# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 18:14:00 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 6-{[(4-hydroxy-3-nitrophenyl)acetyl]amino}hexanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(CC(=O)NCCCCCC([O-])=O)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
 NPC  NPC  6-{[(4-hydroxy-3-nitrophenyl)acetyl]amino}hexanoate  ligand  39  22  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NPC
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
 NPC  C1    C  CR6    0   0.134   2.7779   0.9269   0.5930
 NPC  C2    C  CR16   0  -0.350   3.5351  -0.2019   0.7997
 NPC  C3    C  CR6    0   0.179   4.8425  -0.2908   0.3092
 NPC  N3    N  N      1   0.363   5.5803  -1.4931   0.5675
 NPC  O3A   O  O     -1  -0.368   5.0574  -2.3878   1.1827
 NPC  O3B   O  O      0  -0.431   6.7290  -1.5694   0.1493
 NPC  C4    C  CR6    0   0.355   5.4209   0.7676  -0.4153
 NPC  O4    O  OH1    0  -0.603   6.6489   0.7746  -0.9159
 NPC  C5    C  CR16   0  -0.339   4.6362   1.9079  -0.6173
 NPC  C6    C  CR16   0  -0.253   3.3538   1.9830  -0.1270
 NPC  C7    C  CH2    0  -0.676   1.3744   1.0206   1.1075
 NPC  C8    C  C      0   0.563   0.3418   0.8739  -0.0023
 NPC  O8    O  O      0  -0.491   0.5724   1.2202  -1.1519
 NPC  N9    N  NH1    0  -0.640  -0.8380   0.3809   0.3928
 NPC  C10   C  CH2    0  -0.235  -1.9848   0.2503  -0.4835
 NPC  C11   C  CH2    0  -0.467  -3.2618   0.0737   0.3218
 NPC  C12   C  CH2    0  -0.415  -4.4910  -0.0386  -0.5701
 NPC  C13   C  CH2    0  -0.403  -5.7834  -0.2035   0.2205
 NPC  C14   C  CH2    0  -0.582  -7.0079  -0.3016  -0.6738
 NPC  C15   C  C      0   0.411  -8.3593  -0.4587   0.0450
 NPC  O15   O  O      0  -0.610  -8.3687  -0.3982   1.2903
 NPC  O16   O  OC    -1  -0.635  -9.3538  -0.6295  -0.6927
 NPC  H2    H  HCR6   0   0.294   3.1172  -1.0327   1.3512
 NPC  HO4   H  HOH1   0   0.482   7.0835  -0.0687  -0.6909
 NPC  H5    H  HCR6   0   0.285   5.0640   2.7363  -1.1666
 NPC  H6    H  HCR6   0   0.272   2.7857   2.8891  -0.2931
 NPC  H71   H  HCH2   0   0.281   1.2045   0.2810   1.8918
 NPC  H72   H  HCH2   0   0.301   1.2100   2.0001   1.5674
 NPC  HN9   H  HNH1   0   0.402  -0.9385   0.0742   1.3470
 NPC  H101  H  HCH2   0   0.233  -2.0609   1.1437  -1.1070
 NPC  H102  H  HCH2   0   0.229  -1.8525  -0.5990  -1.1619
 NPC  H111  H  HCH2   0   0.226  -3.1818  -0.8222   0.9471
 NPC  H112  H  HCH2   0   0.227  -3.3797   0.9215   1.0039
 NPC  H121  H  HCH2   0   0.210  -4.5615   0.8531  -1.2032
 NPC  H122  H  HCH2   0   0.211  -4.3680  -0.8852  -1.2547
 NPC  H131  H  HCH2   0   0.203  -5.7098  -1.0961   0.8494
 NPC  H132  H  HCH2   0   0.203  -5.8953   0.6389   0.9091
 NPC  H141  H  HCH2   0   0.218  -7.0664   0.5889  -1.3121
 NPC  H142  H  HCH2   0   0.215  -6.8893  -1.1382  -1.3720

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
 NPC  C1   C2    aromatic  1.375  0.020  1.375
 NPC  C1   C6    aromatic  1.402  0.020  1.402
 NPC  C1   C7    single    1.498  0.020  1.498
 NPC  C2   C3    aromatic  1.399  0.020  1.399
 NPC  C2   H2    single    0.930  0.020  1.080
 NPC  C3   N3    single    1.434  0.020  1.434
 NPC  C3   C4    aromatic  1.407  0.020  1.407
 NPC  N3   O3A   single    1.205  0.020  1.205
 NPC  N3   O3B   double    1.225  0.020  1.225
 NPC  C4   O4    single    1.326  0.020  1.326
 NPC  C4   C5    aromatic  1.399  0.020  1.399
 NPC  O4   HO4   single    0.850  0.020  0.980
 NPC  C5   C6    aromatic  1.375  0.020  1.375
 NPC  C5   H5    single    0.930  0.020  1.080
 NPC  C6   H6    single    0.930  0.020  1.080
 NPC  C7   C8    single    1.523  0.020  1.523
 NPC  C7   H71   single    0.970  0.020  1.090
 NPC  C7   H72   single    0.970  0.020  1.090
 NPC  C8   O8    double    1.223  0.020  1.223
 NPC  C8   N9    single    1.338  0.020  1.338
 NPC  N9   C10   single    1.449  0.020  1.449
 NPC  N9   HN9   single    0.860  0.020  1.020
 NPC  C10  C11   single    1.520  0.020  1.520
 NPC  C10  H101  single    0.970  0.020  1.090
 NPC  C10  H102  single    0.970  0.020  1.090
 NPC  C11  C12   single    1.523  0.020  1.523
 NPC  C11  H111  single    0.970  0.020  1.090
 NPC  C11  H112  single    0.970  0.020  1.090
 NPC  C12  C13   single    1.524  0.020  1.524
 NPC  C12  H121  single    0.970  0.020  1.090
 NPC  C12  H122  single    0.970  0.020  1.090
 NPC  C13  C14   single    1.520  0.020  1.520
 NPC  C13  H131  single    0.970  0.020  1.090
 NPC  C13  H132  single    0.970  0.020  1.090
 NPC  C14  C15   single    1.539  0.020  1.539
 NPC  C14  H141  single    0.970  0.020  1.090
 NPC  C14  H142  single    0.970  0.020  1.090
 NPC  C15  O15   deloc     1.247  0.020  1.247
 NPC  C15  O16   deloc     1.250  0.020  1.250

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
 NPC  C7    C1   C6    120.95  3.000
 NPC  C7    C1   C2    121.05  3.000
 NPC  C6    C1   C2    118.00  3.000
 NPC  H2    C2   C3    119.42  3.000
 NPC  H2    C2   C1    119.65  3.000
 NPC  C3    C2   C1    120.93  3.000
 NPC  C4    C3   N3    120.79  3.000
 NPC  C4    C3   C2    121.12  3.000
 NPC  N3    C3   C2    118.09  3.000
 NPC  O3B   N3   O3A   122.34  3.000
 NPC  O3B   N3   C3    118.25  3.000
 NPC  O3A   N3   C3    119.41  3.000
 NPC  C5    C4   O4    117.43  3.000
 NPC  C5    C4   C3    117.19  3.000
 NPC  O4    C4   C3    125.38  3.000
 NPC  HO4   O4   C4    108.73  3.000
 NPC  H5    C5   C6    120.53  3.000
 NPC  H5    C5   C4    118.39  3.000
 NPC  C6    C5   C4    121.08  3.000
 NPC  H6    C6   C5    118.72  3.000
 NPC  H6    C6   C1    119.60  3.000
 NPC  C5    C6   C1    121.67  3.000
 NPC  H72   C7   H71   106.32  3.000
 NPC  H72   C7   C8    106.89  3.000
 NPC  H71   C7   C8    110.67  3.000
 NPC  H72   C7   C1    109.94  3.000
 NPC  H71   C7   C1    110.51  3.000
 NPC  C8    C7   C1    112.27  3.000
 NPC  N9    C8   O8    123.24  3.000
 NPC  N9    C8   C7    114.71  3.000
 NPC  O8    C8   C7    122.01  3.000
 NPC  HN9   N9   C10   117.80  3.000
 NPC  HN9   N9   C8    118.67  3.000
 NPC  C10   N9   C8    123.53  3.000
 NPC  H102  C10  H101  106.82  3.000
 NPC  H102  C10  C11   109.85  3.000
 NPC  H101  C10  C11   109.82  3.000
 NPC  H102  C10  N9    110.42  3.000
 NPC  H101  C10  N9    109.06  3.000
 NPC  C11   C10  N9    110.79  3.000
 NPC  H112  C11  H111  106.60  3.000
 NPC  H112  C11  C12   109.58  3.000
 NPC  H111  C11  C12   109.45  3.000
 NPC  H112  C11  C10   109.31  3.000
 NPC  H111  C11  C10   109.64  3.000
 NPC  C12   C11  C10   112.11  3.000
 NPC  H122  C12  H121  105.95  3.000
 NPC  H122  C12  C13   109.61  3.000
 NPC  H121  C12  C13   109.46  3.000
 NPC  H122  C12  C11   109.41  3.000
 NPC  H121  C12  C11   109.29  3.000
 NPC  C13   C12  C11   112.87  3.000
 NPC  H132  C13  H131  105.86  3.000
 NPC  H132  C13  C14   109.75  3.000
 NPC  H131  C13  C14   109.86  3.000
 NPC  H132  C13  C12   109.27  3.000
 NPC  H131  C13  C12   109.23  3.000
 NPC  C14   C13  C12   112.65  3.000
 NPC  H142  C14  H141  104.75  3.000
 NPC  H142  C14  C15   108.35  3.000
 NPC  H141  C14  C15   107.93  3.000
 NPC  H142  C14  C13   109.69  3.000
 NPC  H141  C14  C13   109.44  3.000
 NPC  C15   C14  C13   116.07  3.000
 NPC  O16   C15  O15   126.16  3.000
 NPC  O16   C15  C14   115.91  3.000
 NPC  O15   C15  C14   117.92  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
 NPC  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 NPC  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 NPC  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 NPC  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 NPC  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 NPC  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 NPC  CONST_07  N3   C3   C2   C1    180.00   0.0  0
 NPC  CONST_08  O4   C4   C3   C2    180.00   0.0  0
 NPC  CONST_09  C7   C1   C2   C3    180.00   0.0  0
 NPC  CONST_10  C5   C4   C3   N3    180.00   0.0  0
 NPC  CONST_11  C6   C5   C4   O4    180.00   0.0  0
 NPC  CONST_12  C7   C1   C6   C5    180.00   0.0  0
 NPC  CONST_13  H5   C5   C6   C1    180.00   0.0  0
 NPC  CONST_14  H6   C6   C1   C2    180.00   0.0  0
 NPC  CONST_15  H2   C2   C3   C4    180.00   0.0  0
 NPC  CONST_16  O3A  N3   C3   C2      0.00   0.0  0
 NPC  CONST_17  O3B  N3   C3   C2    180.00   0.0  0
 NPC  CONST_18  C4   C3   N3   O3A   180.00   0.0  0
 NPC  CONST_19  C4   C3   N3   O3B     0.00   0.0  0
 NPC  CONST_20  C10  N9   C8   C7    180.00   0.0  0
 NPC  CONST_21  C10  N9   C8   O8      0.00   0.0  0
 NPC  CONST_22  HN9  N9   C8   C7      0.00   0.0  0
 NPC  Var_01    C8   C7   C1   C2   -105.24  30.0  2
 NPC  Var_02    O8   C8   C7   C1    -29.50  30.0  3
 NPC  Var_03    C11  C10  N9   C8   -162.62  30.0  3
 NPC  Var_04    C12  C11  C10  N9    178.85  30.0  3
 NPC  Var_05    C13  C12  C11  C10  -179.47  30.0  3
 NPC  Var_06    C14  C13  C12  C11   179.45  30.0  3
 NPC  Var_07    C15  C14  C13  C12  -179.53  30.0  3
 NPC  Var_08    O15  C15  C14  C13     5.02  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
 NPC  plan-1  C1   0.020
 NPC  plan-1  C2   0.020
 NPC  plan-1  C3   0.020
 NPC  plan-1  N3   0.020
 NPC  plan-1  C4   0.020
 NPC  plan-1  O4   0.020
 NPC  plan-1  C5   0.020
 NPC  plan-1  C6   0.020
 NPC  plan-1  C7   0.020
 NPC  plan-1  H2   0.020
 NPC  plan-1  H5   0.020
 NPC  plan-1  H6   0.020
 NPC  plan-2  C7   0.020
 NPC  plan-2  C8   0.020
 NPC  plan-2  O8   0.020
 NPC  plan-2  N9   0.020
 NPC  plan-2  C10  0.020
 NPC  plan-2  HN9  0.020
 NPC  plan-3  C3   0.020
 NPC  plan-3  N3   0.020
 NPC  plan-3  O3A  0.020
 NPC  plan-3  O3B  0.020
 NPC  plan-4  C14  0.020
 NPC  plan-4  C15  0.020
 NPC  plan-4  O15  0.020
 NPC  plan-4  O16  0.020

