# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 12:13:59 2021
#   Inital geometry file: a 125 line input string
#   Ligand name: (3~{S})-3-(hydroxymethyl)-5-[2-[(2-methoxypyridin-3-yl)amino]pyrimidin-4-yl]-3-methyl-1,2-dihydroindole-7-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ncccc1Nc2nccc(n2)c3cc(C#N)c4NC[C@@](C)(CO)c4c3
#
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
 Q55  Q55  (3~{S})-3-(hydroxymethyl)-5-[2-[(2-methoxypyridin-3-yl)amino]pyrimidin-4-yl]-3-methyl-1,2-dihydroindole-7-carbonitrile  ligand  49  29  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_Q55
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
 Q55  N    N  NR15  0  -0.683  33.4347  12.5671  -14.4797
 Q55  C1   C  CR16  0  -0.356  35.4916  11.3171  -17.3019
 Q55  C2   C  CR6   0   0.037  36.7271  11.7379  -16.8421
 Q55  C19  C  CH3   0  -0.411  44.9671  12.8597  -15.7076
 Q55  C15  C  CR6   0   0.481  42.7136  13.5770  -15.7313
 Q55  N4   N  N     0  -0.452  42.9910  14.3472  -14.7115
 Q55  C16  C  CR16  0  -0.078  42.0258  15.1159  -14.2014
 Q55  C17  C  CR16  0  -0.347  40.7517  15.1410  -14.7199
 Q55  C18  C  CR16  0  -0.190  40.4574  14.3310  -15.8162
 Q55  C14  C  CR6   0   0.194  41.4396  13.5109  -16.3441
 Q55  C13  C  CR6   0   0.588  40.1677  12.0198  -17.8655
 Q55  N1   N  N     0  -0.464  40.3376  11.2552  -18.9483
 Q55  C12  C  CR16  0  -0.023  39.2616  10.6033  -19.3578
 Q55  C11  C  CR16  0  -0.408  38.0304  10.6897  -18.7321
 Q55  C10  C  CR6   0   0.337  37.9577  11.5240  -17.6175
 Q55  C    C  CR6   0  -0.025  34.3187  11.5555  -16.5728
 Q55  C20  C  CSP   0   0.033  33.0581  11.1342  -17.0689
 Q55  N5   N  NS    0  -0.254  32.0219  10.8000  -17.4513
 Q55  C5   C  CR56  0   0.411  34.4047  12.2324  -15.3505
 Q55  C4   C  CR56  0   0.107  35.6620  12.6506  -14.8785
 Q55  C3   C  CR16  0  -0.366  36.7940  12.4128  -15.6008
 Q55  C7   C  CR5   0  -0.201  35.4773  13.2904  -13.5214
 Q55  C8   C  CH3   0  -0.650  36.2527  14.5916  -13.3538
 Q55  C9   C  CH2   0  -0.110  35.8947  12.2550  -12.4722
 Q55  O    O  OH1   0  -0.666  35.6710  12.7802  -11.1874
 Q55  C6   C  CH2   0  -0.259  33.9460  13.5167  -13.4971
 Q55  N2   N  N     0  -0.504  39.0369  12.1802  -17.1972
 Q55  H2   H  HNR5  0   0.399  32.4614  12.5774  -14.7400
 Q55  H    H  HCR6  0   0.274  35.3988  10.8091  -18.2525
 Q55  H17  H  HCH3  0   0.248  45.5663  12.1554  -16.2784
 Q55  H19  H  HCH3  0   0.230  45.3970  13.8580  -15.7977
 Q55  H18  H  HCH3  0   0.231  44.9719  12.5703  -14.6563
 Q55  H14  H  HCR6  0   0.261  42.2967  15.7278  -13.3494
 Q55  H15  H  HCR6  0   0.264  39.9958  15.7850  -14.2933
 Q55  H16  H  HCR6  0   0.284  39.4687  14.3434  -16.2454
 Q55  H13  H  HNH1  0   0.406  42.1253  12.4215  -17.9425
 Q55  H12  H  HCR6  0   0.276  39.3833   9.9728  -20.2318
 Q55  H11  H  HCR6  0   0.271  37.1899  10.1229  -19.1020
 Q55  H1   H  HCR6  0   0.261  37.7601  12.7341  -15.2323
 Q55  H7   H  HCH3  0   0.246  36.0016  15.0829  -12.4145
 Q55  H6   H  HCH3  0   0.228  37.3291  14.4090  -13.3531
 Q55  H5   H  HCH3  0   0.237  36.0294  15.2833  -14.1662
 Q55  H8   H  HCH2  0   0.211  35.3277  11.3280  -12.6335
 Q55  H9   H  HCH2  0   0.206  36.9549  12.0149  -12.6330
 Q55  H10  H  HOH1  0   0.458  35.8774  12.0977  -10.5425
 Q55  H4   H  HCH2  0   0.251  33.7045  14.5423  -13.7952
 Q55  H3   H  HCH2  0   0.255  33.5107  13.3383  -12.5151
 Q55  N3   N  NH1   0  -0.759  41.2865  12.6700  -17.4405
 Q55  O1   O  O2    0  -0.480  43.6620  12.7996  -16.2633

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
 Q55  C12  N1   aromatic  1.323  0.020  1.323
 Q55  C12  C11  aromatic  1.384  0.020  1.384
 Q55  N1   C13  aromatic  1.336  0.020  1.336
 Q55  C11  C10  aromatic  1.394  0.020  1.394
 Q55  C13  N3   single    1.362  0.020  1.362
 Q55  C13  N2   aromatic  1.323  0.020  1.323
 Q55  C10  N2   aromatic  1.331  0.020  1.331
 Q55  C10  C2   single    1.470  0.020  1.470
 Q55  N3   C14  single    1.390  0.020  1.390
 Q55  N5   C20  triple    1.154  0.020  1.154
 Q55  C1   C2   aromatic  1.384  0.020  1.384
 Q55  C1   C    aromatic  1.402  0.020  1.402
 Q55  C20  C    single    1.419  0.020  1.419
 Q55  C2   C3   aromatic  1.415  0.020  1.415
 Q55  C    C5   aromatic  1.400  0.020  1.400
 Q55  O1   C19  single    1.420  0.020  1.420
 Q55  O1   C15  single    1.337  0.020  1.337
 Q55  C14  C15  aromatic  1.415  0.020  1.415
 Q55  C14  C18  aromatic  1.384  0.020  1.384
 Q55  C3   C4   aromatic  1.364  0.020  1.364
 Q55  C15  N4   aromatic  1.308  0.020  1.308
 Q55  C18  C17  aromatic  1.395  0.020  1.395
 Q55  C5   C4   aromatic  1.407  0.020  1.407
 Q55  C5   N    single    1.346  0.020  1.346
 Q55  C4   C7   single    1.512  0.020  1.512
 Q55  N4   C16  aromatic  1.335  0.020  1.335
 Q55  N    C6   single    1.459  0.020  1.459
 Q55  C17  C16  aromatic  1.376  0.020  1.376
 Q55  C8   C7   single    1.524  0.020  1.524
 Q55  C7   C6   single    1.548  0.020  1.548
 Q55  C7   C9   single    1.532  0.020  1.532
 Q55  C9   O    single    1.406  0.020  1.406
 Q55  N    H2   single    0.890  0.020  1.040
 Q55  C1   H    single    0.930  0.020  1.080
 Q55  C19  H17  single    0.970  0.020  1.090
 Q55  C19  H19  single    0.970  0.020  1.090
 Q55  C19  H18  single    0.970  0.020  1.090
 Q55  C16  H14  single    0.930  0.020  1.080
 Q55  C17  H15  single    0.930  0.020  1.080
 Q55  C18  H16  single    0.930  0.020  1.080
 Q55  N3   H13  single    0.860  0.020  1.020
 Q55  C12  H12  single    0.930  0.020  1.080
 Q55  C11  H11  single    0.930  0.020  1.080
 Q55  C3   H1   single    0.930  0.020  1.080
 Q55  C8   H7   single    0.970  0.020  1.090
 Q55  C8   H6   single    0.970  0.020  1.090
 Q55  C8   H5   single    0.970  0.020  1.090
 Q55  C9   H8   single    0.970  0.020  1.090
 Q55  C9   H9   single    0.970  0.020  1.090
 Q55  O    H10  single    0.850  0.020  0.980
 Q55  C6   H4   single    0.970  0.020  1.090
 Q55  C6   H3   single    0.970  0.020  1.090

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
 Q55  H2   N    C6   120.39  3.000
 Q55  H2   N    C5   122.11  3.000
 Q55  C6   N    C5   110.19  3.000
 Q55  H    C1   C    117.73  3.000
 Q55  H    C1   C2   120.76  3.000
 Q55  C    C1   C2   121.51  3.000
 Q55  C3   C2   C10  119.51  3.000
 Q55  C3   C2   C1   118.62  3.000
 Q55  C10  C2   C1   121.86  3.000
 Q55  H18  C19  H19  108.71  3.000
 Q55  H18  C19  H17  109.39  3.000
 Q55  H19  C19  H17  109.42  3.000
 Q55  H18  C19  O1   111.72  3.000
 Q55  H19  C19  O1   111.64  3.000
 Q55  H17  C19  O1   105.89  3.000
 Q55  C14  C15  N4   123.78  3.000
 Q55  N4   C15  O1   120.16  3.000
 Q55  C14  C15  O1   116.05  3.000
 Q55  C16  N4   C15  118.93  3.000
 Q55  H14  C16  C17  121.18  3.000
 Q55  H14  C16  N4   116.41  3.000
 Q55  C17  C16  N4   122.41  3.000
 Q55  H15  C17  C18  120.59  3.000
 Q55  H15  C17  C16  120.65  3.000
 Q55  C18  C17  C16  118.75  3.000
 Q55  H16  C18  C14  120.39  3.000
 Q55  H16  C18  C17  119.99  3.000
 Q55  C14  C18  C17  119.62  3.000
 Q55  N3   C14  C18  125.52  3.000
 Q55  C18  C14  C15  116.49  3.000
 Q55  N3   C14  C15  117.96  3.000
 Q55  N2   C13  N1   125.96  3.000
 Q55  N2   C13  N3   119.11  3.000
 Q55  N1   C13  N3   114.93  3.000
 Q55  C12  N1   C13  115.43  3.000
 Q55  H12  C12  C11  120.03  3.000
 Q55  H12  C12  N1   116.40  3.000
 Q55  C11  C12  N1   123.57  3.000
 Q55  H11  C11  C10  123.22  3.000
 Q55  H11  C11  C12  120.34  3.000
 Q55  C10  C11  C12  116.44  3.000
 Q55  N2   C10  C11  120.34  3.000
 Q55  N2   C10  C2   116.13  3.000
 Q55  C11  C10  C2   123.53  3.000
 Q55  C5   C    C20  120.23  3.000
 Q55  C5   C    C1   119.02  3.000
 Q55  C20  C    C1   120.74  3.000
 Q55  N5   C20  C    180.00  3.000
 Q55  C4   C5   C    119.45  3.000
 Q55  C4   C5   N    110.68  3.000
 Q55  C    C5   N    129.86  3.000
 Q55  C7   C4   C3   130.59  3.000
 Q55  C7   C4   C5   108.54  3.000
 Q55  C3   C4   C5   120.83  3.000
 Q55  H1   C3   C4   120.58  3.000
 Q55  H1   C3   C2   118.85  3.000
 Q55  C4   C3   C2   120.57  3.000
 Q55  C6   C7   C9   110.95  3.000
 Q55  C9   C7   C8   111.29  3.000
 Q55  C6   C7   C8   112.13  3.000
 Q55  C9   C7   C4   107.19  3.000
 Q55  C6   C7   C4   101.35  3.000
 Q55  C8   C7   C4   113.45  3.000
 Q55  H5   C8   H6   107.97  3.000
 Q55  H5   C8   H7   108.01  3.000
 Q55  H6   C8   H7   107.59  3.000
 Q55  H5   C8   C7   110.83  3.000
 Q55  H6   C8   C7   111.03  3.000
 Q55  H7   C8   C7   111.27  3.000
 Q55  H9   C9   H8   106.98  3.000
 Q55  H9   C9   O    111.64  3.000
 Q55  H8   C9   O    111.55  3.000
 Q55  H9   C9   C7   108.07  3.000
 Q55  H8   C9   C7   109.21  3.000
 Q55  O    C9   C7   109.27  3.000
 Q55  H10  O    C9   108.28  3.000
 Q55  H3   C6   H4   108.11  3.000
 Q55  H3   C6   C7   112.68  3.000
 Q55  H4   C6   C7   110.54  3.000
 Q55  H3   C6   N    111.14  3.000
 Q55  H4   C6   N    110.43  3.000
 Q55  C7   C6   N    103.94  3.000
 Q55  C10  N2   C13  118.26  3.000
 Q55  H13  N3   C13  114.22  3.000
 Q55  H13  N3   C14  116.75  3.000
 Q55  C13  N3   C14  128.70  3.000
 Q55  C15  O1   C19  118.15  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
 Q55  CONST_01  C11  C10  C2   C1      0.00   0.0  0
 Q55  CONST_02  N2   C10  C2   C1    180.00   0.0  0
 Q55  CONST_03  C4   C3   C2   C1      0.00   0.0  0
 Q55  CONST_04  C4   C5   C    C1      0.00   0.0  0
 Q55  CONST_05  C12  C11  C10  C2    180.00   0.0  0
 Q55  CONST_06  C13  N2   C10  C2    180.00   0.0  0
 Q55  CONST_07  C5   C    C1   C2      0.00   0.0  0
 Q55  CONST_08  C5   C4   C3   C2      0.00   0.0  0
 Q55  CONST_09  C17  C18  C14  C15     0.00   0.0  0
 Q55  CONST_10  C17  C16  N4   C15     0.00   0.0  0
 Q55  CONST_11  C18  C14  C15  N4      0.00   0.0  0
 Q55  CONST_12  C18  C17  C16  N4      0.00   0.0  0
 Q55  CONST_13  C14  C15  N4   C16     0.00   0.0  0
 Q55  CONST_14  C14  C18  C17  C16     0.00   0.0  0
 Q55  CONST_15  C11  C12  N1   C13     0.00   0.0  0
 Q55  CONST_16  C11  C10  N2   C13     0.00   0.0  0
 Q55  CONST_17  C10  C11  C12  N1      0.00   0.0  0
 Q55  CONST_18  C10  N2   C13  N1      0.00   0.0  0
 Q55  CONST_19  N2   C13  N1   C12     0.00   0.0  0
 Q55  CONST_20  N2   C10  C11  C12     0.00   0.0  0
 Q55  CONST_21  C3   C2   C10  C11   180.00   0.0  0
 Q55  CONST_22  C    C1   C2   C10   180.00   0.0  0
 Q55  CONST_23  C4   C3   C2   C10   180.00   0.0  0
 Q55  CONST_24  C3   C2   C1   C       0.00   0.0  0
 Q55  CONST_25  C3   C4   C5   C       0.00   0.0  0
 Q55  CONST_26  N2   C10  C2   C3      0.00   0.0  0
 Q55  CONST_27  C20  C    C5   N       0.00   0.0  0
 Q55  CONST_28  C20  C    C1   C2    180.00   0.0  0
 Q55  CONST_29  C18  C14  C15  O1    180.00   0.0  0
 Q55  CONST_30  C16  N4   C15  O1    180.00   0.0  0
 Q55  CONST_31  N3   C14  C15  N4    180.00   0.0  0
 Q55  CONST_32  N3   C14  C18  C17   180.00   0.0  0
 Q55  CONST_33  C12  N1   C13  N3    180.00   0.0  0
 Q55  CONST_34  C10  N2   C13  N3    180.00   0.0  0
 Q55  CONST_35  C4   C5   C    C20   180.00   0.0  0
 Q55  CONST_36  H1   C3   C2   C1    180.00   0.0  0
 Q55  CONST_37  H11  C11  C10  C2      0.00   0.0  0
 Q55  CONST_38  H16  C18  C14  C15   180.00   0.0  0
 Q55  CONST_39  H14  C16  N4   C15   180.00   0.0  0
 Q55  CONST_40  H15  C17  C16  N4    180.00   0.0  0
 Q55  CONST_41  H12  C12  N1   C13   180.00   0.0  0
 Q55  CONST_42  H    C1   C2   C10     0.00   0.0  0
 Q55  Var_01    C6   N    C5   C    -167.42  30.0  1
 Q55  Var_02    C7   C6   N    C5    -22.34  30.0  1
 Q55  Var_03    C13  N3   C14  C15   151.13  30.0  3
 Q55  Var_04    N1   C13  N3   C14  -178.79  30.0  1
 Q55  Var_05    C14  C15  O1   C19   178.21  30.0  2
 Q55  Var_06    H17  C19  O1   C15   179.71  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
 Q55  chir_01  C7  C4  C6  C9  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
 Q55  plan-1  C15  0.020
 Q55  plan-1  N4   0.020
 Q55  plan-1  C16  0.020
 Q55  plan-1  C17  0.020
 Q55  plan-1  C18  0.020
 Q55  plan-1  C14  0.020
 Q55  plan-1  H14  0.020
 Q55  plan-1  H15  0.020
 Q55  plan-1  H16  0.020
 Q55  plan-1  N3   0.020
 Q55  plan-1  O1   0.020
 Q55  plan-2  C2   0.020
 Q55  plan-2  C13  0.020
 Q55  plan-2  N1   0.020
 Q55  plan-2  C12  0.020
 Q55  plan-2  C11  0.020
 Q55  plan-2  C10  0.020
 Q55  plan-2  N2   0.020
 Q55  plan-2  H12  0.020
 Q55  plan-2  H11  0.020
 Q55  plan-2  N3   0.020
 Q55  plan-3  N    0.020
 Q55  plan-3  C1   0.020
 Q55  plan-3  C2   0.020
 Q55  plan-3  C10  0.020
 Q55  plan-3  C    0.020
 Q55  plan-3  C20  0.020
 Q55  plan-3  N5   0.020
 Q55  plan-3  C5   0.020
 Q55  plan-3  C4   0.020
 Q55  plan-3  C3   0.020
 Q55  plan-3  C7   0.020
 Q55  plan-3  H    0.020
 Q55  plan-3  H1   0.020

