# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 06:08:12 2021
#   Inital geometry file: a 84 line input string
#   Ligand name: 3-{[6-(hydroxymethyl)pyridin-2-yl]methoxy}-2-methylphenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(O)cccc1OCc2cccc(CO)n2
#
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
 V39  V39  3-{[6-(hydroxymethyl)pyridin-2-yl]methoxy}-2-methylphenol  ligand  33  18  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_V39
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
 V39  C1   C  CH3   0  -0.706  13.8949  -11.2577  -22.5721
 V39  C2   C  CR6   0  -0.117  14.5572  -10.6865  -21.3511
 V39  C3   C  CR6   0   0.343  15.7382   -9.9482  -21.4237
 V39  C4   C  CR16  0  -0.408  16.3390   -9.4277  -20.2760
 V39  C5   C  CR16  0  -0.242  15.7554   -9.6520  -19.0440
 V39  C6   C  CR16  0  -0.409  14.5827  -10.3865  -18.9299
 V39  C7   C  CR6   0   0.374  13.9959  -10.8998  -20.0838
 V39  O8   O  OH1   0  -0.633  16.2833   -9.7569  -22.6445
 V39  O10  O  O2    0  -0.462  12.8612  -11.6297  -20.0823
 V39  C11  C  CH2   0  -0.245  12.2306  -11.9145  -18.8472
 V39  C12  C  CR6   0   0.218  11.0421  -12.7798  -19.1508
 V39  C13  C  CR16  0  -0.341   9.7492  -12.2933  -19.0173
 V39  C14  C  CR16  0  -0.141   8.6948  -13.1402  -19.3215
 V39  C15  C  CR16  0  -0.335   8.9634  -14.4288  -19.7526
 V39  C16  C  CR6   0   0.181  10.2927  -14.8262  -19.8582
 V39  N17  N  N     0  -0.434  11.3015  -14.0168  -19.5566
 V39  C18  C  CH2   0  -0.186  10.6979  -16.1990  -20.3189
 V39  O19  O  OH1   0  -0.665   9.5630  -16.9851  -20.5629
 V39  H1   H  HCH3  0   0.242  13.9665  -12.3473  -22.5922
 V39  H2   H  HCH3  0   0.240  12.8332  -11.0117  -22.6024
 V39  H3   H  HCH3  0   0.246  14.3428  -10.8849  -23.4892
 V39  H4   H  HCR6  0   0.263  17.2549   -8.8527  -20.3526
 V39  H5   H  HCR6  0   0.259  16.2193   -9.2517  -18.1521
 V39  H6   H  HCR6  0   0.275  14.1505  -10.5458  -17.9523
 V39  H7   H  HOH1  0   0.474  17.0863   -9.2304  -22.5691
 V39  H8   H  HCH2  0   0.241  12.9145  -12.4469  -18.1774
 V39  H9   H  HCH2  0   0.241  11.9154  -10.9935  -18.3461
 V39  H10  H  HCR6  0   0.269   9.5729  -11.2789  -18.6856
 V39  H11  H  HCR6  0   0.273   7.6725  -12.7986  -19.2258
 V39  H12  H  HCR6  0   0.269   8.1575  -15.1052  -19.9966
 V39  H13  H  HCH2  0   0.227  11.3194  -16.0842  -21.2166
 V39  H14  H  HCH2  0   0.223  11.3470  -16.6388  -19.5499
 V39  H15  H  HOH1  0   0.466   9.8505  -17.8159  -20.9516

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
 V39  O8   C3   single    1.351  0.020  1.351
 V39  C1   C2   single    1.502  0.020  1.502
 V39  C3   C2   aromatic  1.395  0.020  1.395
 V39  C3   C4   aromatic  1.396  0.020  1.396
 V39  C2   C7   aromatic  1.402  0.020  1.402
 V39  C18  C16  single    1.504  0.020  1.504
 V39  C18  O19  single    1.402  0.020  1.402
 V39  C4   C5   aromatic  1.382  0.020  1.382
 V39  C7   O10  single    1.349  0.020  1.349
 V39  C7   C6   aromatic  1.393  0.020  1.393
 V39  O10  C11  single    1.416  0.020  1.416
 V39  C16  N17  aromatic  1.328  0.020  1.328
 V39  C16  C15  aromatic  1.391  0.020  1.391
 V39  N17  C12  aromatic  1.327  0.020  1.327
 V39  C15  C14  aromatic  1.385  0.020  1.385
 V39  C12  C11  single    1.501  0.020  1.501
 V39  C12  C13  aromatic  1.388  0.020  1.388
 V39  C5   C6   aromatic  1.388  0.020  1.388
 V39  C14  C13  aromatic  1.386  0.020  1.386
 V39  C1   H1   single    0.970  0.020  1.090
 V39  C1   H2   single    0.970  0.020  1.090
 V39  C1   H3   single    0.970  0.020  1.090
 V39  C4   H4   single    0.930  0.020  1.080
 V39  C5   H5   single    0.930  0.020  1.080
 V39  C6   H6   single    0.930  0.020  1.080
 V39  O8   H7   single    0.850  0.020  0.980
 V39  C11  H8   single    0.970  0.020  1.090
 V39  C11  H9   single    0.970  0.020  1.090
 V39  C13  H10  single    0.930  0.020  1.080
 V39  C14  H11  single    0.930  0.020  1.080
 V39  C15  H12  single    0.930  0.020  1.080
 V39  C18  H13  single    0.970  0.020  1.090
 V39  C18  H14  single    0.970  0.020  1.090
 V39  O19  H15  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
 V39  H3   C1   H2   107.49  3.000
 V39  H3   C1   H1   107.45  3.000
 V39  H2   C1   H1   106.77  3.000
 V39  H3   C1   C2   111.96  3.000
 V39  H2   C1   C2   111.48  3.000
 V39  H1   C1   C2   111.43  3.000
 V39  C7   C2   C3   117.81  3.000
 V39  C7   C2   C1   120.02  3.000
 V39  C3   C2   C1   122.17  3.000
 V39  O8   C3   C4   121.10  3.000
 V39  C4   C3   C2   121.26  3.000
 V39  O8   C3   C2   117.64  3.000
 V39  H4   C4   C5   120.40  3.000
 V39  H4   C4   C3   120.21  3.000
 V39  C5   C4   C3   119.39  3.000
 V39  H5   C5   C6   119.34  3.000
 V39  H5   C5   C4   119.59  3.000
 V39  C6   C5   C4   121.07  3.000
 V39  H6   C6   C7   121.78  3.000
 V39  H6   C6   C5   119.35  3.000
 V39  C7   C6   C5   118.87  3.000
 V39  O10  C7   C6   123.57  3.000
 V39  C6   C7   C2   121.60  3.000
 V39  O10  C7   C2   114.83  3.000
 V39  H7   O8   C3   110.07  3.000
 V39  C11  O10  C7   118.97  3.000
 V39  H9   C11  H8   107.98  3.000
 V39  H9   C11  C12  110.46  3.000
 V39  H8   C11  C12  109.75  3.000
 V39  H9   C11  O10  110.99  3.000
 V39  H8   C11  O10  110.68  3.000
 V39  C12  C11  O10  106.99  3.000
 V39  N17  C12  C13  122.56  3.000
 V39  C13  C12  C11  121.07  3.000
 V39  N17  C12  C11  116.37  3.000
 V39  H10  C13  C14  121.08  3.000
 V39  H10  C13  C12  120.67  3.000
 V39  C14  C13  C12  118.25  3.000
 V39  H11  C14  C15  120.29  3.000
 V39  H11  C14  C13  120.42  3.000
 V39  C15  C14  C13  119.28  3.000
 V39  H12  C15  C16  121.12  3.000
 V39  H12  C15  C14  120.54  3.000
 V39  C16  C15  C14  118.34  3.000
 V39  C18  C16  N17  114.92  3.000
 V39  N17  C16  C15  122.30  3.000
 V39  C18  C16  C15  122.78  3.000
 V39  C16  N17  C12  119.27  3.000
 V39  H14  C18  H13  106.26  3.000
 V39  H14  C18  O19  112.07  3.000
 V39  H13  C18  O19  112.00  3.000
 V39  H14  C18  C16  108.08  3.000
 V39  H13  C18  C16  107.91  3.000
 V39  O19  C18  C16  110.31  3.000
 V39  H15  O19  C18  108.24  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
 V39  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 V39  CONST_02  C5   C6   C7   C2      0.00   0.0  0
 V39  CONST_03  C6   C7   C2   C3      0.00   0.0  0
 V39  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 V39  CONST_05  C7   C2   C3   C4      0.00   0.0  0
 V39  CONST_06  C7   C6   C5   C4      0.00   0.0  0
 V39  CONST_07  C15  C16  N17  C12     0.00   0.0  0
 V39  CONST_08  C15  C14  C13  C12     0.00   0.0  0
 V39  CONST_09  C16  N17  C12  C13     0.00   0.0  0
 V39  CONST_10  C16  C15  C14  C13     0.00   0.0  0
 V39  CONST_11  N17  C16  C15  C14     0.00   0.0  0
 V39  CONST_12  N17  C12  C13  C14     0.00   0.0  0
 V39  CONST_13  C4   C3   C2   C1    180.00   0.0  0
 V39  CONST_14  C6   C7   C2   C1    180.00   0.0  0
 V39  CONST_15  O10  C7   C2   C3    180.00   0.0  0
 V39  CONST_16  O8   C3   C4   C5    180.00   0.0  0
 V39  CONST_17  O10  C7   C6   C5    180.00   0.0  0
 V39  CONST_18  O8   C3   C2   C7    180.00   0.0  0
 V39  CONST_19  C16  N17  C12  C11   180.00   0.0  0
 V39  CONST_20  C14  C13  C12  C11   180.00   0.0  0
 V39  CONST_21  C18  C16  N17  C12   180.00   0.0  0
 V39  CONST_22  C18  C16  C15  C14   180.00   0.0  0
 V39  CONST_23  H4   C4   C3   C2    180.00   0.0  0
 V39  CONST_24  H6   C6   C7   C2    180.00   0.0  0
 V39  CONST_25  H5   C5   C4   C3    180.00   0.0  0
 V39  CONST_26  H11  C14  C13  C12   180.00   0.0  0
 V39  CONST_27  H12  C15  C14  C13   180.00   0.0  0
 V39  CONST_28  H10  C13  C14  C15   180.00   0.0  0
 V39  Var_01    C12  C11  O10  C7   -177.63  30.0  3
 V39  Var_02    N17  C12  C11  O10    69.78  30.0  3
 V39  Var_03    O19  C18  C16  C15    -2.11  30.0  2
 V39  Var_04    H1   C1   C2   C3    110.60  30.0  2

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
 V39  plan-1  C1   0.020
 V39  plan-1  C2   0.020
 V39  plan-1  C3   0.020
 V39  plan-1  C4   0.020
 V39  plan-1  C5   0.020
 V39  plan-1  C6   0.020
 V39  plan-1  C7   0.020
 V39  plan-1  O8   0.020
 V39  plan-1  O10  0.020
 V39  plan-1  H4   0.020
 V39  plan-1  H5   0.020
 V39  plan-1  H6   0.020
 V39  plan-2  C11  0.020
 V39  plan-2  C12  0.020
 V39  plan-2  C13  0.020
 V39  plan-2  C14  0.020
 V39  plan-2  C15  0.020
 V39  plan-2  C16  0.020
 V39  plan-2  N17  0.020
 V39  plan-2  C18  0.020
 V39  plan-2  H10  0.020
 V39  plan-2  H11  0.020
 V39  plan-2  H12  0.020

