# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 02:29:32 2021
#   Inital geometry file: a 132 line input string
#   Ligand name: (2S)-3-phenyl-N~1~-[2-(pyridin-4-yl)-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4-yl]propane-1,2-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CNc1nc(nc2sc3CCCCc3c12)c4ccncc4)Cc5ccccc5
#
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
 C58  C58  (2S)-3-phenyl-N~1~-[2-(pyridin-4-yl)-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4-yl]propane-1,2-diamine  ligand  55  30  .  2022-03-15  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C58
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
 C58  C     C  CH1   0  -0.081  16.3765  16.5208  15.2985
 C58  N     N  NH2   0  -0.808  15.3855  15.4809  15.0600
 C58  S     S  S2    0   0.212  17.0768  18.1259   8.4938
 C58  C1    C  CH2   0  -0.278  17.6407  16.2027  14.5049
 C58  N1    N  NH1   0  -0.698  17.4143  16.1361  13.0765
 C58  C2    C  CR6   0   0.525  17.4088  17.2095  12.2734
 C58  N2    N  N     0  -0.490  17.6140  18.3996  12.8309
 C58  C3    C  CR6   0   0.385  17.6558  19.4845  12.0652
 C58  N3    N  N     0  -0.469  17.5119  19.5203  10.7534
 C58  C4    C  CR56  0  -0.035  17.2924  18.3332  10.1967
 C58  N4    N  N     0  -0.404  18.3482  23.2131  14.0472
 C58  C5    C  CR56  0   0.004  17.2064  17.1162  10.8688
 C58  C6    C  CR5   0   0.217  16.9375  16.0128   9.9869
 C58  C7    C  CR5   0  -0.265  16.8601  16.4119   8.6911
 C58  C8    C  CH2   0  -0.480  16.6263  15.5215   7.5148
 C58  C9    C  CH2   0  -0.449  16.8609  14.0666   7.9116
 C58  C10   C  CH2   0  -0.442  16.1650  13.7493   9.2286
 C58  C11   C  CH2   0  -0.556  16.7372  14.5764  10.3790
 C58  C12   C  CR6   0   0.088  17.8944  20.7737  12.7538
 C58  C13   C  CR16  0  -0.358  18.0805  20.8348  14.1323
 C58  C14   C  CR16  0  -0.059  18.3021  22.0696  14.7212
 C58  C15   C  CR16  0  -0.061  18.1697  23.1506  12.7321
 C58  C16   C  CR16  0  -0.356  17.9430  21.9703  12.0436
 C58  C17   C  CH2   0  -0.530  16.6875  16.5707  16.7986
 C58  C18   C  CR6   0   0.132  17.5252  17.7548  17.1929
 C58  C19   C  CR16  0  -0.302  16.9268  18.9952  17.4104
 C58  C20   C  CR16  0  -0.244  17.6847  20.1023  17.7648
 C58  C21   C  CR16  0  -0.272  19.0629  19.9895  17.8996
 C58  C22   C  CR16  0  -0.242  19.6723  18.7613  17.6816
 C58  C23   C  CR16  0  -0.311  18.9073  17.6545  17.3356
 C58  H     H  HCH1  0   0.221  16.0282  17.5185  14.9914
 C58  HN    H  HNH2  0   0.348  14.5246  15.7296  15.5326
 C58  HNA   H  HNH2  0   0.342  15.1496  15.4600  14.0748
 C58  H1    H  HCH2  0   0.255  18.4070  16.9486  14.7115
 C58  H1A   H  HCH2  0   0.250  18.0267  15.2294  14.8136
 C58  HN1   H  HNH1  0   0.424  17.3432  15.2240  12.6619
 C58  H8    H  HCH2  0   0.256  15.6033  15.6514   7.1473
 C58  H8A   H  HCH2  0   0.259  17.2847  15.8022   6.6891
 C58  H9    H  HCH2  0   0.245  16.4958  13.4109   7.1194
 C58  H9A   H  HCH2  0   0.230  17.9344  13.8820   8.0086
 C58  H10   H  HCH2  0   0.231  15.0954  13.9561   9.1299
 C58  H10A  H  HCH2  0   0.245  16.2598  12.6888   9.4666
 C58  H11   H  HCH2  0   0.254  17.6905  14.1439  10.7031
 C58  H11A  H  HCH2  0   0.248  16.0553  14.5114  11.2318
 C58  H13   H  HCR6  0   0.276  18.0519  19.9425  14.7425
 C58  H14   H  HCR6  0   0.260  18.4489  22.1328  15.7934
 C58  H15   H  HCR6  0   0.264  18.2081  24.0904  12.1921
 C58  H16   H  HCR6  0   0.266  17.8081  21.9868  10.9715
 C58  H17   H  HCH2  0   0.252  15.7397  16.6088  17.3430
 C58  H17A  H  HCH2  0   0.243  17.1771  15.6379  17.0929
 C58  H19   H  HCR6  0   0.246  15.8517  19.0933  17.3093
 C58  H20   H  HCR6  0   0.255  17.1986  21.0541  17.9398
 C58  H21   H  HCR6  0   0.254  19.6554  20.8519  18.1775
 C58  H22   H  HCR6  0   0.253  20.7450  18.6607  17.7874
 C58  H23   H  HCR6  0   0.249  19.3926  16.6981  17.1770

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
 C58  C    N     single    1.456  0.020  1.456
 C58  C    C1    single    1.526  0.020  1.526
 C58  C    C17   single    1.533  0.020  1.533
 C58  C    H     single    0.970  0.020  1.090
 C58  N    HN    single    0.890  0.020  1.040
 C58  N    HNA   single    0.890  0.020  1.040
 C58  S    C4    aromatic  1.729  0.020  1.729
 C58  S    C7    aromatic  1.739  0.020  1.739
 C58  C1   N1    single    1.448  0.020  1.448
 C58  C1   H1    single    0.970  0.020  1.090
 C58  C1   H1A   single    0.970  0.020  1.090
 C58  N1   C2    single    1.341  0.020  1.341
 C58  N1   HN1   single    0.860  0.020  1.020
 C58  C2   N2    aromatic  1.330  0.020  1.330
 C58  C2   C5    aromatic  1.422  0.020  1.422
 C58  N2   C3    aromatic  1.329  0.020  1.329
 C58  C3   N3    aromatic  1.320  0.020  1.320
 C58  C3   C12   single    1.481  0.020  1.481
 C58  N3   C4    aromatic  1.329  0.020  1.329
 C58  C4   C5    aromatic  1.393  0.020  1.393
 C58  N4   C14   aromatic  1.328  0.020  1.328
 C58  N4   C15   aromatic  1.329  0.020  1.329
 C58  C5   C6    aromatic  1.438  0.020  1.438
 C58  C6   C7    aromatic  1.358  0.020  1.358
 C58  C6   C11   single    1.502  0.020  1.502
 C58  C7   C8    single    1.494  0.020  1.494
 C58  C8   C9    single    1.526  0.020  1.526
 C58  C8   H8    single    0.970  0.020  1.090
 C58  C8   H8A   single    0.970  0.020  1.090
 C58  C9   C10   single    1.523  0.020  1.523
 C58  C9   H9    single    0.970  0.020  1.090
 C58  C9   H9A   single    0.970  0.020  1.090
 C58  C10  C11   single    1.528  0.020  1.528
 C58  C10  H10   single    0.970  0.020  1.090
 C58  C10  H10A  single    0.970  0.020  1.090
 C58  C11  H11   single    0.970  0.020  1.090
 C58  C11  H11A  single    0.970  0.020  1.090
 C58  C12  C13   aromatic  1.392  0.020  1.392
 C58  C12  C16   aromatic  1.392  0.020  1.392
 C58  C13  C14   aromatic  1.386  0.020  1.386
 C58  C13  H13   single    0.930  0.020  1.080
 C58  C14  H14   single    0.930  0.020  1.080
 C58  C15  C16   aromatic  1.385  0.020  1.385
 C58  C15  H15   single    0.930  0.020  1.080
 C58  C16  H16   single    0.930  0.020  1.080
 C58  C17  C18   single    1.503  0.020  1.503
 C58  C17  H17   single    0.970  0.020  1.090
 C58  C17  H17A  single    0.970  0.020  1.090
 C58  C18  C19   aromatic  1.394  0.020  1.394
 C58  C18  C23   aromatic  1.393  0.020  1.393
 C58  C19  C20   aromatic  1.388  0.020  1.388
 C58  C19  H19   single    0.930  0.020  1.080
 C58  C20  C21   aromatic  1.389  0.020  1.389
 C58  C20  H20   single    0.930  0.020  1.080
 C58  C21  C22   aromatic  1.388  0.020  1.388
 C58  C21  H21   single    0.930  0.020  1.080
 C58  C22  C23   aromatic  1.389  0.020  1.389
 C58  C22  H22   single    0.930  0.020  1.080
 C58  C23  H23   single    0.930  0.020  1.080

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
 C58  H     C    C17  107.93  3.000
 C58  H     C    C1   107.82  3.000
 C58  C17   C    C1   110.34  3.000
 C58  H     C    N    112.73  3.000
 C58  C17   C    N    108.76  3.000
 C58  C1    C    N    109.25  3.000
 C58  HNA   N    HN   105.11  3.000
 C58  HNA   N    C    109.42  3.000
 C58  HN    N    C    109.06  3.000
 C58  C7    S    C4    91.26  3.000
 C58  H1A   C1   H1   107.95  3.000
 C58  H1A   C1   N1   107.06  3.000
 C58  H1    C1   N1   109.19  3.000
 C58  H1A   C1   C    109.37  3.000
 C58  H1    C1   C    109.96  3.000
 C58  N1    C1   C    113.15  3.000
 C58  HN1   N1   C2   118.66  3.000
 C58  HN1   N1   C1   117.39  3.000
 C58  C2    N1   C1   123.70  3.000
 C58  C5    C2   N2   119.64  3.000
 C58  C5    C2   N1   122.66  3.000
 C58  N2    C2   N1   117.69  3.000
 C58  C3    N2   C2   119.60  3.000
 C58  C12   C3   N3   117.13  3.000
 C58  C12   C3   N2   116.61  3.000
 C58  N3    C3   N2   126.25  3.000
 C58  C4    N3   C3   114.20  3.000
 C58  C5    C4   N3   126.04  3.000
 C58  C5    C4   S    111.27  3.000
 C58  N3    C4   S    122.69  3.000
 C58  C15   N4   C14  117.20  3.000
 C58  C6    C5   C4   112.71  3.000
 C58  C6    C5   C2   133.06  3.000
 C58  C4    C5   C2   114.23  3.000
 C58  C11   C6   C7   121.49  3.000
 C58  C11   C6   C5   126.76  3.000
 C58  C7    C6   C5   111.74  3.000
 C58  C8    C7   C6   125.81  3.000
 C58  C8    C7   S    121.18  3.000
 C58  C6    C7   S    113.00  3.000
 C58  H8A   C8   H8   106.20  3.000
 C58  H8A   C8   C9   110.41  3.000
 C58  H8    C8   C9   110.12  3.000
 C58  H8A   C8   C7   110.35  3.000
 C58  H8    C8   C7   109.87  3.000
 C58  C9    C8   C7   109.84  3.000
 C58  H9A   C9   H9   106.94  3.000
 C58  H9A   C9   C10  109.67  3.000
 C58  H9    C9   C10  110.47  3.000
 C58  H9A   C9   C8   109.56  3.000
 C58  H9    C9   C8   109.43  3.000
 C58  C10   C9   C8   110.68  3.000
 C58  H10A  C10  H10  106.77  3.000
 C58  H10A  C10  C11  109.23  3.000
 C58  H10   C10  C11  109.37  3.000
 C58  H10A  C10  C9   110.58  3.000
 C58  H10   C10  C9   109.23  3.000
 C58  C11   C10  C9   111.54  3.000
 C58  H11A  C11  H11  106.75  3.000
 C58  H11A  C11  C10  108.75  3.000
 C58  H11   C11  C10  109.56  3.000
 C58  H11A  C11  C6   110.09  3.000
 C58  H11   C11  C6   109.79  3.000
 C58  C10   C11  C6   111.77  3.000
 C58  C16   C12  C13  117.56  3.000
 C58  C16   C12  C3   121.10  3.000
 C58  C13   C12  C3   121.33  3.000
 C58  H13   C13  C14  119.98  3.000
 C58  H13   C13  C12  121.26  3.000
 C58  C14   C13  C12  118.76  3.000
 C58  H14   C14  C13  119.59  3.000
 C58  H14   C14  N4   116.56  3.000
 C58  C13   C14  N4   123.85  3.000
 C58  H15   C15  C16  119.78  3.000
 C58  H15   C15  N4   116.57  3.000
 C58  C16   C15  N4   123.64  3.000
 C58  H16   C16  C15  120.03  3.000
 C58  H16   C16  C12  120.98  3.000
 C58  C15   C16  C12  118.98  3.000
 C58  H17A  C17  H17  106.49  3.000
 C58  H17A  C17  C18  110.59  3.000
 C58  H17   C17  C18  108.96  3.000
 C58  H17A  C17  C    109.05  3.000
 C58  H17   C17  C    108.21  3.000
 C58  C18   C17  C    113.29  3.000
 C58  C23   C18  C19  118.29  3.000
 C58  C23   C18  C17  121.53  3.000
 C58  C19   C18  C17  120.17  3.000
 C58  H19   C19  C20  119.55  3.000
 C58  H19   C19  C18  119.44  3.000
 C58  C20   C19  C18  121.01  3.000
 C58  H20   C20  C21  120.06  3.000
 C58  H20   C20  C19  119.82  3.000
 C58  C21   C20  C19  120.12  3.000
 C58  H21   C21  C22  120.32  3.000
 C58  H21   C21  C20  120.21  3.000
 C58  C22   C21  C20  119.47  3.000
 C58  H22   C22  C23  119.73  3.000
 C58  H22   C22  C21  120.12  3.000
 C58  C23   C22  C21  120.15  3.000
 C58  H23   C23  C22  119.53  3.000
 C58  H23   C23  C18  119.51  3.000
 C58  C22   C23  C18  120.96  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
 C58  CONST_01  C3   N3   C4   S    180.00   0.0  0
 C58  CONST_02  C2   C5   C4   S    180.00   0.0  0
 C58  CONST_03  C6   C5   C4   S      0.00   0.0  0
 C58  CONST_04  C5   C6   C7   S      0.00   0.0  0
 C58  CONST_05  N3   C3   N2   C2     0.00   0.0  0
 C58  CONST_06  C12  C3   N2   C2   180.00   0.0  0
 C58  CONST_07  N3   C4   C5   C2     0.00   0.0  0
 C58  CONST_08  C7   C6   C5   C2   180.00   0.0  0
 C58  CONST_09  C4   C5   C2   N2     0.00   0.0  0
 C58  CONST_10  C6   C5   C2   N2   180.00   0.0  0
 C58  CONST_11  C4   N3   C3   N2     0.00   0.0  0
 C58  CONST_12  C13  C12  C3   N2     0.00   0.0  0
 C58  CONST_13  C16  C12  C3   N2   180.00   0.0  0
 C58  CONST_14  C5   C2   N2   C3     0.00   0.0  0
 C58  CONST_15  C5   C4   N3   C3     0.00   0.0  0
 C58  CONST_16  C14  C13  C12  C3   180.00   0.0  0
 C58  CONST_17  C15  C16  C12  C3   180.00   0.0  0
 C58  CONST_18  C13  C12  C3   N3   180.00   0.0  0
 C58  CONST_19  C16  C12  C3   N3     0.00   0.0  0
 C58  CONST_20  C7   S    C4   N3   180.00   0.0  0
 C58  CONST_21  C6   C5   C4   N3   180.00   0.0  0
 C58  CONST_22  C6   C7   S    C4     0.00   0.0  0
 C58  CONST_23  C12  C3   N3   C4   180.00   0.0  0
 C58  CONST_24  C7   C6   C5   C4     0.00   0.0  0
 C58  CONST_25  C12  C13  C14  N4     0.00   0.0  0
 C58  CONST_26  C12  C16  C15  N4     0.00   0.0  0
 C58  CONST_27  C7   S    C4   C5     0.00   0.0  0
 C58  CONST_28  C15  C16  C12  C13    0.00   0.0  0
 C58  CONST_29  C15  N4   C14  C13    0.00   0.0  0
 C58  CONST_30  C16  C15  N4   C14    0.00   0.0  0
 C58  CONST_31  C16  C12  C13  C14    0.00   0.0  0
 C58  CONST_32  C21  C20  C19  C18    0.00   0.0  0
 C58  CONST_33  C21  C22  C23  C18    0.00   0.0  0
 C58  CONST_34  C22  C23  C18  C19    0.00   0.0  0
 C58  CONST_35  C22  C21  C20  C19    0.00   0.0  0
 C58  CONST_36  C23  C18  C19  C20    0.00   0.0  0
 C58  CONST_37  C23  C22  C21  C20    0.00   0.0  0
 C58  CONST_38  C3   N2   C2   N1   180.00   0.0  0
 C58  CONST_39  C4   C5   C2   N1   180.00   0.0  0
 C58  CONST_40  C6   C5   C2   N1     0.00   0.0  0
 C58  CONST_41  C20  C19  C18  C17  180.00   0.0  0
 C58  CONST_42  C22  C23  C18  C17  180.00   0.0  0
 C58  CONST_43  H13  C13  C12  C3     0.00   0.0  0
 C58  CONST_44  H16  C16  C12  C3     0.00   0.0  0
 C58  CONST_45  H14  C14  C13  C12  180.00   0.0  0
 C58  CONST_46  H15  C15  C16  C12  180.00   0.0  0
 C58  CONST_47  H20  C20  C19  C18  180.00   0.0  0
 C58  CONST_48  H22  C22  C23  C18  180.00   0.0  0
 C58  CONST_49  H23  C23  C18  C19  180.00   0.0  0
 C58  CONST_50  H21  C21  C20  C19  180.00   0.0  0
 C58  CONST_51  H19  C19  C20  C21  180.00   0.0  0
 C58  CONST_52  N2   C2   N1   C1     0.00   0.0  0
 C58  CONST_53  C5   C2   N1   C1   180.00   0.0  0
 C58  CONST_54  HN1  N1   C2   N2   180.00   0.0  0
 C58  Var_01    C9   C8   C7   S    164.18  30.0  1
 C58  Var_02    C10  C11  C6   C5   167.08  30.0  1
 C58  Var_03    C9   C10  C11  C6    43.94  30.0  1
 C58  Var_04    C10  C9   C8   C7    46.55  30.0  1
 C58  Var_05    C11  C10  C9   C8   -63.19  30.0  1
 C58  Var_06    C19  C18  C17  C     82.46  30.0  2
 C58  Var_07    C2   N1   C1   C     84.23  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
 C58  chir_01  C  N  C1  C17  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
 C58  plan-1  C3   0.020
 C58  plan-1  N4   0.020
 C58  plan-1  C12  0.020
 C58  plan-1  C13  0.020
 C58  plan-1  C14  0.020
 C58  plan-1  C15  0.020
 C58  plan-1  C16  0.020
 C58  plan-1  H13  0.020
 C58  plan-1  H14  0.020
 C58  plan-1  H15  0.020
 C58  plan-1  H16  0.020
 C58  plan-2  C17  0.020
 C58  plan-2  C18  0.020
 C58  plan-2  C19  0.020
 C58  plan-2  C20  0.020
 C58  plan-2  C21  0.020
 C58  plan-2  C22  0.020
 C58  plan-2  C23  0.020
 C58  plan-2  H19  0.020
 C58  plan-2  H20  0.020
 C58  plan-2  H21  0.020
 C58  plan-2  H22  0.020
 C58  plan-2  H23  0.020
 C58  plan-3  S    0.020
 C58  plan-3  N1   0.020
 C58  plan-3  C2   0.020
 C58  plan-3  N2   0.020
 C58  plan-3  C3   0.020
 C58  plan-3  N3   0.020
 C58  plan-3  C4   0.020
 C58  plan-3  C5   0.020
 C58  plan-3  C6   0.020
 C58  plan-3  C7   0.020
 C58  plan-3  C8   0.020
 C58  plan-3  C11  0.020
 C58  plan-3  C12  0.020
 C58  plan-4  C1   0.020
 C58  plan-4  N1   0.020
 C58  plan-4  C2   0.020
 C58  plan-4  HN1  0.020

