# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 08:42:38 2021
#   Inital geometry file: a 114 line input string
#   Ligand name: benzyl [(2S)-1-(3-nitrophenyl)-3-oxobutan-2-yl]carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)[C@H](Cc1cccc(c1)[N+]([O-])=O)NC(=O)OCc2ccccc2
#
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
 Q9D  Q9D  'benzyl [(2S)-1-(3-nitrophenyl)-3-oxobutan-2-yl]carbamate'  ligand  43  25  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_Q9D
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
 Q9D  C22  C  CR16   0  -0.278  -27.9385  -10.1641  12.8719
 Q9D  C24  C  CR16   0  -0.273  -26.1097  -10.2039  14.4340
 Q9D  C28  C  CH2    0  -0.243  -23.0823  -15.5893  11.8695
 Q9D  C02  C  C      0   0.769  -23.6129  -14.1231  13.6433
 Q9D  C04  C  CH1    0  -0.162  -24.3706  -12.6852  15.4408
 Q9D  C05  C  CH2    0  -0.574  -25.7037  -12.1448  15.9784
 Q9D  C06  C  CR6    0   0.155  -26.5000  -11.4569  14.9042
 Q9D  C07  C  CR16   0  -0.351  -27.6194  -12.0613  14.3504
 Q9D  C08  C  CR6    0   0.273  -28.3210  -11.4084  13.3458
 Q9D  C23  C  CR16   0  -0.232  -26.8200   -9.5655  13.4300
 Q9D  C25  C  C      0   0.397  -23.5653  -13.2440  16.6138
 Q9D  C29  C  CR6    0   0.076  -23.8111  -16.5825  11.0174
 Q9D  C30  C  CR16   0  -0.288  -24.4276  -16.1810   9.8358
 Q9D  C31  C  CR16   0  -0.243  -25.1281  -17.0952   9.0611
 Q9D  C32  C  CR16   0  -0.260  -25.2192  -18.4217   9.4634
 Q9D  C33  C  CR16   0  -0.242  -24.6062  -18.8305  10.6406
 Q9D  C34  C  CR16   0  -0.291  -23.9076  -17.9131  11.4136
 Q9D  C56  C  CH3    0  -0.785  -23.7290  -14.6987  16.9450
 Q9D  N03  N  NH1    0  -0.676  -24.6197  -13.6560  14.4087
 Q9D  N09  N  N      1   0.329  -29.4960  -12.0523  12.7747
 Q9D  O01  O  O      0  -0.514  -22.4555  -13.7737  13.7565
 Q9D  O27  O  O2     0  -0.475  -24.0535  -15.0120  12.7547
 Q9D  O41  O  O      0  -0.377  -29.8004  -13.1478  13.1840
 Q9D  O47  O  O     -1  -0.376  -30.1087  -11.4593  11.9188
 Q9D  O52  O  O      0  -0.390  -22.8584  -12.5027  17.2552
 Q9D  H1   H  HCR6   0   0.299  -28.4921   -9.6629  12.0919
 Q9D  H2   H  HCR6   0   0.274  -25.2415   -9.7173  14.8622
 Q9D  H3   H  HCH2   0   0.251  -22.2925  -16.0758  12.4452
 Q9D  H4   H  HCH2   0   0.252  -22.6276  -14.8081  11.2571
 Q9D  H5   H  HCH1   0   0.295  -23.7991  -11.8476  15.0298
 Q9D  H6   H  HCH2   0   0.298  -25.4869  -11.4409  16.7831
 Q9D  H7   H  HCH2   0   0.282  -26.2877  -12.9578  16.4167
 Q9D  H8   H  HCR6   0   0.295  -27.9430  -13.0285  14.7101
 Q9D  H9   H  HCR6   0   0.281  -26.5069   -8.5918  13.0800
 Q9D  H10  H  HCR6   0   0.256  -24.3554  -15.1484   9.5150
 Q9D  H11  H  HCR6   0   0.259  -25.6003  -16.7734   8.1421
 Q9D  H12  H  HCR6   0   0.260  -25.7635  -19.1357   8.8590
 Q9D  H13  H  HCR6   0   0.259  -24.6703  -19.8637  10.9560
 Q9D  H14  H  HCR6   0   0.256  -23.4291  -18.2357  12.3307
 Q9D  H15  H  HCH3   0   0.272  -23.4384  -14.8881  17.9760
 Q9D  H16  H  HCH3   0   0.260  -24.7481  -15.0485  16.7799
 Q9D  H17  H  HCH3   0   0.276  -23.0803  -15.2949  16.2991
 Q9D  H18  H  HNH1   0   0.408  -25.5408  -14.0520  14.3018

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
 Q9D  C31  C32  aromatic  1.389  0.020  1.389
 Q9D  C31  C30  aromatic  1.388  0.020  1.388
 Q9D  C32  C33  aromatic  1.389  0.020  1.389
 Q9D  C30  C29  aromatic  1.392  0.020  1.392
 Q9D  C33  C34  aromatic  1.388  0.020  1.388
 Q9D  C29  C34  aromatic  1.392  0.020  1.392
 Q9D  C29  C28  single    1.498  0.020  1.498
 Q9D  O47  N09  single    1.208  0.020  1.208
 Q9D  C28  O27  single    1.435  0.020  1.435
 Q9D  N09  O41  double    1.208  0.020  1.208
 Q9D  N09  C08  single    1.456  0.020  1.456
 Q9D  O27  C02  single    1.332  0.020  1.332
 Q9D  O01  C02  double    1.214  0.020  1.214
 Q9D  C22  C08  aromatic  1.385  0.020  1.385
 Q9D  C22  C23  aromatic  1.386  0.020  1.386
 Q9D  C08  C07  aromatic  1.388  0.020  1.388
 Q9D  C02  N03  single    1.348  0.020  1.348
 Q9D  C23  C24  aromatic  1.386  0.020  1.386
 Q9D  C07  C06  aromatic  1.387  0.020  1.387
 Q9D  N03  C04  single    1.439  0.020  1.439
 Q9D  C24  C06  aromatic  1.394  0.020  1.394
 Q9D  C06  C05  single    1.504  0.020  1.504
 Q9D  C04  C05  single    1.536  0.020  1.536
 Q9D  C04  C25  single    1.529  0.020  1.529
 Q9D  C25  C56  single    1.501  0.020  1.501
 Q9D  C25  O52  double    1.209  0.020  1.209
 Q9D  C22  H1   single    0.930  0.020  1.080
 Q9D  C24  H2   single    0.930  0.020  1.080
 Q9D  C28  H3   single    0.970  0.020  1.090
 Q9D  C28  H4   single    0.970  0.020  1.090
 Q9D  C04  H5   single    0.970  0.020  1.090
 Q9D  C05  H6   single    0.970  0.020  1.090
 Q9D  C05  H7   single    0.970  0.020  1.090
 Q9D  C07  H8   single    0.930  0.020  1.080
 Q9D  C23  H9   single    0.930  0.020  1.080
 Q9D  C30  H10  single    0.930  0.020  1.080
 Q9D  C31  H11  single    0.930  0.020  1.080
 Q9D  C32  H12  single    0.930  0.020  1.080
 Q9D  C33  H13  single    0.930  0.020  1.080
 Q9D  C34  H14  single    0.930  0.020  1.080
 Q9D  C56  H15  single    0.970  0.020  1.090
 Q9D  C56  H16  single    0.970  0.020  1.090
 Q9D  C56  H17  single    0.970  0.020  1.090
 Q9D  N03  H18  single    0.860  0.020  1.020

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
 Q9D  H1   C22  C23  120.28  3.000
 Q9D  H1   C22  C08  121.50  3.000
 Q9D  C23  C22  C08  118.23  3.000
 Q9D  H2   C24  C23  119.35  3.000
 Q9D  H2   C24  C06  119.65  3.000
 Q9D  C23  C24  C06  121.00  3.000
 Q9D  H4   C28  H3   108.26  3.000
 Q9D  H4   C28  O27  109.87  3.000
 Q9D  H3   C28  O27  110.09  3.000
 Q9D  H4   C28  C29  110.98  3.000
 Q9D  H3   C28  C29  110.88  3.000
 Q9D  O27  C28  C29  106.76  3.000
 Q9D  O27  C02  O01  124.72  3.000
 Q9D  O01  C02  N03  123.99  3.000
 Q9D  O27  C02  N03  111.28  3.000
 Q9D  H5   C04  N03  109.73  3.000
 Q9D  H5   C04  C25  107.03  3.000
 Q9D  N03  C04  C25  113.27  3.000
 Q9D  H5   C04  C05  108.39  3.000
 Q9D  C25  C04  C05  108.50  3.000
 Q9D  N03  C04  C05  109.78  3.000
 Q9D  H7   C05  H6   106.88  3.000
 Q9D  H7   C05  C06  110.11  3.000
 Q9D  H6   C05  C06  109.69  3.000
 Q9D  H7   C05  C04  110.03  3.000
 Q9D  H6   C05  C04  108.23  3.000
 Q9D  C06  C05  C04  111.75  3.000
 Q9D  C07  C06  C05  120.87  3.000
 Q9D  C05  C06  C24  120.26  3.000
 Q9D  C07  C06  C24  118.86  3.000
 Q9D  H8   C07  C08  120.67  3.000
 Q9D  H8   C07  C06  119.88  3.000
 Q9D  C08  C07  C06  119.45  3.000
 Q9D  N09  C08  C07  118.91  3.000
 Q9D  C07  C08  C22  122.03  3.000
 Q9D  N09  C08  C22  119.05  3.000
 Q9D  H9   C23  C24  120.07  3.000
 Q9D  H9   C23  C22  119.50  3.000
 Q9D  C24  C23  C22  120.43  3.000
 Q9D  O52  C25  C56  122.77  3.000
 Q9D  O52  C25  C04  119.42  3.000
 Q9D  C56  C25  C04  117.79  3.000
 Q9D  C34  C29  C30  119.13  3.000
 Q9D  C34  C29  C28  120.38  3.000
 Q9D  C30  C29  C28  120.47  3.000
 Q9D  H10  C30  C31  119.74  3.000
 Q9D  H10  C30  C29  119.78  3.000
 Q9D  C31  C30  C29  120.49  3.000
 Q9D  H11  C31  C32  120.09  3.000
 Q9D  H11  C31  C30  119.89  3.000
 Q9D  C32  C31  C30  120.03  3.000
 Q9D  H12  C32  C33  120.08  3.000
 Q9D  H12  C32  C31  120.08  3.000
 Q9D  C33  C32  C31  119.84  3.000
 Q9D  H13  C33  C34  119.90  3.000
 Q9D  H13  C33  C32  120.12  3.000
 Q9D  C34  C33  C32  119.98  3.000
 Q9D  H14  C34  C33  119.79  3.000
 Q9D  H14  C34  C29  119.67  3.000
 Q9D  C33  C34  C29  120.54  3.000
 Q9D  H17  C56  H16  106.89  3.000
 Q9D  H17  C56  H15  107.86  3.000
 Q9D  H16  C56  H15  109.72  3.000
 Q9D  H17  C56  C25  109.49  3.000
 Q9D  H16  C56  C25  112.31  3.000
 Q9D  H15  C56  C25  110.41  3.000
 Q9D  H18  N03  C04  119.96  3.000
 Q9D  H18  N03  C02  119.07  3.000
 Q9D  C04  N03  C02  120.78  3.000
 Q9D  O47  N09  O41  123.86  3.000
 Q9D  O41  N09  C08  118.11  3.000
 Q9D  O47  N09  C08  118.03  3.000
 Q9D  C02  O27  C28  117.13  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
 Q9D  CONST_01  C06  C07  C08  C22     0.00   0.0  0
 Q9D  CONST_02  C06  C24  C23  C22     0.00   0.0  0
 Q9D  CONST_03  C08  C22  C23  C24     0.00   0.0  0
 Q9D  CONST_04  C08  C07  C06  C24     0.00   0.0  0
 Q9D  CONST_05  C23  C22  C08  C07     0.00   0.0  0
 Q9D  CONST_06  C23  C24  C06  C07     0.00   0.0  0
 Q9D  CONST_07  C32  C31  C30  C29     0.00   0.0  0
 Q9D  CONST_08  C32  C33  C34  C29     0.00   0.0  0
 Q9D  CONST_09  C33  C32  C31  C30     0.00   0.0  0
 Q9D  CONST_10  C33  C34  C29  C30     0.00   0.0  0
 Q9D  CONST_11  C34  C33  C32  C31     0.00   0.0  0
 Q9D  CONST_12  C34  C29  C30  C31     0.00   0.0  0
 Q9D  CONST_13  C31  C30  C29  C28   180.00   0.0  0
 Q9D  CONST_14  C33  C34  C29  C28   180.00   0.0  0
 Q9D  CONST_15  C08  C07  C06  C05   180.00   0.0  0
 Q9D  CONST_16  C23  C24  C06  C05   180.00   0.0  0
 Q9D  CONST_17  N09  C08  C07  C06   180.00   0.0  0
 Q9D  CONST_18  N09  C08  C22  C23   180.00   0.0  0
 Q9D  CONST_19  H8   C07  C08  C22   180.00   0.0  0
 Q9D  CONST_20  H2   C24  C23  C22   180.00   0.0  0
 Q9D  CONST_21  H1   C22  C23  C24   180.00   0.0  0
 Q9D  CONST_22  H9   C23  C24  C06   180.00   0.0  0
 Q9D  CONST_23  H11  C31  C30  C29   180.00   0.0  0
 Q9D  CONST_24  H13  C33  C34  C29   180.00   0.0  0
 Q9D  CONST_25  H12  C32  C31  C30   180.00   0.0  0
 Q9D  CONST_26  H14  C34  C29  C30   180.00   0.0  0
 Q9D  CONST_27  H10  C30  C31  C32   180.00   0.0  0
 Q9D  CONST_28  O47  N09  C08  C22     0.00   0.0  0
 Q9D  CONST_29  O41  N09  C08  C22   180.00   0.0  0
 Q9D  CONST_30  O47  N09  C08  C07   180.00   0.0  0
 Q9D  CONST_31  O41  N09  C08  C07     0.00   0.0  0
 Q9D  Var_01    C04  C05  C06  C24   -73.22  30.0  2
 Q9D  Var_02    O27  C28  C29  C30    87.34  30.0  2
 Q9D  Var_03    C29  C28  O27  C02   177.83  30.0  2
 Q9D  Var_04    O01  C02  O27  C28    -0.19  30.0  3
 Q9D  Var_05    O27  C02  N03  C04   179.83  30.0  1
 Q9D  Var_06    H15  C56  C25  C04  -158.06  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 Q9D  chir_01  C04  N03  C05  C25  negativ

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
 Q9D  plan-1  C22  0.020
 Q9D  plan-1  C24  0.020
 Q9D  plan-1  C05  0.020
 Q9D  plan-1  C06  0.020
 Q9D  plan-1  C07  0.020
 Q9D  plan-1  C08  0.020
 Q9D  plan-1  C23  0.020
 Q9D  plan-1  N09  0.020
 Q9D  plan-1  H1   0.020
 Q9D  plan-1  H2   0.020
 Q9D  plan-1  H8   0.020
 Q9D  plan-1  H9   0.020
 Q9D  plan-2  C28  0.020
 Q9D  plan-2  C29  0.020
 Q9D  plan-2  C30  0.020
 Q9D  plan-2  C31  0.020
 Q9D  plan-2  C32  0.020
 Q9D  plan-2  C33  0.020
 Q9D  plan-2  C34  0.020
 Q9D  plan-2  H10  0.020
 Q9D  plan-2  H11  0.020
 Q9D  plan-2  H12  0.020
 Q9D  plan-2  H13  0.020
 Q9D  plan-2  H14  0.020
 Q9D  plan-3  C08  0.020
 Q9D  plan-3  N09  0.020
 Q9D  plan-3  O41  0.020
 Q9D  plan-3  O47  0.020
 Q9D  plan-4  C04  0.020
 Q9D  plan-4  C25  0.020
 Q9D  plan-4  C56  0.020
 Q9D  plan-4  O52  0.020
 Q9D  plan-5  C02  0.020
 Q9D  plan-5  N03  0.020
 Q9D  plan-5  O01  0.020
 Q9D  plan-5  O27  0.020

