# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 19:51:53 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 4-bromo-5-methyl-N-[1-(3-nitropyridin-2-yl)piperidin-4-yl]-1H-pyrrole-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1[nH]c(cc1Br)C(=O)NC2CCN(CC2)c3ncccc3[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
 08B  08B  4-bromo-5-methyl-N-[1-(3-nitropyridin-2-yl)piperidin-4-yl]-1H-pyrrole-2-carboxamide  ligand  43  25  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_08B
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
 08B  C1   C   CH3    0  -0.735   4.9159   2.8597   0.3084
 08B  C2   C   CR5    0   0.349   4.3998   1.4701   0.2221
 08B  C3   C   CR5    0  -0.225   5.0452   0.2773  -0.0378
 08B  C4   C   CR15   0  -0.315   4.1175  -0.7748   0.0480
 08B  C5   C   CR5    0   0.193   2.9051  -0.1985   0.3539
 08B  N6   N   NR15   0  -0.681   3.1038   1.1528   0.4482
 08B  C8   C   C      0   0.531   1.6253  -0.8990   0.5283
 08B  O9   O   O      0  -0.492   1.6043  -2.1170   0.6608
 08B  N10  N   NH1    0  -0.668   0.5124  -0.1380   0.5416
 08B  C11  C   CH1    0  -0.072  -0.8183  -0.6943   0.6737
 08B  C12  C   CH2    0  -0.439  -1.7480   0.3139   1.3386
 08B  C13  C   CH2    0  -0.330  -3.1476  -0.2683   1.4313
 08B  N14  N   NT     0  -0.470  -3.6497  -0.6540   0.1191
 08B  C15  C   CH2    0  -0.307  -2.8170  -1.6613  -0.5203
 08B  C16  C   CH2    0  -0.431  -1.3968  -1.1324  -0.6704
 08B  C17  C   CR6    0   0.543  -4.9640  -0.5588  -0.2080
 08B  C18  C   CR6    0   0.077  -5.7912   0.5441   0.1294
 08B  C19  C   CR16   0  -0.163  -7.1612   0.4675  -0.0690
 08B  C20  C   CR16   0  -0.357  -7.6929  -0.6392  -0.6998
 08B  C21  C   CR16   0  -0.034  -6.7986  -1.6067  -1.1333
 08B  N22  N   N      0  -0.458  -5.5038  -1.5778  -0.8783
 08B  N23  N   N      1   0.334  -5.2695   1.8255   0.5468
 08B  O24  O   O      0  -0.381  -5.9488   2.5015   1.2874
 08B  O25  O   O     -1  -0.378  -4.2046   2.1832   0.0973
 08B  BR   BR  BR     0  -0.061   6.8628   0.1120  -0.4297
 08B  H1   H   HCH3   0   0.263   5.3867   3.0495   1.2745
 08B  H2   H   HCH3   0   0.259   5.6616   3.0480  -0.4625
 08B  H3   H   HCH3   0   0.262   4.1138   3.5852   0.1811
 08B  H4   H   HCR5   0   0.273   4.3025  -1.8245  -0.1117
 08B  H5   H   HNR5   0   0.417   2.4161   1.8341   0.7299
 08B  H6   H   HNH1   0   0.393   0.5646   0.8202   0.2339
 08B  H7   H   HCH1   0   0.248  -0.7454  -1.5701   1.3239
 08B  H8   H   HCH2   0   0.255  -1.3911   0.5517   2.3425
 08B  H9   H   HCH2   0   0.240  -1.7744   1.2437   0.7647
 08B  H10  H   HCH2   0   0.251  -3.1192  -1.1674   2.0615
 08B  H11  H   HCH2   0   0.268  -3.8194   0.4198   1.9350
 08B  H12  H   HCH2   0   0.230  -2.8120  -2.5865   0.0709
 08B  H13  H   HCH2   0   0.269  -3.2280  -1.9069  -1.4953
 08B  H14  H   HCH2   0   0.230  -1.3959  -0.2834  -1.3601
 08B  H15  H   HCH2   0   0.250  -0.7735  -1.9140  -1.1087
 08B  H16  H   HCR6   0   0.305  -7.7988   1.2934   0.2147
 08B  H17  H   HCR6   0   0.280  -8.7519  -0.7267  -0.8913
 08B  H18  H   HCR6   0   0.277  -7.1509  -2.4575  -1.7056

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
 08B  BR   C3   single    1.867  0.020  1.867
 08B  O25  N23  single    1.210  0.020  1.210
 08B  C3   C4   aromatic  1.405  0.020  1.405
 08B  C3   C2   aromatic  1.381  0.020  1.381
 08B  C4   C5   aromatic  1.377  0.020  1.377
 08B  O24  N23  double    1.211  0.020  1.211
 08B  N23  C18  single    1.445  0.020  1.445
 08B  C2   C1   single    1.485  0.020  1.485
 08B  C2   N6   aromatic  1.353  0.020  1.353
 08B  C19  C18  aromatic  1.386  0.020  1.386
 08B  C19  C20  aromatic  1.380  0.020  1.380
 08B  C18  C17  aromatic  1.419  0.020  1.419
 08B  C5   N6   aromatic  1.369  0.020  1.369
 08B  C5   C8   single    1.469  0.020  1.469
 08B  N10  C8   single    1.348  0.020  1.348
 08B  N10  C11  single    1.448  0.020  1.448
 08B  C20  C21  aromatic  1.387  0.020  1.387
 08B  C12  C11  single    1.524  0.020  1.524
 08B  C12  C13  single    1.519  0.020  1.519
 08B  C17  N14  single    1.358  0.020  1.358
 08B  C17  N22  aromatic  1.334  0.020  1.334
 08B  C16  C11  single    1.528  0.020  1.528
 08B  C16  C15  single    1.523  0.020  1.523
 08B  N14  C13  single    1.457  0.020  1.457
 08B  N14  C15  single    1.455  0.020  1.455
 08B  C8   O9   double    1.225  0.020  1.225
 08B  C21  N22  aromatic  1.320  0.020  1.320
 08B  C1   H1   single    0.970  0.020  1.090
 08B  C1   H2   single    0.970  0.020  1.090
 08B  C1   H3   single    0.970  0.020  1.090
 08B  C4   H4   single    0.930  0.020  1.080
 08B  N6   H5   single    0.860  0.020  1.020
 08B  N10  H6   single    0.860  0.020  1.020
 08B  C11  H7   single    0.970  0.020  1.090
 08B  C12  H8   single    0.970  0.020  1.090
 08B  C12  H9   single    0.970  0.020  1.090
 08B  C13  H10  single    0.970  0.020  1.090
 08B  C13  H11  single    0.970  0.020  1.090
 08B  C15  H12  single    0.970  0.020  1.090
 08B  C15  H13  single    0.970  0.020  1.090
 08B  C16  H14  single    0.970  0.020  1.090
 08B  C16  H15  single    0.970  0.020  1.090
 08B  C19  H16  single    0.930  0.020  1.080
 08B  C20  H17  single    0.930  0.020  1.080
 08B  C21  H18  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
 08B  H3   C1   H2   107.84  3.000
 08B  H3   C1   H1   107.78  3.000
 08B  H2   C1   H1   107.53  3.000
 08B  H3   C1   C2   111.14  3.000
 08B  H2   C1   C2   111.02  3.000
 08B  H1   C1   C2   111.36  3.000
 08B  N6   C2   C3   106.05  3.000
 08B  N6   C2   C1   122.86  3.000
 08B  C3   C2   C1   131.07  3.000
 08B  BR   C3   C4   126.11  3.000
 08B  C4   C3   C2   109.07  3.000
 08B  BR   C3   C2   124.82  3.000
 08B  H4   C4   C5   126.28  3.000
 08B  H4   C4   C3   127.36  3.000
 08B  C5   C4   C3   106.35  3.000
 08B  C8   C5   N6   126.07  3.000
 08B  C8   C5   C4   126.43  3.000
 08B  N6   C5   C4   107.50  3.000
 08B  H5   N6   C5   125.96  3.000
 08B  H5   N6   C2   122.78  3.000
 08B  C5   N6   C2   111.03  3.000
 08B  N10  C8   O9   123.08  3.000
 08B  O9   C8   C5   120.11  3.000
 08B  N10  C8   C5   116.81  3.000
 08B  H6   N10  C11  116.15  3.000
 08B  H6   N10  C8   119.40  3.000
 08B  C11  N10  C8   122.85  3.000
 08B  H7   C11  C16  108.59  3.000
 08B  H7   C11  C12  108.13  3.000
 08B  C16  C11  C12  110.03  3.000
 08B  H7   C11  N10  107.50  3.000
 08B  C16  C11  N10  112.20  3.000
 08B  C12  C11  N10  110.25  3.000
 08B  H9   C12  H8   107.79  3.000
 08B  H9   C12  C13  109.62  3.000
 08B  H8   C12  C13  109.19  3.000
 08B  H9   C12  C11  110.39  3.000
 08B  H8   C12  C11  110.24  3.000
 08B  C13  C12  C11  109.58  3.000
 08B  H11  C13  H10  105.59  3.000
 08B  H11  C13  N14  111.87  3.000
 08B  H10  C13  N14  108.00  3.000
 08B  H11  C13  C12  110.83  3.000
 08B  H10  C13  C12  108.97  3.000
 08B  N14  C13  C12  111.35  3.000
 08B  C17  N14  C15  119.78  3.000
 08B  C15  N14  C13  112.45  3.000
 08B  C17  N14  C13  122.14  3.000
 08B  H13  C15  H12  107.12  3.000
 08B  H13  C15  C16  110.05  3.000
 08B  H12  C15  C16  109.97  3.000
 08B  H13  C15  N14  109.54  3.000
 08B  H12  C15  N14  110.45  3.000
 08B  C16  C15  N14  109.67  3.000
 08B  H15  C16  H14  107.59  3.000
 08B  H15  C16  C15  108.87  3.000
 08B  H14  C16  C15  109.42  3.000
 08B  H15  C16  C11  110.02  3.000
 08B  H14  C16  C11  109.39  3.000
 08B  C15  C16  C11  111.47  3.000
 08B  N22  C17  C18  118.50  3.000
 08B  N22  C17  N14  117.34  3.000
 08B  C18  C17  N14  124.15  3.000
 08B  N23  C18  C19  116.55  3.000
 08B  C19  C18  C17  119.93  3.000
 08B  N23  C18  C17  123.18  3.000
 08B  H16  C19  C20  120.34  3.000
 08B  H16  C19  C18  120.20  3.000
 08B  C20  C19  C18  119.36  3.000
 08B  H17  C20  C21  121.37  3.000
 08B  H17  C20  C19  121.59  3.000
 08B  C21  C20  C19  116.98  3.000
 08B  H18  C21  N22  115.97  3.000
 08B  H18  C21  C20  120.19  3.000
 08B  N22  C21  C20  123.84  3.000
 08B  C21  N22  C17  120.72  3.000
 08B  O25  N23  O24  123.77  3.000
 08B  O24  N23  C18  117.98  3.000
 08B  O25  N23  C18  118.19  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
 08B  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 08B  CONST_02  C4   C5   N6   C2      0.00   0.0  0
 08B  CONST_03  N6   C5   C4   C3      0.00   0.0  0
 08B  CONST_04  C5   N6   C2   C3      0.00   0.0  0
 08B  CONST_05  N6   C2   C3   C4      0.00   0.0  0
 08B  CONST_06  C20  C19  C18  C17     0.00   0.0  0
 08B  CONST_07  C20  C21  N22  C17     0.00   0.0  0
 08B  CONST_08  C21  C20  C19  C18     0.00   0.0  0
 08B  CONST_09  C21  N22  C17  C18     0.00   0.0  0
 08B  CONST_10  N22  C17  C18  C19     0.00   0.0  0
 08B  CONST_11  N22  C21  C20  C19     0.00   0.0  0
 08B  CONST_12  C19  C18  C17  N14   180.00   0.0  0
 08B  CONST_13  C21  N22  C17  N14   180.00   0.0  0
 08B  CONST_14  C4   C3   C2   C1    180.00   0.0  0
 08B  CONST_15  C5   N6   C2   C1    180.00   0.0  0
 08B  CONST_16  C8   C5   N6   C2    180.00   0.0  0
 08B  CONST_17  C8   C5   C4   C3    180.00   0.0  0
 08B  CONST_18  BR   C3   C4   C5    180.00   0.0  0
 08B  CONST_19  BR   C3   C2   N6    180.00   0.0  0
 08B  CONST_21  N23  C18  C19  C20   180.00   0.0  0
 08B  CONST_23  H4   C4   C3   C2    180.00   0.0  0
 08B  CONST_24  H5   N6   C2   C3    180.00   0.0  0
 08B  CONST_25  H16  C19  C18  C17   180.00   0.0  0
 08B  CONST_26  H18  C21  N22  C17   180.00   0.0  0
 08B  CONST_27  H17  C20  C19  C18   180.00   0.0  0
 08B  CONST_28  C11  N10  C8   C5    180.00   0.0  0
 08B  CONST_33  C11  N10  C8   O9      0.00   0.0  0
 08B  CONST_34  H6   N10  C8   C5      0.00   0.0  0
 08B  Var_01    N14  C13  C12  C11   -56.85  30.0  1
 08B  Var_02    N14  C15  C16  C11    55.87  30.0  1
 08B  Var_03    C17  N14  C13  C12  -146.40  30.0  1
 08B  Var_04    C18  C17  N14  C13    42.38  30.0  2
 08B  Var_05    C16  C15  N14  C13   -58.64  30.0  1
 08B  Var_06    N10  C8   C5   C4   -166.23  30.0  2
 08B  Var_07    H1   C1   C2   C3    -79.82  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
 08B  chir_01  C11  N10  C12  C16  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
 08B  plan-1  C1   0.020
 08B  plan-1  C2   0.020
 08B  plan-1  C3   0.020
 08B  plan-1  C4   0.020
 08B  plan-1  C5   0.020
 08B  plan-1  N6   0.020
 08B  plan-1  C8   0.020
 08B  plan-1  BR   0.020
 08B  plan-1  H4   0.020
 08B  plan-1  H5   0.020
 08B  plan-2  N14  0.020
 08B  plan-2  C17  0.020
 08B  plan-2  C18  0.020
 08B  plan-2  C19  0.020
 08B  plan-2  C20  0.020
 08B  plan-2  C21  0.020
 08B  plan-2  N22  0.020
 08B  plan-2  N23  0.020
 08B  plan-2  H16  0.020
 08B  plan-2  H17  0.020
 08B  plan-2  H18  0.020
 08B  plan-3  C18  0.020
 08B  plan-3  N23  0.020
 08B  plan-3  O24  0.020
 08B  plan-3  O25  0.020
 08B  plan-4  C5   0.020
 08B  plan-4  C8   0.020
 08B  plan-4  O9   0.020
 08B  plan-4  N10  0.020
 08B  plan-4  C11  0.020
 08B  plan-4  H6   0.020

