# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 10:00:51 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: (4-pyrimidin-5-ylphenyl)methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCc1ccc(cc1)c2cncnc2
#
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
 SWX  SWX  (4-pyrimidin-5-ylphenyl)methanol  ligand  24  14  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SWX
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
 SWX  C1   C  CR16  0  -0.296   0.5920  -1.1906   0.0918
 SWX  C2   C  CR16  0  -0.295   0.5824   1.1534  -0.4172
 SWX  C3   C  CR16  0  -0.273   1.9748  -1.2005  -0.0016
 SWX  C4   C  CR16  0  -0.270   1.9648   1.1364  -0.5070
 SWX  C5   C  CR16  0  -0.048  -2.3818  -1.0482  -0.4730
 SWX  C6   C  CR16  0  -0.047  -2.2925   1.0766   0.5240
 SWX  C7   C  CR16  0   0.050  -4.2582   0.0389   0.1454
 SWX  C8   C  CR6   0   0.078  -0.1237  -0.0114  -0.1146
 SWX  C9   C  CR6   0  -0.042  -1.5907   0.0048  -0.0214
 SWX  C10  C  CR6   0   0.082   2.6799  -0.0405  -0.3059
 SWX  C11  C  CH2   0  -0.228   4.1800  -0.0450  -0.3587
 SWX  N12  N  N     0  -0.386  -3.7042  -1.0382  -0.3897
 SWX  N13  N  N     0  -0.386  -3.6146   1.1005   0.6063
 SWX  O14  O  OH1   0  -0.666   4.6634   0.3113   0.9209
 SWX  H1   H  HCR6  0   0.259   0.0722  -2.1057   0.3474
 SWX  H2   H  HCR6  0   0.259   0.0502   2.0771  -0.6077
 SWX  H3   H  HCR6  0   0.257   2.5116  -2.1263   0.1677
 SWX  H4   H  HCR6  0   0.257   2.4914   2.0502  -0.7549
 SWX  H6   H  HCR6  0   0.277  -1.7637   1.9376   0.9197
 SWX  H7   H  HCR6  0   0.268  -5.3402   0.0529   0.2126
 SWX  H8   H  HCH2  0   0.211   4.5302  -1.0395  -0.6587
 SWX  H9   H  HCH2  0   0.210   4.5202   0.6605  -1.1262
 SWX  H10  H  HOH1  0   0.456   5.6250   0.3029   0.8840
 SWX  H5   H  HCR6  0   0.276  -1.9295  -1.9218  -0.9305

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
 SWX  C4   C2   aromatic  1.385  0.020  1.385
 SWX  C4   C10  aromatic  1.392  0.020  1.392
 SWX  C11  C10  single    1.501  0.020  1.501
 SWX  C11  O14  single    1.413  0.020  1.413
 SWX  C2   C8   aromatic  1.395  0.020  1.395
 SWX  C10  C3   aromatic  1.391  0.020  1.391
 SWX  C5   N12  aromatic  1.325  0.020  1.325
 SWX  C5   C9   aromatic  1.392  0.020  1.392
 SWX  C8   C9   single    1.470  0.020  1.470
 SWX  C8   C1   aromatic  1.395  0.020  1.395
 SWX  N12  C7   aromatic  1.324  0.020  1.324
 SWX  C9   C6   aromatic  1.392  0.020  1.392
 SWX  C3   C1   aromatic  1.386  0.020  1.386
 SWX  C7   N13  aromatic  1.324  0.020  1.324
 SWX  C6   N13  aromatic  1.325  0.020  1.325
 SWX  C1   H1   single    0.930  0.020  1.080
 SWX  C2   H2   single    0.930  0.020  1.080
 SWX  C3   H3   single    0.930  0.020  1.080
 SWX  C4   H4   single    0.930  0.020  1.080
 SWX  C5   H5   single    0.930  0.020  1.080
 SWX  C6   H6   single    0.930  0.020  1.080
 SWX  C7   H7   single    0.930  0.020  1.080
 SWX  C11  H8   single    0.970  0.020  1.090
 SWX  C11  H9   single    0.970  0.020  1.090
 SWX  O14  H10  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
 SWX  H1   C1   C8   120.20  3.000
 SWX  H1   C1   C3   119.26  3.000
 SWX  C8   C1   C3   120.53  3.000
 SWX  H2   C2   C8   120.10  3.000
 SWX  H2   C2   C4   119.30  3.000
 SWX  C8   C2   C4   120.58  3.000
 SWX  H3   C3   C10  119.71  3.000
 SWX  H3   C3   C1   119.33  3.000
 SWX  C10  C3   C1   120.96  3.000
 SWX  H4   C4   C10  119.77  3.000
 SWX  H4   C4   C2   119.31  3.000
 SWX  C10  C4   C2   120.91  3.000
 SWX  H5   C5   N12  116.66  3.000
 SWX  H5   C5   C9   120.59  3.000
 SWX  N12  C5   C9   122.75  3.000
 SWX  H6   C6   N13  116.70  3.000
 SWX  H6   C6   C9   120.54  3.000
 SWX  N13  C6   C9   122.76  3.000
 SWX  H7   C7   N13  116.94  3.000
 SWX  H7   C7   N12  116.94  3.000
 SWX  N13  C7   N12  126.12  3.000
 SWX  C9   C8   C2   120.63  3.000
 SWX  C9   C8   C1   120.80  3.000
 SWX  C2   C8   C1   118.57  3.000
 SWX  C8   C9   C6   122.43  3.000
 SWX  C6   C9   C5   115.02  3.000
 SWX  C8   C9   C5   122.56  3.000
 SWX  C11  C10  C4   120.73  3.000
 SWX  C11  C10  C3   120.78  3.000
 SWX  C4   C10  C3   118.45  3.000
 SWX  H9   C11  H8   107.03  3.000
 SWX  H9   C11  O14  111.43  3.000
 SWX  H8   C11  O14  111.54  3.000
 SWX  H9   C11  C10  109.44  3.000
 SWX  H8   C11  C10  109.37  3.000
 SWX  O14  C11  C10  108.01  3.000
 SWX  C7   N12  C5   116.68  3.000
 SWX  C7   N13  C6   116.67  3.000
 SWX  H10  O14  C11  107.75  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
 SWX  CONST_01  C4   C2   C8   C1    0.00   0.0  0
 SWX  CONST_04  C4   C10  C3   C1    0.00   0.0  0
 SWX  CONST_05  C3   C10  C4   C2    0.00   0.0  0
 SWX  CONST_08  C3   C1   C8   C2    0.00   0.0  0
 SWX  CONST_09  C9   C8   C1   C3  180.00   0.0  0
 SWX  CONST_10  C9   C8   C2   C4  180.00   0.0  0
 SWX  CONST_11  N13  C7   N12  C5    0.00   0.0  0
 SWX  CONST_12  N13  C6   C9   C5    0.00   0.0  0
 SWX  CONST_13  N12  C5   C9   C6    0.00   0.0  0
 SWX  CONST_14  N12  C7   N13  C6    0.00   0.0  0
 SWX  CONST_15  C9   C5   N12  C7    0.00   0.0  0
 SWX  CONST_16  C9   C6   N13  C7    0.00   0.0  0
 SWX  CONST_17  C10  C4   C2   C8    0.00   0.0  0
 SWX  CONST_18  N12  C5   C9   C8  180.00   0.0  0
 SWX  CONST_19  N13  C6   C9   C8  180.00   0.0  0
 SWX  CONST_20  C10  C3   C1   C8    0.00   0.0  0
 SWX  CONST_21  C11  C10  C3   C1  180.00   0.0  0
 SWX  CONST_22  C11  C10  C4   C2  180.00   0.0  0
 SWX  CONST_23  H2   C2   C8   C1  180.00   0.0  0
 SWX  CONST_24  H1   C1   C8   C2  180.00   0.0  0
 SWX  CONST_25  H4   C4   C10  C3  180.00   0.0  0
 SWX  CONST_26  H3   C3   C10  C4  180.00   0.0  0
 SWX  CONST_27  H7   C7   N12  C5  180.00   0.0  0
 SWX  CONST_28  H6   C6   C9   C5  180.00   0.0  0
 SWX  CONST_29  H5   C5   C9   C6  180.00   0.0  0
 SWX  Var_01    O14  C11  C10  C3  -91.91  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
 SWX  plan-1  C1   0.020
 SWX  plan-1  C2   0.020
 SWX  plan-1  C3   0.020
 SWX  plan-1  C4   0.020
 SWX  plan-1  C8   0.020
 SWX  plan-1  C9   0.020
 SWX  plan-1  C10  0.020
 SWX  plan-1  C11  0.020
 SWX  plan-1  H1   0.020
 SWX  plan-1  H2   0.020
 SWX  plan-1  H3   0.020
 SWX  plan-1  H4   0.020
 SWX  plan-2  C5   0.020
 SWX  plan-2  C6   0.020
 SWX  plan-2  C7   0.020
 SWX  plan-2  C8   0.020
 SWX  plan-2  C9   0.020
 SWX  plan-2  N12  0.020
 SWX  plan-2  N13  0.020
 SWX  plan-2  H6   0.020
 SWX  plan-2  H7   0.020
 SWX  plan-2  H5   0.020

