# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 16:08:03 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: N-[(4-amino-2-methylpyrimidin-5-yl)methyl]-N-(2-hydroxyethyl)formamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CN(CCO)C=O)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
 PF1  PF1  N-[(4-amino-2-methylpyrimidin-5-yl)methyl]-N-(2-hydroxyethyl)formamide  ligand  29  15  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PF1
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
 PF1  OAD   O  OH1   0  -0.660  -1.2482   1.9502  -1.6861
 PF1  CAG   C  CH2   0  -0.151  -2.3646   2.0271  -0.8334
 PF1  CAH   C  CH2   0  -0.333  -2.9772   0.6508  -0.6824
 PF1  NAO   N  NT    0  -0.421  -2.1483  -0.3052   0.0303
 PF1  CAE   C  C1    0   0.254  -2.4849  -0.7107   1.2674
 PF1  OAC   O  O     0  -0.482  -1.8710  -1.5342   1.9212
 PF1  CAI   C  CH2   0  -0.348  -1.0195  -0.9254  -0.6302
 PF1  C5    C  CR6   0  -0.037   0.3271  -0.4333  -0.1790
 PF1  C6    C  CR16  0  -0.067   0.5259   0.5996   0.7007
 PF1  N1    N  N     0  -0.450   1.7294   1.0426   1.0789
 PF1  C2    C  CR6   0   0.344   2.7722   0.4198   0.5522
 PF1  CAA   C  CH3   0  -0.728   4.1384   0.8653   0.9725
 PF1  N3    N  N     0  -0.466   2.7103  -0.5922  -0.3041
 PF1  C4    C  CR6   0   0.456   1.5079  -1.0271  -0.6772
 PF1  NAB   N  NH2   0  -0.834   1.4709  -2.0301  -1.5792
 PF1  HOAD  H  HOH1  0   0.458  -0.7592   2.7756  -1.6268
 PF1  HAG1  H  HCH2  0   0.205  -2.0983   2.4117   0.1588
 PF1  HAG2  H  HCH2  0   0.212  -3.1397   2.6928  -1.2362
 PF1  HAH1  H  HCH2  0   0.262  -3.9174   0.7581  -0.1393
 PF1  HAH2  H  HCH2  0   0.256  -3.2282   0.2434  -1.6651
 PF1  HAE   H  H     0   0.203  -3.3934  -0.2155   1.6426
 PF1  HAI1  H  HCH2  0   0.259  -1.0820  -2.0082  -0.4785
 PF1  HAI2  H  HCH2  0   0.277  -1.1281  -0.7584  -1.7037
 PF1  H6    H  HCR6  0   0.244  -0.3228   1.1140   1.1382
 PF1  HAA1  H  HCH3  0   0.255   4.5328   0.1959   1.7402
 PF1  HAA2  H  HCH3  0   0.247   4.8335   0.8405   0.1349
 PF1  HAA3  H  HCH3  0   0.244   4.1121   1.8697   1.3889
 PF1  HAB1  H  HNH2  0   0.406   0.6285  -2.5594  -1.7231
 PF1  HAB2  H  HNH2  0   0.395   2.3293  -2.5217  -1.7655

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
 PF1  OAD  CAG   single    1.407  0.020  1.407
 PF1  OAD  HOAD  single    0.850  0.020  0.980
 PF1  CAG  CAH   single    1.514  0.020  1.514
 PF1  CAG  HAG1  single    0.970  0.020  1.090
 PF1  CAG  HAG2  single    0.970  0.020  1.090
 PF1  CAH  NAO   single    1.452  0.020  1.452
 PF1  CAH  HAH1  single    0.970  0.020  1.090
 PF1  CAH  HAH2  single    0.970  0.020  1.090
 PF1  NAO  CAE   single    1.345  0.020  1.345
 PF1  NAO  CAI   single    1.447  0.020  1.447
 PF1  CAE  OAC   double    1.218  0.020  1.218
 PF1  CAE  HAE   single    0.930  0.020  1.080
 PF1  CAI  C5    single    1.503  0.020  1.503
 PF1  CAI  HAI1  single    0.970  0.020  1.090
 PF1  CAI  HAI2  single    0.970  0.020  1.090
 PF1  C5   C6    aromatic  1.371  0.020  1.371
 PF1  C5   C4    aromatic  1.412  0.020  1.412
 PF1  C6   N1    aromatic  1.337  0.020  1.337
 PF1  C6   H6    single    0.930  0.020  1.080
 PF1  N1   C2    aromatic  1.324  0.020  1.324
 PF1  C2   CAA   single    1.497  0.020  1.497
 PF1  C2   N3    aromatic  1.327  0.020  1.327
 PF1  CAA  HAA1  single    0.970  0.020  1.090
 PF1  CAA  HAA2  single    0.970  0.020  1.090
 PF1  CAA  HAA3  single    0.970  0.020  1.090
 PF1  N3   C4    aromatic  1.332  0.020  1.332
 PF1  C4   NAB   single    1.349  0.020  1.349
 PF1  NAB  HAB1  single    0.890  0.020  1.040
 PF1  NAB  HAB2  single    0.890  0.020  1.040

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
 PF1  HOAD  OAD  CAG   108.62  3.000
 PF1  HAG2  CAG  HAG1  106.89  3.000
 PF1  HAG2  CAG  CAH   107.58  3.000
 PF1  HAG1  CAG  CAH   109.07  3.000
 PF1  HAG2  CAG  OAD   111.77  3.000
 PF1  HAG1  CAG  OAD   112.01  3.000
 PF1  CAH   CAG  OAD   109.39  3.000
 PF1  HAH2  CAH  HAH1  106.63  3.000
 PF1  HAH2  CAH  NAO   109.08  3.000
 PF1  HAH1  CAH  NAO   108.20  3.000
 PF1  HAH2  CAH  CAG   110.00  3.000
 PF1  HAH1  CAH  CAG   108.00  3.000
 PF1  NAO   CAH  CAG   114.61  3.000
 PF1  CAI   NAO  CAE   119.06  3.000
 PF1  CAI   NAO  CAH   120.22  3.000
 PF1  CAE   NAO  CAH   120.47  3.000
 PF1  HAE   CAE  OAC   122.51  3.000
 PF1  HAE   CAE  NAO   112.62  3.000
 PF1  OAC   CAE  NAO   124.87  3.000
 PF1  HAI2  CAI  HAI1  106.36  3.000
 PF1  HAI2  CAI  C5    109.52  3.000
 PF1  HAI1  CAI  C5    109.47  3.000
 PF1  HAI2  CAI  NAO   107.79  3.000
 PF1  HAI1  CAI  NAO   108.42  3.000
 PF1  C5    CAI  NAO   114.93  3.000
 PF1  C4    C5   C6    114.94  3.000
 PF1  C4    C5   CAI   120.37  3.000
 PF1  C6    C5   CAI   124.69  3.000
 PF1  H6    C6   N1    115.67  3.000
 PF1  H6    C6   C5    120.17  3.000
 PF1  N1    C6   C5    124.17  3.000
 PF1  C2    N1   C6    116.14  3.000
 PF1  N3    C2   CAA   116.78  3.000
 PF1  N3    C2   N1    125.37  3.000
 PF1  CAA   C2   N1    117.84  3.000
 PF1  HAA3  CAA  HAA2  109.33  3.000
 PF1  HAA3  CAA  HAA1  107.79  3.000
 PF1  HAA2  CAA  HAA1  107.23  3.000
 PF1  HAA3  CAA  C2    111.12  3.000
 PF1  HAA2  CAA  C2    111.09  3.000
 PF1  HAA1  CAA  C2    110.15  3.000
 PF1  C4    N3   C2    118.15  3.000
 PF1  NAB   C4   N3    117.04  3.000
 PF1  NAB   C4   C5    121.69  3.000
 PF1  N3    C4   C5    121.24  3.000
 PF1  HAB2  NAB  HAB1  115.53  3.000
 PF1  HAB2  NAB  C4    117.60  3.000
 PF1  HAB1  NAB  C4    120.67  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
 PF1  CONST_01  C2    N1   C6   C5     0.00   0.0  0
 PF1  CONST_02  C2    N3   C4   C5     0.00   0.0  0
 PF1  CONST_03  N3    C4   C5   C6     0.00   0.0  0
 PF1  CONST_04  N3    C2   N1   C6     0.00   0.0  0
 PF1  CONST_05  C4    C5   C6   N1     0.00   0.0  0
 PF1  CONST_06  C4    N3   C2   N1     0.00   0.0  0
 PF1  CONST_07  N1    C6   C5   CAI  180.00   0.0  0
 PF1  CONST_08  N3    C4   C5   CAI  180.00   0.0  0
 PF1  CONST_09  NAB   C4   C5   C6   180.00   0.0  0
 PF1  CONST_10  CAA   C2   N1   C6   180.00   0.0  0
 PF1  CONST_11  NAB   C4   N3   C2   180.00   0.0  0
 PF1  CONST_12  C4    N3   C2   CAA  180.00   0.0  0
 PF1  CONST_13  H6    C6   N1   C2   180.00   0.0  0
 PF1  CONST_15  HAB2  NAB  C4   C5   180.00   0.0  0
 PF1  CONST_16  OAC   CAE  NAO  CAH  180.00   0.0  0
 PF1  CONST_17  CAI   NAO  CAE  OAC    0.00   0.0  0
 PF1  Var_01    C6    C5   CAI  NAO   -5.48  30.0  2
 PF1  Var_02    HAA1  CAA  C2   N1    99.16  30.0  2
 PF1  Var_03    C5    CAI  NAO  CAH  107.15  30.0  3
 PF1  Var_04    NAO   CAH  CAG  OAD   67.39  30.0  3
 PF1  Var_05    CAE   NAO  CAH  CAG  109.07  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
 PF1  plan-1  CAI   0.020
 PF1  plan-1  C5    0.020
 PF1  plan-1  C6    0.020
 PF1  plan-1  N1    0.020
 PF1  plan-1  C2    0.020
 PF1  plan-1  CAA   0.020
 PF1  plan-1  N3    0.020
 PF1  plan-1  C4    0.020
 PF1  plan-1  NAB   0.020
 PF1  plan-1  H6    0.020
 PF1  plan-2  CAH   0.020
 PF1  plan-2  NAO   0.020
 PF1  plan-2  CAE   0.020
 PF1  plan-2  OAC   0.020
 PF1  plan-2  CAI   0.020
 PF1  plan-2  HAE   0.020
 PF1  plan-3  C4    0.020
 PF1  plan-3  NAB   0.020
 PF1  plan-3  HAB1  0.020
 PF1  plan-3  HAB2  0.020

