# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 09:26:57 2021
#   Inital geometry file: a 142 line input string
#   Ligand name: 5-[(2~{R})-2-(4-nitrophenyl)-4-oxidanyl-5-oxidanylidene-3-(phenylcarbonyl)-2~{H}-pyrrol-1-yl]-2-oxidanyl-benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cc(ccc1O)N2[C@H](c3ccc(cc3)[N+](=O)=O)C(=C(O)C2=O)C(=O)c4ccccc4
#
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
 NE5  NE5  '5-[(2~{R})-2-(4-nitrophenyl)-4-oxidanyl-5-oxidanylidene-3-(phenylcarbonyl)-2~{H}-pyrrol-1-yl]-2-oxidanyl-benzoic acid'  ligand  50  34  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NE5
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
 NE5  C10   C  CR5   0   0.255  33.7182  15.0870  18.5625
 NE5  C13   C  C     0   0.388  32.0860  13.7734  19.9483
 NE5  C15   C  CR6   0  -0.051  31.2371  12.5598  19.8856
 NE5  C17   C  CR16  0  -0.241  29.2344  11.4027  20.5437
 NE5  C20   C  CR16  0  -0.289  31.6302  11.4526  19.1363
 NE5  C21   C  CR15  0  -0.250  32.0113  14.0655  17.3378
 NE5  C22   C  CR6   0   0.158  30.5708  14.5259  17.3196
 NE5  C24   C  CR16  0  -0.247  28.9463  16.2920  17.4961
 NE5  C04   C  CR6   0  -0.174  32.9409  16.0995  12.9910
 NE5  C05   C  CR16  0  -0.284  33.2111  15.9982  14.3248
 NE5  C06   C  CR6   0   0.460  32.6262  14.9608  15.1072
 NE5  C08   C  CR5   0   0.518  33.9132  15.4538  17.1454
 NE5  C12   C  CR5   0  -0.100  32.6514  14.2820  18.6840
 NE5  C16   C  CR16  0  -0.262  30.0454  12.5239  20.6066
 NE5  C18   C  CR16  0  -0.243  29.6246  10.3019  19.7901
 NE5  C19   C  CR16  0  -0.238  30.8285  10.3215  19.0981
 NE5  C23   C  CR16  0  -0.281  30.2632  15.8730  17.4773
 NE5  C25   C  CR6   0   0.252  27.9419  15.3432  17.3681
 NE5  C29   C  CR16  0  -0.249  28.2247  13.9960  17.2179
 NE5  C30   C  CR16  0  -0.280  29.5495  13.5951  17.1901
 NE5  C31   C  CR16  0  -0.250  31.7557  14.0307  14.4775
 NE5  C32   C  CR16  0  -0.276  31.4900  14.1187  13.1509
 NE5  C33   C  CR6   0   0.450  32.0692  15.1541  12.3683
 NE5  N07   N  NR5   0  -0.603  32.8571  14.8658  16.4410
 NE5  N26   N  N     1   0.332  26.5504  15.7769  17.3943
 NE5  O01   O  O     0  -0.464  33.2523  17.2535  10.9625
 NE5  O03   O  OH1   0  -0.558  34.2909  18.0007  12.7918
 NE5  O09   O  O     0  -0.377  34.8125  16.1129  16.7002
 NE5  O11   O  OH1   0  -0.555  34.5353  15.5156  19.4922
 NE5  O14   O  O     0  -0.360  32.2880  14.3626  20.9886
 NE5  O27   O  O     0  -0.371  25.6930  14.9311  17.3103
 NE5  O28   O  O     0  -0.371  26.3287  16.9591  17.4991
 NE5  O34   O  OH1   0  -0.510  31.7794  15.1979  11.1142
 NE5  H171  H  HCR6  0   0.269  28.2978  11.3848  21.0847
 NE5  H201  H  HCR6  0   0.281  32.5746  11.4544  18.6046
 NE5  H211  H  HCR5  0   0.349  32.0768  13.0172  17.0374
 NE5  H241  H  HCR6  0   0.307  28.7198  17.3410  17.6149
 NE5  H051  H  HCR6  0   0.341  33.8497  16.7298  14.7920
 NE5  H161  H  HCR6  0   0.269  29.7403  13.3812  21.1928
 NE5  H181  H  HCR6  0   0.270  28.9906   9.4262  19.7473
 NE5  H191  H  HCR6  0   0.270  31.1428   9.4585  18.5267
 NE5  H231  H  HCR6  0   0.281  31.0446  16.6142  17.5893
 NE5  H291  H  HCR6  0   0.307  27.4400  13.2604  17.1220
 NE5  H301  H  HCR6  0   0.287  29.7766  12.5438  17.0685
 NE5  H311  H  HCR6  0   0.330  31.3220  13.2138  15.0327
 NE5  H321  H  HCR6  0   0.336  30.8476  13.3962  12.6662
 NE5  H3    H  HOH1  0   0.512  34.6485  18.6860  12.2037
 NE5  H111  H  HOH1  0   0.499  35.2547  16.0416  19.1114
 NE5  H341  H  HOH1  0   0.513  32.2477  15.9788  10.6995
 NE5  C02   C  C     0   0.652  33.5117  17.1776  12.1497

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
 NE5  O34  C33   single    1.288  0.020  1.288
 NE5  O01  C02   double    1.218  0.020  1.218
 NE5  C33  C32   aromatic  1.421  0.020  1.421
 NE5  C33  C04   aromatic  1.429  0.020  1.429
 NE5  C02  C04   single    1.482  0.020  1.482
 NE5  C02  O03   single    1.303  0.020  1.303
 NE5  C32  C31   aromatic  1.356  0.020  1.356
 NE5  C04  C05   aromatic  1.365  0.020  1.365
 NE5  C31  C06   aromatic  1.421  0.020  1.421
 NE5  C05  C06   aromatic  1.425  0.020  1.425
 NE5  C06  N07   single    1.357  0.020  1.357
 NE5  N07  C08   single    1.399  0.020  1.399
 NE5  N07  C21   single    1.470  0.020  1.470
 NE5  O27  N26   double    1.207  0.020  1.207
 NE5  O09  C08   double    1.201  0.020  1.201
 NE5  C29  C30   aromatic  1.384  0.020  1.384
 NE5  C29  C25   aromatic  1.385  0.020  1.385
 NE5  C30  C22   aromatic  1.388  0.020  1.388
 NE5  N26  C25   single    1.458  0.020  1.458
 NE5  N26  O28   double    1.207  0.020  1.207
 NE5  C25  C24   aromatic  1.388  0.020  1.388
 NE5  C08  C10   single    1.477  0.020  1.477
 NE5  C22  C21   single    1.512  0.020  1.512
 NE5  C22  C23   aromatic  1.391  0.020  1.391
 NE5  C21  C12   single    1.506  0.020  1.506
 NE5  C24  C23   aromatic  1.382  0.020  1.382
 NE5  C10  C12   double    1.342  0.020  1.342
 NE5  C10  O11   single    1.310  0.020  1.310
 NE5  C12  C13   single    1.475  0.020  1.475
 NE5  C20  C19   aromatic  1.387  0.020  1.387
 NE5  C20  C15   aromatic  1.393  0.020  1.393
 NE5  C19  C18   aromatic  1.389  0.020  1.389
 NE5  C13  C15   single    1.482  0.020  1.482
 NE5  C13  O14   double    1.213  0.020  1.213
 NE5  C15  C16   aromatic  1.393  0.020  1.393
 NE5  C18  C17   aromatic  1.390  0.020  1.390
 NE5  C16  C17   aromatic  1.385  0.020  1.385
 NE5  C17  H171  single    0.930  0.020  1.080
 NE5  C20  H201  single    0.930  0.020  1.080
 NE5  C21  H211  single    0.970  0.020  1.090
 NE5  C24  H241  single    0.930  0.020  1.080
 NE5  C05  H051  single    0.930  0.020  1.080
 NE5  C16  H161  single    0.930  0.020  1.080
 NE5  C18  H181  single    0.930  0.020  1.080
 NE5  C19  H191  single    0.930  0.020  1.080
 NE5  C23  H231  single    0.930  0.020  1.080
 NE5  C29  H291  single    0.930  0.020  1.080
 NE5  C30  H301  single    0.930  0.020  1.080
 NE5  C31  H311  single    0.930  0.020  1.080
 NE5  C32  H321  single    0.930  0.020  1.080
 NE5  O03  H3    single    0.850  0.020  0.980
 NE5  O11  H111  single    0.850  0.020  0.980
 NE5  O34  H341  single    0.850  0.020  0.980

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
 NE5  O11   C10  C12  128.90  3.000
 NE5  O11   C10  C08  121.17  3.000
 NE5  C12   C10  C08  109.93  3.000
 NE5  O14   C13  C12  120.25  3.000
 NE5  O14   C13  C15  121.97  3.000
 NE5  C12   C13  C15  117.74  3.000
 NE5  C16   C15  C20  119.94  3.000
 NE5  C16   C15  C13  119.28  3.000
 NE5  C20   C15  C13  120.78  3.000
 NE5  H171  C17  C18  120.07  3.000
 NE5  H171  C17  C16  119.84  3.000
 NE5  C18   C17  C16  120.08  3.000
 NE5  H201  C20  C19  119.44  3.000
 NE5  H201  C20  C15  120.55  3.000
 NE5  C19   C20  C15  119.98  3.000
 NE5  H211  C21  N07  108.68  3.000
 NE5  H211  C21  C12  110.99  3.000
 NE5  N07   C21  C12  102.86  3.000
 NE5  H211  C21  C22  110.24  3.000
 NE5  C12   C21  C22  111.83  3.000
 NE5  N07   C21  C22  112.02  3.000
 NE5  C30   C22  C23  119.83  3.000
 NE5  C23   C22  C21  120.27  3.000
 NE5  C30   C22  C21  119.86  3.000
 NE5  H241  C24  C25  121.51  3.000
 NE5  H241  C24  C23  119.73  3.000
 NE5  C25   C24  C23  118.76  3.000
 NE5  C33   C04  C05  119.84  3.000
 NE5  C05   C04  C02  122.19  3.000
 NE5  C33   C04  C02  117.97  3.000
 NE5  H051  C05  C06  119.97  3.000
 NE5  H051  C05  C04  119.38  3.000
 NE5  C06   C05  C04  120.63  3.000
 NE5  N07   C06  C31  119.60  3.000
 NE5  N07   C06  C05  121.38  3.000
 NE5  C31   C06  C05  118.99  3.000
 NE5  O09   C08  N07  127.55  3.000
 NE5  O09   C08  C10  126.23  3.000
 NE5  N07   C08  C10  106.21  3.000
 NE5  C21   C12  C13  123.60  3.000
 NE5  C13   C12  C10  126.09  3.000
 NE5  C21   C12  C10  110.07  3.000
 NE5  H161  C16  C17  120.04  3.000
 NE5  H161  C16  C15  120.06  3.000
 NE5  C17   C16  C15  119.87  3.000
 NE5  H181  C18  C19  119.98  3.000
 NE5  H181  C18  C17  119.86  3.000
 NE5  C19   C18  C17  120.16  3.000
 NE5  H191  C19  C18  120.26  3.000
 NE5  H191  C19  C20  119.82  3.000
 NE5  C18   C19  C20  119.92  3.000
 NE5  H231  C23  C24  118.60  3.000
 NE5  H231  C23  C22  121.01  3.000
 NE5  C24   C23  C22  120.39  3.000
 NE5  N26   C25  C29  119.10  3.000
 NE5  N26   C25  C24  119.07  3.000
 NE5  C29   C25  C24  121.83  3.000
 NE5  H291  C29  C30  119.76  3.000
 NE5  H291  C29  C25  121.60  3.000
 NE5  C30   C29  C25  118.64  3.000
 NE5  H301  C30  C29  118.97  3.000
 NE5  H301  C30  C22  120.50  3.000
 NE5  C29   C30  C22  120.54  3.000
 NE5  H311  C31  C32  118.29  3.000
 NE5  H311  C31  C06  120.92  3.000
 NE5  C32   C31  C06  120.74  3.000
 NE5  H321  C32  C33  118.81  3.000
 NE5  H321  C32  C31  120.77  3.000
 NE5  C33   C32  C31  120.41  3.000
 NE5  O34   C33  C32  117.99  3.000
 NE5  C32   C33  C04  119.39  3.000
 NE5  O34   C33  C04  122.63  3.000
 NE5  C08   N07  C06  126.44  3.000
 NE5  C08   N07  C21  110.86  3.000
 NE5  C06   N07  C21  122.68  3.000
 NE5  O28   N26  O27  124.16  3.000
 NE5  O28   N26  C25  117.92  3.000
 NE5  O27   N26  C25  117.92  3.000
 NE5  H3    O03  C02  111.57  3.000
 NE5  H111  O11  C10  111.21  3.000
 NE5  H341  O34  C33  108.95  3.000
 NE5  O03   C02  O01  124.66  3.000
 NE5  O03   C02  C04  114.22  3.000
 NE5  O01   C02  C04  121.12  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
 NE5  CONST_01  C18   C19  C20  C15     0.00   0.0  0
 NE5  CONST_02  C18   C17  C16  C15     0.00   0.0  0
 NE5  CONST_03  C20   C19  C18  C17     0.00   0.0  0
 NE5  CONST_04  C20   C15  C16  C17     0.00   0.0  0
 NE5  CONST_05  C25   C29  C30  C22     0.00   0.0  0
 NE5  CONST_06  C25   C24  C23  C22     0.00   0.0  0
 NE5  CONST_07  C30   C29  C25  C24     0.00   0.0  0
 NE5  CONST_08  C30   C22  C23  C24     0.00   0.0  0
 NE5  CONST_09  C31   C32  C33  C04     0.00   0.0  0
 NE5  CONST_10  C31   C06  C05  C04     0.00   0.0  0
 NE5  CONST_11  C32   C33  C04  C05     0.00   0.0  0
 NE5  CONST_12  C32   C31  C06  C05     0.00   0.0  0
 NE5  CONST_13  C33   C32  C31  C06     0.00   0.0  0
 NE5  CONST_14  C33   C04  C05  C06     0.00   0.0  0
 NE5  CONST_15  C19   C20  C15  C16     0.00   0.0  0
 NE5  CONST_16  C19   C18  C17  C16     0.00   0.0  0
 NE5  CONST_17  C29   C30  C22  C23     0.00   0.0  0
 NE5  CONST_18  C29   C25  C24  C23     0.00   0.0  0
 NE5  CONST_19  C29   C30  C22  C21   180.00   0.0  0
 NE5  CONST_20  C24   C23  C22  C21   180.00   0.0  0
 NE5  CONST_21  N07   C06  C05  C04   180.00   0.0  0
 NE5  CONST_22  N07   C06  C31  C32   180.00   0.0  0
 NE5  CONST_23  C06   N07  C08  C10   180.00   0.0  0
 NE5  CONST_24  C21   N07  C08  C10     0.00   0.0  0
 NE5  CONST_25  C19   C20  C15  C13   180.00   0.0  0
 NE5  CONST_26  C17   C16  C15  C13   180.00   0.0  0
 NE5  CONST_27  C32   C33  C04  C02   180.00   0.0  0
 NE5  CONST_28  C06   C05  C04  C02   180.00   0.0  0
 NE5  CONST_29  O34   C33  C04  C05   180.00   0.0  0
 NE5  CONST_30  N26   C25  C24  C23   180.00   0.0  0
 NE5  CONST_31  N26   C25  C29  C30   180.00   0.0  0
 NE5  CONST_32  O34   C33  C32  C31   180.00   0.0  0
 NE5  CONST_33  O09   C08  N07  C21   180.00   0.0  0
 NE5  CONST_34  O09   C08  N07  C06     0.00   0.0  0
 NE5  CONST_35  H191  C19  C20  C15   180.00   0.0  0
 NE5  CONST_36  H171  C17  C16  C15   180.00   0.0  0
 NE5  CONST_37  H181  C18  C19  C20   180.00   0.0  0
 NE5  CONST_38  H161  C16  C15  C20   180.00   0.0  0
 NE5  CONST_39  H301  C30  C22  C21     0.00   0.0  0
 NE5  CONST_40  H231  C23  C22  C21     0.00   0.0  0
 NE5  CONST_41  H291  C29  C30  C22   180.00   0.0  0
 NE5  CONST_42  H241  C24  C23  C22   180.00   0.0  0
 NE5  CONST_43  H321  C32  C33  C04   180.00   0.0  0
 NE5  CONST_44  H311  C31  C06  C05   180.00   0.0  0
 NE5  CONST_45  H201  C20  C15  C16   180.00   0.0  0
 NE5  CONST_46  H051  C05  C06  C31   180.00   0.0  0
 NE5  CONST_47  O27   N26  C25  C24   180.00   0.0  0
 NE5  CONST_48  O28   N26  C25  C24     0.00   0.0  0
 NE5  CONST_49  O27   N26  C25  C29     0.00   0.0  0
 NE5  CONST_50  O28   N26  C25  C29   180.00   0.0  0
 NE5  CONST_51  H3    O03  C02  C04   180.00   0.0  0
 NE5  Var_01    C31   C06  N07  C21   -15.48  30.0  2
 NE5  Var_02    C08   C10  C12  C21    -1.39  30.0  1
 NE5  Var_03    N07   C08  C10  C12     2.69  30.0  1
 NE5  Var_04    C15   C13  C12  C10  -159.14  30.0  2
 NE5  Var_05    C12   C13  C15  C20    45.49  30.0  2
 NE5  Var_06    O01   C02  C04  C05  -179.64  30.0  2

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
 NE5  chir_01  C21  N07  C22  C12  positiv

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
 NE5  plan-1  C13   0.020
 NE5  plan-1  C15   0.020
 NE5  plan-1  C17   0.020
 NE5  plan-1  C20   0.020
 NE5  plan-1  C16   0.020
 NE5  plan-1  C18   0.020
 NE5  plan-1  C19   0.020
 NE5  plan-1  H171  0.020
 NE5  plan-1  H201  0.020
 NE5  plan-1  H161  0.020
 NE5  plan-1  H181  0.020
 NE5  plan-1  H191  0.020
 NE5  plan-2  C21   0.020
 NE5  plan-2  C22   0.020
 NE5  plan-2  C24   0.020
 NE5  plan-2  C23   0.020
 NE5  plan-2  C25   0.020
 NE5  plan-2  C29   0.020
 NE5  plan-2  C30   0.020
 NE5  plan-2  N26   0.020
 NE5  plan-2  H241  0.020
 NE5  plan-2  H231  0.020
 NE5  plan-2  H291  0.020
 NE5  plan-2  H301  0.020
 NE5  plan-3  C04   0.020
 NE5  plan-3  C05   0.020
 NE5  plan-3  C06   0.020
 NE5  plan-3  C31   0.020
 NE5  plan-3  C32   0.020
 NE5  plan-3  C33   0.020
 NE5  plan-3  N07   0.020
 NE5  plan-3  O34   0.020
 NE5  plan-3  H051  0.020
 NE5  plan-3  H311  0.020
 NE5  plan-3  H321  0.020
 NE5  plan-3  C02   0.020
 NE5  plan-4  C25   0.020
 NE5  plan-4  N26   0.020
 NE5  plan-4  O27   0.020
 NE5  plan-4  O28   0.020
 NE5  plan-5  C13   0.020
 NE5  plan-5  C15   0.020
 NE5  plan-5  C12   0.020
 NE5  plan-5  O14   0.020
 NE5  plan-6  C10   0.020
 NE5  plan-6  C21   0.020
 NE5  plan-6  C06   0.020
 NE5  plan-6  C08   0.020
 NE5  plan-6  N07   0.020
 NE5  plan-6  O09   0.020
 NE5  plan-7  C04   0.020
 NE5  plan-7  O01   0.020
 NE5  plan-7  O03   0.020
 NE5  plan-7  H3    0.020
 NE5  plan-7  C02   0.020

