# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 18:33:05 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: ~{O}3-ethyl ~{O}5-methyl (4~{S})-2-(2-azanylethoxymethyl)-4-(2-chlorophenyl)-6-methyl-1,4-dihydropyridine-3,5-dicarboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)C1=C(COCCN)NC(=C([C@@H]1c2ccccc2Cl)C(=O)OC)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
 6UB  6UB  '~{O}3-ethyl ~{O}5-methyl (4~{S})-2-(2-azanylethoxymethyl)-4-(2-chlorophenyl)-6-methyl-1,4-dihydropyridine-3,5-dicarboxylate'  ligand  53  28  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6UB
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
 6UB  CAA   C   CH3   0  -0.687  -2.2108  -4.9908   1.6188
 6UB  CAL   C   CH2   0  -0.176  -0.8658  -4.3468   1.3843
 6UB  OAS   O   O2    0  -0.474  -1.0903  -2.9566   1.1202
 6UB  CAV   C   C     0   0.583  -0.0351  -2.1806   0.8855
 6UB  OAF   O   O     0  -0.463   1.1024  -2.6001   0.9264
 6UB  CAY   C   C     0  -0.164  -0.3561  -0.7848   0.5956
 6UB  CAW   C   C     0   0.299  -1.6065  -0.2999   0.3877
 6UB  NAP   N   NH1   0  -0.737  -1.7887   1.0400   0.2095
 6UB  CAT   C   C     0   0.350  -0.8117   1.9748   0.4099
 6UB  CAX   C   C     0  -0.163   0.4679   1.5745   0.6209
 6UB  CBB   C   CH1   0  -0.398   0.8582   0.1156   0.4730
 6UB  CBA   C   CR6   0   0.303   1.5658  -0.1215  -0.8542
 6UB  CAK   C   CR16  0  -0.312   0.8629   0.1224  -2.0346
 6UB  CAI   C   CR16  0  -0.232   1.4285  -0.0608  -3.2851
 6UB  CAH   C   CR16  0  -0.285   2.7400  -0.5040  -3.3851
 6UB  CAJ   C   CR16  0  -0.204   3.4657  -0.7563  -2.2331
 6UB  CAZ   C   CR6   0  -0.135   2.8791  -0.5646  -0.9872
 6UB  CLAG  CL  CL    0  -0.138   3.8714  -0.9032   0.3973
 6UB  CAU   C   C     0   0.567   1.5116   2.5491   0.9323
 6UB  OAE   O   O     0  -0.473   1.3619   3.7371   1.1360
 6UB  OAQ   O   O2    0  -0.457   2.7107   1.9718   0.9752
 6UB  CAB   C   CH3   0  -0.417   3.8354   2.7856   1.2758
 6UB  CAC   C   CH3   0  -0.737  -1.3192   3.3851   0.3850
 6UB  C24   C   CH2   0  -0.218  -2.9036  -1.1007   0.3688
 6UB  O25   O   O2    0  -0.491  -3.9892  -0.3317  -0.0596
 6UB  C26   C   CH2   0  -0.183  -4.1907  -0.2907  -1.4614
 6UB  C27   C   CH2   0  -0.304  -4.9131   0.9964  -1.7942
 6UB  N28   N   NH2   0  -0.804  -4.0736   2.1442  -1.4768
 6UB  H1    H   HCH3  0   0.238  -2.0704  -6.0524   1.8201
 6UB  H2    H   HCH3  0   0.234  -2.7207  -4.5522   2.4767
 6UB  H3    H   HCH3  0   0.235  -2.8574  -4.8983   0.7461
 6UB  H4    H   HCH2  0   0.231  -0.2239  -4.4571   2.2606
 6UB  H5    H   HCH2  0   0.231  -0.3556  -4.8088   0.5363
 6UB  H6    H   HNH1  0   0.434  -2.7143   1.3760  -0.0679
 6UB  H9    H   HCH1  0   0.269   1.5485  -0.1433   1.2751
 6UB  H10   H   HCR6  0   0.255  -0.1621   0.4675  -1.9711
 6UB  H11   H   HCR6  0   0.257   0.8490   0.1417  -4.1760
 6UB  H12   H   HCR6  0   0.262   3.2008  -0.6546  -4.3523
 6UB  H13   H   HCR6  0   0.272   4.4889  -1.1014  -2.2998
 6UB  H14   H   HCH3  0   0.232   3.7538   3.2409   2.2634
 6UB  H15   H   HCH3  0   0.244   4.6938   2.1201   1.2581
 6UB  H16   H   HCH3  0   0.232   3.9756   3.5718   0.5335
 6UB  H17   H   HCH3  0   0.252  -2.3320   3.4116  -0.0128
 6UB  H18   H   HCH3  0   0.264  -1.3440   3.8072   1.3894
 6UB  H19   H   HCH3  0   0.260  -0.6921   4.0305  -0.2233
 6UB  H20   H   HCH2  0   0.247  -2.7841  -1.9956  -0.2456
 6UB  H21   H   HCH2  0   0.273  -3.1239  -1.4337   1.3848
 6UB  H22   H   HCH2  0   0.213  -3.2381  -0.3295  -2.0075
 6UB  H23   H   HCH2  0   0.234  -4.7823  -1.1546  -1.7861
 6UB  H24   H   HCH2  0   0.219  -5.2240   0.9565  -2.8444
 6UB  H25   H   HCH2  0   0.237  -5.8274   1.0554  -1.2004
 6UB  H26   H   HNH2  0   0.356  -3.4195   2.3121  -2.2314
 6UB  H27   H   HNH2  0   0.367  -4.6341   2.9824  -1.4018

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
 6UB  CAH   CAJ  aromatic  1.385  0.020  1.385
 6UB  CAH   CAI  aromatic  1.388  0.020  1.388
 6UB  CAJ   CAZ  aromatic  1.390  0.020  1.390
 6UB  CAI   CAK  aromatic  1.385  0.020  1.385
 6UB  CLAG  CAZ  single    1.737  0.020  1.737
 6UB  CAZ   CBA  aromatic  1.392  0.020  1.392
 6UB  CAK   CBA  aromatic  1.395  0.020  1.395
 6UB  CBA   CBB  single    1.523  0.020  1.523
 6UB  OAE   CAU  double    1.215  0.020  1.215
 6UB  CBB   CAX  single    1.517  0.020  1.517
 6UB  CBB   CAY  single    1.517  0.020  1.517
 6UB  CAX   CAU  single    1.462  0.020  1.462
 6UB  CAX   CAT  double    1.357  0.020  1.357
 6UB  CAU   OAQ  single    1.332  0.020  1.332
 6UB  CAY   CAV  single    1.461  0.020  1.461
 6UB  CAY   CAW  double    1.357  0.020  1.357
 6UB  CAL   OAS  single    1.433  0.020  1.433
 6UB  CAL   CAA  single    1.510  0.020  1.510
 6UB  CAV   OAF  double    1.213  0.020  1.213
 6UB  CAV   OAS  single    1.331  0.020  1.331
 6UB  NAP   CAT  single    1.367  0.020  1.367
 6UB  NAP   CAW  single    1.364  0.020  1.364
 6UB  CAT   CAC  single    1.499  0.020  1.499
 6UB  CAW   C24  single    1.524  0.020  1.524
 6UB  OAQ   CAB  single    1.420  0.020  1.420
 6UB  C24   O25  single    1.398  0.020  1.398
 6UB  O25   C26  single    1.417  0.020  1.417
 6UB  C26   C27  single    1.513  0.020  1.513
 6UB  C27   N28  single    1.457  0.020  1.457
 6UB  CAA   H1   single    0.970  0.020  1.090
 6UB  CAA   H2   single    0.970  0.020  1.090
 6UB  CAA   H3   single    0.970  0.020  1.090
 6UB  CAL   H4   single    0.970  0.020  1.090
 6UB  CAL   H5   single    0.970  0.020  1.090
 6UB  NAP   H6   single    0.860  0.020  1.020
 6UB  CBB   H9   single    0.970  0.020  1.090
 6UB  CAK   H10  single    0.930  0.020  1.080
 6UB  CAI   H11  single    0.930  0.020  1.080
 6UB  CAH   H12  single    0.930  0.020  1.080
 6UB  CAJ   H13  single    0.930  0.020  1.080
 6UB  CAB   H14  single    0.970  0.020  1.090
 6UB  CAB   H15  single    0.970  0.020  1.090
 6UB  CAB   H16  single    0.970  0.020  1.090
 6UB  CAC   H17  single    0.970  0.020  1.090
 6UB  CAC   H18  single    0.970  0.020  1.090
 6UB  CAC   H19  single    0.970  0.020  1.090
 6UB  C24   H20  single    0.970  0.020  1.090
 6UB  C24   H21  single    0.970  0.020  1.090
 6UB  C26   H22  single    0.970  0.020  1.090
 6UB  C26   H23  single    0.970  0.020  1.090
 6UB  C27   H24  single    0.970  0.020  1.090
 6UB  C27   H25  single    0.970  0.020  1.090
 6UB  N28   H26  single    0.890  0.020  1.040
 6UB  N28   H27  single    0.890  0.020  1.040

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
 6UB  H3    CAA  H2   108.57  3.000
 6UB  H3    CAA  H1   107.88  3.000
 6UB  H2    CAA  H1   107.87  3.000
 6UB  H3    CAA  CAL  111.59  3.000
 6UB  H2    CAA  CAL  111.55  3.000
 6UB  H1    CAA  CAL  109.24  3.000
 6UB  H5    CAL  H4   107.80  3.000
 6UB  H5    CAL  OAS  109.91  3.000
 6UB  H4    CAL  OAS  109.76  3.000
 6UB  H5    CAL  CAA  110.87  3.000
 6UB  H4    CAL  CAA  110.86  3.000
 6UB  OAS   CAL  CAA  107.64  3.000
 6UB  CAV   OAS  CAL  118.30  3.000
 6UB  CAY   CAV  OAF  122.89  3.000
 6UB  OAF   CAV  OAS  122.41  3.000
 6UB  CAY   CAV  OAS  114.70  3.000
 6UB  CBB   CAY  CAW  120.88  3.000
 6UB  CAW   CAY  CAV  125.04  3.000
 6UB  CBB   CAY  CAV  114.03  3.000
 6UB  C24   CAW  NAP  113.63  3.000
 6UB  C24   CAW  CAY  126.73  3.000
 6UB  NAP   CAW  CAY  119.61  3.000
 6UB  H6    NAP  CAT  117.50  3.000
 6UB  H6    NAP  CAW  118.61  3.000
 6UB  CAT   NAP  CAW  123.86  3.000
 6UB  CAC   CAT  CAX  126.82  3.000
 6UB  CAC   CAT  NAP  113.52  3.000
 6UB  CAX   CAT  NAP  119.66  3.000
 6UB  CAU   CAX  CBB  118.56  3.000
 6UB  CAU   CAX  CAT  120.65  3.000
 6UB  CBB   CAX  CAT  120.73  3.000
 6UB  H9    CBB  CBA  108.08  3.000
 6UB  H9    CBB  CAX  108.64  3.000
 6UB  CBA   CBB  CAX  110.75  3.000
 6UB  H9    CBB  CAY  107.86  3.000
 6UB  CAX   CBB  CAY  110.91  3.000
 6UB  CBA   CBB  CAY  110.49  3.000
 6UB  CAZ   CBA  CAK  116.74  3.000
 6UB  CAK   CBA  CBB  118.43  3.000
 6UB  CAZ   CBA  CBB  124.83  3.000
 6UB  H10   CAK  CAI  118.79  3.000
 6UB  H10   CAK  CBA  118.86  3.000
 6UB  CAI   CAK  CBA  122.35  3.000
 6UB  H11   CAI  CAH  120.43  3.000
 6UB  H11   CAI  CAK  120.01  3.000
 6UB  CAH   CAI  CAK  119.56  3.000
 6UB  H12   CAH  CAJ  119.68  3.000
 6UB  H12   CAH  CAI  120.75  3.000
 6UB  CAJ   CAH  CAI  119.56  3.000
 6UB  H13   CAJ  CAZ  119.88  3.000
 6UB  H13   CAJ  CAH  120.16  3.000
 6UB  CAZ   CAJ  CAH  119.95  3.000
 6UB  CLAG  CAZ  CAJ  116.51  3.000
 6UB  CLAG  CAZ  CBA  121.66  3.000
 6UB  CAJ   CAZ  CBA  121.83  3.000
 6UB  OAQ   CAU  OAE  121.98  3.000
 6UB  OAQ   CAU  CAX  111.16  3.000
 6UB  OAE   CAU  CAX  126.86  3.000
 6UB  CAB   OAQ  CAU  118.13  3.000
 6UB  H16   CAB  H15  109.21  3.000
 6UB  H16   CAB  H14  108.98  3.000
 6UB  H15   CAB  H14  109.25  3.000
 6UB  H16   CAB  OAQ  111.77  3.000
 6UB  H15   CAB  OAQ  105.74  3.000
 6UB  H14   CAB  OAQ  111.81  3.000
 6UB  H19   CAC  H18  107.41  3.000
 6UB  H19   CAC  H17  108.54  3.000
 6UB  H18   CAC  H17  107.84  3.000
 6UB  H19   CAC  CAT  111.89  3.000
 6UB  H18   CAC  CAT  110.90  3.000
 6UB  H17   CAC  CAT  110.12  3.000
 6UB  H21   C24  H20  107.20  3.000
 6UB  H21   C24  O25  107.24  3.000
 6UB  H20   C24  O25  111.31  3.000
 6UB  H21   C24  CAW  108.69  3.000
 6UB  H20   C24  CAW  110.14  3.000
 6UB  O25   C24  CAW  112.06  3.000
 6UB  C26   O25  C24  115.45  3.000
 6UB  H23   C26  H22  107.03  3.000
 6UB  H23   C26  C27  110.34  3.000
 6UB  H22   C26  C27  109.55  3.000
 6UB  H23   C26  O25  110.31  3.000
 6UB  H22   C26  O25  111.55  3.000
 6UB  C27   C26  O25  108.07  3.000
 6UB  H25   C27  H24  106.59  3.000
 6UB  H25   C27  N28  108.75  3.000
 6UB  H24   C27  N28  113.63  3.000
 6UB  H25   C27  C26  109.03  3.000
 6UB  H24   C27  C26  108.38  3.000
 6UB  N28   C27  C26  110.31  3.000
 6UB  H27   N28  H26  106.02  3.000
 6UB  H27   N28  C27  110.47  3.000
 6UB  H26   N28  C27  109.90  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
 6UB  CONST_01  CAH   CAJ  CAZ  CBA     0.00   0.0  0
 6UB  CONST_02  CAH   CAI  CAK  CBA     0.00   0.0  0
 6UB  CONST_03  CAJ   CAH  CAI  CAK     0.00   0.0  0
 6UB  CONST_04  CAJ   CAZ  CBA  CAK     0.00   0.0  0
 6UB  CONST_05  CAZ   CAJ  CAH  CAI     0.00   0.0  0
 6UB  CONST_06  CAZ   CBA  CAK  CAI     0.00   0.0  0
 6UB  CONST_07  CAJ   CAZ  CBA  CBB   180.00   0.0  0
 6UB  CONST_08  CAI   CAK  CBA  CBB   180.00   0.0  0
 6UB  CONST_09  CLAG  CAZ  CBA  CBB     0.00   0.0  0
 6UB  CONST_10  CLAG  CAZ  CBA  CAK   180.00   0.0  0
 6UB  CONST_11  CLAG  CAZ  CAJ  CAH   180.00   0.0  0
 6UB  CONST_12  H10   CAK  CBA  CBB     0.00   0.0  0
 6UB  CONST_13  H13   CAJ  CAZ  CBA   180.00   0.0  0
 6UB  CONST_14  H11   CAI  CAK  CBA   180.00   0.0  0
 6UB  CONST_15  H12   CAH  CAI  CAK   180.00   0.0  0
 6UB  Var_01    CAT   NAP  CAW  CAY    -9.56  30.0  1
 6UB  Var_02    CAX   CAT  NAP  CAW     9.45  30.0  1
 6UB  Var_03    CBB   CAX  CAT  NAP     7.37  30.0  1
 6UB  Var_04    CBB   CAY  CAW  NAP    -7.17  30.0  1
 6UB  Var_05    O25   C24  CAW  CAY  -171.47  30.0  3
 6UB  Var_06    OAE   CAU  CAX  CAT     6.12  30.0  2
 6UB  Var_07    H17   CAC  CAT  NAP   -12.91  30.0  3
 6UB  Var_08    CAY   CAV  OAS  CAL   178.66  30.0  1
 6UB  Var_09    C27   C26  O25  C24  -154.23  30.0  3
 6UB  Var_10    N28   C27  C26  O25    64.60  30.0  3
 6UB  Var_11    H1    CAA  CAL  OAS   179.85  30.0  3
 6UB  Var_12    H4    CAL  OAS  CAV    59.06  30.0  1
 6UB  Var_13    H14   CAB  OAQ  CAU    61.20  30.0  3
 6UB  Var_14    H26   N28  C27  C26    82.07  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
 6UB  chir_01  CBB  CBA  CAX  CAY  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
 6UB  plan-1  CBB   0.020
 6UB  plan-1  CBA   0.020
 6UB  plan-1  CAK   0.020
 6UB  plan-1  CAI   0.020
 6UB  plan-1  CAH   0.020
 6UB  plan-1  CAJ   0.020
 6UB  plan-1  CAZ   0.020
 6UB  plan-1  CLAG  0.020
 6UB  plan-1  H10   0.020
 6UB  plan-1  H11   0.020
 6UB  plan-1  H12   0.020
 6UB  plan-1  H13   0.020
 6UB  plan-2  CAW   0.020
 6UB  plan-2  NAP   0.020
 6UB  plan-2  CAT   0.020
 6UB  plan-2  H6    0.020
 6UB  plan-3  CAX   0.020
 6UB  plan-3  CAU   0.020
 6UB  plan-3  OAE   0.020
 6UB  plan-3  OAQ   0.020
 6UB  plan-4  OAS   0.020
 6UB  plan-4  CAV   0.020
 6UB  plan-4  OAF   0.020
 6UB  plan-4  CAY   0.020

