# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 17:33:23 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 7-(4-methoxyphenyl)-5-phenyl-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)n2cc(c3ccccc3)c4C(=O)NC=Nc24
#
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
 BKE  BKE  7-(4-methoxyphenyl)-5-phenyl-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one  ligand  39  24  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BKE
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
 BKE  C    C  CH3   0  -0.439   6.8600   0.6459   0.7059
 BKE  N    N  NR5   0  -0.607   0.5366  -0.0377  -0.0416
 BKE  O    O  O2    0  -0.468   5.9416   1.1741  -0.2317
 BKE  C1   C  CR6   0   0.389   4.6471   0.8291  -0.1323
 BKE  N1   N  N     0  -0.440   0.6471  -2.4264  -0.1708
 BKE  C2   C  CR16  0  -0.341   3.7798   1.4036  -1.0649
 BKE  N2   N  NR16  0  -0.660  -1.4592  -3.4367  -0.1167
 BKE  C3   C  CR16  0  -0.265   2.4317   1.1048  -1.0410
 BKE  C4   C  CR6   0   0.288   1.9239   0.2412  -0.0759
 BKE  C5   C  CR16  0  -0.259   2.7782  -0.3272   0.8544
 BKE  C6   C  CR16  0  -0.385   4.1368  -0.0444   0.8265
 BKE  C7   C  CR15  0  -0.069  -0.4596   0.9073   0.0218
 BKE  C8   C  CR5   0   0.006  -1.6864   0.2995   0.0148
 BKE  C9   C  CR56  0  -0.203  -1.4219  -1.1042  -0.0597
 BKE  C10  C  CR56  0   0.491  -0.0389  -1.2661  -0.0937
 BKE  C11  C  CR16  0   0.154  -0.1097  -3.4711  -0.1832
 BKE  C12  C  CR6   0   0.488  -2.2386  -2.2814  -0.0344
 BKE  C13  C  CR6   0   0.043  -2.9683   1.0098   0.0724
 BKE  C14  C  CR16  0  -0.320  -3.1245   2.1005   0.9308
 BKE  C15  C  CR16  0  -0.242  -4.3162   2.8101   0.9710
 BKE  C16  C  CR16  0  -0.269  -5.3786   2.4363   0.1592
 BKE  C17  C  CR16  0  -0.244  -5.2346   1.3521  -0.6977
 BKE  C18  C  CR16  0  -0.301  -4.0421   0.6454  -0.7420
 BKE  H    H  HCH3  0   0.231   6.6049   0.9273   1.7305
 BKE  HA   H  HCH3  0   0.231   6.9255  -0.4434   0.6446
 BKE  HB   H  HCH3  0   0.262   7.8302   1.0685   0.4576
 BKE  H2   H  HCR6  0   0.271   4.1726   2.0776  -1.8156
 BKE  HN2  H  HNR6  0   0.431  -1.9526  -4.3201  -0.1123
 BKE  H3   H  HCR6  0   0.276   1.7736   1.5445  -1.7798
 BKE  H5   H  HCR6  0   0.274   2.3912  -0.9896   1.6170
 BKE  H6   H  HCR6  0   0.286   4.7744  -0.5066   1.5669
 BKE  H7   H  HCR5  0   0.301  -0.2137   1.9567   0.0600
 BKE  H11  H  HCR6  0   0.298   0.3292  -4.4581  -0.2475
 BKE  H14  H  HCR6  0   0.248  -2.3105   2.3870   1.5852
 BKE  H15  H  HCR6  0   0.256  -4.4153   3.6508   1.6456
 BKE  H16  H  HCR6  0   0.255  -6.3110   2.9847   0.1939
 BKE  H17  H  HCR6  0   0.255  -6.0542   1.0571  -1.3405
 BKE  H18  H  HCR6  0   0.244  -3.9411  -0.1847  -1.4271
 BKE  O1   O  O     0  -0.467  -3.4535  -2.3615   0.0516

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
 BKE  C    O    single    1.415  0.020  1.415
 BKE  N    C4   single    1.415  0.020  1.415
 BKE  N    C7   aromatic  1.375  0.020  1.375
 BKE  N    C10  aromatic  1.358  0.020  1.358
 BKE  O    C1   single    1.343  0.020  1.343
 BKE  C1   C2   aromatic  1.397  0.020  1.397
 BKE  C1   C6   aromatic  1.394  0.020  1.394
 BKE  N1   C10  single    1.350  0.020  1.350
 BKE  N1   C11  double    1.290  0.020  1.290
 BKE  O1   C12  double    1.221  0.020  1.221
 BKE  C2   C3   aromatic  1.381  0.020  1.381
 BKE  N2   C11  single    1.352  0.020  1.352
 BKE  N2   C12  single    1.396  0.020  1.396
 BKE  C3   C4   aromatic  1.391  0.020  1.391
 BKE  C4   C5   aromatic  1.385  0.020  1.385
 BKE  C5   C6   aromatic  1.388  0.020  1.388
 BKE  C7   C8   aromatic  1.369  0.020  1.369
 BKE  C8   C9   aromatic  1.430  0.020  1.430
 BKE  C8   C13  single    1.467  0.020  1.467
 BKE  C9   C10  aromatic  1.393  0.020  1.393
 BKE  C9   C12  single    1.433  0.020  1.433
 BKE  C13  C14  aromatic  1.397  0.020  1.397
 BKE  C13  C18  aromatic  1.396  0.020  1.396
 BKE  C14  C15  aromatic  1.388  0.020  1.388
 BKE  C15  C16  aromatic  1.388  0.020  1.388
 BKE  C16  C17  aromatic  1.389  0.020  1.389
 BKE  C17  C18  aromatic  1.387  0.020  1.387
 BKE  C    H    single    0.970  0.020  1.090
 BKE  C    HA   single    0.970  0.020  1.090
 BKE  C    HB   single    0.970  0.020  1.090
 BKE  C2   H2   single    0.930  0.020  1.080
 BKE  N2   HN2  single    0.860  0.020  1.020
 BKE  C3   H3   single    0.930  0.020  1.080
 BKE  C5   H5   single    0.930  0.020  1.080
 BKE  C6   H6   single    0.930  0.020  1.080
 BKE  C7   H7   single    0.930  0.020  1.080
 BKE  C11  H11  single    0.930  0.020  1.080
 BKE  C14  H14  single    0.930  0.020  1.080
 BKE  C15  H15  single    0.930  0.020  1.080
 BKE  C16  H16  single    0.930  0.020  1.080
 BKE  C17  H17  single    0.930  0.020  1.080
 BKE  C18  H18  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
 BKE  HB   C    HA   108.74  3.000
 BKE  HB   C    H    108.81  3.000
 BKE  HA   C    H    108.86  3.000
 BKE  HB   C    O    106.43  3.000
 BKE  HA   C    O    111.95  3.000
 BKE  H    C    O    111.94  3.000
 BKE  C10  N    C7   108.46  3.000
 BKE  C10  N    C4   126.36  3.000
 BKE  C7   N    C4   125.17  3.000
 BKE  C1   O    C    118.72  3.000
 BKE  C6   C1   C2   119.32  3.000
 BKE  C6   C1   O    124.38  3.000
 BKE  C2   C1   O    116.30  3.000
 BKE  C11  N1   C10  113.48  3.000
 BKE  H2   C2   C3   120.05  3.000
 BKE  H2   C2   C1   119.58  3.000
 BKE  C3   C2   C1   120.36  3.000
 BKE  HN2  N2   C12  116.75  3.000
 BKE  HN2  N2   C11  117.70  3.000
 BKE  C12  N2   C11  125.54  3.000
 BKE  H3   C3   C4   120.24  3.000
 BKE  H3   C3   C2   119.58  3.000
 BKE  C4   C3   C2   120.18  3.000
 BKE  C5   C4   C3   119.71  3.000
 BKE  C5   C4   N    120.49  3.000
 BKE  C3   C4   N    119.80  3.000
 BKE  H5   C5   C6   119.28  3.000
 BKE  H5   C5   C4   120.27  3.000
 BKE  C6   C5   C4   120.44  3.000
 BKE  H6   C6   C5   118.46  3.000
 BKE  H6   C6   C1   121.55  3.000
 BKE  C5   C6   C1   119.99  3.000
 BKE  H7   C7   C8   129.53  3.000
 BKE  H7   C7   N    120.36  3.000
 BKE  C8   C7   N    110.12  3.000
 BKE  C13  C8   C9   129.71  3.000
 BKE  C13  C8   C7   124.61  3.000
 BKE  C9   C8   C7   105.68  3.000
 BKE  C12  C9   C10  118.09  3.000
 BKE  C12  C9   C8   134.42  3.000
 BKE  C10  C9   C8   107.40  3.000
 BKE  C9   C10  N1   127.29  3.000
 BKE  C9   C10  N    108.35  3.000
 BKE  N1   C10  N    124.37  3.000
 BKE  H11  C11  N2   115.54  3.000
 BKE  H11  C11  N1   120.09  3.000
 BKE  N2   C11  N1   124.38  3.000
 BKE  C9   C12  N2   111.14  3.000
 BKE  C9   C12  O1   128.49  3.000
 BKE  N2   C12  O1   120.36  3.000
 BKE  C18  C13  C14  118.45  3.000
 BKE  C18  C13  C8   121.52  3.000
 BKE  C14  C13  C8   120.01  3.000
 BKE  H14  C14  C15  119.51  3.000
 BKE  H14  C14  C13  119.60  3.000
 BKE  C15  C14  C13  120.88  3.000
 BKE  H15  C15  C16  120.23  3.000
 BKE  H15  C15  C14  119.60  3.000
 BKE  C16  C15  C14  120.17  3.000
 BKE  H16  C16  C17  120.30  3.000
 BKE  H16  C16  C15  120.27  3.000
 BKE  C17  C16  C15  119.43  3.000
 BKE  H17  C17  C18  119.54  3.000
 BKE  H17  C17  C16  120.03  3.000
 BKE  C18  C17  C16  120.43  3.000
 BKE  H18  C18  C17  119.46  3.000
 BKE  H18  C18  C13  119.89  3.000
 BKE  C17  C18  C13  120.64  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
 BKE  CONST_01  C2   C3   C4   N    180.00   0.0  0
 BKE  CONST_02  C6   C5   C4   N    180.00   0.0  0
 BKE  CONST_03  C9   C8   C7   N      0.00   0.0  0
 BKE  CONST_04  C13  C8   C7   N    180.00   0.0  0
 BKE  CONST_05  C8   C9   C10  N      0.00   0.0  0
 BKE  CONST_06  C4   C3   C2   C1     0.00   0.0  0
 BKE  CONST_07  C4   C5   C6   C1     0.00   0.0  0
 BKE  CONST_08  C5   C6   C1   C2     0.00   0.0  0
 BKE  CONST_09  C5   C4   C3   C2     0.00   0.0  0
 BKE  CONST_10  C6   C1   C2   C3     0.00   0.0  0
 BKE  CONST_13  C6   C5   C4   C3     0.00   0.0  0
 BKE  CONST_14  C8   C7   N    C4   180.00   0.0  0
 BKE  CONST_15  C9   C10  N    C4   180.00   0.0  0
 BKE  CONST_18  C9   C10  N    C7     0.00   0.0  0
 BKE  CONST_19  C10  C9   C8   C7     0.00   0.0  0
 BKE  CONST_22  C10  N    C7   C8     0.00   0.0  0
 BKE  CONST_23  C15  C14  C13  C8   180.00   0.0  0
 BKE  CONST_24  C17  C18  C13  C8   180.00   0.0  0
 BKE  CONST_27  C13  C8   C9   C10  180.00   0.0  0
 BKE  CONST_28  C16  C15  C14  C13    0.00   0.0  0
 BKE  CONST_29  C16  C17  C18  C13    0.00   0.0  0
 BKE  CONST_30  C17  C18  C13  C14    0.00   0.0  0
 BKE  CONST_31  C17  C16  C15  C14    0.00   0.0  0
 BKE  CONST_32  C18  C13  C14  C15    0.00   0.0  0
 BKE  CONST_33  C18  C17  C16  C15    0.00   0.0  0
 BKE  CONST_34  C4   N    C10  N1     0.00   0.0  0
 BKE  CONST_35  C13  C8   C9   C12    0.00   0.0  0
 BKE  CONST_36  C12  N2   C11  N1     0.00   0.0  0
 BKE  CONST_37  C10  N1   C11  N2     0.00   0.0  0
 BKE  CONST_38  C11  N2   C12  C9     0.00   0.0  0
 BKE  CONST_39  C3   C2   C1   O    180.00   0.0  0
 BKE  CONST_40  C5   C6   C1   O    180.00   0.0  0
 BKE  CONST_41  C11  N2   C12  O1   180.00   0.0  0
 BKE  CONST_42  H3   C3   C4   N      0.00   0.0  0
 BKE  CONST_43  H5   C5   C4   N      0.00   0.0  0
 BKE  CONST_44  H6   C6   C1   C2   180.00   0.0  0
 BKE  CONST_45  H7   C7   N    C4     0.00   0.0  0
 BKE  CONST_46  H2   C2   C3   C4   180.00   0.0  0
 BKE  CONST_47  H14  C14  C13  C8     0.00   0.0  0
 BKE  CONST_48  H18  C18  C13  C8     0.00   0.0  0
 BKE  CONST_49  H15  C15  C14  C13  180.00   0.0  0
 BKE  CONST_50  H17  C17  C18  C13  180.00   0.0  0
 BKE  CONST_51  H16  C16  C15  C14  180.00   0.0  0
 BKE  CONST_52  HN2  N2   C11  N1   180.00   0.0  0
 BKE  CONST_53  H11  C11  N1   C10  180.00   0.0  0
 BKE  Var_01    C2   C1   O    C    178.59  30.0  2
 BKE  Var_02    H    C    O    C1   -59.91  30.0  3

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
 BKE  plan-1  N    0.020
 BKE  plan-1  O    0.020
 BKE  plan-1  C1   0.020
 BKE  plan-1  C2   0.020
 BKE  plan-1  C3   0.020
 BKE  plan-1  C4   0.020
 BKE  plan-1  C5   0.020
 BKE  plan-1  C6   0.020
 BKE  plan-1  H2   0.020
 BKE  plan-1  H3   0.020
 BKE  plan-1  H5   0.020
 BKE  plan-1  H6   0.020
 BKE  plan-2  C8   0.020
 BKE  plan-2  C13  0.020
 BKE  plan-2  C14  0.020
 BKE  plan-2  C15  0.020
 BKE  plan-2  C16  0.020
 BKE  plan-2  C17  0.020
 BKE  plan-2  C18  0.020
 BKE  plan-2  H14  0.020
 BKE  plan-2  H15  0.020
 BKE  plan-2  H16  0.020
 BKE  plan-2  H17  0.020
 BKE  plan-2  H18  0.020
 BKE  plan-3  N    0.020
 BKE  plan-3  N1   0.020
 BKE  plan-3  N2   0.020
 BKE  plan-3  C4   0.020
 BKE  plan-3  C7   0.020
 BKE  plan-3  C8   0.020
 BKE  plan-3  C9   0.020
 BKE  plan-3  C10  0.020
 BKE  plan-3  C11  0.020
 BKE  plan-3  C12  0.020
 BKE  plan-3  C13  0.020
 BKE  plan-3  HN2  0.020
 BKE  plan-3  H7   0.020
 BKE  plan-3  H11  0.020
 BKE  plan-3  O1   0.020

