# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 09:50:41 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: N-(4-nitro-2-phenoxyphenyl)methanesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)Nc1ccc(cc1Oc2ccccc2)[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
 NIM  NIM  N-(4-nitro-2-phenoxyphenyl)methanesulfonamide  ligand  33  21  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NIM
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
 NIM  O4    O  O     -1  -0.372  -1.4396   4.6649   0.0439
 NIM  N2    N  N      1   0.329  -1.7618   3.5010   0.0513
 NIM  O3    O  O      0  -0.374  -2.8904   3.1131   0.2392
 NIM  C5    C  CR6    0   0.276  -0.7241   2.5050  -0.1795
 NIM  C4    C  CR16   0  -0.293   0.5708   2.9255  -0.4244
 NIM  C3    C  CR16   0  -0.254   1.5409   1.9640  -0.6478
 NIM  C2    C  CR6    0   0.228   1.2286   0.6133  -0.6087
 NIM  N1    N  NC1    0  -0.809   2.2274  -0.3524  -0.8363
 NIM  S1    S  S      0   1.320   3.3472  -0.6701   0.3611
 NIM  O1    O  OS     0  -0.655   4.2697  -1.6328  -0.2110
 NIM  O2    O  OS     0  -0.648   3.8339   0.6122   0.8358
 NIM  C1    C  CH3    0  -0.794   2.4450  -1.4507   1.6778
 NIM  C6    C  CR16   0  -0.378  -1.0793   1.1642  -0.1472
 NIM  C7    C  CR6    0   0.389  -0.0928   0.2162  -0.3549
 NIM  O5    O  O2     0  -0.513  -0.3095  -1.1166  -0.3281
 NIM  C8    C  CR6    0   0.291  -1.5795  -1.5902  -0.0692
 NIM  C13   C  CR16   0  -0.293  -2.4448  -1.8171  -1.1270
 NIM  C12   C  CR16   0  -0.253  -3.7070  -2.3316  -0.8630
 NIM  C11   C  CR16   0  -0.250  -4.0925  -2.6075   0.4425
 NIM  C10   C  CR16   0  -0.254  -3.2114  -2.3718   1.4899
 NIM  C9    C  CR16   0  -0.294  -1.9461  -1.8579   1.2395
 NIM  H4    H  HCR6   0   0.302   0.8312   3.9724  -0.4617
 NIM  H3    H  HCR6   0   0.292   2.5530   2.2661  -0.8730
 NIM  HN1   H  HNC1   0   0.426   1.9194  -1.1999  -1.3039
 NIM  H11A  H  HCH3   0   0.290   1.6693  -0.7780   2.0374
 NIM  H12A  H  HCH3   0   0.298   2.0098  -2.3783   1.3147
 NIM  H13A  H  HCH3   0   0.314   3.1487  -1.6571   2.4827
 NIM  H6    H  HCR6   0   0.321  -2.0989   0.8683   0.0530
 NIM  H13   H  HCR6   0   0.281  -2.1346  -1.6009  -2.1414
 NIM  H12   H  HCR6   0   0.268  -4.3891  -2.5164  -1.6822
 NIM  H11   H  HCR6   0   0.265  -5.0764  -3.0094   0.6444
 NIM  H10   H  HCR6   0   0.269  -3.5075  -2.5866   2.5078
 NIM  H9    H  HCR6   0   0.276  -1.2529  -1.6757   2.0512

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
 NIM  O4   N2    single    1.208  0.020  1.208
 NIM  N2   O3    double    1.208  0.020  1.208
 NIM  N2   C5    single    1.457  0.020  1.457
 NIM  C5   C4    aromatic  1.383  0.020  1.383
 NIM  C5   C6    aromatic  1.387  0.020  1.387
 NIM  C4   C3    aromatic  1.384  0.020  1.384
 NIM  C4   H4    single    0.930  0.020  1.080
 NIM  C3   C2    aromatic  1.387  0.020  1.387
 NIM  C3   H3    single    0.930  0.020  1.080
 NIM  C2   N1    single    1.408  0.020  1.408
 NIM  C2   C7    aromatic  1.403  0.020  1.403
 NIM  N1   S1    single    1.670  0.020  1.670
 NIM  N1   HN1   single    0.890  0.020  1.040
 NIM  S1   O1    double    1.451  0.020  1.451
 NIM  S1   O2    double    1.451  0.020  1.451
 NIM  S1   C1    single    1.777  0.020  1.777
 NIM  C1   H11A  single    0.970  0.020  1.090
 NIM  C1   H12A  single    0.970  0.020  1.090
 NIM  C1   H13A  single    0.970  0.020  1.090
 NIM  C6   C7    aromatic  1.384  0.020  1.384
 NIM  C6   H6    single    0.930  0.020  1.080
 NIM  C7   O5    single    1.351  0.020  1.351
 NIM  O5   C8    single    1.380  0.020  1.380
 NIM  C8   C13   aromatic  1.385  0.020  1.385
 NIM  C8   C9    aromatic  1.385  0.020  1.385
 NIM  C13  C12   aromatic  1.388  0.020  1.388
 NIM  C13  H13   single    0.930  0.020  1.080
 NIM  C12  C11   aromatic  1.389  0.020  1.389
 NIM  C12  H12   single    0.930  0.020  1.080
 NIM  C11  C10   aromatic  1.389  0.020  1.389
 NIM  C11  H11   single    0.930  0.020  1.080
 NIM  C10  C9    aromatic  1.388  0.020  1.388
 NIM  C10  H10   single    0.930  0.020  1.080
 NIM  C9   H9    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
 NIM  C5    N2   O3    118.08  3.000
 NIM  C5    N2   O4    117.90  3.000
 NIM  O3    N2   O4    124.03  3.000
 NIM  C6    C5   C4    122.51  3.000
 NIM  C6    C5   N2    118.34  3.000
 NIM  C4    C5   N2    119.15  3.000
 NIM  H4    C4   C3    119.94  3.000
 NIM  H4    C4   C5    121.79  3.000
 NIM  C3    C4   C5    118.26  3.000
 NIM  H3    C3   C2    119.29  3.000
 NIM  H3    C3   C4    119.75  3.000
 NIM  C2    C3   C4    120.95  3.000
 NIM  C7    C2   N1    120.22  3.000
 NIM  C7    C2   C3    119.53  3.000
 NIM  N1    C2   C3    120.25  3.000
 NIM  HN1   N1   S1    112.00  3.000
 NIM  HN1   N1   C2    115.58  3.000
 NIM  S1    N1   C2    119.36  3.000
 NIM  C1    S1   O2    108.42  3.000
 NIM  C1    S1   O1    108.88  3.000
 NIM  O2    S1   O1    120.13  3.000
 NIM  C1    S1   N1    105.93  3.000
 NIM  O2    S1   N1    106.94  3.000
 NIM  O1    S1   N1    105.66  3.000
 NIM  H13A  C1   H12A  110.11  3.000
 NIM  H13A  C1   H11A  109.49  3.000
 NIM  H12A  C1   H11A  110.65  3.000
 NIM  H13A  C1   S1    107.64  3.000
 NIM  H12A  C1   S1    109.31  3.000
 NIM  H11A  C1   S1    109.60  3.000
 NIM  H6    C6   C7    120.86  3.000
 NIM  H6    C6   C5    120.70  3.000
 NIM  C7    C6   C5    118.43  3.000
 NIM  O5    C7   C6    123.97  3.000
 NIM  O5    C7   C2    115.73  3.000
 NIM  C6    C7   C2    120.30  3.000
 NIM  C8    O5   C7    119.35  3.000
 NIM  C9    C8   C13   121.63  3.000
 NIM  C9    C8   O5    119.15  3.000
 NIM  C13   C8   O5    119.20  3.000
 NIM  H13   C13  C12   120.84  3.000
 NIM  H13   C13  C8    120.25  3.000
 NIM  C12   C13  C8    118.90  3.000
 NIM  H12   C12  C11   120.19  3.000
 NIM  H12   C12  C13   119.50  3.000
 NIM  C11   C12  C13   120.31  3.000
 NIM  H11   C11  C10   119.95  3.000
 NIM  H11   C11  C12   120.11  3.000
 NIM  C10   C11  C12   119.94  3.000
 NIM  H10   C10  C9    119.52  3.000
 NIM  H10   C10  C11   120.15  3.000
 NIM  C9    C10  C11   120.33  3.000
 NIM  H9    C9   C10   120.70  3.000
 NIM  H9    C9   C8    120.41  3.000
 NIM  C10   C9   C8    118.89  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
 NIM  CONST_01  C2    C3   C4   C5      0.00   0.0  0
 NIM  CONST_02  C2    C7   C6   C5      0.00   0.0  0
 NIM  CONST_03  C7    C6   C5   C4      0.00   0.0  0
 NIM  CONST_04  C7    C2   C3   C4      0.00   0.0  0
 NIM  CONST_05  C6    C5   C4   C3      0.00   0.0  0
 NIM  CONST_06  C6    C7   C2   C3      0.00   0.0  0
 NIM  CONST_07  C11   C12  C13  C8      0.00   0.0  0
 NIM  CONST_08  C11   C10  C9   C8      0.00   0.0  0
 NIM  CONST_09  C10   C9   C8   C13     0.00   0.0  0
 NIM  CONST_10  C10   C11  C12  C13     0.00   0.0  0
 NIM  CONST_11  C9    C8   C13  C12     0.00   0.0  0
 NIM  CONST_12  C9    C10  C11  C12     0.00   0.0  0
 NIM  CONST_13  C3    C4   C5   N2    180.00   0.0  0
 NIM  CONST_14  C7    C6   C5   N2    180.00   0.0  0
 NIM  CONST_15  O5    C7   C6   C5    180.00   0.0  0
 NIM  CONST_16  N1    C2   C3   C4    180.00   0.0  0
 NIM  CONST_17  O5    C7   C2   C3    180.00   0.0  0
 NIM  CONST_18  C6    C7   C2   N1    180.00   0.0  0
 NIM  CONST_19  C12   C13  C8   O5    180.00   0.0  0
 NIM  CONST_20  C10   C9   C8   O5    180.00   0.0  0
 NIM  CONST_21  H3    C3   C4   C5    180.00   0.0  0
 NIM  CONST_22  H6    C6   C5   C4    180.00   0.0  0
 NIM  CONST_23  H4    C4   C3   C2    180.00   0.0  0
 NIM  CONST_24  H12   C12  C13  C8    180.00   0.0  0
 NIM  CONST_25  H10   C10  C9   C8    180.00   0.0  0
 NIM  CONST_26  H9    C9   C8   C13   180.00   0.0  0
 NIM  CONST_27  H11   C11  C12  C13   180.00   0.0  0
 NIM  CONST_28  H13   C13  C12  C11   180.00   0.0  0
 NIM  CONST_29  C4    C5   N2   O4      0.00   0.0  0
 NIM  CONST_30  C6    C5   N2   O4    180.00   0.0  0
 NIM  CONST_31  C4    C5   N2   O3    180.00   0.0  0
 NIM  CONST_32  C6    C5   N2   O3      0.00   0.0  0
 NIM  Var_01    C13   C8   O5   C7     90.57  30.0  2
 NIM  Var_02    O1    S1   N1   C2   -176.52  30.0  3
 NIM  Var_03    H11A  C1   S1   N1    -60.16  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
 NIM  plan-1  N2   0.020
 NIM  plan-1  C5   0.020
 NIM  plan-1  C4   0.020
 NIM  plan-1  C3   0.020
 NIM  plan-1  C2   0.020
 NIM  plan-1  N1   0.020
 NIM  plan-1  C6   0.020
 NIM  plan-1  C7   0.020
 NIM  plan-1  O5   0.020
 NIM  plan-1  H4   0.020
 NIM  plan-1  H3   0.020
 NIM  plan-1  H6   0.020
 NIM  plan-2  O5   0.020
 NIM  plan-2  C8   0.020
 NIM  plan-2  C13  0.020
 NIM  plan-2  C12  0.020
 NIM  plan-2  C11  0.020
 NIM  plan-2  C10  0.020
 NIM  plan-2  C9   0.020
 NIM  plan-2  H13  0.020
 NIM  plan-2  H12  0.020
 NIM  plan-2  H11  0.020
 NIM  plan-2  H10  0.020
 NIM  plan-2  H9   0.020
 NIM  plan-3  O4   0.020
 NIM  plan-3  N2   0.020
 NIM  plan-3  O3   0.020
 NIM  plan-3  C5   0.020
 NIM  plan-4  C2   0.020
 NIM  plan-4  N1   0.020
 NIM  plan-4  S1   0.020
 NIM  plan-4  HN1  0.020

