# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 05:03:37 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: (3E,5R)-8-(2-chlorophenyl)-5-methyl-2,6-dioxooct-3-enoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](\C=C\C(=O)C([O-])=O)C(=O)CCc1ccccc1Cl
#
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
 KEK  KEK  (3E,5R)-8-(2-chlorophenyl)-5-methyl-2,6-dioxooct-3-enoate  ligand  34  20  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_KEK
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
 KEK  CL    CL  CL     0  -0.133   4.0251  -1.6512   0.9181
 KEK  C02   C   CR6    0  -0.121   4.2890   0.0074   0.4647
 KEK  C03   C   CR16   0  -0.194   5.3784   0.6664   1.0150
 KEK  C04   C   CR16   0  -0.282   5.6173   1.9891   0.6744
 KEK  C05   C   CR16   0  -0.228   4.7682   2.6364  -0.2116
 KEK  C06   C   CR16   0  -0.329   3.6863   1.9569  -0.7506
 KEK  C07   C   CR6    0   0.212   3.4178   0.6275  -0.4287
 KEK  C08   C   CH2    0  -0.512   2.2195  -0.0642  -1.0135
 KEK  C09   C   CH2    0  -0.569   1.0637  -0.1077  -0.0197
 KEK  C10   C   C      0   0.440  -0.1862  -0.7556  -0.5472
 KEK  C11   C   CH1    0  -0.455  -1.2568  -1.0448   0.4957
 KEK  C12   C   C1     0  -0.092  -2.6283  -0.8274  -0.0501
 KEK  C13   C   C1     0  -0.369  -3.5345  -0.0369   0.5274
 KEK  C14   C   C      0   0.189  -4.8884   0.1445  -0.0384
 KEK  C15   C   C      0   0.348  -5.8441   1.1266   0.6990
 KEK  O16   O   OC    -1  -0.583  -6.9251   1.3414   0.1356
 KEK  O17   O   O      0  -0.574  -5.4205   1.5870   1.7739
 KEK  O18   O   O      0  -0.401  -5.2565  -0.4397  -1.0362
 KEK  C19   C   CH3    0  -0.648  -1.0763  -2.5020   0.9558
 KEK  O20   O   O      0  -0.396  -0.3326  -1.0546  -1.7090
 KEK  H03   H   HCR6   0   0.278   6.0343   0.1502   1.7030
 KEK  H04   H   HCR6   0   0.266   6.4659   2.5064   1.1015
 KEK  H05   H   HCR6   0   0.262   4.9485   3.6670  -0.4864
 KEK  H06   H   HCR6   0   0.259   3.0280   2.4647  -1.4452
 KEK  H081  H   HCH2   0   0.265   1.9093   0.4703  -1.9121
 KEK  H082  H   HCH2   0   0.258   2.4791  -1.0776  -1.3260
 KEK  H091  H   HCH2   0   0.273   1.3519  -0.6158   0.9057
 KEK  H092  H   HCH2   0   0.294   0.7842   0.9058   0.2916
 KEK  H11   H   HCH1   0   0.278  -1.0967  -0.3908   1.3575
 KEK  H12   H   H      0   0.266  -2.8856  -1.3642  -0.9587
 KEK  H191  H   HCH3   0   0.255  -1.7784  -2.7292   1.7566
 KEK  H192  H   HCH3   0   0.240  -1.2541  -3.1994   0.1372
 KEK  H193  H   HCH3   0   0.245  -0.0687  -2.6730   1.3372
 KEK  H13   H   H      0   0.259  -3.2925   0.5030   1.4333

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
 KEK  CL   C02   single    1.740  0.020  1.740
 KEK  C02  C03   aromatic  1.387  0.020  1.387
 KEK  C02  C07   aromatic  1.393  0.020  1.393
 KEK  C03  C04   aromatic  1.387  0.020  1.387
 KEK  C04  C05   aromatic  1.387  0.020  1.387
 KEK  C05  C06   aromatic  1.387  0.020  1.387
 KEK  C06  C07   aromatic  1.394  0.020  1.394
 KEK  C07  C08   single    1.502  0.020  1.502
 KEK  C08  C09   single    1.525  0.020  1.525
 KEK  C09  C10   single    1.503  0.020  1.503
 KEK  C10  C11   single    1.522  0.020  1.522
 KEK  C10  O20   double    1.209  0.020  1.209
 KEK  C11  C12   single    1.492  0.020  1.492
 KEK  C11  C19   single    1.539  0.020  1.539
 KEK  C12  C13   double    1.334  0.020  1.334
 KEK  C13  C14   single    1.478  0.020  1.478
 KEK  C14  C15   single    1.556  0.020  1.556
 KEK  C14  O18   double    1.213  0.020  1.213
 KEK  C15  O16   deloc     1.238  0.020  1.238
 KEK  C15  O17   deloc     1.244  0.020  1.244
 KEK  C03  H03   single    0.930  0.020  1.080
 KEK  C04  H04   single    0.930  0.020  1.080
 KEK  C05  H05   single    0.930  0.020  1.080
 KEK  C06  H06   single    0.930  0.020  1.080
 KEK  C08  H081  single    0.970  0.020  1.090
 KEK  C08  H082  single    0.970  0.020  1.090
 KEK  C09  H091  single    0.970  0.020  1.090
 KEK  C09  H092  single    0.970  0.020  1.090
 KEK  C11  H11   single    0.970  0.020  1.090
 KEK  C12  H12   single    0.930  0.020  1.080
 KEK  C19  H191  single    0.970  0.020  1.090
 KEK  C19  H192  single    0.970  0.020  1.090
 KEK  C19  H193  single    0.970  0.020  1.090
 KEK  C13  H13   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
 KEK  C07   C02  C03   122.28  3.000
 KEK  C07   C02  CL    119.77  3.000
 KEK  C03   C02  CL    117.95  3.000
 KEK  H03   C03  C04   120.47  3.000
 KEK  H03   C03  C02   120.12  3.000
 KEK  C04   C03  C02   119.41  3.000
 KEK  H04   C04  C05   120.61  3.000
 KEK  H04   C04  C03   119.63  3.000
 KEK  C05   C04  C03   119.77  3.000
 KEK  H05   C05  C06   119.88  3.000
 KEK  H05   C05  C04   120.31  3.000
 KEK  C06   C05  C04   119.81  3.000
 KEK  H06   C06  C07   118.56  3.000
 KEK  H06   C06  C05   119.58  3.000
 KEK  C07   C06  C05   121.86  3.000
 KEK  C08   C07  C06   120.19  3.000
 KEK  C08   C07  C02   122.92  3.000
 KEK  C06   C07  C02   116.87  3.000
 KEK  H082  C08  H081  106.66  3.000
 KEK  H082  C08  C09   109.90  3.000
 KEK  H081  C08  C09   109.60  3.000
 KEK  H082  C08  C07   110.44  3.000
 KEK  H081  C08  C07   108.78  3.000
 KEK  C09   C08  C07   111.35  3.000
 KEK  H092  C09  H091  104.85  3.000
 KEK  H092  C09  C10   106.62  3.000
 KEK  H091  C09  C10   108.40  3.000
 KEK  H092  C09  C08   110.60  3.000
 KEK  H091  C09  C08   111.39  3.000
 KEK  C10   C09  C08   114.44  3.000
 KEK  O20   C10  C11   121.76  3.000
 KEK  O20   C10  C09   123.00  3.000
 KEK  C11   C10  C09   115.23  3.000
 KEK  H11   C11  C19   108.27  3.000
 KEK  H11   C11  C12   109.61  3.000
 KEK  C19   C11  C12   110.81  3.000
 KEK  H11   C11  C10   108.86  3.000
 KEK  C19   C11  C10   107.60  3.000
 KEK  C12   C11  C10   111.60  3.000
 KEK  H12   C12  C13   119.60  3.000
 KEK  H12   C12  C11   116.85  3.000
 KEK  C13   C12  C11   123.53  3.000
 KEK  H13   C13  C14   117.64  3.000
 KEK  H13   C13  C12   120.41  3.000
 KEK  C14   C13  C12   121.94  3.000
 KEK  O18   C14  C15   120.47  3.000
 KEK  O18   C14  C13   122.24  3.000
 KEK  C15   C14  C13   117.29  3.000
 KEK  O17   C15  O16   128.81  3.000
 KEK  O17   C15  C14   115.71  3.000
 KEK  O16   C15  C14   115.48  3.000
 KEK  H193  C19  H192  108.23  3.000
 KEK  H193  C19  H191  107.80  3.000
 KEK  H192  C19  H191  108.27  3.000
 KEK  H193  C19  C11   111.19  3.000
 KEK  H192  C19  C11   111.24  3.000
 KEK  H191  C19  C11   110.00  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
 KEK  CONST_01  C05  C04  C03  C02     0.00   0.0  0
 KEK  CONST_02  C05  C06  C07  C02     0.00   0.0  0
 KEK  CONST_03  C06  C07  C02  C03     0.00   0.0  0
 KEK  CONST_04  C06  C05  C04  C03     0.00   0.0  0
 KEK  CONST_05  C07  C02  C03  C04     0.00   0.0  0
 KEK  CONST_06  C07  C06  C05  C04     0.00   0.0  0
 KEK  CONST_07  C04  C03  C02  CL    180.00   0.0  0
 KEK  CONST_08  C06  C07  C02  CL    180.00   0.0  0
 KEK  CONST_09  C08  C07  C02  C03   180.00   0.0  0
 KEK  CONST_10  C08  C07  C06  C05   180.00   0.0  0
 KEK  CONST_11  H04  C04  C03  C02   180.00   0.0  0
 KEK  CONST_12  H06  C06  C07  C02   180.00   0.0  0
 KEK  CONST_13  H05  C05  C04  C03   180.00   0.0  0
 KEK  CONST_14  H03  C03  C04  C05   180.00   0.0  0
 KEK  Var_01    C09  C08  C07  C02    78.61  30.0  2
 KEK  Var_02    C10  C09  C08  C07   178.51  30.0  3
 KEK  Var_03    C14  C13  C12  C11  -179.48   0.0  2
 KEK  Var_04    C11  C10  C09  C08   169.05  30.0  3
 KEK  Var_05    C15  C14  C13  C12  -178.12  30.0  2
 KEK  Var_06    O16  C15  C14  C13   174.05  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
 KEK  chir_01  C11  C10  C12  C19  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
 KEK  plan-1  CL   0.020
 KEK  plan-1  C02  0.020
 KEK  plan-1  C03  0.020
 KEK  plan-1  C04  0.020
 KEK  plan-1  C05  0.020
 KEK  plan-1  C06  0.020
 KEK  plan-1  C07  0.020
 KEK  plan-1  C08  0.020
 KEK  plan-1  H03  0.020
 KEK  plan-1  H04  0.020
 KEK  plan-1  H05  0.020
 KEK  plan-1  H06  0.020
 KEK  plan-2  C09  0.020
 KEK  plan-2  C10  0.020
 KEK  plan-2  C11  0.020
 KEK  plan-2  O20  0.020
 KEK  plan-3  C13  0.020
 KEK  plan-3  C14  0.020
 KEK  plan-3  C15  0.020
 KEK  plan-3  O18  0.020
 KEK  plan-4  C14  0.020
 KEK  plan-4  C15  0.020
 KEK  plan-4  O16  0.020
 KEK  plan-4  O17  0.020
 KEK  plan-5  C11  0.020
 KEK  plan-5  C12  0.020
 KEK  plan-5  C13  0.020
 KEK  plan-5  C14  0.020
 KEK  plan-5  H12  0.020
 KEK  plan-5  H13  0.020

