# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 10:02:00 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: 2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]ethanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(C)nc(SCCO)n1
#
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
 KI5  KI5  2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]ethanol  ligand  24  12  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KI5
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
 KI5  O     O  OH1   0  -0.668   4.6180   0.6596   0.0290
 KI5  C6    C  CH2   0  -0.141   3.7097  -0.4158   0.0476
 KI5  C5    C  CH2   0  -0.573   2.3103   0.1774   0.0361
 KI5  S     S  S2    0   0.031   1.1257  -1.1935   0.0663
 KI5  C4    C  CR6   0   0.214  -0.4221  -0.3670   0.0277
 KI5  N     N  N     0  -0.438  -1.4560  -1.1964   0.0323
 KI5  C3    C  CR6   0   0.283  -2.6647  -0.6423   0.0013
 KI5  C7    C  CH3   0  -0.720  -3.8383  -1.5661   0.0041
 KI5  C2    C  CR16  0  -0.397  -2.8131   0.7403  -0.0337
 KI5  N1    N  N     0  -0.424  -0.4560   0.9502  -0.0029
 KI5  C1    C  CR6   0   0.296  -1.6644   1.5172  -0.0340
 KI5  C     C  CH3   0  -0.717  -1.7135   3.0089  -0.0652
 KI5  H     H  HOH1  0   0.459   5.5090   0.2981   0.0312
 KI5  H61C  H  HCH2  0   0.209   3.8378  -1.0705  -0.8235
 KI5  H62C  H  HCH2  0   0.209   3.8376  -1.0397   0.9412
 KI5  H51C  H  HCH2  0   0.279   2.1538   0.8132   0.9075
 KI5  H52C  H  HCH2  0   0.279   2.1523   0.7739  -0.8624
 KI5  H71C  H  HCH3  0   0.262  -3.8275  -2.1883   0.8997
 KI5  H72C  H  HCH3  0   0.251  -4.7803  -1.0232  -0.0275
 KI5  H73C  H  HCH3  0   0.262  -3.7943  -2.2355  -0.8555
 KI5  H2    H  HCR6  0   0.271  -3.7933   1.1949  -0.0607
 KI5  HC1   H  HCH3  0   0.262  -1.2674   3.4207   0.8411
 KI5  HC2   H  HCH3  0   0.261  -1.1384   3.3905  -0.9094
 KI5  HC3   H  HCH3  0   0.250  -2.7342   3.3768  -0.1448

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
 KI5  O   C6    single    1.408  0.020  1.408
 KI5  C6  C5    single    1.520  0.020  1.520
 KI5  C5  S     single    1.812  0.020  1.812
 KI5  S   C4    single    1.755  0.020  1.755
 KI5  C4  N     aromatic  1.325  0.020  1.325
 KI5  C4  N1    aromatic  1.318  0.020  1.318
 KI5  N   C3    aromatic  1.330  0.020  1.330
 KI5  C3  C7    single    1.494  0.020  1.494
 KI5  C3  C2    aromatic  1.391  0.020  1.391
 KI5  C2  C1    aromatic  1.387  0.020  1.387
 KI5  N1  C1    aromatic  1.335  0.020  1.335
 KI5  C1  C     single    1.493  0.020  1.493
 KI5  O   H     single    0.850  0.020  0.980
 KI5  C6  H61C  single    0.970  0.020  1.090
 KI5  C6  H62C  single    0.970  0.020  1.090
 KI5  C5  H51C  single    0.970  0.020  1.090
 KI5  C5  H52C  single    0.970  0.020  1.090
 KI5  C7  H71C  single    0.970  0.020  1.090
 KI5  C7  H72C  single    0.970  0.020  1.090
 KI5  C7  H73C  single    0.970  0.020  1.090
 KI5  C2  H2    single    0.930  0.020  1.080
 KI5  C   HC1   single    0.970  0.020  1.090
 KI5  C   HC2   single    0.970  0.020  1.090
 KI5  C   HC3   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
 KI5  H     O   C6    108.09  3.000
 KI5  H62C  C6  H61C  107.08  3.000
 KI5  H62C  C6  C5    109.59  3.000
 KI5  H61C  C6  C5    109.53  3.000
 KI5  H62C  C6  O     111.71  3.000
 KI5  H61C  C6  O     111.72  3.000
 KI5  C5    C6  O     107.20  3.000
 KI5  H52C  C5  H51C  108.61  3.000
 KI5  H52C  C5  S     109.45  3.000
 KI5  H51C  C5  S     109.52  3.000
 KI5  H52C  C5  C6    110.69  3.000
 KI5  H51C  C5  C6    110.72  3.000
 KI5  S     C5  C6    107.85  3.000
 KI5  C4    S   C5    102.70  3.000
 KI5  N1    C4  N     127.26  3.000
 KI5  N1    C4  S     119.59  3.000
 KI5  N     C4  S     113.15  3.000
 KI5  C3    N   C4    116.62  3.000
 KI5  C2    C3  C7    122.08  3.000
 KI5  C2    C3  N     120.77  3.000
 KI5  C7    C3  N     117.15  3.000
 KI5  H73C  C7  H72C  108.57  3.000
 KI5  H73C  C7  H71C  107.26  3.000
 KI5  H72C  C7  H71C  108.49  3.000
 KI5  H73C  C7  C3    110.28  3.000
 KI5  H72C  C7  C3    111.82  3.000
 KI5  H71C  C7  C3    110.28  3.000
 KI5  H2    C2  C1    121.04  3.000
 KI5  H2    C2  C3    121.02  3.000
 KI5  C1    C2  C3    117.94  3.000
 KI5  C1    N1  C4    116.63  3.000
 KI5  C     C1  N1    117.04  3.000
 KI5  C     C1  C2    122.18  3.000
 KI5  N1    C1  C2    120.78  3.000
 KI5  HC3   C   HC2   108.66  3.000
 KI5  HC3   C   HC1   108.47  3.000
 KI5  HC2   C   HC1   107.18  3.000
 KI5  HC3   C   C1    111.73  3.000
 KI5  HC2   C   C1    110.40  3.000
 KI5  HC1   C   C1    110.26  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
 KI5  CONST_01  C2    C3  N   C4     0.00   0.0  0
 KI5  CONST_02  C2    C1  N1  C4     0.00   0.0  0
 KI5  CONST_03  C1    N1  C4  N      0.00   0.0  0
 KI5  CONST_04  C1    C2  C3  N      0.00   0.0  0
 KI5  CONST_05  N1    C4  N   C3     0.00   0.0  0
 KI5  CONST_06  N1    C1  C2  C3     0.00   0.0  0
 KI5  CONST_07  C3    N   C4  S    180.00   0.0  0
 KI5  CONST_08  C1    N1  C4  S    180.00   0.0  0
 KI5  CONST_09  C7    C3  N   C4   180.00   0.0  0
 KI5  CONST_10  C     C1  N1  C4   180.00   0.0  0
 KI5  CONST_11  C     C1  C2  C3   180.00   0.0  0
 KI5  CONST_12  C1    C2  C3  C7   180.00   0.0  0
 KI5  CONST_13  H2    C2  C3  N    180.00   0.0  0
 KI5  Var_01    N     C4  S   C5   179.49  30.0  2
 KI5  Var_02    H71C  C7  C3  N     59.47  30.0  2
 KI5  Var_03    HC1   C   C1  C2   117.42  30.0  2
 KI5  Var_04    H51C  C5  S   C4    60.18  30.0  1
 KI5  Var_05    S     C5  C6  O   -179.79  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
 KI5  plan-1  S   0.020
 KI5  plan-1  C4  0.020
 KI5  plan-1  N   0.020
 KI5  plan-1  C3  0.020
 KI5  plan-1  C7  0.020
 KI5  plan-1  C2  0.020
 KI5  plan-1  N1  0.020
 KI5  plan-1  C1  0.020
 KI5  plan-1  C   0.020
 KI5  plan-1  H2  0.020

