# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 18:34:43 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 4-(dimethylamino)-N-{[(2S)-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
 C57  C57  4-(dimethylamino)-N-{[(2S)-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_C57
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
 C57  O16   O  O      0  -0.483  -1.4328  -2.1887  -0.7863
 C57  C15   C  C      0   0.523  -1.0311  -1.4561   0.1047
 C57  C2    C  CR6    0  -0.200   0.3658  -0.9229   0.1028
 C57  C3    C  CR6    0   0.448   1.4814  -1.7733  -0.0561
 C57  O13   O  O2     0  -0.448   1.2234  -3.0780  -0.0936
 C57  C14   C  CH3    0  -0.447   2.2973  -4.0014  -0.1668
 C57  C4    C  CR16   0  -0.541   2.7548  -1.2433  -0.1620
 C57  C5    C  CR6    0   0.450   3.0035   0.1428  -0.1084
 C57  N10   N  NT     0  -0.472   4.2526   0.6132  -0.3492
 C57  C12   C  CH3    0  -0.562   5.3870  -0.2846  -0.3047
 C57  C11   C  CH3    0  -0.545   4.4910   1.8344  -1.0942
 C57  C6    C  CR6    0   0.129   1.8818   0.9673   0.1589
 C57  N7    N  N      1   0.332   1.9966   2.3435   0.5497
 C57  O9    O  O     -1  -0.398   1.0506   3.0802   0.3519
 C57  O8    O  O      0  -0.394   3.0067   2.7052   1.1165
 C57  C1    C  CR16   0  -0.294   0.5981   0.4243   0.2179
 C57  N17   N  NH1    0  -0.620  -1.7732  -1.0594   1.1518
 C57  C18   C  CH2    0  -0.267  -3.1901  -1.2934   1.2705
 C57  C07   C  CH2    0  -0.470  -5.6815  -0.5467  -0.6200
 C57  C06   C  CH2    0  -0.474  -5.5081  -0.3880   0.8867
 C57  C05   C  CR15   0  -0.081  -4.0241  -0.0324   1.0187
 C57  N09   N  NR5    0  -0.402  -3.6549   0.5949  -0.2503
 C57  C10   C  CH2    0  -0.288  -3.0157   1.8861  -0.1403
 C57  C08   C  CH2    0  -0.258  -4.7974   0.5697  -1.1531
 C57  C13   C  CH3    0  -0.675  -2.3770   2.3335  -1.4437
 C57  H1    H  HCR6   0   0.299  -0.2389   1.0861   0.3933
 C57  H17   H  HNH1   0   0.401  -1.3229  -0.5243   1.8766
 C57  H4    H  HCR6   0   0.312   3.5849  -1.9051  -0.3537
 C57  H141  H  HCH3   0   0.238   2.9993  -3.8692   0.6589
 C57  H142  H  HCH3   0   0.270   1.8520  -4.9901  -0.1005
 C57  H143  H  HCH3   0   0.239   2.8367  -3.9207  -1.1132
 C57  H121  H  HCH3   0   0.240   5.4874  -0.8884  -1.2127
 C57  H122  H  HCH3   0   0.271   6.2929   0.3090  -0.1965
 C57  H123  H  HCH3   0   0.257   5.3274  -0.9481   0.5561
 C57  H111  H  HCH3   0   0.250   3.5702   2.2401  -1.5071
 C57  H112  H  HCH3   0   0.248   4.9798   2.6016  -0.4934
 C57  H113  H  HCH3   0   0.257   5.1388   1.6032  -1.9417
 C57  H181  H  HCH2   0   0.241  -3.4631  -2.0691   0.5555
 C57  H182  H  HCH2   0   0.241  -3.4055  -1.6794   2.2699
 C57  H05   H  HCR5   0   0.228  -3.8653   0.6619   1.8526
 C57  H071  H  HCH2   0   0.228  -5.3159  -1.5211  -0.9530
 C57  H072  H  HCH2   0   0.241  -6.7166  -0.4537  -0.9486
 C57  H061  H  HCH2   0   0.237  -6.1262   0.4378   1.2467
 C57  H062  H  HCH2   0   0.240  -5.7869  -1.2771   1.4553
 C57  H081  H  HCH2   0   0.224  -4.4898   0.4027  -2.1884
 C57  H082  H  HCH2   0   0.187  -5.3521   1.5227  -1.1303
 C57  H101  H  HCH2   0   0.189  -3.7253   2.6625   0.1980
 C57  H102  H  HCH2   0   0.224  -2.2445   1.8281   0.6312
 C57  H131  H  HCH3   0   0.220  -1.6472   1.6004  -1.7908
 C57  H132  H  HCH3   0   0.229  -3.1176   2.4705  -2.2327
 C57  H133  H  HCH3   0   0.228  -1.8630   3.2853  -1.3071

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
 C57  O16  C15   double    1.221  0.020  1.221
 C57  C15  C2    single    1.495  0.020  1.495
 C57  C15  N17   single    1.343  0.020  1.343
 C57  C2   C3    aromatic  1.412  0.020  1.412
 C57  C2   C1    aromatic  1.372  0.020  1.372
 C57  C6   C1    aromatic  1.395  0.020  1.395
 C57  C3   O13   single    1.330  0.020  1.330
 C57  C3   C4    aromatic  1.383  0.020  1.383
 C57  O13  C14   single    1.418  0.020  1.418
 C57  C4   C5    aromatic  1.409  0.020  1.409
 C57  C5   N10   single    1.356  0.020  1.356
 C57  C5   C6    aromatic  1.417  0.020  1.417
 C57  N10  C12   single    1.447  0.020  1.447
 C57  N10  C11   single    1.450  0.020  1.450
 C57  C6   N7    single    1.435  0.020  1.435
 C57  N7   O9    single    1.215  0.020  1.215
 C57  N7   O8    double    1.213  0.020  1.213
 C57  N17  C18   single    1.441  0.020  1.441
 C57  C18  C05   single    1.533  0.020  1.533
 C57  C07  C06   single    1.525  0.020  1.525
 C57  C07  C08   single    1.521  0.020  1.521
 C57  C06  C05   single    1.532  0.020  1.532
 C57  C05  N09   single    1.463  0.020  1.463
 C57  N09  C10   single    1.445  0.020  1.445
 C57  N09  C08   single    1.456  0.020  1.456
 C57  C10  C13   single    1.519  0.020  1.519
 C57  C1   H1    single    0.930  0.020  1.080
 C57  N17  H17   single    0.860  0.020  1.020
 C57  C4   H4    single    0.930  0.020  1.080
 C57  C14  H141  single    0.970  0.020  1.090
 C57  C14  H142  single    0.970  0.020  1.090
 C57  C14  H143  single    0.970  0.020  1.090
 C57  C12  H121  single    0.970  0.020  1.090
 C57  C12  H122  single    0.970  0.020  1.090
 C57  C12  H123  single    0.970  0.020  1.090
 C57  C13  H131  single    0.970  0.020  1.090
 C57  C13  H132  single    0.970  0.020  1.090
 C57  C13  H133  single    0.970  0.020  1.090
 C57  C11  H111  single    0.970  0.020  1.090
 C57  C11  H112  single    0.970  0.020  1.090
 C57  C11  H113  single    0.970  0.020  1.090
 C57  C18  H181  single    0.970  0.020  1.090
 C57  C18  H182  single    0.970  0.020  1.090
 C57  C05  H05   single    0.970  0.020  1.090
 C57  C07  H071  single    0.970  0.020  1.090
 C57  C07  H072  single    0.970  0.020  1.090
 C57  C06  H061  single    0.970  0.020  1.090
 C57  C06  H062  single    0.970  0.020  1.090
 C57  C08  H081  single    0.970  0.020  1.090
 C57  C08  H082  single    0.970  0.020  1.090
 C57  C10  H101  single    0.970  0.020  1.090
 C57  C10  H102  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
 C57  N17   C15  C2    114.32  3.000
 C57  N17   C15  O16   124.34  3.000
 C57  C2    C15  O16   121.35  3.000
 C57  C1    C2   C3    117.86  3.000
 C57  C1    C2   C15   120.55  3.000
 C57  C3    C2   C15   121.57  3.000
 C57  C4    C3   O13   123.50  3.000
 C57  C4    C3   C2    120.35  3.000
 C57  O13   C3   C2    116.15  3.000
 C57  C14   O13  C3    119.55  3.000
 C57  H143  C14  H142  108.82  3.000
 C57  H143  C14  H141  109.20  3.000
 C57  H142  C14  H141  109.13  3.000
 C57  H143  C14  O13   111.75  3.000
 C57  H142  C14  O13   106.20  3.000
 C57  H141  C14  O13   111.65  3.000
 C57  H4    C4   C5    118.31  3.000
 C57  H4    C4   C3    119.14  3.000
 C57  C5    C4   C3    122.44  3.000
 C57  C6    C5   N10   124.09  3.000
 C57  C6    C5   C4    116.08  3.000
 C57  N10   C5   C4    119.80  3.000
 C57  C11   N10  C12   114.16  3.000
 C57  C11   N10  C5    122.32  3.000
 C57  C12   N10  C5    120.08  3.000
 C57  H123  C12  H122  107.42  3.000
 C57  H123  C12  H121  108.95  3.000
 C57  H122  C12  H121  107.87  3.000
 C57  H123  C12  N10   111.06  3.000
 C57  H122  C12  N10   108.48  3.000
 C57  H121  C12  N10   112.86  3.000
 C57  H113  C11  H112  108.11  3.000
 C57  H113  C11  H111  106.66  3.000
 C57  H112  C11  H111  109.05  3.000
 C57  H113  C11  N10   108.55  3.000
 C57  H112  C11  N10   112.53  3.000
 C57  H111  C11  N10   111.71  3.000
 C57  C1    C6   N7    115.80  3.000
 C57  N7    C6   C5    123.08  3.000
 C57  C1    C6   C5    120.65  3.000
 C57  O8    N7   O9    122.92  3.000
 C57  O8    N7   C6    118.65  3.000
 C57  O9    N7   C6    118.34  3.000
 C57  H1    C1   C6    118.75  3.000
 C57  H1    C1   C2    118.92  3.000
 C57  C6    C1   C2    122.30  3.000
 C57  H17   N17  C18   117.81  3.000
 C57  H17   N17  C15   118.09  3.000
 C57  C18   N17  C15   124.02  3.000
 C57  H182  C18  H181  107.41  3.000
 C57  H182  C18  C05   109.49  3.000
 C57  H181  C18  C05   109.98  3.000
 C57  H182  C18  N17   109.05  3.000
 C57  H181  C18  N17   107.93  3.000
 C57  C05   C18  N17   112.82  3.000
 C57  H072  C07  H071  107.57  3.000
 C57  H072  C07  C08   112.57  3.000
 C57  H071  C07  C08   110.69  3.000
 C57  H072  C07  C06   113.39  3.000
 C57  H071  C07  C06   110.85  3.000
 C57  C08   C07  C06   101.76  3.000
 C57  H062  C06  H061  107.43  3.000
 C57  H062  C06  C05   113.06  3.000
 C57  H061  C06  C05   110.14  3.000
 C57  H062  C06  C07   113.63  3.000
 C57  H061  C06  C07   109.87  3.000
 C57  C05   C06  C07   102.68  3.000
 C57  H05   C05  N09   110.59  3.000
 C57  H05   C05  C06   110.66  3.000
 C57  N09   C05  C06   105.62  3.000
 C57  H05   C05  C18   108.49  3.000
 C57  N09   C05  C18   110.98  3.000
 C57  C06   C05  C18   110.51  3.000
 C57  C08   N09  C10   114.19  3.000
 C57  C08   N09  C05   109.41  3.000
 C57  C10   N09  C05   115.39  3.000
 C57  H102  C10  H101  105.94  3.000
 C57  H102  C10  C13   108.95  3.000
 C57  H101  C10  C13   109.01  3.000
 C57  H102  C10  N09   108.58  3.000
 C57  H101  C10  N09   111.54  3.000
 C57  C13   C10  N09   112.58  3.000
 C57  H082  C08  H081  107.05  3.000
 C57  H082  C08  N09   111.52  3.000
 C57  H081  C08  N09   111.66  3.000
 C57  H082  C08  C07   109.56  3.000
 C57  H081  C08  C07   112.56  3.000
 C57  N09   C08  C07   104.57  3.000
 C57  H133  C13  H132  107.52  3.000
 C57  H133  C13  H131  108.13  3.000
 C57  H132  C13  H131  107.96  3.000
 C57  H133  C13  C10   110.36  3.000
 C57  H132  C13  C10   111.85  3.000
 C57  H131  C13  C10   110.87  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
 C57  CONST_01  C5    C4   C3   C2      0.00   0.0  0
 C57  CONST_02  C5    C6   C1   C2      0.00   0.0  0
 C57  CONST_03  C6    C1   C2   C3      0.00   0.0  0
 C57  CONST_04  C6    C5   C4   C3      0.00   0.0  0
 C57  CONST_05  C1    C2   C3   C4      0.00   0.0  0
 C57  CONST_06  C1    C6   C5   C4      0.00   0.0  0
 C57  CONST_07  C4    C3   C2   C15   180.00   0.0  0
 C57  CONST_08  C6    C1   C2   C15   180.00   0.0  0
 C57  CONST_09  N7    C6   C1   C2    180.00   0.0  0
 C57  CONST_10  N10   C5   C4   C3    180.00   0.0  0
 C57  CONST_11  C1    C2   C3   O13   180.00   0.0  0
 C57  CONST_12  C5    C4   C3   O13   180.00   0.0  0
 C57  CONST_13  N7    C6   C5   C4    180.00   0.0  0
 C57  CONST_14  C1    C6   C5   N10   180.00   0.0  0
 C57  CONST_15  H4    C4   C3   C2    180.00   0.0  0
 C57  CONST_16  H1    C1   C2   C3    180.00   0.0  0
 C57  CONST_21  C6    C5   N10  C12   180.00   0.0  0
 C57  CONST_25  C18   N17  C15  C2    180.00   0.0  0
 C57  CONST_26  H17   N17  C15  C2      0.00   0.0  0
 C57  CONST_27  C18   N17  C15  O16     0.00   0.0  0
 C57  Var_01    C05   N09  C08  C07   -21.52  30.0  1
 C57  Var_02    N09   C08  C07  C06    37.19  30.0  1
 C57  Var_03    C08   C07  C06  C05   -38.42  30.0  1
 C57  Var_04    C3    C2   C15  O16   -51.20  30.0  2
 C57  Var_05    C4    C3   O13  C14     3.86  30.0  2
 C57  Var_06    C13   C10  N09  C05   166.82  30.0  3
 C57  Var_07    C05   C18  N17  C15  -105.06  30.0  3
 C57  Var_08    H141  C14  O13  C3     56.47  30.0  3
 C57  Var_09    H121  C12  N10  C5     78.84  30.0  3
 C57  Var_10    H111  C11  N10  C5     -6.06  30.0  3
 C57  Var_11    H131  C13  C10  N09   -57.35  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
 C57  chir_01  C05  C18  C06  N09  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
 C57  plan-1  C15  0.020
 C57  plan-1  C2   0.020
 C57  plan-1  C3   0.020
 C57  plan-1  O13  0.020
 C57  plan-1  C4   0.020
 C57  plan-1  C5   0.020
 C57  plan-1  N10  0.020
 C57  plan-1  C6   0.020
 C57  plan-1  N7   0.020
 C57  plan-1  C1   0.020
 C57  plan-1  H1   0.020
 C57  plan-1  H4   0.020
 C57  plan-2  C5   0.020
 C57  plan-2  N10  0.020
 C57  plan-2  C12  0.020
 C57  plan-2  C11  0.020
 C57  plan-3  C6   0.020
 C57  plan-3  N7   0.020
 C57  plan-3  O9   0.020
 C57  plan-3  O8   0.020
 C57  plan-4  O16  0.020
 C57  plan-4  C15  0.020
 C57  plan-4  C2   0.020
 C57  plan-4  N17  0.020
 C57  plan-4  C18  0.020
 C57  plan-4  H17  0.020

