# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 11:27:55 2021
#   Inital geometry file: a 68 line input string
#   Ligand name: 1-(pyridin-2-yl)-1,4-diazepane
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CNCCN(C1)c2ccccn2
#
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
 W6J  W6J  1-(pyridin-2-yl)-1,4-diazepane  ligand  28  13  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_W6J
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
 W6J  C10   C  CH2   0  -0.307  -38.3669  -0.9973  17.9785
 W6J  N12   N  N     0  -0.472  -35.7490   0.6991  17.5508
 W6J  C13   C  CR16  0  -0.069  -34.8145   1.4406  18.1332
 W6J  C01   C  CR16  0  -0.369  -34.6716   2.8012  17.9424
 W6J  C02   C  CR16  0  -0.155  -35.5783   3.4131  17.0797
 W6J  C03   C  CR16  0  -0.394  -36.5575   2.6668  16.4622
 W6J  C04   C  CR6   0   0.518  -36.6171   1.2785  16.7174
 W6J  C06   C  CH2   0  -0.343  -38.6575   0.9968  15.3784
 W6J  C07   C  CH2   0  -0.443  -39.8219   1.4306  16.2613
 W6J  C08   C  CH2   0  -0.302  -40.3007   0.3675  17.2529
 W6J  C11   C  CH2   0  -0.336  -37.6984  -0.8968  16.5939
 W6J  N05   N  NT    0  -0.471  -37.5291   0.4599  16.1163
 W6J  N09   N  NH1   0  -0.591  -39.3543   0.0129  18.2969
 W6J  H101  H  HCH2  0   0.222  -38.8218  -1.9911  18.0471
 W6J  H102  H  HCH2  0   0.232  -37.6028  -0.9513  18.7542
 W6J  H011  H  HCR6  0   0.255  -33.8951   3.3581  18.4467
 W6J  H021  H  HCR6  0   0.264  -35.5238   4.4776  16.8899
 W6J  H031  H  HCR6  0   0.263  -37.2580   3.1547  15.8009
 W6J  H062  H  HCH2  0   0.255  -38.3344   1.8230  14.7450
 W6J  H061  H  HCH2  0   0.252  -38.9922   0.2167  14.6912
 W6J  H072  H  HCH2  0   0.223  -39.5488   2.3304  16.8225
 W6J  H071  H  HCH2  0   0.230  -40.6553   1.7184  15.6135
 W6J  H081  H  HCH2  0   0.232  -41.2159   0.7411  17.7221
 W6J  H082  H  HCH2  0   0.222  -40.5912  -0.5455  16.7237
 W6J  H112  H  HCH2  0   0.240  -38.3113  -1.4120  15.8528
 W6J  H111  H  HCH2  0   0.249  -36.7404  -1.4178  16.6191
 W6J  H1    H  HNH1  0   0.343  -38.8994   0.8461  18.6459
 W6J  H131  H  HCR6  0   0.251  -34.1408   0.9101  18.7986

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
 W6J  C06  N05   single    1.451  0.020  1.451
 W6J  C06  C07   single    1.524  0.020  1.524
 W6J  N05  C04   single    1.365  0.020  1.365
 W6J  N05  C11   single    1.448  0.020  1.448
 W6J  C07  C08   single    1.531  0.020  1.531
 W6J  C03  C04   aromatic  1.413  0.020  1.413
 W6J  C03  C02   aromatic  1.377  0.020  1.377
 W6J  C04  N12   aromatic  1.336  0.020  1.336
 W6J  C11  C10   single    1.541  0.020  1.541
 W6J  C02  C01   aromatic  1.393  0.020  1.393
 W6J  C08  N09   single    1.453  0.020  1.453
 W6J  N12  C13   aromatic  1.328  0.020  1.328
 W6J  C01  C13   aromatic  1.381  0.020  1.381
 W6J  N09  C10   single    1.448  0.020  1.448
 W6J  C10  H101  single    0.970  0.020  1.090
 W6J  C10  H102  single    0.970  0.020  1.090
 W6J  C13  H131  single    0.930  0.020  1.080
 W6J  C01  H011  single    0.930  0.020  1.080
 W6J  C02  H021  single    0.930  0.020  1.080
 W6J  C03  H031  single    0.930  0.020  1.080
 W6J  C06  H062  single    0.970  0.020  1.090
 W6J  C06  H061  single    0.970  0.020  1.090
 W6J  C07  H072  single    0.970  0.020  1.090
 W6J  C07  H071  single    0.970  0.020  1.090
 W6J  C08  H081  single    0.970  0.020  1.090
 W6J  C08  H082  single    0.970  0.020  1.090
 W6J  C11  H112  single    0.970  0.020  1.090
 W6J  C11  H111  single    0.970  0.020  1.090
 W6J  N09  H1    single    0.890  0.020  1.040

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
 W6J  H102  C10  H101  106.56  3.000
 W6J  H102  C10  N09   106.99  3.000
 W6J  H101  C10  N09   109.64  3.000
 W6J  H102  C10  C11   109.43  3.000
 W6J  H101  C10  C11   107.20  3.000
 W6J  N09   C10  C11   116.61  3.000
 W6J  C04   N12  C13   119.27  3.000
 W6J  H131  C13  C01   120.13  3.000
 W6J  H131  C13  N12   115.65  3.000
 W6J  C01   C13  N12   124.23  3.000
 W6J  H011  C01  C02   122.03  3.000
 W6J  H011  C01  C13   121.17  3.000
 W6J  C02   C01  C13   116.80  3.000
 W6J  H021  C02  C03   119.34  3.000
 W6J  H021  C02  C01   120.51  3.000
 W6J  C03   C02  C01   120.16  3.000
 W6J  H031  C03  C04   121.82  3.000
 W6J  H031  C03  C02   119.40  3.000
 W6J  C04   C03  C02   118.78  3.000
 W6J  N05   C04  C03   122.55  3.000
 W6J  C03   C04  N12   120.77  3.000
 W6J  N05   C04  N12   116.67  3.000
 W6J  H061  C06  H062  105.47  3.000
 W6J  H061  C06  N05   107.10  3.000
 W6J  H062  C06  N05   110.21  3.000
 W6J  H061  C06  C07   109.49  3.000
 W6J  H062  C06  C07   110.32  3.000
 W6J  N05   C06  C07   113.87  3.000
 W6J  H071  C07  H072  106.10  3.000
 W6J  H071  C07  C08   109.15  3.000
 W6J  H072  C07  C08   108.46  3.000
 W6J  H071  C07  C06   108.29  3.000
 W6J  H072  C07  C06   109.89  3.000
 W6J  C08   C07  C06   114.62  3.000
 W6J  H082  C08  H081  105.68  3.000
 W6J  H082  C08  N09   108.46  3.000
 W6J  H081  C08  N09   108.66  3.000
 W6J  H082  C08  C07   110.43  3.000
 W6J  H081  C08  C07   107.59  3.000
 W6J  N09   C08  C07   115.55  3.000
 W6J  H111  C11  H112  106.47  3.000
 W6J  H111  C11  N05   110.63  3.000
 W6J  H112  C11  N05   106.50  3.000
 W6J  H111  C11  C10   109.22  3.000
 W6J  H112  C11  C10   109.63  3.000
 W6J  N05   C11  C10   114.09  3.000
 W6J  C11   N05  C06   115.05  3.000
 W6J  C11   N05  C04   119.65  3.000
 W6J  C06   N05  C04   121.44  3.000
 W6J  H1    N09  C08   109.87  3.000
 W6J  H1    N09  C10   110.11  3.000
 W6J  C08   N09  C10   117.16  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
 W6J  CONST_01  C02   C03  C04  N12    0.00  0.0  0
 W6J  CONST_02  C02   C01  C13  N12    0.00  0.0  0
 W6J  CONST_03  C03   C04  N12  C13    0.00  0.0  0
 W6J  CONST_04  C03   C02  C01  C13    0.00  0.0  0
 W6J  CONST_05  C04   C03  C02  C01    0.00  0.0  0
 W6J  CONST_06  C04   N12  C13  C01    0.00  0.0  0
 W6J  CONST_07  N05   C04  N12  C13  180.00  0.0  0
 W6J  CONST_08  N05   C04  C03  C02  180.00  0.0  0
 W6J  CONST_09  H031  C03  C04  N12  180.00  0.0  0
 W6J  CONST_10  H011  C01  C13  N12  180.00  0.0  0
 W6J  CONST_11  H021  C02  C01  C13  180.00  0.0  0
 W6J  CONST_12  H131  C13  C01  C02  180.00  0.0  0

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
 W6J  plan-1  N12   0.020
 W6J  plan-1  C13   0.020
 W6J  plan-1  C01   0.020
 W6J  plan-1  C02   0.020
 W6J  plan-1  C03   0.020
 W6J  plan-1  C04   0.020
 W6J  plan-1  N05   0.020
 W6J  plan-1  H011  0.020
 W6J  plan-1  H021  0.020
 W6J  plan-1  H031  0.020
 W6J  plan-1  H131  0.020

