# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 08:58:47 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: (4R)-4-[(7-methoxy-2-{2-[(2-methylpropanoyl)amino]-1,3-thiazol-4-yl}quinolin-4-yl)oxy]-L-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2c(O[C@H]3CN[C@@H](C3)C(O)=O)cc(nc2c1)c4csc(NC(=O)C(C)C)n4
#
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
 12Y  12Y  (4R)-4-[(7-methoxy-2-{2-[(2-methylpropanoyl)amino]-1,3-thiazol-4-yl}quinolin-4-yl)oxy]-L-proline  L-peptide  56  32  .  2022-03-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_12Y
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
 12Y  C10  C  C     0   0.527   0.9716   6.1081  -0.5347
 12Y  O11  O  O     0  -0.433  -0.1996   6.3283  -0.6981
 12Y  C12  C  CR15  0  -0.173   1.5507   5.0372   0.3628
 12Y  C13  C  CH2   0  -0.507   2.2842   3.9304  -0.4355
 12Y  C14  C  CR15  0   0.018   1.5369   2.6514  -0.0638
 12Y  C15  C  CH2   0  -0.300   0.9550   2.9805   1.3059
 12Y  N16  N  NR15  0  -0.612   0.5087   4.3406   1.0893
 12Y  O33  O  O2    0  -0.467   2.4562   1.5705  -0.0579
 12Y  C34  C  CR6   0   0.493   2.0197   0.3123  -0.0385
 12Y  C35  C  CR16  0  -0.461   0.7021  -0.0729  -0.0219
 12Y  C36  C  CR6   0   0.165   0.4045  -1.4534  -0.0167
 12Y  N37  N  N     0  -0.496   1.3079  -2.4014  -0.0193
 12Y  C38  C  CR66  0   0.230   2.6123  -2.0423  -0.0312
 12Y  C39  C  CR66  0  -0.055   3.0314  -0.6883  -0.0433
 12Y  C40  C  CR16  0  -0.281   4.4086  -0.4014  -0.0594
 12Y  C41  C  CR16  0  -0.372   5.3416  -1.4053  -0.0632
 12Y  C42  C  CR6   0   0.399   4.9261  -2.7563  -0.0504
 12Y  C43  C  CR16  0  -0.429   3.5822  -3.0605  -0.0341
 12Y  O45  O  O2    0  -0.469   5.7813  -3.7915  -0.0534
 12Y  C46  C  CH3   0  -0.440   7.1738  -3.5375  -0.0749
 12Y  C47  C  CR5   0   0.332  -1.0019  -1.8806  -0.0056
 12Y  C48  C  CR15  0  -0.551  -1.4258  -3.1718   0.0359
 12Y  S49  S  S2    0   0.251  -3.1416  -3.2393   0.0366
 12Y  C50  C  CR5   0   0.295  -3.1626  -1.5075  -0.0201
 12Y  N51  N  N     0  -0.455  -2.0005  -0.9445  -0.0368
 12Y  N52  N  NH1   0  -0.700  -4.3216  -0.7749  -0.0527
 12Y  C53  C  C     0   0.590  -5.5765  -1.3078  -0.0156
 12Y  O54  O  O     0  -0.454  -5.7385  -2.5132   0.0283
 12Y  C55  C  CH1   0  -0.403  -6.6994  -0.2969   0.0157
 12Y  C56  C  CH3   0  -0.649  -7.9553  -0.8512  -0.6419
 12Y  C57  C  CH3   0  -0.649  -6.9616   0.0985   1.4736
 12Y  H9   H  HCR5  0   0.275   2.2759   5.5330   1.0220
 12Y  H10  H  HCH2  0   0.274   2.2928   4.0994  -1.5114
 12Y  H11  H  HCH2  0   0.270   3.3204   3.8600  -0.1054
 12Y  H12  H  HCR5  0   0.258   0.7344   2.4575  -0.7823
 12Y  H13  H  HCH2  0   0.248   0.1189   2.3421   1.5946
 12Y  H14  H  HCH2  0   0.218   1.7416   2.8739   2.0682
 12Y  H35  H  HCR6  0   0.287  -0.1126   0.6344  -0.0098
 12Y  H36  H  HCR6  0   0.266   4.7483   0.6253  -0.0683
 12Y  H37  H  HCR6  0   0.286   6.3905  -1.1433  -0.0760
 12Y  H38  H  HCR6  0   0.262   3.2539  -4.0927  -0.0246
 12Y  H39  H  HCH3  0   0.232   7.5018  -2.9803   0.8059
 12Y  H40  H  HCH3  0   0.262   7.6613  -4.5092  -0.0751
 12Y  H41  H  HCH3  0   0.232   7.4766  -2.9936  -0.9730
 12Y  H42  H  HCR5  0   0.302  -0.8262  -4.0671   0.0673
 12Y  H43  H  HNH1  0   0.429  -4.2034   0.2274  -0.1060
 12Y  H44  H  HCH1  0   0.270  -6.3756   0.5957  -0.5281
 12Y  H45  H  HCH3  0   0.230  -8.3274  -1.7251  -0.1077
 12Y  H46  H  HCH3  0   0.240  -8.7394  -0.0945  -0.6318
 12Y  H47  H  HCH3  0   0.240  -7.7800  -1.1341  -1.6798
 12Y  H48  H  HCH3  0   0.235  -7.3020  -0.7602   2.0541
 12Y  H49  H  HCH3  0   0.241  -6.0726   0.5050   1.9558
 12Y  H50  H  HCH3  0   0.248  -7.7388   0.8613   1.5142
 12Y  OXT  O  OH1   0  -0.596   1.9397   6.7962  -1.1323
 12Y  HXT  H  HOH1  0   0.482   1.5585   7.4707  -1.7138
 12Y  H2   H  HNR5  0   0.364   0.2573   4.8085   1.9483

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
 12Y  S49  C48  aromatic  1.717  0.020  1.717
 12Y  S49  C50  aromatic  1.733  0.020  1.733
 12Y  C48  C47  aromatic  1.360  0.020  1.360
 12Y  O45  C46  single    1.416  0.020  1.416
 12Y  O45  C42  single    1.343  0.020  1.343
 12Y  O54  C53  double    1.217  0.020  1.217
 12Y  C43  C42  aromatic  1.378  0.020  1.378
 12Y  C43  C38  aromatic  1.406  0.020  1.406
 12Y  N37  C38  aromatic  1.353  0.020  1.353
 12Y  N37  C36  aromatic  1.310  0.020  1.310
 12Y  C42  C41  aromatic  1.414  0.020  1.414
 12Y  C47  C36  single    1.470  0.020  1.470
 12Y  C47  N51  aromatic  1.369  0.020  1.369
 12Y  C50  N52  single    1.371  0.020  1.371
 12Y  C50  N51  aromatic  1.291  0.020  1.291
 12Y  C38  C39  aromatic  1.417  0.020  1.417
 12Y  C53  N52  single    1.364  0.020  1.364
 12Y  C53  C55  single    1.511  0.020  1.511
 12Y  C57  C55  single    1.533  0.020  1.533
 12Y  C36  C35  aromatic  1.412  0.020  1.412
 12Y  C41  C40  aromatic  1.370  0.020  1.370
 12Y  C55  C56  single    1.522  0.020  1.522
 12Y  C39  C40  aromatic  1.407  0.020  1.407
 12Y  C39  C34  aromatic  1.423  0.020  1.423
 12Y  C35  C34  aromatic  1.373  0.020  1.373
 12Y  C34  O33  single    1.332  0.020  1.332
 12Y  O33  C14  single    1.419  0.020  1.419
 12Y  C13  C14  single    1.527  0.020  1.527
 12Y  C13  C12  single    1.549  0.020  1.549
 12Y  C14  C15  single    1.524  0.020  1.524
 12Y  C12  C10  single    1.513  0.020  1.513
 12Y  C12  N16  single    1.449  0.020  1.449
 12Y  C10  O11  double    1.203  0.020  1.203
 12Y  C15  N16  single    1.448  0.020  1.448
 12Y  C12  H9   single    0.970  0.020  1.090
 12Y  C13  H10  single    0.970  0.020  1.090
 12Y  C13  H11  single    0.970  0.020  1.090
 12Y  C14  H12  single    0.970  0.020  1.090
 12Y  C15  H13  single    0.970  0.020  1.090
 12Y  C15  H14  single    0.970  0.020  1.090
 12Y  C35  H35  single    0.930  0.020  1.080
 12Y  C40  H36  single    0.930  0.020  1.080
 12Y  C41  H37  single    0.930  0.020  1.080
 12Y  C43  H38  single    0.930  0.020  1.080
 12Y  C46  H39  single    0.970  0.020  1.090
 12Y  C46  H40  single    0.970  0.020  1.090
 12Y  C46  H41  single    0.970  0.020  1.090
 12Y  C48  H42  single    0.930  0.020  1.080
 12Y  N52  H43  single    0.860  0.020  1.020
 12Y  C55  H44  single    0.970  0.020  1.090
 12Y  C56  H45  single    0.970  0.020  1.090
 12Y  C56  H46  single    0.970  0.020  1.090
 12Y  C56  H47  single    0.970  0.020  1.090
 12Y  C57  H48  single    0.970  0.020  1.090
 12Y  C57  H49  single    0.970  0.020  1.090
 12Y  C57  H50  single    0.970  0.020  1.090
 12Y  C10  OXT  single    1.330  0.020  1.330
 12Y  OXT  HXT  single    0.850  0.020  0.980
 12Y  N16  H2   single    0.890  0.020  1.040

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
 12Y  OXT  C10  C12  110.76  3.000
 12Y  OXT  C10  O11  123.58  3.000
 12Y  C12  C10  O11  125.66  3.000
 12Y  H9   C12  N16  113.02  3.000
 12Y  H9   C12  C13  108.61  3.000
 12Y  N16  C12  C13  104.80  3.000
 12Y  H9   C12  C10  106.82  3.000
 12Y  N16  C12  C10  111.26  3.000
 12Y  C13  C12  C10  112.41  3.000
 12Y  H11  C13  H10  107.56  3.000
 12Y  H11  C13  C14  109.72  3.000
 12Y  H10  C13  C14  111.97  3.000
 12Y  H11  C13  C12  109.89  3.000
 12Y  H10  C13  C12  113.70  3.000
 12Y  C14  C13  C12  103.96  3.000
 12Y  H12  C14  O33  110.05  3.000
 12Y  H12  C14  C15  110.38  3.000
 12Y  O33  C14  C15  114.08  3.000
 12Y  H12  C14  C13  110.33  3.000
 12Y  C15  C14  C13  102.98  3.000
 12Y  O33  C14  C13  108.78  3.000
 12Y  H14  C15  H13  107.93  3.000
 12Y  H14  C15  N16  114.52  3.000
 12Y  H13  C15  N16  110.68  3.000
 12Y  H14  C15  C14  109.19  3.000
 12Y  H13  C15  C14  113.83  3.000
 12Y  N16  C15  C14  100.72  3.000
 12Y  H2   N16  C15  112.62  3.000
 12Y  H2   N16  C12  112.51  3.000
 12Y  C15  N16  C12  107.76  3.000
 12Y  C34  O33  C14  120.49  3.000
 12Y  C39  C34  C35  119.02  3.000
 12Y  C35  C34  O33  125.43  3.000
 12Y  C39  C34  O33  115.55  3.000
 12Y  H35  C35  C36  118.79  3.000
 12Y  H35  C35  C34  122.75  3.000
 12Y  C36  C35  C34  118.46  3.000
 12Y  C47  C36  N37  116.72  3.000
 12Y  C47  C36  C35  119.07  3.000
 12Y  N37  C36  C35  124.22  3.000
 12Y  C38  N37  C36  118.22  3.000
 12Y  C43  C38  C39  119.19  3.000
 12Y  C39  C38  N37  122.59  3.000
 12Y  C43  C38  N37  118.22  3.000
 12Y  C40  C39  C38  118.97  3.000
 12Y  C40  C39  C34  123.55  3.000
 12Y  C38  C39  C34  117.49  3.000
 12Y  H36  C40  C41  118.78  3.000
 12Y  H36  C40  C39  120.08  3.000
 12Y  C41  C40  C39  121.14  3.000
 12Y  H37  C41  C42  121.12  3.000
 12Y  H37  C41  C40  118.88  3.000
 12Y  C42  C41  C40  120.00  3.000
 12Y  O45  C42  C43  116.81  3.000
 12Y  C43  C42  C41  119.85  3.000
 12Y  O45  C42  C41  123.34  3.000
 12Y  H38  C43  C42  120.40  3.000
 12Y  H38  C43  C38  118.74  3.000
 12Y  C42  C43  C38  120.85  3.000
 12Y  C46  O45  C42  119.22  3.000
 12Y  H41  C46  H40  108.69  3.000
 12Y  H41  C46  H39  109.00  3.000
 12Y  H40  C46  H39  108.75  3.000
 12Y  H41  C46  O45  111.98  3.000
 12Y  H40  C46  O45  106.31  3.000
 12Y  H39  C46  O45  112.00  3.000
 12Y  N51  C47  C48  115.00  3.000
 12Y  N51  C47  C36  119.93  3.000
 12Y  C48  C47  C36  125.07  3.000
 12Y  H42  C48  S49  121.54  3.000
 12Y  H42  C48  C47  128.04  3.000
 12Y  S49  C48  C47  110.42  3.000
 12Y  C50  S49  C48   88.44  3.000
 12Y  N52  C50  N51  121.82  3.000
 12Y  N51  C50  S49  115.16  3.000
 12Y  N52  C50  S49  123.01  3.000
 12Y  C50  N51  C47  110.98  3.000
 12Y  H43  N52  C53  119.77  3.000
 12Y  H43  N52  C50  115.61  3.000
 12Y  C53  N52  C50  124.63  3.000
 12Y  C55  C53  O54  124.25  3.000
 12Y  C55  C53  N52  115.02  3.000
 12Y  O54  C53  N52  120.69  3.000
 12Y  H44  C55  C57  108.23  3.000
 12Y  H44  C55  C56  109.06  3.000
 12Y  C57  C55  C56  111.32  3.000
 12Y  H44  C55  C53  108.39  3.000
 12Y  C56  C55  C53  111.14  3.000
 12Y  C57  C55  C53  108.62  3.000
 12Y  H47  C56  H46  107.74  3.000
 12Y  H47  C56  H45  108.27  3.000
 12Y  H46  C56  H45  107.85  3.000
 12Y  H47  C56  C55  111.92  3.000
 12Y  H46  C56  C55  109.69  3.000
 12Y  H45  C56  C55  111.22  3.000
 12Y  H50  C57  H49  107.71  3.000
 12Y  H50  C57  H48  107.98  3.000
 12Y  H49  C57  H48  108.21  3.000
 12Y  H50  C57  C55  109.75  3.000
 12Y  H49  C57  C55  112.17  3.000
 12Y  H48  C57  C55  110.88  3.000
 12Y  HXT  OXT  C10  110.10  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
 12Y  CONST_01  C43  C38  C39  C34  180.00   0.0  0
 12Y  CONST_02  N37  C38  C39  C34    0.00   0.0  0
 12Y  CONST_03  C41  C40  C39  C34  180.00   0.0  0
 12Y  CONST_04  N37  C36  C35  C34    0.00   0.0  0
 12Y  CONST_05  C47  C36  C35  C34  180.00   0.0  0
 12Y  CONST_06  C38  N37  C36  C35    0.00   0.0  0
 12Y  CONST_07  C48  C47  C36  C35  180.00   0.0  0
 12Y  CONST_08  N51  C47  C36  C35    0.00   0.0  0
 12Y  CONST_09  C38  C39  C34  C35    0.00   0.0  0
 12Y  CONST_10  C40  C39  C34  C35  180.00   0.0  0
 12Y  CONST_11  C43  C38  N37  C36  180.00   0.0  0
 12Y  CONST_12  C39  C38  N37  C36    0.00   0.0  0
 12Y  CONST_13  S49  C48  C47  C36  180.00   0.0  0
 12Y  CONST_14  C50  N51  C47  C36  180.00   0.0  0
 12Y  CONST_15  C39  C34  C35  C36    0.00   0.0  0
 12Y  CONST_16  C42  C43  C38  N37  180.00   0.0  0
 12Y  CONST_17  C40  C39  C38  N37  180.00   0.0  0
 12Y  CONST_18  C48  C47  C36  N37    0.00   0.0  0
 12Y  CONST_19  N51  C47  C36  N37  180.00   0.0  0
 12Y  CONST_20  C41  C42  C43  C38    0.00   0.0  0
 12Y  CONST_21  C47  C36  N37  C38  180.00   0.0  0
 12Y  CONST_22  C41  C40  C39  C38    0.00   0.0  0
 12Y  CONST_23  C42  C43  C38  C39    0.00   0.0  0
 12Y  CONST_24  C42  C41  C40  C39    0.00   0.0  0
 12Y  CONST_25  C43  C42  C41  C40    0.00   0.0  0
 12Y  CONST_26  C43  C38  C39  C40    0.00   0.0  0
 12Y  CONST_27  C50  S49  C48  C47    0.00   0.0  0
 12Y  CONST_28  S49  C50  N51  C47    0.00   0.0  0
 12Y  CONST_29  N51  C50  S49  C48    0.00   0.0  0
 12Y  CONST_30  C50  N51  C47  C48    0.00   0.0  0
 12Y  CONST_31  N51  C47  C48  S49    0.00   0.0  0
 12Y  CONST_32  C38  C39  C34  O33  180.00   0.0  0
 12Y  CONST_33  C40  C39  C34  O33    0.00   0.0  0
 12Y  CONST_34  C36  C35  C34  O33  180.00   0.0  0
 12Y  CONST_35  O45  C42  C43  C38  180.00   0.0  0
 12Y  CONST_36  O45  C42  C41  C40  180.00   0.0  0
 12Y  CONST_37  N52  C50  N51  C47  180.00   0.0  0
 12Y  CONST_38  N52  C50  S49  C48  180.00   0.0  0
 12Y  CONST_39  H36  C40  C39  C34    0.00   0.0  0
 12Y  CONST_40  H42  C48  C47  C36    0.00   0.0  0
 12Y  CONST_41  H38  C43  C38  N37    0.00   0.0  0
 12Y  CONST_42  H35  C35  C36  N37  180.00   0.0  0
 12Y  CONST_43  H37  C41  C40  C39  180.00   0.0  0
 12Y  CONST_44  C53  N52  C50  S49    0.00   0.0  0
 12Y  CONST_45  C53  N52  C50  N51  180.00   0.0  0
 12Y  CONST_46  H43  N52  C50  S49  180.00   0.0  0
 12Y  CONST_47  O54  C53  N52  C50    0.00   0.0  0
 12Y  CONST_48  C55  C53  N52  C50  180.00   0.0  0
 12Y  CONST_49  HXT  OXT  C10  C12  180.00   0.0  0
 12Y  Var_01    C14  C15  N16  C12  -43.55  30.0  1
 12Y  Var_02    C39  C34  O33  C14  179.60  30.0  3
 12Y  Var_03    H39  C46  O45  C42   61.46  30.0  3
 12Y  Var_04    C57  C55  C53  N52  -86.49  30.0  3
 12Y  Var_05    H48  C57  C55  C53  -63.33  30.0  3
 12Y  Var_06    H45  C56  C55  C53   62.38  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
 12Y  chir_01  C12  C13  C10  N16  negativ
 12Y  chir_02  C14  O33  C15  C13  negativ

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
 12Y  plan-1  C36  0.020
 12Y  plan-1  C47  0.020
 12Y  plan-1  C48  0.020
 12Y  plan-1  S49  0.020
 12Y  plan-1  C50  0.020
 12Y  plan-1  N51  0.020
 12Y  plan-1  N52  0.020
 12Y  plan-1  H42  0.020
 12Y  plan-2  O33  0.020
 12Y  plan-2  C34  0.020
 12Y  plan-2  C35  0.020
 12Y  plan-2  C36  0.020
 12Y  plan-2  N37  0.020
 12Y  plan-2  C38  0.020
 12Y  plan-2  C39  0.020
 12Y  plan-2  C40  0.020
 12Y  plan-2  C41  0.020
 12Y  plan-2  C42  0.020
 12Y  plan-2  C43  0.020
 12Y  plan-2  O45  0.020
 12Y  plan-2  C47  0.020
 12Y  plan-2  H35  0.020
 12Y  plan-2  H36  0.020
 12Y  plan-2  H37  0.020
 12Y  plan-2  H38  0.020
 12Y  plan-3  C50  0.020
 12Y  plan-3  N52  0.020
 12Y  plan-3  C53  0.020
 12Y  plan-3  O54  0.020
 12Y  plan-3  C55  0.020
 12Y  plan-3  H43  0.020
 12Y  plan-4  C10  0.020
 12Y  plan-4  O11  0.020
 12Y  plan-4  C12  0.020
 12Y  plan-4  OXT  0.020
 12Y  plan-4  HXT  0.020

