# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 14:49:26 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: N-[3-(benzyloxy)phenyl]-3-nitrobenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)c1cccc(c1)C(=O)Nc2cccc(OCc3ccccc3)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
 6BH  6BH  N-[3-(benzyloxy)phenyl]-3-nitrobenzamide  ligand  42  26  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_6BH
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
 6BH  OAB  O  O      0  -0.371  -7.3441  -2.0386   0.2340
 6BH  NBA  N  N      1   0.330  -6.1412  -2.0408   0.3380
 6BH  OAC  O  O     -1  -0.373  -5.4972  -2.9834   0.7310
 6BH  CAY  C  CR6    0   0.282  -5.4226  -0.8284  -0.0362
 6BH  CAP  C  CR16   0  -0.292  -4.0451  -0.8044   0.0876
 6BH  CAN  C  CR16   0  -0.263  -6.1396   0.2602  -0.5117
 6BH  CAM  C  CR16   0  -0.235  -5.4439   1.4007  -0.8715
 6BH  CAW  C  CR16   0  -0.271  -4.0634   1.4509  -0.7440
 6BH  CAZ  C  CR6    0  -0.034  -3.3586   0.3539  -0.2552
 6BH  CAT  C  C      0   0.547  -1.8665   0.3308  -0.1266
 6BH  OAA  O  O      0  -0.452  -1.2541  -0.7172  -0.2225
 6BH  NAR  N  NH1    0  -0.762  -1.2966   1.5358   0.1089
 6BH  CAV  C  CR6    0   0.397   0.0585   1.8665   0.2214
 6BH  CAO  C  CR16   0  -0.430   1.0961   0.9540   0.0832
 6BH  CAK  C  CR16   0  -0.375   0.3472   3.2108   0.4849
 6BH  CAH  C  CR16   0  -0.227   1.6604   3.6160   0.6049
 6BH  CAL  C  CR16   0  -0.401   2.7136   2.7178   0.4700
 6BH  CAX  C  CR6    0   0.416   2.4200   1.3842   0.2071
 6BH  OAS  O  O2     0  -0.470   3.3475   0.4183   0.0548
 6BH  CAQ  C  CH2    0  -0.270   4.7197   0.7631   0.1975
 6BH  CAU  C  CR6    0   0.100   5.5164  -0.4900  -0.0041
 6BH  CAI  C  CR16   0  -0.296   6.0462  -0.8007  -1.2524
 6BH  CAF  C  CR16   0  -0.242   6.7593  -1.9771  -1.4433
 6BH  CAE  C  CR16   0  -0.261   6.9439  -2.8564  -0.3846
 6BH  CAG  C  CR16   0  -0.243   6.4159  -2.5546   0.8648
 6BH  CAJ  C  CR16   0  -0.288   5.7052  -1.3776   1.0519
 6BH  H1   H  HCR6   0   0.302  -3.5038  -1.6656   0.4518
 6BH  H2   H  HCR6   0   0.307  -7.2147   0.2273  -0.6080
 6BH  H3   H  HCR6   0   0.289  -5.9798   2.2553  -1.2591
 6BH  H4   H  HCR6   0   0.283  -3.5478   2.3494  -1.0575
 6BH  H5   H  HNH1   0   0.426  -1.9227   2.3092   0.2742
 6BH  H6   H  HCR6   0   0.287   0.9093  -0.0886  -0.1165
 6BH  H7   H  HCR6   0   0.270  -0.4556   3.9301   0.5886
 6BH  H8   H  HCR6   0   0.265   1.8777   4.6564   0.8073
 6BH  H9   H  HCR6   0   0.282   3.7295   3.0729   0.5708
 6BH  H10  H  HCH2   0   0.243   5.0020   1.5219  -0.5392
 6BH  H11  H  HCH2   0   0.242   4.9041   1.1784   1.1939
 6BH  H12  H  HCR6   0   0.255   5.9062  -0.1165  -2.0810
 6BH  H13  H  HCR6   0   0.259   7.1720  -2.2056  -2.4174
 6BH  H14  H  HCR6   0   0.259   7.5019  -3.7722  -0.5315
 6BH  H15  H  HCR6   0   0.258   6.5613  -3.2343   1.6944
 6BH  H16  H  HCR6   0   0.255   5.3011  -1.1425   2.0296

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
 6BH  CAE  CAG  aromatic  1.390  0.020  1.390
 6BH  CAE  CAF  aromatic  1.388  0.020  1.388
 6BH  CAG  CAJ  aromatic  1.388  0.020  1.388
 6BH  CAF  CAI  aromatic  1.389  0.020  1.389
 6BH  CAJ  CAU  aromatic  1.392  0.020  1.392
 6BH  CAI  CAU  aromatic  1.391  0.020  1.391
 6BH  CAU  CAQ  single    1.499  0.020  1.499
 6BH  CAQ  OAS  single    1.422  0.020  1.422
 6BH  OAS  CAX  single    1.348  0.020  1.348
 6BH  CAX  CAL  aromatic  1.391  0.020  1.391
 6BH  CAX  CAO  aromatic  1.397  0.020  1.397
 6BH  CAL  CAH  aromatic  1.391  0.020  1.391
 6BH  CAO  CAV  aromatic  1.389  0.020  1.389
 6BH  CAH  CAK  aromatic  1.379  0.020  1.379
 6BH  CAV  CAK  aromatic  1.400  0.020  1.400
 6BH  CAV  NAR  single    1.399  0.020  1.399
 6BH  NAR  CAT  single    1.354  0.020  1.354
 6BH  OAA  CAT  double    1.218  0.020  1.218
 6BH  CAT  CAZ  single    1.498  0.020  1.498
 6BH  CAZ  CAP  aromatic  1.389  0.020  1.389
 6BH  CAZ  CAW  aromatic  1.393  0.020  1.393
 6BH  CAP  CAY  aromatic  1.383  0.020  1.383
 6BH  OAC  NBA  single    1.207  0.020  1.207
 6BH  CAW  CAM  aromatic  1.387  0.020  1.387
 6BH  CAY  NBA  single    1.458  0.020  1.458
 6BH  CAY  CAN  aromatic  1.388  0.020  1.388
 6BH  NBA  OAB  double    1.207  0.020  1.207
 6BH  CAM  CAN  aromatic  1.384  0.020  1.384
 6BH  CAP  H1   single    0.930  0.020  1.080
 6BH  CAN  H2   single    0.930  0.020  1.080
 6BH  CAM  H3   single    0.930  0.020  1.080
 6BH  CAW  H4   single    0.930  0.020  1.080
 6BH  NAR  H5   single    0.860  0.020  1.020
 6BH  CAO  H6   single    0.930  0.020  1.080
 6BH  CAK  H7   single    0.930  0.020  1.080
 6BH  CAH  H8   single    0.930  0.020  1.080
 6BH  CAL  H9   single    0.930  0.020  1.080
 6BH  CAQ  H10  single    0.970  0.020  1.090
 6BH  CAQ  H11  single    0.970  0.020  1.090
 6BH  CAI  H12  single    0.930  0.020  1.080
 6BH  CAF  H13  single    0.930  0.020  1.080
 6BH  CAE  H14  single    0.930  0.020  1.080
 6BH  CAG  H15  single    0.930  0.020  1.080
 6BH  CAJ  H16  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
 6BH  CAY  NBA  OAC  118.02  3.000
 6BH  CAY  NBA  OAB  117.87  3.000
 6BH  OAC  NBA  OAB  124.12  3.000
 6BH  CAN  CAY  CAP  122.11  3.000
 6BH  CAN  CAY  NBA  119.05  3.000
 6BH  CAP  CAY  NBA  118.83  3.000
 6BH  H1   CAP  CAZ  120.01  3.000
 6BH  H1   CAP  CAY  121.01  3.000
 6BH  CAZ  CAP  CAY  118.98  3.000
 6BH  H2   CAN  CAM  120.17  3.000
 6BH  H2   CAN  CAY  121.40  3.000
 6BH  CAM  CAN  CAY  118.42  3.000
 6BH  H3   CAM  CAW  119.86  3.000
 6BH  H3   CAM  CAN  119.72  3.000
 6BH  CAW  CAM  CAN  120.42  3.000
 6BH  H4   CAW  CAZ  120.96  3.000
 6BH  H4   CAW  CAM  118.52  3.000
 6BH  CAZ  CAW  CAM  120.50  3.000
 6BH  CAT  CAZ  CAW  123.13  3.000
 6BH  CAW  CAZ  CAP  119.55  3.000
 6BH  CAT  CAZ  CAP  117.27  3.000
 6BH  NAR  CAT  OAA  124.62  3.000
 6BH  OAA  CAT  CAZ  120.50  3.000
 6BH  NAR  CAT  CAZ  114.88  3.000
 6BH  H5   NAR  CAV  113.99  3.000
 6BH  H5   NAR  CAT  116.73  3.000
 6BH  CAV  NAR  CAT  129.21  3.000
 6BH  CAK  CAV  CAO  119.71  3.000
 6BH  CAK  CAV  NAR  116.22  3.000
 6BH  CAO  CAV  NAR  124.07  3.000
 6BH  H6   CAO  CAX  118.58  3.000
 6BH  H6   CAO  CAV  121.64  3.000
 6BH  CAX  CAO  CAV  119.78  3.000
 6BH  H7   CAK  CAH  120.15  3.000
 6BH  H7   CAK  CAV  120.19  3.000
 6BH  CAH  CAK  CAV  119.65  3.000
 6BH  H8   CAH  CAL  119.14  3.000
 6BH  H8   CAH  CAK  119.34  3.000
 6BH  CAL  CAH  CAK  121.52  3.000
 6BH  H9   CAL  CAX  122.08  3.000
 6BH  H9   CAL  CAH  119.38  3.000
 6BH  CAX  CAL  CAH  118.54  3.000
 6BH  OAS  CAX  CAL  124.28  3.000
 6BH  CAL  CAX  CAO  120.80  3.000
 6BH  OAS  CAX  CAO  114.92  3.000
 6BH  CAQ  OAS  CAX  118.62  3.000
 6BH  H11  CAQ  H10  107.82  3.000
 6BH  H11  CAQ  CAU  110.49  3.000
 6BH  H10  CAQ  CAU  110.61  3.000
 6BH  H11  CAQ  OAS  110.23  3.000
 6BH  H10  CAQ  OAS  110.45  3.000
 6BH  CAU  CAQ  OAS  107.27  3.000
 6BH  CAJ  CAU  CAI  119.12  3.000
 6BH  CAI  CAU  CAQ  120.66  3.000
 6BH  CAJ  CAU  CAQ  120.21  3.000
 6BH  H12  CAI  CAF  119.74  3.000
 6BH  H12  CAI  CAU  119.73  3.000
 6BH  CAF  CAI  CAU  120.53  3.000
 6BH  H13  CAF  CAE  120.12  3.000
 6BH  H13  CAF  CAI  119.89  3.000
 6BH  CAE  CAF  CAI  119.99  3.000
 6BH  H14  CAE  CAG  120.11  3.000
 6BH  H14  CAE  CAF  120.06  3.000
 6BH  CAG  CAE  CAF  119.83  3.000
 6BH  H15  CAG  CAJ  119.88  3.000
 6BH  H15  CAG  CAE  120.11  3.000
 6BH  CAJ  CAG  CAE  120.00  3.000
 6BH  H16  CAJ  CAG  119.78  3.000
 6BH  H16  CAJ  CAU  119.70  3.000
 6BH  CAG  CAJ  CAU  120.53  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
 6BH  CONST_01  CAW  CAZ  CAP  CAY     0.00   0.0  0
 6BH  CONST_02  CAW  CAM  CAN  CAY     0.00   0.0  0
 6BH  CONST_03  CAM  CAW  CAZ  CAP     0.00   0.0  0
 6BH  CONST_04  CAM  CAN  CAY  CAP     0.00   0.0  0
 6BH  CONST_05  CAZ  CAP  CAY  CAN     0.00   0.0  0
 6BH  CONST_06  CAZ  CAW  CAM  CAN     0.00   0.0  0
 6BH  CONST_07  CAL  CAX  CAO  CAV     0.00   0.0  0
 6BH  CONST_08  CAL  CAH  CAK  CAV     0.00   0.0  0
 6BH  CONST_09  CAH  CAL  CAX  CAO     0.00   0.0  0
 6BH  CONST_10  CAH  CAK  CAV  CAO     0.00   0.0  0
 6BH  CONST_11  CAX  CAL  CAH  CAK     0.00   0.0  0
 6BH  CONST_12  CAX  CAO  CAV  CAK     0.00   0.0  0
 6BH  CONST_13  CAE  CAG  CAJ  CAU     0.00   0.0  0
 6BH  CONST_14  CAE  CAF  CAI  CAU     0.00   0.0  0
 6BH  CONST_15  CAG  CAE  CAF  CAI     0.00   0.0  0
 6BH  CONST_16  CAG  CAJ  CAU  CAI     0.00   0.0  0
 6BH  CONST_17  CAJ  CAG  CAE  CAF     0.00   0.0  0
 6BH  CONST_18  CAJ  CAU  CAI  CAF     0.00   0.0  0
 6BH  CONST_19  CAZ  CAP  CAY  NBA   180.00   0.0  0
 6BH  CONST_20  CAM  CAN  CAY  NBA   180.00   0.0  0
 6BH  CONST_21  CAT  CAZ  CAP  CAY   180.00   0.0  0
 6BH  CONST_22  CAT  CAZ  CAW  CAM   180.00   0.0  0
 6BH  CONST_23  CAX  CAO  CAV  NAR   180.00   0.0  0
 6BH  CONST_24  CAH  CAK  CAV  NAR   180.00   0.0  0
 6BH  CONST_25  OAS  CAX  CAO  CAV   180.00   0.0  0
 6BH  CONST_26  OAS  CAX  CAL  CAH   180.00   0.0  0
 6BH  CONST_27  CAG  CAJ  CAU  CAQ   180.00   0.0  0
 6BH  CONST_28  CAF  CAI  CAU  CAQ   180.00   0.0  0
 6BH  CONST_29  H3   CAM  CAN  CAY   180.00   0.0  0
 6BH  CONST_30  H4   CAW  CAZ  CAP   180.00   0.0  0
 6BH  CONST_31  H2   CAN  CAY  CAP   180.00   0.0  0
 6BH  CONST_32  H1   CAP  CAY  CAN   180.00   0.0  0
 6BH  CONST_33  H8   CAH  CAK  CAV   180.00   0.0  0
 6BH  CONST_34  H9   CAL  CAX  CAO   180.00   0.0  0
 6BH  CONST_35  H7   CAK  CAV  CAO   180.00   0.0  0
 6BH  CONST_36  H6   CAO  CAV  CAK   180.00   0.0  0
 6BH  CONST_37  H15  CAG  CAJ  CAU   180.00   0.0  0
 6BH  CONST_38  H13  CAF  CAI  CAU   180.00   0.0  0
 6BH  CONST_39  H14  CAE  CAF  CAI   180.00   0.0  0
 6BH  CONST_40  H16  CAJ  CAU  CAI   180.00   0.0  0
 6BH  CONST_41  H12  CAI  CAF  CAE   180.00   0.0  0
 6BH  CONST_42  CAV  NAR  CAT  CAZ   180.00   0.0  0
 6BH  CONST_43  CAP  CAY  NBA  OAB   180.00   0.0  0
 6BH  CONST_44  CAN  CAY  NBA  OAB     0.00   0.0  0
 6BH  CONST_45  CAP  CAY  NBA  OAC     0.00   0.0  0
 6BH  CONST_46  CAN  CAY  NBA  OAC   180.00   0.0  0
 6BH  CONST_47  CAO  CAV  NAR  CAT     0.00   0.0  0
 6BH  CONST_48  CAK  CAV  NAR  CAT   180.00   0.0  0
 6BH  CONST_49  H5   NAR  CAV  CAO   180.00   0.0  0
 6BH  CONST_50  CAV  NAR  CAT  OAA     0.00   0.0  0
 6BH  Var_01    NAR  CAT  CAZ  CAP  -152.38  30.0  2
 6BH  Var_02    CAU  CAQ  OAS  CAX   179.33  30.0  1
 6BH  Var_03    CAJ  CAU  CAQ  OAS   -83.26  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
 6BH  plan-1  NBA  0.020
 6BH  plan-1  CAY  0.020
 6BH  plan-1  CAP  0.020
 6BH  plan-1  CAN  0.020
 6BH  plan-1  CAM  0.020
 6BH  plan-1  CAW  0.020
 6BH  plan-1  CAZ  0.020
 6BH  plan-1  CAT  0.020
 6BH  plan-1  H1   0.020
 6BH  plan-1  H2   0.020
 6BH  plan-1  H3   0.020
 6BH  plan-1  H4   0.020
 6BH  plan-2  NAR  0.020
 6BH  plan-2  CAV  0.020
 6BH  plan-2  CAO  0.020
 6BH  plan-2  CAK  0.020
 6BH  plan-2  CAH  0.020
 6BH  plan-2  CAL  0.020
 6BH  plan-2  CAX  0.020
 6BH  plan-2  OAS  0.020
 6BH  plan-2  H6   0.020
 6BH  plan-2  H7   0.020
 6BH  plan-2  H8   0.020
 6BH  plan-2  H9   0.020
 6BH  plan-3  CAQ  0.020
 6BH  plan-3  CAU  0.020
 6BH  plan-3  CAI  0.020
 6BH  plan-3  CAF  0.020
 6BH  plan-3  CAE  0.020
 6BH  plan-3  CAG  0.020
 6BH  plan-3  CAJ  0.020
 6BH  plan-3  H12  0.020
 6BH  plan-3  H13  0.020
 6BH  plan-3  H14  0.020
 6BH  plan-3  H15  0.020
 6BH  plan-3  H16  0.020
 6BH  plan-4  CAZ  0.020
 6BH  plan-4  CAT  0.020
 6BH  plan-4  OAA  0.020
 6BH  plan-4  NAR  0.020
 6BH  plan-4  CAV  0.020
 6BH  plan-4  H5   0.020
 6BH  plan-5  OAB  0.020
 6BH  plan-5  NBA  0.020
 6BH  plan-5  OAC  0.020
 6BH  plan-5  CAY  0.020

