# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 10:06:56 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: (2Z)-4-[(3S)-1-benzyl-3-(4-chlorobenzyl)piperidin-3-yl]-2-hydroxy-4-oxobut-2-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C(/O)=C/C(=O)[C@@]1(CCCN(Cc2ccccc2)C1)Cc3ccc(Cl)cc3
#
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
 CI3  CI3  '(2Z)-4-[(3S)-1-benzyl-3-(4-chlorobenzyl)piperidin-3-yl]-2-hydroxy-4-oxobut-2-enoic acid'  ligand  53  29  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CI3
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
 CI3  CL    CL  CL    0  -0.135  -0.9414  -5.4679  -0.5782
 CI3  CZB   C   CR6   0  -0.058  -0.7639  -3.8173  -0.0733
 CI3  CEA   C   CR16  0  -0.198   0.4993  -3.2490  -0.0274
 CI3  CDA   C   CR16  0  -0.324   0.6289  -1.9306   0.3817
 CI3  CEB   C   CR16  0  -0.195  -1.8855  -3.0898   0.2897
 CI3  CDB   C   CR16  0  -0.314  -1.7327  -1.7722   0.6964
 CI3  CGA   C   CR6   0   0.151  -0.4791  -1.1662   0.7429
 CI3  CO    C   CH2   0  -0.510  -0.3170   0.2640   1.1747
 CI3  CF    C   CT    0  -0.263  -0.3729   1.3010   0.0240
 CI3  CH    C   CH2   0  -0.246   0.7541   1.0680  -0.9848
 CI3  CB    C   C     0   0.460  -1.7182   1.1811  -0.6865
 CI3  O13   O   O     0  -0.399  -1.7916   0.8369  -1.8500
 CI3  CM    C   C1    0  -0.445  -2.9075   1.4979   0.1129
 CI3  CA    C   C     0   0.240  -4.1751   1.4410  -0.3329
 CI3  O14   O   OH1   0  -0.572  -4.5063   1.0882  -1.5650
 CI3  CE    C   C     0   0.517  -5.2878   1.7946   0.6209
 CI3  CG    C   CH2   0  -0.428  -0.2171   2.7233   0.5987
 CI3  OAO   O   O     0  -0.404  -5.1168   2.1401   1.7581
 CI3  OAN   O   OH1   0  -0.605  -6.4631   1.6687   0.0317
 CI3  CK    C   CH2   0  -0.447   1.1953   2.9686   1.1192
 CI3  CI    C   CH2   0  -0.277   2.2446   2.5868   0.0902
 CI3  NJ    N   NT    0  -0.419   2.0537   1.2189  -0.3596
 CI3  CP    C   CH2   0  -0.319   3.1159   0.7901  -1.2450
 CI3  CGB   C   CR6   0   0.082   4.4387   0.6221  -0.5416
 CI3  CD1   C   CR16  0  -0.291   4.5075   0.0587   0.7316
 CI3  CE1   C   CR16  0  -0.237   5.7320  -0.1403   1.3528
 CI3  CZ    C   CR16  0  -0.272   6.9105   0.2208   0.7098
 CI3  CE2   C   CR16  0  -0.241   6.8522   0.7850  -0.5567
 CI3  CD2   C   CR16  0  -0.316   5.6232   0.9872  -1.1735
 CI3  HEB   H   HCR6  0   0.277  -2.8677  -3.5419   0.2638
 CI3  HEA   H   HCR6  0   0.276   1.3740  -3.8244  -0.2991
 CI3  HDB   H   HCR6  0   0.257  -2.6146  -1.2173   0.9928
 CI3  HDA   H   HCR6  0   0.269   1.6176  -1.4907   0.4303
 CI3  HO1C  H   HCH2  0   0.257  -1.0802   0.5086   1.9171
 CI3  HO2C  H   HCH2  0   0.277   0.6447   0.3741   1.6760
 CI3  HG1C  H   HCH2  0   0.240  -0.4332   3.4470  -0.1947
 CI3  HG2C  H   HCH2  0   0.244  -0.9422   2.9058   1.3948
 CI3  HH1C  H   HCH2  0   0.246   0.6815   0.0624  -1.4027
 CI3  HH2C  H   HCH2  0   0.213   0.6380   1.7707  -1.8281
 CI3  HM    H   H     0   0.288  -2.7716   1.7975   1.1412
 CI3  H14   H   HOH1  0   0.490  -5.4647   1.1071  -1.6897
 CI3  HAN   H   HOH1  0   0.505  -7.1899   1.8887   0.6351
 CI3  HK1C  H   HCH2  0   0.243   1.3078   4.0240   1.3752
 CI3  HK2C  H   HCH2  0   0.229   1.3723   2.4074   2.0396
 CI3  HI1C  H   HCH2  0   0.190   2.1976   3.2856  -0.7648
 CI3  HI2C  H   HCH2  0   0.242   3.2406   2.6873   0.5255
 CI3  HP1C  H   HCH2  0   0.251   2.8253  -0.1749  -1.6736
 CI3  HP2C  H   HCH2  0   0.215   3.2411   1.4748  -2.1010
 CI3  HD1   H   HCR6  0   0.249   3.5918  -0.2137   1.2416
 CI3  HD2   H   HCR6  0   0.246   5.5870   1.4376  -2.1589
 CI3  HE1   H   HCR6  0   0.252   5.7679  -0.5788   2.3422
 CI3  HZ    H   HCR6  0   0.253   7.8657   0.0658   1.1948
 CI3  HE2   H   HCR6  0   0.253   7.7635   1.0735  -1.0647

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
 CI3  CL   CZB   single    1.735  0.020  1.735
 CI3  CZB  CEB   aromatic  1.385  0.020  1.385
 CI3  CZB  CEA   aromatic  1.386  0.020  1.386
 CI3  CEB  CDB   aromatic  1.387  0.020  1.387
 CI3  CDB  CGA   aromatic  1.393  0.020  1.393
 CI3  CEA  CDA   aromatic  1.387  0.020  1.387
 CI3  CDA  CGA   aromatic  1.394  0.020  1.394
 CI3  CGA  CO    single    1.503  0.020  1.503
 CI3  CO   CF    single    1.550  0.020  1.550
 CI3  CF   CB    single    1.526  0.020  1.526
 CI3  CF   CG    single    1.542  0.020  1.542
 CI3  CF   CH    single    1.530  0.020  1.530
 CI3  CB   CM    single    1.468  0.020  1.468
 CI3  CB   O13   double    1.216  0.020  1.216
 CI3  CM   CA    double    1.345  0.020  1.345
 CI3  CA   CE    single    1.508  0.020  1.508
 CI3  CA   O14   single    1.324  0.020  1.324
 CI3  CE   OAO   double    1.201  0.020  1.201
 CI3  CE   OAN   single    1.321  0.020  1.321
 CI3  CG   CK    single    1.525  0.020  1.525
 CI3  CK   CI    single    1.518  0.020  1.518
 CI3  CI   NJ    single    1.453  0.020  1.453
 CI3  NJ   CH    single    1.450  0.020  1.450
 CI3  NJ   CP    single    1.448  0.020  1.448
 CI3  CP   CGB   single    1.508  0.020  1.508
 CI3  CGB  CD1   aromatic  1.394  0.020  1.394
 CI3  CGB  CD2   aromatic  1.391  0.020  1.391
 CI3  CD1  CE1   aromatic  1.387  0.020  1.387
 CI3  CE1  CZ    aromatic  1.390  0.020  1.390
 CI3  CZ   CE2   aromatic  1.388  0.020  1.388
 CI3  CE2  CD2   aromatic  1.390  0.020  1.390
 CI3  CEB  HEB   single    0.930  0.020  1.080
 CI3  CEA  HEA   single    0.930  0.020  1.080
 CI3  CDB  HDB   single    0.930  0.020  1.080
 CI3  CDA  HDA   single    0.930  0.020  1.080
 CI3  CO   HO1C  single    0.970  0.020  1.090
 CI3  CO   HO2C  single    0.970  0.020  1.090
 CI3  CG   HG1C  single    0.970  0.020  1.090
 CI3  CG   HG2C  single    0.970  0.020  1.090
 CI3  CH   HH1C  single    0.970  0.020  1.090
 CI3  CH   HH2C  single    0.970  0.020  1.090
 CI3  CM   HM    single    0.930  0.020  1.080
 CI3  O14  H14   single    0.850  0.020  0.980
 CI3  OAN  HAN   single    0.850  0.020  0.980
 CI3  CK   HK1C  single    0.970  0.020  1.090
 CI3  CK   HK2C  single    0.970  0.020  1.090
 CI3  CI   HI1C  single    0.970  0.020  1.090
 CI3  CI   HI2C  single    0.970  0.020  1.090
 CI3  CP   HP1C  single    0.970  0.020  1.090
 CI3  CP   HP2C  single    0.970  0.020  1.090
 CI3  CD1  HD1   single    0.930  0.020  1.080
 CI3  CD2  HD2   single    0.930  0.020  1.080
 CI3  CE1  HE1   single    0.930  0.020  1.080
 CI3  CZ   HZ    single    0.930  0.020  1.080
 CI3  CE2  HE2   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
 CI3  CEB   CZB  CEA   120.93  3.000
 CI3  CEA   CZB  CL    119.53  3.000
 CI3  CEB   CZB  CL    119.53  3.000
 CI3  HEA   CEA  CDA   120.29  3.000
 CI3  HEA   CEA  CZB   120.71  3.000
 CI3  CDA   CEA  CZB   119.00  3.000
 CI3  HDA   CDA  CGA   119.42  3.000
 CI3  HDA   CDA  CEA   118.99  3.000
 CI3  CGA   CDA  CEA   121.58  3.000
 CI3  HEB   CEB  CDB   120.27  3.000
 CI3  HEB   CEB  CZB   120.63  3.000
 CI3  CDB   CEB  CZB   119.10  3.000
 CI3  HDB   CDB  CGA   120.04  3.000
 CI3  HDB   CDB  CEB   118.49  3.000
 CI3  CGA   CDB  CEB   121.47  3.000
 CI3  CO    CGA  CDB   121.37  3.000
 CI3  CO    CGA  CDA   120.71  3.000
 CI3  CDB   CGA  CDA   117.91  3.000
 CI3  HO2C  CO   HO1C  106.34  3.000
 CI3  HO2C  CO   CF    107.80  3.000
 CI3  HO1C  CO   CF    109.24  3.000
 CI3  HO2C  CO   CGA   108.87  3.000
 CI3  HO1C  CO   CGA   109.45  3.000
 CI3  CF    CO   CGA   114.80  3.000
 CI3  CG    CF   CB    109.57  3.000
 CI3  CG    CF   CH    108.16  3.000
 CI3  CB    CF   CH    109.28  3.000
 CI3  CH    CF   CO    111.16  3.000
 CI3  CG    CF   CO    109.68  3.000
 CI3  CB    CF   CO    108.96  3.000
 CI3  HH2C  CH   HH1C  106.69  3.000
 CI3  HH2C  CH   NJ    110.94  3.000
 CI3  HH1C  CH   NJ    108.70  3.000
 CI3  HH2C  CH   CF    109.22  3.000
 CI3  HH1C  CH   CF    110.10  3.000
 CI3  NJ    CH   CF    111.09  3.000
 CI3  CM    CB   O13   122.24  3.000
 CI3  O13   CB   CF    121.41  3.000
 CI3  CM    CB   CF    116.35  3.000
 CI3  HM    CM   CA    116.50  3.000
 CI3  HM    CM   CB    118.47  3.000
 CI3  CA    CM   CB    125.04  3.000
 CI3  CE    CA   O14   117.82  3.000
 CI3  O14   CA   CM    123.76  3.000
 CI3  CE    CA   CM    118.42  3.000
 CI3  H14   O14  CA    111.28  3.000
 CI3  OAN   CE   OAO   125.21  3.000
 CI3  OAN   CE   CA    110.62  3.000
 CI3  OAO   CE   CA    124.16  3.000
 CI3  HG2C  CG   HG1C  106.65  3.000
 CI3  HG2C  CG   CK    109.82  3.000
 CI3  HG1C  CG   CK    108.88  3.000
 CI3  HG2C  CG   CF    111.03  3.000
 CI3  HG1C  CG   CF    108.64  3.000
 CI3  CK    CG   CF    111.66  3.000
 CI3  HAN   OAN  CE    111.57  3.000
 CI3  HK2C  CK   HK1C  106.40  3.000
 CI3  HK2C  CK   CI    109.25  3.000
 CI3  HK1C  CK   CI    109.31  3.000
 CI3  HK2C  CK   CG    110.79  3.000
 CI3  HK1C  CK   CG    109.33  3.000
 CI3  CI    CK   CG    111.61  3.000
 CI3  HI2C  CI   HI1C  106.80  3.000
 CI3  HI2C  CI   NJ    109.28  3.000
 CI3  HI1C  CI   NJ    110.50  3.000
 CI3  HI2C  CI   CK    109.71  3.000
 CI3  HI1C  CI   CK    109.62  3.000
 CI3  NJ    CI   CK    110.84  3.000
 CI3  CP    NJ   CI    111.83  3.000
 CI3  CP    NJ   CH    111.29  3.000
 CI3  CI    NJ   CH    110.45  3.000
 CI3  HP2C  CP   HP1C  105.86  3.000
 CI3  HP2C  CP   CGB   109.37  3.000
 CI3  HP1C  CP   CGB   108.49  3.000
 CI3  HP2C  CP   NJ    111.96  3.000
 CI3  HP1C  CP   NJ    107.80  3.000
 CI3  CGB   CP   NJ    113.04  3.000
 CI3  CD2   CGB  CD1   118.61  3.000
 CI3  CD2   CGB  CP    120.39  3.000
 CI3  CD1   CGB  CP    120.96  3.000
 CI3  HD1   CD1  CE1   119.96  3.000
 CI3  HD1   CD1  CGB   119.34  3.000
 CI3  CE1   CD1  CGB   120.69  3.000
 CI3  HE1   CE1  CZ    119.98  3.000
 CI3  HE1   CE1  CD1   119.76  3.000
 CI3  CZ    CE1  CD1   120.26  3.000
 CI3  HZ    CZ   CE2   120.28  3.000
 CI3  HZ    CZ   CE1   120.24  3.000
 CI3  CE2   CZ   CE1   119.47  3.000
 CI3  HE2   CE2  CD2   119.83  3.000
 CI3  HE2   CE2  CZ    120.08  3.000
 CI3  CD2   CE2  CZ    120.09  3.000
 CI3  HD2   CD2  CE2   119.56  3.000
 CI3  HD2   CD2  CGB   119.57  3.000
 CI3  CE2   CD2  CGB   120.87  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
 CI3  CONST_01  CGA  CDB  CEB  CZB     0.00   0.0  0
 CI3  CONST_02  CGA  CDA  CEA  CZB     0.00   0.0  0
 CI3  CONST_03  CDB  CEB  CZB  CEA     0.00   0.0  0
 CI3  CONST_04  CDB  CGA  CDA  CEA     0.00   0.0  0
 CI3  CONST_05  CEB  CZB  CEA  CDA     0.00   0.0  0
 CI3  CONST_06  CEB  CDB  CGA  CDA     0.00   0.0  0
 CI3  CONST_07  CZ   CE1  CD1  CGB     0.00   0.0  0
 CI3  CONST_08  CZ   CE2  CD2  CGB     0.00   0.0  0
 CI3  CONST_09  CE2  CD2  CGB  CD1     0.00   0.0  0
 CI3  CONST_10  CE2  CZ   CE1  CD1     0.00   0.0  0
 CI3  CONST_11  CD2  CGB  CD1  CE1     0.00   0.0  0
 CI3  CONST_12  CD2  CE2  CZ   CE1     0.00   0.0  0
 CI3  CONST_13  CDB  CEB  CZB  CL    180.00   0.0  0
 CI3  CONST_14  CDA  CEA  CZB  CL    180.00   0.0  0
 CI3  CONST_15  CO   CGA  CDA  CEA   180.00   0.0  0
 CI3  CONST_16  CO   CGA  CDB  CEB   180.00   0.0  0
 CI3  CONST_17  CE1  CD1  CGB  CP    180.00   0.0  0
 CI3  CONST_18  CE2  CD2  CGB  CP    180.00   0.0  0
 CI3  CONST_19  HDB  CDB  CEB  CZB   180.00   0.0  0
 CI3  CONST_20  HDA  CDA  CEA  CZB   180.00   0.0  0
 CI3  CONST_21  HEB  CEB  CZB  CEA   180.00   0.0  0
 CI3  CONST_22  HEA  CEA  CZB  CEB   180.00   0.0  0
 CI3  CONST_23  HE1  CE1  CD1  CGB   180.00   0.0  0
 CI3  CONST_24  HE2  CE2  CD2  CGB   180.00   0.0  0
 CI3  CONST_25  HD2  CD2  CGB  CD1   180.00   0.0  0
 CI3  CONST_26  HZ   CZ   CE1  CD1   180.00   0.0  0
 CI3  CONST_27  HD1  CD1  CE1  CZ    180.00   0.0  0
 CI3  CONST_28  HAN  OAN  CE   CA    180.00   0.0  0
 CI3  Var_01    CI   CK   CG   CF     50.41  30.0  1
 CI3  Var_02    CI   NJ   CH   CF    -64.49  30.0  1
 CI3  Var_03    CK   CI   NJ   CH     60.94  30.0  1
 CI3  Var_04    NJ   CI   CK   CG    -54.06  30.0  1
 CI3  Var_05    CF   CO   CGA  CDA    89.19  30.0  2
 CI3  Var_06    CGB  CP   NJ   CH   -166.54  30.0  3
 CI3  Var_07    CD1  CGB  CP   NJ     40.05  30.0  2
 CI3  Var_08    CA   CM   CB   CF   -179.50  30.0  2
 CI3  Var_09    CE   CA   CM   CB    179.78   0.0  2
 CI3  Var_10    OAO  CE   CA   CM      0.82  30.0  2

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
 CI3  chir_01  CF  CB  CG  CH  positiv

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
 CI3  plan-1  CL   0.020
 CI3  plan-1  CZB  0.020
 CI3  plan-1  CEA  0.020
 CI3  plan-1  CDA  0.020
 CI3  plan-1  CEB  0.020
 CI3  plan-1  CDB  0.020
 CI3  plan-1  CGA  0.020
 CI3  plan-1  CO   0.020
 CI3  plan-1  HEB  0.020
 CI3  plan-1  HEA  0.020
 CI3  plan-1  HDB  0.020
 CI3  plan-1  HDA  0.020
 CI3  plan-2  CP   0.020
 CI3  plan-2  CGB  0.020
 CI3  plan-2  CD1  0.020
 CI3  plan-2  CE1  0.020
 CI3  plan-2  CZ   0.020
 CI3  plan-2  CE2  0.020
 CI3  plan-2  CD2  0.020
 CI3  plan-2  HD1  0.020
 CI3  plan-2  HD2  0.020
 CI3  plan-2  HE1  0.020
 CI3  plan-2  HZ   0.020
 CI3  plan-2  HE2  0.020
 CI3  plan-3  CA   0.020
 CI3  plan-3  CE   0.020
 CI3  plan-3  OAO  0.020
 CI3  plan-3  OAN  0.020
 CI3  plan-3  HAN  0.020
 CI3  plan-4  CF   0.020
 CI3  plan-4  CB   0.020
 CI3  plan-4  O13  0.020
 CI3  plan-4  CM   0.020
 CI3  plan-5  CB   0.020
 CI3  plan-5  CM   0.020
 CI3  plan-5  CA   0.020
 CI3  plan-5  O14  0.020
 CI3  plan-5  CE   0.020
 CI3  plan-5  HM   0.020

