# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 13:32:11 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: methyl 2-[2-(2-benzylphenyl)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)c1CCc2ccccc2Cc3ccccc3
#
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
 VC5  VC5  'methyl 2-[2-(2-benzylphenyl)ethyl]-3-chloro-4,6-dihydroxybenzoate'  ligand  49  28  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VC5
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
 VC5  O01  O   OH1   0  -0.617   5.6873   0.1827   0.1144
 VC5  C02  C   CR6   0   0.405   4.4875   0.7737   0.0218
 VC5  C03  C   CR16  0  -0.500   4.3493   2.1054  -0.3309
 VC5  C04  C   CR6   0   0.464   3.0846   2.6712  -0.4176
 VC5  O05  O   OH1   0  -0.607   3.0079   3.9626  -0.7481
 VC5  C06  C   CR6   0  -0.289   1.9656   1.8770  -0.1564
 VC5  CL7  CL  CL    0  -0.110   0.4072   2.6446  -0.2421
 VC5  C08  C   CR6   0   0.266   2.0800   0.5312   0.1792
 VC5  C09  C   CH2   0  -0.544   0.8523  -0.3006   0.4364
 VC5  C10  C   CH2   0  -0.524   0.1858  -0.7694  -0.8679
 VC5  C11  C   CR6   0   0.106  -0.9804  -1.6843  -0.6031
 VC5  C12  C   CR6   0   0.065  -2.2701  -1.1986  -0.3310
 VC5  C13  C   CH2   0  -0.584  -2.5337   0.2945  -0.3391
 VC5  C14  C   CR6   0   0.102  -3.9600   0.6942  -0.0879
 VC5  C15  C   CR16  0  -0.294  -4.4159   0.9215   1.2083
 VC5  C16  C   CR16  0  -0.242  -5.7368   1.2767   1.4459
 VC5  C17  C   CR16  0  -0.270  -6.6237   1.4108   0.3854
 VC5  C18  C   CR16  0  -0.243  -6.1796   1.1881  -0.9117
 VC5  C19  C   CR16  0  -0.294  -4.8578   0.8318  -1.1436
 VC5  C20  C   CR16  0  -0.285  -3.2863  -2.1123  -0.0643
 VC5  C21  C   CR16  0  -0.260  -3.0490  -3.4808  -0.0573
 VC5  C22  C   CR16  0  -0.256  -1.7772  -3.9600  -0.3258
 VC5  C23  C   CR16  0  -0.310  -0.7579  -3.0585  -0.5967
 VC5  C24  C   CR6   0  -0.225   3.3604  -0.0188   0.2656
 VC5  C25  C   C     0   0.503   3.5852  -1.4364   0.6694
 VC5  O26  O   O2    0  -0.439   3.1037  -2.2899  -0.2206
 VC5  C27  C   CH3   0  -0.432   3.2254  -3.6847   0.0700
 VC5  O28  O   O     0  -0.427   4.1522  -1.7679   1.6789
 VC5  H1   H   HOH1  0   0.485   6.3931   0.8087  -0.0857
 VC5  H2   H   HCR6  0   0.293   5.2193   2.7177  -0.5385
 VC5  H3   H   HOH1  0   0.473   2.0894   4.2565  -0.8096
 VC5  H4   H   HCH2  0   0.270   1.1026  -1.1722   1.0415
 VC5  H5   H   HCH2  0   0.273   0.1414   0.2715   1.0348
 VC5  H6   H   HCH2  0   0.254  -0.1222   0.0975  -1.4552
 VC5  H7   H   HCH2  0   0.269   0.9274  -1.2995  -1.4666
 VC5  H8   H   HCH2  0   0.260  -1.9002   0.7725   0.4125
 VC5  H9   H   HCH2  0   0.264  -2.2116   0.7079  -1.2992
 VC5  H10  H   HCR6  0   0.248  -3.7286   0.8204   2.0403
 VC5  H11  H   HCR6  0   0.254  -6.0731   1.4518   2.4598
 VC5  H12  H   HCR6  0   0.254  -7.6533   1.6895   0.5689
 VC5  H13  H   HCR6  0   0.254  -6.8624   1.2946  -1.7449
 VC5  H14  H   HCR6  0   0.248  -4.5187   0.6587  -2.1584
 VC5  H15  H   HCR6  0   0.247  -4.2865  -1.7556   0.1447
 VC5  H16  H   HCR6  0   0.251  -3.8601  -4.1659   0.1539
 VC5  H17  H   HCR6  0   0.251  -1.5781  -5.0239  -0.3292
 VC5  H18  H   HCR6  0   0.246   0.2363  -3.4297  -0.8181
 VC5  H19  H   HCH3  0   0.243   2.7141  -3.9452   0.9965
 VC5  H20  H   HCH3  0   0.254   2.7569  -4.2031  -0.7612
 VC5  H21  H   HCH3  0   0.250   4.2708  -3.9838   0.1390

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
 VC5  O01  C02  single    1.341  0.020  1.341
 VC5  C02  C03  aromatic  1.385  0.020  1.385
 VC5  C02  C24  aromatic  1.399  0.020  1.399
 VC5  O28  C25  double    1.204  0.020  1.204
 VC5  C03  C04  aromatic  1.388  0.020  1.388
 VC5  C25  C24  single    1.491  0.020  1.491
 VC5  C25  O26  single    1.324  0.020  1.324
 VC5  C27  O26  single    1.430  0.020  1.430
 VC5  C24  C08  aromatic  1.396  0.020  1.396
 VC5  C04  O05  single    1.335  0.020  1.335
 VC5  C04  C06  aromatic  1.397  0.020  1.397
 VC5  C16  C17  aromatic  1.389  0.020  1.389
 VC5  C16  C15  aromatic  1.388  0.020  1.388
 VC5  C17  C18  aromatic  1.389  0.020  1.389
 VC5  C08  C06  aromatic  1.392  0.020  1.392
 VC5  C08  C09  single    1.505  0.020  1.505
 VC5  C06  CL7  single    1.739  0.020  1.739
 VC5  C15  C14  aromatic  1.393  0.020  1.393
 VC5  C18  C19  aromatic  1.388  0.020  1.388
 VC5  C09  C10  single    1.538  0.020  1.538
 VC5  C19  C14  aromatic  1.393  0.020  1.393
 VC5  C14  C13  single    1.502  0.020  1.502
 VC5  C10  C11  single    1.506  0.020  1.506
 VC5  C13  C12  single    1.516  0.020  1.516
 VC5  C11  C12  aromatic  1.405  0.020  1.405
 VC5  C11  C23  aromatic  1.392  0.020  1.392
 VC5  C12  C20  aromatic  1.392  0.020  1.392
 VC5  C23  C22  aromatic  1.387  0.020  1.387
 VC5  C20  C21  aromatic  1.389  0.020  1.389
 VC5  C22  C21  aromatic  1.385  0.020  1.385
 VC5  O01  H1   single    0.850  0.020  0.980
 VC5  C03  H2   single    0.930  0.020  1.080
 VC5  O05  H3   single    0.850  0.020  0.980
 VC5  C09  H4   single    0.970  0.020  1.090
 VC5  C09  H5   single    0.970  0.020  1.090
 VC5  C10  H6   single    0.970  0.020  1.090
 VC5  C10  H7   single    0.970  0.020  1.090
 VC5  C13  H8   single    0.970  0.020  1.090
 VC5  C13  H9   single    0.970  0.020  1.090
 VC5  C15  H10  single    0.930  0.020  1.080
 VC5  C16  H11  single    0.930  0.020  1.080
 VC5  C17  H12  single    0.930  0.020  1.080
 VC5  C18  H13  single    0.930  0.020  1.080
 VC5  C19  H14  single    0.930  0.020  1.080
 VC5  C20  H15  single    0.930  0.020  1.080
 VC5  C21  H16  single    0.930  0.020  1.080
 VC5  C22  H17  single    0.930  0.020  1.080
 VC5  C23  H18  single    0.930  0.020  1.080
 VC5  C27  H19  single    0.970  0.020  1.090
 VC5  C27  H20  single    0.970  0.020  1.090
 VC5  C27  H21  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
 VC5  H1   O01  C02  110.77  3.000
 VC5  C24  C02  C03  120.58  3.000
 VC5  C24  C02  O01  117.34  3.000
 VC5  C03  C02  O01  122.07  3.000
 VC5  H2   C03  C04  119.28  3.000
 VC5  H2   C03  C02  120.80  3.000
 VC5  C04  C03  C02  119.92  3.000
 VC5  C06  C04  O05  123.38  3.000
 VC5  C06  C04  C03  119.10  3.000
 VC5  O05  C04  C03  117.51  3.000
 VC5  H3   O05  C04  111.38  3.000
 VC5  C08  C06  CL7  120.82  3.000
 VC5  CL7  C06  C04  117.23  3.000
 VC5  C08  C06  C04  121.95  3.000
 VC5  C24  C08  C09  121.32  3.000
 VC5  C09  C08  C06  120.57  3.000
 VC5  C24  C08  C06  118.11  3.000
 VC5  H5   C09  H4   105.33  3.000
 VC5  H5   C09  C10  110.03  3.000
 VC5  H4   C09  C10  109.06  3.000
 VC5  H5   C09  C08  109.60  3.000
 VC5  H4   C09  C08  110.45  3.000
 VC5  C10  C09  C08  112.15  3.000
 VC5  H7   C10  H6   106.41  3.000
 VC5  H7   C10  C11  109.14  3.000
 VC5  H6   C10  C11  111.02  3.000
 VC5  H7   C10  C09  108.60  3.000
 VC5  H6   C10  C09  109.66  3.000
 VC5  C11  C10  C09  111.82  3.000
 VC5  C23  C11  C12  119.16  3.000
 VC5  C23  C11  C10  118.48  3.000
 VC5  C12  C11  C10  122.34  3.000
 VC5  C20  C12  C13  121.35  3.000
 VC5  C20  C12  C11  118.70  3.000
 VC5  C13  C12  C11  119.94  3.000
 VC5  H9   C13  H8   105.52  3.000
 VC5  H9   C13  C14  109.01  3.000
 VC5  H8   C13  C14  108.60  3.000
 VC5  H9   C13  C12  109.00  3.000
 VC5  H8   C13  C12  109.04  3.000
 VC5  C14  C13  C12  115.23  3.000
 VC5  C19  C14  C15  118.58  3.000
 VC5  C19  C14  C13  120.77  3.000
 VC5  C15  C14  C13  120.64  3.000
 VC5  H10  C15  C16  119.72  3.000
 VC5  H10  C15  C14  119.45  3.000
 VC5  C16  C15  C14  120.83  3.000
 VC5  H11  C16  C17  120.08  3.000
 VC5  H11  C16  C15  119.82  3.000
 VC5  C17  C16  C15  120.10  3.000
 VC5  H12  C17  C18  120.25  3.000
 VC5  H12  C17  C16  120.18  3.000
 VC5  C18  C17  C16  119.57  3.000
 VC5  H13  C18  C19  119.81  3.000
 VC5  H13  C18  C17  120.09  3.000
 VC5  C19  C18  C17  120.10  3.000
 VC5  H14  C19  C18  119.68  3.000
 VC5  H14  C19  C14  119.49  3.000
 VC5  C18  C19  C14  120.82  3.000
 VC5  H15  C20  C21  118.80  3.000
 VC5  H15  C20  C12  119.68  3.000
 VC5  C21  C20  C12  121.52  3.000
 VC5  H16  C21  C22  120.45  3.000
 VC5  H16  C21  C20  119.77  3.000
 VC5  C22  C21  C20  119.78  3.000
 VC5  H17  C22  C23  120.19  3.000
 VC5  H17  C22  C21  120.63  3.000
 VC5  C23  C22  C21  119.18  3.000
 VC5  H18  C23  C22  119.41  3.000
 VC5  H18  C23  C11  118.92  3.000
 VC5  C22  C23  C11  121.66  3.000
 VC5  C25  C24  C08  121.98  3.000
 VC5  C08  C24  C02  120.32  3.000
 VC5  C25  C24  C02  117.66  3.000
 VC5  O28  C25  O26  123.87  3.000
 VC5  O26  C25  C24  112.09  3.000
 VC5  O28  C25  C24  124.04  3.000
 VC5  C27  O26  C25  117.47  3.000
 VC5  H21  C27  H20  109.35  3.000
 VC5  H21  C27  H19  109.32  3.000
 VC5  H20  C27  H19  109.53  3.000
 VC5  H21  C27  O26  111.24  3.000
 VC5  H20  C27  O26  105.87  3.000
 VC5  H19  C27  O26  111.47  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
 VC5  CONST_01  C06  C04  C03  C02    0.00   0.0  0
 VC5  CONST_02  C06  C08  C24  C02    0.00   0.0  0
 VC5  CONST_03  C08  C24  C02  C03    0.00   0.0  0
 VC5  CONST_04  C08  C06  C04  C03    0.00   0.0  0
 VC5  CONST_05  C24  C02  C03  C04    0.00   0.0  0
 VC5  CONST_06  C24  C08  C06  C04    0.00   0.0  0
 VC5  CONST_07  C21  C20  C12  C11    0.00   0.0  0
 VC5  CONST_08  C21  C22  C23  C11    0.00   0.0  0
 VC5  CONST_09  C22  C23  C11  C12    0.00   0.0  0
 VC5  CONST_10  C22  C21  C20  C12    0.00   0.0  0
 VC5  CONST_11  C17  C16  C15  C14    0.00   0.0  0
 VC5  CONST_12  C17  C18  C19  C14    0.00   0.0  0
 VC5  CONST_13  C18  C17  C16  C15    0.00   0.0  0
 VC5  CONST_14  C18  C19  C14  C15    0.00   0.0  0
 VC5  CONST_15  C19  C18  C17  C16    0.00   0.0  0
 VC5  CONST_16  C19  C14  C15  C16    0.00   0.0  0
 VC5  CONST_17  C23  C11  C12  C20    0.00   0.0  0
 VC5  CONST_18  C23  C22  C21  C20    0.00   0.0  0
 VC5  CONST_19  C04  C03  C02  O01  180.00   0.0  0
 VC5  CONST_20  C08  C24  C02  O01  180.00   0.0  0
 VC5  CONST_21  O05  C04  C03  C02  180.00   0.0  0
 VC5  CONST_22  C09  C08  C24  C02  180.00   0.0  0
 VC5  CONST_23  C25  C24  C02  C03  180.00   0.0  0
 VC5  CONST_24  CL7  C06  C04  C03  180.00   0.0  0
 VC5  CONST_25  C09  C08  C06  C04  180.00   0.0  0
 VC5  CONST_26  C08  C06  C04  O05  180.00   0.0  0
 VC5  CONST_27  C25  C24  C08  C06  180.00   0.0  0
 VC5  CONST_28  C24  C08  C06  CL7  180.00   0.0  0
 VC5  CONST_29  C20  C12  C11  C10  180.00   0.0  0
 VC5  CONST_30  C22  C23  C11  C10  180.00   0.0  0
 VC5  CONST_31  C16  C15  C14  C13  180.00   0.0  0
 VC5  CONST_32  C18  C19  C14  C13  180.00   0.0  0
 VC5  CONST_33  C23  C11  C12  C13  180.00   0.0  0
 VC5  CONST_34  C21  C20  C12  C13  180.00   0.0  0
 VC5  CONST_35  H2   C03  C04  C06  180.00   0.0  0
 VC5  CONST_36  H15  C20  C12  C11  180.00   0.0  0
 VC5  CONST_37  H17  C22  C23  C11  180.00   0.0  0
 VC5  CONST_38  H18  C23  C11  C12  180.00   0.0  0
 VC5  CONST_39  H16  C21  C20  C12  180.00   0.0  0
 VC5  CONST_40  H11  C16  C15  C14  180.00   0.0  0
 VC5  CONST_41  H13  C18  C19  C14  180.00   0.0  0
 VC5  CONST_42  H12  C17  C16  C15  180.00   0.0  0
 VC5  CONST_43  H14  C19  C14  C15  180.00   0.0  0
 VC5  CONST_44  H10  C15  C16  C17  180.00   0.0  0
 VC5  Var_01    C14  C13  C12  C11  177.70  30.0  1
 VC5  Var_02    C15  C14  C13  C12   89.66  30.0  2
 VC5  Var_03    O28  C25  C24  C02   62.66  30.0  3
 VC5  Var_04    C10  C09  C08  C06   80.10  30.0  2
 VC5  Var_05    C11  C10  C09  C08  175.76  30.0  3
 VC5  Var_06    C12  C11  C10  C09   84.83  30.0  2
 VC5  Var_07    H19  C27  O26  C25   59.78  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
 VC5  plan-1  O01  0.020
 VC5  plan-1  C02  0.020
 VC5  plan-1  C03  0.020
 VC5  plan-1  C04  0.020
 VC5  plan-1  O05  0.020
 VC5  plan-1  C06  0.020
 VC5  plan-1  CL7  0.020
 VC5  plan-1  C08  0.020
 VC5  plan-1  C09  0.020
 VC5  plan-1  C24  0.020
 VC5  plan-1  C25  0.020
 VC5  plan-1  H2   0.020
 VC5  plan-2  C10  0.020
 VC5  plan-2  C11  0.020
 VC5  plan-2  C12  0.020
 VC5  plan-2  C13  0.020
 VC5  plan-2  C20  0.020
 VC5  plan-2  C21  0.020
 VC5  plan-2  C22  0.020
 VC5  plan-2  C23  0.020
 VC5  plan-2  H15  0.020
 VC5  plan-2  H16  0.020
 VC5  plan-2  H17  0.020
 VC5  plan-2  H18  0.020
 VC5  plan-3  C13  0.020
 VC5  plan-3  C14  0.020
 VC5  plan-3  C15  0.020
 VC5  plan-3  C16  0.020
 VC5  plan-3  C17  0.020
 VC5  plan-3  C18  0.020
 VC5  plan-3  C19  0.020
 VC5  plan-3  H10  0.020
 VC5  plan-3  H11  0.020
 VC5  plan-3  H12  0.020
 VC5  plan-3  H13  0.020
 VC5  plan-3  H14  0.020
 VC5  plan-4  C24  0.020
 VC5  plan-4  C25  0.020
 VC5  plan-4  O26  0.020
 VC5  plan-4  O28  0.020

