# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 22:46:54 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: 1-[(3,4-dichlorophenyl)methyl]-7~{H}-pyrrolo[3,2-c]pyridin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(Cn2ccc3C(=O)N=CCc23)cc1Cl
#
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
 JJ5  JJ5  1-[(3,4-dichlorophenyl)methyl]-7~{H}-pyrrolo[3,2-c]pyridin-4-one  ligand  29  19  .  2021-08-12  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JJ5
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
 JJ5  O    O   O     0  -0.424   5.0030   0.7916   1.8545
 JJ5  C13  C   CR6   0   0.414   4.1825   0.2288   1.1584
 JJ5  C    C   CR56  0  -0.192   3.2305   0.9135   0.3161
 JJ5  C3   C   CR15  0  -0.385   2.9968   2.2968   0.0793
 JJ5  C2   C   CR15  0  -0.046   1.9739   2.3611  -0.8206
 JJ5  N1   N   N     0  -0.417   4.1522  -1.1889   1.1666
 JJ5  C12  C   CR16  0   0.005   3.3167  -1.8251   0.4487
 JJ5  C11  C   C     0  -0.606   2.2799  -1.2669  -0.4702
 JJ5  C1   C   CR56  0   0.448   2.3366   0.2036  -0.4534
 JJ5  N    N   NR5   0  -0.495   1.5800   1.0809  -1.1424
 JJ5  C4   C   CH2   0  -0.372   0.5083   0.7349  -2.0490
 JJ5  C5   C   CR6   0   0.082  -0.6616   0.0890  -1.3510
 JJ5  C10  C   CR16  0  -0.301  -1.3457  -0.9559  -1.9592
 JJ5  C9   C   CR16  0  -0.200  -2.4418  -1.5368  -1.3425
 JJ5  C8   C   CR6   0  -0.016  -2.8604  -1.0822  -0.1021
 JJ5  CL   CL  CL    0  -0.094  -4.2174  -1.8166   0.6614
 JJ5  C7   C   CR6   0   0.021  -2.1756  -0.0405   0.5155
 JJ5  CL1  CL  CL    0  -0.092  -2.6711   0.5391   2.0595
 JJ5  C6   C   CR16  0  -0.235  -1.0841   0.5421  -0.1078
 JJ5  H1   H   HCR5  0   0.256   3.5177   3.1345   0.5136
 JJ5  H2   H   HCR5  0   0.293   1.4851   3.2097  -1.2716
 JJ5  H3   H   HCR6  0   0.284   3.3476  -2.9110   0.5018
 JJ5  H4   H   H     0   0.315   2.4518  -1.6897  -1.4676
 JJ5  H5   H   H     0   0.308   1.3065  -1.6627  -0.1557
 JJ5  H6   H   HCH2  0   0.304   0.1891   1.6532  -2.5431
 JJ5  H7   H   HCH2  0   0.292   0.8889   0.0758  -2.8313
 JJ5  H8   H   HCR6  0   0.275  -1.0260  -1.3273  -2.9245
 JJ5  H9   H   HCR6  0   0.292  -2.9697  -2.3498  -1.8217
 JJ5  H10  H   HCR6  0   0.286  -0.5642   1.3504   0.3914

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
 JJ5  CL   C8   single    1.722  0.020  1.722
 JJ5  C9   C8   aromatic  1.386  0.020  1.386
 JJ5  C9   C10  aromatic  1.385  0.020  1.385
 JJ5  C8   C7   aromatic  1.391  0.020  1.391
 JJ5  C10  C5   aromatic  1.389  0.020  1.389
 JJ5  C12  C11  single    1.494  0.020  1.494
 JJ5  C12  N1   double    1.272  0.020  1.272
 JJ5  C7   CL1  single    1.722  0.020  1.722
 JJ5  C7   C6   aromatic  1.385  0.020  1.385
 JJ5  C11  C1   single    1.472  0.020  1.472
 JJ5  C5   C6   aromatic  1.389  0.020  1.389
 JJ5  C5   C4   single    1.508  0.020  1.508
 JJ5  N1   C13  single    1.418  0.020  1.418
 JJ5  C4   N    single    1.446  0.020  1.446
 JJ5  C1   N    aromatic  1.348  0.020  1.348
 JJ5  C1   C    aromatic  1.377  0.020  1.377
 JJ5  C13  C    single    1.444  0.020  1.444
 JJ5  C13  O    double    1.214  0.020  1.214
 JJ5  N    C2   aromatic  1.378  0.020  1.378
 JJ5  C    C3   aromatic  1.423  0.020  1.423
 JJ5  C2   C3   aromatic  1.364  0.020  1.364
 JJ5  C3   H1   single    0.930  0.020  1.080
 JJ5  C2   H2   single    0.930  0.020  1.080
 JJ5  C12  H3   single    0.930  0.020  1.080
 JJ5  C11  H4   single    0.970  0.020  1.090
 JJ5  C11  H5   single    0.970  0.020  1.090
 JJ5  C4   H6   single    0.970  0.020  1.090
 JJ5  C4   H7   single    0.970  0.020  1.090
 JJ5  C10  H8   single    0.930  0.020  1.080
 JJ5  C9   H9   single    0.930  0.020  1.080
 JJ5  C6   H10  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
 JJ5  N1   C13  C    117.61  3.000
 JJ5  C    C13  O    124.06  3.000
 JJ5  N1   C13  O    118.33  3.000
 JJ5  C1   C    C3   107.56  3.000
 JJ5  C3   C    C13  131.80  3.000
 JJ5  C1   C    C13  120.64  3.000
 JJ5  H1   C3   C2   126.28  3.000
 JJ5  H1   C3   C    127.53  3.000
 JJ5  C2   C3   C    106.19  3.000
 JJ5  H2   C2   N    120.27  3.000
 JJ5  H2   C2   C3   130.78  3.000
 JJ5  N    C2   C3   108.95  3.000
 JJ5  C12  N1   C13  120.71  3.000
 JJ5  H3   C12  C11  115.02  3.000
 JJ5  H3   C12  N1   116.94  3.000
 JJ5  C11  C12  N1   128.04  3.000
 JJ5  H5   C11  H4   105.11  3.000
 JJ5  H5   C11  C1   113.05  3.000
 JJ5  H4   C11  C1   112.92  3.000
 JJ5  H5   C11  C12  107.74  3.000
 JJ5  H4   C11  C12  107.86  3.000
 JJ5  C1   C11  C12  109.86  3.000
 JJ5  N    C1   C11  128.53  3.000
 JJ5  N    C1   C    108.34  3.000
 JJ5  C11  C1   C    123.14  3.000
 JJ5  C4   N    C1   125.51  3.000
 JJ5  C1   N    C2   108.96  3.000
 JJ5  C4   N    C2   125.51  3.000
 JJ5  H7   C4   H6   106.61  3.000
 JJ5  H7   C4   C5   110.10  3.000
 JJ5  H6   C4   C5   110.09  3.000
 JJ5  H7   C4   N    109.60  3.000
 JJ5  H6   C4   N    107.43  3.000
 JJ5  C5   C4   N    112.79  3.000
 JJ5  C6   C5   C10  119.17  3.000
 JJ5  C6   C5   C4   120.70  3.000
 JJ5  C10  C5   C4   120.12  3.000
 JJ5  H8   C10  C9   119.13  3.000
 JJ5  H8   C10  C5   120.19  3.000
 JJ5  C9   C10  C5   120.68  3.000
 JJ5  H9   C9   C8   119.72  3.000
 JJ5  H9   C9   C10  120.28  3.000
 JJ5  C8   C9   C10  119.99  3.000
 JJ5  C7   C8   CL   120.70  3.000
 JJ5  C7   C8   C9   119.62  3.000
 JJ5  CL   C8   C9   119.68  3.000
 JJ5  C6   C7   CL1  119.24  3.000
 JJ5  C6   C7   C8   120.20  3.000
 JJ5  CL1  C7   C8   120.56  3.000
 JJ5  H10  C6   C7   118.99  3.000
 JJ5  H10  C6   C5   120.67  3.000
 JJ5  C7   C6   C5   120.34  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
 JJ5  CONST_01  C2   N    C1   C       0.00   0.0  0
 JJ5  CONST_02  N    C2   C3   C       0.00   0.0  0
 JJ5  CONST_03  N    C1   C    C3      0.00   0.0  0
 JJ5  CONST_04  C1   N    C2   C3      0.00   0.0  0
 JJ5  CONST_05  C1   C    C3   C2      0.00   0.0  0
 JJ5  CONST_06  C8   C9   C10  C5      0.00   0.0  0
 JJ5  CONST_07  C8   C7   C6   C5      0.00   0.0  0
 JJ5  CONST_08  C7   C8   C9   C10     0.00   0.0  0
 JJ5  CONST_09  C7   C6   C5   C10     0.00   0.0  0
 JJ5  CONST_10  C6   C7   C8   C9      0.00   0.0  0
 JJ5  CONST_11  C6   C5   C10  C9      0.00   0.0  0
 JJ5  CONST_12  C4   N    C1   C     180.00   0.0  0
 JJ5  CONST_13  C4   N    C2   C3    180.00   0.0  0
 JJ5  CONST_14  C4   N    C1   C11     0.00   0.0  0
 JJ5  CONST_15  C9   C10  C5   C4    180.00   0.0  0
 JJ5  CONST_16  C7   C6   C5   C4    180.00   0.0  0
 JJ5  CONST_17  CL1  C7   C6   C5    180.00   0.0  0
 JJ5  CONST_18  CL   C8   C9   C10   180.00   0.0  0
 JJ5  CONST_19  CL1  C7   C8   C9    180.00   0.0  0
 JJ5  CONST_20  C6   C7   C8   CL    180.00   0.0  0
 JJ5  CONST_21  H1   C3   C    C13     0.00   0.0  0
 JJ5  CONST_22  H2   C2   C3   C     180.00   0.0  0
 JJ5  CONST_23  H9   C9   C10  C5    180.00   0.0  0
 JJ5  CONST_24  H10  C6   C5   C10   180.00   0.0  0
 JJ5  CONST_25  H8   C10  C9   C8    180.00   0.0  0
 JJ5  Var_01    C11  C12  N1   C13    -0.18  30.0  1
 JJ5  Var_02    C12  C11  C1   C      -0.14  30.0  1
 JJ5  Var_03    N1   C13  C    C3   -179.98  30.0  1
 JJ5  Var_04    C1   C11  C12  N1      0.06  30.0  1
 JJ5  Var_05    C5   C4   N    C2   -112.47  30.0  2
 JJ5  Var_06    C10  C5   C4   N    -141.63  30.0  2

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
 JJ5  plan-1  C4   0.020
 JJ5  plan-1  C5   0.020
 JJ5  plan-1  C10  0.020
 JJ5  plan-1  C9   0.020
 JJ5  plan-1  C8   0.020
 JJ5  plan-1  CL   0.020
 JJ5  plan-1  C7   0.020
 JJ5  plan-1  CL1  0.020
 JJ5  plan-1  C6   0.020
 JJ5  plan-1  H8   0.020
 JJ5  plan-1  H9   0.020
 JJ5  plan-1  H10  0.020
 JJ5  plan-2  C13  0.020
 JJ5  plan-2  C    0.020
 JJ5  plan-2  C3   0.020
 JJ5  plan-2  C2   0.020
 JJ5  plan-2  C11  0.020
 JJ5  plan-2  C1   0.020
 JJ5  plan-2  N    0.020
 JJ5  plan-2  C4   0.020
 JJ5  plan-2  H1   0.020
 JJ5  plan-2  H2   0.020
 JJ5  plan-3  O    0.020
 JJ5  plan-3  C13  0.020
 JJ5  plan-3  C    0.020
 JJ5  plan-3  N1   0.020

