# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 11:40:57 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: N-{5-[(4-nitrobenzyl)amino]-5-oxopentanoyl}glycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CNC(=O)CCCC(=O)NCc1ccc(cc1)[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
 PNC  PNC  N-{5-[(4-nitrobenzyl)amino]-5-oxopentanoyl}glycine  ligand  39  23  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PNC
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
 PNC  C1    C  C      0   0.109  -0.4675   0.9265  -3.5021
 PNC  C2    C  C1     0  -0.282   0.5232   0.0498  -3.0722
 PNC  C3    C  C1     0  -0.252   0.8126  -1.1009  -3.7852
 PNC  C4    C  C      0   0.235   0.0992  -1.3707  -4.9437
 PNC  C5    C  C1     0  -0.254  -0.8947  -0.5132  -5.3961
 PNC  C6    C  C1     0  -0.287  -1.1697   0.6285  -4.6679
 PNC  C7    C  CH2    0  -0.333  -0.7745   2.2125  -2.7755
 PNC  C8    C  CH2    0  -0.573  -0.4134   1.7472   0.9584
 PNC  C9    C  CH2    0  -0.418  -0.2416   0.4230   1.6941
 PNC  C10   C  CH2    0  -0.573   0.2787   0.6452   3.1079
 PNC  C11   C  C      0   0.554   0.5455  -0.6514   3.8444
 PNC  C12   C  CH2    0  -0.411   0.4085  -1.7697   6.0234
 PNC  C13   C  C      0   0.397  -0.1060  -1.4528   7.4426
 PNC  C14   C  C      0   0.558  -0.9727   1.5663  -0.4336
 PNC  N1    N  N      1   0.329   0.3959  -2.5750  -5.6982
 PNC  N2    N  NH1    0  -0.631   0.1842  -0.6635   5.1295
 PNC  N3    N  NH1    0  -0.642  -0.3398   2.2493  -1.4061
 PNC  O2    O  O      0  -0.490  -1.9425   0.8592  -0.6655
 PNC  O4    O  O      0  -0.382  -0.2484  -2.7945  -6.6979
 PNC  O5    O  O     -1  -0.382   1.2732  -3.3013  -5.2921
 PNC  O6    O  O      0  -0.519   1.0798  -1.6102   3.2940
 PNC  O7    O  O      0  -0.600  -0.6239  -0.3343   7.6250
 PNC  O8    O  OC    -1  -0.610   0.0490  -2.3616   8.2764
 PNC  H2    H  H      0   0.263   1.0801   0.2583  -2.1686
 PNC  H3    H  H      0   0.296   1.5848  -1.7689  -3.4325
 PNC  H5    H  H      0   0.296  -1.4512  -0.7243  -6.2974
 PNC  H6    H  H      0   0.270  -1.9471   1.2975  -5.0157
 PNC  H71   H  HCH2   0   0.266  -1.8463   2.4120  -2.8385
 PNC  H72   H  HCH2   0   0.291  -0.2783   3.0324  -3.2968
 PNC  H81   H  HCH2   0   0.268  -1.1102   2.3881   1.5084
 PNC  H82   H  HCH2   0   0.252   0.5382   2.2830   0.9288
 PNC  H91   H  HCH2   0   0.236   0.4519  -0.2169   1.1450
 PNC  H92   H  HCH2   0   0.238  -1.1973  -0.1034   1.7316
 PNC  H101  H  HCH2   0   0.248  -0.4166   1.2735   3.6700
 PNC  H102  H  HCH2   0   0.263   1.2246   1.1966   3.0686
 PNC  H121  H  HCH2   0   0.239   1.4741  -2.0137   6.0808
 PNC  H122  H  HCH2   0   0.239  -0.0926  -2.6723   5.6598
 PNC  HN2   H  HNH1   0   0.385  -0.2604   0.1404   5.5487
 PNC  HN3   H  HNH1   0   0.408   0.4694   2.8012  -1.1770

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
 PNC  C1   C2    aromatic  1.391  0.020  1.391
 PNC  C1   C6    aromatic  1.393  0.020  1.393
 PNC  C1   C7    single    1.509  0.020  1.509
 PNC  C2   C3    aromatic  1.384  0.020  1.384
 PNC  C2   H2    single    0.930  0.020  1.080
 PNC  C3   C4    aromatic  1.387  0.020  1.387
 PNC  C3   H3    single    0.930  0.020  1.080
 PNC  C4   C5    aromatic  1.388  0.020  1.388
 PNC  C4   N1    single    1.452  0.020  1.452
 PNC  C5   C6    aromatic  1.382  0.020  1.382
 PNC  C5   H5    single    0.930  0.020  1.080
 PNC  C6   H6    single    0.930  0.020  1.080
 PNC  C7   N3    single    1.437  0.020  1.437
 PNC  C7   H71   single    0.970  0.020  1.090
 PNC  C7   H72   single    0.970  0.020  1.090
 PNC  C8   C9    single    1.525  0.020  1.525
 PNC  C8   C14   single    1.511  0.020  1.511
 PNC  C8   H81   single    0.970  0.020  1.090
 PNC  C8   H82   single    0.970  0.020  1.090
 PNC  C9   C10   single    1.523  0.020  1.523
 PNC  C9   H91   single    0.970  0.020  1.090
 PNC  C9   H92   single    0.970  0.020  1.090
 PNC  C10  C11   single    1.515  0.020  1.515
 PNC  C10  H101  single    0.970  0.020  1.090
 PNC  C10  H102  single    0.970  0.020  1.090
 PNC  C11  N2    single    1.335  0.020  1.335
 PNC  C11  O6    double    1.228  0.020  1.228
 PNC  C12  C13   single    1.542  0.020  1.542
 PNC  C12  N2    single    1.440  0.020  1.440
 PNC  C12  H121  single    0.970  0.020  1.090
 PNC  C12  H122  single    0.970  0.020  1.090
 PNC  C13  O7    deloc     1.246  0.020  1.246
 PNC  C13  O8    deloc     1.243  0.020  1.243
 PNC  C14  N3    single    1.346  0.020  1.346
 PNC  C14  O2    double    1.222  0.020  1.222
 PNC  N1   O4    double    1.209  0.020  1.209
 PNC  N1   O5    single    1.209  0.020  1.209
 PNC  N2   HN2   single    0.860  0.020  1.020
 PNC  N3   HN3   single    0.860  0.020  1.020

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
 PNC  C7    C1   C6    118.87  3.000
 PNC  C7    C1   C2    122.23  3.000
 PNC  C6    C1   C2    118.87  3.000
 PNC  H2    C2   C3    118.87  3.000
 PNC  H2    C2   C1    120.22  3.000
 PNC  C3    C2   C1    120.91  3.000
 PNC  H3    C3   C4    121.34  3.000
 PNC  H3    C3   C2    119.69  3.000
 PNC  C4    C3   C2    118.97  3.000
 PNC  N1    C4   C5    119.29  3.000
 PNC  N1    C4   C3    119.37  3.000
 PNC  C5    C4   C3    121.34  3.000
 PNC  H5    C5   C6    119.92  3.000
 PNC  H5    C5   C4    121.33  3.000
 PNC  C6    C5   C4    118.76  3.000
 PNC  H6    C6   C5    118.95  3.000
 PNC  H6    C6   C1    119.89  3.000
 PNC  C5    C6   C1    121.16  3.000
 PNC  H72   C7   H71   106.35  3.000
 PNC  H72   C7   N3    107.37  3.000
 PNC  H71   C7   N3    110.32  3.000
 PNC  H72   C7   C1    108.53  3.000
 PNC  H71   C7   C1    109.13  3.000
 PNC  N3    C7   C1    114.79  3.000
 PNC  H82   C8   H81   106.31  3.000
 PNC  H82   C8   C14   110.86  3.000
 PNC  H81   C8   C14   107.29  3.000
 PNC  H82   C8   C9    109.94  3.000
 PNC  H81   C8   C9    109.74  3.000
 PNC  C14   C8   C9    112.48  3.000
 PNC  H92   C9   H91   106.91  3.000
 PNC  H92   C9   C10   109.73  3.000
 PNC  H91   C9   C10   109.60  3.000
 PNC  H92   C9   C8    109.68  3.000
 PNC  H91   C9   C8    109.75  3.000
 PNC  C10   C9   C8    111.09  3.000
 PNC  H102  C10  H101  106.17  3.000
 PNC  H102  C10  C11   107.23  3.000
 PNC  H101  C10  C11   110.74  3.000
 PNC  H102  C10  C9    109.58  3.000
 PNC  H101  C10  C9    110.13  3.000
 PNC  C11   C10  C9    112.75  3.000
 PNC  O6    C11  N2    122.83  3.000
 PNC  O6    C11  C10   121.80  3.000
 PNC  N2    C11  C10   115.35  3.000
 PNC  H122  C12  H121  106.22  3.000
 PNC  H122  C12  N2    110.86  3.000
 PNC  H121  C12  N2    110.82  3.000
 PNC  H122  C12  C13   108.81  3.000
 PNC  H121  C12  C13   108.80  3.000
 PNC  N2    C12  C13   111.19  3.000
 PNC  O8    C13  O7    127.58  3.000
 PNC  O8    C13  C12   115.18  3.000
 PNC  O7    C13  C12   117.24  3.000
 PNC  O2    C14  N3    121.96  3.000
 PNC  O2    C14  C8    122.52  3.000
 PNC  N3    C14  C8    115.51  3.000
 PNC  O5    N1   O4    123.72  3.000
 PNC  O5    N1   C4    118.16  3.000
 PNC  O4    N1   C4    118.12  3.000
 PNC  HN2   N2   C12   114.99  3.000
 PNC  HN2   N2   C11   120.77  3.000
 PNC  C12   N2   C11   124.23  3.000
 PNC  HN3   N3   C14   119.47  3.000
 PNC  HN3   N3   C7    118.32  3.000
 PNC  C14   N3   C7    122.21  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
 PNC  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 PNC  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 PNC  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 PNC  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 PNC  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 PNC  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 PNC  CONST_07  N1   C4   C3   C2    180.00   0.0  0
 PNC  CONST_08  C7   C1   C2   C3    180.00   0.0  0
 PNC  CONST_09  C7   C1   C6   C5    180.00   0.0  0
 PNC  CONST_10  N1   C4   C5   C6    180.00   0.0  0
 PNC  CONST_11  H3   C3   C2   C1    180.00   0.0  0
 PNC  CONST_12  H5   C5   C6   C1    180.00   0.0  0
 PNC  CONST_13  H6   C6   C1   C2    180.00   0.0  0
 PNC  CONST_14  H2   C2   C3   C4    180.00   0.0  0
 PNC  CONST_15  O4   N1   C4   C3    180.00   0.0  0
 PNC  CONST_16  O5   N1   C4   C3      0.00   0.0  0
 PNC  CONST_17  O4   N1   C4   C5      0.00   0.0  0
 PNC  CONST_18  O5   N1   C4   C5    180.00   0.0  0
 PNC  CONST_19  C8   C14  N3   C7    180.00   0.0  0
 PNC  CONST_20  O2   C14  N3   C7      0.00   0.0  0
 PNC  CONST_21  C12  N2   C11  C10   180.00   0.0  0
 PNC  CONST_22  O6   C11  N2   C12     0.00   0.0  0
 PNC  CONST_23  HN3  N3   C14  C8      0.00   0.0  0
 PNC  CONST_24  HN2  N2   C11  C10     0.00   0.0  0
 PNC  Var_01    N3   C7   C1   C2    -20.93  30.0  2
 PNC  Var_02    C14  N3   C7   C1    -73.96  30.0  3
 PNC  Var_03    C11  C10  C9   C8   -176.42  30.0  3
 PNC  Var_04    N3   C14  C8   C9   -133.27  30.0  3
 PNC  Var_05    N2   C11  C10  C9   -139.57  30.0  3
 PNC  Var_06    C14  C8   C9   C10  -178.09  30.0  1
 PNC  Var_07    C13  C12  N2   C11   179.03  30.0  1
 PNC  Var_08    O7   C13  C12  N2     -0.03  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
 PNC  plan-1  C1   0.020
 PNC  plan-1  C2   0.020
 PNC  plan-1  C3   0.020
 PNC  plan-1  C4   0.020
 PNC  plan-1  C5   0.020
 PNC  plan-1  C6   0.020
 PNC  plan-1  C7   0.020
 PNC  plan-1  N1   0.020
 PNC  plan-1  H2   0.020
 PNC  plan-1  H3   0.020
 PNC  plan-1  H5   0.020
 PNC  plan-1  H6   0.020
 PNC  plan-2  C10  0.020
 PNC  plan-2  C11  0.020
 PNC  plan-2  C12  0.020
 PNC  plan-2  N2   0.020
 PNC  plan-2  O6   0.020
 PNC  plan-2  HN2  0.020
 PNC  plan-3  C7   0.020
 PNC  plan-3  C8   0.020
 PNC  plan-3  C14  0.020
 PNC  plan-3  N3   0.020
 PNC  plan-3  O2   0.020
 PNC  plan-3  HN3  0.020
 PNC  plan-4  C4   0.020
 PNC  plan-4  N1   0.020
 PNC  plan-4  O4   0.020
 PNC  plan-4  O5   0.020
 PNC  plan-5  C12  0.020
 PNC  plan-5  C13  0.020
 PNC  plan-5  O7   0.020
 PNC  plan-5  O8   0.020

