# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 18:23:05 2021
#   Inital geometry file: a 119 line input string
#   Ligand name: N-[(5S)-5-amino-5-carboxypentanoyl]-L-cysteinyl-D-methionine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCC[C@@H](NC(=O)[C@H](CS)NC(=O)CCC[C@H](N)C(O)=O)C(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 M8F  M8F  N-[(5S)-5-amino-5-carboxypentanoyl]-L-cysteinyl-D-methionine  ligand  50  25  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_M8F
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 M8F  C8    C  C     0   0.566  11.7701  39.2586  5.4316
 M8F  O9    O  O     0  -0.498  11.0885  38.9906  6.4109
 M8F  O4    O  O     0  -0.455  17.7315  36.2649  4.8807
 M8F  C7    C  CH2   0  -0.574  13.2744  39.1288  5.4278
 M8F  C2    C  C     0   0.524  17.2431  36.1607  5.9805
 M8F  C1    C  CH1   0  -0.208  15.7395  36.2239  6.2362
 M8F  C5    C  CH2   0  -0.434  15.2451  37.6248  5.8526
 M8F  C6    C  CH2   0  -0.412  13.7276  37.7343  5.8537
 M8F  N1    N  NH2   0  -0.780  15.2880  35.8642  7.5585
 M8F  N10   N  NH1   0  -0.624  11.2241  39.7093  4.2866
 M8F  C11   C  CH1   0  -0.219   9.8031  39.7906  4.1171
 M8F  C14   C  C     0   0.566   9.1708  38.3918  4.1091
 M8F  O15   O  O     0  -0.467   9.8180  37.3896  3.8678
 M8F  C12   C  CH2   0  -0.566   9.4639  40.5349  2.8294
 M8F  S13   S  S2    0  -0.241  10.0180  39.5742  1.3774
 M8F  N16   N  NH1   0  -0.644   7.8494  38.3921  4.3438
 M8F  C17   C  CH1   0  -0.205   7.0450  37.1960  4.2658
 M8F  C22   C  C     0   0.558   5.7968  37.2979  5.1258
 M8F  O24   O  O     0  -0.441   4.8971  36.4982  5.0635
 M8F  C18   C  CH2   0  -0.430   6.7302  36.7732  2.8249
 M8F  C19   C  CH2   0  -0.577   6.3591  37.9239  1.9037
 M8F  S20   S  S2    0  -0.049   5.0848  39.0415  2.5446
 M8F  C21   C  CH3   0  -0.765   3.5945  38.0488  2.3069
 M8F  O23   O  OH1   0  -0.587   5.8434  38.2801  6.0114
 M8F  H7    H  HCH2  0   0.265  13.6739  39.8714  6.1252
 M8F  H7A   H  HCH2  0   0.249  13.6841  39.3738  4.4454
 M8F  H1    H  HCH1  0   0.272  15.3005  35.5148  5.5257
 M8F  H5    H  HCH2  0   0.234  15.6693  38.3602  6.5457
 M8F  H5A   H  HCH2  0   0.241  15.6281  37.8746  4.8608
 M8F  H6    H  HCH2  0   0.228  13.3107  36.9882  5.1699
 M8F  H6A   H  HCH2  0   0.238  13.3377  37.5057  6.8450
 M8F  HN1   H  HNH2  0   0.355  15.5649  34.9200  7.7921
 M8F  HN1A  H  HNH2  0   0.345  15.6967  36.4715  8.2576
 M8F  HO3   H  HOH1  0   0.480  18.9069  35.9697  6.8525
 M8F  HN10  H  HNH1  0   0.400  11.8081  39.8118  3.4707
 M8F  H11   H  HCH1  0   0.306   9.3693  40.3689  4.9386
 M8F  H12   H  HCH2  0   0.286   8.3907  40.7097  2.7730
 M8F  H12A  H  HCH2  0   0.310   9.9615  41.5035  2.8339
 M8F  HS13  H  HSH1  0   0.238   9.9386  40.5742  0.4943
 M8F  HN16  H  HNH1  0   0.406   7.3903  39.2703  4.5294
 M8F  H17   H  HCH1  0   0.318   7.6166  36.3797  4.7229
 M8F  H18   H  HCH2  0   0.262   7.6157  36.2893  2.4080
 M8F  H18A  H  HCH2  0   0.260   5.9494  36.0126  2.8405
 M8F  H19   H  HCH2  0   0.276   7.2310  38.5519  1.7093
 M8F  H19A  H  HCH2  0   0.286   6.0356  37.5385  0.9352
 M8F  H21   H  HCH3  0   0.265   3.6062  37.1501  2.9190
 M8F  H21A  H  HCH3  0   0.274   2.7474  38.6621  2.6092
 M8F  H21B  H  HCH3  0   0.263   3.4729  37.7807  1.2586
 M8F  HO23  H  HOH1  0   0.487   5.0386  38.2774  6.5519
 M8F  O3    O  OH1   0  -0.585  17.9647  35.9885  7.0785

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 M8F  C5   C1    single  1.534  0.020  1.534
 M8F  C2   C1    single  1.526  0.020  1.526
 M8F  C1   N1    single  1.443  0.020  1.443
 M8F  C1   H1    single  0.970  0.020  1.090
 M8F  N1   HN1   single  0.890  0.020  1.040
 M8F  N1   HN1A  single  0.890  0.020  1.040
 M8F  O4   C2    double  1.208  0.020  1.208
 M8F  C2   O3    single  1.325  0.020  1.325
 M8F  O3   HO3   single  0.850  0.020  0.980
 M8F  C5   C6    single  1.521  0.020  1.521
 M8F  C5   H5    single  0.970  0.020  1.090
 M8F  C5   H5A   single  0.970  0.020  1.090
 M8F  C7   C6    single  1.527  0.020  1.527
 M8F  C6   H6    single  0.970  0.020  1.090
 M8F  C6   H6A   single  0.970  0.020  1.090
 M8F  C7   C8    single  1.510  0.020  1.510
 M8F  C7   H7    single  0.970  0.020  1.090
 M8F  C7   H7A   single  0.970  0.020  1.090
 M8F  N10  C8    single  1.346  0.020  1.346
 M8F  C8   O9    double  1.223  0.020  1.223
 M8F  N10  C11   single  1.433  0.020  1.433
 M8F  N10  HN10  single  0.860  0.020  1.020
 M8F  C12  C11   single  1.526  0.020  1.526
 M8F  C14  C11   single  1.535  0.020  1.535
 M8F  C11  H11   single  0.970  0.020  1.090
 M8F  S13  C12   single  1.827  0.020  1.827
 M8F  C12  H12   single  0.970  0.020  1.090
 M8F  C12  H12A  single  0.970  0.020  1.090
 M8F  S13  HS13  single  1.200  0.020  1.300
 M8F  O15  C14   double  1.217  0.020  1.217
 M8F  N16  C14   single  1.342  0.020  1.342
 M8F  C17  N16   single  1.443  0.020  1.443
 M8F  N16  HN16  single  0.860  0.020  1.020
 M8F  C18  C17   single  1.534  0.020  1.534
 M8F  C17  C22   single  1.519  0.020  1.519
 M8F  C17  H17   single  0.970  0.020  1.090
 M8F  C19  C18   single  1.520  0.020  1.520
 M8F  C18  H18   single  0.970  0.020  1.090
 M8F  C18  H18A  single  0.970  0.020  1.090
 M8F  S20  C19   single  1.812  0.020  1.812
 M8F  C19  H19   single  0.970  0.020  1.090
 M8F  C19  H19A  single  0.970  0.020  1.090
 M8F  C21  S20   single  1.806  0.020  1.806
 M8F  C21  H21   single  0.970  0.020  1.090
 M8F  C21  H21A  single  0.970  0.020  1.090
 M8F  C21  H21B  single  0.970  0.020  1.090
 M8F  O24  C22   double  1.205  0.020  1.205
 M8F  C22  O23   single  1.323  0.020  1.323
 M8F  O23  HO23  single  0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 M8F  N10   C8   C7    115.51  3.000
 M8F  N10   C8   O9    121.90  3.000
 M8F  C7    C8   O9    122.58  3.000
 M8F  H7A   C7   H7    106.51  3.000
 M8F  H7A   C7   C6    110.14  3.000
 M8F  H7    C7   C6    109.49  3.000
 M8F  H7A   C7   C8    110.90  3.000
 M8F  H7    C7   C8    107.68  3.000
 M8F  C6    C7   C8    111.93  3.000
 M8F  O3    C2   C1    113.76  3.000
 M8F  O3    C2   O4    123.05  3.000
 M8F  C1    C2   O4    123.18  3.000
 M8F  H1    C1   N1    107.91  3.000
 M8F  H1    C1   C5    107.44  3.000
 M8F  N1    C1   C5    110.85  3.000
 M8F  H1    C1   C2    105.02  3.000
 M8F  N1    C1   C2    116.84  3.000
 M8F  C5    C1   C2    108.26  3.000
 M8F  H5A   C5   H5    106.57  3.000
 M8F  H5A   C5   C6    109.52  3.000
 M8F  H5    C5   C6    109.71  3.000
 M8F  H5A   C5   C1    108.84  3.000
 M8F  H5    C5   C1    109.25  3.000
 M8F  C6    C5   C1    112.76  3.000
 M8F  H6A   C6   H6    106.81  3.000
 M8F  H6A   C6   C5    110.03  3.000
 M8F  H6    C6   C5    109.30  3.000
 M8F  H6A   C6   C7    109.83  3.000
 M8F  H6    C6   C7    109.58  3.000
 M8F  C5    C6   C7    111.19  3.000
 M8F  HN1A  N1   HN1   106.86  3.000
 M8F  HN1A  N1   C1    110.91  3.000
 M8F  HN1   N1   C1    111.03  3.000
 M8F  HN10  N10  C11   118.21  3.000
 M8F  HN10  N10  C8    119.15  3.000
 M8F  C11   N10  C8    121.44  3.000
 M8F  H11   C11  C12   106.73  3.000
 M8F  H11   C11  C14   108.80  3.000
 M8F  C12   C11  C14   110.41  3.000
 M8F  H11   C11  N10   109.52  3.000
 M8F  C14   C11  N10   110.93  3.000
 M8F  C12   C11  N10   110.36  3.000
 M8F  N16   C14  O15   123.95  3.000
 M8F  N16   C14  C11   113.85  3.000
 M8F  O15   C14  C11   122.16  3.000
 M8F  H12A  C12  H12   107.93  3.000
 M8F  H12A  C12  S13   109.42  3.000
 M8F  H12   C12  S13   110.01  3.000
 M8F  H12A  C12  C11   109.20  3.000
 M8F  H12   C12  C11   109.95  3.000
 M8F  S13   C12  C11   110.30  3.000
 M8F  HS13  S13  C12    96.53  3.000
 M8F  HN16  N16  C17   118.56  3.000
 M8F  HN16  N16  C14   118.73  3.000
 M8F  C17   N16  C14   122.61  3.000
 M8F  H17   C17  C18   107.06  3.000
 M8F  H17   C17  C22   104.02  3.000
 M8F  C18   C17  C22   112.43  3.000
 M8F  H17   C17  N16   107.69  3.000
 M8F  C22   C17  N16   111.82  3.000
 M8F  C18   C17  N16   113.17  3.000
 M8F  O23   C22  O24   123.59  3.000
 M8F  O23   C22  C17   113.56  3.000
 M8F  O24   C22  C17   122.65  3.000
 M8F  H18A  C18  H18   106.09  3.000
 M8F  H18A  C18  C19   111.22  3.000
 M8F  H18   C18  C19   107.58  3.000
 M8F  H18A  C18  C17   109.02  3.000
 M8F  H18   C18  C17   108.32  3.000
 M8F  C19   C18  C17   114.24  3.000
 M8F  H19A  C19  H19   106.37  3.000
 M8F  H19A  C19  S20   108.85  3.000
 M8F  H19   C19  S20   105.65  3.000
 M8F  H19A  C19  C18   110.05  3.000
 M8F  H19   C19  C18   110.39  3.000
 M8F  S20   C19  C18   115.10  3.000
 M8F  C21   S20  C19   101.23  3.000
 M8F  H21B  C21  H21A  108.61  3.000
 M8F  H21B  C21  H21   109.86  3.000
 M8F  H21A  C21  H21   108.53  3.000
 M8F  H21B  C21  S20   110.74  3.000
 M8F  H21A  C21  S20   107.21  3.000
 M8F  H21   C21  S20   111.79  3.000
 M8F  HO23  O23  C22   109.99  3.000
 M8F  HO3   O3   C2    109.80  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 M8F  CONST_01  C11   N10  C8   O9      0.00   0.0  0
 M8F  CONST_02  C11   N10  C8   C7    180.00   0.0  0
 M8F  CONST_03  C17   N16  C14  C11   180.00   0.0  0
 M8F  CONST_04  C17   N16  C14  O15     0.00   0.0  0
 M8F  CONST_05  HN10  N10  C8   O9    180.00   0.0  0
 M8F  CONST_06  HN16  N16  C14  C11     0.00   0.0  0
 M8F  CONST_07  HO3   O3   C2   O4      0.00   0.0  0
 M8F  CONST_08  HO23  O23  C22  C17   180.00   0.0  0
 M8F  Var_01    C5    C6   C7   C8   -179.64  30.0  3
 M8F  Var_02    C6    C7   C8   O9     54.02  30.0  1
 M8F  Var_03    C1    C5   C6   C7   -178.33  30.0  1
 M8F  Var_04    S20   C19  C18  C17   -49.89  30.0  1
 M8F  Var_05    H21   C21  S20  C19    64.61  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 M8F  chir_01  C1   C5   C2   N1   negativ
 M8F  chir_02  C11  N10  C12  C14  negativ
 M8F  chir_03  C17  N16  C18  C22  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 M8F  plan-1  C8    0.020
 M8F  plan-1  O9    0.020
 M8F  plan-1  C7    0.020
 M8F  plan-1  N10   0.020
 M8F  plan-1  C11   0.020
 M8F  plan-1  HN10  0.020
 M8F  plan-2  C11   0.020
 M8F  plan-2  C14   0.020
 M8F  plan-2  O15   0.020
 M8F  plan-2  N16   0.020
 M8F  plan-2  C17   0.020
 M8F  plan-2  HN16  0.020
 M8F  plan-3  O4    0.020
 M8F  plan-3  C2    0.020
 M8F  plan-3  C1    0.020
 M8F  plan-3  HO3   0.020
 M8F  plan-3  O3    0.020
 M8F  plan-4  C17   0.020
 M8F  plan-4  C22   0.020
 M8F  plan-4  O24   0.020
 M8F  plan-4  O23   0.020
 M8F  plan-4  HO23  0.020

