# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 00:13:45 2020
#   Inital geometry file: a 157 line input string
#   Ligand name: 2-[benzyl(methyl)amino]ethyl methyl 2,6-dimethyl-4-(3-nitrophenyl)pyridine-3,5-dicarboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)c1c(C)nc(C)c(C(=O)OCCN(C)Cc2ccccc2)c1c3cccc(c3)[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
 93U  93U  '2-[benzyl(methyl)amino]ethyl methyl 2,6-dimethyl-4-(3-nitrophenyl)pyridine-3,5-dicarboxylate'  ligand  62  35  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_93U
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
 93U  C1   C  CR6    0   0.259  -3.0748  -2.2416  -1.3077
 93U  O1   O  O2     0  -0.439   0.8577  -2.7345   1.5408
 93U  O2   O  O      0  -0.374  -1.4671   4.9113   1.4997
 93U  C2   C  CR6    0  -0.136  -2.4947  -0.9909  -1.0802
 93U  C3   C  CR6    0   0.306  -1.5225  -0.8633  -0.0911
 93U  C4   C  CR6    0  -0.159  -1.1411  -2.0019   0.6145
 93U  C5   C  CR6    0   0.263  -1.7706  -3.2178   0.3295
 93U  O3   O  O     -1  -0.376  -3.1569   3.6099   1.4992
 93U  O4   O  O      0  -0.425  -4.0456   0.5800  -1.9799
 93U  O5   O  O2     0  -0.430  -1.8808   0.7313  -2.5146
 93U  C24  C  C      0   0.456  -2.9100   0.1868  -1.8952
 93U  C25  C  CH3    0  -0.423  -2.1139   1.9269  -3.2625
 93U  C18  C  CR6    0   0.012  -0.9169   0.4600   0.1862
 93U  C23  C  CR16   0  -0.231   0.4396   0.6770  -0.0306
 93U  C22  C  CR16   0  -0.236   0.9904   1.9326   0.1679
 93U  C21  C  CR16   0  -0.273   0.2027   2.9840   0.6052
 93U  C20  C  CR6    0   0.267  -1.1436   2.7461   0.8377
 93U  N2   N  N      1   0.326  -1.9843   3.8356   1.3141
 93U  C19  C  CR16   0  -0.316  -1.7180   1.5014   0.6307
 93U  C6   C  CH3    0  -0.736  -1.4655  -4.4845   1.0708
 93U  N    N  N      0  -0.452  -2.7087  -3.3060  -0.6063
 93U  C    C  CH3    0  -0.739  -4.1231  -2.4608  -2.3555
 93U  C7   C  C      0   0.479  -0.1339  -1.8818   1.7090
 93U  O    O  O      0  -0.421  -0.2409  -1.0968   2.6153
 93U  C8   C  CH2    0  -0.218   1.9512  -2.7721   2.4687
 93U  C9   C  CH2    0  -0.295   3.2416  -2.4764   1.7337
 93U  N1   N  NT     0  -0.398   3.2798  -1.1642   1.1192
 93U  C10  C  CH3    0  -0.536   3.3189  -0.1017   2.1031
 93U  C11  C  CH2    0  -0.354   4.3951  -1.0587   0.1870
 93U  C12  C  CR6    0   0.109   4.2420   0.1074  -0.7530
 93U  C17  C  CR16   0  -0.304   4.9666   1.2822  -0.5787
 93U  C16  C  CR16   0  -0.245   4.7942   2.3593  -1.4409
 93U  C15  C  CR16   0  -0.268   3.8943   2.2695  -2.4937
 93U  C14  C  CR16   0  -0.237   3.1719   1.0968  -2.6826
 93U  C13  C  CR16   0  -0.298   3.3487   0.0260  -1.8195
 93U  H1   H  HCH3   0   0.255  -1.1432   2.2366  -3.6363
 93U  H2   H  HCH3   0   0.247  -2.7870   1.7442  -4.0992
 93U  H3   H  HCH3   0   0.240  -2.5281   2.7127  -2.6313
 93U  H4   H  HCR6   0   0.272   1.0754  -0.1353  -0.3561
 93U  H5   H  HCR6   0   0.277   2.0410   2.0963  -0.0300
 93U  H6   H  HCR6   0   0.300   0.6363   3.9609   0.7602
 93U  H7   H  HCR6   0   0.305  -2.7690   1.3376   0.8256
 93U  H8   H  HCH3   0   0.266  -0.5139  -4.9098   0.7502
 93U  H9   H  HCH3   0   0.253  -1.4077  -4.3308   2.1481
 93U  H10  H  HCH3   0   0.260  -2.2454  -5.2154   0.8717
 93U  H11  H  HCH3   0   0.254  -3.8469  -2.0150  -3.3110
 93U  H12  H  HCH3   0   0.260  -4.2738  -3.5270  -2.5042
 93U  H13  H  HCH3   0   0.266  -5.0742  -2.0213  -2.0541
 93U  H14  H  HCH2   0   0.252   1.7782  -2.0926   3.3006
 93U  H15  H  HCH2   0   0.266   1.9930  -3.7859   2.8683
 93U  H16  H  HCH2   0   0.209   4.0608  -2.6315   2.4571
 93U  H17  H  HCH2   0   0.247   3.3746  -3.2283   0.9523
 93U  H19  H  HCH3   0   0.201   4.1982  -0.1689   2.7625
 93U  H20  H  HCH3   0   0.243   3.3482   0.8678   1.6089
 93U  H21  H  HCH3   0   0.240   2.4264  -0.1086   2.7263
 93U  H22  H  HCH2   0   0.215   5.3609  -0.9863   0.7139
 93U  H23  H  HCH2   0   0.251   4.4297  -1.9789  -0.4009
 93U  H24  H  HCR6   0   0.252   5.6719   1.3576   0.2410
 93U  H25  H  HCR6   0   0.254   5.3641   3.2672  -1.2892
 93U  H26  H  HCR6   0   0.255   3.7570   3.1067  -3.1658
 93U  H27  H  HCR6   0   0.252   2.4698   1.0178  -3.5027
 93U  H28  H  HCR6   0   0.251   2.7827  -0.8865  -1.9705

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
 93U  C6   C5   single    1.499  0.020  1.499
 93U  O    C7   double    1.204  0.020  1.204
 93U  C5   N    aromatic  1.328  0.020  1.328
 93U  C5   C4   aromatic  1.399  0.020  1.399
 93U  N    C1   aromatic  1.326  0.020  1.326
 93U  C7   C4   single    1.492  0.020  1.492
 93U  C7   O1   single    1.319  0.020  1.319
 93U  C4   C3   aromatic  1.393  0.020  1.393
 93U  C8   O1   single    1.435  0.020  1.435
 93U  C8   C9   single    1.514  0.020  1.514
 93U  C1   C    single    1.498  0.020  1.498
 93U  C1   C2   aromatic  1.397  0.020  1.397
 93U  C3   C2   aromatic  1.393  0.020  1.393
 93U  C3   C18  single    1.481  0.020  1.481
 93U  C14  C13  aromatic  1.387  0.020  1.387
 93U  C14  C15  aromatic  1.390  0.020  1.390
 93U  N1   C9   single    1.449  0.020  1.449
 93U  N1   C10  single    1.449  0.020  1.449
 93U  N1   C11  single    1.457  0.020  1.457
 93U  C2   C24  single    1.491  0.020  1.491
 93U  C13  C12  aromatic  1.394  0.020  1.394
 93U  C23  C18  aromatic  1.391  0.020  1.391
 93U  C23  C22  aromatic  1.385  0.020  1.385
 93U  C15  C16  aromatic  1.388  0.020  1.388
 93U  C18  C19  aromatic  1.387  0.020  1.387
 93U  C12  C11  single    1.506  0.020  1.506
 93U  C12  C17  aromatic  1.391  0.020  1.391
 93U  C22  C21  aromatic  1.385  0.020  1.385
 93U  C24  O4   double    1.205  0.020  1.205
 93U  C24  O5   single    1.319  0.020  1.319
 93U  C16  C17  aromatic  1.390  0.020  1.390
 93U  C19  C20  aromatic  1.386  0.020  1.386
 93U  O5   C25  single    1.429  0.020  1.429
 93U  C21  C20  aromatic  1.387  0.020  1.387
 93U  C20  N2   single    1.456  0.020  1.456
 93U  N2   O2   double    1.208  0.020  1.208
 93U  N2   O3   single    1.208  0.020  1.208
 93U  C25  H1   single    0.970  0.020  1.090
 93U  C25  H2   single    0.970  0.020  1.090
 93U  C25  H3   single    0.970  0.020  1.090
 93U  C23  H4   single    0.930  0.020  1.080
 93U  C22  H5   single    0.930  0.020  1.080
 93U  C21  H6   single    0.930  0.020  1.080
 93U  C19  H7   single    0.930  0.020  1.080
 93U  C6   H8   single    0.970  0.020  1.090
 93U  C6   H9   single    0.970  0.020  1.090
 93U  C6   H10  single    0.970  0.020  1.090
 93U  C    H11  single    0.970  0.020  1.090
 93U  C    H12  single    0.970  0.020  1.090
 93U  C    H13  single    0.970  0.020  1.090
 93U  C8   H14  single    0.970  0.020  1.090
 93U  C8   H15  single    0.970  0.020  1.090
 93U  C9   H16  single    0.970  0.020  1.090
 93U  C9   H17  single    0.970  0.020  1.090
 93U  C10  H19  single    0.970  0.020  1.090
 93U  C10  H20  single    0.970  0.020  1.090
 93U  C10  H21  single    0.970  0.020  1.090
 93U  C11  H22  single    0.970  0.020  1.090
 93U  C11  H23  single    0.970  0.020  1.090
 93U  C17  H24  single    0.930  0.020  1.080
 93U  C16  H25  single    0.930  0.020  1.080
 93U  C15  H26  single    0.930  0.020  1.080
 93U  C14  H27  single    0.930  0.020  1.080
 93U  C13  H28  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
 93U  C    C1   N    116.46  3.000
 93U  C    C1   C2   122.37  3.000
 93U  N    C1   C2   121.17  3.000
 93U  C8   O1   C7   120.51  3.000
 93U  C24  C2   C3   120.67  3.000
 93U  C24  C2   C1   120.15  3.000
 93U  C3   C2   C1   119.18  3.000
 93U  C18  C3   C4   121.56  3.000
 93U  C18  C3   C2   120.01  3.000
 93U  C4   C3   C2   118.43  3.000
 93U  C7   C4   C5   121.55  3.000
 93U  C7   C4   C3   119.38  3.000
 93U  C5   C4   C3   118.96  3.000
 93U  N    C5   C6   115.85  3.000
 93U  N    C5   C4   121.29  3.000
 93U  C6   C5   C4   122.84  3.000
 93U  C25  O5   C24  117.63  3.000
 93U  O5   C24  O4   124.60  3.000
 93U  O5   C24  C2   111.43  3.000
 93U  O4   C24  C2   123.96  3.000
 93U  H3   C25  H2   109.33  3.000
 93U  H3   C25  H1   109.49  3.000
 93U  H2   C25  H1   109.63  3.000
 93U  H3   C25  O5   111.23  3.000
 93U  H2   C25  O5   111.25  3.000
 93U  H1   C25  O5   105.85  3.000
 93U  C19  C18  C23  119.75  3.000
 93U  C19  C18  C3   119.64  3.000
 93U  C23  C18  C3   120.59  3.000
 93U  H4   C23  C22  119.35  3.000
 93U  H4   C23  C18  120.20  3.000
 93U  C22  C23  C18  120.45  3.000
 93U  H5   C22  C21  119.70  3.000
 93U  H5   C22  C23  119.81  3.000
 93U  C21  C22  C23  120.49  3.000
 93U  H6   C21  C20  121.39  3.000
 93U  H6   C21  C22  120.26  3.000
 93U  C20  C21  C22  118.36  3.000
 93U  C19  C20  N2   118.77  3.000
 93U  N2   C20  C21  119.14  3.000
 93U  C19  C20  C21  122.09  3.000
 93U  C20  N2   O3   118.07  3.000
 93U  O3   N2   O2   123.94  3.000
 93U  C20  N2   O2   117.99  3.000
 93U  H7   C19  C20  120.78  3.000
 93U  H7   C19  C18  120.35  3.000
 93U  C20  C19  C18  118.86  3.000
 93U  H10  C6   H9   108.30  3.000
 93U  H10  C6   H8   108.06  3.000
 93U  H9   C6   H8   107.42  3.000
 93U  H10  C6   C5   109.36  3.000
 93U  H9   C6   C5   112.36  3.000
 93U  H8   C6   C5   111.21  3.000
 93U  C5   N    C1   120.96  3.000
 93U  H13  C    H12  108.20  3.000
 93U  H13  C    H11  107.37  3.000
 93U  H12  C    H11  108.45  3.000
 93U  H13  C    C1   110.98  3.000
 93U  H12  C    C1   109.65  3.000
 93U  H11  C    C1   112.08  3.000
 93U  O    C7   C4   123.01  3.000
 93U  C4   C7   O1   111.23  3.000
 93U  O    C7   O1   125.77  3.000
 93U  H15  C8   H14  107.85  3.000
 93U  H15  C8   C9   109.07  3.000
 93U  H14  C8   C9   112.62  3.000
 93U  H15  C8   O1   106.89  3.000
 93U  H14  C8   O1   110.92  3.000
 93U  C9   C8   O1   109.30  3.000
 93U  H17  C9   H16  106.36  3.000
 93U  H17  C9   N1   108.46  3.000
 93U  H16  C9   N1   112.68  3.000
 93U  H17  C9   C8   108.45  3.000
 93U  H16  C9   C8   106.67  3.000
 93U  N1   C9   C8   113.89  3.000
 93U  C11  N1   C10  111.14  3.000
 93U  C11  N1   C9   110.91  3.000
 93U  C10  N1   C9   112.13  3.000
 93U  H21  C10  H20  106.71  3.000
 93U  H21  C10  H19  108.15  3.000
 93U  H20  C10  H19  107.74  3.000
 93U  H21  C10  N1   111.22  3.000
 93U  H20  C10  N1   110.22  3.000
 93U  H19  C10  N1   112.56  3.000
 93U  H23  C11  H22  106.54  3.000
 93U  H23  C11  C12  108.64  3.000
 93U  H22  C11  C12  109.67  3.000
 93U  H23  C11  N1   107.91  3.000
 93U  H22  C11  N1   111.68  3.000
 93U  C12  C11  N1   112.18  3.000
 93U  C13  C12  C17  118.63  3.000
 93U  C17  C12  C11  121.52  3.000
 93U  C13  C12  C11  119.85  3.000
 93U  H24  C17  C16  119.71  3.000
 93U  H24  C17  C12  119.50  3.000
 93U  C16  C17  C12  120.79  3.000
 93U  H25  C16  C15  120.12  3.000
 93U  H25  C16  C17  119.84  3.000
 93U  C15  C16  C17  120.04  3.000
 93U  H26  C15  C14  120.15  3.000
 93U  H26  C15  C16  120.21  3.000
 93U  C14  C15  C16  119.64  3.000
 93U  H27  C14  C13  119.86  3.000
 93U  H27  C14  C15  120.10  3.000
 93U  C13  C14  C15  120.04  3.000
 93U  H28  C13  C14  119.77  3.000
 93U  H28  C13  C12  119.36  3.000
 93U  C14  C13  C12  120.86  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
 93U  CONST_01  C4   C5   N    C1      0.00   0.0  0
 93U  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 93U  CONST_03  C18  C3   C2   C1    180.00   0.0  0
 93U  CONST_04  C5   N    C1   C2      0.00   0.0  0
 93U  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 93U  CONST_08  N    C5   C4   C3      0.00   0.0  0
 93U  CONST_09  N    C1   C2   C3      0.00   0.0  0
 93U  CONST_10  C22  C23  C18  C3    180.00   0.0  0
 93U  CONST_11  C20  C19  C18  C3    180.00   0.0  0
 93U  CONST_14  C18  C3   C4   C5    180.00   0.0  0
 93U  CONST_15  C21  C22  C23  C18     0.00   0.0  0
 93U  CONST_16  C21  C20  C19  C18     0.00   0.0  0
 93U  CONST_17  C20  C19  C18  C23     0.00   0.0  0
 93U  CONST_18  C20  C21  C22  C23     0.00   0.0  0
 93U  CONST_19  C19  C18  C23  C22     0.00   0.0  0
 93U  CONST_20  C19  C20  C21  C22     0.00   0.0  0
 93U  CONST_21  C15  C14  C13  C12     0.00   0.0  0
 93U  CONST_22  C15  C16  C17  C12     0.00   0.0  0
 93U  CONST_23  C14  C13  C12  C17     0.00   0.0  0
 93U  CONST_24  C14  C15  C16  C17     0.00   0.0  0
 93U  CONST_25  C13  C14  C15  C16     0.00   0.0  0
 93U  CONST_26  C13  C12  C17  C16     0.00   0.0  0
 93U  CONST_27  C6   C5   N    C1    180.00   0.0  0
 93U  CONST_28  C7   C4   C3   C2    180.00   0.0  0
 93U  CONST_29  C6   C5   C4   C3    180.00   0.0  0
 93U  CONST_30  C    C1   C2   C3    180.00   0.0  0
 93U  CONST_31  C24  C2   C3   C4    180.00   0.0  0
 93U  CONST_32  C    C1   N    C5    180.00   0.0  0
 93U  CONST_33  N    C1   C2   C24   180.00   0.0  0
 93U  CONST_34  C18  C3   C2   C24     0.00   0.0  0
 93U  CONST_35  C7   C4   C3   C18     0.00   0.0  0
 93U  CONST_36  N2   C20  C19  C18   180.00   0.0  0
 93U  CONST_37  N2   C20  C21  C22   180.00   0.0  0
 93U  CONST_38  C7   C4   C5   N     180.00   0.0  0
 93U  CONST_39  C14  C13  C12  C11   180.00   0.0  0
 93U  CONST_40  C16  C17  C12  C11   180.00   0.0  0
 93U  CONST_41  H4   C23  C18  C3      0.00   0.0  0
 93U  CONST_42  H7   C19  C18  C3      0.00   0.0  0
 93U  CONST_43  H5   C22  C23  C18   180.00   0.0  0
 93U  CONST_44  H6   C21  C22  C23   180.00   0.0  0
 93U  CONST_45  H27  C14  C13  C12   180.00   0.0  0
 93U  CONST_46  H25  C16  C17  C12   180.00   0.0  0
 93U  CONST_47  H28  C13  C12  C17   180.00   0.0  0
 93U  CONST_48  H26  C15  C16  C17   180.00   0.0  0
 93U  CONST_49  H24  C17  C16  C15   180.00   0.0  0
 93U  CONST_50  C19  C20  N2   O2    180.00   0.0  0
 93U  CONST_51  C21  C20  N2   O2      0.00   0.0  0
 93U  CONST_52  C19  C20  N2   O3      0.00   0.0  0
 93U  CONST_53  C21  C20  N2   O3    180.00   0.0  0
 93U  Var_01    O4   C24  C2   C1     56.94  30.0  2
 93U  Var_02    C5   C4   C7   O1     56.44  30.0  2
 93U  Var_03    C13  C12  C11  N1    -76.08  30.0  2
 93U  Var_04    H11  C    C1   C2     47.40  30.0  2
 93U  Var_05    H8   C6   C5   C4    -75.97  30.0  2
 93U  Var_06    C12  C11  N1   C9    163.28  30.0  3
 93U  Var_07    N1   C9   C8   O1     61.50  30.0  3
 93U  Var_08    C9   C8   O1   C7   -120.17  30.0  1
 93U  Var_09    C10  N1   C9   C8     68.10  30.0  1
 93U  Var_10    H1   C25  O5   C24   176.74  30.0  3
 93U  Var_11    H19  C10  N1   C9     59.62  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
 93U  plan-1  C1   0.020
 93U  plan-1  C2   0.020
 93U  plan-1  C3   0.020
 93U  plan-1  C4   0.020
 93U  plan-1  C5   0.020
 93U  plan-1  C24  0.020
 93U  plan-1  C18  0.020
 93U  plan-1  C6   0.020
 93U  plan-1  N    0.020
 93U  plan-1  C    0.020
 93U  plan-1  C7   0.020
 93U  plan-2  C3   0.020
 93U  plan-2  C18  0.020
 93U  plan-2  C23  0.020
 93U  plan-2  C22  0.020
 93U  plan-2  C21  0.020
 93U  plan-2  C20  0.020
 93U  plan-2  N2   0.020
 93U  plan-2  C19  0.020
 93U  plan-2  H4   0.020
 93U  plan-2  H5   0.020
 93U  plan-2  H6   0.020
 93U  plan-2  H7   0.020
 93U  plan-3  C11  0.020
 93U  plan-3  C12  0.020
 93U  plan-3  C17  0.020
 93U  plan-3  C16  0.020
 93U  plan-3  C15  0.020
 93U  plan-3  C14  0.020
 93U  plan-3  C13  0.020
 93U  plan-3  H24  0.020
 93U  plan-3  H25  0.020
 93U  plan-3  H26  0.020
 93U  plan-3  H27  0.020
 93U  plan-3  H28  0.020
 93U  plan-4  O2   0.020
 93U  plan-4  O3   0.020
 93U  plan-4  C20  0.020
 93U  plan-4  N2   0.020
 93U  plan-5  O1   0.020
 93U  plan-5  C4   0.020
 93U  plan-5  C7   0.020
 93U  plan-5  O    0.020
 93U  plan-6  C2   0.020
 93U  plan-6  O4   0.020
 93U  plan-6  O5   0.020
 93U  plan-6  C24  0.020

