# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 01:14:34 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: (9~{b}~{R})-9~{b}-(4-chlorophenyl)-1-pyridin-3-ylcarbonyl-2,3-dihydroimidazo[5,6]pyrrolo[1,2-~{a}]pyridin-5-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(cc1)[C@]23N(CCN2C(=O)c4ccncc34)C(=O)c5cccnc5
#
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
 5NP  5NP  (9~{b}~{R})-9~{b}-(4-chlorophenyl)-1-pyridin-3-ylcarbonyl-2,3-dihydroimidazo[5,6]pyrrolo[1,2-~{a}]pyridin-5-one  ligand  43  28  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5NP
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
 5NP  C10  C   CH2   0  -0.303   1.5456  -0.1058  -1.8136
 5NP  C13  C   CR5   0   0.532  -0.4216  -2.6523  -1.5165
 5NP  C15  C   C     0   0.518   1.6081   0.6153   0.5969
 5NP  C17  C   CR16  0  -0.306  -1.1640   1.7662  -0.4637
 5NP  C20  C   CR6   0  -0.137   2.9810   1.1588   0.3942
 5NP  C21  C   CR16  0  -0.051  -0.6767  -4.1204   1.9623
 5NP  C22  C   CR16  0  -0.200  -2.1878   2.6987  -0.3807
 5NP  C24  C   CR6   0  -0.052  -3.4515   2.2832   0.0024
 5NP  C26  C   CR16  0  -0.063   3.2266   2.4862   0.7354
 5NP  C28  C   CR16  0  -0.053   5.4355   2.3045   0.2304
 5NP  CL1  CL  CL    0  -0.122  -4.7347   3.4398   0.1145
 5NP  O02  O   O     0  -0.422  -0.3500  -3.4344  -2.4363
 5NP  O03  O   O     0  -0.454   1.0251   0.7850   1.6552
 5NP  N04  N   N     0  -0.489  -0.4282  -1.2875  -1.6096
 5NP  N05  N   NR5   0  -0.507   1.0448  -0.0451  -0.4353
 5NP  N06  N   N     0  -0.400  -0.6147  -2.9917   2.6632
 5NP  N07  N   N     0  -0.399   4.4195   3.0539   0.6443
 5NP  C08  C   C     0   0.160  -0.2979  -0.6202  -0.3207
 5NP  C09  C   CH2   0  -0.355   0.3101  -0.5399  -2.6016
 5NP  C11  C   CR56  0   0.035  -0.4125  -1.7775   0.6470
 5NP  C12  C   CR6   0   0.254  -1.3880   0.4293  -0.1612
 5NP  C14  C   CR56  0   0.037  -0.5080  -2.9556  -0.0676
 5NP  C16  C   CR16  0  -0.081  -0.4926  -1.8309   2.0284
 5NP  C18  C   CR16  0  -0.318  -2.6692   0.0350   0.2122
 5NP  C19  C   CR16  0  -0.365  -0.6354  -4.1697   0.5750
 5NP  C23  C   CR16  0  -0.197  -3.7034   0.9525   0.2976
 5NP  C25  C   CR16  0  -0.152   4.0513   0.3836  -0.0346
 5NP  C27  C   CR16  0  -0.319   5.3046   0.9672  -0.1122
 5NP  H1   H   HCH2  0   0.287   1.9302   0.8592  -2.1398
 5NP  H2   H   HCH2  0   0.276   2.3344  -0.8520  -1.9139
 5NP  H3   H   HCR6  0   0.264  -0.1873   2.1128  -0.7740
 5NP  H4   H   HCR6  0   0.281  -0.7759  -5.0354   2.5343
 5NP  H5   H   HCR6  0   0.286  -1.9894   3.7383  -0.6039
 5NP  H6   H   HCR6  0   0.273   2.4164   3.1164   1.0873
 5NP  H7   H   HCR6  0   0.275   6.4034   2.7893   0.1736
 5NP  H8   H   HCH2  0   0.282  -0.2746   0.3132  -2.9470
 5NP  H9   H   HCH2  0   0.300   0.5529  -1.1611  -3.4598
 5NP  H10  H   HCR6  0   0.279  -0.4638  -0.9394   2.6393
 5NP  H11  H   HCR6  0   0.268  -2.8830  -1.0003   0.4436
 5NP  H12  H   HCR6  0   0.285  -0.7102  -5.1072   0.0414
 5NP  H13  H   HCR6  0   0.286  -4.6919   0.6292   0.5931
 5NP  H14  H   HCR6  0   0.287   3.9230  -0.6623  -0.2820
 5NP  H15  H   HCR6  0   0.282   6.1669   0.3977  -0.4287

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
 5NP  CL1  C24  single    1.731  0.020  1.731
 5NP  C22  C24  aromatic  1.384  0.020  1.384
 5NP  C22  C17  aromatic  1.387  0.020  1.387
 5NP  C24  C23  aromatic  1.386  0.020  1.386
 5NP  C17  C12  aromatic  1.389  0.020  1.389
 5NP  C23  C18  aromatic  1.385  0.020  1.385
 5NP  N06  C16  aromatic  1.329  0.020  1.329
 5NP  N06  C21  aromatic  1.330  0.020  1.330
 5NP  C16  C11  aromatic  1.385  0.020  1.385
 5NP  C12  C18  aromatic  1.392  0.020  1.392
 5NP  C12  C08  single    1.522  0.020  1.522
 5NP  C21  C19  aromatic  1.389  0.020  1.389
 5NP  C11  C08  single    1.513  0.020  1.513
 5NP  C11  C14  aromatic  1.381  0.020  1.381
 5NP  O03  C15  double    1.220  0.020  1.220
 5NP  C08  N05  single    1.465  0.020  1.465
 5NP  C08  N04  single    1.457  0.020  1.457
 5NP  C19  C14  aromatic  1.379  0.020  1.379
 5NP  C15  N05  single    1.349  0.020  1.349
 5NP  C15  C20  single    1.490  0.020  1.490
 5NP  C14  C13  single    1.483  0.020  1.483
 5NP  N05  C10  single    1.468  0.020  1.468
 5NP  C26  C20  aromatic  1.392  0.020  1.392
 5NP  C26  N07  aromatic  1.324  0.020  1.324
 5NP  C20  C25  aromatic  1.389  0.020  1.389
 5NP  N04  C13  single    1.368  0.020  1.368
 5NP  N04  C09  single    1.445  0.020  1.445
 5NP  C10  C09  single    1.528  0.020  1.528
 5NP  C13  O02  double    1.209  0.020  1.209
 5NP  N07  C28  aromatic  1.329  0.020  1.329
 5NP  C25  C27  aromatic  1.385  0.020  1.385
 5NP  C28  C27  aromatic  1.387  0.020  1.387
 5NP  C10  H1   single    0.970  0.020  1.090
 5NP  C10  H2   single    0.970  0.020  1.090
 5NP  C17  H3   single    0.930  0.020  1.080
 5NP  C21  H4   single    0.930  0.020  1.080
 5NP  C22  H5   single    0.930  0.020  1.080
 5NP  C26  H6   single    0.930  0.020  1.080
 5NP  C28  H7   single    0.930  0.020  1.080
 5NP  C09  H8   single    0.970  0.020  1.090
 5NP  C09  H9   single    0.970  0.020  1.090
 5NP  C16  H10  single    0.930  0.020  1.080
 5NP  C18  H11  single    0.930  0.020  1.080
 5NP  C19  H12  single    0.930  0.020  1.080
 5NP  C23  H13  single    0.930  0.020  1.080
 5NP  C25  H14  single    0.930  0.020  1.080
 5NP  C27  H15  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
 5NP  H2   C10  H1   108.87  3.000
 5NP  H2   C10  C09  110.06  3.000
 5NP  H1   C10  C09  112.51  3.000
 5NP  H2   C10  N05  111.19  3.000
 5NP  H1   C10  N05  111.42  3.000
 5NP  C09  C10  N05  102.71  3.000
 5NP  C14  C13  N04  105.68  3.000
 5NP  N04  C13  O02  126.42  3.000
 5NP  C14  C13  O02  127.90  3.000
 5NP  N05  C15  O03  122.17  3.000
 5NP  N05  C15  C20  117.34  3.000
 5NP  O03  C15  C20  120.49  3.000
 5NP  H3   C17  C12  121.10  3.000
 5NP  H3   C17  C22  117.90  3.000
 5NP  C12  C17  C22  121.00  3.000
 5NP  C25  C20  C26  118.14  3.000
 5NP  C25  C20  C15  123.24  3.000
 5NP  C26  C20  C15  118.48  3.000
 5NP  H4   C21  C19  120.01  3.000
 5NP  H4   C21  N06  116.27  3.000
 5NP  C19  C21  N06  123.72  3.000
 5NP  H5   C22  C24  120.87  3.000
 5NP  H5   C22  C17  119.89  3.000
 5NP  C24  C22  C17  119.24  3.000
 5NP  C23  C24  CL1  119.53  3.000
 5NP  C23  C24  C22  120.86  3.000
 5NP  CL1  C24  C22  119.61  3.000
 5NP  H6   C26  N07  116.48  3.000
 5NP  H6   C26  C20  120.10  3.000
 5NP  N07  C26  C20  123.42  3.000
 5NP  H7   C28  C27  120.17  3.000
 5NP  H7   C28  N07  116.54  3.000
 5NP  C27  C28  N07  123.29  3.000
 5NP  C09  N04  C08  108.94  3.000
 5NP  C09  N04  C13  124.08  3.000
 5NP  C08  N04  C13  113.34  3.000
 5NP  C08  N05  C15  121.01  3.000
 5NP  C15  N05  C10  126.61  3.000
 5NP  C08  N05  C10  111.71  3.000
 5NP  C16  N06  C21  119.60  3.000
 5NP  C28  N07  C26  117.93  3.000
 5NP  C12  C08  C11  113.97  3.000
 5NP  C11  C08  N05  114.82  3.000
 5NP  C12  C08  N05  113.20  3.000
 5NP  N05  C08  N04  101.10  3.000
 5NP  C11  C08  N04  102.05  3.000
 5NP  C12  C08  N04  110.15  3.000
 5NP  H9   C09  H8   108.47  3.000
 5NP  H9   C09  N04  111.13  3.000
 5NP  H8   C09  N04  110.38  3.000
 5NP  H9   C09  C10  112.88  3.000
 5NP  H8   C09  C10  112.00  3.000
 5NP  N04  C09  C10  101.89  3.000
 5NP  C16  C11  C14  118.64  3.000
 5NP  C14  C11  C08  109.07  3.000
 5NP  C16  C11  C08  132.22  3.000
 5NP  C18  C12  C08  119.49  3.000
 5NP  C08  C12  C17  121.71  3.000
 5NP  C18  C12  C17  118.67  3.000
 5NP  C19  C14  C11  121.07  3.000
 5NP  C19  C14  C13  129.83  3.000
 5NP  C11  C14  C13  109.09  3.000
 5NP  H10  C16  C11  122.03  3.000
 5NP  H10  C16  N06  116.93  3.000
 5NP  C11  C16  N06  121.04  3.000
 5NP  H11  C18  C23  118.23  3.000
 5NP  H11  C18  C12  120.68  3.000
 5NP  C23  C18  C12  121.08  3.000
 5NP  H12  C19  C14  122.65  3.000
 5NP  H12  C19  C21  121.44  3.000
 5NP  C14  C19  C21  115.90  3.000
 5NP  H13  C23  C18  120.10  3.000
 5NP  H13  C23  C24  120.75  3.000
 5NP  C18  C23  C24  119.15  3.000
 5NP  H14  C25  C27  120.11  3.000
 5NP  H14  C25  C20  121.22  3.000
 5NP  C27  C25  C20  118.65  3.000
 5NP  H15  C27  C25  121.10  3.000
 5NP  H15  C27  C28  120.35  3.000
 5NP  C25  C27  C28  118.55  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
 5NP  CONST_01  C23  C24  C22  C17    0.00   0.0  0
 5NP  CONST_02  C23  C18  C12  C17    0.00   0.0  0
 5NP  CONST_03  C28  N07  C26  C20    0.00   0.0  0
 5NP  CONST_04  C28  C27  C25  C20    0.00   0.0  0
 5NP  CONST_05  C11  C16  N06  C21    0.00   0.0  0
 5NP  CONST_06  C11  C14  C19  C21    0.00   0.0  0
 5NP  CONST_07  C18  C23  C24  C22    0.00   0.0  0
 5NP  CONST_08  C18  C12  C17  C22    0.00   0.0  0
 5NP  CONST_09  C12  C17  C22  C24    0.00   0.0  0
 5NP  CONST_10  C12  C18  C23  C24    0.00   0.0  0
 5NP  CONST_11  C27  C25  C20  C26    0.00   0.0  0
 5NP  CONST_12  C27  C28  N07  C26    0.00   0.0  0
 5NP  CONST_13  C14  C11  C16  N06    0.00   0.0  0
 5NP  CONST_14  C14  C19  C21  N06    0.00   0.0  0
 5NP  CONST_15  C25  C20  C26  N07    0.00   0.0  0
 5NP  CONST_16  C25  C27  C28  N07    0.00   0.0  0
 5NP  CONST_17  C19  C21  N06  C16    0.00   0.0  0
 5NP  CONST_18  C19  C14  C11  C16    0.00   0.0  0
 5NP  CONST_19  C08  C12  C17  C22  180.00   0.0  0
 5NP  CONST_20  C23  C18  C12  C08  180.00   0.0  0
 5NP  CONST_21  C14  C13  N04  C08    0.00   0.0  0
 5NP  CONST_23  N07  C26  C20  C15  180.00   0.0  0
 5NP  CONST_24  C27  C25  C20  C15  180.00   0.0  0
 5NP  CONST_25  CL1  C24  C22  C17  180.00   0.0  0
 5NP  CONST_26  C18  C23  C24  CL1  180.00   0.0  0
 5NP  CONST_27  C20  C15  N05  C10    0.00   0.0  0
 5NP  CONST_28  C08  N05  C15  C20  180.00   0.0  0
 5NP  CONST_29  C08  N04  C13  O02  180.00   0.0  0
 5NP  CONST_31  H12  C19  C14  C13    0.00   0.0  0
 5NP  CONST_32  H11  C18  C12  C17  180.00   0.0  0
 5NP  CONST_33  H15  C27  C25  C20  180.00   0.0  0
 5NP  CONST_34  H10  C16  N06  C21  180.00   0.0  0
 5NP  CONST_35  H13  C23  C24  C22  180.00   0.0  0
 5NP  CONST_36  H3   C17  C22  C24  180.00   0.0  0
 5NP  CONST_37  H14  C25  C20  C26  180.00   0.0  0
 5NP  CONST_38  H7   C28  N07  C26  180.00   0.0  0
 5NP  CONST_39  H6   C26  N07  C28  180.00   0.0  0
 5NP  CONST_40  H5   C22  C17  C12  180.00   0.0  0
 5NP  CONST_41  H4   C21  C19  C14  180.00   0.0  0
 5NP  CONST_42  O03  C15  N05  C10  180.00   0.0  0
 5NP  CONST_43  C08  N05  C15  O03    0.00   0.0  0
 5NP  Var_01    C08  N04  C09  C10   38.41  30.0  1
 5NP  Var_02    N05  C10  C09  N04  -27.98  30.0  1
 5NP  Var_03    C09  C10  N05  C08    9.67  30.0  1
 5NP  Var_04    N05  C15  C20  C26  130.69  30.0  2

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
 5NP  chir_01  C08  C11  N05  N04  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
 5NP  plan-1  C17  0.020
 5NP  plan-1  C22  0.020
 5NP  plan-1  C24  0.020
 5NP  plan-1  CL1  0.020
 5NP  plan-1  C08  0.020
 5NP  plan-1  C12  0.020
 5NP  plan-1  C18  0.020
 5NP  plan-1  C23  0.020
 5NP  plan-1  H3   0.020
 5NP  plan-1  H5   0.020
 5NP  plan-1  H11  0.020
 5NP  plan-1  H13  0.020
 5NP  plan-2  C15  0.020
 5NP  plan-2  C20  0.020
 5NP  plan-2  C26  0.020
 5NP  plan-2  C28  0.020
 5NP  plan-2  N07  0.020
 5NP  plan-2  C25  0.020
 5NP  plan-2  C27  0.020
 5NP  plan-2  H6   0.020
 5NP  plan-2  H7   0.020
 5NP  plan-2  H14  0.020
 5NP  plan-2  H15  0.020
 5NP  plan-3  C10  0.020
 5NP  plan-3  C15  0.020
 5NP  plan-3  C20  0.020
 5NP  plan-3  O03  0.020
 5NP  plan-3  N05  0.020
 5NP  plan-3  C08  0.020
 5NP  plan-4  C13  0.020
 5NP  plan-4  C21  0.020
 5NP  plan-4  O02  0.020
 5NP  plan-4  N04  0.020
 5NP  plan-4  N06  0.020
 5NP  plan-4  C08  0.020
 5NP  plan-4  C09  0.020
 5NP  plan-4  C11  0.020
 5NP  plan-4  C14  0.020
 5NP  plan-4  C16  0.020
 5NP  plan-4  C19  0.020
 5NP  plan-4  H4   0.020
 5NP  plan-4  H10  0.020
 5NP  plan-4  H12  0.020

