# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 17:03:54 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 4-(dimethylamino)-N-{[(2R)-1-ethylpyrrolidin-2-yl]methyl}-2-methoxy-5-nitrobenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN1CCC[C@@H]1CNC(=O)c2cc(c(cc2OC)N(C)C)[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
 C56  C56  4-(dimethylamino)-N-{[(2R)-1-ethylpyrrolidin-2-yl]methyl}-2-methoxy-5-nitrobenzamide  ligand  51  25  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_C56
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
 C56  O16   O  O      0  -0.484  -0.8870  -1.9213  -1.6404
 C56  C15   C  C      0   0.522  -0.6140  -1.1522  -0.7307
 C56  C2    C  CR6    0  -0.196   0.7949  -0.7675  -0.4149
 C56  C3    C  CR6    0   0.448   1.7895  -1.7428  -0.1893
 C56  O13   O  O2     0  -0.449   1.3745  -3.0069  -0.1762
 C56  C14   C  CH3    0  -0.446   2.2942  -4.0425   0.1283
 C56  C4    C  CR16   0  -0.537   3.1074  -1.3676  -0.0002
 C56  C5    C  CR6    0   0.448   3.5154  -0.0194  -0.0170
 C56  N10   N  NT     0  -0.473   4.8361   0.2848   0.0459
 C56  C12   C  CH3    0  -0.563   5.7878  -0.7133   0.4855
 C56  C11   C  CH3    0  -0.545   5.4216   1.3649  -0.7245
 C56  C6    C  CR6    0   0.130   2.4850   0.9446  -0.1459
 C56  N7    N  N      1   0.333   2.6881   2.3421   0.1145
 C56  O9    O  O     -1  -0.399   1.9508   3.1425  -0.4257
 C56  O8    O  O      0  -0.392   3.5467   2.6668   0.9075
 C56  C1    C  CR16   0  -0.282   1.1662   0.5539  -0.3783
 C56  N17   N  NH1    0  -0.629  -1.5401  -0.5504   0.0317
 C56  C18   C  CH2    0  -0.263  -2.9636  -0.7120  -0.1650
 C56  C05   C  CH1    0  -0.133  -3.7172   0.4559   0.4860
 C56  C06   C  CH2    0  -0.444  -3.4510   1.7803  -0.2229
 C56  C07   C  CH2    0  -0.492  -4.4423   1.7567  -1.3929
 C56  C08   C  CH2    0  -0.268  -5.5659   0.8113  -0.9322
 C56  N09   N  NT     0  -0.422  -5.1612   0.3608   0.3928
 C56  C10   C  CH2    0  -0.283  -5.7813  -0.8582   0.8598
 C56  C13   C  CH3    0  -0.668  -7.2666  -0.6765   1.1293
 C56  H17   H  HNH1   0   0.405  -1.2338  -0.0656   0.8614
 C56  H1    H  HCR6   0   0.291   0.4106   1.3178  -0.5032
 C56  H4    H  HCR6   0   0.311   3.8654  -2.1301   0.0904
 C56  H141  H  HCH3   0   0.238   2.7481  -3.9028   1.1116
 C56  H142  H  HCH3   0   0.270   1.7208  -4.9652   0.1317
 C56  H143  H  HCH3   0   0.239   3.0815  -4.1195  -0.6245
 C56  H121  H  HCH3   0   0.239   6.0258  -1.4456  -0.2930
 C56  H122  H  HCH3   0   0.271   6.7106  -0.2091   0.7655
 C56  H123  H  HCH3   0   0.258   5.4231  -1.2410   1.3654
 C56  H111  H  HCH3   0   0.251   4.7033   1.8034  -1.4143
 C56  H112  H  HCH3   0   0.248   5.8363   2.1518  -0.0935
 C56  H113  H  HCH3   0   0.257   6.2305   0.9587  -1.3346
 C56  H181  H  HCH2   0   0.240  -3.1697  -0.7559  -1.2366
 C56  H182  H  HCH2   0   0.247  -3.3003  -1.6616   0.2625
 C56  H05   H  HCH1   0   0.243  -3.4269   0.4989   1.5432
 C56  H061  H  HCH2   0   0.241  -3.6710   2.6039   0.4584
 C56  H062  H  HCH2   0   0.237  -2.4163   1.8963  -0.5465
 C56  H071  H  HCH2   0   0.245  -4.8117   2.7528  -1.6343
 C56  H072  H  HCH2   0   0.236  -3.9660   1.3713  -2.2953
 C56  H081  H  HCH2   0   0.227  -6.5353   1.3137  -0.8877
 C56  H082  H  HCH2   0   0.198  -5.6802  -0.0254  -1.6385
 C56  H101  H  HCH2   0   0.190  -5.6487  -1.6906   0.1489
 C56  H102  H  HCH2   0   0.229  -5.2835  -1.1584   1.7857
 C56  H131  H  HCH3   0   0.227  -7.8114  -0.4053   0.2240
 C56  H132  H  HCH3   0   0.228  -7.7016  -1.6023   1.5064
 C56  H133  H  HCH3   0   0.220  -7.4355   0.1055   1.8706

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
 C56  O16  C15   double    1.222  0.020  1.222
 C56  C15  C2    single    1.494  0.020  1.494
 C56  C15  N17   single    1.342  0.020  1.342
 C56  C2   C3    aromatic  1.411  0.020  1.411
 C56  C2   C1    aromatic  1.373  0.020  1.373
 C56  C3   O13   single    1.331  0.020  1.331
 C56  C3   C4    aromatic  1.383  0.020  1.383
 C56  O13  C14   single    1.418  0.020  1.418
 C56  C4   C5    aromatic  1.409  0.020  1.409
 C56  C5   N10   single    1.357  0.020  1.357
 C56  C5   C6    aromatic  1.417  0.020  1.417
 C56  N10  C12   single    1.447  0.020  1.447
 C56  N10  C11   single    1.450  0.020  1.450
 C56  C6   N7    single    1.436  0.020  1.436
 C56  C6   C1    aromatic  1.395  0.020  1.395
 C56  N7   O9    single    1.215  0.020  1.215
 C56  N7   O8    double    1.213  0.020  1.213
 C56  N17  C18   single    1.446  0.020  1.446
 C56  C05  C06   single    1.526  0.020  1.526
 C56  C05  N09   single    1.450  0.020  1.450
 C56  C05  C18   single    1.535  0.020  1.535
 C56  C06  C07   single    1.534  0.020  1.534
 C56  C07  C08   single    1.539  0.020  1.539
 C56  C08  N09   single    1.457  0.020  1.457
 C56  N09  C10   single    1.445  0.020  1.445
 C56  C10  C13   single    1.521  0.020  1.521
 C56  N17  H17   single    0.860  0.020  1.020
 C56  C1   H1    single    0.930  0.020  1.080
 C56  C4   H4    single    0.930  0.020  1.080
 C56  C14  H141  single    0.970  0.020  1.090
 C56  C14  H142  single    0.970  0.020  1.090
 C56  C14  H143  single    0.970  0.020  1.090
 C56  C12  H121  single    0.970  0.020  1.090
 C56  C12  H122  single    0.970  0.020  1.090
 C56  C12  H123  single    0.970  0.020  1.090
 C56  C11  H111  single    0.970  0.020  1.090
 C56  C11  H112  single    0.970  0.020  1.090
 C56  C11  H113  single    0.970  0.020  1.090
 C56  C18  H181  single    0.970  0.020  1.090
 C56  C18  H182  single    0.970  0.020  1.090
 C56  C05  H05   single    0.970  0.020  1.090
 C56  C06  H061  single    0.970  0.020  1.090
 C56  C06  H062  single    0.970  0.020  1.090
 C56  C07  H071  single    0.970  0.020  1.090
 C56  C07  H072  single    0.970  0.020  1.090
 C56  C08  H081  single    0.970  0.020  1.090
 C56  C08  H082  single    0.970  0.020  1.090
 C56  C10  H101  single    0.970  0.020  1.090
 C56  C10  H102  single    0.970  0.020  1.090
 C56  C13  H131  single    0.970  0.020  1.090
 C56  C13  H132  single    0.970  0.020  1.090
 C56  C13  H133  single    0.970  0.020  1.090

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
 C56  N17   C15  C2    114.53  3.000
 C56  N17   C15  O16   123.43  3.000
 C56  C2    C15  O16   122.00  3.000
 C56  C1    C2   C3    118.05  3.000
 C56  C1    C2   C15   120.55  3.000
 C56  C3    C2   C15   121.36  3.000
 C56  C4    C3   O13   123.60  3.000
 C56  C4    C3   C2    120.39  3.000
 C56  O13   C3   C2    116.00  3.000
 C56  C14   O13  C3    119.58  3.000
 C56  H143  C14  H142  108.83  3.000
 C56  H143  C14  H141  109.28  3.000
 C56  H142  C14  H141  108.98  3.000
 C56  H143  C14  O13   111.78  3.000
 C56  H142  C14  O13   106.18  3.000
 C56  H141  C14  O13   111.68  3.000
 C56  H4    C4   C5    118.29  3.000
 C56  H4    C4   C3    119.29  3.000
 C56  C5    C4   C3    122.26  3.000
 C56  C6    C5   N10   124.03  3.000
 C56  C6    C5   C4    116.21  3.000
 C56  N10   C5   C4    119.73  3.000
 C56  C11   N10  C12   114.17  3.000
 C56  C11   N10  C5    122.37  3.000
 C56  C12   N10  C5    119.97  3.000
 C56  H123  C12  H122  107.50  3.000
 C56  H123  C12  H121  108.85  3.000
 C56  H122  C12  H121  107.97  3.000
 C56  H123  C12  N10   111.06  3.000
 C56  H122  C12  N10   108.44  3.000
 C56  H121  C12  N10   112.84  3.000
 C56  H113  C11  H112  108.07  3.000
 C56  H113  C11  H111  106.55  3.000
 C56  H112  C11  H111  109.08  3.000
 C56  H113  C11  N10   108.60  3.000
 C56  H112  C11  N10   112.56  3.000
 C56  H111  C11  N10   111.74  3.000
 C56  C1    C6   N7    115.88  3.000
 C56  C1    C6   C5    120.81  3.000
 C56  N7    C6   C5    122.87  3.000
 C56  O8    N7   O9    122.95  3.000
 C56  O8    N7   C6    118.62  3.000
 C56  O9    N7   C6    118.34  3.000
 C56  H1    C1   C6    118.80  3.000
 C56  H1    C1   C2    119.19  3.000
 C56  C6    C1   C2    121.98  3.000
 C56  H17   N17  C18   117.68  3.000
 C56  H17   N17  C15   118.25  3.000
 C56  C18   N17  C15   123.50  3.000
 C56  H182  C18  H181  106.89  3.000
 C56  H182  C18  C05   110.09  3.000
 C56  H181  C18  C05   110.74  3.000
 C56  H182  C18  N17   110.28  3.000
 C56  H181  C18  N17   108.89  3.000
 C56  C05   C18  N17   109.91  3.000
 C56  H05   C05  N09   109.15  3.000
 C56  H05   C05  C06   111.57  3.000
 C56  N09   C05  C06   101.58  3.000
 C56  H05   C05  C18   107.98  3.000
 C56  N09   C05  C18   114.31  3.000
 C56  C06   C05  C18   112.20  3.000
 C56  H062  C06  H061  107.24  3.000
 C56  H062  C06  C07   112.87  3.000
 C56  H061  C06  C07   110.95  3.000
 C56  H062  C06  C05   113.32  3.000
 C56  H061  C06  C05   109.26  3.000
 C56  C07   C06  C05   103.20  3.000
 C56  H072  C07  H071  106.72  3.000
 C56  H072  C07  C08   110.45  3.000
 C56  H071  C07  C08   112.36  3.000
 C56  H072  C07  C06   110.75  3.000
 C56  H071  C07  C06   111.97  3.000
 C56  C08   C07  C06   104.65  3.000
 C56  H082  C08  H081  106.47  3.000
 C56  H082  C08  N09   112.17  3.000
 C56  H081  C08  N09   110.58  3.000
 C56  H082  C08  C07   110.52  3.000
 C56  H081  C08  C07   112.17  3.000
 C56  N09   C08  C07   105.03  3.000
 C56  C10   N09  C08   115.81  3.000
 C56  C10   N09  C05   117.50  3.000
 C56  C08   N09  C05   108.35  3.000
 C56  H102  C10  H101  106.50  3.000
 C56  H102  C10  C13   109.11  3.000
 C56  H101  C10  C13   108.78  3.000
 C56  H102  C10  N09   108.06  3.000
 C56  H101  C10  N09   112.14  3.000
 C56  C13   C10  N09   112.06  3.000
 C56  H133  C13  H132  108.18  3.000
 C56  H133  C13  H131  107.97  3.000
 C56  H132  C13  H131  107.39  3.000
 C56  H133  C13  C10   110.95  3.000
 C56  H132  C13  C10   110.46  3.000
 C56  H131  C13  C10   111.74  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
 C56  CONST_01  C5    C4   C3   C2      0.00   0.0  0
 C56  CONST_02  C5    C6   C1   C2      0.00   0.0  0
 C56  CONST_03  C6    C1   C2   C3      0.00   0.0  0
 C56  CONST_04  C6    C5   C4   C3      0.00   0.0  0
 C56  CONST_05  C1    C2   C3   C4      0.00   0.0  0
 C56  CONST_06  C1    C6   C5   C4      0.00   0.0  0
 C56  CONST_07  C4    C3   C2   C15   180.00   0.0  0
 C56  CONST_08  C6    C1   C2   C15   180.00   0.0  0
 C56  CONST_09  N7    C6   C1   C2    180.00   0.0  0
 C56  CONST_10  N10   C5   C4   C3    180.00   0.0  0
 C56  CONST_11  C1    C2   C3   O13   180.00   0.0  0
 C56  CONST_12  C5    C4   C3   O13   180.00   0.0  0
 C56  CONST_13  N7    C6   C5   C4    180.00   0.0  0
 C56  CONST_14  C1    C6   C5   N10   180.00   0.0  0
 C56  CONST_15  H4    C4   C3   C2    180.00   0.0  0
 C56  CONST_16  H1    C1   C2   C3    180.00   0.0  0
 C56  CONST_21  C6    C5   N10  C12   180.00   0.0  0
 C56  CONST_25  C18   N17  C15  C2    180.00   0.0  0
 C56  CONST_26  H17   N17  C15  C2      0.00   0.0  0
 C56  CONST_27  C18   N17  C15  O16     0.00   0.0  0
 C56  Var_01    C08   C07  C06  C05    24.43  30.0  1
 C56  Var_02    C07   C08  N09  C05   -25.16  30.0  1
 C56  Var_03    N09   C08  C07  C06    -0.77  30.0  1
 C56  Var_04    C3    C2   C15  O16   -53.15  30.0  2
 C56  Var_05    C4    C3   O13  C14     4.14  30.0  2
 C56  Var_06    C13   C10  N09  C05   161.61  30.0  3
 C56  Var_07    C05   C18  N17  C15  -159.22  30.0  3
 C56  Var_08    H141  C14  O13  C3     58.29  30.0  3
 C56  Var_09    H121  C12  N10  C5     78.06  30.0  3
 C56  Var_10    H111  C11  N10  C5     -6.21  30.0  3
 C56  Var_11    H131  C13  C10  N09    62.11  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
 C56  chir_01  C05  C06  N09  C18  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
 C56  plan-1  C15  0.020
 C56  plan-1  C2   0.020
 C56  plan-1  C3   0.020
 C56  plan-1  O13  0.020
 C56  plan-1  C4   0.020
 C56  plan-1  C5   0.020
 C56  plan-1  N10  0.020
 C56  plan-1  C6   0.020
 C56  plan-1  N7   0.020
 C56  plan-1  C1   0.020
 C56  plan-1  H1   0.020
 C56  plan-1  H4   0.020
 C56  plan-2  C5   0.020
 C56  plan-2  N10  0.020
 C56  plan-2  C12  0.020
 C56  plan-2  C11  0.020
 C56  plan-3  C6   0.020
 C56  plan-3  N7   0.020
 C56  plan-3  O9   0.020
 C56  plan-3  O8   0.020
 C56  plan-4  O16  0.020
 C56  plan-4  C15  0.020
 C56  plan-4  C2   0.020
 C56  plan-4  N17  0.020
 C56  plan-4  C18  0.020
 C56  plan-4  H17  0.020

