# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 18:14:02 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: 2-methoxyethyl propan-2-yl 2,6-dimethyl-4-(3-nitrophenyl)pyridine-3,5-dicarboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCOC(=O)c1c(C)nc(C)c(C(=O)OC(C)C)c1c2cccc(c2)[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
 NIW  NIW  '2-methoxyethyl propan-2-yl 2,6-dimethyl-4-(3-nitrophenyl)pyridine-3,5-dicarboxylate'  ligand  54  30  .  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_NIW
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
 NIW  O4   O  O      0  -0.412   2.4986  -0.9053   1.7610
 NIW  O3   O  O     -1  -0.372   0.1403   5.0431   1.1563
 NIW  C5   C  CR6    0   0.258  -2.1390  -2.5443   1.1552
 NIW  C4   C  CR6    0  -0.156  -1.8318  -1.2522   0.7162
 NIW  C3   C  CR6    0   0.326  -0.4933  -0.8859   0.5815
 NIW  C2   C  CR6    0  -0.131   0.4804  -1.8247   0.8957
 NIW  O2   O  O      0  -0.374  -0.8856   3.7379   2.4960
 NIW  C1   C  CR6    0   0.263   0.0955  -3.0950   1.3213
 NIW  C7   C  C      0   0.467  -2.9198  -0.2824   0.4015
 NIW  C13  C  CR6    0   0.271   0.0490   2.8220   0.6191
 NIW  C12  C  CR16   0  -0.310  -0.3652   1.5556   1.0007
 NIW  C11  C  CR6    0  -0.031  -0.0845   0.4792   0.1709
 NIW  C10  C  CH3    0  -0.664  -2.8020   2.1806  -2.1630
 NIW  C9   C  CH3    0  -0.672  -4.8624   0.7459  -1.8822
 NIW  C17  C  C      0   0.455   1.9241  -1.4404   0.8497
 NIW  C19  C  CH2    0  -0.168   4.0830  -1.5327  -2.0367
 NIW  O6   O  O2     0  -0.473   3.2776  -0.6447  -2.7640
 NIW  C20  C  CH3    0  -0.395   3.4623  -0.7570  -4.1525
 NIW  O    O  O      0  -0.431  -3.8266  -0.0317   1.1559
 NIW  N    N  N      0  -0.452  -1.1843  -3.4246   1.4342
 NIW  C    C  CH3    0  -0.752   1.1097  -4.1299   1.6973
 NIW  C16  C  CR16   0  -0.241   0.6085   0.6871  -1.0189
 NIW  C15  C  CR16   0  -0.235   1.0239   1.9610  -1.3743
 NIW  C14  C  CR16   0  -0.272   0.7458   3.0448  -0.5590
 NIW  H1   H  HCH3   0   0.264  -4.0087  -2.5961   2.2079
 NIW  H2   H  HCH3   0   0.250  -4.1779  -2.7681   0.4685
 NIW  H3   H  HCH3   0   0.258  -3.5496  -4.1095   1.4291
 NIW  H4   H  HCH1   0   0.244  -3.9136   1.9151  -0.3507
 NIW  H5   H  HCR6   0   0.304  -0.8871   1.4002   1.9351
 NIW  H6   H  HCH3   0   0.232  -2.5180   1.6297  -3.0606
 NIW  H7   H  HCH3   0   0.240  -3.3846   3.0486  -2.4705
 NIW  H8   H  HCH3   0   0.243  -1.8949   2.5394  -1.6770
 NIW  H9   H  HCH3   0   0.234  -4.5955   0.1213  -2.7358
 NIW  H10  H  HCH3   0   0.243  -5.4546   0.1531  -1.1860
 NIW  H11  H  HCH3   0   0.241  -5.4935   1.5573  -2.2455
 NIW  H12  H  HCH2   0   0.250   3.9641  -0.3114  -0.2725
 NIW  H13  H  HCH2   0   0.259   4.5088  -1.9730   0.0113
 NIW  H14  H  HCH2   0   0.220   5.1514  -1.3393  -2.2041
 NIW  H15  H  HCH2   0   0.215   3.8989  -2.5752  -2.3330
 NIW  H16  H  HCH3   0   0.207   3.2154  -1.7596  -4.5209
 NIW  H17  H  HCH3   0   0.235   2.8015  -0.0391  -4.6362
 NIW  H18  H  HCH3   0   0.206   4.4937  -0.5341  -4.4495
 NIW  H19  H  HCH3   0   0.267   1.6187  -3.8529   2.6226
 NIW  H20  H  HCH3   0   0.269   0.6275  -5.0918   1.8525
 NIW  H21  H  HCH3   0   0.256   1.8740  -4.2472   0.9284
 NIW  H22  H  HCR6   0   0.280   0.8279  -0.1431  -1.6758
 NIW  H23  H  HCR6   0   0.281   1.5652   2.1130  -2.2974
 NIW  H24  H  HCR6   0   0.304   1.0668   4.0359  -0.8437
 NIW  C6   C  CH3    0  -0.735  -3.5480  -3.0278   1.3189
 NIW  O5   O  O2     0  -0.436   2.4662  -1.7559  -0.3095
 NIW  O1   O  O2     0  -0.444  -2.7533   0.2529  -0.7900
 NIW  N1   N  N      1   0.328  -0.2535   3.9510   1.4888
 NIW  C8   C  CH1    0   0.001  -3.6261   1.3257  -1.2243
 NIW  C18  C  CH2    0  -0.214   3.8207  -1.3531  -0.5663

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
 NIW  C9   C8   single    1.516  0.020  1.516
 NIW  C8   O1   single    1.450  0.020  1.450
 NIW  C8   C10  single    1.514  0.020  1.514
 NIW  O1   C7   single    1.317  0.020  1.317
 NIW  O    C7   double    1.206  0.020  1.206
 NIW  C7   C4   single    1.491  0.020  1.491
 NIW  C6   C5   single    1.499  0.020  1.499
 NIW  C4   C5   aromatic  1.399  0.020  1.399
 NIW  C4   C3   aromatic  1.394  0.020  1.394
 NIW  C5   N    aromatic  1.328  0.020  1.328
 NIW  C3   C11  single    1.483  0.020  1.483
 NIW  C3   C2   aromatic  1.389  0.020  1.389
 NIW  O6   C20  single    1.405  0.020  1.405
 NIW  O6   C19  single    1.402  0.020  1.402
 NIW  C16  C11  aromatic  1.393  0.020  1.393
 NIW  C16  C15  aromatic  1.386  0.020  1.386
 NIW  C11  C12  aromatic  1.388  0.020  1.388
 NIW  N    C1   aromatic  1.326  0.020  1.326
 NIW  C2   C1   aromatic  1.394  0.020  1.394
 NIW  C2   C17  single    1.495  0.020  1.495
 NIW  O5   C17  single    1.318  0.020  1.318
 NIW  O5   C18  single    1.436  0.020  1.436
 NIW  C15  C14  aromatic  1.384  0.020  1.384
 NIW  C1   C    single    1.497  0.020  1.497
 NIW  C19  C18  single    1.504  0.020  1.504
 NIW  C17  O4   double    1.203  0.020  1.203
 NIW  C12  C13  aromatic  1.386  0.020  1.386
 NIW  C14  C13  aromatic  1.387  0.020  1.387
 NIW  C13  N1   single    1.457  0.020  1.457
 NIW  N1   O2   double    1.208  0.020  1.208
 NIW  N1   O3   single    1.208  0.020  1.208
 NIW  C6   H1   single    0.970  0.020  1.090
 NIW  C6   H2   single    0.970  0.020  1.090
 NIW  C6   H3   single    0.970  0.020  1.090
 NIW  C8   H4   single    0.970  0.020  1.090
 NIW  C12  H5   single    0.930  0.020  1.080
 NIW  C10  H6   single    0.970  0.020  1.090
 NIW  C10  H7   single    0.970  0.020  1.090
 NIW  C10  H8   single    0.970  0.020  1.090
 NIW  C9   H9   single    0.970  0.020  1.090
 NIW  C9   H10  single    0.970  0.020  1.090
 NIW  C9   H11  single    0.970  0.020  1.090
 NIW  C18  H12  single    0.970  0.020  1.090
 NIW  C18  H13  single    0.970  0.020  1.090
 NIW  C19  H14  single    0.970  0.020  1.090
 NIW  C19  H15  single    0.970  0.020  1.090
 NIW  C20  H16  single    0.970  0.020  1.090
 NIW  C20  H17  single    0.970  0.020  1.090
 NIW  C20  H18  single    0.970  0.020  1.090
 NIW  C    H19  single    0.970  0.020  1.090
 NIW  C    H20  single    0.970  0.020  1.090
 NIW  C    H21  single    0.970  0.020  1.090
 NIW  C16  H22  single    0.930  0.020  1.080
 NIW  C15  H23  single    0.930  0.020  1.080
 NIW  C14  H24  single    0.930  0.020  1.080

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
 NIW  N    C5   C6   116.04  3.000
 NIW  N    C5   C4   121.35  3.000
 NIW  C6   C5   C4   122.60  3.000
 NIW  C7   C4   C3   120.61  3.000
 NIW  C3   C4   C5   118.93  3.000
 NIW  C7   C4   C5   120.45  3.000
 NIW  C11  C3   C2   119.45  3.000
 NIW  C2   C3   C4   118.28  3.000
 NIW  C11  C3   C4   122.22  3.000
 NIW  C17  C2   C1   120.69  3.000
 NIW  C17  C2   C3   119.77  3.000
 NIW  C1   C2   C3   119.44  3.000
 NIW  C    C1   N    117.42  3.000
 NIW  C    C1   C2   121.31  3.000
 NIW  N    C1   C2   121.26  3.000
 NIW  O    C7   O1   125.22  3.000
 NIW  O    C7   C4   123.49  3.000
 NIW  O1   C7   C4   111.29  3.000
 NIW  C14  C13  C12  122.07  3.000
 NIW  C14  C13  N1   119.14  3.000
 NIW  C12  C13  N1   118.79  3.000
 NIW  H5   C12  C11  120.18  3.000
 NIW  H5   C12  C13  120.89  3.000
 NIW  C11  C12  C13  118.92  3.000
 NIW  C16  C11  C12  119.72  3.000
 NIW  C12  C11  C3   119.52  3.000
 NIW  C16  C11  C3   120.74  3.000
 NIW  H8   C10  H7   107.98  3.000
 NIW  H8   C10  H6   108.45  3.000
 NIW  H7   C10  H6   108.02  3.000
 NIW  H8   C10  C8   111.25  3.000
 NIW  H7   C10  C8   109.50  3.000
 NIW  H6   C10  C8   111.52  3.000
 NIW  H11  C9   H10  107.66  3.000
 NIW  H11  C9   H9   107.88  3.000
 NIW  H10  C9   H9   108.75  3.000
 NIW  H11  C9   C8   109.39  3.000
 NIW  H10  C9   C8   111.97  3.000
 NIW  H9   C9   C8   111.05  3.000
 NIW  O5   C17  C2   111.27  3.000
 NIW  O5   C17  O4   125.19  3.000
 NIW  C2   C17  O4   123.53  3.000
 NIW  H15  C19  H14  106.78  3.000
 NIW  H15  C19  O6   111.38  3.000
 NIW  H14  C19  O6   111.60  3.000
 NIW  H15  C19  C18  110.33  3.000
 NIW  H14  C19  C18  107.31  3.000
 NIW  O6   C19  C18  109.34  3.000
 NIW  C20  O6   C19  112.73  3.000
 NIW  H18  C20  H17  108.45  3.000
 NIW  H18  C20  H16  107.86  3.000
 NIW  H17  C20  H16  108.48  3.000
 NIW  H18  C20  O6   112.03  3.000
 NIW  H17  C20  O6   107.85  3.000
 NIW  H16  C20  O6   112.06  3.000
 NIW  C1   N    C5   120.73  3.000
 NIW  H21  C    H20  108.44  3.000
 NIW  H21  C    H19  107.35  3.000
 NIW  H20  C    H19  108.08  3.000
 NIW  H21  C    C1   111.84  3.000
 NIW  H20  C    C1   110.30  3.000
 NIW  H19  C    C1   110.69  3.000
 NIW  H22  C16  C15  119.28  3.000
 NIW  H22  C16  C11  120.37  3.000
 NIW  C15  C16  C11  120.35  3.000
 NIW  H23  C15  C14  119.57  3.000
 NIW  H23  C15  C16  119.88  3.000
 NIW  C14  C15  C16  120.55  3.000
 NIW  H24  C14  C15  120.23  3.000
 NIW  H24  C14  C13  121.38  3.000
 NIW  C15  C14  C13  118.39  3.000
 NIW  H3   C6   H2   108.39  3.000
 NIW  H3   C6   H1   108.10  3.000
 NIW  H2   C6   H1   107.32  3.000
 NIW  H3   C6   C5   109.47  3.000
 NIW  H2   C6   C5   112.42  3.000
 NIW  H1   C6   C5   111.01  3.000
 NIW  C18  O5   C17  118.55  3.000
 NIW  C8   O1   C7   119.72  3.000
 NIW  C13  N1   O2   118.01  3.000
 NIW  O2   N1   O3   124.04  3.000
 NIW  C13  N1   O3   117.95  3.000
 NIW  H4   C8   C9   109.81  3.000
 NIW  H4   C8   C10  109.54  3.000
 NIW  C9   C8   C10  113.01  3.000
 NIW  H4   C8   O1   108.56  3.000
 NIW  C10  C8   O1   106.02  3.000
 NIW  C9   C8   O1   109.76  3.000
 NIW  H13  C18  H12  108.47  3.000
 NIW  H13  C18  C19  109.85  3.000
 NIW  H12  C18  C19  110.73  3.000
 NIW  H13  C18  O5   109.92  3.000
 NIW  H12  C18  O5   110.08  3.000
 NIW  C19  C18  O5   107.80  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
 NIW  CONST_01  C11  C3   C4   C5    180.00   0.0  0
 NIW  CONST_02  C2   C3   C4   C5      0.00   0.0  0
 NIW  CONST_03  C2   C1   N    C5      0.00   0.0  0
 NIW  CONST_04  C1   N    C5   C4      0.00   0.0  0
 NIW  CONST_07  C1   C2   C3   C4      0.00   0.0  0
 NIW  CONST_08  N    C5   C4   C3      0.00   0.0  0
 NIW  CONST_09  C15  C16  C11  C3    180.00   0.0  0
 NIW  CONST_10  C13  C12  C11  C3    180.00   0.0  0
 NIW  CONST_11  N    C1   C2   C3      0.00   0.0  0
 NIW  CONST_14  C11  C3   C2   C1    180.00   0.0  0
 NIW  CONST_15  C16  C11  C12  C13     0.00   0.0  0
 NIW  CONST_16  C16  C15  C14  C13     0.00   0.0  0
 NIW  CONST_17  C15  C16  C11  C12     0.00   0.0  0
 NIW  CONST_18  C15  C14  C13  C12     0.00   0.0  0
 NIW  CONST_19  C14  C15  C16  C11     0.00   0.0  0
 NIW  CONST_20  C14  C13  C12  C11     0.00   0.0  0
 NIW  CONST_21  C    C1   N    C5    180.00   0.0  0
 NIW  CONST_22  C17  C2   C3   C4    180.00   0.0  0
 NIW  CONST_23  C6   C5   C4   C3    180.00   0.0  0
 NIW  CONST_24  C    C1   C2   C3    180.00   0.0  0
 NIW  CONST_25  C7   C4   C3   C2    180.00   0.0  0
 NIW  CONST_26  C11  C12  C13  N1    180.00   0.0  0
 NIW  CONST_27  C15  C14  C13  N1    180.00   0.0  0
 NIW  CONST_28  C6   C5   N    C1    180.00   0.0  0
 NIW  CONST_29  N    C5   C4   C7    180.00   0.0  0
 NIW  CONST_30  C11  C3   C4   C7      0.00   0.0  0
 NIW  CONST_31  C17  C2   C3   C11     0.00   0.0  0
 NIW  CONST_32  N    C1   C2   C17   180.00   0.0  0
 NIW  CONST_33  H22  C16  C11  C3      0.00   0.0  0
 NIW  CONST_34  H5   C12  C11  C3      0.00   0.0  0
 NIW  CONST_35  H23  C15  C14  C13   180.00   0.0  0
 NIW  CONST_36  H24  C14  C13  C12   180.00   0.0  0
 NIW  CONST_37  C12  C13  N1   O3    180.00   0.0  0
 NIW  CONST_38  C14  C13  N1   O3      0.00   0.0  0
 NIW  CONST_39  C12  C13  N1   O2      0.00   0.0  0
 NIW  CONST_40  C14  C13  N1   O2    180.00   0.0  0
 NIW  Var_01    C3   C2   C17  O4     84.55  30.0  3
 NIW  Var_02    O1   C7   C4   C5   -128.80  30.0  3
 NIW  Var_03    H1   C6   C5   C4    -74.49  30.0  2
 NIW  Var_04    H19  C    C1   C2     69.12  30.0  2
 NIW  Var_05    C9   C8   O1   C7    -87.65  30.0  2
 NIW  Var_06    O6   C19  C18  O5     65.50  30.0  2
 NIW  Var_07    C19  C18  O5   C17  -166.68  30.0  3
 NIW  Var_08    H9   C9   C8   O1    -58.56  30.0  3
 NIW  Var_09    H6   C10  C8   O1     64.48  30.0  3
 NIW  Var_10    H16  C20  O6   C19    60.52  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
 NIW  plan-1  C5   0.020
 NIW  plan-1  C4   0.020
 NIW  plan-1  C3   0.020
 NIW  plan-1  C2   0.020
 NIW  plan-1  C1   0.020
 NIW  plan-1  C7   0.020
 NIW  plan-1  C11  0.020
 NIW  plan-1  C17  0.020
 NIW  plan-1  N    0.020
 NIW  plan-1  C    0.020
 NIW  plan-1  C6   0.020
 NIW  plan-2  C3   0.020
 NIW  plan-2  C13  0.020
 NIW  plan-2  C12  0.020
 NIW  plan-2  C11  0.020
 NIW  plan-2  C16  0.020
 NIW  plan-2  C15  0.020
 NIW  plan-2  C14  0.020
 NIW  plan-2  H5   0.020
 NIW  plan-2  H22  0.020
 NIW  plan-2  H23  0.020
 NIW  plan-2  H24  0.020
 NIW  plan-2  N1   0.020
 NIW  plan-3  O3   0.020
 NIW  plan-3  O2   0.020
 NIW  plan-3  C13  0.020
 NIW  plan-3  N1   0.020
 NIW  plan-4  C4   0.020
 NIW  plan-4  C7   0.020
 NIW  plan-4  O    0.020
 NIW  plan-4  O1   0.020
 NIW  plan-5  O4   0.020
 NIW  plan-5  C2   0.020
 NIW  plan-5  C17  0.020
 NIW  plan-5  O5   0.020

