# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 00:28:37 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: {6-[(4-methoxy-2-methylphenoxy)methyl]pyridin-2-yl}methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(OCc2cccc(CO)n2)c(C)c1
#
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
 GJ1  GJ1  {6-[(4-methoxy-2-methylphenoxy)methyl]pyridin-2-yl}methanol  ligand  36  19  .  2021-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GJ1
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
 GJ1  C7   C  CR6   0   0.355   1.6236  -0.1763  -0.0064
 GJ1  C6   C  CR16  0  -0.368   2.0918   1.1265  -0.0059
 GJ1  C5   C  CR16  0  -0.387   3.4614   1.3934   0.0138
 GJ1  C4   C  CR6   0   0.372   4.3669   0.3453   0.0337
 GJ1  C2   C  CR6   0   0.014   2.5313  -1.2485   0.0152
 GJ1  C13  C  CR16  0  -0.346  -2.2582  -1.4773  -0.0052
 GJ1  C11  C  CH2   0  -0.204  -0.6525   0.5015  -0.0223
 GJ1  C1   C  CH3   0  -0.715   2.0369  -2.6643   0.0096
 GJ1  C3   C  CR16  0  -0.380   3.8850  -0.9671   0.0353
 GJ1  O8   O  O2    0  -0.478   5.7117   0.4865   0.0525
 GJ1  C9   C  CH3   0  -0.434   6.2405   1.7955   0.0490
 GJ1  O10  O  O2    0  -0.478   0.3123  -0.5175  -0.0262
 GJ1  C12  C  CR6   0   0.182  -2.0273  -0.1077  -0.0163
 GJ1  C14  C  CR16  0  -0.140  -3.5749  -1.9110   0.0004
 GJ1  C15  C  CR16  0  -0.340  -4.6060  -0.9856  -0.0051
 GJ1  C16  C  CR6   0   0.183  -4.2727   0.3637  -0.0161
 GJ1  N17  N  N     0  -0.451  -3.0123   0.7819  -0.0211
 GJ1  C18  C  CH2   0  -0.186  -5.3030   1.4580  -0.0242
 GJ1  O19  O  OH1   0  -0.665  -6.5936   0.9105  -0.0104
 GJ1  H1   H  HCR6  0   0.282   1.4137   1.9688  -0.0215
 GJ1  H2   H  HCR6  0   0.277   3.7830   2.4261   0.0130
 GJ1  H4   H  HCH2  0   0.246  -0.5463   1.1469   0.8588
 GJ1  H5   H  HCH2  0   0.246  -0.5540   1.1472  -0.9041
 GJ1  H6   H  HCH3  0   0.245   1.5086  -2.9003  -0.9162
 GJ1  H7   H  HCH3  0   0.245   2.8660  -3.3633   0.1046
 GJ1  H8   H  HCH3  0   0.244   1.3415  -2.8538   0.8286
 GJ1  H9   H  HCR6  0   0.256   4.5963  -1.7849   0.0521
 GJ1  H10  H  HCH3  0   0.224   5.9473   2.3524  -0.8453
 GJ1  H11  H  HCH3  0   0.224   5.9312   2.3635   0.9310
 GJ1  H12  H  HCH3  0   0.257   7.3233   1.6952   0.0593
 GJ1  H13  H  HCR6  0   0.270  -3.7950  -2.9708   0.0090
 GJ1  H14  H  HCR6  0   0.266  -5.6368  -1.3080  -0.0012
 GJ1  H15  H  HCH2  0   0.224  -5.1211   2.1039   0.8450
 GJ1  H16  H  HCH2  0   0.224  -5.1304   2.0825  -0.9107
 GJ1  H17  H  HOH1  0   0.465  -7.2269   1.6334  -0.0187
 GJ1  H3   H  HCR6  0   0.270  -1.4450  -2.1878  -0.0001

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
 GJ1  C1   C2   single    1.500  0.020  1.500
 GJ1  C3   C2   aromatic  1.383  0.020  1.383
 GJ1  C3   C4   aromatic  1.398  0.020  1.398
 GJ1  C2   C7   aromatic  1.405  0.020  1.405
 GJ1  O8   C4   single    1.352  0.020  1.352
 GJ1  O8   C9   single    1.412  0.020  1.412
 GJ1  C4   C5   aromatic  1.385  0.020  1.385
 GJ1  O19  C18  single    1.402  0.020  1.402
 GJ1  C7   O10  single    1.355  0.020  1.355
 GJ1  C7   C6   aromatic  1.384  0.020  1.384
 GJ1  O10  C11  single    1.403  0.020  1.403
 GJ1  C15  C14  aromatic  1.386  0.020  1.386
 GJ1  C15  C16  aromatic  1.390  0.020  1.390
 GJ1  C14  C13  aromatic  1.386  0.020  1.386
 GJ1  C18  C16  single    1.503  0.020  1.503
 GJ1  C16  N17  aromatic  1.328  0.020  1.328
 GJ1  C13  C12  aromatic  1.389  0.020  1.389
 GJ1  N17  C12  aromatic  1.327  0.020  1.327
 GJ1  C12  C11  single    1.504  0.020  1.504
 GJ1  C5   C6   aromatic  1.395  0.020  1.395
 GJ1  C6   H1   single    0.930  0.020  1.080
 GJ1  C5   H2   single    0.930  0.020  1.080
 GJ1  C13  H3   single    0.930  0.020  1.080
 GJ1  C11  H4   single    0.970  0.020  1.090
 GJ1  C11  H5   single    0.970  0.020  1.090
 GJ1  C1   H6   single    0.970  0.020  1.090
 GJ1  C1   H7   single    0.970  0.020  1.090
 GJ1  C1   H8   single    0.970  0.020  1.090
 GJ1  C3   H9   single    0.930  0.020  1.080
 GJ1  C9   H10  single    0.970  0.020  1.090
 GJ1  C9   H11  single    0.970  0.020  1.090
 GJ1  C9   H12  single    0.970  0.020  1.090
 GJ1  C14  H13  single    0.930  0.020  1.080
 GJ1  C15  H14  single    0.930  0.020  1.080
 GJ1  C18  H15  single    0.970  0.020  1.090
 GJ1  C18  H16  single    0.970  0.020  1.090
 GJ1  O19  H17  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
 GJ1  O10  C7   C2   115.67  3.000
 GJ1  O10  C7   C6   124.34  3.000
 GJ1  C2   C7   C6   119.98  3.000
 GJ1  H1   C6   C5   117.82  3.000
 GJ1  H1   C6   C7   121.40  3.000
 GJ1  C5   C6   C7   120.79  3.000
 GJ1  H2   C5   C4   121.87  3.000
 GJ1  H2   C5   C6   118.32  3.000
 GJ1  C4   C5   C6   119.81  3.000
 GJ1  O8   C4   C3   116.15  3.000
 GJ1  O8   C4   C5   124.84  3.000
 GJ1  C3   C4   C5   119.01  3.000
 GJ1  C3   C2   C1   120.99  3.000
 GJ1  C3   C2   C7   118.51  3.000
 GJ1  C1   C2   C7   120.49  3.000
 GJ1  H3   C13  C14  120.62  3.000
 GJ1  H3   C13  C12  121.58  3.000
 GJ1  C14  C13  C12  117.80  3.000
 GJ1  H5   C11  H4   106.88  3.000
 GJ1  H5   C11  C12  108.88  3.000
 GJ1  H4   C11  C12  108.88  3.000
 GJ1  H5   C11  O10  111.31  3.000
 GJ1  H4   C11  O10  111.27  3.000
 GJ1  C12  C11  O10  109.54  3.000
 GJ1  H8   C1   H7   107.96  3.000
 GJ1  H8   C1   H6   106.90  3.000
 GJ1  H7   C1   H6   107.69  3.000
 GJ1  H8   C1   C2   111.80  3.000
 GJ1  H7   C1   C2   110.78  3.000
 GJ1  H6   C1   C2   111.52  3.000
 GJ1  H9   C3   C2   119.28  3.000
 GJ1  H9   C3   C4   118.82  3.000
 GJ1  C2   C3   C4   121.90  3.000
 GJ1  C9   O8   C4   117.98  3.000
 GJ1  H12  C9   H11  108.77  3.000
 GJ1  H12  C9   H10  108.76  3.000
 GJ1  H11  C9   H10  108.61  3.000
 GJ1  H12  C9   O8   106.70  3.000
 GJ1  H11  C9   O8   111.94  3.000
 GJ1  H10  C9   O8   111.95  3.000
 GJ1  C11  O10  C7   118.85  3.000
 GJ1  N17  C12  C11  114.01  3.000
 GJ1  C11  C12  C13  123.47  3.000
 GJ1  N17  C12  C13  122.52  3.000
 GJ1  H13  C14  C15  120.17  3.000
 GJ1  H13  C14  C13  119.96  3.000
 GJ1  C15  C14  C13  119.86  3.000
 GJ1  H14  C15  C16  121.24  3.000
 GJ1  H14  C15  C14  120.73  3.000
 GJ1  C16  C15  C14  118.03  3.000
 GJ1  C18  C16  N17  114.92  3.000
 GJ1  N17  C16  C15  122.24  3.000
 GJ1  C18  C16  C15  122.85  3.000
 GJ1  C16  N17  C12  119.55  3.000
 GJ1  H16  C18  H15  106.17  3.000
 GJ1  H16  C18  O19  112.01  3.000
 GJ1  H15  C18  O19  111.99  3.000
 GJ1  H16  C18  C16  108.10  3.000
 GJ1  H15  C18  C16  108.09  3.000
 GJ1  O19  C18  C16  110.28  3.000
 GJ1  H17  O19  C18  108.23  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
 GJ1  CONST_01  C4   C3   C2   C7      0.00   0.0  0
 GJ1  CONST_02  C4   C5   C6   C7      0.00   0.0  0
 GJ1  CONST_03  C3   C2   C7   C6      0.00   0.0  0
 GJ1  CONST_04  C3   C4   C5   C6      0.00   0.0  0
 GJ1  CONST_05  C2   C3   C4   C5      0.00   0.0  0
 GJ1  CONST_06  C2   C7   C6   C5      0.00   0.0  0
 GJ1  CONST_07  C16  C15  C14  C13     0.00   0.0  0
 GJ1  CONST_08  C16  N17  C12  C13     0.00   0.0  0
 GJ1  CONST_09  C15  C14  C13  C12     0.00   0.0  0
 GJ1  CONST_10  C15  C16  N17  C12     0.00   0.0  0
 GJ1  CONST_11  N17  C16  C15  C14     0.00   0.0  0
 GJ1  CONST_12  N17  C12  C13  C14     0.00   0.0  0
 GJ1  CONST_13  C1   C2   C7   C6    180.00   0.0  0
 GJ1  CONST_14  O8   C4   C5   C6    180.00   0.0  0
 GJ1  CONST_15  O10  C7   C6   C5    180.00   0.0  0
 GJ1  CONST_16  C1   C2   C3   C4    180.00   0.0  0
 GJ1  CONST_17  O8   C4   C3   C2    180.00   0.0  0
 GJ1  CONST_18  C14  C13  C12  C11   180.00   0.0  0
 GJ1  CONST_19  C16  N17  C12  C11   180.00   0.0  0
 GJ1  CONST_20  O10  C7   C2   C3    180.00   0.0  0
 GJ1  CONST_21  C18  C16  N17  C12   180.00   0.0  0
 GJ1  CONST_22  C18  C16  C15  C14   180.00   0.0  0
 GJ1  CONST_23  H9   C3   C2   C7    180.00   0.0  0
 GJ1  CONST_24  H2   C5   C6   C7    180.00   0.0  0
 GJ1  CONST_25  H1   C6   C5   C4    180.00   0.0  0
 GJ1  CONST_26  H14  C15  C14  C13   180.00   0.0  0
 GJ1  CONST_27  H13  C14  C13  C12   180.00   0.0  0
 GJ1  CONST_28  H3   C13  C14  C15   180.00   0.0  0
 GJ1  Var_01    C12  C11  O10  C7   -178.77  30.0  3
 GJ1  Var_02    O10  C11  C12  C13     0.49  30.0  2
 GJ1  Var_03    O19  C18  C16  C15     0.37  30.0  2
 GJ1  Var_04    H6   C1   C2   C7     64.37  30.0  2
 GJ1  Var_05    H10  C9   O8   C4    -60.76  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
 GJ1  plan-1  C7   0.020
 GJ1  plan-1  C6   0.020
 GJ1  plan-1  C5   0.020
 GJ1  plan-1  C4   0.020
 GJ1  plan-1  C2   0.020
 GJ1  plan-1  C1   0.020
 GJ1  plan-1  C3   0.020
 GJ1  plan-1  O8   0.020
 GJ1  plan-1  O10  0.020
 GJ1  plan-1  H1   0.020
 GJ1  plan-1  H2   0.020
 GJ1  plan-1  H9   0.020
 GJ1  plan-2  C13  0.020
 GJ1  plan-2  C11  0.020
 GJ1  plan-2  C12  0.020
 GJ1  plan-2  C14  0.020
 GJ1  plan-2  C15  0.020
 GJ1  plan-2  C16  0.020
 GJ1  plan-2  N17  0.020
 GJ1  plan-2  C18  0.020
 GJ1  plan-2  H13  0.020
 GJ1  plan-2  H14  0.020
 GJ1  plan-2  H3   0.020

