# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 06:38:44 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: 2-amino-7-methyl-1,7-dihydro-6H-purin-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cnc2N=C(N)NC(=O)c12
#
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
 MY6  MY6  2-amino-7-methyl-1,7-dihydro-6H-purin-6-one  ligand  19  12  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MY6
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
 MY6  C1    C  CH3   0  -0.519   2.9885   0.9085  -0.0180
 MY6  N2    N  N     0  -0.475   0.9441  -2.0736   0.1047
 MY6  C3    C  CR15  0   0.108   2.0832  -1.4128   0.0753
 MY6  N4    N  NR5   0  -0.465   1.9353  -0.0811   0.0253
 MY6  C5    C  CR56  0   0.086   0.5807   0.1415   0.0225
 MY6  C6    C  CR6   0   0.520  -0.1938   1.3295  -0.0150
 MY6  O7    O  O     0  -0.477   0.1805   2.4917  -0.0568
 MY6  N8    N  NR16  0  -0.720  -1.5499   1.0067   0.0043
 MY6  C9    C  CR6   0   0.663  -2.0731  -0.2582   0.0489
 MY6  N10   N  NH2   0  -0.833  -3.4178  -0.3444   0.1033
 MY6  N11   N  N     0  -0.502  -1.3430  -1.3371   0.0815
 MY6  C12   C  CR56  0   0.292  -0.0102  -1.1113   0.0722
 MY6  H1    H  HCH3  0   0.263   2.9211   1.4995  -0.9282
 MY6  H1A   H  HCH3  0   0.263   2.9268   1.5700   0.8425
 MY6  H1B   H  HCH3  0   0.265   3.9467   0.3973  -0.0014
 MY6  HN8   H  HNR6  0   0.425  -2.1876   1.7922  -0.0042
 MY6  HN10  H  HNH2  0   0.408  -3.9836   0.4282  -0.2069
 MY6  HN1A  H  HNH2  0   0.406  -3.8131  -1.2561  -0.0558
 MY6  H3    H  HCR5  0   0.292   3.0626  -1.8683   0.0890

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
 MY6  N4   C1    single    1.446  0.020  1.446
 MY6  C1   H1    single    0.970  0.020  1.090
 MY6  C1   H1A   single    0.970  0.020  1.090
 MY6  C1   H1B   single    0.970  0.020  1.090
 MY6  C3   N2    aromatic  1.317  0.020  1.317
 MY6  N2   C12   aromatic  1.356  0.020  1.356
 MY6  C3   N4    aromatic  1.341  0.020  1.341
 MY6  C3   H3    single    0.930  0.020  1.080
 MY6  N4   C5    aromatic  1.373  0.020  1.373
 MY6  C12  C5    aromatic  1.386  0.020  1.386
 MY6  C5   C6    single    1.419  0.020  1.419
 MY6  C6   N8    single    1.394  0.020  1.394
 MY6  C6   O7    double    1.222  0.020  1.222
 MY6  C9   N8    single    1.370  0.020  1.370
 MY6  N8   HN8   single    0.860  0.020  1.020
 MY6  N11  C9    double    1.303  0.020  1.303
 MY6  C9   N10   single    1.349  0.020  1.349
 MY6  N10  HN10  single    0.890  0.020  1.040
 MY6  N10  HN1A  single    0.890  0.020  1.040
 MY6  C12  N11   single    1.352  0.020  1.352

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
 MY6  H1B   C1   H1A   108.93  3.000
 MY6  H1B   C1   H1    108.86  3.000
 MY6  H1A   C1   H1    109.17  3.000
 MY6  H1B   C1   N4    108.67  3.000
 MY6  H1A   C1   N4    110.58  3.000
 MY6  H1    C1   N4    110.60  3.000
 MY6  C12   N2   C3    104.60  3.000
 MY6  H3    C3   N4    121.28  3.000
 MY6  H3    C3   N2    124.91  3.000
 MY6  N4    C3   N2    113.81  3.000
 MY6  C5    N4   C3    105.66  3.000
 MY6  C5    N4   C1    127.43  3.000
 MY6  C3    N4   C1    126.91  3.000
 MY6  C12   C5   C6    121.68  3.000
 MY6  C6    C5   N4    132.42  3.000
 MY6  C12   C5   N4    105.90  3.000
 MY6  N8    C6   O7    121.25  3.000
 MY6  O7    C6   C5    129.07  3.000
 MY6  N8    C6   C5    109.68  3.000
 MY6  HN8   N8   C9    118.46  3.000
 MY6  HN8   N8   C6    115.67  3.000
 MY6  C9    N8   C6    125.87  3.000
 MY6  N11   C9   N10   120.32  3.000
 MY6  N10   C9   N8    116.19  3.000
 MY6  N11   C9   N8    123.46  3.000
 MY6  HN1A  N10  HN10  115.21  3.000
 MY6  HN1A  N10  C9    116.31  3.000
 MY6  HN10  N10  C9    119.93  3.000
 MY6  C12   N11  C9    114.46  3.000
 MY6  N11   C12  C5    124.86  3.000
 MY6  N11   C12  N2    125.12  3.000
 MY6  C5    C12  N2    110.02  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
 MY6  CONST_01  C5    N4   C3   N2     0.00   0.0  0
 MY6  CONST_02  N4    C5   C12  N2     0.00   0.0  0
 MY6  CONST_03  C5    C12  N2   C3     0.00   0.0  0
 MY6  CONST_04  C12   C5   N4   C3     0.00   0.0  0
 MY6  CONST_05  C12   N2   C3   N4     0.00   0.0  0
 MY6  CONST_06  C9    N8   C6   C5     0.00   0.0  0
 MY6  CONST_07  N11   C9   N8   C6     0.00   0.0  0
 MY6  CONST_08  C12   N11  C9   N8     0.00   0.0  0
 MY6  CONST_09  N2    C3   N4   C1   180.00   0.0  0
 MY6  CONST_10  C12   C5   N4   C1   180.00   0.0  0
 MY6  CONST_11  C6    C5   N4   C1     0.00   0.0  0
 MY6  CONST_12  N10   C9   N8   C6   180.00   0.0  0
 MY6  CONST_13  C9    N8   C6   O7   180.00   0.0  0
 MY6  CONST_14  C12   N11  C9   N10  180.00   0.0  0
 MY6  CONST_15  H3    C3   N4   C5   180.00   0.0  0
 MY6  CONST_16  HN8   N8   C6   C5   180.00   0.0  0
 MY6  CONST_18  HN1A  N10  C9   N8   180.00   0.0  0
 MY6  Var_01    H1    C1   N4   C3   119.32  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
 MY6  plan-1  C1    0.020
 MY6  plan-1  N2    0.020
 MY6  plan-1  C3    0.020
 MY6  plan-1  N4    0.020
 MY6  plan-1  C5    0.020
 MY6  plan-1  C6    0.020
 MY6  plan-1  O7    0.020
 MY6  plan-1  N8    0.020
 MY6  plan-1  C9    0.020
 MY6  plan-1  N10   0.020
 MY6  plan-1  N11   0.020
 MY6  plan-1  C12   0.020
 MY6  plan-1  HN8   0.020
 MY6  plan-1  HN10  0.020
 MY6  plan-1  HN1A  0.020
 MY6  plan-1  H3    0.020

