# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 05:15:34 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: 2-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]phenyl}ethanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(Cc2cccc(CCO)c2)c(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
 26G  26G  2-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]phenyl}ethanol  ligand  35  18  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_26G
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
 26G  CM2  C  CH3   0  -0.728   5.2247   0.9969  -1.2263
 26G  C02  C  CH2   0  -0.130  -4.0267   1.6596   0.0003
 26G  C2   C  CR16  0  -0.301  -0.5235  -1.8496  -0.7145
 26G  C5   C  CR6   0   0.131  -2.8895  -0.5558   0.0148
 26G  C4   C  CR16  0  -0.400  -1.7659  -0.5181   0.8398
 26G  C01  C  CR6   0   0.170  -0.5795  -1.1512   0.4896
 26G  C7A  C  CH2   0  -0.626   0.6295  -1.0905   1.3961
 26G  C4A  C  CR6   0   0.461   1.9379   0.8292   0.3197
 26G  N3A  N  N     0  -0.468   3.0250   1.2864  -0.3008
 26G  C2A  C  CR6   0   0.349   4.0176   0.4372  -0.5395
 26G  N1A  N  N     0  -0.449   4.0318  -0.8444  -0.2075
 26G  C6A  C  CR16  0  -0.098   2.9384  -1.2952   0.4169
 26G  C5A  C  CR6   0  -0.020   1.8418  -0.5266   0.7165
 26G  C28  C  CR16  0  -0.325  -2.8100  -1.2578  -1.1827
 26G  C30  C  CR16  0  -0.224  -1.6339  -1.9052  -1.5420
 26G  O31  O  OH1   0  -0.671  -5.2172   2.3163   0.3722
 26G  H1   H  HCH3  0   0.253   5.7555   1.6804  -0.5610
 26G  H2   H  HCH3  0   0.243   5.9096   0.2051  -1.5199
 26G  H3   H  HCH3  0   0.249   4.9396   1.5670  -2.1103
 26G  H4   H  HNH2  0   0.407   0.1425   1.4674   1.0941
 26G  H5   H  HNH2  0   0.398   1.0907   2.6762   0.3325
 26G  H6   H  HCH2  0   0.194  -3.1508   2.0992   0.4964
 26G  H7   H  HCH2  0   0.197  -3.8457   1.7290  -1.0805
 26G  H8   H  HCH2  0   0.246  -4.3059   0.1212   1.4706
 26G  H9   H  HCH2  0   0.247  -5.0032  -0.2505  -0.1032
 26G  H10  H  HCR6  0   0.247   0.3907  -2.3537  -1.0055
 26G  H11  H  HCR6  0   0.246  -1.8213   0.0188   1.7829
 26G  H12  H  HCH2  0   0.270   0.3835  -0.5110   2.2914
 26G  H13  H  HCH2  0   0.283   0.8704  -2.0962   1.7506
 26G  H14  H  HCR6  0   0.259   2.9415  -2.3455   0.6953
 26G  H15  H  HCR6  0   0.248  -3.6724  -1.2990  -1.8376
 26G  H16  H  HCR6  0   0.253  -1.5852  -2.4560  -2.4729
 26G  H17  H  HOH1  0   0.454  -5.1417   3.2408   0.1199
 26G  N4A  N  NH2   0  -0.827   0.9417   1.7023   0.5342
 26G  C6   C  CH2   0  -0.540  -4.1365   0.1925   0.3931

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
 26G  CM2  C2A  single    1.497  0.020  1.497
 26G  C2A  N3A  aromatic  1.328  0.020  1.328
 26G  C2A  N1A  aromatic  1.324  0.020  1.324
 26G  N3A  C4A  aromatic  1.333  0.020  1.333
 26G  N1A  C6A  aromatic  1.337  0.020  1.337
 26G  C30  C2   aromatic  1.386  0.020  1.386
 26G  C30  C28  aromatic  1.390  0.020  1.390
 26G  C4A  N4A  single    1.342  0.020  1.342
 26G  C4A  C5A  aromatic  1.416  0.020  1.416
 26G  C2   C01  aromatic  1.393  0.020  1.393
 26G  C6A  C5A  aromatic  1.372  0.020  1.372
 26G  C5A  C7A  single    1.500  0.020  1.500
 26G  C28  C5   aromatic  1.390  0.020  1.390
 26G  C01  C7A  single    1.512  0.020  1.512
 26G  C01  C4   aromatic  1.390  0.020  1.390
 26G  C5   C4   aromatic  1.394  0.020  1.394
 26G  C5   C6   single    1.503  0.020  1.503
 26G  C6   C02  single    1.523  0.020  1.523
 26G  C02  O31  single    1.410  0.020  1.410
 26G  CM2  H1   single    0.970  0.020  1.090
 26G  CM2  H2   single    0.970  0.020  1.090
 26G  CM2  H3   single    0.970  0.020  1.090
 26G  N4A  H4   single    0.860  0.020  1.020
 26G  N4A  H5   single    0.860  0.020  1.020
 26G  C02  H6   single    0.970  0.020  1.090
 26G  C02  H7   single    0.970  0.020  1.090
 26G  C6   H8   single    0.970  0.020  1.090
 26G  C6   H9   single    0.970  0.020  1.090
 26G  C2   H10  single    0.930  0.020  1.080
 26G  C4   H11  single    0.930  0.020  1.080
 26G  C7A  H12  single    0.970  0.020  1.090
 26G  C7A  H13  single    0.970  0.020  1.090
 26G  C6A  H14  single    0.930  0.020  1.080
 26G  C28  H15  single    0.930  0.020  1.080
 26G  C30  H16  single    0.930  0.020  1.080
 26G  O31  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
 26G  H3   CM2  H2   109.07  3.000
 26G  H3   CM2  H1   107.09  3.000
 26G  H2   CM2  H1   108.31  3.000
 26G  H3   CM2  C2A  110.90  3.000
 26G  H2   CM2  C2A  111.07  3.000
 26G  H1   CM2  C2A  110.27  3.000
 26G  H7   C02  H6   106.73  3.000
 26G  H7   C02  O31  111.68  3.000
 26G  H6   C02  O31  111.58  3.000
 26G  H7   C02  C6   109.07  3.000
 26G  H6   C02  C6   109.07  3.000
 26G  O31  C02  C6   108.65  3.000
 26G  H10  C2   C30  119.79  3.000
 26G  H10  C2   C01  119.94  3.000
 26G  C30  C2   C01  120.27  3.000
 26G  C28  C5   C4   118.50  3.000
 26G  C4   C5   C6   120.41  3.000
 26G  C28  C5   C6   121.04  3.000
 26G  H11  C4   C01  119.17  3.000
 26G  H11  C4   C5   119.07  3.000
 26G  C01  C4   C5   121.77  3.000
 26G  C7A  C01  C4   120.87  3.000
 26G  C4   C01  C2   118.72  3.000
 26G  C7A  C01  C2   120.41  3.000
 26G  H13  C7A  H12  105.74  3.000
 26G  H13  C7A  C5A  108.34  3.000
 26G  H12  C7A  C5A  110.69  3.000
 26G  H13  C7A  C01  109.48  3.000
 26G  H12  C7A  C01  109.38  3.000
 26G  C5A  C7A  C01  112.94  3.000
 26G  C5A  C4A  N3A  120.96  3.000
 26G  C5A  C4A  N4A  121.86  3.000
 26G  N3A  C4A  N4A  117.18  3.000
 26G  C2A  N3A  C4A  118.30  3.000
 26G  N1A  C2A  N3A  125.59  3.000
 26G  N1A  C2A  CM2  117.92  3.000
 26G  N3A  C2A  CM2  116.49  3.000
 26G  C6A  N1A  C2A  115.76  3.000
 26G  H14  C6A  C5A  119.19  3.000
 26G  H14  C6A  N1A  116.30  3.000
 26G  C5A  C6A  N1A  124.51  3.000
 26G  C6A  C5A  C4A  114.89  3.000
 26G  C6A  C5A  C7A  122.30  3.000
 26G  C4A  C5A  C7A  122.81  3.000
 26G  H15  C28  C30  119.96  3.000
 26G  H15  C28  C5   119.62  3.000
 26G  C30  C28  C5   120.42  3.000
 26G  H16  C30  C28  119.82  3.000
 26G  H16  C30  C2   119.85  3.000
 26G  C28  C30  C2   120.32  3.000
 26G  H17  O31  C02  108.21  3.000
 26G  H5   N4A  H4   117.16  3.000
 26G  H5   N4A  C4A  119.22  3.000
 26G  H4   N4A  C4A  121.87  3.000
 26G  H9   C6   H8   107.36  3.000
 26G  H9   C6   C5   110.00  3.000
 26G  H8   C6   C5   110.13  3.000
 26G  H9   C6   C02  109.31  3.000
 26G  H8   C6   C02  109.17  3.000
 26G  C5   C6   C02  110.79  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
 26G  CONST_01  C5   C28  C30  C2     0.00   0.0  0
 26G  CONST_02  C5   C4   C01  C2     0.00   0.0  0
 26G  CONST_03  C30  C2   C01  C4     0.00   0.0  0
 26G  CONST_04  C30  C28  C5   C4     0.00   0.0  0
 26G  CONST_05  C28  C30  C2   C01    0.00   0.0  0
 26G  CONST_06  C28  C5   C4   C01    0.00   0.0  0
 26G  CONST_07  N1A  C2A  N3A  C4A    0.00   0.0  0
 26G  CONST_08  N1A  C6A  C5A  C4A    0.00   0.0  0
 26G  CONST_09  C6A  N1A  C2A  N3A    0.00   0.0  0
 26G  CONST_10  C6A  C5A  C4A  N3A    0.00   0.0  0
 26G  CONST_11  C5A  C4A  N3A  C2A    0.00   0.0  0
 26G  CONST_12  C5A  C6A  N1A  C2A    0.00   0.0  0
 26G  CONST_13  C4A  N3A  C2A  CM2  180.00   0.0  0
 26G  CONST_14  C6A  N1A  C2A  CM2  180.00   0.0  0
 26G  CONST_15  C2A  N3A  C4A  N4A  180.00   0.0  0
 26G  CONST_16  C6A  C5A  C4A  N4A  180.00   0.0  0
 26G  CONST_17  C30  C28  C5   C6   180.00   0.0  0
 26G  CONST_18  C01  C4   C5   C6   180.00   0.0  0
 26G  CONST_19  C7A  C01  C4   C5   180.00   0.0  0
 26G  CONST_20  N3A  C4A  C5A  C7A  180.00   0.0  0
 26G  CONST_21  N1A  C6A  C5A  C7A  180.00   0.0  0
 26G  CONST_22  C30  C2   C01  C7A  180.00   0.0  0
 26G  CONST_23  H15  C28  C30  C2   180.00   0.0  0
 26G  CONST_24  H11  C4   C01  C2   180.00   0.0  0
 26G  CONST_25  H16  C30  C28  C5   180.00   0.0  0
 26G  CONST_26  H10  C2   C01  C4   180.00   0.0  0
 26G  CONST_27  H14  C6A  C5A  C4A  180.00   0.0  0
 26G  CONST_28  H4   N4A  C4A  N3A  180.00   0.0  0
 26G  CONST_29  H5   N4A  C4A  N3A    0.00   0.0  0
 26G  Var_01    C5A  C7A  C01  C2    56.97  30.0  2
 26G  Var_02    C4A  C5A  C7A  C01   68.28  30.0  2
 26G  Var_03    C28  C5   C6   C02  -95.53  30.0  2
 26G  Var_04    H1   CM2  C2A  N3A   68.99  30.0  2
 26G  Var_05    O31  C02  C6   C5   179.89  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
 26G  plan-1  CM2  0.020
 26G  plan-1  C7A  0.020
 26G  plan-1  C4A  0.020
 26G  plan-1  N3A  0.020
 26G  plan-1  C2A  0.020
 26G  plan-1  N1A  0.020
 26G  plan-1  C6A  0.020
 26G  plan-1  C5A  0.020
 26G  plan-1  H14  0.020
 26G  plan-1  N4A  0.020
 26G  plan-2  C2   0.020
 26G  plan-2  C5   0.020
 26G  plan-2  C4   0.020
 26G  plan-2  C01  0.020
 26G  plan-2  C7A  0.020
 26G  plan-2  C28  0.020
 26G  plan-2  C30  0.020
 26G  plan-2  H10  0.020
 26G  plan-2  H11  0.020
 26G  plan-2  H15  0.020
 26G  plan-2  H16  0.020
 26G  plan-2  C6   0.020
 26G  plan-3  C4A  0.020
 26G  plan-3  H4   0.020
 26G  plan-3  H5   0.020
 26G  plan-3  N4A  0.020

