# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 18:55:27 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: 2-amino-6-(hydroxymethyl)-7,8-dihydropteridin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC2=C(N=C(CO)CN2)C(=O)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
 PH2  PH2  2-amino-6-(hydroxymethyl)-7,8-dihydropteridin-4(3H)-one  ligand  23  14  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PH2
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
 PH2  N1    N  N     0  -0.378  -0.5812   0.0173  -1.3161
 PH2  C2    C  CR6   0   0.149   0.4022  -0.0780  -2.1105
 PH2  C3    C  C     0  -0.321   1.8096  -0.3722  -1.6491
 PH2  N4    N  NR16  0  -0.652   1.9714   0.0970  -0.2931
 PH2  N5    N  N     0  -0.525   1.2363   0.1360   1.8814
 PH2  C6    C  CR6   0   0.697   0.2216   0.0918   2.7116
 PH2  N6    N  NH2   0  -0.825   0.4405   0.1982   4.0257
 PH2  N7    N  NR16  0  -0.714  -1.0575  -0.0389   2.2937
 PH2  C8    C  CR6   0   0.484  -1.4437  -0.0897   0.9474
 PH2  O8    O  OC    0  -0.501  -2.6362  -0.1548   0.6723
 PH2  C9    C  CR66  0  -0.121  -0.3441  -0.0603   0.0508
 PH2  C10   C  CR66  0   0.511   0.9452   0.0409   0.5719
 PH2  C11   C  CH2   0  -0.208   0.2326   0.0391  -3.5910
 PH2  O4    O  OH1   0  -0.658  -1.1176   0.1551  -3.9305
 PH2  H31   H  H     0   0.252   1.9970  -1.4527  -1.7373
 PH2  H32   H  H     0   0.264   2.5397   0.1253  -2.2898
 PH2  HN4   H  HNR6  0   0.398   2.9022   0.1330   0.0914
 PH2  HN61  H  HNH2  0   0.413   1.3908   0.1745   4.3538
 PH2  HN62  H  HNH2  0   0.417  -0.2816   0.0053   4.6984
 PH2  HN7   H  HNR6  0   0.418  -1.8040  -0.0612   2.9753
 PH2  H111  H  HCH2  0   0.222   0.8276   0.9019  -3.9297
 PH2  H112  H  HCH2  0   0.219   0.7065  -0.8415  -4.0534
 PH2  HO4   H  HOH1  0   0.460  -1.1753   0.1954  -4.8892

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
 PH2  N1   C2    double    1.268  0.020  1.268
 PH2  N1   C9    single    1.389  0.020  1.389
 PH2  C2   C3    single    1.510  0.020  1.510
 PH2  C2   C11   single    1.495  0.020  1.495
 PH2  C3   N4    single    1.444  0.020  1.444
 PH2  C3   H31   single    0.970  0.020  1.090
 PH2  C3   H32   single    0.970  0.020  1.090
 PH2  N4   C10   single    1.343  0.020  1.343
 PH2  N4   HN4   single    0.890  0.020  1.040
 PH2  N5   C6    aromatic  1.312  0.020  1.312
 PH2  N5   C10   aromatic  1.345  0.020  1.345
 PH2  C6   N6    single    1.336  0.020  1.336
 PH2  C6   N7    aromatic  1.352  0.020  1.352
 PH2  N6   HN61  single    0.860  0.020  1.020
 PH2  N6   HN62  single    0.860  0.020  1.020
 PH2  N7   C8    aromatic  1.402  0.020  1.402
 PH2  N7   HN7   single    0.860  0.020  1.020
 PH2  C8   O8    double    1.226  0.020  1.226
 PH2  C8   C9    aromatic  1.419  0.020  1.419
 PH2  C9   C10   aromatic  1.394  0.020  1.394
 PH2  C11  O4    single    1.397  0.020  1.397
 PH2  C11  H111  single    0.970  0.020  1.090
 PH2  C11  H112  single    0.970  0.020  1.090
 PH2  O4   HO4   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
 PH2  C9    N1   C2    118.68  3.000
 PH2  C11   C2   C3    115.07  3.000
 PH2  C11   C2   N1    121.79  3.000
 PH2  C3    C2   N1    123.10  3.000
 PH2  H32   C3   H31   106.66  3.000
 PH2  H32   C3   N4    109.16  3.000
 PH2  H31   C3   N4    112.04  3.000
 PH2  H32   C3   C2    110.81  3.000
 PH2  H31   C3   C2    109.01  3.000
 PH2  N4    C3   C2    109.15  3.000
 PH2  HN4   N4   C10   117.47  3.000
 PH2  HN4   N4   C3    118.26  3.000
 PH2  C10   N4   C3    120.37  3.000
 PH2  C10   N5   C6    116.51  3.000
 PH2  N7    C6   N6    117.81  3.000
 PH2  N7    C6   N5    122.65  3.000
 PH2  N6    C6   N5    119.53  3.000
 PH2  HN62  N6   HN61  117.12  3.000
 PH2  HN62  N6   C6    121.66  3.000
 PH2  HN61  N6   C6    118.27  3.000
 PH2  HN7   N7   C8    116.32  3.000
 PH2  HN7   N7   C6    119.49  3.000
 PH2  C8    N7   C6    124.13  3.000
 PH2  C9    C8   O8    127.82  3.000
 PH2  C9    C8   N7    113.12  3.000
 PH2  O8    C8   N7    119.06  3.000
 PH2  C10   C9   C8    118.80  3.000
 PH2  C10   C9   N1    121.43  3.000
 PH2  C8    C9   N1    119.38  3.000
 PH2  C9    C10  N5    124.70  3.000
 PH2  C9    C10  N4    117.95  3.000
 PH2  N5    C10  N4    117.31  3.000
 PH2  H112  C11  H111  105.35  3.000
 PH2  H112  C11  O4    112.34  3.000
 PH2  H111  C11  O4    112.48  3.000
 PH2  H112  C11  C2    107.72  3.000
 PH2  H111  C11  C2    107.74  3.000
 PH2  O4    C11  C2    110.91  3.000
 PH2  HO4   O4   C11   107.69  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
 PH2  CONST_01  C8    N7   C6   N5     0.00   0.0  0
 PH2  CONST_02  C8    C9   C10  N5     0.00   0.0  0
 PH2  CONST_03  C9    C10  N5   C6     0.00   0.0  0
 PH2  CONST_04  C9    C8   N7   C6     0.00   0.0  0
 PH2  CONST_05  C10   N5   C6   N7     0.00   0.0  0
 PH2  CONST_06  C10   C9   C8   N7     0.00   0.0  0
 PH2  CONST_07  O8    C8   C9   N1     0.00   0.0  0
 PH2  CONST_08  O8    C8   N7   C6   180.00   0.0  0
 PH2  CONST_09  C10   N5   C6   N6   180.00   0.0  0
 PH2  CONST_10  C8    N7   C6   N6   180.00   0.0  0
 PH2  CONST_11  C10   C9   C8   O8   180.00   0.0  0
 PH2  CONST_12  HN7   N7   C6   N5   180.00   0.0  0
 PH2  CONST_13  HN61  N6   C6   N5     0.00   0.0  0
 PH2  CONST_14  HN62  N6   C6   N5   180.00   0.0  0
 PH2  Var_01    N4    C3   C2   N1   -27.00  30.0  1
 PH2  Var_02    C8    C9   N1   C2  -173.76  30.0  1
 PH2  Var_03    C10   N4   C3   C2    34.34  30.0  1
 PH2  Var_04    N5    C10  N4   C3   162.14  30.0  1
 PH2  Var_05    O4    C11  C2   N1    -4.50  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
 PH2  plan-1  C6    0.020
 PH2  plan-1  N6    0.020
 PH2  plan-1  HN61  0.020
 PH2  plan-1  HN62  0.020
 PH2  plan-2  N1    0.020
 PH2  plan-2  N4    0.020
 PH2  plan-2  N5    0.020
 PH2  plan-2  C6    0.020
 PH2  plan-2  N6    0.020
 PH2  plan-2  N7    0.020
 PH2  plan-2  C8    0.020
 PH2  plan-2  O8    0.020
 PH2  plan-2  C9    0.020
 PH2  plan-2  C10   0.020
 PH2  plan-2  HN7   0.020

