# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 13:47:08 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: methyl 2-[2-(2-benzylpyridin-3-yl)ethyl]-3-chloro-4,6-dihydroxybenzoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)c1c(O)cc(O)c(Cl)c1CCc2cccnc2Cc3ccccc3
#
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
 VC4  VC4  'methyl 2-[2-(2-benzylpyridin-3-yl)ethyl]-3-chloro-4,6-dihydroxybenzoate'  ligand  48  28  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_VC4
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
 VC4  O01  O   OH1   0  -0.616  -4.9594  -0.1519  -1.3208
 VC4  C02  C   CR6   0   0.417  -3.9216  -0.6865  -0.6623
 VC4  C03  C   CR16  0  -0.543  -3.8246  -2.0505  -0.4285
 VC4  C04  C   CR6   0   0.465  -2.7220  -2.5614   0.2402
 VC4  O05  O   OH1   0  -0.605  -2.5759  -3.8632   0.4999
 VC4  C06  C   CR6   0  -0.268  -1.7153  -1.6913   0.6639
 VC4  CL7  CL  CL    0  -0.099  -0.3723  -2.3872   1.5107
 VC4  C08  C   CR6   0   0.250  -1.7862  -0.3232   0.4268
 VC4  C09  C   CH2   0  -0.539  -0.6770   0.5902   0.8692
 VC4  C10  C   CH2   0  -0.528   0.4646   0.6456  -0.1593
 VC4  C11  C   CR6   0   0.044   1.5099   1.6464   0.2434
 VC4  C12  C   CR6   0   0.211   2.6790   1.3021   0.9324
 VC4  C13  C   CH2   0  -0.607   3.0255  -0.1309   1.2530
 VC4  C14  C   CR6   0   0.139   3.6667  -0.8325   0.0772
 VC4  C15  C   CR16  0  -0.317   3.1070  -1.9824  -0.4718
 VC4  C16  C   CR16  0  -0.245   3.7046  -2.6200  -1.5531
 VC4  C17  C   CR16  0  -0.271   4.8747  -2.1145  -2.1005
 VC4  C18  C   CR16  0  -0.240   5.4444  -0.9687  -1.5570
 VC4  C19  C   CR16  0  -0.286   4.8452  -0.3349  -0.4786
 VC4  N20  N   N     0  -0.422   3.5748   2.2115   1.3115
 VC4  C21  C   CR16  0  -0.084   3.3622   3.4901   1.0301
 VC4  C22  C   CR16  0  -0.324   2.2387   3.9365   0.3552
 VC4  C23  C   CR16  0  -0.185   1.3043   2.9929  -0.0363
 VC4  C24  C   CR6   0  -0.220  -2.9077   0.1776  -0.2420
 VC4  C25  C   C     0   0.516  -3.0240   1.6296  -0.5601
 VC4  O26  O   O2    0  -0.434  -4.0584   2.1844   0.0457
 VC4  C27  C   CH3   0  -0.426  -4.3153   3.5651  -0.2214
 VC4  O28  O   O     0  -0.432  -2.2650   2.2321  -1.2787
 VC4  H1   H   HOH1  0   0.485  -5.5897  -0.8350  -1.5777
 VC4  H2   H   HCR6  0   0.299  -4.6076  -2.7188  -0.7702
 VC4  H3   H   HOH1  0   0.487  -3.3231  -4.3640   0.1514
 VC4  H4   H   HCH2  0   0.271  -1.0579   1.5983   1.0371
 VC4  H5   H   HCH2  0   0.269  -0.2853   0.2604   1.8330
 VC4  H6   H   HCH2  0   0.261   0.8944  -0.3478  -0.2862
 VC4  H7   H   HCH2  0   0.273   0.0545   0.9282  -1.1293
 VC4  H8   H   HCH2  0   0.278   3.7206  -0.1252   2.0947
 VC4  H9   H   HCH2  0   0.255   2.1451  -0.6857   1.5801
 VC4  H10  H   HCR6  0   0.235   2.1949  -2.3903  -0.0517
 VC4  H11  H   HCR6  0   0.254   3.2527  -3.5132  -1.9654
 VC4  H12  H   HCR6  0   0.254   5.3425  -2.6101  -2.9413
 VC4  H13  H   HCR6  0   0.254   6.3602  -0.5689  -1.9736
 VC4  H14  H   HCR6  0   0.249   5.2995   0.5563  -0.0619
 VC4  H15  H   HCR6  0   0.260   4.1216   4.1909   1.3596
 VC4  H16  H   HCR6  0   0.267   2.1014   4.9880   0.1443
 VC4  H17  H   HCR6  0   0.263   0.4078   3.2977  -0.5641
 VC4  H18  H   HCH3  0   0.254  -5.1894   3.8243   0.3680
 VC4  H19  H   HCH3  0   0.242  -3.4759   4.1909   0.0804
 VC4  H20  H   HCH3  0   0.242  -4.5265   3.7313  -1.2774

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
 VC4  C21  C22  aromatic  1.384  0.020  1.384
 VC4  C21  N20  aromatic  1.326  0.020  1.326
 VC4  C22  C23  aromatic  1.384  0.020  1.384
 VC4  N20  C12  aromatic  1.332  0.020  1.332
 VC4  C23  C11  aromatic  1.391  0.020  1.391
 VC4  C12  C11  aromatic  1.400  0.020  1.400
 VC4  C12  C13  single    1.509  0.020  1.509
 VC4  C11  C10  single    1.502  0.020  1.502
 VC4  C13  C14  single    1.512  0.020  1.512
 VC4  C14  C19  aromatic  1.395  0.020  1.395
 VC4  C14  C15  aromatic  1.392  0.020  1.392
 VC4  C10  C09  single    1.537  0.020  1.537
 VC4  C19  C18  aromatic  1.387  0.020  1.387
 VC4  CL7  C06  single    1.734  0.020  1.734
 VC4  C09  C08  single    1.503  0.020  1.503
 VC4  C15  C16  aromatic  1.390  0.020  1.390
 VC4  C18  C17  aromatic  1.390  0.020  1.390
 VC4  C06  C08  aromatic  1.390  0.020  1.390
 VC4  C06  C04  aromatic  1.396  0.020  1.396
 VC4  C08  C24  aromatic  1.399  0.020  1.399
 VC4  C16  C17  aromatic  1.387  0.020  1.387
 VC4  O05  C04  single    1.335  0.020  1.335
 VC4  O26  C27  single    1.430  0.020  1.430
 VC4  O26  C25  single    1.321  0.020  1.321
 VC4  C04  C03  aromatic  1.387  0.020  1.387
 VC4  C24  C25  single    1.491  0.020  1.491
 VC4  C24  C02  aromatic  1.397  0.020  1.397
 VC4  C25  O28  double    1.206  0.020  1.206
 VC4  C03  C02  aromatic  1.387  0.020  1.387
 VC4  C02  O01  single    1.340  0.020  1.340
 VC4  O01  H1   single    0.850  0.020  0.980
 VC4  C03  H2   single    0.930  0.020  1.080
 VC4  O05  H3   single    0.850  0.020  0.980
 VC4  C09  H4   single    0.970  0.020  1.090
 VC4  C09  H5   single    0.970  0.020  1.090
 VC4  C10  H6   single    0.970  0.020  1.090
 VC4  C10  H7   single    0.970  0.020  1.090
 VC4  C13  H8   single    0.970  0.020  1.090
 VC4  C13  H9   single    0.970  0.020  1.090
 VC4  C15  H10  single    0.930  0.020  1.080
 VC4  C16  H11  single    0.930  0.020  1.080
 VC4  C17  H12  single    0.930  0.020  1.080
 VC4  C18  H13  single    0.930  0.020  1.080
 VC4  C19  H14  single    0.930  0.020  1.080
 VC4  C21  H15  single    0.930  0.020  1.080
 VC4  C22  H16  single    0.930  0.020  1.080
 VC4  C23  H17  single    0.930  0.020  1.080
 VC4  C27  H18  single    0.970  0.020  1.090
 VC4  C27  H19  single    0.970  0.020  1.090
 VC4  C27  H20  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
 VC4  H1   O01  C02  110.76  3.000
 VC4  C24  C02  C03  120.45  3.000
 VC4  C03  C02  O01  121.95  3.000
 VC4  C24  C02  O01  117.58  3.000
 VC4  H2   C03  C04  119.92  3.000
 VC4  H2   C03  C02  120.14  3.000
 VC4  C04  C03  C02  119.93  3.000
 VC4  C06  C04  O05  118.00  3.000
 VC4  O05  C04  C03  122.67  3.000
 VC4  C06  C04  C03  119.33  3.000
 VC4  H3   O05  C04  110.56  3.000
 VC4  C08  C06  CL7  121.18  3.000
 VC4  C08  C06  C04  121.65  3.000
 VC4  CL7  C06  C04  117.17  3.000
 VC4  C24  C08  C09  120.98  3.000
 VC4  C24  C08  C06  118.35  3.000
 VC4  C09  C08  C06  120.67  3.000
 VC4  H5   C09  H4   105.58  3.000
 VC4  H5   C09  C10  109.58  3.000
 VC4  H4   C09  C10  109.21  3.000
 VC4  H5   C09  C08  109.94  3.000
 VC4  H4   C09  C08  110.44  3.000
 VC4  C10  C09  C08  111.89  3.000
 VC4  H7   C10  H6   106.32  3.000
 VC4  H7   C10  C11  109.11  3.000
 VC4  H6   C10  C11  111.35  3.000
 VC4  H7   C10  C09  108.97  3.000
 VC4  H6   C10  C09  109.75  3.000
 VC4  C11  C10  C09  111.18  3.000
 VC4  C23  C11  C12  117.43  3.000
 VC4  C12  C11  C10  123.31  3.000
 VC4  C23  C11  C10  119.23  3.000
 VC4  N20  C12  C13  115.70  3.000
 VC4  C13  C12  C11  122.00  3.000
 VC4  N20  C12  C11  122.27  3.000
 VC4  H9   C13  H8   106.58  3.000
 VC4  H9   C13  C14  109.84  3.000
 VC4  H8   C13  C14  109.39  3.000
 VC4  H9   C13  C12  111.19  3.000
 VC4  H8   C13  C12  107.77  3.000
 VC4  C14  C13  C12  111.90  3.000
 VC4  C19  C14  C15  118.51  3.000
 VC4  C15  C14  C13  121.31  3.000
 VC4  C19  C14  C13  120.18  3.000
 VC4  H10  C15  C16  119.38  3.000
 VC4  H10  C15  C14  119.76  3.000
 VC4  C16  C15  C14  120.86  3.000
 VC4  H11  C16  C17  120.17  3.000
 VC4  H11  C16  C15  119.68  3.000
 VC4  C17  C16  C15  120.15  3.000
 VC4  H12  C17  C18  120.26  3.000
 VC4  H12  C17  C16  120.28  3.000
 VC4  C18  C17  C16  119.46  3.000
 VC4  H13  C18  C19  119.73  3.000
 VC4  H13  C18  C17  120.04  3.000
 VC4  C19  C18  C17  120.23  3.000
 VC4  H14  C19  C18  119.59  3.000
 VC4  H14  C19  C14  119.63  3.000
 VC4  C18  C19  C14  120.79  3.000
 VC4  C21  N20  C12  119.35  3.000
 VC4  H15  C21  C22  120.53  3.000
 VC4  H15  C21  N20  116.49  3.000
 VC4  C22  C21  N20  122.98  3.000
 VC4  H16  C22  C23  121.46  3.000
 VC4  H16  C22  C21  120.77  3.000
 VC4  C23  C22  C21  117.76  3.000
 VC4  H17  C23  C22  120.27  3.000
 VC4  H17  C23  C11  119.51  3.000
 VC4  C22  C23  C11  120.22  3.000
 VC4  C25  C24  C08  120.89  3.000
 VC4  C25  C24  C02  118.79  3.000
 VC4  C08  C24  C02  120.29  3.000
 VC4  O28  C25  O26  123.79  3.000
 VC4  O28  C25  C24  124.35  3.000
 VC4  O26  C25  C24  111.86  3.000
 VC4  C27  O26  C25  117.43  3.000
 VC4  H20  C27  H19  109.28  3.000
 VC4  H20  C27  H18  109.49  3.000
 VC4  H19  C27  H18  109.43  3.000
 VC4  H20  C27  O26  111.30  3.000
 VC4  H19  C27  O26  111.38  3.000
 VC4  H18  C27  O26  105.89  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
 VC4  CONST_01  C06  C08  C24  C02     0.00   0.0  0
 VC4  CONST_02  C06  C04  C03  C02     0.00   0.0  0
 VC4  CONST_03  C08  C06  C04  C03     0.00   0.0  0
 VC4  CONST_04  C08  C24  C02  C03     0.00   0.0  0
 VC4  CONST_05  C24  C08  C06  C04     0.00   0.0  0
 VC4  CONST_06  C24  C02  C03  C04     0.00   0.0  0
 VC4  CONST_07  C21  C22  C23  C11     0.00   0.0  0
 VC4  CONST_08  C21  N20  C12  C11     0.00   0.0  0
 VC4  CONST_09  C22  C21  N20  C12     0.00   0.0  0
 VC4  CONST_10  C22  C23  C11  C12     0.00   0.0  0
 VC4  CONST_11  C17  C18  C19  C14     0.00   0.0  0
 VC4  CONST_12  C17  C16  C15  C14     0.00   0.0  0
 VC4  CONST_13  C18  C19  C14  C15     0.00   0.0  0
 VC4  CONST_14  C18  C17  C16  C15     0.00   0.0  0
 VC4  CONST_15  C19  C14  C15  C16     0.00   0.0  0
 VC4  CONST_16  C19  C18  C17  C16     0.00   0.0  0
 VC4  CONST_17  C23  C22  C21  N20     0.00   0.0  0
 VC4  CONST_18  C23  C11  C12  N20     0.00   0.0  0
 VC4  CONST_19  C08  C24  C02  O01   180.00   0.0  0
 VC4  CONST_20  C04  C03  C02  O01   180.00   0.0  0
 VC4  CONST_21  C09  C08  C24  C02   180.00   0.0  0
 VC4  CONST_22  O05  C04  C03  C02   180.00   0.0  0
 VC4  CONST_23  CL7  C06  C04  C03   180.00   0.0  0
 VC4  CONST_24  C25  C24  C02  C03   180.00   0.0  0
 VC4  CONST_25  C09  C08  C06  C04   180.00   0.0  0
 VC4  CONST_26  C08  C06  C04  O05   180.00   0.0  0
 VC4  CONST_27  C25  C24  C08  C06   180.00   0.0  0
 VC4  CONST_28  C24  C08  C06  CL7   180.00   0.0  0
 VC4  CONST_29  C22  C23  C11  C10   180.00   0.0  0
 VC4  CONST_30  N20  C12  C11  C10   180.00   0.0  0
 VC4  CONST_31  C21  N20  C12  C13   180.00   0.0  0
 VC4  CONST_32  C23  C11  C12  C13   180.00   0.0  0
 VC4  CONST_33  C18  C19  C14  C13   180.00   0.0  0
 VC4  CONST_34  C16  C15  C14  C13   180.00   0.0  0
 VC4  CONST_35  H2   C03  C04  C06   180.00   0.0  0
 VC4  CONST_36  H16  C22  C23  C11   180.00   0.0  0
 VC4  CONST_37  H15  C21  N20  C12   180.00   0.0  0
 VC4  CONST_38  H17  C23  C11  C12   180.00   0.0  0
 VC4  CONST_39  H13  C18  C19  C14   180.00   0.0  0
 VC4  CONST_40  H11  C16  C15  C14   180.00   0.0  0
 VC4  CONST_41  H14  C19  C14  C15   180.00   0.0  0
 VC4  CONST_42  H12  C17  C16  C15   180.00   0.0  0
 VC4  CONST_43  H10  C15  C16  C17   180.00   0.0  0
 VC4  Var_01    C14  C13  C12  C11    81.81  30.0  2
 VC4  Var_02    C19  C14  C13  C12    58.68  30.0  2
 VC4  Var_03    O26  C25  C24  C02    64.52  30.0  2
 VC4  Var_04    C10  C09  C08  C06    84.36  30.0  2
 VC4  Var_05    C11  C10  C09  C08   175.33  30.0  1
 VC4  Var_06    C23  C11  C10  C09   -81.75  30.0  2
 VC4  Var_07    H18  C27  O26  C25  -179.70  30.0  3

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
 VC4  plan-1  O01  0.020
 VC4  plan-1  C02  0.020
 VC4  plan-1  C03  0.020
 VC4  plan-1  C04  0.020
 VC4  plan-1  O05  0.020
 VC4  plan-1  C06  0.020
 VC4  plan-1  CL7  0.020
 VC4  plan-1  C08  0.020
 VC4  plan-1  C09  0.020
 VC4  plan-1  C24  0.020
 VC4  plan-1  C25  0.020
 VC4  plan-1  H2   0.020
 VC4  plan-2  C13  0.020
 VC4  plan-2  C14  0.020
 VC4  plan-2  C15  0.020
 VC4  plan-2  C16  0.020
 VC4  plan-2  C17  0.020
 VC4  plan-2  C18  0.020
 VC4  plan-2  C19  0.020
 VC4  plan-2  H10  0.020
 VC4  plan-2  H11  0.020
 VC4  plan-2  H12  0.020
 VC4  plan-2  H13  0.020
 VC4  plan-2  H14  0.020
 VC4  plan-3  C10  0.020
 VC4  plan-3  C11  0.020
 VC4  plan-3  C12  0.020
 VC4  plan-3  C13  0.020
 VC4  plan-3  N20  0.020
 VC4  plan-3  C21  0.020
 VC4  plan-3  C22  0.020
 VC4  plan-3  C23  0.020
 VC4  plan-3  H15  0.020
 VC4  plan-3  H16  0.020
 VC4  plan-3  H17  0.020
 VC4  plan-4  C24  0.020
 VC4  plan-4  C25  0.020
 VC4  plan-4  O26  0.020
 VC4  plan-4  O28  0.020

