# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 23:55:25 2020
#   Inital geometry file: a 58 line input string
#   Ligand name: 4-(2-hydroxyethyl)benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCc1ccc(cc1)C#N
#
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
 JMD  JMD  4-(2-hydroxyethyl)benzonitrile  ligand  20  11  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_JMD
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
 JMD  C10   C  CSP   0   0.054   3.3548   0.0221   0.2147
 JMD  O01   O  OH1   0  -0.669  -4.4112   0.0333   0.4037
 JMD  C02   C  CH2   0  -0.133  -3.0262   0.0619   0.6605
 JMD  C03   C  CH2   0  -0.540  -2.2907  -0.1047  -0.6636
 JMD  C04   C  CR6   0   0.126  -0.8045  -0.0760  -0.4588
 JMD  C05   C  CR16  0  -0.288  -0.1439   1.1376  -0.2660
 JMD  C06   C  CR16  0  -0.224   1.2197   1.1797  -0.0416
 JMD  C07   C  CR6   0  -0.013   1.9465  -0.0110  -0.0107
 JMD  C08   C  CR16  0  -0.222   1.3031  -1.2327  -0.2034
 JMD  C09   C  CR16  0  -0.297  -0.0631  -1.2551  -0.4237
 JMD  N11   N  NS    0  -0.255   4.4926   0.0486   0.3972
 JMD  H011  H  HOH1  0   0.456  -4.8730   0.1920   1.2319
 JMD  H021  H  HCH2  0   0.201  -2.7210   1.0082   1.1257
 JMD  H022  H  HCH2  0   0.201  -2.7234  -0.7415   1.3449
 JMD  H032  H  HCH2  0   0.254  -2.5860  -1.0492  -1.1257
 JMD  H031  H  HCH2  0   0.255  -2.5873   0.6990  -1.3422
 JMD  H051  H  HCR6  0   0.268  -0.7046   2.0639  -0.2969
 JMD  H061  H  HCR6  0   0.280   1.7209   2.1267   0.1064
 JMD  H081  H  HCR6  0   0.280   1.8687  -2.1544  -0.1820
 JMD  H091  H  HCR6  0   0.267  -0.5590  -2.2053  -0.5776

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
 JMD  N11  C10   triple    1.153  0.020  1.153
 JMD  C06  C05   aromatic  1.383  0.020  1.383
 JMD  C06  C07   aromatic  1.395  0.020  1.395
 JMD  C10  C07   single    1.427  0.020  1.427
 JMD  C05  C04   aromatic  1.395  0.020  1.395
 JMD  C07  C08   aromatic  1.394  0.020  1.394
 JMD  C04  C09   aromatic  1.393  0.020  1.393
 JMD  C04  C03   single    1.501  0.020  1.501
 JMD  C08  C09   aromatic  1.384  0.020  1.384
 JMD  C02  O01   single    1.409  0.020  1.409
 JMD  C02  C03   single    1.524  0.020  1.524
 JMD  O01  H011  single    0.850  0.020  0.980
 JMD  C02  H021  single    0.970  0.020  1.090
 JMD  C02  H022  single    0.970  0.020  1.090
 JMD  C03  H032  single    0.970  0.020  1.090
 JMD  C03  H031  single    0.970  0.020  1.090
 JMD  C05  H051  single    0.930  0.020  1.080
 JMD  C06  H061  single    0.930  0.020  1.080
 JMD  C08  H081  single    0.930  0.020  1.080
 JMD  C09  H091  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
 JMD  N11   C10  C07   180.00  3.000
 JMD  H011  O01  C02   108.17  3.000
 JMD  H022  C02  H021  106.85  3.000
 JMD  H022  C02  C03   109.18  3.000
 JMD  H021  C02  C03   109.17  3.000
 JMD  H022  C02  O01   111.71  3.000
 JMD  H021  C02  O01   111.59  3.000
 JMD  C03   C02  O01   108.30  3.000
 JMD  H031  C03  H032  107.45  3.000
 JMD  H031  C03  C04   109.85  3.000
 JMD  H032  C03  C04   110.00  3.000
 JMD  H031  C03  C02   109.16  3.000
 JMD  H032  C03  C02   109.37  3.000
 JMD  C04   C03  C02   110.94  3.000
 JMD  C09   C04  C05   118.73  3.000
 JMD  C09   C04  C03   120.95  3.000
 JMD  C05   C04  C03   120.30  3.000
 JMD  H051  C05  C06   119.28  3.000
 JMD  H051  C05  C04   119.66  3.000
 JMD  C06   C05  C04   121.06  3.000
 JMD  H061  C06  C07   120.18  3.000
 JMD  H061  C06  C05   120.39  3.000
 JMD  C07   C06  C05   119.43  3.000
 JMD  C08   C07  C06   120.28  3.000
 JMD  C08   C07  C10   119.85  3.000
 JMD  C06   C07  C10   119.86  3.000
 JMD  H081  C08  C09   120.37  3.000
 JMD  H081  C08  C07   120.18  3.000
 JMD  C09   C08  C07   119.46  3.000
 JMD  H091  C09  C08   119.27  3.000
 JMD  H091  C09  C04   119.70  3.000
 JMD  C08   C09  C04   121.03  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
 JMD  CONST_01  C07   C06  C05  C04    0.00   0.0  0
 JMD  CONST_02  C07   C08  C09  C04    0.00   0.0  0
 JMD  CONST_03  C08   C07  C06  C05    0.00   0.0  0
 JMD  CONST_04  C08   C09  C04  C05    0.00   0.0  0
 JMD  CONST_05  C09   C04  C05  C06    0.00   0.0  0
 JMD  CONST_06  C09   C08  C07  C06    0.00   0.0  0
 JMD  CONST_07  C05   C06  C07  C10  180.00   0.0  0
 JMD  CONST_08  C09   C08  C07  C10  180.00   0.0  0
 JMD  CONST_09  C06   C05  C04  C03  180.00   0.0  0
 JMD  CONST_10  C08   C09  C04  C03  180.00   0.0  0
 JMD  CONST_11  H061  C06  C05  C04  180.00   0.0  0
 JMD  CONST_12  H081  C08  C09  C04  180.00   0.0  0
 JMD  CONST_13  H091  C09  C04  C05  180.00   0.0  0
 JMD  CONST_14  H051  C05  C06  C07  180.00   0.0  0
 JMD  Var_01    C05   C04  C03  C02  -78.05  30.0  2
 JMD  Var_02    C04   C03  C02  O01  179.72  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
 JMD  plan-1  C10   0.020
 JMD  plan-1  C03   0.020
 JMD  plan-1  C04   0.020
 JMD  plan-1  C05   0.020
 JMD  plan-1  C06   0.020
 JMD  plan-1  C07   0.020
 JMD  plan-1  C08   0.020
 JMD  plan-1  C09   0.020
 JMD  plan-1  N11   0.020
 JMD  plan-1  H051  0.020
 JMD  plan-1  H061  0.020
 JMD  plan-1  H081  0.020
 JMD  plan-1  H091  0.020

