# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 04:04:33 2020
#   Inital geometry file: a 58 line input string
#   Ligand name: N-[(4-amino-2-methylpyrimidin-5-yl)methyl]formamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CNC=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
 NFM  NFM  N-[(4-amino-2-methylpyrimidin-5-yl)methyl]formamide  ligand  22  12  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NFM
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
 NFM  C1    C  CR6   0   0.460   0.5269   0.8352   0.2323
 NFM  N1    N  N     0  -0.470   1.8330   0.9734  -0.0089
 NFM  O1    O  O     0  -0.505  -3.1018   1.5820  -0.1663
 NFM  C2    C  CR6   0   0.353   2.5719  -0.1202  -0.1399
 NFM  N2    N  N     0  -0.451   2.1313  -1.3674  -0.0486
 NFM  C3    C  CR16  0  -0.079   0.8251  -1.5011   0.1963
 NFM  N3    N  NH2   0  -0.847  -0.1894   1.9560   0.3910
 NFM  C4    C  CR6   0  -0.028  -0.0502  -0.4544   0.3447
 NFM  N4    N  NH1   0  -0.561  -2.3556  -0.5321  -0.5525
 NFM  C5    C  CH3   0  -0.729   4.0329   0.0862  -0.3926
 NFM  C6    C  CH2   0  -0.426  -1.5076  -0.6909   0.6154
 NFM  C7    C  C1    0   0.265  -3.0819   0.5510  -0.8275
 NFM  H3    H  HCR6  0   0.261   0.4545  -2.5193   0.2821
 NFM  HN3   H  HNH2  0   0.415  -1.2005   1.9452   0.3995
 NFM  HN3A  H  HNH2  0   0.393   0.2612   2.8384   0.2168
 NFM  HN4   H  HNH1  0   0.415  -2.4071  -1.3031  -1.1992
 NFM  H5    H  HCH3  0   0.255   4.5229   0.4561   0.5103
 NFM  H5A   H  HCH3  0   0.244   4.5158  -0.8438  -0.6828
 NFM  H5B   H  HCH3  0   0.249   4.1925   0.8308  -1.1719
 NFM  H6    H  HCH2  0   0.287  -1.6377  -1.7107   0.9785
 NFM  H6A   H  HCH2  0   0.275  -1.8771  -0.0334   1.4037
 NFM  H7    H  H     0   0.227  -3.6865   0.4295  -1.7361

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
 NFM  N1  C1    aromatic  1.335  0.020  1.335
 NFM  N3  C1    single    1.340  0.020  1.340
 NFM  C1  C4    aromatic  1.417  0.020  1.417
 NFM  N1  C2    aromatic  1.326  0.020  1.326
 NFM  C7  O1    double    1.225  0.020  1.225
 NFM  C5  C2    single    1.497  0.020  1.497
 NFM  C2  N2    aromatic  1.326  0.020  1.326
 NFM  N2  C3    aromatic  1.336  0.020  1.336
 NFM  C4  C3    aromatic  1.373  0.020  1.373
 NFM  C3  H3    single    0.930  0.020  1.080
 NFM  N3  HN3   single    0.860  0.020  1.020
 NFM  N3  HN3A  single    0.860  0.020  1.020
 NFM  C4  C6    single    1.501  0.020  1.501
 NFM  N4  C6    single    1.452  0.020  1.452
 NFM  N4  C7    single    1.333  0.020  1.333
 NFM  N4  HN4   single    0.860  0.020  1.020
 NFM  C5  H5    single    0.970  0.020  1.090
 NFM  C5  H5A   single    0.970  0.020  1.090
 NFM  C5  H5B   single    0.970  0.020  1.090
 NFM  C6  H6    single    0.970  0.020  1.090
 NFM  C6  H6A   single    0.970  0.020  1.090
 NFM  C7  H7    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
 NFM  C4    C1  N3   122.29  3.000
 NFM  C4    C1  N1   120.45  3.000
 NFM  N3    C1  N1   117.24  3.000
 NFM  C2    N1  C1   118.52  3.000
 NFM  C5    C2  N2   117.75  3.000
 NFM  N2    C2  N1   125.71  3.000
 NFM  C5    C2  N1   116.53  3.000
 NFM  C3    N2  C2   115.58  3.000
 NFM  H3    C3  C4   119.24  3.000
 NFM  H3    C3  N2   116.21  3.000
 NFM  C4    C3  N2   124.55  3.000
 NFM  HN3A  N3  HN3  117.30  3.000
 NFM  HN3A  N3  C1   118.30  3.000
 NFM  HN3   N3  C1   121.78  3.000
 NFM  C6    C4  C3   121.23  3.000
 NFM  C6    C4  C1   123.57  3.000
 NFM  C3    C4  C1   115.20  3.000
 NFM  HN4   N4  C7   117.49  3.000
 NFM  HN4   N4  C6   117.54  3.000
 NFM  C7    N4  C6   124.97  3.000
 NFM  H5B   C5  H5A  109.18  3.000
 NFM  H5B   C5  H5   107.11  3.000
 NFM  H5A   C5  H5   108.13  3.000
 NFM  H5B   C5  C2   110.98  3.000
 NFM  H5A   C5  C2   111.13  3.000
 NFM  H5    C5  C2   110.18  3.000
 NFM  H6A   C6  H6   106.42  3.000
 NFM  H6A   C6  N4   108.51  3.000
 NFM  H6    C6  N4   107.49  3.000
 NFM  H6A   C6  C4   111.36  3.000
 NFM  H6    C6  C4   108.86  3.000
 NFM  N4    C6  C4   113.87  3.000
 NFM  H7    C7  N4   112.39  3.000
 NFM  H7    C7  O1   122.06  3.000
 NFM  N4    C7  O1   125.56  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
 NFM  CONST_01  N2    C2  N1  C1     0.00   0.0  0
 NFM  CONST_02  N2    C3  C4  C1     0.00   0.0  0
 NFM  CONST_03  C3    C4  C1  N1     0.00   0.0  0
 NFM  CONST_04  C3    N2  C2  N1     0.00   0.0  0
 NFM  CONST_05  C4    C1  N1  C2     0.00   0.0  0
 NFM  CONST_06  C4    C3  N2  C2     0.00   0.0  0
 NFM  CONST_07  C5    C2  N1  C1   180.00   0.0  0
 NFM  CONST_08  C6    C4  C1  N1   180.00   0.0  0
 NFM  CONST_09  N3    C1  N1  C2   180.00   0.0  0
 NFM  CONST_10  C6    C4  C3  N2   180.00   0.0  0
 NFM  CONST_11  C5    C2  N2  C3   180.00   0.0  0
 NFM  CONST_12  N3    C1  C4  C3   180.00   0.0  0
 NFM  CONST_13  H3    C3  C4  C1   180.00   0.0  0
 NFM  CONST_14  HN3   N3  C1  N1   180.00   0.0  0
 NFM  CONST_15  HN3A  N3  C1  N1     0.00   0.0  0
 NFM  CONST_16  C6    N4  C7  O1     0.00   0.0  0
 NFM  CONST_17  HN4   N4  C7  O1   180.00   0.0  0
 NFM  Var_01    N4    C6  C4  C1    78.70  30.0  2
 NFM  Var_02    H5    C5  C2  N1    71.60  30.0  2
 NFM  Var_03    C7    N4  C6  C4  -100.14  30.0  1

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
 NFM  plan-1  C1    0.020
 NFM  plan-1  N1    0.020
 NFM  plan-1  C2    0.020
 NFM  plan-1  N2    0.020
 NFM  plan-1  C3    0.020
 NFM  plan-1  N3    0.020
 NFM  plan-1  C4    0.020
 NFM  plan-1  C5    0.020
 NFM  plan-1  C6    0.020
 NFM  plan-1  H3    0.020
 NFM  plan-2  O1    0.020
 NFM  plan-2  N4    0.020
 NFM  plan-2  C6    0.020
 NFM  plan-2  C7    0.020
 NFM  plan-2  HN4   0.020
 NFM  plan-2  H7    0.020
 NFM  plan-3  C1    0.020
 NFM  plan-3  N3    0.020
 NFM  plan-3  HN3   0.020
 NFM  plan-3  HN3A  0.020

