# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 18:58:16 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 8-bromo-2-{2-chloro-4-[(piperidin-4-ylmethyl)amino]phenyl}[1]benzofuro[3,2-d]pyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cc(NCC2CCNCC2)ccc1C3=Nc4c(oc5ccc(Br)cc45)C(=O)N3
#
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
 R9P  R9P  8-bromo-2-{2-chloro-4-[(piperidin-4-ylmethyl)amino]phenyl}[1]benzofuro[3,2-d]pyrimidin-4(3H)-one  ligand  50  30  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_R9P
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
 R9P  C13   C   CH2   0  -0.429   -8.7458  -0.3581   0.1367
 R9P  C14   C   CH2   0  -0.316  -10.0007   0.5130   0.1047
 R9P  N3    N   NH1   0  -0.576   -9.9814   1.5436  -0.9204
 R9P  C15   C   CH2   0  -0.317   -8.7869   2.3679  -0.8276
 R9P  C16   C   CH2   0  -0.419   -7.4832   1.5726  -0.8259
 R9P  C12   C   CH1   0  -0.288   -7.4922   0.5047   0.2671
 R9P  C11   C   CH2   0  -0.244   -6.2376  -0.3583   0.2438
 R9P  N2    N   NH1   0  -0.695   -5.0695   0.4298   0.5673
 R9P  C10   C   CR6   0   0.406   -3.8018  -0.0440   0.5300
 R9P  C17   C   CR16  0  -0.300   -2.7687   0.6995   1.1307
 R9P  C18   C   CR6   0  -0.079   -1.4642   0.2646   1.0839
 R9P  CL1   CL  CL    0  -0.118   -0.2881   1.2206   1.9203
 R9P  C9    C   CR16  0  -0.338   -3.4596  -1.2531  -0.0972
 R9P  C8    C   CR16  0  -0.287   -2.1448  -1.6675  -0.1282
 R9P  C7    C   CR6   0   0.038   -1.1065  -0.9307   0.4473
 R9P  C6    C   CR6   0   0.469    0.2748  -1.4158   0.3551
 R9P  N4    N   N     0  -0.433    1.2448  -0.6159   0.0375
 R9P  C19   C   CR56  0   0.178    2.4643  -1.1930  -0.0260
 R9P  C20   C   CR56  0   0.017    3.7485  -0.6126  -0.3086
 R9P  C21   C   CR16  0  -0.303    4.1993   0.6753  -0.5856
 R9P  C22   C   CR6   0  -0.120    5.5553   0.8322  -0.7924
 R9P  BR1   BR  BR    0  -0.036    6.2371   2.5527  -1.1668
 R9P  C1    C   CR16  0  -0.229    6.4512  -0.2443  -0.7315
 R9P  C2    C   CR16  0  -0.325    6.0054  -1.5251  -0.4581
 R9P  C3    C   CR56  0   0.364    4.6466  -1.6806  -0.2489
 R9P  O1    O   O     0  -0.455    4.0152  -2.8429   0.0400
 R9P  C4    C   CR56  0   0.152    2.7075  -2.5250   0.1722
 R9P  C5    C   CR6   0   0.499    1.6676  -3.4415   0.5101
 R9P  O2    O   O     0  -0.456    1.7502  -4.6370   0.7221
 R9P  N1    N   NR16  0  -0.705    0.4644  -2.7471   0.5953
 R9P  H131  H   HCH2  0   0.230   -8.8088  -1.0667   0.9677
 R9P  H132  H   HCH2  0   0.215   -8.6902  -0.9532  -0.7827
 R9P  H141  H   HCH2  0   0.234  -10.8880  -0.1079  -0.0363
 R9P  H142  H   HCH2  0   0.214  -10.1158   1.0051   1.0770
 R9P  H12   H   HCH1  0   0.226   -7.5388   1.0080   1.2439
 R9P  H3    H   HNH1  0   0.337   -9.9984   1.0976  -1.8311
 R9P  H151  H   HCH2  0   0.235   -8.7894   3.0822  -1.6533
 R9P  H152  H   HCH2  0   0.214   -8.8505   2.9578   0.0937
 R9P  H161  H   HCH2  0   0.212   -7.3570   1.0854  -1.8003
 R9P  H162  H   HCH2  0   0.229   -6.6364   2.2523  -0.7019
 R9P  H111  H   HCH2  0   0.234   -6.3490  -1.1968   0.9443
 R9P  H112  H   HCH2  0   0.231   -6.1258  -0.7917  -0.7548
 R9P  H2    H   HNH1  0   0.390   -5.2283   1.2100   1.1859
 R9P  H17   H   HCR6  0   0.285   -3.0082   1.6219   1.6446
 R9P  H9    H   HCR6  0   0.277   -4.2131  -1.8658  -0.5715
 R9P  H8    H   HCR6  0   0.274   -1.9150  -2.5916  -0.6445
 R9P  H1    H   HNR6  0   0.439   -0.3336  -3.2944   0.8955
 R9P  H21   H   HCR6  0   0.285    3.5077   1.5057  -0.6311
 R9P  HA    H   HCR6  0   0.292    7.5075  -0.0824  -0.8966
 R9P  HB    H   HCR6  0   0.291    6.6954  -2.3559  -0.4091

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
 R9P  C13  C14   single    1.528  0.020  1.528
 R9P  C13  C12   single    1.527  0.020  1.527
 R9P  C14  N3    single    1.454  0.020  1.454
 R9P  N3   C15   single    1.454  0.020  1.454
 R9P  C15  C16   single    1.527  0.020  1.527
 R9P  C16  C12   single    1.528  0.020  1.528
 R9P  C12  C11   single    1.523  0.020  1.523
 R9P  C11  N2    single    1.446  0.020  1.446
 R9P  N2   C10   single    1.354  0.020  1.354
 R9P  C10  C17   aromatic  1.407  0.020  1.407
 R9P  C10  C9    aromatic  1.404  0.020  1.404
 R9P  C17  C18   aromatic  1.376  0.020  1.376
 R9P  C18  CL1   single    1.731  0.020  1.731
 R9P  C18  C7    aromatic  1.401  0.020  1.401
 R9P  C9   C8    aromatic  1.379  0.020  1.379
 R9P  C8   C7    aromatic  1.397  0.020  1.397
 R9P  C7   C6    single    1.467  0.020  1.467
 R9P  C6   N4    double    1.297  0.020  1.297
 R9P  C6   N1    single    1.366  0.020  1.366
 R9P  N4   C19   single    1.351  0.020  1.351
 R9P  C19  C20   aromatic  1.437  0.020  1.437
 R9P  C19  C4    aromatic  1.368  0.020  1.368
 R9P  C20  C21   aromatic  1.392  0.020  1.392
 R9P  C20  C3    aromatic  1.397  0.020  1.397
 R9P  C21  C22   aromatic  1.381  0.020  1.381
 R9P  C22  BR1   single    1.888  0.020  1.888
 R9P  C22  C1    aromatic  1.402  0.020  1.402
 R9P  C1   C2    aromatic  1.384  0.020  1.384
 R9P  C2   C3    aromatic  1.384  0.020  1.384
 R9P  C3   O1    aromatic  1.354  0.020  1.354
 R9P  O1   C4    aromatic  1.352  0.020  1.352
 R9P  C4   C5    single    1.427  0.020  1.427
 R9P  C5   O2    double    1.217  0.020  1.217
 R9P  C5   N1    single    1.392  0.020  1.392
 R9P  C13  H131  single    0.970  0.020  1.090
 R9P  C13  H132  single    0.970  0.020  1.090
 R9P  C14  H141  single    0.970  0.020  1.090
 R9P  C14  H142  single    0.970  0.020  1.090
 R9P  C12  H12   single    0.970  0.020  1.090
 R9P  N3   H3    single    0.890  0.020  1.040
 R9P  C15  H151  single    0.970  0.020  1.090
 R9P  C15  H152  single    0.970  0.020  1.090
 R9P  C16  H161  single    0.970  0.020  1.090
 R9P  C16  H162  single    0.970  0.020  1.090
 R9P  C11  H111  single    0.970  0.020  1.090
 R9P  C11  H112  single    0.970  0.020  1.090
 R9P  N2   H2    single    0.890  0.020  1.040
 R9P  C17  H17   single    0.930  0.020  1.080
 R9P  C9   H9    single    0.930  0.020  1.080
 R9P  C8   H8    single    0.930  0.020  1.080
 R9P  N1   H1    single    0.860  0.020  1.020
 R9P  C21  H21   single    0.930  0.020  1.080
 R9P  C1   HA    single    0.930  0.020  1.080
 R9P  C2   HB    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
 R9P  H132  C13  H131  106.76  3.000
 R9P  H132  C13  C12   109.67  3.000
 R9P  H131  C13  C12   110.38  3.000
 R9P  H132  C13  C14   109.48  3.000
 R9P  H131  C13  C14   109.75  3.000
 R9P  C12   C13  C14   110.72  3.000
 R9P  H142  C14  H141  106.53  3.000
 R9P  H142  C14  N3    107.98  3.000
 R9P  H141  C14  N3    108.83  3.000
 R9P  H142  C14  C13   108.89  3.000
 R9P  H141  C14  C13   110.24  3.000
 R9P  N3    C14  C13   114.08  3.000
 R9P  H3    N3   C15   108.68  3.000
 R9P  H3    N3   C14   108.74  3.000
 R9P  C15   N3   C14   111.57  3.000
 R9P  H152  C15  H151  106.47  3.000
 R9P  H152  C15  C16   109.21  3.000
 R9P  H151  C15  C16   110.09  3.000
 R9P  H152  C15  N3    108.12  3.000
 R9P  H151  C15  N3    108.71  3.000
 R9P  C16   C15  N3    113.96  3.000
 R9P  H162  C16  H161  106.73  3.000
 R9P  H162  C16  C12   110.98  3.000
 R9P  H161  C16  C12   109.02  3.000
 R9P  H162  C16  C15   109.73  3.000
 R9P  H161  C16  C15   109.19  3.000
 R9P  C12   C16  C15   111.08  3.000
 R9P  H12   C12  C11   107.92  3.000
 R9P  H12   C12  C16   108.41  3.000
 R9P  C11   C12  C16   112.34  3.000
 R9P  H12   C12  C13   107.44  3.000
 R9P  C11   C12  C13   110.77  3.000
 R9P  C16   C12  C13   109.79  3.000
 R9P  H112  C11  H111  106.86  3.000
 R9P  H112  C11  N2    109.72  3.000
 R9P  H111  C11  N2    110.82  3.000
 R9P  H112  C11  C12   108.82  3.000
 R9P  H111  C11  C12   109.84  3.000
 R9P  N2    C11  C12   110.68  3.000
 R9P  H2    N2   C10   115.80  3.000
 R9P  H2    N2   C11   115.59  3.000
 R9P  C10   N2   C11   124.03  3.000
 R9P  C9    C10  C17   117.81  3.000
 R9P  C9    C10  N2    122.80  3.000
 R9P  C17   C10  N2    119.39  3.000
 R9P  H17   C17  C18   119.68  3.000
 R9P  H17   C17  C10   119.35  3.000
 R9P  C18   C17  C10   120.97  3.000
 R9P  C7    C18  CL1   121.16  3.000
 R9P  C7    C18  C17   121.82  3.000
 R9P  CL1   C18  C17   116.95  3.000
 R9P  H9    C9   C8    118.99  3.000
 R9P  H9    C9   C10   120.94  3.000
 R9P  C8    C9   C10   120.07  3.000
 R9P  H8    C8   C7    119.25  3.000
 R9P  H8    C8   C9    117.99  3.000
 R9P  C7    C8   C9    122.74  3.000
 R9P  C6    C7   C8    119.96  3.000
 R9P  C6    C7   C18   123.46  3.000
 R9P  C8    C7   C18   116.58  3.000
 R9P  N1    C6   N4    122.71  3.000
 R9P  N1    C6   C7    116.23  3.000
 R9P  N4    C6   C7    121.04  3.000
 R9P  C19   N4   C6    115.04  3.000
 R9P  C4    C19  C20   105.23  3.000
 R9P  C4    C19  N4    124.72  3.000
 R9P  C20   C19  N4    130.05  3.000
 R9P  C3    C20  C21   120.51  3.000
 R9P  C3    C20  C19   104.91  3.000
 R9P  C21   C20  C19   134.58  3.000
 R9P  H21   C21  C22   122.31  3.000
 R9P  H21   C21  C20   120.76  3.000
 R9P  C22   C21  C20   116.93  3.000
 R9P  C1    C22  BR1   118.53  3.000
 R9P  C1    C22  C21   122.27  3.000
 R9P  BR1   C22  C21   119.20  3.000
 R9P  HA    C1   C2    118.92  3.000
 R9P  HA    C1   C22   120.18  3.000
 R9P  C2    C1   C22   120.90  3.000
 R9P  HB    C2   C3    122.25  3.000
 R9P  HB    C2   C1    120.98  3.000
 R9P  C3    C2   C1    116.77  3.000
 R9P  O1    C3   C2    125.92  3.000
 R9P  O1    C3   C20   111.45  3.000
 R9P  C2    C3   C20   122.62  3.000
 R9P  C4    O1   C3    105.66  3.000
 R9P  C5    C4   O1    125.24  3.000
 R9P  C5    C4   C19   122.01  3.000
 R9P  O1    C4   C19   112.74  3.000
 R9P  N1    C5   O2    122.56  3.000
 R9P  N1    C5   C4    108.91  3.000
 R9P  O2    C5   C4    128.52  3.000
 R9P  H1    N1   C5    115.44  3.000
 R9P  H1    N1   C6    117.99  3.000
 R9P  C5    N1   C6    126.54  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
 R9P  CONST_01  C7   C18  C17  C10     0.00   0.0  0
 R9P  CONST_02  C7   C8   C9   C10     0.00   0.0  0
 R9P  CONST_03  C8   C9   C10  C17     0.00   0.0  0
 R9P  CONST_04  C8   C7   C18  C17     0.00   0.0  0
 R9P  CONST_05  C9   C10  C17  C18     0.00   0.0  0
 R9P  CONST_06  C9   C8   C7   C18     0.00   0.0  0
 R9P  CONST_07  C22  C21  C20  C19   180.00   0.0  0
 R9P  CONST_08  C2   C3   C20  C19   180.00   0.0  0
 R9P  CONST_09  O1   C3   C20  C19     0.00   0.0  0
 R9P  CONST_10  C3   O1   C4   C19     0.00   0.0  0
 R9P  CONST_11  O1   C4   C19  C20     0.00   0.0  0
 R9P  CONST_12  C1   C22  C21  C20     0.00   0.0  0
 R9P  CONST_13  C1   C2   C3   C20     0.00   0.0  0
 R9P  CONST_14  C4   O1   C3   C20     0.00   0.0  0
 R9P  CONST_15  C4   C19  C20  C21   180.00   0.0  0
 R9P  CONST_16  C2   C3   C20  C21     0.00   0.0  0
 R9P  CONST_17  O1   C3   C20  C21   180.00   0.0  0
 R9P  CONST_18  C2   C1   C22  C21     0.00   0.0  0
 R9P  CONST_19  C3   C20  C21  C22     0.00   0.0  0
 R9P  CONST_20  C3   C2   C1   C22     0.00   0.0  0
 R9P  CONST_21  O1   C3   C2   C1    180.00   0.0  0
 R9P  CONST_22  C4   O1   C3   C2    180.00   0.0  0
 R9P  CONST_23  C4   C19  C20  C3      0.00   0.0  0
 R9P  CONST_24  C6   C7   C18  C17   180.00   0.0  0
 R9P  CONST_25  C6   C7   C8   C9    180.00   0.0  0
 R9P  CONST_26  C19  N4   C6   C7    180.00   0.0  0
 R9P  CONST_27  C5   N1   C6   C7    180.00   0.0  0
 R9P  CONST_28  C4   C5   N1   C6      0.00   0.0  0
 R9P  CONST_29  C5   N1   C6   N4      0.00   0.0  0
 R9P  CONST_30  N1   C6   N4   C19     0.00   0.0  0
 R9P  CONST_31  C18  C17  C10  N2    180.00   0.0  0
 R9P  CONST_32  C8   C9   C10  N2    180.00   0.0  0
 R9P  CONST_33  CL1  C18  C17  C10   180.00   0.0  0
 R9P  CONST_34  C8   C7   C18  CL1   180.00   0.0  0
 R9P  CONST_35  C6   C7   C18  CL1     0.00   0.0  0
 R9P  CONST_36  BR1  C22  C21  C20   180.00   0.0  0
 R9P  CONST_37  C2   C1   C22  BR1   180.00   0.0  0
 R9P  CONST_38  O2   C5   N1   C6    180.00   0.0  0
 R9P  CONST_39  H8   C8   C9   C10   180.00   0.0  0
 R9P  CONST_40  H9   C9   C10  C17   180.00   0.0  0
 R9P  CONST_41  H17  C17  C10  C9    180.00   0.0  0
 R9P  CONST_42  H21  C21  C20  C19     0.00   0.0  0
 R9P  CONST_43  HB   C2   C3   C20   180.00   0.0  0
 R9P  CONST_44  HA   C1   C22  C21   180.00   0.0  0
 R9P  CONST_45  H1   N1   C6   C7      0.00   0.0  0
 R9P  CONST_46  C17  C10  N2   C11   180.00   0.0  0
 R9P  CONST_47  C9   C10  N2   C11     0.00   0.0  0
 R9P  CONST_48  H2   N2   C10  C17     0.00   0.0  0
 R9P  Var_01    C15  N3   C14  C13   -53.68  30.0  1
 R9P  Var_02    C16  C15  N3   C14    53.29  30.0  1
 R9P  Var_03    C12  C13  C14  N3     54.53  30.0  1
 R9P  Var_04    C12  C16  C15  N3    -53.99  30.0  1
 R9P  Var_05    N4   C6   C7   C18   -44.66  30.0  2
 R9P  Var_06    C10  N2   C11  C12  -175.04  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
 R9P  chir_01  C12  C13  C16  C11  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
 R9P  plan-1  N2   0.020
 R9P  plan-1  C10  0.020
 R9P  plan-1  C17  0.020
 R9P  plan-1  C18  0.020
 R9P  plan-1  CL1  0.020
 R9P  plan-1  C9   0.020
 R9P  plan-1  C8   0.020
 R9P  plan-1  C7   0.020
 R9P  plan-1  C6   0.020
 R9P  plan-1  H17  0.020
 R9P  plan-1  H9   0.020
 R9P  plan-1  H8   0.020
 R9P  plan-2  C7   0.020
 R9P  plan-2  C6   0.020
 R9P  plan-2  N4   0.020
 R9P  plan-2  C19  0.020
 R9P  plan-2  C20  0.020
 R9P  plan-2  C21  0.020
 R9P  plan-2  C22  0.020
 R9P  plan-2  BR1  0.020
 R9P  plan-2  C1   0.020
 R9P  plan-2  C2   0.020
 R9P  plan-2  C3   0.020
 R9P  plan-2  O1   0.020
 R9P  plan-2  C4   0.020
 R9P  plan-2  C5   0.020
 R9P  plan-2  O2   0.020
 R9P  plan-2  N1   0.020
 R9P  plan-2  H1   0.020
 R9P  plan-2  H21  0.020
 R9P  plan-2  HA   0.020
 R9P  plan-2  HB   0.020
 R9P  plan-3  C11  0.020
 R9P  plan-3  N2   0.020
 R9P  plan-3  C10  0.020
 R9P  plan-3  H2   0.020

