# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 02:17:17 2021
#   Inital geometry file: a 83 line input string
#   Ligand name: (4-nitrophenyl) hexanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC(=O)Oc1ccc(cc1)[N+]([O-])=O
#
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
 D8F  D8F  '(4-nitrophenyl) hexanoate'  ligand  32  17  .  2022-03-18  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D8F
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
 D8F  CAF   C  CH2    0  -0.434   -8.7734  -22.7714  -12.7189
 D8F  CAG   C  CH2    0  -0.449  -10.2380  -22.5743  -13.1061
 D8F  CAH   C  CH2    0  -0.436   -8.0580  -21.5084  -12.2424
 D8F  CAI   C  CH2    0  -0.599  -10.4691  -21.5437  -14.2036
 D8F  CAJ   C  CH3    0  -0.668   -8.7126  -20.8467  -11.0368
 D8F  CAK   C  C      0   0.587   -9.9367  -21.9595  -15.5423
 D8F  CAL   C  CR6    0   0.391   -9.3400  -21.1188  -17.6393
 D8F  CAM   C  CR16   0  -0.305  -10.2848  -21.3120  -18.6351
 D8F  CAN   C  CR16   0  -0.307   -7.9839  -21.1076  -17.9254
 D8F  CAO   C  CR6    0   0.254   -8.5108  -21.4754  -20.2245
 D8F  CAP   C  CR16   0  -0.264   -9.8693  -21.4890  -19.9421
 D8F  CAQ   C  CR16   0  -0.263   -7.5617  -21.2858  -19.2303
 D8F  NAE   N  N      1   0.331   -8.0709  -21.6619  -21.5979
 D8F  OAA   O  O2     0  -0.498   -9.7567  -20.8874  -16.3518
 D8F  OAB   O  O      0  -0.411   -9.7137  -23.0775  -15.9108
 D8F  OAC   O  O     -1  -0.376   -8.9159  -21.7886  -22.4521
 D8F  OAD   O  O      0  -0.377   -6.8827  -21.6805  -21.8161
 D8F  HAF1  H  HCH2   0   0.225   -8.7316  -23.5209  -11.9230
 D8F  HAF2  H  HCH2   0   0.226   -8.2209  -23.1988  -13.5598
 D8F  HAG2  H  HCH2   0   0.242  -10.8080  -22.2555  -12.2306
 D8F  HAG1  H  HCH2   0   0.242  -10.6673  -23.5320  -13.4070
 D8F  HAH1  H  HCH2   0   0.228   -7.0281  -21.7739  -11.9905
 D8F  HAH2  H  HCH2   0   0.213   -7.9810  -20.7850  -13.0601
 D8F  HAI1  H  HCH2   0   0.274  -10.0599  -20.5681  -13.9338
 D8F  HAI2  H  HCH2   0   0.304  -11.5440  -21.3804  -14.3395
 D8F  HAJ2  H  HCH3   0   0.230   -8.1194  -20.0037  -10.6810
 D8F  HAJ3  H  HCH3   0   0.219   -9.7082  -20.4645  -11.2677
 D8F  HAJ1  H  HCH3   0   0.218   -8.8167  -21.5511  -10.2088
 D8F  HAM1  H  HCR6   0   0.295  -11.3402  -21.3143  -18.3983
 D8F  HAN1  H  HCR6   0   0.294   -7.2588  -20.9525  -17.1379
 D8F  HAP1  H  HCR6   0   0.306  -10.6039  -21.6360  -20.7199
 D8F  HAQ1  H  HCR6   0   0.306   -6.5053  -21.2759  -19.4541

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
 D8F  OAD  NAE   double    1.208  0.020  1.208
 D8F  OAC  NAE   single    1.208  0.020  1.208
 D8F  NAE  CAO   single    1.454  0.020  1.454
 D8F  CAO  CAQ   aromatic  1.387  0.020  1.387
 D8F  CAO  CAP   aromatic  1.388  0.020  1.388
 D8F  CAQ  CAN   aromatic  1.383  0.020  1.383
 D8F  CAP  CAM   aromatic  1.383  0.020  1.383
 D8F  CAN  CAL   aromatic  1.386  0.020  1.386
 D8F  CAM  CAL   aromatic  1.386  0.020  1.386
 D8F  CAL  OAA   single    1.373  0.020  1.373
 D8F  OAA  CAK   single    1.355  0.020  1.355
 D8F  CAK  OAB   double    1.198  0.020  1.198
 D8F  CAK  CAI   single    1.500  0.020  1.500
 D8F  CAI  CAG   single    1.523  0.020  1.523
 D8F  CAG  CAF   single    1.528  0.020  1.528
 D8F  CAF  CAH   single    1.528  0.020  1.528
 D8F  CAH  CAJ   single    1.523  0.020  1.523
 D8F  CAF  HAF1  single    0.970  0.020  1.090
 D8F  CAF  HAF2  single    0.970  0.020  1.090
 D8F  CAG  HAG2  single    0.970  0.020  1.090
 D8F  CAG  HAG1  single    0.970  0.020  1.090
 D8F  CAH  HAH1  single    0.970  0.020  1.090
 D8F  CAH  HAH2  single    0.970  0.020  1.090
 D8F  CAI  HAI1  single    0.970  0.020  1.090
 D8F  CAI  HAI2  single    0.970  0.020  1.090
 D8F  CAJ  HAJ2  single    0.970  0.020  1.090
 D8F  CAJ  HAJ3  single    0.970  0.020  1.090
 D8F  CAJ  HAJ1  single    0.970  0.020  1.090
 D8F  CAM  HAM1  single    0.930  0.020  1.080
 D8F  CAN  HAN1  single    0.930  0.020  1.080
 D8F  CAP  HAP1  single    0.930  0.020  1.080
 D8F  CAQ  HAQ1  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
 D8F  HAF2  CAF  HAF1  105.82  3.000
 D8F  HAF2  CAF  CAH   109.06  3.000
 D8F  HAF1  CAF  CAH   108.76  3.000
 D8F  HAF2  CAF  CAG   109.87  3.000
 D8F  HAF1  CAF  CAG   108.02  3.000
 D8F  CAH   CAF  CAG   114.92  3.000
 D8F  HAG1  CAG  HAG2  105.77  3.000
 D8F  HAG1  CAG  CAI   109.59  3.000
 D8F  HAG2  CAG  CAI   107.51  3.000
 D8F  HAG1  CAG  CAF   109.49  3.000
 D8F  HAG2  CAG  CAF   109.56  3.000
 D8F  CAI   CAG  CAF   114.54  3.000
 D8F  HAH2  CAH  HAH1  105.45  3.000
 D8F  HAH2  CAH  CAJ   109.55  3.000
 D8F  HAH1  CAH  CAJ   109.15  3.000
 D8F  HAH2  CAH  CAF   110.27  3.000
 D8F  HAH1  CAH  CAF   108.19  3.000
 D8F  CAJ   CAH  CAF   113.88  3.000
 D8F  HAI2  CAI  HAI1  105.38  3.000
 D8F  HAI2  CAI  CAK   106.19  3.000
 D8F  HAI1  CAI  CAK   109.60  3.000
 D8F  HAI2  CAI  CAG   109.81  3.000
 D8F  HAI1  CAI  CAG   111.70  3.000
 D8F  CAK   CAI  CAG   113.69  3.000
 D8F  HAJ1  CAJ  HAJ3  107.42  3.000
 D8F  HAJ1  CAJ  HAJ2  107.65  3.000
 D8F  HAJ3  CAJ  HAJ2  107.13  3.000
 D8F  HAJ1  CAJ  CAH   111.16  3.000
 D8F  HAJ3  CAJ  CAH   112.13  3.000
 D8F  HAJ2  CAJ  CAH   111.12  3.000
 D8F  OAB   CAK  OAA   121.99  3.000
 D8F  OAB   CAK  CAI   126.83  3.000
 D8F  OAA   CAK  CAI   111.16  3.000
 D8F  OAA   CAL  CAN   119.29  3.000
 D8F  OAA   CAL  CAM   119.36  3.000
 D8F  CAN   CAL  CAM   121.31  3.000
 D8F  HAM1  CAM  CAP   119.98  3.000
 D8F  HAM1  CAM  CAL   120.54  3.000
 D8F  CAP   CAM  CAL   119.48  3.000
 D8F  HAN1  CAN  CAQ   120.05  3.000
 D8F  HAN1  CAN  CAL   120.45  3.000
 D8F  CAQ   CAN  CAL   119.50  3.000
 D8F  NAE   CAO  CAQ   119.17  3.000
 D8F  CAQ   CAO  CAP   121.68  3.000
 D8F  NAE   CAO  CAP   119.15  3.000
 D8F  HAP1  CAP  CAO   121.39  3.000
 D8F  HAP1  CAP  CAM   119.59  3.000
 D8F  CAO   CAP  CAM   119.03  3.000
 D8F  HAQ1  CAQ  CAO   121.46  3.000
 D8F  HAQ1  CAQ  CAN   119.54  3.000
 D8F  CAO   CAQ  CAN   119.01  3.000
 D8F  OAD   NAE  OAC   123.95  3.000
 D8F  OAC   NAE  CAO   118.01  3.000
 D8F  OAD   NAE  CAO   118.04  3.000
 D8F  CAL   OAA  CAK   117.84  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
 D8F  CONST_01  CAO   CAQ  CAN  CAL     0.00   0.0  0
 D8F  CONST_02  CAO   CAP  CAM  CAL     0.00   0.0  0
 D8F  CONST_03  CAQ   CAO  CAP  CAM     0.00   0.0  0
 D8F  CONST_04  CAQ   CAN  CAL  CAM     0.00   0.0  0
 D8F  CONST_05  CAP   CAO  CAQ  CAN     0.00   0.0  0
 D8F  CONST_06  CAP   CAM  CAL  CAN     0.00   0.0  0
 D8F  CONST_07  NAE   CAO  CAP  CAM   180.00   0.0  0
 D8F  CONST_08  NAE   CAO  CAQ  CAN   180.00   0.0  0
 D8F  CONST_09  OAA   CAL  CAM  CAP   180.00   0.0  0
 D8F  CONST_10  OAA   CAL  CAN  CAQ   180.00   0.0  0
 D8F  CONST_11  HAQ1  CAQ  CAN  CAL   180.00   0.0  0
 D8F  CONST_12  HAP1  CAP  CAM  CAL   180.00   0.0  0
 D8F  CONST_13  HAN1  CAN  CAL  CAM   180.00   0.0  0
 D8F  CONST_14  HAM1  CAM  CAL  CAN   180.00   0.0  0
 D8F  CONST_15  OAD   NAE  CAO  CAP   180.00   0.0  0
 D8F  CONST_16  OAC   NAE  CAO  CAP     0.00   0.0  0
 D8F  CONST_17  OAD   NAE  CAO  CAQ     0.00   0.0  0
 D8F  CONST_18  OAC   NAE  CAO  CAQ   180.00   0.0  0
 D8F  Var_01    CAN   CAL  OAA  CAK   -92.31  30.0  2
 D8F  Var_02    OAB   CAK  OAA  CAL     1.76  30.0  3
 D8F  Var_03    CAK   CAI  CAG  CAF    67.65  30.0  1
 D8F  Var_04    OAA   CAK  CAI  CAG  -159.59  30.0  1
 D8F  Var_05    CAJ   CAH  CAF  CAG    58.12  30.0  3
 D8F  Var_06    CAI   CAG  CAF  CAH    57.88  30.0  1
 D8F  Var_07    HAJ2  CAJ  CAH  CAF   175.00  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
 D8F  plan-1  CAL   0.020
 D8F  plan-1  CAM   0.020
 D8F  plan-1  CAN   0.020
 D8F  plan-1  CAO   0.020
 D8F  plan-1  CAP   0.020
 D8F  plan-1  CAQ   0.020
 D8F  plan-1  NAE   0.020
 D8F  plan-1  OAA   0.020
 D8F  plan-1  HAM1  0.020
 D8F  plan-1  HAN1  0.020
 D8F  plan-1  HAP1  0.020
 D8F  plan-1  HAQ1  0.020
 D8F  plan-2  CAO   0.020
 D8F  plan-2  NAE   0.020
 D8F  plan-2  OAC   0.020
 D8F  plan-2  OAD   0.020
 D8F  plan-3  CAI   0.020
 D8F  plan-3  CAK   0.020
 D8F  plan-3  OAA   0.020
 D8F  plan-3  OAB   0.020

