# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 11:16:17 2022
#   Inital geometry file: a 99 line input string
#   Ligand name: 2-[[6-[(4-nitrophenyl)amino]-3-oxidanyl-pyridin-2-yl]carbonylamino]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CNC(=O)c1nc(Nc2ccc(cc2)[N+]([O-])=O)ccc1O
#
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
 HZX  HZX  "2-[[6-[(4-nitrophenyl)amino]-3-oxidanyl-pyridin-2-yl]carbonylamino]ethanoic acid"  ligand  35  24  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HZX
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
 HZX  C1   C  CH2    0  -0.415  -10.4268  -31.7105  -32.7447
 HZX  C10  C  CR16   0  -0.330   -7.8470  -26.7122  -25.8934
 HZX  C11  C  CR16   0  -0.350   -7.6055  -29.3682  -27.5114
 HZX  C12  C  CR16   0  -0.267   -7.8861  -30.7086  -27.6704
 HZX  C2   C  C      0   0.504  -10.2241  -30.4588  -30.6415
 HZX  C3   C  CR6    0   0.003   -9.2843  -30.1359  -29.5084
 HZX  C4   C  CR6    0   0.437   -8.2374  -28.4526  -28.3544
 HZX  C5   C  CR6    0   0.405   -7.6953  -26.2987  -27.2271
 HZX  C6   C  CR16   0  -0.340   -7.2310  -24.9932  -27.4711
 HZX  C7   C  CR16   0  -0.255   -6.9082  -24.1486  -26.4365
 HZX  C8   C  CR6    0   0.218   -7.0392  -24.5898  -25.1220
 HZX  C9   C  CR16   0  -0.257   -7.5169  -25.8682  -24.8560
 HZX  N2   N  NH1    0  -0.763   -8.0101  -27.0812  -28.3000
 HZX  O1   O  O      0  -0.394   -6.3127  -22.5937  -24.2998
 HZX  N    N  NH1    0  -0.613   -9.7162  -31.2551  -31.5777
 HZX  C    C  C      0   0.399   -9.5323  -32.6541  -33.5816
 HZX  O    O  OC    -1  -0.594   -8.3619  -32.8147  -33.1831
 HZX  C13  C  CR6    0   0.313   -8.7480  -31.1216  -28.6827
 HZX  N1   N  N      0  -0.439   -9.0491  -28.8448  -29.3205
 HZX  N3   N  N      1   0.321   -6.6874  -23.7164  -24.0360
 HZX  O2   O  O     -1  -0.395   -6.7791  -24.1398  -22.9033
 HZX  O4   O  O      0  -0.487  -11.3500  -29.9796  -30.6731
 HZX  H1   H  HCH2   0   0.241  -10.7362  -30.8659  -33.3690
 HZX  H2   H  HCH2   0   0.240  -11.3423  -32.2376  -32.4612
 HZX  H3   H  HCR6   0   0.293   -8.2524  -27.6844  -25.6542
 HZX  H4   H  HCR6   0   0.298   -6.8920  -29.0555  -26.7629
 HZX  H5   H  HCR6   0   0.293   -7.4165  -31.4373  -27.0193
 HZX  H6   H  HCR6   0   0.283   -7.1156  -24.6507  -28.4919
 HZX  H7   H  HCR6   0   0.293   -6.5454  -23.1554  -26.6586
 HZX  H8   H  HCR6   0   0.294   -7.6512  -26.2104  -23.8400
 HZX  H9   H  HNH1   0   0.409   -8.1420  -26.6058  -29.1809
 HZX  H10  H  HOH1   0   0.481   -8.6414  -32.9834  -28.2637
 HZX  H11  H  HNH1   0   0.392   -8.7663  -31.5989  -31.5188
 HZX  O3   O  OH1    0  -0.618   -9.0845  -32.4054  -28.8958
 HZX  O5   O  O      0  -0.598  -10.0793  -33.1559  -34.5764

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
 HZX  O5   C    deloc     1.241  0.020  1.241
 HZX  C    O    deloc     1.247  0.020  1.247
 HZX  C    C1   single    1.546  0.020  1.546
 HZX  C1   N    single    1.440  0.020  1.440
 HZX  N    C2   single    1.330  0.020  1.330
 HZX  C2   O4   double    1.224  0.020  1.224
 HZX  C2   C3   single    1.507  0.020  1.507
 HZX  C3   N1   aromatic  1.326  0.020  1.326
 HZX  C3   C13  aromatic  1.393  0.020  1.393
 HZX  N1   C4   aromatic  1.321  0.020  1.321
 HZX  O3   C13  single    1.344  0.020  1.344
 HZX  C13  C12  aromatic  1.392  0.020  1.392
 HZX  C4   N2   single    1.391  0.020  1.391
 HZX  C4   C11  aromatic  1.396  0.020  1.396
 HZX  N2   C5   single    1.365  0.020  1.365
 HZX  C12  C11  aromatic  1.379  0.020  1.379
 HZX  C6   C5   aromatic  1.407  0.020  1.407
 HZX  C6   C7   aromatic  1.374  0.020  1.374
 HZX  C5   C10  aromatic  1.405  0.020  1.405
 HZX  C7   C8   aromatic  1.393  0.020  1.393
 HZX  C10  C9   aromatic  1.378  0.020  1.378
 HZX  C8   C9   aromatic  1.390  0.020  1.390
 HZX  C8   N3   single    1.437  0.020  1.437
 HZX  O1   N3   double    1.213  0.020  1.213
 HZX  N3   O2   single    1.213  0.020  1.213
 HZX  C1   H1   single    0.970  0.020  1.090
 HZX  C1   H2   single    0.970  0.020  1.090
 HZX  C10  H3   single    0.930  0.020  1.080
 HZX  C11  H4   single    0.930  0.020  1.080
 HZX  C12  H5   single    0.930  0.020  1.080
 HZX  C6   H6   single    0.930  0.020  1.080
 HZX  C7   H7   single    0.930  0.020  1.080
 HZX  C9   H8   single    0.930  0.020  1.080
 HZX  N2   H9   single    0.860  0.020  1.020
 HZX  O3   H10  single    0.850  0.020  0.980
 HZX  N    H11  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
 HZX  H2   C1   H1   106.44  3.000
 HZX  H2   C1   C    109.29  3.000
 HZX  H1   C1   C    109.00  3.000
 HZX  H2   C1   N    110.82  3.000
 HZX  H1   C1   N    110.95  3.000
 HZX  C    C1   N    110.25  3.000
 HZX  H3   C10  C9   118.34  3.000
 HZX  H3   C10  C5   121.05  3.000
 HZX  C9   C10  C5   120.59  3.000
 HZX  H4   C11  C4   121.84  3.000
 HZX  H4   C11  C12  119.72  3.000
 HZX  C4   C11  C12  118.42  3.000
 HZX  H5   C12  C13  120.36  3.000
 HZX  H5   C12  C11  119.74  3.000
 HZX  C13  C12  C11  119.89  3.000
 HZX  O4   C2   N    124.58  3.000
 HZX  O4   C2   C3   120.61  3.000
 HZX  N    C2   C3   114.80  3.000
 HZX  N1   C3   C13  122.46  3.000
 HZX  C13  C3   C2   122.28  3.000
 HZX  N1   C3   C2   115.21  3.000
 HZX  N1   C4   N2   114.94  3.000
 HZX  N2   C4   C11  123.30  3.000
 HZX  N1   C4   C11  121.66  3.000
 HZX  N2   C5   C6   118.15  3.000
 HZX  C6   C5   C10  118.26  3.000
 HZX  N2   C5   C10  123.56  3.000
 HZX  H6   C6   C7   119.36  3.000
 HZX  H6   C6   C5   119.49  3.000
 HZX  C7   C6   C5   121.15  3.000
 HZX  H7   C7   C8   121.12  3.000
 HZX  H7   C7   C6   119.28  3.000
 HZX  C8   C7   C6   119.59  3.000
 HZX  N3   C8   C9   119.88  3.000
 HZX  N3   C8   C7   119.84  3.000
 HZX  C9   C8   C7   120.28  3.000
 HZX  H8   C9   C8   120.93  3.000
 HZX  H8   C9   C10  118.96  3.000
 HZX  C8   C9   C10  120.10  3.000
 HZX  H9   N2   C5   116.50  3.000
 HZX  H9   N2   C4   114.12  3.000
 HZX  C5   N2   C4   129.32  3.000
 HZX  H11  N    C2   121.40  3.000
 HZX  H11  N    C1   113.76  3.000
 HZX  C2   N    C1   124.84  3.000
 HZX  O    C    O5   128.16  3.000
 HZX  O    C    C1   116.66  3.000
 HZX  O5   C    C1   115.18  3.000
 HZX  O3   C13  C3   119.04  3.000
 HZX  O3   C13  C12  123.62  3.000
 HZX  C3   C13  C12  117.34  3.000
 HZX  C4   N1   C3   120.11  3.000
 HZX  O2   N3   O1   123.35  3.000
 HZX  O2   N3   C8   118.36  3.000
 HZX  O1   N3   C8   118.28  3.000
 HZX  H10  O3   C13  110.70  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
 HZX  CONST_01  C7   C6   C5   C10     0.00   0.0  0
 HZX  CONST_02  C7   C8   C9   C10     0.00   0.0  0
 HZX  CONST_03  C3   N1   C4   C11     0.00   0.0  0
 HZX  CONST_04  C3   C13  C12  C11     0.00   0.0  0
 HZX  CONST_05  N1   C3   C13  C12     0.00   0.0  0
 HZX  CONST_06  N1   C4   C11  C12     0.00   0.0  0
 HZX  CONST_07  C13  C3   N1   C4      0.00   0.0  0
 HZX  CONST_08  C13  C12  C11  C4      0.00   0.0  0
 HZX  CONST_09  C8   C7   C6   C5      0.00   0.0  0
 HZX  CONST_10  C8   C9   C10  C5      0.00   0.0  0
 HZX  CONST_11  C9   C10  C5   C6      0.00   0.0  0
 HZX  CONST_12  C9   C8   C7   C6      0.00   0.0  0
 HZX  CONST_13  N3   C8   C9   C10   180.00   0.0  0
 HZX  CONST_14  O3   C13  C12  C11   180.00   0.0  0
 HZX  CONST_15  C2   C3   C13  C12   180.00   0.0  0
 HZX  CONST_16  N2   C4   C11  C12   180.00   0.0  0
 HZX  CONST_17  C4   N1   C3   C2    180.00   0.0  0
 HZX  CONST_18  N2   C4   N1   C3    180.00   0.0  0
 HZX  CONST_19  N3   C8   C7   C6    180.00   0.0  0
 HZX  CONST_20  N2   C5   C6   C7    180.00   0.0  0
 HZX  CONST_21  N2   C5   C10  C9    180.00   0.0  0
 HZX  CONST_22  N1   C3   C13  O3    180.00   0.0  0
 HZX  CONST_23  H6   C6   C5   C10   180.00   0.0  0
 HZX  CONST_24  H5   C12  C13  C3    180.00   0.0  0
 HZX  CONST_25  H5   C12  C11  C4    180.00   0.0  0
 HZX  CONST_26  H7   C7   C6   C5    180.00   0.0  0
 HZX  CONST_27  H8   C9   C10  C5    180.00   0.0  0
 HZX  CONST_28  H3   C10  C5   C6    180.00   0.0  0
 HZX  CONST_29  H8   C9   C8   C7    180.00   0.0  0
 HZX  CONST_30  H6   C6   C7   C8    180.00   0.0  0
 HZX  CONST_31  H3   C10  C9   C8    180.00   0.0  0
 HZX  CONST_32  H7   C7   C8   C9    180.00   0.0  0
 HZX  CONST_33  H4   C11  C12  C13   180.00   0.0  0
 HZX  CONST_34  H4   C11  C4   N1    180.00   0.0  0
 HZX  CONST_35  O1   N3   C8   C7      0.00   0.0  0
 HZX  CONST_36  O2   N3   C8   C7    180.00   0.0  0
 HZX  CONST_37  O1   N3   C8   C9    180.00   0.0  0
 HZX  CONST_38  O2   N3   C8   C9      0.00   0.0  0
 HZX  CONST_39  C3   C2   N    C1    180.00   0.0  0
 HZX  CONST_40  H11  N    C2   C3      0.00   0.0  0
 HZX  CONST_41  O4   C2   N    C1      0.00   0.0  0
 HZX  CONST_42  H11  N    C2   O4    180.00   0.0  0
 HZX  Var_01    C4   N2   C5   C10   -15.57  30.0  2
 HZX  Var_02    C5   N2   C4   C11   -31.55  30.0  2
 HZX  Var_03    C6   C5   N2   C4    166.37  30.0  2
 HZX  Var_04    N1   C4   N2   C5    152.02  30.0  1
 HZX  Var_05    N1   C3   C2   N     122.11  30.0  2
 HZX  Var_06    C13  C3   C2   N     -60.55  30.0  2
 HZX  Var_07    O4   C2   C3   C13   120.97  30.0  2
 HZX  Var_08    O4   C2   C3   N1    -56.38  30.0  2
 HZX  Var_09    H9   N2   C5   C10   161.28  30.0  2
 HZX  Var_10    H9   N2   C4   C11   151.53  30.0  2
 HZX  Var_11    H9   N2   C5   C6    -16.77  30.0  2
 HZX  Var_12    H9   N2   C4   N1    -24.90  30.0  2
 HZX  Var_13    C    C1   N    C2   -178.24  30.0  1
 HZX  Var_14    N    C1   C    O5    176.49  30.0  3
 HZX  Var_15    O    C    C1   N      -3.70  30.0  2
 HZX  Var_16    H1   C1   N    C2     60.91  30.0  1
 HZX  Var_17    H2   C1   N    C2    -57.10  30.0  1
 HZX  Var_18    H1   C1   C    O5    -61.50  30.0  3
 HZX  Var_19    H2   C1   C    O5     54.45  30.0  3
 HZX  Var_20    H11  N    C1   C       1.69  30.0  3
 HZX  Var_21    H1   C1   C    O     118.31  30.0  3
 HZX  Var_22    H2   C1   C    O    -125.73  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
 HZX  plan-1  C11  0.020
 HZX  plan-1  C12  0.020
 HZX  plan-1  C2   0.020
 HZX  plan-1  C3   0.020
 HZX  plan-1  C4   0.020
 HZX  plan-1  N2   0.020
 HZX  plan-1  C13  0.020
 HZX  plan-1  N1   0.020
 HZX  plan-1  H4   0.020
 HZX  plan-1  H5   0.020
 HZX  plan-1  O3   0.020
 HZX  plan-2  C10  0.020
 HZX  plan-2  C5   0.020
 HZX  plan-2  C6   0.020
 HZX  plan-2  C7   0.020
 HZX  plan-2  C8   0.020
 HZX  plan-2  C9   0.020
 HZX  plan-2  N2   0.020
 HZX  plan-2  N3   0.020
 HZX  plan-2  H3   0.020
 HZX  plan-2  H6   0.020
 HZX  plan-2  H7   0.020
 HZX  plan-2  H8   0.020
 HZX  plan-3  C1   0.020
 HZX  plan-3  C2   0.020
 HZX  plan-3  C3   0.020
 HZX  plan-3  N    0.020
 HZX  plan-3  O4   0.020
 HZX  plan-3  H11  0.020
 HZX  plan-4  C8   0.020
 HZX  plan-4  O1   0.020
 HZX  plan-4  N3   0.020
 HZX  plan-4  O2   0.020
 HZX  plan-5  C1   0.020
 HZX  plan-5  C    0.020
 HZX  plan-5  O    0.020
 HZX  plan-5  O5   0.020

