# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 22:34:51 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: {3-[(4-amino-2-methylpyrimidin-5-yl)methyl]phenyl}methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(Cc2cccc(CO)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
 XX8  XX8  {3-[(4-amino-2-methylpyrimidin-5-yl)methyl]phenyl}methanol  ligand  32  17  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_XX8
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
 XX8  CM2  C  CH3   0  -0.728  -5.1712   0.1278   1.1709
 XX8  O01  O  OH1   0  -0.666   4.1757   2.0318  -1.2725
 XX8  C2   C  CR16  0  -0.291   1.0144  -1.2823   0.6770
 XX8  C5   C  CR6   0   0.067   3.2732   0.1827  -0.0624
 XX8  C4   C  CR16  0  -0.367   2.1488   0.1436  -0.8838
 XX8  C01  C  CR6   0   0.117   1.0165  -0.5831  -0.5274
 XX8  C7A  C  CH2   0  -0.588  -0.1823  -0.6241  -1.4500
 XX8  C4A  C  CR6   0   0.455  -1.8426   0.7948  -0.1272
 XX8  N3A  N  N     0  -0.466  -3.0191   0.9437   0.4784
 XX8  C2A  C  CR6   0   0.349  -3.8578  -0.0866   0.4851
 XX8  N1A  N  N     0  -0.448  -3.6272  -1.2705  -0.0603
 XX8  C6A  C  CR16  0  -0.094  -2.4438  -1.4118  -0.6678
 XX8  C5A  C  CR6   0  -0.035  -1.4921  -0.4269  -0.7496
 XX8  C28  C  CR16  0  -0.313   3.2504  -0.5192   1.1377
 XX8  C30  C  CR16  0  -0.227   2.1285  -1.2515   1.5017
 XX8  H1   H  HCH3  0   0.252  -5.7239   0.9368   0.6911
 XX8  H2   H  HCH3  0   0.244  -5.7793  -0.7728   1.1430
 XX8  H3   H  HCH3  0   0.251  -5.0205   0.4168   2.2117
 XX8  H4   H  HNH2  0   0.396  -1.2569   2.6543   0.4207
 XX8  H5   H  HNH2  0   0.407  -0.0497   1.7576  -0.3873
 XX8  H6   H  HOH1  0   0.460   4.9844   2.3772  -1.6610
 XX8  H7   H  HCH2  0   0.222   5.1759   0.2351  -1.0049
 XX8  H8   H  HCH2  0   0.212   5.0590   1.2355   0.4340
 XX8  H9   H  HCR6  0   0.248   0.1395  -1.8475   0.9758
 XX8  H10  H  HCR6  0   0.251   2.1475   0.6888  -1.8206
 XX8  H11  H  HCH2  0   0.267  -0.0582   0.1305  -2.2327
 XX8  H12  H  HCH2  0   0.281  -0.2053  -1.5882  -1.9663
 XX8  H13  H  HCR6  0   0.259  -2.2481  -2.3801  -1.1203
 XX8  H14  H  HCR6  0   0.250   4.1107  -0.4895   1.7962
 XX8  H15  H  HCR6  0   0.255   2.1205  -1.7930   2.4391
 XX8  N4A  N  NH2   0  -0.825  -1.0218   1.8607  -0.1521
 XX8  C6   C  CH2   0  -0.192   4.5147   0.9286  -0.4685

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
 XX8  C2   C30  aromatic  1.387  0.020  1.387
 XX8  C2   C01  aromatic  1.393  0.020  1.393
 XX8  C30  C28  aromatic  1.388  0.020  1.388
 XX8  C7A  C01  single    1.513  0.020  1.513
 XX8  C7A  C5A  single    1.498  0.020  1.498
 XX8  C01  C4   aromatic  1.392  0.020  1.392
 XX8  C28  C5   aromatic  1.390  0.020  1.390
 XX8  C5A  C6A  aromatic  1.372  0.020  1.372
 XX8  C5A  C4A  aromatic  1.415  0.020  1.415
 XX8  C4   C5   aromatic  1.393  0.020  1.393
 XX8  C6A  N1A  aromatic  1.338  0.020  1.338
 XX8  C5   C6   single    1.504  0.020  1.504
 XX8  N4A  C4A  single    1.346  0.020  1.346
 XX8  C4A  N3A  aromatic  1.332  0.020  1.332
 XX8  N1A  C2A  aromatic  1.324  0.020  1.324
 XX8  C6   O01  single    1.407  0.020  1.407
 XX8  N3A  C2A  aromatic  1.329  0.020  1.329
 XX8  C2A  CM2  single    1.497  0.020  1.497
 XX8  CM2  H1   single    0.970  0.020  1.090
 XX8  CM2  H2   single    0.970  0.020  1.090
 XX8  CM2  H3   single    0.970  0.020  1.090
 XX8  N4A  H4   single    0.890  0.020  1.040
 XX8  N4A  H5   single    0.890  0.020  1.040
 XX8  O01  H6   single    0.850  0.020  0.980
 XX8  C6   H7   single    0.970  0.020  1.090
 XX8  C6   H8   single    0.970  0.020  1.090
 XX8  C2   H9   single    0.930  0.020  1.080
 XX8  C4   H10  single    0.930  0.020  1.080
 XX8  C7A  H11  single    0.970  0.020  1.090
 XX8  C7A  H12  single    0.970  0.020  1.090
 XX8  C6A  H13  single    0.930  0.020  1.080
 XX8  C28  H14  single    0.930  0.020  1.080
 XX8  C30  H15  single    0.930  0.020  1.080

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
 XX8  H3   CM2  H2   108.74  3.000
 XX8  H3   CM2  H1   107.06  3.000
 XX8  H2   CM2  H1   108.65  3.000
 XX8  H3   CM2  C2A  110.73  3.000
 XX8  H2   CM2  C2A  111.12  3.000
 XX8  H1   CM2  C2A  110.43  3.000
 XX8  H6   O01  C6   108.06  3.000
 XX8  H9   C2   C30  119.75  3.000
 XX8  H9   C2   C01  120.11  3.000
 XX8  C30  C2   C01  120.14  3.000
 XX8  C28  C5   C4   118.79  3.000
 XX8  C4   C5   C6   121.39  3.000
 XX8  C28  C5   C6   119.79  3.000
 XX8  H10  C4   C01  118.88  3.000
 XX8  H10  C4   C5   119.77  3.000
 XX8  C01  C4   C5   121.35  3.000
 XX8  C7A  C01  C4   120.17  3.000
 XX8  C4   C01  C2   119.00  3.000
 XX8  C7A  C01  C2   120.83  3.000
 XX8  H12  C7A  H11  105.82  3.000
 XX8  H12  C7A  C5A  108.56  3.000
 XX8  H11  C7A  C5A  110.04  3.000
 XX8  H12  C7A  C01  109.17  3.000
 XX8  H11  C7A  C01  109.12  3.000
 XX8  C5A  C7A  C01  113.82  3.000
 XX8  C5A  C4A  N3A  121.02  3.000
 XX8  N3A  C4A  N4A  117.31  3.000
 XX8  C5A  C4A  N4A  121.64  3.000
 XX8  C2A  N3A  C4A  118.25  3.000
 XX8  N1A  C2A  N3A  125.56  3.000
 XX8  N3A  C2A  CM2  116.42  3.000
 XX8  N1A  C2A  CM2  118.01  3.000
 XX8  C6A  N1A  C2A  115.83  3.000
 XX8  H13  C6A  C5A  119.33  3.000
 XX8  H13  C6A  N1A  116.28  3.000
 XX8  C5A  C6A  N1A  124.39  3.000
 XX8  C6A  C5A  C4A  114.94  3.000
 XX8  C4A  C5A  C7A  122.39  3.000
 XX8  C6A  C5A  C7A  122.66  3.000
 XX8  H14  C28  C30  119.77  3.000
 XX8  H14  C28  C5   119.84  3.000
 XX8  C30  C28  C5   120.38  3.000
 XX8  H15  C30  C28  119.79  3.000
 XX8  H15  C30  C2   119.87  3.000
 XX8  C28  C30  C2   120.34  3.000
 XX8  H5   N4A  H4   116.09  3.000
 XX8  H5   N4A  C4A  120.86  3.000
 XX8  H4   N4A  C4A  118.13  3.000
 XX8  H8   C6   H7   106.23  3.000
 XX8  H8   C6   C5   109.02  3.000
 XX8  H7   C6   C5   108.40  3.000
 XX8  H8   C6   O01  111.73  3.000
 XX8  H7   C6   O01  111.18  3.000
 XX8  C5   C6   O01  110.14  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
 XX8  CONST_01  C5   C28  C30  C2      0.00   0.0  0
 XX8  CONST_02  C5   C4   C01  C2      0.00   0.0  0
 XX8  CONST_03  C30  C2   C01  C4      0.00   0.0  0
 XX8  CONST_04  C30  C28  C5   C4      0.00   0.0  0
 XX8  CONST_05  C28  C30  C2   C01     0.00   0.0  0
 XX8  CONST_06  C28  C5   C4   C01     0.00   0.0  0
 XX8  CONST_07  N1A  C6A  C5A  C4A     0.00   0.0  0
 XX8  CONST_08  N1A  C2A  N3A  C4A     0.00   0.0  0
 XX8  CONST_09  C6A  C5A  C4A  N3A     0.00   0.0  0
 XX8  CONST_10  C6A  N1A  C2A  N3A     0.00   0.0  0
 XX8  CONST_11  C5A  C6A  N1A  C2A     0.00   0.0  0
 XX8  CONST_12  C5A  C4A  N3A  C2A     0.00   0.0  0
 XX8  CONST_13  C6A  N1A  C2A  CM2   180.00   0.0  0
 XX8  CONST_14  C4A  N3A  C2A  CM2   180.00   0.0  0
 XX8  CONST_15  C6A  C5A  C4A  N4A   180.00   0.0  0
 XX8  CONST_16  C2A  N3A  C4A  N4A   180.00   0.0  0
 XX8  CONST_17  C30  C28  C5   C6    180.00   0.0  0
 XX8  CONST_18  C01  C4   C5   C6    180.00   0.0  0
 XX8  CONST_19  C7A  C01  C4   C5    180.00   0.0  0
 XX8  CONST_20  C30  C2   C01  C7A   180.00   0.0  0
 XX8  CONST_21  N1A  C6A  C5A  C7A   180.00   0.0  0
 XX8  CONST_22  N3A  C4A  C5A  C7A   180.00   0.0  0
 XX8  CONST_23  H14  C28  C30  C2    180.00   0.0  0
 XX8  CONST_24  H10  C4   C01  C2    180.00   0.0  0
 XX8  CONST_25  H15  C30  C28  C5    180.00   0.0  0
 XX8  CONST_26  H9   C2   C01  C4    180.00   0.0  0
 XX8  CONST_27  H13  C6A  C5A  C4A   180.00   0.0  0
 XX8  CONST_28  H4   N4A  C4A  N3A     0.00   0.0  0
 XX8  Var_01    C5A  C7A  C01  C2     45.92  30.0  2
 XX8  Var_02    C6A  C5A  C7A  C01  -114.11  30.0  2
 XX8  Var_03    C28  C5   C6   O01  -151.23  30.0  2
 XX8  Var_04    H1   CM2  C2A  N3A    60.53  30.0  2

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
 XX8  plan-1  C2   0.020
 XX8  plan-1  C5   0.020
 XX8  plan-1  C4   0.020
 XX8  plan-1  C01  0.020
 XX8  plan-1  C7A  0.020
 XX8  plan-1  C28  0.020
 XX8  plan-1  C30  0.020
 XX8  plan-1  H9   0.020
 XX8  plan-1  H10  0.020
 XX8  plan-1  H14  0.020
 XX8  plan-1  H15  0.020
 XX8  plan-1  C6   0.020
 XX8  plan-2  CM2  0.020
 XX8  plan-2  C7A  0.020
 XX8  plan-2  C4A  0.020
 XX8  plan-2  N3A  0.020
 XX8  plan-2  C2A  0.020
 XX8  plan-2  N1A  0.020
 XX8  plan-2  C6A  0.020
 XX8  plan-2  C5A  0.020
 XX8  plan-2  H13  0.020
 XX8  plan-2  N4A  0.020
 XX8  plan-3  C4A  0.020
 XX8  plan-3  H4   0.020
 XX8  plan-3  H5   0.020
 XX8  plan-3  N4A  0.020

