# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:20:00 2022
#   Inital geometry file: a 142 line input string
#   Ligand name: ~{O}3-(2-methoxyethyl) ~{O}5-propan-2-yl (4~{S})-2,6-dimethyl-4-(3-nitrophenyl)-1,4-dihydropyridine-3,5-dicarboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCOC(=O)C1=C(C)NC(=C([C@H]1c2cccc(c2)[N+]([O-])=O)C(=O)OC(C)C)C
#
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
 6U9  6U9  '~{O}3-(2-methoxyethyl) ~{O}5-propan-2-yl (4~{S})-2,6-dimethyl-4-(3-nitrophenyl)-1,4-dihydropyridine-3,5-dicarboxylate'  ligand  56  30  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6U9
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
 6U9  C13  C  CH3    0  -0.727   1.7412  -3.7569  -1.7036
 6U9  C12  C  C      0   0.362   0.9476  -2.6359  -1.1061
 6U9  C10  C  CH3    0  -0.734  -2.7500  -2.3828  -1.0763
 6U9  C01  C  CH3    0  -0.394  -6.8953  -1.8181   0.8435
 6U9  O02  O  O2     0  -0.479  -5.6530  -1.3239   1.2721
 6U9  C03  C  CH2    0  -0.164  -5.4671   0.0254   0.9389
 6U9  C04  C  CH2    0  -0.208  -4.0919   0.4676   1.3625
 6U9  O05  O  O2     0  -0.462  -3.1467  -0.2822   0.6024
 6U9  C06  C  C      0   0.593  -1.8546  -0.0315   0.7724
 6U9  O07  O  O      0  -0.474  -1.4556   0.8383   1.5205
 6U9  C08  C  C      0  -0.171  -0.9573  -0.8845  -0.0058
 6U9  C09  C  C      0   0.358  -1.3515  -1.9283  -0.7774
 6U9  N11  N  NH1    0  -0.723  -0.3933  -2.7059  -1.3726
 6U9  C14  C  C      0  -0.171   1.4195  -1.6122  -0.3535
 6U9  C15  C  CH1    0  -0.399   0.5032  -0.4919   0.0910
 6U9  C16  C  CR6    0   0.217   0.7604   0.7676  -0.7193
 6U9  C17  C  CR16   0  -0.328   1.1271   1.9506  -0.0959
 6U9  C18  C  CR6    0   0.261   1.3651   3.0822  -0.8617
 6U9  C19  C  CR16   0  -0.288   1.2411   3.0766  -2.2438
 6U9  C20  C  CR16   0  -0.235   0.8678   1.8941  -2.8595
 6U9  C21  C  CR16   0  -0.277   0.6304   0.7536  -2.1050
 6U9  N22  N  N      1   0.327   1.7633   4.3118  -0.1934
 6U9  O23  O  O     -1  -0.379   1.9043   4.2898   1.0072
 6U9  O24  O  O      0  -0.381   1.9367   5.2984  -0.8707
 6U9  C25  C  C      0   0.580   2.8412  -1.5234  -0.0135
 6U9  O26  O  O      0  -0.470   3.7061  -2.3111  -0.3384
 6U9  O27  O  O2     0  -0.473   3.0932  -0.4350   0.7104
 6U9  C28  C  CH1    0   0.020   4.4430  -0.1410   1.1154
 6U9  C29  C  CH3    0  -0.669   4.5155   1.3621   1.2930
 6U9  C30  C  CH3    0  -0.676   4.7798  -0.8906   2.3914
 6U9  H1   H  HCH3   0   0.250   1.0958  -4.4191  -2.2782
 6U9  H2   H  HCH3   0   0.267   2.5200  -3.3832  -2.3641
 6U9  H3   H  HCH3   0   0.269   2.2275  -4.3511  -0.9331
 6U9  H5   H  HCH3   0   0.268  -3.3316  -1.5952  -1.5492
 6U9  H6   H  HCH3   0   0.252  -2.7342  -3.2390  -1.7485
 6U9  H7   H  HCH3   0   0.272  -3.2792  -2.6782  -0.1731
 6U9  H8   H  HCH3   0   0.204  -7.7344  -1.2918   1.3143
 6U9  H9   H  HCH3   0   0.204  -7.0160  -1.7380  -0.2435
 6U9  H10  H  HCH3   0   0.234  -6.9526  -2.8706   1.1182
 6U9  H11  H  HCH2   0   0.209  -5.5963   0.1897  -0.1404
 6U9  H12  H  HCH2   0   0.214  -6.1988   0.6689   1.4478
 6U9  H13  H  HCH2   0   0.241  -3.9854   1.5373   1.1694
 6U9  H14  H  HCH2   0   0.239  -3.9414   0.2999   2.4321
 6U9  H17  H  HNH1   0   0.413  -0.7114  -3.4802  -1.9331
 6U9  H20  H  HCH1   0   0.273   0.7186  -0.2539   1.1339
 6U9  H21  H  HCR6   0   0.280   1.2298   1.9792   0.9789
 6U9  H22  H  HCR6   0   0.294   1.4312   3.9616  -2.8328
 6U9  H23  H  HCR6   0   0.274   0.7653   1.8627  -3.9355
 6U9  H24  H  HCR6   0   0.267   0.3426  -0.1604  -2.6109
 6U9  H25  H  HCH1   0   0.234   5.1269  -0.4448   0.3196
 6U9  H26  H  HCH3   0   0.228   3.8440   1.7032   2.0826
 6U9  H27  H  HCH3   0   0.236   5.5304   1.6473   1.5693
 6U9  H28  H  HCH3   0   0.239   4.2576   1.8851   0.3721
 6U9  H29  H  HCH3   0   0.235   5.7965  -0.6480   2.7029
 6U9  H30  H  HCH3   0   0.228   4.1051  -0.6056   3.2006
 6U9  H31  H  HCH3   0   0.241   4.7243  -1.9702   2.2556

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
 6U9  O24  N22  double    1.209  0.020  1.209
 6U9  N22  O23  single    1.209  0.020  1.209
 6U9  N22  C18  single    1.455  0.020  1.455
 6U9  C01  O02  single    1.404  0.020  1.404
 6U9  O02  C03  single    1.402  0.020  1.402
 6U9  C19  C18  aromatic  1.388  0.020  1.388
 6U9  C19  C20  aromatic  1.384  0.020  1.384
 6U9  C03  C04  single    1.505  0.020  1.505
 6U9  C18  C17  aromatic  1.387  0.020  1.387
 6U9  C20  C21  aromatic  1.388  0.020  1.388
 6U9  C17  C16  aromatic  1.387  0.020  1.387
 6U9  C04  O05  single    1.426  0.020  1.426
 6U9  C21  C16  aromatic  1.392  0.020  1.392
 6U9  O05  C06  single    1.327  0.020  1.327
 6U9  C16  C15  single    1.520  0.020  1.520
 6U9  C06  O07  double    1.215  0.020  1.215
 6U9  C06  C08  single    1.462  0.020  1.462
 6U9  C15  C08  single    1.515  0.020  1.515
 6U9  C15  C14  single    1.514  0.020  1.514
 6U9  O26  C25  double    1.214  0.020  1.214
 6U9  C08  C09  double    1.357  0.020  1.357
 6U9  C25  C14  single    1.464  0.020  1.464
 6U9  C25  O27  single    1.331  0.020  1.331
 6U9  C14  C12  double    1.355  0.020  1.355
 6U9  C09  C10  single    1.500  0.020  1.500
 6U9  C09  N11  single    1.370  0.020  1.370
 6U9  C28  O27  single    1.439  0.020  1.439
 6U9  C28  C30  single    1.518  0.020  1.518
 6U9  C28  C29  single    1.515  0.020  1.515
 6U9  C12  N11  single    1.369  0.020  1.369
 6U9  C12  C13  single    1.498  0.020  1.498
 6U9  C13  H1   single    0.970  0.020  1.090
 6U9  C13  H2   single    0.970  0.020  1.090
 6U9  C13  H3   single    0.970  0.020  1.090
 6U9  C10  H5   single    0.970  0.020  1.090
 6U9  C10  H6   single    0.970  0.020  1.090
 6U9  C10  H7   single    0.970  0.020  1.090
 6U9  C01  H8   single    0.970  0.020  1.090
 6U9  C01  H9   single    0.970  0.020  1.090
 6U9  C01  H10  single    0.970  0.020  1.090
 6U9  C03  H11  single    0.970  0.020  1.090
 6U9  C03  H12  single    0.970  0.020  1.090
 6U9  C04  H13  single    0.970  0.020  1.090
 6U9  C04  H14  single    0.970  0.020  1.090
 6U9  N11  H17  single    0.860  0.020  1.020
 6U9  C15  H20  single    0.970  0.020  1.090
 6U9  C17  H21  single    0.930  0.020  1.080
 6U9  C19  H22  single    0.930  0.020  1.080
 6U9  C20  H23  single    0.930  0.020  1.080
 6U9  C21  H24  single    0.930  0.020  1.080
 6U9  C28  H25  single    0.970  0.020  1.090
 6U9  C29  H26  single    0.970  0.020  1.090
 6U9  C29  H27  single    0.970  0.020  1.090
 6U9  C29  H28  single    0.970  0.020  1.090
 6U9  C30  H29  single    0.970  0.020  1.090
 6U9  C30  H30  single    0.970  0.020  1.090
 6U9  C30  H31  single    0.970  0.020  1.090

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
 6U9  H3   C13  H2   107.32  3.000
 6U9  H3   C13  H1   107.86  3.000
 6U9  H2   C13  H1   108.24  3.000
 6U9  H3   C13  C12  111.30  3.000
 6U9  H2   C13  C12  111.38  3.000
 6U9  H1   C13  C12  110.59  3.000
 6U9  C14  C12  N11  119.19  3.000
 6U9  N11  C12  C13  113.77  3.000
 6U9  C14  C12  C13  127.04  3.000
 6U9  H7   C10  H6   107.82  3.000
 6U9  H7   C10  H5   107.32  3.000
 6U9  H6   C10  H5   107.99  3.000
 6U9  H7   C10  C09  111.74  3.000
 6U9  H6   C10  C09  110.34  3.000
 6U9  H5   C10  C09  111.46  3.000
 6U9  H10  C01  H9   108.34  3.000
 6U9  H10  C01  H8   108.38  3.000
 6U9  H9   C01  H8   107.84  3.000
 6U9  H10  C01  O02  108.04  3.000
 6U9  H9   C01  O02  111.98  3.000
 6U9  H8   C01  O02  112.15  3.000
 6U9  C03  O02  C01  112.55  3.000
 6U9  H12  C03  H11  106.79  3.000
 6U9  H12  C03  C04  107.81  3.000
 6U9  H11  C03  C04  109.86  3.000
 6U9  H12  C03  O02  111.40  3.000
 6U9  H11  C03  O02  111.19  3.000
 6U9  C04  C03  O02  109.69  3.000
 6U9  H14  C04  H13  108.05  3.000
 6U9  H14  C04  O05  110.47  3.000
 6U9  H13  C04  O05  110.86  3.000
 6U9  H14  C04  C03  110.86  3.000
 6U9  H13  C04  C03  109.09  3.000
 6U9  O05  C04  C03  107.52  3.000
 6U9  C06  O05  C04  118.54  3.000
 6U9  C08  C06  O07  122.95  3.000
 6U9  C08  C06  O05  114.78  3.000
 6U9  O07  C06  O05  122.27  3.000
 6U9  C15  C08  C09  121.04  3.000
 6U9  C09  C08  C06  124.97  3.000
 6U9  C15  C08  C06  113.97  3.000
 6U9  N11  C09  C08  118.72  3.000
 6U9  N11  C09  C10  113.17  3.000
 6U9  C08  C09  C10  128.11  3.000
 6U9  H17  N11  C09  117.20  3.000
 6U9  H17  N11  C12  117.18  3.000
 6U9  C09  N11  C12  124.86  3.000
 6U9  C25  C14  C15  118.33  3.000
 6U9  C25  C14  C12  120.84  3.000
 6U9  C15  C14  C12  120.74  3.000
 6U9  H20  C15  C16  107.18  3.000
 6U9  H20  C15  C14  108.82  3.000
 6U9  C16  C15  C14  110.75  3.000
 6U9  H20  C15  C08  107.92  3.000
 6U9  C14  C15  C08  111.90  3.000
 6U9  C16  C15  C08  110.11  3.000
 6U9  C21  C16  C17  118.74  3.000
 6U9  C21  C16  C15  120.44  3.000
 6U9  C17  C16  C15  120.82  3.000
 6U9  H21  C17  C18  120.76  3.000
 6U9  H21  C17  C16  119.68  3.000
 6U9  C18  C17  C16  119.56  3.000
 6U9  N22  C18  C19  119.04  3.000
 6U9  C19  C18  C17  122.09  3.000
 6U9  N22  C18  C17  118.88  3.000
 6U9  H22  C19  C20  120.33  3.000
 6U9  H22  C19  C18  121.61  3.000
 6U9  C20  C19  C18  118.07  3.000
 6U9  H23  C20  C21  120.06  3.000
 6U9  H23  C20  C19  119.53  3.000
 6U9  C21  C20  C19  120.41  3.000
 6U9  H24  C21  C20  118.99  3.000
 6U9  H24  C21  C16  119.88  3.000
 6U9  C20  C21  C16  121.13  3.000
 6U9  O24  N22  O23  123.66  3.000
 6U9  O23  N22  C18  118.21  3.000
 6U9  O24  N22  C18  118.13  3.000
 6U9  O27  C25  O26  122.76  3.000
 6U9  O27  C25  C14  111.08  3.000
 6U9  O26  C25  C14  126.16  3.000
 6U9  C28  O27  C25  119.83  3.000
 6U9  H25  C28  C30  109.64  3.000
 6U9  H25  C28  C29  109.34  3.000
 6U9  C30  C28  C29  112.38  3.000
 6U9  H25  C28  O27  108.98  3.000
 6U9  C29  C28  O27  106.29  3.000
 6U9  C30  C28  O27  110.11  3.000
 6U9  H28  C29  H27  107.99  3.000
 6U9  H28  C29  H26  108.41  3.000
 6U9  H27  C29  H26  107.93  3.000
 6U9  H28  C29  C28  111.45  3.000
 6U9  H27  C29  C28  109.51  3.000
 6U9  H26  C29  C28  111.44  3.000
 6U9  H31  C30  H30  108.64  3.000
 6U9  H31  C30  H29  107.67  3.000
 6U9  H30  C30  H29  107.84  3.000
 6U9  H31  C30  C28  111.92  3.000
 6U9  H30  C30  C28  110.92  3.000
 6U9  H29  C30  C28  109.70  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
 6U9  CONST_01  C19  C18  C17  C16     0.00   0.0  0
 6U9  CONST_02  C19  C20  C21  C16     0.00   0.0  0
 6U9  CONST_03  C20  C19  C18  C17     0.00   0.0  0
 6U9  CONST_04  C20  C21  C16  C17     0.00   0.0  0
 6U9  CONST_05  C21  C20  C19  C18     0.00   0.0  0
 6U9  CONST_06  C21  C16  C17  C18     0.00   0.0  0
 6U9  CONST_07  C18  C17  C16  C15   180.00   0.0  0
 6U9  CONST_08  C20  C21  C16  C15   180.00   0.0  0
 6U9  CONST_09  N22  C18  C17  C16   180.00   0.0  0
 6U9  CONST_10  N22  C18  C19  C20   180.00   0.0  0
 6U9  CONST_11  H21  C17  C16  C15     0.00   0.0  0
 6U9  CONST_12  H24  C21  C16  C15     0.00   0.0  0
 6U9  CONST_13  H23  C20  C21  C16   180.00   0.0  0
 6U9  CONST_14  H22  C19  C18  C17   180.00   0.0  0
 6U9  CONST_15  O24  N22  C18  C17   180.00   0.0  0
 6U9  CONST_16  O23  N22  C18  C17     0.00   0.0  0
 6U9  CONST_17  O24  N22  C18  C19     0.00   0.0  0
 6U9  CONST_18  O23  N22  C18  C19   180.00   0.0  0
 6U9  Var_01    C08  C09  N11  C12     9.70  30.0  1
 6U9  Var_02    C14  C12  N11  C09   -10.16  30.0  1
 6U9  Var_03    C15  C08  C09  N11     6.10  30.0  1
 6U9  Var_04    C15  C14  C12  N11    -5.24  30.0  1
 6U9  Var_05    O26  C25  C14  C12    -0.48  30.0  1
 6U9  Var_06    H5   C10  C09  C08    58.72  30.0  3
 6U9  Var_07    H1   C13  C12  N11     1.78  30.0  3
 6U9  Var_08    C08  C06  O05  C04   177.58  30.0  3
 6U9  Var_09    C04  C03  O02  C01  -177.06  30.0  3
 6U9  Var_10    O05  C04  C03  O02    64.05  30.0  3
 6U9  Var_11    C30  C28  O27  C25   -84.67  30.0  2
 6U9  Var_12    H8   C01  O02  C03   -61.90  30.0  3
 6U9  Var_13    H29  C30  C28  O27  -178.89  30.0  3
 6U9  Var_14    H26  C29  C28  O27    62.54  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 6U9  chir_01  C15  C16  C08  C14  negativ

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
 6U9  plan-1  C15  0.020
 6U9  plan-1  C16  0.020
 6U9  plan-1  C17  0.020
 6U9  plan-1  C18  0.020
 6U9  plan-1  C19  0.020
 6U9  plan-1  C20  0.020
 6U9  plan-1  C21  0.020
 6U9  plan-1  N22  0.020
 6U9  plan-1  H21  0.020
 6U9  plan-1  H22  0.020
 6U9  plan-1  H23  0.020
 6U9  plan-1  H24  0.020
 6U9  plan-2  C18  0.020
 6U9  plan-2  N22  0.020
 6U9  plan-2  O23  0.020
 6U9  plan-2  O24  0.020
 6U9  plan-3  C12  0.020
 6U9  plan-3  C09  0.020
 6U9  plan-3  N11  0.020
 6U9  plan-3  H17  0.020
 6U9  plan-4  O05  0.020
 6U9  plan-4  C06  0.020
 6U9  plan-4  O07  0.020
 6U9  plan-4  C08  0.020
 6U9  plan-5  C14  0.020
 6U9  plan-5  C25  0.020
 6U9  plan-5  O26  0.020
 6U9  plan-5  O27  0.020

