# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 20:55:13 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 3-[6-amino-5-(3,4,5-trimethoxyphenyl)pyridin-3-yl]phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(cc(OC)c1OC)c2cc(cnc2N)c3cccc(O)c3
#
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
 A3F  A3F  3-[6-amino-5-(3,4,5-trimethoxyphenyl)pyridin-3-yl]phenol  ligand  46  26  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A3F
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
 A3F  CAA   C  CH3   0  -0.440   4.1917   2.4481  -1.9706
 A3F  CAB   C  CH3   0  -0.440   2.3171  -3.4418   1.6262
 A3F  CAC   C  CH3   0  -0.409   5.9858  -0.9488   0.4723
 A3F  CAF   C  CR16  0  -0.227  -4.7687  -1.6876  -1.8058
 A3F  CAG   C  CR16  0  -0.354  -5.9597  -1.5865  -1.1051
 A3F  CAH   C  CR16  0  -0.350  -3.6437  -0.9761  -1.4147
 A3F  CAI   C  CR16  0  -0.110  -2.6206   1.8894   0.6904
 A3F  CAJ   C  CR16  0  -0.466  -4.8948  -0.0480   0.4163
 A3F  CAK   C  CR16  0  -0.466   2.2002   1.0731  -0.5520
 A3F  CAL   C  CR16  0  -0.469   1.5626  -0.9218   0.6508
 A3F  CAM   C  CR16  0  -0.242  -1.2148   0.1384  -0.0338
 A3F  NAN   N  N     0  -0.447  -1.5885   2.6205   1.0831
 A3F  OAO   O  O2    0  -0.463   4.4472   1.1598  -1.4458
 A3F  CAR   C  CR6   0   0.384  -6.0215  -0.7569   0.0126
 A3F  CAS   C  CR6   0   0.404  -0.3544   2.1468   0.9294
 A3F  CAT   C  CR6   0   0.111  -3.6975  -0.1448  -0.2948
 A3F  CAU   C  CR6   0  -0.006  -2.5152   0.6240   0.1285
 A3F  CAV   C  CR6   0   0.077   1.2504   0.3407   0.1560
 A3F  CAW   C  CR6   0   0.352   3.4680   0.5389  -0.7679
 A3F  CAX   C  CR6   0   0.349   2.8306  -1.4583   0.4363
 A3F  CAY   C  CR6   0  -0.046  -0.1137   0.8791   0.3463
 A3F  CAZ   C  CR6   0   0.169   3.7852  -0.7315  -0.2792
 A3F  HAA   H  HCH3  0   0.262   5.0988   2.7555  -2.4847
 A3F  HAAA  H  HCH3  0   0.230   3.3663   2.4417  -2.6865
 A3F  HAAB  H  HCH3  0   0.229   3.9710   3.1734  -1.1830
 A3F  HAB   H  HCH3  0   0.262   2.8383  -4.3599   1.8850
 A3F  HABA  H  HCH3  0   0.230   2.0135  -2.9367   2.5464
 A3F  HABB  H  HCH3  0   0.230   1.4231  -3.6960   1.0513
 A3F  HAC   H  HCH3  0   0.237   6.9140  -1.4319   0.1725
 A3F  HACA  H  HCH3  0   0.223   6.1580   0.1280   0.5391
 A3F  HACB  H  HCH3  0   0.221   5.6997  -1.3218   1.4586
 A3F  HNAD  H  HNH2  0   0.387   0.4086   3.7130   1.9479
 A3F  HNAA  H  HNH2  0   0.395   1.5587   2.5400   1.5290
 A3F  HOAE  H  HOH1  0   0.474  -7.1187  -0.0844   1.4262
 A3F  HAF   H  HCR6  0   0.258  -4.7205  -2.3264  -2.6782
 A3F  HAG   H  HCR6  0   0.263  -6.8344  -2.1445  -1.4149
 A3F  HAH   H  HCR6  0   0.248  -2.7330  -1.0521  -1.9945
 A3F  HAI   H  HCR6  0   0.256  -3.5951   2.3500   0.8201
 A3F  HAJ   H  HCR6  0   0.265  -4.9474   0.5717   1.3054
 A3F  HAK   H  HCR6  0   0.283   1.9351   2.0426  -0.9502
 A3F  HAL   H  HCR6  0   0.279   0.8158  -1.4661   1.2128
 A3F  HAM   H  HCR6  0   0.261  -1.0530  -0.8424  -0.4661
 A3F  NAD   N  NH2   0  -0.827   0.6619   2.9539   1.3366
 A3F  OAP   O  O2    0  -0.464   3.2281  -2.6640   0.8743
 A3F  OAQ   O  O2    0  -0.481   5.0113  -1.2669  -0.5135
 A3F  OAE   O  OH1   0  -0.634  -7.1930  -0.6845   0.6758

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
 A3F  CAA  OAO   single    1.414  0.020  1.414
 A3F  CAB  OAP   single    1.414  0.020  1.414
 A3F  CAC  OAQ   single    1.422  0.020  1.422
 A3F  NAD  CAS   single    1.360  0.020  1.360
 A3F  OAE  CAR   single    1.348  0.020  1.348
 A3F  CAF  CAG   aromatic  1.385  0.020  1.385
 A3F  CAF  CAH   aromatic  1.387  0.020  1.387
 A3F  CAG  CAR   aromatic  1.393  0.020  1.393
 A3F  CAH  CAT   aromatic  1.396  0.020  1.396
 A3F  CAI  NAN   aromatic  1.324  0.020  1.324
 A3F  CAI  CAU   aromatic  1.389  0.020  1.389
 A3F  CAJ  CAR   aromatic  1.391  0.020  1.391
 A3F  CAJ  CAT   aromatic  1.396  0.020  1.396
 A3F  CAK  CAV   aromatic  1.393  0.020  1.393
 A3F  CAK  CAW   aromatic  1.393  0.020  1.393
 A3F  CAL  CAV   aromatic  1.391  0.020  1.391
 A3F  CAL  CAX   aromatic  1.393  0.020  1.393
 A3F  CAM  CAU   aromatic  1.398  0.020  1.398
 A3F  CAM  CAY   aromatic  1.380  0.020  1.380
 A3F  NAN  CAS   aromatic  1.331  0.020  1.331
 A3F  OAO  CAW   single    1.343  0.020  1.343
 A3F  OAP  CAX   single    1.343  0.020  1.343
 A3F  OAQ  CAZ   single    1.358  0.020  1.358
 A3F  CAS  CAY   aromatic  1.416  0.020  1.416
 A3F  CAT  CAU   single    1.472  0.020  1.472
 A3F  CAV  CAY   single    1.479  0.020  1.479
 A3F  CAW  CAZ   aromatic  1.398  0.020  1.398
 A3F  CAX  CAZ   aromatic  1.397  0.020  1.397
 A3F  CAA  HAA   single    0.970  0.020  1.090
 A3F  CAA  HAAA  single    0.970  0.020  1.090
 A3F  CAA  HAAB  single    0.970  0.020  1.090
 A3F  CAB  HAB   single    0.970  0.020  1.090
 A3F  CAB  HABA  single    0.970  0.020  1.090
 A3F  CAB  HABB  single    0.970  0.020  1.090
 A3F  CAC  HAC   single    0.970  0.020  1.090
 A3F  CAC  HACA  single    0.970  0.020  1.090
 A3F  CAC  HACB  single    0.970  0.020  1.090
 A3F  NAD  HNAD  single    0.890  0.020  1.040
 A3F  NAD  HNAA  single    0.890  0.020  1.040
 A3F  OAE  HOAE  single    0.850  0.020  0.980
 A3F  CAF  HAF   single    0.930  0.020  1.080
 A3F  CAG  HAG   single    0.930  0.020  1.080
 A3F  CAH  HAH   single    0.930  0.020  1.080
 A3F  CAI  HAI   single    0.930  0.020  1.080
 A3F  CAJ  HAJ   single    0.930  0.020  1.080
 A3F  CAK  HAK   single    0.930  0.020  1.080
 A3F  CAL  HAL   single    0.930  0.020  1.080
 A3F  CAM  HAM   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
 A3F  HAAB  CAA  HAAA  108.87  3.000
 A3F  HAAB  CAA  HAA   108.76  3.000
 A3F  HAAA  CAA  HAA   108.79  3.000
 A3F  HAAB  CAA  OAO   111.93  3.000
 A3F  HAAA  CAA  OAO   111.98  3.000
 A3F  HAA   CAA  OAO   106.40  3.000
 A3F  HABB  CAB  HABA  108.86  3.000
 A3F  HABB  CAB  HAB   108.72  3.000
 A3F  HABA  CAB  HAB   108.85  3.000
 A3F  HABB  CAB  OAP   112.04  3.000
 A3F  HABA  CAB  OAP   111.87  3.000
 A3F  HAB   CAB  OAP   106.39  3.000
 A3F  HACB  CAC  HACA  108.82  3.000
 A3F  HACB  CAC  HAC   108.69  3.000
 A3F  HACA  CAC  HAC   108.65  3.000
 A3F  HACB  CAC  OAQ   111.71  3.000
 A3F  HACA  CAC  OAQ   111.77  3.000
 A3F  HAC   CAC  OAQ   107.10  3.000
 A3F  HAF   CAF  CAH   119.59  3.000
 A3F  HAF   CAF  CAG   119.27  3.000
 A3F  CAH   CAF  CAG   121.13  3.000
 A3F  HAG   CAG  CAR   120.03  3.000
 A3F  HAG   CAG  CAF   120.80  3.000
 A3F  CAR   CAG  CAF   119.16  3.000
 A3F  HAH   CAH  CAT   120.28  3.000
 A3F  HAH   CAH  CAF   119.69  3.000
 A3F  CAT   CAH  CAF   120.02  3.000
 A3F  HAI   CAI  CAU   120.20  3.000
 A3F  HAI   CAI  NAN   115.46  3.000
 A3F  CAU   CAI  NAN   124.33  3.000
 A3F  HAJ   CAJ  CAT   119.91  3.000
 A3F  HAJ   CAJ  CAR   119.32  3.000
 A3F  CAT   CAJ  CAR   120.77  3.000
 A3F  HAK   CAK  CAW   120.67  3.000
 A3F  HAK   CAK  CAV   119.45  3.000
 A3F  CAW   CAK  CAV   119.86  3.000
 A3F  HAL   CAL  CAX   120.96  3.000
 A3F  HAL   CAL  CAV   119.11  3.000
 A3F  CAX   CAL  CAV   119.92  3.000
 A3F  HAM   CAM  CAY   118.44  3.000
 A3F  HAM   CAM  CAU   119.97  3.000
 A3F  CAY   CAM  CAU   121.59  3.000
 A3F  CAS   NAN  CAI   119.46  3.000
 A3F  CAW   OAO  CAA   118.47  3.000
 A3F  CAJ   CAR  CAG   120.02  3.000
 A3F  CAJ   CAR  OAE   122.25  3.000
 A3F  CAG   CAR  OAE   117.72  3.000
 A3F  CAY   CAS  NAN   121.60  3.000
 A3F  CAY   CAS  NAD   121.84  3.000
 A3F  NAN   CAS  NAD   116.55  3.000
 A3F  CAU   CAT  CAJ   120.40  3.000
 A3F  CAU   CAT  CAH   120.71  3.000
 A3F  CAJ   CAT  CAH   118.89  3.000
 A3F  CAT   CAU  CAM   122.17  3.000
 A3F  CAT   CAU  CAI   122.09  3.000
 A3F  CAM   CAU  CAI   115.73  3.000
 A3F  CAY   CAV  CAL   119.44  3.000
 A3F  CAY   CAV  CAK   120.20  3.000
 A3F  CAL   CAV  CAK   120.32  3.000
 A3F  CAZ   CAW  OAO   115.54  3.000
 A3F  CAZ   CAW  CAK   120.07  3.000
 A3F  OAO   CAW  CAK   124.38  3.000
 A3F  CAZ   CAX  OAP   115.59  3.000
 A3F  CAZ   CAX  CAL   120.03  3.000
 A3F  OAP   CAX  CAL   124.39  3.000
 A3F  CAV   CAY  CAS   122.40  3.000
 A3F  CAV   CAY  CAM   120.34  3.000
 A3F  CAS   CAY  CAM   117.26  3.000
 A3F  CAX   CAZ  CAW   119.79  3.000
 A3F  CAX   CAZ  OAQ   120.01  3.000
 A3F  CAW   CAZ  OAQ   120.19  3.000
 A3F  HNAA  NAD  HNAD  114.72  3.000
 A3F  HNAA  NAD  CAS   118.62  3.000
 A3F  HNAD  NAD  CAS   116.17  3.000
 A3F  CAX   OAP  CAB   118.46  3.000
 A3F  CAZ   OAQ  CAC   114.26  3.000
 A3F  HOAE  OAE  CAR   110.46  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
 A3F  CONST_01  CAJ  CAR  CAG  CAF     0.00   0.0  0
 A3F  CONST_02  CAJ  CAT  CAH  CAF     0.00   0.0  0
 A3F  CONST_03  CAU  CAT  CAH  CAF   180.00   0.0  0
 A3F  CONST_04  CAT  CAH  CAF  CAG     0.00   0.0  0
 A3F  CONST_05  CAT  CAJ  CAR  CAG     0.00   0.0  0
 A3F  CONST_06  CAR  CAG  CAF  CAH     0.00   0.0  0
 A3F  CONST_07  CAR  CAJ  CAT  CAH     0.00   0.0  0
 A3F  CONST_10  CAY  CAS  NAN  CAI     0.00   0.0  0
 A3F  CONST_11  CAY  CAM  CAU  CAI     0.00   0.0  0
 A3F  CONST_14  CAX  CAL  CAV  CAK     0.00   0.0  0
 A3F  CONST_17  CAX  CAZ  CAW  CAK     0.00   0.0  0
 A3F  CONST_18  CAW  CAK  CAV  CAL     0.00   0.0  0
 A3F  CONST_21  CAW  CAZ  CAX  CAL     0.00   0.0  0
 A3F  CONST_22  NAN  CAI  CAU  CAM     0.00   0.0  0
 A3F  CONST_23  NAN  CAS  CAY  CAM     0.00   0.0  0
 A3F  CONST_24  CAT  CAU  CAI  NAN   180.00   0.0  0
 A3F  CONST_25  CAV  CAY  CAS  NAN   180.00   0.0  0
 A3F  CONST_26  CAU  CAT  CAJ  CAR   180.00   0.0  0
 A3F  CONST_27  CAU  CAI  NAN  CAS     0.00   0.0  0
 A3F  CONST_28  CAU  CAM  CAY  CAS     0.00   0.0  0
 A3F  CONST_29  CAY  CAM  CAU  CAT   180.00   0.0  0
 A3F  CONST_30  CAV  CAY  CAM  CAU   180.00   0.0  0
 A3F  CONST_31  CAZ  CAW  CAK  CAV     0.00   0.0  0
 A3F  CONST_32  CAZ  CAX  CAL  CAV     0.00   0.0  0
 A3F  CONST_33  CAY  CAV  CAK  CAW   180.00   0.0  0
 A3F  CONST_34  CAY  CAV  CAL  CAX   180.00   0.0  0
 A3F  CONST_35  CAI  NAN  CAS  NAD   180.00   0.0  0
 A3F  CONST_36  CAM  CAY  CAS  NAD   180.00   0.0  0
 A3F  CONST_37  CAV  CAY  CAS  NAD     0.00   0.0  0
 A3F  CONST_38  CAF  CAG  CAR  OAE   180.00   0.0  0
 A3F  CONST_39  CAT  CAJ  CAR  OAE   180.00   0.0  0
 A3F  CONST_40  OAQ  CAZ  CAW  CAK   180.00   0.0  0
 A3F  CONST_41  OAQ  CAZ  CAX  CAL   180.00   0.0  0
 A3F  CONST_42  CAV  CAK  CAW  OAO   180.00   0.0  0
 A3F  CONST_43  CAX  CAZ  CAW  OAO   180.00   0.0  0
 A3F  CONST_44  CAV  CAL  CAX  OAP   180.00   0.0  0
 A3F  CONST_45  CAW  CAZ  CAX  OAP   180.00   0.0  0
 A3F  CONST_46  HAH  CAH  CAF  CAG   180.00   0.0  0
 A3F  CONST_47  HAJ  CAJ  CAR  CAG   180.00   0.0  0
 A3F  CONST_48  HAG  CAG  CAF  CAH   180.00   0.0  0
 A3F  CONST_49  HAM  CAM  CAU  CAI   180.00   0.0  0
 A3F  CONST_50  HAL  CAL  CAV  CAK   180.00   0.0  0
 A3F  CONST_51  HAK  CAK  CAV  CAL   180.00   0.0  0
 A3F  CONST_52  HAI  CAI  CAU  CAM   180.00   0.0  0
 A3F  CONST_53  HAF  CAF  CAG  CAR   180.00   0.0  0
 A3F  Var_01    CAK  CAW  OAO  CAA     0.62  30.0  2
 A3F  Var_02    CAL  CAX  OAP  CAB    -1.23  30.0  2
 A3F  Var_03    CAW  CAZ  OAQ  CAC    89.13  30.0  2
 A3F  Var_04    HAA  CAA  OAO  CAW  -179.27  30.0  3
 A3F  Var_05    HAB  CAB  OAP  CAX  -179.39  30.0  3
 A3F  Var_06    HAC  CAC  OAQ  CAZ   179.99  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
 A3F  plan-1  CAF   0.020
 A3F  plan-1  CAG   0.020
 A3F  plan-1  CAH   0.020
 A3F  plan-1  CAJ   0.020
 A3F  plan-1  CAR   0.020
 A3F  plan-1  CAT   0.020
 A3F  plan-1  CAU   0.020
 A3F  plan-1  HAF   0.020
 A3F  plan-1  HAG   0.020
 A3F  plan-1  HAH   0.020
 A3F  plan-1  HAJ   0.020
 A3F  plan-1  OAE   0.020
 A3F  plan-2  CAI   0.020
 A3F  plan-2  CAM   0.020
 A3F  plan-2  NAN   0.020
 A3F  plan-2  CAS   0.020
 A3F  plan-2  CAT   0.020
 A3F  plan-2  CAU   0.020
 A3F  plan-2  CAV   0.020
 A3F  plan-2  CAY   0.020
 A3F  plan-2  HAI   0.020
 A3F  plan-2  HAM   0.020
 A3F  plan-2  NAD   0.020
 A3F  plan-3  CAK   0.020
 A3F  plan-3  CAL   0.020
 A3F  plan-3  OAO   0.020
 A3F  plan-3  CAV   0.020
 A3F  plan-3  CAW   0.020
 A3F  plan-3  CAX   0.020
 A3F  plan-3  CAY   0.020
 A3F  plan-3  CAZ   0.020
 A3F  plan-3  HAK   0.020
 A3F  plan-3  HAL   0.020
 A3F  plan-3  OAP   0.020
 A3F  plan-3  OAQ   0.020
 A3F  plan-4  CAS   0.020
 A3F  plan-4  HNAD  0.020
 A3F  plan-4  HNAA  0.020
 A3F  plan-4  NAD   0.020

