# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 20:33:18 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: 3-(2-azanyl-6-methyl-pyrimidin-4-yl)oxypropan-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(OCCCO)nc(N)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
 6Q3  6Q3  3-(2-azanyl-6-methyl-pyrimidin-4-yl)oxypropan-1-ol  ligand  26  13  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6Q3
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
 6Q3  N3    N  N     0  -0.496  -0.7585  -0.9145  -0.0311
 6Q3  C2    C  CR6   0   0.538  -2.0515  -1.2645  -0.0563
 6Q3  N2    N  NH2   0  -0.760  -2.3139  -2.5874  -0.1222
 6Q3  N1    N  N     0  -0.564  -3.0866  -0.4315  -0.0523
 6Q3  C6    C  CR6   0   0.260  -2.8053   0.8741  -0.0290
 6Q3  C7    C  CH3   0  -0.704  -3.9720   1.8084  -0.0172
 6Q3  C4    C  CR6   0   0.513  -0.5027   0.3735  -0.0084
 6Q3  C5    C  CR16  0  -0.386  -1.5084   1.3463  -0.0113
 6Q3  O1'   O  OH1   0  -0.645   5.4852   0.3430  -0.0387
 6Q3  C1'   C  CH2   0  -0.116   4.2850  -0.3963  -0.0288
 6Q3  C2'   C  CH2   0  -0.499   3.1185   0.5739  -0.0020
 6Q3  C3'   C  CH2   0  -0.130   1.8033  -0.1773   0.0003
 6Q3  O3'   O  O2    0  -0.356   0.7555   0.7916   0.0206
 6Q3  H21N  H  HNH2  0   0.353  -1.5757  -3.2313   0.1019
 6Q3  H22N  H  HNH2  0   0.374  -3.2506  -2.8958   0.0708
 6Q3  H71C  H  HCH3  0   0.228  -4.5879   1.6366   0.8664
 6Q3  H72C  H  HCH3  0   0.249  -3.6574   2.8497  -0.0180
 6Q3  H73C  H  HCH3  0   0.221  -4.6068   1.6387  -0.8874
 6Q3  H5    H  HCR6  0   0.229  -1.2799   2.4020   0.0086
 6Q3  H1'   H  HOH1  0   0.439   6.2167  -0.2783  -0.0813
 6Q3  H1'1  H  HCH2  0   0.180   4.2031  -1.0385  -0.9156
 6Q3  H1'2  H  HCH2  0   0.192   4.2286  -1.0582   0.8454
 6Q3  H2'1  H  HCH2  0   0.198   3.1869   1.2045   0.8885
 6Q3  H2'2  H  HCH2  0   0.271   3.1686   1.2280  -0.8765
 6Q3  H3'1  H  HCH2  0   0.199   1.7138  -0.8084  -0.8881
 6Q3  H3'2  H  HCH2  0   0.212   1.7267  -0.8308   0.8736

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
 6Q3  N3   C2    aromatic  1.340  0.020  1.340
 6Q3  N3   C4    aromatic  1.313  0.020  1.313
 6Q3  C2   N2    single    1.350  0.020  1.350
 6Q3  C2   N1    aromatic  1.329  0.020  1.329
 6Q3  N1   C6    aromatic  1.336  0.020  1.336
 6Q3  C6   C7    single    1.495  0.020  1.495
 6Q3  C6   C5    aromatic  1.380  0.020  1.380
 6Q3  C4   C5    aromatic  1.399  0.020  1.399
 6Q3  C4   O3'   single    1.326  0.020  1.326
 6Q3  O1'  C1'   single    1.410  0.020  1.410
 6Q3  C1'  C2'   single    1.517  0.020  1.517
 6Q3  C2'  C3'   single    1.515  0.020  1.515
 6Q3  C3'  O3'   single    1.427  0.020  1.427
 6Q3  N2   H21N  single    0.890  0.020  1.040
 6Q3  N2   H22N  single    0.890  0.020  1.040
 6Q3  C7   H71C  single    0.970  0.020  1.090
 6Q3  C7   H72C  single    0.970  0.020  1.090
 6Q3  C7   H73C  single    0.970  0.020  1.090
 6Q3  C5   H5    single    0.930  0.020  1.080
 6Q3  O1'  H1'   single    0.850  0.020  0.980
 6Q3  C1'  H1'1  single    0.970  0.020  1.090
 6Q3  C1'  H1'2  single    0.970  0.020  1.090
 6Q3  C2'  H2'1  single    0.970  0.020  1.090
 6Q3  C2'  H2'2  single    0.970  0.020  1.090
 6Q3  C3'  H3'1  single    0.970  0.020  1.090
 6Q3  C3'  H3'2  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
 6Q3  C4    N3   C2    116.39  3.000
 6Q3  N1    C2   N2    117.58  3.000
 6Q3  N1    C2   N3    126.01  3.000
 6Q3  N2    C2   N3    116.39  3.000
 6Q3  H22N  N2   H21N  116.44  3.000
 6Q3  H22N  N2   C2    118.19  3.000
 6Q3  H21N  N2   C2    118.30  3.000
 6Q3  C6    N1   C2    116.67  3.000
 6Q3  C5    C6   C7    121.29  3.000
 6Q3  C5    C6   N1    122.17  3.000
 6Q3  C7    C6   N1    116.53  3.000
 6Q3  H73C  C7   H72C  108.47  3.000
 6Q3  H73C  C7   H71C  107.06  3.000
 6Q3  H72C  C7   H71C  108.34  3.000
 6Q3  H73C  C7   C6    110.53  3.000
 6Q3  H72C  C7   C6    111.88  3.000
 6Q3  H71C  C7   C6    110.41  3.000
 6Q3  O3'   C4   C5    117.56  3.000
 6Q3  O3'   C4   N3    119.63  3.000
 6Q3  C5    C4   N3    122.81  3.000
 6Q3  H5    C5   C4    121.83  3.000
 6Q3  H5    C5   C6    122.22  3.000
 6Q3  C4    C5   C6    115.94  3.000
 6Q3  H1'   O1'  C1'   108.02  3.000
 6Q3  H1'2  C1'  H1'1  106.66  3.000
 6Q3  H1'2  C1'  C2'   109.38  3.000
 6Q3  H1'1  C1'  C2'   109.32  3.000
 6Q3  H1'2  C1'  O1'   111.44  3.000
 6Q3  H1'1  C1'  O1'   111.38  3.000
 6Q3  C2'   C1'  O1'   108.62  3.000
 6Q3  H2'2  C2'  H2'1  107.67  3.000
 6Q3  H2'2  C2'  C3'   109.74  3.000
 6Q3  H2'1  C2'  C3'   109.83  3.000
 6Q3  H2'2  C2'  C1'   109.46  3.000
 6Q3  H2'1  C2'  C1'   109.58  3.000
 6Q3  C3'   C2'  C1'   110.52  3.000
 6Q3  H3'2  C3'  H3'1  107.35  3.000
 6Q3  H3'2  C3'  O3'   110.06  3.000
 6Q3  H3'1  C3'  O3'   110.08  3.000
 6Q3  H3'2  C3'  C2'   111.00  3.000
 6Q3  H3'1  C3'  C2'   110.86  3.000
 6Q3  O3'   C3'  C2'   107.51  3.000
 6Q3  C3'   O3'  C4    118.83  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
 6Q3  CONST_01  C6    N1   C2   N3      0.00   0.0  0
 6Q3  CONST_02  C6    C5   C4   N3      0.00   0.0  0
 6Q3  CONST_03  C5    C4   N3   C2      0.00   0.0  0
 6Q3  CONST_04  C5    C6   N1   C2      0.00   0.0  0
 6Q3  CONST_05  C4    N3   C2   N1      0.00   0.0  0
 6Q3  CONST_06  C4    C5   C6   N1      0.00   0.0  0
 6Q3  CONST_07  O3'   C4   N3   C2    180.00   0.0  0
 6Q3  CONST_08  C7    C6   N1   C2    180.00   0.0  0
 6Q3  CONST_09  C4    N3   C2   N2    180.00   0.0  0
 6Q3  CONST_10  C6    N1   C2   N2    180.00   0.0  0
 6Q3  CONST_11  O3'   C4   C5   C6    180.00   0.0  0
 6Q3  CONST_12  C4    C5   C6   C7    180.00   0.0  0
 6Q3  CONST_13  H5    C5   C4   N3    180.00   0.0  0
 6Q3  CONST_15  H22N  N2   C2   N3    180.00   0.0  0
 6Q3  Var_01    H71C  C7   C6   N1     60.37  30.0  2
 6Q3  Var_02    C2'   C3'  O3'  C4    178.29  30.0  1
 6Q3  Var_03    C3'   C2'  C1'  O1'   179.63  30.0  3
 6Q3  Var_04    O3'   C3'  C2'  C1'  -179.78  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
 6Q3  plan-1  N3    0.020
 6Q3  plan-1  C2    0.020
 6Q3  plan-1  N2    0.020
 6Q3  plan-1  N1    0.020
 6Q3  plan-1  C6    0.020
 6Q3  plan-1  C7    0.020
 6Q3  plan-1  C4    0.020
 6Q3  plan-1  C5    0.020
 6Q3  plan-1  O3'   0.020
 6Q3  plan-1  H5    0.020
 6Q3  plan-2  C2    0.020
 6Q3  plan-2  N2    0.020
 6Q3  plan-2  H21N  0.020
 6Q3  plan-2  H22N  0.020

