# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 06:51:39 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: N-[2-(benzyloxy)phenyl]-3-nitrobenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)c1cccc(c1)C(=O)Nc2ccccc2OCc3ccccc3
#
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
 B05  B05  N-[2-(benzyloxy)phenyl]-3-nitrobenzamide  ligand  42  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_B05
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
 B05  OAB  O  O      0  -0.372  -5.8834   0.6930   0.3666
 B05  OAC  O  O     -1  -0.371  -5.6935   2.8067   0.1486
 B05  CAZ  C  CR6    0  -0.032  -1.9081   0.1138  -0.3711
 B05  CAK  C  CR16   0  -0.305   4.3389   1.8182   1.2178
 B05  CAJ  C  CR16   0  -0.288   3.1418   1.7010  -0.8591
 B05  CAI  C  CR16   0  -0.256   2.6776  -4.5322  -0.0245
 B05  NBA  N  N      1   0.330  -5.2366   1.6891   0.1490
 B05  CAY  C  CR6    0   0.340   2.1653  -2.1919   0.1425
 B05  CAX  C  CR6    0   0.276   0.7952  -2.4749  -0.0320
 B05  CAW  C  CR6    0   0.283  -3.8137   1.5346  -0.1300
 B05  CAV  C  CR16   0  -0.266  -1.1325   1.2387  -0.6449
 B05  CAU  C  CR6    0   0.096   3.7676   1.0558   0.2069
 B05  CAQ  C  CH2    0  -0.254   3.8020  -0.4422   0.2584
 B05  CAP  C  CR16   0  -0.293  -3.2673   0.2635  -0.1283
 B05  CAO  C  CR16   0  -0.375   3.0970  -3.2160   0.1466
 B05  CAN  C  CR16   0  -0.262  -3.0524   2.6640  -0.3939
 B05  CAM  C  CR16   0  -0.233  -1.7039   2.5021  -0.6596
 B05  CAL  C  CR16   0  -0.310   0.3915  -3.7935  -0.1933
 B05  OAA  O  O      0  -0.455  -2.0627  -2.2310  -0.6541
 B05  NAR  N  NH1    0  -0.750  -0.0539  -1.3624  -0.0244
 B05  CAH  C  CR16   0  -0.270   1.3352  -4.8167  -0.1924
 B05  CAF  C  CR16   0  -0.240   3.0885   3.0853  -0.9085
 B05  CAE  C  CR16   0  -0.262   3.6667   3.8424   0.1049
 B05  CAG  C  CR16   0  -0.240   4.2945   3.2069   1.1660
 B05  H2   H  HCR6   0   0.255   2.6972   1.1213  -1.6599
 B05  H3   H  HCR6   0   0.261   3.4115  -5.3266  -0.0213
 B05  H4   H  HCR6   0   0.264  -0.0783   1.1480  -0.8776
 B05  H5   H  HCH2   0   0.248   4.2957  -0.8499  -0.6304
 B05  H6   H  HCH2   0   0.250   4.3512  -0.7898   1.1388
 B05  H7   H  HCR6   0   0.302  -3.8784  -0.6063   0.0653
 B05  H8   H  HCR6   0   0.286   4.1498  -3.0069   0.2829
 B05  H9   H  HCR6   0   0.308  -3.4909   3.6511  -0.3993
 B05  H10  H  HCR6   0   0.287  -1.0967   3.3680  -0.8830
 B05  H11  H  HCR6   0   0.281  -0.6512  -4.0316  -0.3244
 B05  H12  H  HNH1   0   0.421   0.3941  -0.5085   0.2697
 B05  H13  H  HCR6   0   0.257   1.0054  -5.8386  -0.3224
 B05  H14  H  HCR6   0   0.259   2.5992   3.5749  -1.7405
 B05  H15  H  HCR6   0   0.259   3.6267   4.9232   0.0647
 B05  H16  H  HCR6   0   0.259   4.7448   3.7884   1.9599
 B05  CAT  C  C      0   0.545  -1.3562  -1.2800  -0.3709
 B05  OAS  O  O2     0  -0.491   2.4528  -0.8847   0.3044
 B05  H1   H  HCR6   0   0.257   4.8184   1.3260   2.0552

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
 B05  OAB  NBA  double    1.207  0.020  1.207
 B05  CAN  CAM  aromatic  1.384  0.020  1.384
 B05  CAN  CAW  aromatic  1.387  0.020  1.387
 B05  CAM  CAV  aromatic  1.387  0.020  1.387
 B05  NBA  CAW  single    1.458  0.020  1.458
 B05  NBA  OAC  single    1.207  0.020  1.207
 B05  CAW  CAP  aromatic  1.384  0.020  1.384
 B05  CAV  CAZ  aromatic  1.394  0.020  1.394
 B05  CAE  CAF  aromatic  1.391  0.020  1.391
 B05  CAE  CAG  aromatic  1.387  0.020  1.387
 B05  CAF  CAJ  aromatic  1.386  0.020  1.386
 B05  CAP  CAZ  aromatic  1.389  0.020  1.389
 B05  CAZ  CAT  single    1.499  0.020  1.499
 B05  CAG  CAK  aromatic  1.390  0.020  1.390
 B05  CAJ  CAU  aromatic  1.394  0.020  1.394
 B05  CAT  OAA  double    1.218  0.020  1.218
 B05  CAT  NAR  single    1.350  0.020  1.350
 B05  CAK  CAU  aromatic  1.389  0.020  1.389
 B05  CAU  CAQ  single    1.499  0.020  1.499
 B05  NAR  CAX  single    1.399  0.020  1.399
 B05  CAQ  OAS  single    1.421  0.020  1.421
 B05  OAS  CAY  single    1.348  0.020  1.348
 B05  CAX  CAY  aromatic  1.410  0.020  1.410
 B05  CAX  CAL  aromatic  1.388  0.020  1.388
 B05  CAY  CAO  aromatic  1.385  0.020  1.385
 B05  CAL  CAH  aromatic  1.392  0.020  1.392
 B05  CAO  CAI  aromatic  1.392  0.020  1.392
 B05  CAH  CAI  aromatic  1.382  0.020  1.382
 B05  CAK  H1   single    0.930  0.020  1.080
 B05  CAJ  H2   single    0.930  0.020  1.080
 B05  CAI  H3   single    0.930  0.020  1.080
 B05  CAV  H4   single    0.930  0.020  1.080
 B05  CAQ  H5   single    0.970  0.020  1.090
 B05  CAQ  H6   single    0.970  0.020  1.090
 B05  CAP  H7   single    0.930  0.020  1.080
 B05  CAO  H8   single    0.930  0.020  1.080
 B05  CAN  H9   single    0.930  0.020  1.080
 B05  CAM  H10  single    0.930  0.020  1.080
 B05  CAL  H11  single    0.930  0.020  1.080
 B05  NAR  H12  single    0.860  0.020  1.020
 B05  CAH  H13  single    0.930  0.020  1.080
 B05  CAF  H14  single    0.930  0.020  1.080
 B05  CAE  H15  single    0.930  0.020  1.080
 B05  CAG  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
 B05  CAP  CAZ  CAT  117.42  3.000
 B05  CAT  CAZ  CAV  123.07  3.000
 B05  CAP  CAZ  CAV  119.47  3.000
 B05  H1   CAK  CAG  119.78  3.000
 B05  H1   CAK  CAU  119.69  3.000
 B05  CAG  CAK  CAU  120.53  3.000
 B05  H2   CAJ  CAF  119.47  3.000
 B05  H2   CAJ  CAU  120.10  3.000
 B05  CAF  CAJ  CAU  120.43  3.000
 B05  H3   CAI  CAH  120.54  3.000
 B05  H3   CAI  CAO  119.32  3.000
 B05  CAH  CAI  CAO  120.14  3.000
 B05  CAW  NBA  OAC  117.86  3.000
 B05  OAC  NBA  OAB  124.12  3.000
 B05  CAW  NBA  OAB  118.02  3.000
 B05  OAS  CAY  CAO  124.98  3.000
 B05  CAO  CAY  CAX  120.39  3.000
 B05  OAS  CAY  CAX  114.63  3.000
 B05  NAR  CAX  CAL  125.39  3.000
 B05  CAL  CAX  CAY  119.18  3.000
 B05  NAR  CAX  CAY  115.43  3.000
 B05  CAN  CAW  CAP  122.10  3.000
 B05  CAP  CAW  NBA  118.85  3.000
 B05  CAN  CAW  NBA  119.05  3.000
 B05  H4   CAV  CAM  118.36  3.000
 B05  H4   CAV  CAZ  121.07  3.000
 B05  CAM  CAV  CAZ  120.55  3.000
 B05  CAQ  CAU  CAJ  119.93  3.000
 B05  CAQ  CAU  CAK  120.93  3.000
 B05  CAJ  CAU  CAK  119.14  3.000
 B05  H6   CAQ  H5   107.96  3.000
 B05  H6   CAQ  OAS  110.59  3.000
 B05  H5   CAQ  OAS  109.78  3.000
 B05  H6   CAQ  CAU  110.89  3.000
 B05  H5   CAQ  CAU  110.75  3.000
 B05  OAS  CAQ  CAU  106.89  3.000
 B05  H7   CAP  CAW  121.09  3.000
 B05  H7   CAP  CAZ  119.87  3.000
 B05  CAW  CAP  CAZ  119.03  3.000
 B05  H8   CAO  CAY  120.81  3.000
 B05  H8   CAO  CAI  119.44  3.000
 B05  CAY  CAO  CAI  119.75  3.000
 B05  H9   CAN  CAM  120.10  3.000
 B05  H9   CAN  CAW  121.47  3.000
 B05  CAM  CAN  CAW  118.42  3.000
 B05  H10  CAM  CAN  119.56  3.000
 B05  H10  CAM  CAV  120.04  3.000
 B05  CAN  CAM  CAV  120.40  3.000
 B05  H11  CAL  CAH  119.59  3.000
 B05  H11  CAL  CAX  120.35  3.000
 B05  CAH  CAL  CAX  120.06  3.000
 B05  H12  NAR  CAT  116.86  3.000
 B05  H12  NAR  CAX  113.90  3.000
 B05  CAT  NAR  CAX  129.23  3.000
 B05  H13  CAH  CAL  119.19  3.000
 B05  H13  CAH  CAI  120.34  3.000
 B05  CAL  CAH  CAI  120.47  3.000
 B05  H14  CAF  CAE  120.12  3.000
 B05  H14  CAF  CAJ  119.77  3.000
 B05  CAE  CAF  CAJ  120.11  3.000
 B05  H15  CAE  CAG  120.18  3.000
 B05  H15  CAE  CAF  120.08  3.000
 B05  CAG  CAE  CAF  119.75  3.000
 B05  H16  CAG  CAE  120.22  3.000
 B05  H16  CAG  CAK  119.74  3.000
 B05  CAE  CAG  CAK  120.04  3.000
 B05  NAR  CAT  OAA  124.85  3.000
 B05  NAR  CAT  CAZ  114.33  3.000
 B05  OAA  CAT  CAZ  120.82  3.000
 B05  CAQ  OAS  CAY  120.04  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
 B05  CONST_01  CAN  CAM  CAV  CAZ     0.00   0.0  0
 B05  CONST_02  CAN  CAW  CAP  CAZ     0.00   0.0  0
 B05  CONST_03  CAF  CAE  CAG  CAK     0.00   0.0  0
 B05  CONST_04  CAF  CAJ  CAU  CAK     0.00   0.0  0
 B05  CONST_05  CAG  CAE  CAF  CAJ     0.00   0.0  0
 B05  CONST_06  CAG  CAK  CAU  CAJ     0.00   0.0  0
 B05  CONST_07  CAX  CAY  CAO  CAI     0.00   0.0  0
 B05  CONST_08  CAX  CAL  CAH  CAI     0.00   0.0  0
 B05  CONST_09  CAH  CAL  CAX  CAY     0.00   0.0  0
 B05  CONST_10  CAH  CAI  CAO  CAY     0.00   0.0  0
 B05  CONST_11  CAV  CAM  CAN  CAW     0.00   0.0  0
 B05  CONST_12  CAV  CAZ  CAP  CAW     0.00   0.0  0
 B05  CONST_13  CAE  CAF  CAJ  CAU     0.00   0.0  0
 B05  CONST_14  CAE  CAG  CAK  CAU     0.00   0.0  0
 B05  CONST_15  CAM  CAN  CAW  CAP     0.00   0.0  0
 B05  CONST_16  CAM  CAV  CAZ  CAP     0.00   0.0  0
 B05  CONST_17  CAL  CAX  CAY  CAO     0.00   0.0  0
 B05  CONST_18  CAL  CAH  CAI  CAO     0.00   0.0  0
 B05  CONST_19  NBA  CAW  CAP  CAZ   180.00   0.0  0
 B05  CONST_20  OAS  CAY  CAO  CAI   180.00   0.0  0
 B05  CONST_21  CAM  CAN  CAW  NBA   180.00   0.0  0
 B05  CONST_22  CAT  CAZ  CAP  CAW   180.00   0.0  0
 B05  CONST_23  CAM  CAV  CAZ  CAT   180.00   0.0  0
 B05  CONST_24  CAF  CAJ  CAU  CAQ   180.00   0.0  0
 B05  CONST_25  CAG  CAK  CAU  CAQ   180.00   0.0  0
 B05  CONST_26  NAR  CAX  CAY  CAO   180.00   0.0  0
 B05  CONST_27  OAS  CAY  CAX  CAL   180.00   0.0  0
 B05  CONST_28  CAH  CAL  CAX  NAR   180.00   0.0  0
 B05  CONST_29  H10  CAM  CAV  CAZ   180.00   0.0  0
 B05  CONST_30  H15  CAE  CAG  CAK   180.00   0.0  0
 B05  CONST_31  H2   CAJ  CAU  CAK   180.00   0.0  0
 B05  CONST_32  H1   CAK  CAU  CAJ   180.00   0.0  0
 B05  CONST_33  H11  CAL  CAH  CAI   180.00   0.0  0
 B05  CONST_34  H3   CAI  CAO  CAY   180.00   0.0  0
 B05  CONST_35  H8   CAO  CAY  CAX   180.00   0.0  0
 B05  CONST_36  H13  CAH  CAL  CAX   180.00   0.0  0
 B05  CONST_37  H9   CAN  CAM  CAV   180.00   0.0  0
 B05  CONST_38  H7   CAP  CAZ  CAV   180.00   0.0  0
 B05  CONST_39  H14  CAF  CAJ  CAU   180.00   0.0  0
 B05  CONST_40  H16  CAG  CAK  CAU   180.00   0.0  0
 B05  CONST_41  H4   CAV  CAZ  CAP   180.00   0.0  0
 B05  CONST_42  CAX  NAR  CAT  CAZ   180.00   0.0  0
 B05  CONST_43  CAN  CAW  NBA  OAB   180.00   0.0  0
 B05  CONST_44  CAP  CAW  NBA  OAB     0.00   0.0  0
 B05  CONST_45  CAN  CAW  NBA  OAC     0.00   0.0  0
 B05  CONST_46  CAP  CAW  NBA  OAC   180.00   0.0  0
 B05  CONST_47  CAT  NAR  CAX  CAY   180.00   0.0  0
 B05  CONST_48  CAL  CAX  NAR  CAT     0.00   0.0  0
 B05  CONST_49  H12  NAR  CAX  CAY     0.00   0.0  0
 B05  CONST_50  OAA  CAT  NAR  CAX     0.00   0.0  0
 B05  Var_01    OAS  CAQ  CAU  CAK   118.26  30.0  2
 B05  Var_02    CAU  CAQ  OAS  CAY   169.44  30.0  1
 B05  Var_03    OAA  CAT  CAZ  CAV  -150.74  30.0  2
 B05  Var_04    CAO  CAY  OAS  CAQ    11.24  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
 B05  plan-1  CAI  0.020
 B05  plan-1  CAY  0.020
 B05  plan-1  CAX  0.020
 B05  plan-1  CAO  0.020
 B05  plan-1  CAL  0.020
 B05  plan-1  NAR  0.020
 B05  plan-1  CAH  0.020
 B05  plan-1  H3   0.020
 B05  plan-1  H8   0.020
 B05  plan-1  H11  0.020
 B05  plan-1  H13  0.020
 B05  plan-1  OAS  0.020
 B05  plan-2  CAZ  0.020
 B05  plan-2  NBA  0.020
 B05  plan-2  CAW  0.020
 B05  plan-2  CAV  0.020
 B05  plan-2  CAP  0.020
 B05  plan-2  CAN  0.020
 B05  plan-2  CAM  0.020
 B05  plan-2  H4   0.020
 B05  plan-2  H7   0.020
 B05  plan-2  H9   0.020
 B05  plan-2  H10  0.020
 B05  plan-2  CAT  0.020
 B05  plan-3  CAK  0.020
 B05  plan-3  CAJ  0.020
 B05  plan-3  CAU  0.020
 B05  plan-3  CAQ  0.020
 B05  plan-3  CAF  0.020
 B05  plan-3  CAE  0.020
 B05  plan-3  CAG  0.020
 B05  plan-3  H2   0.020
 B05  plan-3  H14  0.020
 B05  plan-3  H15  0.020
 B05  plan-3  H16  0.020
 B05  plan-3  H1   0.020
 B05  plan-4  CAZ  0.020
 B05  plan-4  CAX  0.020
 B05  plan-4  OAA  0.020
 B05  plan-4  NAR  0.020
 B05  plan-4  H12  0.020
 B05  plan-4  CAT  0.020
 B05  plan-5  OAB  0.020
 B05  plan-5  OAC  0.020
 B05  plan-5  NBA  0.020
 B05  plan-5  CAW  0.020

