# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 02:04:24 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 3-[7-(1H-benzimidazol-5-yl)-2-(morpholin-4-yl)-6,7-dihydro-5H-pyrrolo[2,3-d]pyrimidin-4-yl]phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cccc(c1)c2nc(nc3N(CCc23)c4ccc5[nH]cnc5c4)N6CCOCC6
#
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
 BMW  BMW  3-[7-(1H-benzimidazol-5-yl)-2-(morpholin-4-yl)-6,7-dihydro-5H-pyrrolo[2,3-d]pyrimidin-4-yl]phenol  ligand  53  31  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_BMW
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
 BMW  C1    C  CR16  0  -0.403  -3.1953   0.3781  -0.5544
 BMW  C2    C  CR56  0   0.152  -4.5772   0.2265  -0.4720
 BMW  N3    N  N     0  -0.468  -5.3654  -0.8120  -0.9139
 BMW  C5    C  CR15  0   0.102  -6.5825  -0.4571  -0.6092
 BMW  N6    N  NR15  0  -0.661  -6.6577   0.7450   0.0063
 BMW  C7    C  CR56  0   0.323  -5.3770   1.2199   0.1125
 BMW  C8    C  CR16  0  -0.289  -4.8261   2.3810   0.6347
 BMW  C9    C  CR16  0  -0.363  -3.4533   2.5188   0.5627
 BMW  C10   C  CR6   0   0.350  -2.6279   1.5336  -0.0253
 BMW  N11   N  NR5   0  -0.631  -1.2510   1.7757  -0.0905
 BMW  C12   C  CH2   0  -0.290  -0.6908   3.1120   0.1271
 BMW  C13   C  CH2   0  -0.546   0.7937   2.9828  -0.2436
 BMW  C14   C  CR56  0  -0.132   1.0067   1.5011  -0.2170
 BMW  C15   C  CR56  0   0.595  -0.2450   0.8600  -0.1642
 BMW  N16   N  N     0  -0.528  -0.4105  -0.4429  -0.1604
 BMW  C17   C  CR6   0   0.639   0.7250  -1.1609  -0.1783
 BMW  N18   N  NT    0  -0.521   0.5891  -2.5153  -0.1512
 BMW  C19   C  CH2   0  -0.312   1.7212  -3.3803  -0.4229
 BMW  C20   C  CH2   0  -0.190   1.5541  -4.6983   0.3084
 BMW  O21   O  O2    0  -0.484   0.3228  -5.3161   0.0088
 BMW  C22   C  CH2   0  -0.186  -0.7499  -4.4750   0.3675
 BMW  C23   C  CH2   0  -0.312  -0.6994  -3.1463  -0.3640
 BMW  N24   N  N     0  -0.531   1.9539  -0.6649  -0.2001
 BMW  C25   C  CR6   0   0.234   2.1019   0.6711  -0.2276
 BMW  C26   C  CR6   0   0.066   3.4953   1.1658  -0.2313
 BMW  C27   C  CR16  0  -0.438   4.4798   0.4108   0.4063
 BMW  C28   C  CR16  0  -0.339   3.8476   2.3576  -0.8607
 BMW  C29   C  CR16  0  -0.229   5.1691   2.7835  -0.8378
 BMW  C30   C  CR16  0  -0.345   6.1454   2.0467  -0.1892
 BMW  C31   C  CR6   0   0.384   5.7969   0.8519   0.4390
 BMW  O32   O  OH1   0  -0.633   6.7744   0.1635   1.0614
 BMW  H1    H  HCR6  0   0.274  -2.5937  -0.3876  -1.0186
 BMW  H5    H  HCR5  0   0.286  -7.4694  -1.0389  -0.8109
 BMW  HN6   H  HNR5  0   0.421  -7.5028   1.2002   0.3118
 BMW  H8    H  HCR6  0   0.270  -5.4322   3.1545   1.0870
 BMW  H9    H  HCR6  0   0.275  -3.0142   3.4142   0.9787
 BMW  H12   H  HCH2  0   0.263  -1.2096   3.8480  -0.4859
 BMW  H12A  H  HCH2  0   0.254  -0.8063   3.4032   1.1747
 BMW  H13   H  HCH2  0   0.267   0.9750   3.3958  -1.2389
 BMW  H13A  H  HCH2  0   0.269   1.4290   3.5297   0.4531
 BMW  H19   H  HCH2  0   0.227   1.8135  -3.5599  -1.5023
 BMW  H19A  H  HCH2  0   0.269   2.6388  -2.9008  -0.0913
 BMW  H20   H  HCH2  0   0.242   2.3481  -5.3845   0.0107
 BMW  H20A  H  HCH2  0   0.205   1.6425  -4.5276   1.3909
 BMW  H22   H  HCH2  0   0.242  -1.6753  -4.9946   0.1151
 BMW  H22A  H  HCH2  0   0.205  -0.7474  -4.2929   1.4516
 BMW  H23   H  HCH2  0   0.268  -1.4933  -2.5054   0.0108
 BMW  H23A  H  HCH2  0   0.227  -0.8776  -3.3024  -1.4364
 BMW  H27   H  HCR6  0   0.270   4.2056  -0.5231   0.8833
 BMW  H28   H  HCR6  0   0.253   3.1137   2.9405  -1.3982
 BMW  H29   H  HCR6  0   0.261   5.4433   3.7038  -1.3365
 BMW  H30   H  HCR6  0   0.266   7.1731   2.3874  -0.1698
 BMW  HO32  H  HOH1  0   0.474   6.4209  -0.6424   1.4544

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
 BMW  C1   C2    aromatic  1.393  0.020  1.393
 BMW  C1   C10   aromatic  1.392  0.020  1.392
 BMW  C2   N3    aromatic  1.377  0.020  1.377
 BMW  C2   C7    aromatic  1.403  0.020  1.403
 BMW  N3   C5    aromatic  1.304  0.020  1.304
 BMW  C5   N6    aromatic  1.353  0.020  1.353
 BMW  N6   C7    aromatic  1.370  0.020  1.370
 BMW  C7   C8    aromatic  1.387  0.020  1.387
 BMW  C8   C9    aromatic  1.382  0.020  1.382
 BMW  C9   C10   aromatic  1.413  0.020  1.413
 BMW  C10  N11   single    1.400  0.020  1.400
 BMW  N11  C12   single    1.465  0.020  1.465
 BMW  N11  C15   single    1.362  0.020  1.362
 BMW  C12  C13   single    1.536  0.020  1.536
 BMW  C13  C14   single    1.497  0.020  1.497
 BMW  C14  C15   aromatic  1.407  0.020  1.407
 BMW  C14  C25   aromatic  1.374  0.020  1.374
 BMW  C15  N16   aromatic  1.313  0.020  1.313
 BMW  N16  C17   aromatic  1.344  0.020  1.344
 BMW  C17  N18   single    1.361  0.020  1.361
 BMW  C17  N24   aromatic  1.325  0.020  1.325
 BMW  N18  C19   single    1.450  0.020  1.450
 BMW  N18  C23   single    1.450  0.020  1.450
 BMW  C19  C20   single    1.517  0.020  1.517
 BMW  C20  O21   single    1.410  0.020  1.410
 BMW  O21  C22   single    1.410  0.020  1.410
 BMW  C22  C23   single    1.518  0.020  1.518
 BMW  N24  C25   aromatic  1.344  0.020  1.344
 BMW  C25  C26   single    1.479  0.020  1.479
 BMW  C26  C27   aromatic  1.395  0.020  1.395
 BMW  C26  C28   aromatic  1.393  0.020  1.393
 BMW  C27  C31   aromatic  1.389  0.020  1.389
 BMW  C28  C29   aromatic  1.389  0.020  1.389
 BMW  C29  C30   aromatic  1.384  0.020  1.384
 BMW  C30  C31   aromatic  1.394  0.020  1.394
 BMW  C31  O32   single    1.348  0.020  1.348
 BMW  C1   H1    single    0.930  0.020  1.080
 BMW  C5   H5    single    0.930  0.020  1.080
 BMW  N6   HN6   single    0.860  0.020  1.020
 BMW  C8   H8    single    0.930  0.020  1.080
 BMW  C9   H9    single    0.930  0.020  1.080
 BMW  C12  H12   single    0.970  0.020  1.090
 BMW  C12  H12A  single    0.970  0.020  1.090
 BMW  C13  H13   single    0.970  0.020  1.090
 BMW  C13  H13A  single    0.970  0.020  1.090
 BMW  C19  H19   single    0.970  0.020  1.090
 BMW  C19  H19A  single    0.970  0.020  1.090
 BMW  C20  H20   single    0.970  0.020  1.090
 BMW  C20  H20A  single    0.970  0.020  1.090
 BMW  C22  H22   single    0.970  0.020  1.090
 BMW  C22  H22A  single    0.970  0.020  1.090
 BMW  C23  H23   single    0.970  0.020  1.090
 BMW  C23  H23A  single    0.970  0.020  1.090
 BMW  C27  H27   single    0.930  0.020  1.080
 BMW  C28  H28   single    0.930  0.020  1.080
 BMW  C29  H29   single    0.930  0.020  1.080
 BMW  C30  H30   single    0.930  0.020  1.080
 BMW  O32  HO32  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
 BMW  H1    C1   C10  121.71  3.000
 BMW  H1    C1   C2   120.11  3.000
 BMW  C10   C1   C2   118.19  3.000
 BMW  C7    C2   N3   109.96  3.000
 BMW  C7    C2   C1   120.88  3.000
 BMW  N3    C2   C1   129.15  3.000
 BMW  C5    N3   C2   104.72  3.000
 BMW  H5    C5   N6   121.22  3.000
 BMW  H5    C5   N3   125.19  3.000
 BMW  N6    C5   N3   113.58  3.000
 BMW  HN6   N6   C7   127.17  3.000
 BMW  HN6   N6   C5   125.89  3.000
 BMW  C7    N6   C5   106.94  3.000
 BMW  C8    C7   N6   133.67  3.000
 BMW  C8    C7   C2   121.54  3.000
 BMW  N6    C7   C2   104.79  3.000
 BMW  H8    C8   C9   120.48  3.000
 BMW  H8    C8   C7   122.24  3.000
 BMW  C9    C8   C7   117.29  3.000
 BMW  H9    C9   C10  120.03  3.000
 BMW  H9    C9   C8   117.80  3.000
 BMW  C10   C9   C8   122.17  3.000
 BMW  N11   C10  C9   118.26  3.000
 BMW  N11   C10  C1   121.80  3.000
 BMW  C9    C10  C1   119.92  3.000
 BMW  C15   N11  C12  109.80  3.000
 BMW  C15   N11  C10  127.79  3.000
 BMW  C12   N11  C10  121.80  3.000
 BMW  H12A  C12  H12  107.99  3.000
 BMW  H12A  C12  C13  110.84  3.000
 BMW  H12   C12  C13  112.42  3.000
 BMW  H12A  C12  N11  110.17  3.000
 BMW  H12   C12  N11  110.52  3.000
 BMW  C13   C12  N11  104.89  3.000
 BMW  H13A  C13  H13  107.21  3.000
 BMW  H13A  C13  C14  113.72  3.000
 BMW  H13   C13  C14  111.51  3.000
 BMW  H13A  C13  C12  111.52  3.000
 BMW  H13   C13  C12  110.39  3.000
 BMW  C14   C13  C12  102.51  3.000
 BMW  C25   C14  C15  115.72  3.000
 BMW  C25   C14  C13  135.31  3.000
 BMW  C15   C14  C13  108.97  3.000
 BMW  N16   C15  C14  124.34  3.000
 BMW  N16   C15  N11  125.00  3.000
 BMW  C14   C15  N11  110.65  3.000
 BMW  C17   N16  C15  115.06  3.000
 BMW  N24   C17  N18  117.72  3.000
 BMW  N24   C17  N16  125.72  3.000
 BMW  N18   C17  N16  116.55  3.000
 BMW  C23   N18  C19  113.99  3.000
 BMW  C23   N18  C17  121.23  3.000
 BMW  C19   N18  C17  120.77  3.000
 BMW  H19A  C19  H19  107.52  3.000
 BMW  H19A  C19  C20  109.22  3.000
 BMW  H19   C19  C20  109.94  3.000
 BMW  H19A  C19  N18  109.80  3.000
 BMW  H19   C19  N18  110.32  3.000
 BMW  C20   C19  N18  110.00  3.000
 BMW  H20A  C20  H20  107.93  3.000
 BMW  H20A  C20  O21  110.34  3.000
 BMW  H20   C20  O21  107.58  3.000
 BMW  H20A  C20  C19  109.33  3.000
 BMW  H20   C20  C19  109.57  3.000
 BMW  O21   C20  C19  112.00  3.000
 BMW  C22   O21  C20  110.43  3.000
 BMW  H22A  C22  H22  108.00  3.000
 BMW  H22A  C22  C23  109.28  3.000
 BMW  H22   C22  C23  109.50  3.000
 BMW  H22A  C22  O21  110.37  3.000
 BMW  H22   C22  O21  107.61  3.000
 BMW  C23   C22  O21  111.99  3.000
 BMW  H23A  C23  H23  107.57  3.000
 BMW  H23A  C23  C22  109.92  3.000
 BMW  H23   C23  C22  109.01  3.000
 BMW  H23A  C23  N18  110.44  3.000
 BMW  H23   C23  N18  109.98  3.000
 BMW  C22   C23  N18  109.86  3.000
 BMW  C25   N24  C17  118.31  3.000
 BMW  C26   C25  N24  115.87  3.000
 BMW  C26   C25  C14  123.30  3.000
 BMW  N24   C25  C14  120.82  3.000
 BMW  C28   C26  C27  119.41  3.000
 BMW  C28   C26  C25  121.71  3.000
 BMW  C27   C26  C25  118.87  3.000
 BMW  H27   C27  C31  120.20  3.000
 BMW  H27   C27  C26  119.27  3.000
 BMW  C31   C27  C26  120.53  3.000
 BMW  H28   C28  C29  119.29  3.000
 BMW  H28   C28  C26  120.97  3.000
 BMW  C29   C28  C26  119.71  3.000
 BMW  H29   C29  C30  119.33  3.000
 BMW  H29   C29  C28  119.63  3.000
 BMW  C30   C29  C28  121.04  3.000
 BMW  H30   C30  C31  119.93  3.000
 BMW  H30   C30  C29  120.68  3.000
 BMW  C31   C30  C29  119.39  3.000
 BMW  O32   C31  C30  117.67  3.000
 BMW  O32   C31  C27  122.43  3.000
 BMW  C30   C31  C27  119.90  3.000
 BMW  HO32  O32  C31  110.45  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
 BMW  CONST_01  C5   N3   C2   C1    180.00   0.0  0
 BMW  CONST_02  N6   C7   C2   C1    180.00   0.0  0
 BMW  CONST_03  C8   C7   C2   C1      0.00   0.0  0
 BMW  CONST_04  C8   C9   C10  C1      0.00   0.0  0
 BMW  CONST_05  C9   C10  C1   C2      0.00   0.0  0
 BMW  CONST_06  N6   C5   N3   C2      0.00   0.0  0
 BMW  CONST_07  C5   N6   C7   C2      0.00   0.0  0
 BMW  CONST_08  C9   C8   C7   C2      0.00   0.0  0
 BMW  CONST_09  C10  C1   C2   N3    180.00   0.0  0
 BMW  CONST_10  N6   C7   C2   N3      0.00   0.0  0
 BMW  CONST_11  C8   C7   C2   N3    180.00   0.0  0
 BMW  CONST_12  C7   N6   C5   N3      0.00   0.0  0
 BMW  CONST_13  C7   C2   N3   C5      0.00   0.0  0
 BMW  CONST_14  C8   C7   N6   C5    180.00   0.0  0
 BMW  CONST_15  C9   C8   C7   N6    180.00   0.0  0
 BMW  CONST_16  C10  C1   C2   C7      0.00   0.0  0
 BMW  CONST_17  C10  C9   C8   C7      0.00   0.0  0
 BMW  CONST_18  C17  N16  C15  C14     0.00   0.0  0
 BMW  CONST_19  C17  N24  C25  C14     0.00   0.0  0
 BMW  CONST_22  N24  C25  C14  C15     0.00   0.0  0
 BMW  CONST_23  C26  C25  C14  C15   180.00   0.0  0
 BMW  CONST_24  N24  C17  N16  C15     0.00   0.0  0
 BMW  CONST_25  C25  C14  C15  N16     0.00   0.0  0
 BMW  CONST_26  C25  N24  C17  N16     0.00   0.0  0
 BMW  CONST_27  C26  C25  N24  C17   180.00   0.0  0
 BMW  CONST_30  C31  C27  C26  C25   180.00   0.0  0
 BMW  CONST_31  C29  C28  C26  C25   180.00   0.0  0
 BMW  CONST_32  C30  C31  C27  C26     0.00   0.0  0
 BMW  CONST_33  C30  C29  C28  C26     0.00   0.0  0
 BMW  CONST_34  C29  C28  C26  C27     0.00   0.0  0
 BMW  CONST_35  C29  C30  C31  C27     0.00   0.0  0
 BMW  CONST_36  C31  C27  C26  C28     0.00   0.0  0
 BMW  CONST_37  C31  C30  C29  C28     0.00   0.0  0
 BMW  CONST_38  N11  C10  C1   C2    180.00   0.0  0
 BMW  CONST_39  N11  C10  C9   C8    180.00   0.0  0
 BMW  CONST_40  C26  C25  C14  C13     0.00   0.0  0
 BMW  CONST_41  N18  C17  N16  C15   180.00   0.0  0
 BMW  CONST_42  C25  N24  C17  N18   180.00   0.0  0
 BMW  CONST_43  O32  C31  C27  C26   180.00   0.0  0
 BMW  CONST_44  O32  C31  C30  C29   180.00   0.0  0
 BMW  CONST_45  H9   C9   C10  C1    180.00   0.0  0
 BMW  CONST_46  H5   C5   N3   C2    180.00   0.0  0
 BMW  CONST_47  HN6  N6   C7   C2    180.00   0.0  0
 BMW  CONST_48  H8   C8   C7   C2    180.00   0.0  0
 BMW  CONST_49  H1   C1   C2   N3      0.00   0.0  0
 BMW  CONST_50  H27  C27  C26  C25     0.00   0.0  0
 BMW  CONST_51  H28  C28  C26  C25     0.00   0.0  0
 BMW  CONST_52  H29  C29  C28  C26   180.00   0.0  0
 BMW  CONST_53  H30  C30  C31  C27   180.00   0.0  0
 BMW  Var_01    C12  N11  C10  C1    163.29  30.0  2
 BMW  Var_02    C13  C12  N11  C10  -171.54  30.0  1
 BMW  Var_03    C14  C15  N11  C10   179.85  30.0  1
 BMW  Var_04    C14  C13  C12  N11   -17.21  30.0  1
 BMW  Var_05    C15  C14  C13  C12    12.63  30.0  1
 BMW  Var_06    C19  N18  C17  N16   168.13  30.0  2
 BMW  Var_07    C20  C19  N18  C17   151.60  30.0  1
 BMW  Var_08    C22  C23  N18  C17  -151.65  30.0  1
 BMW  Var_09    O21  C20  C19  N18    54.28  30.0  1
 BMW  Var_10    O21  C22  C23  N18   -54.50  30.0  1
 BMW  Var_11    C23  C22  O21  C20    59.50  30.0  1

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
 BMW  plan-1  C25  0.020
 BMW  plan-1  C26  0.020
 BMW  plan-1  C27  0.020
 BMW  plan-1  C28  0.020
 BMW  plan-1  C29  0.020
 BMW  plan-1  C30  0.020
 BMW  plan-1  C31  0.020
 BMW  plan-1  O32  0.020
 BMW  plan-1  H27  0.020
 BMW  plan-1  H28  0.020
 BMW  plan-1  H29  0.020
 BMW  plan-1  H30  0.020
 BMW  plan-2  N11  0.020
 BMW  plan-2  C13  0.020
 BMW  plan-2  C14  0.020
 BMW  plan-2  C15  0.020
 BMW  plan-2  N16  0.020
 BMW  plan-2  C17  0.020
 BMW  plan-2  N18  0.020
 BMW  plan-2  N24  0.020
 BMW  plan-2  C25  0.020
 BMW  plan-2  C26  0.020
 BMW  plan-3  C1   0.020
 BMW  plan-3  C2   0.020
 BMW  plan-3  N3   0.020
 BMW  plan-3  C5   0.020
 BMW  plan-3  N6   0.020
 BMW  plan-3  C7   0.020
 BMW  plan-3  C8   0.020
 BMW  plan-3  C9   0.020
 BMW  plan-3  C10  0.020
 BMW  plan-3  N11  0.020
 BMW  plan-3  H1   0.020
 BMW  plan-3  H5   0.020
 BMW  plan-3  HN6  0.020
 BMW  plan-3  H8   0.020
 BMW  plan-3  H9   0.020

