# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 06:19:06 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: ethyl 3-[4-(2-hydroxyphenyl)-3-oxidanyl-phenyl]propanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)CCc1ccc(c(O)c1)c2ccccc2O
#
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
 5VK  5VK  'ethyl 3-[4-(2-hydroxyphenyl)-3-oxidanyl-phenyl]propanoate'  ligand  39  21  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_5VK
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
 5VK  CAA  C  CH3   0  -0.689   7.3987   1.4266  -1.1262
 5VK  CAL  C  CH2   0  -0.182   6.7651   0.4035  -0.2152
 5VK  OAO  O  O2    0  -0.459   5.3390   0.5308  -0.3345
 5VK  CAP  C  C     0   0.605   4.5774  -0.2861   0.3800
 5VK  OAB  O  O     0  -0.455   5.0176  -1.1400   1.1097
 5VK  CAM  C  CH2   0  -0.575   3.1134  -0.0014   0.1699
 5VK  CAN  C  CH2   0  -0.512   2.2031  -0.9968   0.8819
 5VK  CAQ  C  CR6   0   0.132   0.7543  -0.6459   0.6840
 5VK  CAK  C  CR16  0  -0.434   0.0957  -1.0144  -0.4851
 5VK  CAS  C  CR6   0   0.355  -1.2364  -0.6742  -0.6976
 5VK  OAD  O  OH1   0  -0.622  -1.8831  -0.9923  -1.8345
 5VK  CAI  C  CR16  0  -0.332   0.0584   0.0816   1.6425
 5VK  CAJ  C  CR16  0  -0.264  -1.2723   0.4144   1.4316
 5VK  CAU  C  CR6   0  -0.046  -1.9458   0.0412   0.2742
 5VK  CAT  C  CR6   0  -0.031  -3.3587   0.4273   0.0691
 5VK  CAH  C  CR16  0  -0.280  -3.7187   1.7696  -0.0036
 5VK  CAF  C  CR16  0  -0.274  -5.0406   2.1630  -0.1649
 5VK  CAE  C  CR16  0  -0.252  -6.0275   1.1927  -0.2559
 5VK  CAG  C  CR16  0  -0.380  -5.6956  -0.1522  -0.1772
 5VK  CAR  C  CR6   0   0.334  -4.3687  -0.5395  -0.0101
 5VK  OAC  O  OH1   0  -0.621  -4.0080  -1.8312   0.1056
 5VK  H1   H  HCH3  0   0.236   7.1312   1.2574  -2.1691
 5VK  H2   H  HCH3  0   0.236   7.1113   2.4416  -0.8527
 5VK  H3   H  HCH3  0   0.239   8.4828   1.3534  -1.0437
 5VK  H4   H  HCH2  0   0.235   7.0698  -0.6070  -0.4940
 5VK  H5   H  HCH2  0   0.234   7.0619   0.5698   0.8223
 5VK  H6   H  HCH2  0   0.286   2.9117   1.0160   0.5196
 5VK  H7   H  HCH2  0   0.281   2.9082   0.0098  -0.9042
 5VK  H8   H  HCH2  0   0.254   2.3961  -2.0032   0.5046
 5VK  H9   H  HCH2  0   0.254   2.4325  -1.0099   1.9485
 5VK  H10  H  HCR6  0   0.260   0.6309  -1.5743  -1.2468
 5VK  H11  H  HOH1  0   0.473  -1.2993  -1.4823  -2.4243
 5VK  H12  H  HCR6  0   0.244   0.5504   0.3821   2.5594
 5VK  H13  H  HCR6  0   0.249  -1.8112   0.9691   2.1902
 5VK  H14  H  HCR6  0   0.251  -2.9389   2.5187   0.0597
 5VK  H15  H  HCR6  0   0.251  -5.2924   3.2134  -0.2235
 5VK  H16  H  HCR6  0   0.258  -7.0640   1.4761  -0.3851
 5VK  H17  H  HCR6  0   0.268  -6.4739  -0.9047  -0.2357
 5VK  H18  H  HOH1  0   0.473  -4.7837  -2.4003   0.0489

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
 5VK  CAA  CAL  single    1.509  0.020  1.509
 5VK  CAL  OAO  single    1.437  0.020  1.437
 5VK  CAG  CAE  aromatic  1.387  0.020  1.387
 5VK  CAG  CAR  aromatic  1.392  0.020  1.392
 5VK  OAO  CAP  single    1.326  0.020  1.326
 5VK  CAE  CAF  aromatic  1.387  0.020  1.387
 5VK  OAC  CAR  single    1.346  0.020  1.346
 5VK  CAR  CAT  aromatic  1.400  0.020  1.400
 5VK  OAB  CAP  double    1.206  0.020  1.206
 5VK  CAF  CAH  aromatic  1.389  0.020  1.389
 5VK  CAP  CAM  single    1.506  0.020  1.506
 5VK  CAT  CAH  aromatic  1.392  0.020  1.392
 5VK  CAT  CAU  single    1.479  0.020  1.479
 5VK  CAU  CAJ  aromatic  1.390  0.020  1.390
 5VK  CAU  CAS  aromatic  1.400  0.020  1.400
 5VK  CAJ  CAI  aromatic  1.388  0.020  1.388
 5VK  OAD  CAS  single    1.346  0.020  1.346
 5VK  CAS  CAK  aromatic  1.391  0.020  1.391
 5VK  CAI  CAQ  aromatic  1.390  0.020  1.390
 5VK  CAM  CAN  single    1.525  0.020  1.525
 5VK  CAK  CAQ  aromatic  1.392  0.020  1.392
 5VK  CAQ  CAN  single    1.504  0.020  1.504
 5VK  CAA  H1   single    0.970  0.020  1.090
 5VK  CAA  H2   single    0.970  0.020  1.090
 5VK  CAA  H3   single    0.970  0.020  1.090
 5VK  CAL  H4   single    0.970  0.020  1.090
 5VK  CAL  H5   single    0.970  0.020  1.090
 5VK  CAM  H6   single    0.970  0.020  1.090
 5VK  CAM  H7   single    0.970  0.020  1.090
 5VK  CAN  H8   single    0.970  0.020  1.090
 5VK  CAN  H9   single    0.970  0.020  1.090
 5VK  CAK  H10  single    0.930  0.020  1.080
 5VK  OAD  H11  single    0.850  0.020  0.980
 5VK  CAI  H12  single    0.930  0.020  1.080
 5VK  CAJ  H13  single    0.930  0.020  1.080
 5VK  CAH  H14  single    0.930  0.020  1.080
 5VK  CAF  H15  single    0.930  0.020  1.080
 5VK  CAE  H16  single    0.930  0.020  1.080
 5VK  CAG  H17  single    0.930  0.020  1.080
 5VK  OAC  H18  single    0.850  0.020  0.980

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
 5VK  H3   CAA  H2   107.81  3.000
 5VK  H3   CAA  H1   107.83  3.000
 5VK  H2   CAA  H1   108.66  3.000
 5VK  H3   CAA  CAL  109.05  3.000
 5VK  H2   CAA  CAL  111.66  3.000
 5VK  H1   CAA  CAL  111.68  3.000
 5VK  H5   CAL  H4   107.93  3.000
 5VK  H5   CAL  OAO  109.59  3.000
 5VK  H4   CAL  OAO  109.75  3.000
 5VK  H5   CAL  CAA  110.86  3.000
 5VK  H4   CAL  CAA  110.86  3.000
 5VK  OAO  CAL  CAA  107.85  3.000
 5VK  CAP  OAO  CAL  118.09  3.000
 5VK  CAM  CAP  OAB  124.94  3.000
 5VK  CAM  CAP  OAO  111.51  3.000
 5VK  OAB  CAP  OAO  123.54  3.000
 5VK  H7   CAM  H6   105.65  3.000
 5VK  H7   CAM  CAN  110.68  3.000
 5VK  H6   CAM  CAN  110.34  3.000
 5VK  H7   CAM  CAP  108.74  3.000
 5VK  H6   CAM  CAP  108.07  3.000
 5VK  CAN  CAM  CAP  113.06  3.000
 5VK  H9   CAN  H8   106.83  3.000
 5VK  H9   CAN  CAQ  109.51  3.000
 5VK  H8   CAN  CAQ  109.87  3.000
 5VK  H9   CAN  CAM  109.79  3.000
 5VK  H8   CAN  CAM  109.56  3.000
 5VK  CAQ  CAN  CAM  111.18  3.000
 5VK  CAI  CAQ  CAK  118.75  3.000
 5VK  CAK  CAQ  CAN  120.32  3.000
 5VK  CAI  CAQ  CAN  120.91  3.000
 5VK  H10  CAK  CAS  119.39  3.000
 5VK  H10  CAK  CAQ  119.50  3.000
 5VK  CAS  CAK  CAQ  121.12  3.000
 5VK  CAU  CAS  OAD  117.62  3.000
 5VK  OAD  CAS  CAK  122.09  3.000
 5VK  CAU  CAS  CAK  120.28  3.000
 5VK  H11  OAD  CAS  110.25  3.000
 5VK  H12  CAI  CAJ  119.85  3.000
 5VK  H12  CAI  CAQ  120.10  3.000
 5VK  CAJ  CAI  CAQ  120.05  3.000
 5VK  H13  CAJ  CAU  118.65  3.000
 5VK  H13  CAJ  CAI  119.56  3.000
 5VK  CAU  CAJ  CAI  121.78  3.000
 5VK  CAT  CAU  CAJ  120.54  3.000
 5VK  CAJ  CAU  CAS  118.02  3.000
 5VK  CAT  CAU  CAS  121.42  3.000
 5VK  CAR  CAT  CAH  118.45  3.000
 5VK  CAH  CAT  CAU  120.41  3.000
 5VK  CAR  CAT  CAU  121.10  3.000
 5VK  H14  CAH  CAF  119.74  3.000
 5VK  H14  CAH  CAT  118.55  3.000
 5VK  CAF  CAH  CAT  121.71  3.000
 5VK  H15  CAF  CAE  120.68  3.000
 5VK  H15  CAF  CAH  120.20  3.000
 5VK  CAE  CAF  CAH  119.13  3.000
 5VK  H16  CAE  CAG  119.32  3.000
 5VK  H16  CAE  CAF  120.40  3.000
 5VK  CAG  CAE  CAF  120.28  3.000
 5VK  H17  CAG  CAR  119.84  3.000
 5VK  H17  CAG  CAE  119.87  3.000
 5VK  CAR  CAG  CAE  120.29  3.000
 5VK  OAC  CAR  CAG  122.18  3.000
 5VK  OAC  CAR  CAT  117.67  3.000
 5VK  CAG  CAR  CAT  120.14  3.000
 5VK  H18  OAC  CAR  110.23  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
 5VK  CONST_01  CAU  CAJ  CAI  CAQ    0.00   0.0  0
 5VK  CONST_02  CAU  CAS  CAK  CAQ    0.00   0.0  0
 5VK  CONST_03  CAT  CAU  CAS  CAK  180.00   0.0  0
 5VK  CONST_04  CAJ  CAU  CAS  CAK    0.00   0.0  0
 5VK  CONST_05  CAJ  CAI  CAQ  CAK    0.00   0.0  0
 5VK  CONST_08  CAI  CAJ  CAU  CAS    0.00   0.0  0
 5VK  CONST_09  CAI  CAQ  CAK  CAS    0.00   0.0  0
 5VK  CONST_10  CAT  CAU  CAJ  CAI  180.00   0.0  0
 5VK  CONST_13  CAG  CAR  CAT  CAU  180.00   0.0  0
 5VK  CONST_14  CAF  CAH  CAT  CAU  180.00   0.0  0
 5VK  CONST_15  CAE  CAG  CAR  CAT    0.00   0.0  0
 5VK  CONST_16  CAE  CAF  CAH  CAT    0.00   0.0  0
 5VK  CONST_17  CAG  CAE  CAF  CAH    0.00   0.0  0
 5VK  CONST_18  CAG  CAR  CAT  CAH    0.00   0.0  0
 5VK  CONST_19  CAR  CAG  CAE  CAF    0.00   0.0  0
 5VK  CONST_20  CAR  CAT  CAH  CAF    0.00   0.0  0
 5VK  CONST_21  CAJ  CAI  CAQ  CAN  180.00   0.0  0
 5VK  CONST_22  CAS  CAK  CAQ  CAN  180.00   0.0  0
 5VK  CONST_23  OAD  CAS  CAK  CAQ  180.00   0.0  0
 5VK  CONST_24  CAT  CAU  CAS  OAD    0.00   0.0  0
 5VK  CONST_25  CAJ  CAU  CAS  OAD  180.00   0.0  0
 5VK  CONST_26  OAC  CAR  CAT  CAU    0.00   0.0  0
 5VK  CONST_27  OAC  CAR  CAT  CAH  180.00   0.0  0
 5VK  CONST_28  OAC  CAR  CAG  CAE  180.00   0.0  0
 5VK  CONST_29  H13  CAJ  CAI  CAQ  180.00   0.0  0
 5VK  CONST_30  H12  CAI  CAQ  CAK  180.00   0.0  0
 5VK  CONST_31  H10  CAK  CAQ  CAI  180.00   0.0  0
 5VK  CONST_32  H14  CAH  CAT  CAU    0.00   0.0  0
 5VK  CONST_33  H17  CAG  CAR  CAT  180.00   0.0  0
 5VK  CONST_34  H15  CAF  CAH  CAT  180.00   0.0  0
 5VK  CONST_35  H16  CAE  CAF  CAH  180.00   0.0  0
 5VK  Var_01    CAI  CAQ  CAN  CAM  -96.71  30.0  2
 5VK  Var_02    CAQ  CAN  CAM  CAP  178.02  30.0  3
 5VK  Var_03    OAB  CAP  OAO  CAL   -1.01  30.0  3
 5VK  Var_04    CAN  CAM  CAP  OAO  175.08  30.0  3
 5VK  Var_05    H1   CAA  CAL  OAO  -61.47  30.0  3
 5VK  Var_06    H4   CAL  OAO  CAP   58.69  30.0  1

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
 5VK  plan-1  CAN  0.020
 5VK  plan-1  CAQ  0.020
 5VK  plan-1  CAK  0.020
 5VK  plan-1  CAS  0.020
 5VK  plan-1  OAD  0.020
 5VK  plan-1  CAI  0.020
 5VK  plan-1  CAJ  0.020
 5VK  plan-1  CAU  0.020
 5VK  plan-1  CAT  0.020
 5VK  plan-1  H10  0.020
 5VK  plan-1  H12  0.020
 5VK  plan-1  H13  0.020
 5VK  plan-2  CAU  0.020
 5VK  plan-2  CAT  0.020
 5VK  plan-2  CAH  0.020
 5VK  plan-2  CAF  0.020
 5VK  plan-2  CAE  0.020
 5VK  plan-2  CAG  0.020
 5VK  plan-2  CAR  0.020
 5VK  plan-2  OAC  0.020
 5VK  plan-2  H14  0.020
 5VK  plan-2  H15  0.020
 5VK  plan-2  H16  0.020
 5VK  plan-2  H17  0.020
 5VK  plan-3  OAO  0.020
 5VK  plan-3  CAP  0.020
 5VK  plan-3  OAB  0.020
 5VK  plan-3  CAM  0.020

