# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 15:22:40 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: 3,3'-dimethoxybiphenyl-4,4'-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(ccc1N)c2ccc(N)c(OC)c2
#
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
 DDJ  DDJ  3,3'-dimethoxybiphenyl-4,4'-diamine  ligand  34  18  .  2021-08-08  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DDJ
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
 DDJ  NAA   N  NH2   0  -0.848   4.7218  -1.4068   0.4262
 DDJ  OAC   O  O2    0  -0.480   4.0866   1.0824  -0.3428
 DDJ  CAD   C  CR16  0  -0.469  -1.7413  -0.6627  -0.1084
 DDJ  CAE   C  CR16  0  -0.469   1.7157   0.6759  -0.0572
 DDJ  CAF   C  CR6   0   0.371   3.0425   0.2843  -0.0210
 DDJ  CAG   C  CR6   0   0.193   3.3917  -1.0306   0.3503
 DDJ  CAH   C  CR6   0   0.097   0.6819  -0.2061   0.2877
 DDJ  CAI   C  CR16  0  -0.345   1.0310  -1.4982   0.6625
 DDJ  CAJ   C  CR16  0  -0.310   2.3603  -1.8999   0.6866
 DDJ  CAK   C  CR6   0   0.370  -3.0687  -0.2743  -0.1469
 DDJ  CAL   C  CR6   0   0.096  -0.7252   0.2347   0.2489
 DDJ  CAM   C  CR6   0   0.195  -3.4384   1.0472   0.1790
 DDJ  CAN   C  CR16  0  -0.311  -2.4247   1.9311   0.5314
 DDJ  CAO   C  CR16  0  -0.345  -1.0930   1.5372   0.5653
 DDJ  CAP   C  CH3   0  -0.434  -3.8158  -2.4315  -0.8084
 DDJ  CAQ   C  CH3   0  -0.434   3.8219   2.4086  -0.7465
 DDJ  NAR   N  NH2   0  -0.848  -4.7601   1.4450   0.0824
 DDJ  HNAA  H  HNH2  0   0.374   5.3411  -0.9314  -0.2113
 DDJ  HNAB  H  HNH2  0   0.376   4.8677  -2.4036   0.3874
 DDJ  HAD   H  HCR6  0   0.269  -1.4684  -1.6718  -0.3877
 DDJ  HAE   H  HCR6  0   0.269   1.4588   1.6757  -0.3814
 DDJ  HAI   H  HCR6  0   0.240   0.2675  -2.2075   0.9566
 DDJ  HAJ   H  HCR6  0   0.255   2.6062  -2.9127   0.9840
 DDJ  HAN   H  HCR6  0   0.255  -2.6866   2.9491   0.7959
 DDJ  HAO   H  HCR6  0   0.240  -0.3444   2.2586   0.8686
 DDJ  HAP   H  HCH3  0   0.226  -3.3548  -2.9614   0.0298
 DDJ  HAPA  H  HCH3  0   0.260  -4.7692  -2.9018  -1.0373
 DDJ  HAPB  H  HCH3  0   0.226  -3.1633  -2.5201  -1.6812
 DDJ  HAQ   H  HCH3  0   0.227   3.2167   2.4465  -1.6563
 DDJ  HAQA  H  HCH3  0   0.225   3.3158   2.9804   0.0362
 DDJ  HAQB  H  HCH3  0   0.260   4.7853   2.8705  -0.9489
 DDJ  HNAR  H  HNH2  0   0.374  -5.4413   0.7250   0.2644
 DDJ  HNAC  H  HNH2  0   0.376  -4.9774   2.2824   0.5995
 DDJ  OAB   O  O2    0  -0.479  -4.0954  -1.0845  -0.4931

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
 DDJ  NAA  CAG   single    1.384  0.020  1.384
 DDJ  OAB  CAK   single    1.353  0.020  1.353
 DDJ  OAB  CAP   single    1.411  0.020  1.411
 DDJ  OAC  CAF   single    1.353  0.020  1.353
 DDJ  OAC  CAQ   single    1.411  0.020  1.411
 DDJ  CAD  CAK   aromatic  1.384  0.020  1.384
 DDJ  CAD  CAL   aromatic  1.402  0.020  1.402
 DDJ  CAE  CAF   aromatic  1.384  0.020  1.384
 DDJ  CAE  CAH   aromatic  1.402  0.020  1.402
 DDJ  CAF  CAG   aromatic  1.410  0.020  1.410
 DDJ  CAG  CAJ   aromatic  1.390  0.020  1.390
 DDJ  CAH  CAI   aromatic  1.390  0.020  1.390
 DDJ  CAH  CAL   single    1.475  0.020  1.475
 DDJ  CAI  CAJ   aromatic  1.389  0.020  1.389
 DDJ  CAK  CAM   aromatic  1.410  0.020  1.410
 DDJ  CAL  CAO   aromatic  1.390  0.020  1.390
 DDJ  CAM  CAN   aromatic  1.390  0.020  1.390
 DDJ  CAM  NAR   single    1.384  0.020  1.384
 DDJ  CAN  CAO   aromatic  1.389  0.020  1.389
 DDJ  NAA  HNAA  single    0.890  0.020  1.040
 DDJ  NAA  HNAB  single    0.890  0.020  1.040
 DDJ  CAD  HAD   single    0.930  0.020  1.080
 DDJ  CAE  HAE   single    0.930  0.020  1.080
 DDJ  CAI  HAI   single    0.930  0.020  1.080
 DDJ  CAJ  HAJ   single    0.930  0.020  1.080
 DDJ  CAN  HAN   single    0.930  0.020  1.080
 DDJ  CAO  HAO   single    0.930  0.020  1.080
 DDJ  CAP  HAP   single    0.970  0.020  1.090
 DDJ  CAP  HAPA  single    0.970  0.020  1.090
 DDJ  CAP  HAPB  single    0.970  0.020  1.090
 DDJ  CAQ  HAQ   single    0.970  0.020  1.090
 DDJ  CAQ  HAQA  single    0.970  0.020  1.090
 DDJ  CAQ  HAQB  single    0.970  0.020  1.090
 DDJ  NAR  HNAR  single    0.890  0.020  1.040
 DDJ  NAR  HNAC  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
 DDJ  HNAB  NAA  HNAA  110.67  3.000
 DDJ  HNAB  NAA  CAG   113.93  3.000
 DDJ  HNAA  NAA  CAG   115.31  3.000
 DDJ  CAQ   OAC  CAF   118.53  3.000
 DDJ  HAD   CAD  CAL   118.68  3.000
 DDJ  HAD   CAD  CAK   119.78  3.000
 DDJ  CAL   CAD  CAK   121.51  3.000
 DDJ  HAE   CAE  CAH   118.68  3.000
 DDJ  HAE   CAE  CAF   119.80  3.000
 DDJ  CAH   CAE  CAF   121.50  3.000
 DDJ  CAG   CAF  CAE   120.54  3.000
 DDJ  CAG   CAF  OAC   114.93  3.000
 DDJ  CAE   CAF  OAC   124.52  3.000
 DDJ  CAJ   CAG  CAF   117.58  3.000
 DDJ  CAJ   CAG  NAA   121.99  3.000
 DDJ  CAF   CAG  NAA   120.38  3.000
 DDJ  CAL   CAH  CAI   121.64  3.000
 DDJ  CAL   CAH  CAE   120.59  3.000
 DDJ  CAI   CAH  CAE   117.77  3.000
 DDJ  HAI   CAI  CAJ   118.73  3.000
 DDJ  HAI   CAI  CAH   120.33  3.000
 DDJ  CAJ   CAI  CAH   120.93  3.000
 DDJ  HAJ   CAJ  CAI   119.48  3.000
 DDJ  HAJ   CAJ  CAG   118.84  3.000
 DDJ  CAI   CAJ  CAG   121.67  3.000
 DDJ  CAM   CAK  CAD   120.54  3.000
 DDJ  CAM   CAK  OAB   114.92  3.000
 DDJ  CAD   CAK  OAB   124.55  3.000
 DDJ  CAO   CAL  CAH   121.77  3.000
 DDJ  CAO   CAL  CAD   117.78  3.000
 DDJ  CAH   CAL  CAD   120.45  3.000
 DDJ  NAR   CAM  CAN   122.10  3.000
 DDJ  NAR   CAM  CAK   120.24  3.000
 DDJ  CAN   CAM  CAK   117.59  3.000
 DDJ  HAN   CAN  CAO   119.47  3.000
 DDJ  HAN   CAN  CAM   118.87  3.000
 DDJ  CAO   CAN  CAM   121.66  3.000
 DDJ  HAO   CAO  CAN   118.73  3.000
 DDJ  HAO   CAO  CAL   120.33  3.000
 DDJ  CAN   CAO  CAL   120.92  3.000
 DDJ  HAPB  CAP  HAPA  108.67  3.000
 DDJ  HAPB  CAP  HAP   108.72  3.000
 DDJ  HAPA  CAP  HAP   108.75  3.000
 DDJ  HAPB  CAP  OAB   111.96  3.000
 DDJ  HAPA  CAP  OAB   106.63  3.000
 DDJ  HAP   CAP  OAB   112.01  3.000
 DDJ  HAQB  CAQ  HAQA  108.73  3.000
 DDJ  HAQB  CAQ  HAQ   108.72  3.000
 DDJ  HAQA  CAQ  HAQ   108.74  3.000
 DDJ  HAQB  CAQ  OAC   106.63  3.000
 DDJ  HAQA  CAQ  OAC   111.92  3.000
 DDJ  HAQ   CAQ  OAC   111.99  3.000
 DDJ  HNAC  NAR  HNAR  110.81  3.000
 DDJ  HNAC  NAR  CAM   114.14  3.000
 DDJ  HNAR  NAR  CAM   115.33  3.000
 DDJ  CAP   OAB  CAK   118.58  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
 DDJ  CONST_01  CAN  CAM  CAK  CAD    0.00   0.0  0
 DDJ  CONST_04  CAN  CAO  CAL  CAD    0.00   0.0  0
 DDJ  CONST_05  CAJ  CAG  CAF  CAE    0.00   0.0  0
 DDJ  CONST_06  CAJ  CAI  CAH  CAE    0.00   0.0  0
 DDJ  CONST_08  CAI  CAH  CAE  CAF    0.00   0.0  0
 DDJ  CONST_09  CAL  CAH  CAE  CAF  180.00   0.0  0
 DDJ  CONST_10  CAI  CAJ  CAG  CAF    0.00   0.0  0
 DDJ  CONST_11  CAH  CAE  CAF  CAG    0.00   0.0  0
 DDJ  CONST_12  CAH  CAI  CAJ  CAG    0.00   0.0  0
 DDJ  CONST_13  CAK  CAD  CAL  CAH  180.00   0.0  0
 DDJ  CONST_14  CAN  CAO  CAL  CAH  180.00   0.0  0
 DDJ  CONST_16  CAL  CAH  CAI  CAJ  180.00   0.0  0
 DDJ  CONST_17  CAO  CAL  CAD  CAK    0.00   0.0  0
 DDJ  CONST_18  CAO  CAN  CAM  CAK    0.00   0.0  0
 DDJ  CONST_19  CAM  CAK  CAD  CAL    0.00   0.0  0
 DDJ  CONST_20  CAM  CAN  CAO  CAL    0.00   0.0  0
 DDJ  CONST_21  CAE  CAF  CAG  NAA  180.00   0.0  0
 DDJ  CONST_22  CAI  CAJ  CAG  NAA  180.00   0.0  0
 DDJ  CONST_23  CAL  CAD  CAK  OAB  180.00   0.0  0
 DDJ  CONST_24  CAN  CAM  CAK  OAB  180.00   0.0  0
 DDJ  CONST_25  CAH  CAE  CAF  OAC  180.00   0.0  0
 DDJ  CONST_26  CAJ  CAG  CAF  OAC  180.00   0.0  0
 DDJ  CONST_27  NAR  CAM  CAK  CAD  180.00   0.0  0
 DDJ  CONST_28  NAR  CAM  CAN  CAO  180.00   0.0  0
 DDJ  CONST_29  HAO  CAO  CAL  CAD  180.00   0.0  0
 DDJ  CONST_30  HAI  CAI  CAH  CAE  180.00   0.0  0
 DDJ  CONST_31  HAJ  CAJ  CAG  CAF  180.00   0.0  0
 DDJ  CONST_32  HAE  CAE  CAF  CAG  180.00   0.0  0
 DDJ  CONST_33  HAD  CAD  CAL  CAH    0.00   0.0  0
 DDJ  CONST_34  HAN  CAN  CAM  CAK  180.00   0.0  0
 DDJ  Var_01    HAQ  CAQ  OAC  CAF  -61.59  30.0  3
 DDJ  Var_02    HAP  CAP  OAB  CAK   60.15  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
 DDJ  plan-1  CAD   0.020
 DDJ  plan-1  CAH   0.020
 DDJ  plan-1  CAK   0.020
 DDJ  plan-1  CAL   0.020
 DDJ  plan-1  CAM   0.020
 DDJ  plan-1  CAN   0.020
 DDJ  plan-1  CAO   0.020
 DDJ  plan-1  NAR   0.020
 DDJ  plan-1  HAD   0.020
 DDJ  plan-1  HAN   0.020
 DDJ  plan-1  HAO   0.020
 DDJ  plan-1  OAB   0.020
 DDJ  plan-2  NAA   0.020
 DDJ  plan-2  OAC   0.020
 DDJ  plan-2  CAE   0.020
 DDJ  plan-2  CAF   0.020
 DDJ  plan-2  CAG   0.020
 DDJ  plan-2  CAH   0.020
 DDJ  plan-2  CAI   0.020
 DDJ  plan-2  CAJ   0.020
 DDJ  plan-2  CAL   0.020
 DDJ  plan-2  HAE   0.020
 DDJ  plan-2  HAI   0.020
 DDJ  plan-2  HAJ   0.020
 DDJ  plan-3  NAA   0.020
 DDJ  plan-3  CAG   0.020
 DDJ  plan-3  HNAA  0.020
 DDJ  plan-3  HNAB  0.020
 DDJ  plan-4  CAM   0.020
 DDJ  plan-4  NAR   0.020
 DDJ  plan-4  HNAR  0.020
 DDJ  plan-4  HNAC  0.020

