protenix/data/constants.py

# Copyright 2024 ByteDance and/or its affiliates.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#      http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

from rdkit.Chem import GetPeriodicTable

EvaluationChainInterface = [
    "intra_ligand",
    "intra_dna",
    "intra_rna",
    "intra_prot",
    "ligand_prot",
    "rna_prot",
    "dna_prot",
    "prot_prot",
    "antibody_antigen",
    "antibody",
]

EntityPolyTypeDict = {
    "nuc": [
        "peptide nucleic acid",
        "polydeoxyribonucleotide",
        "polydeoxyribonucleotide/polyribonucleotide hybrid",
        "polyribonucleotide",
    ],
    "protein": ["polypeptide(D)", "polypeptide(L)"],
    "ligand": ["cyclic-pseudo-peptide", "other"],
}

CRYSTALLIZATION_METHODS = {
    "X-RAY DIFFRACTION",
    "NEUTRON DIFFRACTION",
    "ELECTRON CRYSTALLOGRAPHY",
    "POWDER CRYSTALLOGRAPHY",
    "FIBER DIFFRACTION",
}

### Protein Constants ###
# https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_entity_poly.pdbx_seq_one_letter_code_can.html

mmcif_restype_1to3 = {
    "A": "ALA",
    "R": "ARG",
    "N": "ASN",
    "D": "ASP",
    "C": "CYS",
    "Q": "GLN",
    "E": "GLU",
    "G": "GLY",
    "H": "HIS",
    "I": "ILE",
    "L": "LEU",
    "K": "LYS",
    "M": "MET",
    "F": "PHE",
    "P": "PRO",
    "S": "SER",
    "T": "THR",
    "W": "TRP",
    "Y": "TYR",
    "V": "VAL",
    "B": "ASX",  # additional
    "Z": "GLX",  # additional
    # "X": "UNK",
}

mmcif_restype_3to1 = {v: k for k, v in mmcif_restype_1to3.items()}

"""
vdw table from rdkit; indices match those of the ligand atom_types.
https://github.com/rdkit/rdkit/blob/master/Code/GraphMol/atomic_data.cpp#L46
"""

rdkit_vdws = [
    1.2,
    1.4,
    2.2,
    1.9,
    1.8,
    1.7,
    1.6,
    1.55,
    1.5,
    1.54,
    2.4,
    2.2,
    2.1,
    2.1,
    1.95,
    1.8,
    1.8,
    1.88,
    2.8,
    2.4,
    2.3,
    2.15,
    2.05,
    2.05,
    2.05,
    2.05,
    2.0,
    2.0,
    2.0,
    2.1,
    2.1,
    2.1,
    2.05,
    1.9,
    1.9,
    2.02,
    2.9,
    2.55,
    2.4,
    2.3,
    2.15,
    2.1,
    2.05,
    2.05,
    2.0,
    2.05,
    2.1,
    2.2,
    2.2,
    2.25,
    2.2,
    2.1,
    2.1,
    2.16,
    3.0,
    2.7,
    2.5,
    2.48,
    2.47,
    2.45,
    2.43,
    2.42,
    2.4,
    2.38,
    2.37,
    2.35,
    2.33,
    2.32,
    2.3,
    2.28,
    2.27,
    2.25,
    2.2,
    2.1,
    2.05,
    2.0,
    2.0,
    2.05,
    2.1,
    2.05,
    2.2,
    2.3,
    2.3,
    2.0,
    2.0,
    2.0,
    2.0,
    2.0,
    2.0,
    2.4,
    2.0,
    2.3,
    2.0,
    2.0,
    2.0,
    2.0,
    2.0,
    2.0,
    2.0,
    2.0,
    2.0,
    2.0,
    2.0,
    2.0,
    2.0,
    2.0,
    2.0,
    2.0,
    2.0,
    2.0,
    2.0,
    2.0,
    2.0,
    2.0,
    2.0,
    2.0,
    2.0,
    2.0,
]


"""
atom37 vdw table. Orders match atom37 indices. Note: the vdw's for N and O are different from rdkit_van_der_waals in this file. 
We used the rdkit values for consistency.
Ref to https://github.com/aqlaboratory/openfold/blob/80c85b54e1a81d9a66df3f1b6c257ff97f10acd3/openfold/utils/loss.py#L1208C5-L1211C6
rdkit_van_der_waals_radius = {
    "C": 1.7,
    "N": 1.6,
    "O": 1.55,
    "S": 1.8,
}

atom37_vdw = [
        rdkit_van_der_waals_radius[name[0]]
        for name in residue_constants.atom_types
    ]

"""
atom37_vdw = [
    1.55,
    1.7,
    1.7,
    1.7,
    1.52,
    1.7,
    1.7,
    1.7,
    1.52,
    1.52,
    1.8,
    1.7,
    1.7,
    1.7,
    1.55,
    1.55,
    1.52,
    1.52,
    1.8,
    1.7,
    1.7,
    1.7,
    1.7,
    1.55,
    1.55,
    1.55,
    1.52,
    1.52,
    1.7,
    1.55,
    1.55,
    1.52,
    1.7,
    1.7,
    1.7,
    1.55,
    1.52,
]


# Standard residues (AlphaFold3 SI Talbe 13)
PRO_STD_RESIDUES = {
    "ALA": 0,
    "ARG": 1,
    "ASN": 2,
    "ASP": 3,
    "CYS": 4,
    "GLN": 5,
    "GLU": 6,
    "GLY": 7,
    "HIS": 8,
    "ILE": 9,
    "LEU": 10,
    "LYS": 11,
    "MET": 12,
    "PHE": 13,
    "PRO": 14,
    "SER": 15,
    "THR": 16,
    "TRP": 17,
    "TYR": 18,
    "VAL": 19,
    "UNK": 20,
}

RNA_STD_RESIDUES = {
    "A": 21,
    "G": 22,
    "C": 23,
    "U": 24,
    "N": 29,
}

DNA_STD_RESIDUES = {
    "DA": 25,
    "DG": 26,
    "DC": 27,
    "DT": 28,
    "DN": 30,
}

STD_RESIDUES = PRO_STD_RESIDUES | RNA_STD_RESIDUES | DNA_STD_RESIDUES

rna_order_with_x = {
    "A": 0,
    "G": 1,
    "C": 2,
    "U": 3,
    "N": 4,
}

RNA_NT_TO_ID = {
    "A": 0,
    "G": 1,
    "C": 2,
    "U": 3,
    "N": 4,
    "R": 4,  # A or G
    "Y": 4,  # C or U
    "S": 4,  # G or C
    "W": 4,  # A or U
    "K": 4,  # G or U
    "M": 4,  # A or C
    "B": 4,  # C, G, U
    "D": 4,  # A, G, U
    "H": 4,  # A, C, U
    "V": 4,  # A, C, G
    "X": 4,
    "I": 4,
    "T": 4,
    "-": 5,
}

# Partial inversion of RNA_NT_TO_ID
RNA_ID_TO_NT = {
    0: "A",
    1: "G",
    2: "C",
    3: "U",
    4: "N",  # Also R, Y, S, W, K, M, B, D, H
    5: "-",
}


def get_all_elems():
    """
    Retrieve a list of all element symbols from the RDKit periodic table up to a specified cutoff.

    Returns:
        list: A list of element symbols strings.
    """
    elem_list = []
    pt = GetPeriodicTable()
    for i in range(1, 119):
        elem_list.append(pt.GetElementSymbol(i).upper())

    # 128 elements in the AlphaFold3 SI Table 5 ref_element
    elem_list += [f"UNK_ELEM_{i}" for i in range(119, 129)]
    return elem_list


# len(STD_RESIDUES) + Atomic number up to 118 + 10 UNK_ELEM
ELEMS = dict([(i, len(STD_RESIDUES) + idx) for idx, i in enumerate(get_all_elems())])

RES_ATOMS_DICT = {
    "ALA": {"N": 0, "CA": 1, "C": 2, "O": 3, "CB": 4, "OXT": 5},
    "ARG": {
        "N": 0,
        "CA": 1,
        "C": 2,
        "O": 3,
        "CB": 4,
        "CG": 5,
        "CD": 6,
        "NE": 7,
        "CZ": 8,
        "NH1": 9,
        "NH2": 10,
        "OXT": 11,
    },
    "ASN": {
        "N": 0,
        "CA": 1,
        "C": 2,
        "O": 3,
        "CB": 4,
        "CG": 5,
        "OD1": 6,
        "ND2": 7,
        "OXT": 8,
    },
    "ASP": {
        "N": 0,
        "CA": 1,
        "C": 2,
        "O": 3,
        "CB": 4,
        "CG": 5,
        "OD1": 6,
        "OD2": 7,
        "OXT": 8,
    },
    "CYS": {"N": 0, "CA": 1, "C": 2, "O": 3, "CB": 4, "SG": 5, "OXT": 6},
    "GLN": {
        "N": 0,
        "CA": 1,
        "C": 2,
        "O": 3,
        "CB": 4,
        "CG": 5,
        "CD": 6,
        "OE1": 7,
        "NE2": 8,
        "OXT": 9,
    },
    "GLU": {
        "N": 0,
        "CA": 1,
        "C": 2,
        "O": 3,
        "CB": 4,
        "CG": 5,
        "CD": 6,
        "OE1": 7,
        "OE2": 8,
        "OXT": 9,
    },
    "GLY": {"N": 0, "CA": 1, "C": 2, "O": 3, "OXT": 4},
    "HIS": {
        "N": 0,
        "CA": 1,
        "C": 2,
        "O": 3,
        "CB": 4,
        "CG": 5,
        "ND1": 6,
        "CD2": 7,
        "CE1": 8,
        "NE2": 9,
        "OXT": 10,
    },
    "ILE": {
        "N": 0,
        "CA": 1,
        "C": 2,
        "O": 3,
        "CB": 4,
        "CG1": 5,
        "CG2": 6,
        "CD1": 7,
        "OXT": 8,
    },
    "LEU": {
        "N": 0,
        "CA": 1,
        "C": 2,
        "O": 3,
        "CB": 4,
        "CG": 5,
        "CD1": 6,
        "CD2": 7,
        "OXT": 8,
    },
    "LYS": {
        "N": 0,
        "CA": 1,
        "C": 2,
        "O": 3,
        "CB": 4,
        "CG": 5,
        "CD": 6,
        "CE": 7,
        "NZ": 8,
        "OXT": 9,
    },
    "MET": {
        "N": 0,
        "CA": 1,
        "C": 2,
        "O": 3,
        "CB": 4,
        "CG": 5,
        "SD": 6,
        "CE": 7,
        "OXT": 8,
    },
    "PHE": {
        "N": 0,
        "CA": 1,
        "C": 2,
        "O": 3,
        "CB": 4,
        "CG": 5,
        "CD1": 6,
        "CD2": 7,
        "CE1": 8,
        "CE2": 9,
        "CZ": 10,
        "OXT": 11,
    },
    "PRO": {"N": 0, "CA": 1, "C": 2, "O": 3, "CB": 4, "CG": 5, "CD": 6, "OXT": 7},
    "SER": {"N": 0, "CA": 1, "C": 2, "O": 3, "CB": 4, "OG": 5, "OXT": 6},
    "THR": {"N": 0, "CA": 1, "C": 2, "O": 3, "CB": 4, "OG1": 5, "CG2": 6, "OXT": 7},
    "TRP": {
        "N": 0,
        "CA": 1,
        "C": 2,
        "O": 3,
        "CB": 4,
        "CG": 5,
        "CD1": 6,
        "CD2": 7,
        "NE1": 8,
        "CE2": 9,
        "CE3": 10,
        "CZ2": 11,
        "CZ3": 12,
        "CH2": 13,
        "OXT": 14,
    },
    "TYR": {
        "N": 0,
        "CA": 1,
        "C": 2,
        "O": 3,
        "CB": 4,
        "CG": 5,
        "CD1": 6,
        "CD2": 7,
        "CE1": 8,
        "CE2": 9,
        "CZ": 10,
        "OH": 11,
        "OXT": 12,
    },
    "VAL": {"N": 0, "CA": 1, "C": 2, "O": 3, "CB": 4, "CG1": 5, "CG2": 6, "OXT": 7},
    "UNK": {"N": 0, "CA": 1, "C": 2, "O": 3, "CB": 4, "CG": 5, "OXT": 6},
    "DA": {
        "OP3": 0,
        "P": 1,
        "OP1": 2,
        "OP2": 3,
        "O5'": 4,
        "C5'": 5,
        "C4'": 6,
        "O4'": 7,
        "C3'": 8,
        "O3'": 9,
        "C2'": 10,
        "C1'": 11,
        "N9": 12,
        "C8": 13,
        "N7": 14,
        "C5": 15,
        "C6": 16,
        "N6": 17,
        "N1": 18,
        "C2": 19,
        "N3": 20,
        "C4": 21,
    },
    "DC": {
        "OP3": 0,
        "P": 1,
        "OP1": 2,
        "OP2": 3,
        "O5'": 4,
        "C5'": 5,
        "C4'": 6,
        "O4'": 7,
        "C3'": 8,
        "O3'": 9,
        "C2'": 10,
        "C1'": 11,
        "N1": 12,
        "C2": 13,
        "O2": 14,
        "N3": 15,
        "C4": 16,
        "N4": 17,
        "C5": 18,
        "C6": 19,
    },
    "DG": {
        "OP3": 0,
        "P": 1,
        "OP1": 2,
        "OP2": 3,
        "O5'": 4,
        "C5'": 5,
        "C4'": 6,
        "O4'": 7,
        "C3'": 8,
        "O3'": 9,
        "C2'": 10,
        "C1'": 11,
        "N9": 12,
        "C8": 13,
        "N7": 14,
        "C5": 15,
        "C6": 16,
        "O6": 17,
        "N1": 18,
        "C2": 19,
        "N2": 20,
        "N3": 21,
        "C4": 22,
    },
    "DT": {
        "OP3": 0,
        "P": 1,
        "OP1": 2,
        "OP2": 3,
        "O5'": 4,
        "C5'": 5,
        "C4'": 6,
        "O4'": 7,
        "C3'": 8,
        "O3'": 9,
        "C2'": 10,
        "C1'": 11,
        "N1": 12,
        "C2": 13,
        "O2": 14,
        "N3": 15,
        "C4": 16,
        "O4": 17,
        "C5": 18,
        "C7": 19,
        "C6": 20,
    },
    "DN": {
        "OP3": 0,
        "P": 1,
        "OP1": 2,
        "OP2": 3,
        "O5'": 4,
        "C5'": 5,
        "C4'": 6,
        "O4'": 7,
        "C3'": 8,
        "O3'": 9,
        "C2'": 10,
        "C1'": 11,
    },
    "A": {
        "OP3": 0,
        "P": 1,
        "OP1": 2,
        "OP2": 3,
        "O5'": 4,
        "C5'": 5,
        "C4'": 6,
        "O4'": 7,
        "C3'": 8,
        "O3'": 9,
        "C2'": 10,
        "O2'": 11,
        "C1'": 12,
        "N9": 13,
        "C8": 14,
        "N7": 15,
        "C5": 16,
        "C6": 17,
        "N6": 18,
        "N1": 19,
        "C2": 20,
        "N3": 21,
        "C4": 22,
    },
    "C": {
        "OP3": 0,
        "P": 1,
        "OP1": 2,
        "OP2": 3,
        "O5'": 4,
        "C5'": 5,
        "C4'": 6,
        "O4'": 7,
        "C3'": 8,
        "O3'": 9,
        "C2'": 10,
        "O2'": 11,
        "C1'": 12,
        "N1": 13,
        "C2": 14,
        "O2": 15,
        "N3": 16,
        "C4": 17,
        "N4": 18,
        "C5": 19,
        "C6": 20,
    },
    "G": {
        "OP3": 0,
        "P": 1,
        "OP1": 2,
        "OP2": 3,
        "O5'": 4,
        "C5'": 5,
        "C4'": 6,
        "O4'": 7,
        "C3'": 8,
        "O3'": 9,
        "C2'": 10,
        "O2'": 11,
        "C1'": 12,
        "N9": 13,
        "C8": 14,
        "N7": 15,
        "C5": 16,
        "C6": 17,
        "O6": 18,
        "N1": 19,
        "C2": 20,
        "N2": 21,
        "N3": 22,
        "C4": 23,
    },
    "U": {
        "OP3": 0,
        "P": 1,
        "OP1": 2,
        "OP2": 3,
        "O5'": 4,
        "C5'": 5,
        "C4'": 6,
        "O4'": 7,
        "C3'": 8,
        "O3'": 9,
        "C2'": 10,
        "O2'": 11,
        "C1'": 12,
        "N1": 13,
        "C2": 14,
        "O2": 15,
        "N3": 16,
        "C4": 17,
        "O4": 18,
        "C5": 19,
        "C6": 20,
    },
    "N": {
        "OP3": 0,
        "P": 1,
        "OP1": 2,
        "OP2": 3,
        "O5'": 4,
        "C5'": 5,
        "C4'": 6,
        "O4'": 7,
        "C3'": 8,
        "O3'": 9,
        "C2'": 10,
        "O2'": 11,
        "C1'": 12,
    },
}

CRYSTALLIZATION_AIDS = (
    "SO4",
    "GOL",
    "EDO",
    "PO4",
    "ACT",
    "PEG",
    "DMS",
    "TRS",
    "PGE",
    "PG4",
    "FMT",
    "EPE",
    "MPD",
    "MES",
    "CD",
    "IOD",
)

PROT_STD_RESIDUES_ONE_TO_THREE = {
    "A": "ALA",
    "R": "ARG",
    "N": "ASN",
    "D": "ASP",
    "C": "CYS",
    "Q": "GLN",
    "E": "GLU",
    "G": "GLY",
    "H": "HIS",
    "I": "ILE",
    "L": "LEU",
    "K": "LYS",
    "M": "MET",
    "F": "PHE",
    "P": "PRO",
    "S": "SER",
    "T": "THR",
    "W": "TRP",
    "Y": "TYR",
    "V": "VAL",
    "X": "UNK",
}

CRYSTALLIZATION_AIDS = (
    "SO4",
    "GOL",
    "EDO",
    "PO4",
    "ACT",
    "PEG",
    "DMS",
    "TRS",
    "PGE",
    "PG4",
    "FMT",
    "EPE",
    "MPD",
    "MES",
    "CD",
    "IOD",
)


### Molecule Constants ###
# AlphaFold3 SI Tabel 9
LIGAND_EXCLUSION = {'144', 'SEP', 'PG0', 'BEN', 'NH4', 'PO4', '3SY', 'BO3', 'UNL', 'MES', 'FLC', 'PGR', '15P', 'MYR', 
                    'POL', 'CIT', 'N', 'SPD', 'CAQ', 'IPA', 'EGL', 'SAR', 'NO3', 'STU', 'NHE', 'BU1', 'OXA', 'TPO', 
                    'EEE', 'CAD', 'CBM', 'SPM', 'BCN', 'FMT', 'PEP', 'CM', 'BAM', 'ETF', 'IOD', 'MLI', 'MRD', 'SCN', 
                    'GSH', 'CCN', 'SR', '1PE', 'ACY', 'STE', '9JE', 'SEO', 'IHS', 'MLA', 'TBU', 'DEP', 'STO', 'ACE', 
                    'NA', 'TRS', 'CPT', 'OHE', 'TME', 'CL', 'BME', 'DN', '3HR', 'LDA', 'SO4', 'MPD', 'OLC', 'DOD', 
                    'PE4', 'DOX', 'CMO', 'POP', 'PG4', '2F2', 'DMS', 'IMD', 'NH2', 'EOX', 'IPH', 'ACT', '7PE', 'UNX', 
                    'GTT', '7N5', 'AZI', 'FCY', 'SIN', 'AAE', 'BTB', 'BTC', 'PGE', 'PE3', 'MB3', 'EDO', 'PLM', 'BCT', 
                    'EOH', 'P6G', 'ACN', 'D10', 'EPE', 'DIO', 'CO3', 'PVO', 'TAR', 'URE', 'BDN', 'GOL', 'MSE', 'HED', 
                    'CLR', 'MEG', 'IHP', 'PEO', 'CXS', 'MOH', 'GYF', 'PEG', 'FJO', 'FW5', 'OLA', '2JC', 'ABA', 'O4B', 
                    'UPL', 'OME', 'C8E', 'OMB', 'UNK'}  # fmt: skip


# AlphaFold3 SI Tabel 11
GLYCANS = {'79J', 'LXZ', 'KO1', 'Z57', 'XDX', '8OQ', 'G0S', '14T', 'ZB3', '9PG', 'BGL', 'GYU', 'AHG', 'SUC', 'ADA', 'NGR', 
           '4R1', 'EBQ', 'GAF', 'NAA', 'GYP', 'NDG', 'U2D', 'ISL', '9GP', 'KDM', 'HSX', 'NYT', 'V3P', '4NN', 'Z3L', 'ZCZ', 
           'D5E', 'RIP', '3LR', 'GL1', 'K99', 'MQG', 'RAM', 'TUP', 'KDB', 'SIO', 'Z5L', 'GUL', 'GU2', 'EQV', '0V4', 'ABD', 
           'RY7', '5II', 'GAL', '2GL', 'DR5', '4RS', 'MNA', 'DFX', '0WK', 'HTG', 'RP5', 'A1Q', 'B1N', 'GUF', 'NGA', 'TMR', 
           'C3X', '9S7', 'XLS', 'MAG', 'RST', 'SDY', 'HSH', 'GN4', 'GTR', 'KBA', '6YR', 'CKB', 'DDA', 'RHC', 'OPM', 'SIZ', 
           'GE3', 'TS8', 'Z6W', 'BZD', '56N', 'RIB', 'GL6', '8GA', 'GLC', 'TAG', 'QIF', 'TA6', 'UAP', 'TVY', 'GC1', 'ARW', 
           'GU3', 'LBS', 'KDD', 'NPF', '49V', 'CDR', '12E', '6LA', '2M4', 'SA0', 'HNW', 'AOG', 'G8Z', '8LR', 'GPH', 'XXX', 
           'GPM', 'MTT', 'JFZ', 'LOG', 'LMO', '5TH', '8I4', 'GUP', '5KQ', 'R2G', 'SSG', 'P8E', 'RF5', 'TOC', 'CT3', '2FL', 
           '73E', 'VJ4', '0H0', 'ERI', 'AMG', '3GR', 'BO1', 'AFD', 'FYJ', 'IDF', 'NBY', 'DOM', 'MBF', 'QDK', 'TDG', '6GR', 
           'MAV', '1X4', 'AF1', 'EEN', 'ZB1', 'Z2D', '445', 'KHP', 'LKS', '10M', '491', 'OTU', 'BNG', 'AY9', 'KDR', 'LEC', 
           'FFX', 'AFO', 'SGA', '16F', 'X34', 'SEJ', 'LAG', 'DNO', '6PZ', 'LBT', 'OSU', '3BU', '6K3', 'SFU', 'YDR', 'SIA', 
           '2WP', '25E', 'SMD', 'NBG', 'DO8', 'LGU', 'S81', 'Z3Q', 'TWA', 'G6S', '2WS', 'G6D', '18D', 'IN1', '64K', 'QPS', 
           'PTQ', 'FX1', 'RVM', '8GP', 'NLC', 'FCA', 'JLT', 'AH8', 'MFB', 'RRJ', 'SOL', 'TM5', 'TCB', 'GU5', 'TWY', 'ETT', 
           '8YV', 'SG6', 'XMM', '17T', 'BGC', 'MLR', 'Z6J', '9SJ', 'R2B', 'BBK', 'BEM', 'LTG', '0NZ', 'DKZ', '3YW', 'ASO', 
           'FUB', '4GL', 'GLT', 'KTU', 'CBF', 'ARI', 'FIF', 'LCN', 'SG5', 'AC1', 'SUP', 'ZMR', 'GU8', 'YYH', 'XKJ', 'JSV', 
           'DQR', 'M6D', 'FBP', 'AFP', 'F6P', 'GLG', 'JZR', 'DLG', '9C1', 'AAL', 'RRY', 'ZDC', 'TVS', 'B1H', 'XXM', '8B7', 
           'RCD', 'UBO', '7D1', 'XYT', 'WZ2', 'X1X', 'LRH', 'GDA', 'GLS', 'G6P', '49A', 'NM9', 'DVC', 'MG5', 'SCR', 'MAF', 
           '149', 'LFC', 'FMF', 'FRU', 'BG8', 'GP4', 'GU1', 'XXR', '4V5', 'MA2', '293', '6KH', 'GAA', 'MXY', 'QV4', 'MSX', 
           'GU6', '95Z', 'Z9M', 'ARB', 'FNY', 'H1S', 'VG1', 'VTB', 'Z61', 'H6Z', '7K3', 'XGP', 'SOE', 'Z6H', 'GYV', 'MLB', 
           'DR3', 'ISD', 'BGN', 'AXR', 'SCG', 'Z8T', '6UD', 'KDF', 'GLA', 'BNX', '3MG', 'BDP', 'KFN', 'Z9N', '2FG', 'PNA', 
           'MUB', 'ZDO', '9WJ', 'GMB', 'LER', 'TVM', '89Y', 'Z4Y', '9SM', 'NGS', 'LAO', 'KGM', 'FKD', 'M1F', 'BG6', 'LAK', 
           '8GG', '6LS', 'GBH', 'CEG', 'BDR', 'RR7', 'SOG', 'AZC', 'AMU', 'BS7', '3S6', 'MXZ', 'Z3U', 'MDP', '6MJ', 'M3M', 
           'DT6', 'PRP', 'TUG', 'Z16', 'IDG', 'TUR', 'Z4S', 'GM0', 'A0K', 'GCN', 'ZEE', 'UEA', 'HVC', 'CE5', 'FUD', 'NAG', 
           'GPO', '22S', '3J4', 'DKX', 'FMO', 'BXP', 'NSQ', '50A', 'MAT', '5TM', '0MK', '9OK', 'RI2', 'SZZ', 'IDS', 'JRV', 
           '18O', '1CF', 'RAO', 'P53', '27C', 'Z3K', 'Z4U', 'Z4R', 'B4G', '6KU', 'HBZ', '07E', 'KBG', '98U', 'GFP', 'LFR', 
           'G2F', '51N', 'FUF', 'LGC', '6S2', 'E3M', 'G7P', 'OTN', 'MVP', 'TVD', 'BBV', 'E5G', 'MJJ', 'IEM', 'FSA', 'CE8', 
           'U1Y', '1FT', 'HTM', 'DLD', 'YO5', 'W9T', '5N6', 'PNG', 'NGY', 'DSR', 'M3N', 'GP0', '3MK', 'RBL', 'GTM', 'FSW', 
           '4JA', 'YYM', 'Z4V', '3HD', '2DR', 'AIG', 'GL0', 'BND', 'TM6', 'TUJ', 'DAN', '5GF', '4QY', '3FM', '6KW', 'LNV', 
           '289', 'BFN', 'PSG', 'U9J', 'YX0', 'EQP', 'YZ0', '0BD', 'GAT', 'LVZ', 'FUL', '22O', 'DLF', 'MA1', 'BXY', 'C3G', 
           'CR6', 'GNS', 'EEQ', 'IDY', 'FFC', 'NBX', 'SID', '9KJ', '9WZ', 'M2F', 'FK9', 'SSH', 'TWG', 'RVG', 'BXX', '24S', 
           'FSM', 'GDL', 'F1X', '3R3', 'ALX', '4GC', 'GL2', 'DL6', 'GS1', 'AMV', 'TVV', '2DG', 'RGG', 'TFU', '1GN', 'N3U', 
           'SOR', 'MA3', 'GCT', 'H1M', '16G', '49T', 'BCD', 'GPW', 'DAG', 'GN1', 'IAB', 'EBG', 'GPU', '38J', '1LL', 'DR2', 
           'YIO', 'YKR', '15L', 'WZ1', 'BTG', 'GPK', '5MM', '26O', 'AMN', 'DEL', 'CTT', '83Y', 'GMT', 'CTO', 'MBE', '1SD', 
           '6ZC', 'AXP', 'OX2', '5LT', 'MRH', '6BG', 'MDA', 'SG7', '045', 'GC4', 'LDY', 'YYJ', '07Y', 'KDO', 'GP1', 'BHG', 
           'DPC', 'BM3', 'GU4', 'ISX', 'P6P', 'GPQ', '1S4', '475', 'GYE', 'CBK', 'CEZ', 'SGD', 'TH1', 'V3M', 'RWI', 'RM4', 
           'U9M', 'U2A', '7GP', '05L', 'Z0F', 'GLO', 'LXB', 'TGA', '61J', 'GYG', 'GCU', 'GE1', 'F1P', 'GLP', 'CTR', 'AHR', 
           '3LJ', 'FUY', 'JVA', 'LAT', 'NHF', 'RB5', 'XYS', 'LXC', 'SLT', 'U8V', 'GMH', 'EAG', 'GCV', 'B6D', 'IDU', 'KG1', 
           'BDF', 'NTP', 'IXD', 'RZM', 'PH5', 'SHB', 'X6Y', 'B16', 'Z9E', '9VP', 'LAH', 'H2P', 'TNX', '5GO', 'TGY', '5SP', 
           'RHA', '5KV', 'GTK', 'SUS', 'DAF', '6DM', '8S0', '6MN', 'G4D', 'NT1', 'XYF', '5TJ', '46Z', '9AM', '7K2', '6C2', 
           'WIA', '9YW', 'G4S', '46D', 'Z9W', 'ABL', 'XYZ', 'G3I', 'S7P', 'GC9', 'GQ1', 'GCO', 'M6P', 'WUN', 'U63', 'ZB2', 
           'GLD', 'T6P', 'ZEL', '145', '2OS', 'BGP', 'C4W', 'IDX', 'MUR', '3SA', 'CR1', '34V', 'DEG', 'F55', 'L0W', 'TYV', 
           'CJB', 'TW7', 'DDL', '5L3', 'NGC', 'ACX', 'JVS', 'NA1', 'GAD', '7JZ', 'BOG', 'GCW', 'BDG', 'Z15', '0LP', 'ABE', 
           'RG1', 'DGU', 'N1L', 'NGE', 'PUF', 'B9D', '49S', '5LS', '4N2', '23V', 'RUU', 'B0D', 'RTV', '42D', 'M1P', 'MAB', 
           '2F8', 'TQY', 'L6S', 'V71', '2H5', 'M8C', 'NTF', 'H3S', 'LM2', 'MN0', 'JV4', '9WN', 'U9G', 'LZ0', 'X0X', 'TXB', 
           '3DO', 'SG4', 'IDR', '8B9', 'TOA', 'CRA', 'HSJ', '0HX', 'FDQ', 'FUC', 'ABF', 'ALL', 'G20', 'GL9', 'IDC', 'LOX', 
           'Z2T', 'RP6', '2HA', 'AHM', 'DRI', 'EMZ', 'GMZ', 'HD4', 'GU9', 'L1L', 'PNW', 'PPC', 'MMA', 'CE6', '5KS', 'MGC', 
           'XLF', 'KO2', 'RUG', 'HSG', 'SF6', 'IPT', 'TF0', 'GCD', 'B8D', '0YT', 'GRX', 'HNV', 'FVQ', 'RV7', 'J5B', 'ERE', 
           'DFR', 'LVO', '4GP', 'BQY', 'BMA', 'KDA', 'ARA', 'KDN', 'ZCD', 'A5C', 'T68', 'XYL', 'YJM', 'NM6', '9CD', 'CNP', 
           'U97', '9T1', 'C5X', 'R1X', 'BW3', '09X', 'GNX', 'PDX', 'Z9D', 'DGO', 'SLM', '66O', '4CQ', 'X6X', 'RTG', 'HSY', 
           '20X', 'GCB', 'EUS', 'FNG', '1S3', 'EGA', 'MQT', 'NXD', '5TK', 'Z9K', 'TGR', '9MR', 'M7P', 'PA1', 'MFU', 'UBH', 
           'CBI', 'TMX', 'T6D', '32O', 'JHM', 'X2F', '4SG', '3DY', 'SGC', 'PAV', 'A2G', 'LAI', '0UB', 'BXF', '3J3', '9T7', 
           'T6T', 'OI7', 'ANA', '9QG', 'K5B', 'KOT', 'GIV', 'MGL', 'GL4', '9SP', 'FDP', 'GPV', '6KS', 'GXV', 'NFG', 'M7B', 
           'DG0', '57S', 'GUZ', '96O', 'GCS', 'MAN', 'YYB', 'TWD', 'MGS', 'TT7', 'PNJ', 'GXL', 'TRE', 'G28', '7NU', '8PK', 
           'LKA', 'ASG', 'SF9', '2M8', '1GL', '5KT', 'BWG', 'OTG', 'VJ1', 'ZGE', '40J', 'Z4K', 'F58', 'KME', 'SR1', 'ZB0', 
           'UDC', '6KL', '6LW', '8EX', 'D1M', '62I', 'H6Q', 'RAE', 'SHD', 'AGL', 'DGS', 'VKN', 'TWJ', 'MRP', 'TGK', 'HSQ', 
           'ASC', 'F8X', '6GB', '0XY', 'BMX', 'SN5', 'Z5J', 'ZD0', 'DJB', 'KDE', 'TEU', 'M55', 'YYQ', 'DK4', 'D6G', 'KD5', 
           'AH2', '4AM', 'RER', '16O', 'C3B', 'G1P', 'NG6', 'MBG', 'Z4W', 'MAW', '147', 'NGK', 'CKP', 'DJE', 'GL5', 'TVG', 
           'PKM', 'L6T', 'XS2', '2GS', 'BTU', 'G16', 'PSV', 'AQA', 'MCU', 'SNG', '2M5', 'SLB', 'BM7', 'H53', 'MA8', 'OAK', 
           'GRF', 'BGS', 'NTO', 'YYK', 'EPG', '6GP', 'MYG', 'FCT', 'Z9H', 'GL7', '48Z', '4UZ', '7CV', 'DYM', 'GLF', 'GU0', 
           'CGF', 'STZ', '44S', 'LB2', 'TU4', 'Z8H', '5QP', 'A6P', 'XYP', 'B2G', 'U9A', 'SWE', 'NGZ', 'SGN', 'B7G', 'MAL', 
           '291', 'FSI', 'R1P', 'ACR', 'PZU', 'X2Y', 'Z9L', 'STW', 'U9D', 'X1P', 'TTV', 'GS9', 'QKH', 'SHG', 'N9S', 'NNG', 
           'RP3', 'G3F', 'YX1', 'EMP', 'XIL', '08U', 'WOO', 'FCB', 'NG1', 'TRV', '20S', 'RAF', 'GZL', 'C4B', '9SG', 'GAC'}  # fmt: skip


# AlphaFold3 SI Tabel 12
IONS = {'XGP', 'Z4K', '147', 'B0D', 'G6D', 'RIB', 'AXR', 'SOG', 'NTF', 'SHB', 'RG1', 'G6S', 'GPO', 'BTG', '5LT', 'CEG', 'KG1', 
        'TDG', 'TRV', 'WZ1', 'ARI', 'HVC', 'TM6', '2DG', '6K3', 'ARA', 'ASO', '6GB', 'NBX', 'OTG', 'ASG', 'YO5', 'MRH', 'GYP', 
        'C4B', 'GDA', 'MUB', 'XXM', 'M6D', 'OPM', 'GYV', 'DKX', '9SG', 'LOG', 'TRE', 'DLG', 'FNG', 'BBK', 'ABF', 'AQA', '3BU', 
        'SIA', 'CGF', 'LBS', 'QV4', 'NAA', 'GLC', 'BHG', 'MSX', 'ZB1', 'YYJ', 'TUP', '6ZC', '0WK', 'RY7', 'L1L', 'RRY', 'M55', 
        '9PG', '5GF', '4V5', 'FMO', 'SWE', 'KDA', 'P8E', '14T', 'DL6', 'CKB', '2M8', 'AHR', 'NGY', '8GP', 'YYQ', 'LVO', 'CRA', 
        'GU9', 'PPC', '6GP', 'CR1', 'G20', 'T6P', 'EMZ', 'RHA', 'GC4', 'AH2', 'FCT', 'QDK', 'DDA', 'RTV', '8S0', 'TVG', 'HNV', 
        'FYJ', 'BDP', 'GYE', 'TS8', 'CEZ', '42D', 'NHF', 'NT1', 'WOO', '0LP', 'HBZ', 'SG5', 'NM9', 'CJB', 'DLF', 'EUS', 'IDY', 
        '2GL', 'NTO', 'PNG', 'B2G', '7NU', '4UZ', '5LS', '475', 'DJE', 'Z9E', 'GC9', 'QPS', '0NZ', 'F1X', 'G8Z', '2F8', '3SA', 
        '46D', '3DO', '6PZ', 'OI7', 'SLM', 'A0K', '9SJ', 'TWD', 'AOG', 'TW7', '2WS', 'GU5', 'NSQ', 'FUD', 'GLO', 'TNX', 'XYP', 
        'JFZ', '2HA', 'G16', 'V3M', 'RTG', 'C4W', 'R2G', 'HD4', '66O', 'MFB', 'GXL', '8YV', 'NFG', 'FFC', '3YW', 'XYZ', '445', 
        'IXD', 'GUL', 'CTO', '05L', 'Z3L', 'RBL', 'DR5', 'S81', 'CTR', '15L', 'GLP', '7K3', 'LDY', 'Z4S', 'H2P', '4GP', '5SP', 
        '18O', 'DGS', 'OX2', 'DFR', 'GN1', 'BGL', 'Z9K', 'GU4', '0V4', 'MA2', 'U2A', 'MXZ', 'PA1', '9YW', 'GS9', '3MK', 'AAL', 
        'NBY', 'XXX', 'ISD', 'SEJ', 'DKZ', 'GL9', '23V', 'AMN', 'AHG', '25E', 'DJB', '7K2', 'GDL', '08U', 'TT7', 'DRI', 'HSY', 
        'LB2', 'GCV', 'X1P', 'MN0', 'BW3', 'U9J', 'FFX', 'Z3U', 'LOX', 'MQG', 'HSG', 'GCO', 'GPQ', 'IDR', '2GS', 'AGL', 'RUU', 
        '5KV', 'R1X', 'LZ0', 'P6P', '0H0', '32O', 'LAG', 'YYK', '07E', '6KS', 'KOT', '17T', 'TQY', 'RM4', 'LNV', 'BGN', 'STW', 
        'NGC', 'GLF', '2WP', 'GL5', 'KHP', '9SP', 'LAI', 'KDB', 'JVA', 'OTN', 'NA1', 'RR7', 'B16', 'PSV', 'NXD', 'C5X', 'G1P', 
        'RRJ', 'DAF', '5N6', 'SG4', 'KDN', '95Z', 'FDQ', 'K5B', 'MDP', 'GTK', '4SG', 'ALL', 'LXC', 'TM5', 'NGA', '98U', '7JZ', 
        'A6P', 'UBH', '293', '9T7', 'PUF', '5TM', 'VTB', 'BGP', 'JV4', 'SN5', 'FSA', 'LAK', 'G7P', 'BGC', 'ZCD', '7GP', '79J', 
        'FKD', 'TWY', 'ZGE', 'OAK', 'FMF', 'ZCZ', 'GL2', 'MAV', 'ZB3', 'SA0', '3LR', 'SHD', 'XLS', 'DOM', 'Z4R', 'GP0', '5KS', 
        'KO1', 'FCB', 'LFC', 'AC1', 'NPF', 'X6Y', 'IDF', '20X', '6KL', '6LW', '49S', '0YT', 'BDR', 'GBH', 'LAH', 'KO2', '40J', 
        '4CQ', 'D5E', 'T6D', 'SUP', 'TGR', 'Z57', 'SDY', '4NN', 'MNA', 'Z5J', '20S', 'CT3', 'DQR', '5MM', '83Y', '49T', 'BDG', 
        'GL1', 'TOC', '6UD', 'GM0', 'GU3', '18D', 'ADA', '4AM', '9WZ', 'HSX', 'QIF', '6DM', '4RS', 'KDF', 'GAL', 'ISL', 'Z9H', 
        'GC1', 'Z9W', 'NBG', 'MAL', 'BGS', 'W9T', 'U9A', '62I', 'M6P', 'AFO', 'C3G', 'M2F', 'RUG', 'ARW', 'LEC', 'B8D', '61J', 
        'GL7', 'F58', 'GP4', 'GFP', 'TVY', 'ZB0', 'FSM', 'BDF', 'TCB', 'ZEL', 'IDG', '9CD', 'PNA', 'SF9', 'DSR', 'MG5', 'E5G', 
        'PNW', 'TH1', '1S4', 'PTQ', 'KDD', 'SSH', 'F55', 'V71', 'VG1', '9T1', '145', 'GU2', '2M5', '8I4', 'H1S', 'YYB', '1LL', 
        '4N2', 'BG6', 'R2B', 'MAT', 'LMO', 'OSU', 'PSG', 'RCD', '26O', 'DGO', 'SID', 'FUB', '2FL', '3HD', '34V', 'FK9', 'AMG', 
        'G4D', 'EPG', 'BWG', 'KTU', '491', 'JHM', 'NG1', 'DLD', 'MCU', 'MQT', 'EQV', 'CBF', '4GL', 'GS1', 'DEG', 'DDL', 'SGA', 
        '16O', 'X6X', 'H53', 'FUC', 'IDS', 'LTG', 'TMX', '9SM', '045', 'DAN', 'FRU', 'Z5L', 'AHM', 'BNG', 'AFP', 'MAF', 'UBO', 
        'BOG', '2H5', 'NG6', '10M', 'NM6', 'RST', 'C3X', '9S7', '49A', 'AXP', 'PH5', 'ISX', 'B6D', 'GU6', 'TWG', '6GR', 'H3S', 
        'Z61', '9WJ', 'BMA', 'U63', 'LKA', 'GRF', 'VJ1', 'RZM', 'MA3', '0XY', 'GAF', 'GAD', '1FT', '149', 'DPC', 'LFR', 'B9D', 
        'CE5', 'SOR', '6KU', 'SFU', 'BEM', 'YKR', '38J', 'N3U', 'ARB', 'CBK', 'SGD', '8EX', 'WZ2', '8B9', 'TF0', 'X2Y', 'PKM', 
        'RF5', 'D1M', 'AF1', 'DR2', 'EQP', 'AMV', 'PRP', 'VJ4', 'BCD', '1GN', 'SMD', '9QG', 'GCW', 'A5C', 'M3N', 'SZZ', 'B1H', 
        'GPH', 'NDG', '5KT', 'TYV', 'KDM', 'A2G', 'CE6', 'H1M', 'JVS', 'ABL', 'LAO', 'P53', 'GCN', 'QKH', 'U2D', 'YYH', '6S2', 
        'L0W', 'DEL', 'G2F', 'LER', 'MGC', 'RI2', '5KQ', 'DT6', 'U97', 'BG8', '1X4', 'GYG', 'U9D', 'SG7', '8B7', 'FCA', 'RWI', 
        '8GG', 'TAG', 'ERE', '46Z', '5QP', 'UDC', '51N', 'SGN', 'NLC', '8LR', 'L6T', 'WIA', 'TMR', 'IDC', 'GLT', 'FDP', 'GCT', 
        'FSW', 'XYS', 'GAA', 'N9S', 'DO8', 'UAP', 'TUG', 'F1P', '2FG', '12E', '56N', 'IAB', 'LAT', 'X1X', 'MBE', 'GP1', 'X34', 
        '6MJ', '6KH', 'G3F', '3DY', 'XYF', 'GE1', 'MAB', 'Z9L', '289', 'GIV', 'F8X', '9WN', 'KDO', 'GLA', 'SIZ', 'G0S', 'EGA', 
        'MJJ', 'B7G', 'BND', 'JRV', '1S3', 'DAG', 'GL0', 'GPV', 'HTM', '3R3', 'SHG', 'DR3', 'TTV', 'DK4', '22S', 'IDU', 'XIL', 
        'RER', '6BG', 'GXV', 'BTU', 'GE3', 'H6Z', 'ZD0', 'SF6', 'VKN', 'GYU', '16F', 'K99', 'KGM', 'FX1', 'NGS', 'RVG', 'YX1', 
        '4GC', 'EEQ', 'XDX', 'MVP', 'PNJ', 'BS7', 'M7B', '0BD', 'AIG', 'TVV', 'BXY', 'T68', 'SIO', '8OQ', '2OS', 'S7P', 'GNX', 
        'TUR', 'YX0', 'DVC', 'NGK', 'M8C', 'RHC', 'GPM', 'LKS', '64K', 'GMT', 'JLT', 'XS2', 'LBT', 'TVM', '6MN', 'DYM', 'E3M', 
        'NGR', 'G6P', 'RAO', 'SCR', 'YJM', 'MRP', 'YIO', 'ACR', '291', '3GR', 'M1F', 'L6S', 'XLF', 'GU1', 'LVZ', 'DNO', '22O', 
        'SOL', 'GPW', 'KD5', 'GCU', 'ERI', 'YZ0', 'TXB', 'ABD', 'YYM', 'BFN', 'G4S', 'GAC', 'PAV', 'MMA', 'RV7', 'MBG', '16G', 
        'MA8', 'GU8', '4JA', 'NTP', 'FNY', '07Y', '1CF', 'KDE', 'Z16', 'CBI', '50A', 'Z4W', 'U9G', 'D6G', 'JSV', 'YDR', 'DGU', 
        'Z15', 'G3I', 'XKJ', 'IEM', 'CDR', 'GLG', '0HX', 'TA6', '57S', 'LGU', '27C', 'BO1', 'EEN', 'HSJ', 'GLD', 'RP3', 'FSI', 
        'LRH', '8PK', 'GTR', 'B1N', 'XXR', 'TFU', 'RAF', 'ETT', 'AY9', '3FM', 'G28', '2DR', 'FUL', 'CE8', 'GQ1', 'TGA', '6C2', 
        'NGZ', '6LS', 'SOE', 'BQY', 'HSH', 'XYL', '5TH', 'A1Q', 'HTG', 'Z3K', '3MG', 'GMH', 'M1P', 'ASC', '73E', 'Z8T', 'STZ', 
        'RAE', 'GL6', '7CV', 'GPU', '5L3', '7D1', 'CKP', 'BXP', 'M7P', 'RVM', 'TWA', '4R1', 'N1L', 'X2F', 'TVD', '3J3', 'TOA', 
        'B4G', 'WUN', '0MK', '6YR', 'H6Q', 'CNP', 'TEU', 'MBF', '44S', 'Z9N', 'BM7', 'NGE', 'U9M', 'GMB', 'MTT', '9GP', 'DG0', 
        'RP5', 'KBA', 'ALX', 'FVQ', 'TGY', 'EBG', 'BXF', '9C1', 'BBV', 'AFD', '4QY', 'GCD', 'FBP', '96O', 'GNS', 'OTU', 'ACX', 
        'RP6', 'UEA', 'SGC', 'Z4V', 'RAM', 'AZC', 'J5B', '1GL', 'TGK', 'HSQ', 'LM2', 'MYG', 'PDX', 'Z6W', 'ZDC', '09X', 'IDX', 
        '9MR', 'MFU', 'CR6', 'Z8H', 'SUS', 'PZU', '89Y', '5TK', 'KME', 'U1Y', 'Z4U', 'LCN', 'GPK', 'MUR', '5TJ', 'NYT', '24S', 
        'SR1', '0UB', '48Z', 'MGL', 'Z6J', 'BMX', 'C3B', 'TVS', 'SLB', 'IPT', 'MLB', 'SLT', 'Z9D', 'GRX', 'AH8', 'F6P', 'BNX', 
        'JZR', 'LXB', 'M3M', 'XYT', 'MA1', 'GTM', 'SCG', 'Z3Q', 'KFN', 'LGC', 'ZB2', 'FIF', 'GLS', 'SSG', 'Z4Y', 'T6T', 'GCS', 
        'GZL', 'U8V', 'V3P', 'ABE', 'MGS', '6KW', '8GA', 'BZD', 'FUF', 'GMZ', 'FUY', 'HNW', 'LXZ', 'IN1', 'SNG', 'GAT', 'Z9M', 
        'BM3', 'ZDO', '9AM', '3LJ', 'X0X', 'MAN', '5GO', 'AMU', 'GUF', 'XMM', 'EAG', 'SUC', 'BXX', 'Z0F', '9OK', 'CTT', 'MLR', 
        '49V', 'ZMR', 'TWJ', 'MAW', '5II', 'ZEE', 'KBG', 'EMP', 'GUZ', 'TUJ', 'RB5', 'GCB', '9KJ', 'MAG', 'Z2D', '6LA', '2M4', 
        'GN4', 'MDA', 'TU4', 'Z2T', 'GL4', 'EBQ', 'NNG', '1SD', 'ANA', 'MXY', 'Z6H', 'GU0', 'GUP', 'SG6', 'NAG', '9VP', 'RIP', 
        '3S6', 'KDR', 'R1P', '3J4', 'DFX', 'RGG'}  # fmt: skip


# AlphaFold3 SI Tabel 15
PBV2_COMMON_NATURAL_LIGANDS = {'UPG', 'CDP', 'DSG', 'APC', 'GSP', 'FAD', 'IPE', 'NAI', '2BA', 'PGA', 'A3P', 'PRP', 'NAD', 'PLG', 
                               'SFG', 'MFU', 'APR', 'GTP', 'PLP', 'UDP', 'SAH', 'ACP', 'GSH', 'CTP', 'AKG', 'F15', '5AD', 'BCN', 
                               'BDP', 'H4B', 'PHO', 'FMN', 'MTA', 'NGA', 'OGA', 'SLB', 'SIN', 'C5P', 'TPP', 'BGC', 'NCA', 'UD1', 
                               'ANP', 'DGL', 'FDA', 'URI', 'ADP', 'MTE', 'PJ8', 'ATP'}  # fmt: skip