# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 02:54:25 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: (6R)-2-amino-6-[(1R,2S)-1,2-dihydroxypropyl]-7,8-dihydropteridin-4(6H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](O)[C@H](O)[C@H]1CNC2=NC(=NC(=O)C2=N1)N
#
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
 H2B  H2B  (6R)-2-amino-6-[(1R,2S)-1,2-dihydroxypropyl]-7,8-dihydropteridin-4(6H)-one  ligand  30  17  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_H2B
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
 H2B  N1    N  N     0  -0.508  -1.1974  -0.1373  -2.7775
 H2B  C2    C  CR6   0   0.580  -0.0226  -0.1317  -3.4737
 H2B  N2    N  NH2   0  -0.775  -0.1699  -0.3392  -4.7736
 H2B  N3    N  N     0  -0.530   1.2121   0.0744  -3.0299
 H2B  C4    C  CR6   0   0.432   1.4114   0.2353  -1.7129
 H2B  O4    O  O     0  -0.455   2.5006   0.4593  -1.2120
 H2B  C4A   C  CR6   0   0.016   0.2070   0.0991  -0.8158
 H2B  C8A   C  CR6   0   0.547  -1.1077   0.0139  -1.4898
 H2B  N5    N  N     0  -0.356   0.3556  -0.0328   0.4294
 H2B  N8    N  NH1   0  -0.626  -2.1681   0.0510  -0.7078
 H2B  C6    C  CH1   0  -0.178  -0.7983  -0.2168   1.2838
 H2B  C7    C  CH2   0  -0.272  -2.0645   0.3927   0.6990
 H2B  C9    C  CH1   0   0.018  -0.4979   0.3435   2.6872
 H2B  O9    O  OH1   0  -0.657  -1.6082   0.1115   3.5180
 H2B  C10   C  CH1   0   0.017   0.8160  -0.2075   3.2814
 H2B  C11   C  CH3   0  -0.670   0.9573   0.1512   4.7502
 H2B  O10   O  OH1   0  -0.691   1.9399   0.3192   2.6109
 H2B  H22   H  HNH2  0   0.412   0.6313  -0.3511  -5.3814
 H2B  H21   H  HNH2  0   0.414  -1.0813  -0.4966  -5.1683
 H2B  H8    H  HNH1  0   0.420  -3.0808   0.0131  -1.1393
 H2B  H6    H  HCH1  0   0.293  -0.9219  -1.3058   1.3771
 H2B  H71   H  HCH2  0   0.288  -2.9446   0.0093   1.2069
 H2B  H72   H  HCH2  0   0.263  -2.0534   1.4813   0.8178
 H2B  H9    H  HCH1  0   0.243  -0.3979   1.4326   2.6143
 H2B  H9O1  H  HOH1  0   0.450  -1.7019  -0.8373   3.6610
 H2B  H10   H  HCH1  0   0.192   0.7914  -1.3075   3.1944
 H2B  H113  H  HCH3  0   0.236   1.9237  -0.1899   5.1234
 H2B  H112  H  HCH3  0   0.222   0.8975   1.2313   4.8993
 H2B  H111  H  HCH3  0   0.228   0.1871  -0.3195   5.3577
 H2B  H1O1  H  HOH1  0   0.448   1.7950   0.1804   1.6606

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
 H2B  N1   C2    single  1.366  0.020  1.366
 H2B  N1   C8A   double  1.300  0.020  1.300
 H2B  C2   N2    single  1.325  0.020  1.325
 H2B  C2   N3    double  1.328  0.020  1.328
 H2B  N2   H22   single  0.860  0.020  1.020
 H2B  N2   H21   single  0.860  0.020  1.020
 H2B  N3   C4    single  1.342  0.020  1.342
 H2B  C4   O4    double  1.220  0.020  1.220
 H2B  C4   C4A   single  1.508  0.020  1.508
 H2B  C4A  C8A   single  1.480  0.020  1.480
 H2B  C4A  N5    double  1.261  0.020  1.261
 H2B  C8A  N8    single  1.318  0.020  1.318
 H2B  N5   C6    single  1.448  0.020  1.448
 H2B  N8   C7    single  1.451  0.020  1.451
 H2B  N8   H8    single  0.860  0.020  1.020
 H2B  C6   C7    single  1.522  0.020  1.522
 H2B  C6   C9    single  1.541  0.020  1.541
 H2B  C6   H6    single  0.970  0.020  1.090
 H2B  C7   H71   single  0.970  0.020  1.090
 H2B  C7   H72   single  0.970  0.020  1.090
 H2B  C9   O9    single  1.406  0.020  1.406
 H2B  C9   C10   single  1.544  0.020  1.544
 H2B  C9   H9    single  0.970  0.020  1.090
 H2B  O9   H9O1  single  0.850  0.020  0.980
 H2B  C10  C11   single  1.519  0.020  1.519
 H2B  C10  O10   single  1.411  0.020  1.411
 H2B  C10  H10   single  0.970  0.020  1.090
 H2B  C11  H113  single  0.970  0.020  1.090
 H2B  C11  H112  single  0.970  0.020  1.090
 H2B  C11  H111  single  0.970  0.020  1.090
 H2B  O10  H1O1  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
 H2B  C8A   N1   C2    116.44  3.000
 H2B  N3    C2   N2    117.11  3.000
 H2B  N3    C2   N1    129.06  3.000
 H2B  N2    C2   N1    113.83  3.000
 H2B  H21   N2   H22   118.88  3.000
 H2B  H21   N2   C2    120.70  3.000
 H2B  H22   N2   C2    120.42  3.000
 H2B  C4    N3   C2    119.00  3.000
 H2B  C4A   C4   O4    119.05  3.000
 H2B  C4A   C4   N3    117.03  3.000
 H2B  O4    C4   N3    123.91  3.000
 H2B  N5    C4A  C8A   123.25  3.000
 H2B  N5    C4A  C4    120.19  3.000
 H2B  C8A   C4A  C4    116.35  3.000
 H2B  N8    C8A  C4A   116.29  3.000
 H2B  N8    C8A  N1    122.38  3.000
 H2B  C4A   C8A  N1    121.28  3.000
 H2B  C6    N5   C4A   120.15  3.000
 H2B  H8    N8   C7    119.17  3.000
 H2B  H8    N8   C8A   118.18  3.000
 H2B  C7    N8   C8A   121.62  3.000
 H2B  H6    C6   C9    107.74  3.000
 H2B  H6    C6   C7    109.61  3.000
 H2B  C9    C6   C7    111.50  3.000
 H2B  H6    C6   N5    105.40  3.000
 H2B  C9    C6   N5    109.63  3.000
 H2B  C7    C6   N5    112.67  3.000
 H2B  H72   C7   H71   107.96  3.000
 H2B  H72   C7   C6    110.36  3.000
 H2B  H71   C7   C6    110.67  3.000
 H2B  H72   C7   N8    109.88  3.000
 H2B  H71   C7   N8    108.20  3.000
 H2B  C6    C7   N8    109.73  3.000
 H2B  H9    C9   C10   107.62  3.000
 H2B  H9    C9   O9    105.98  3.000
 H2B  C10   C9   O9    112.70  3.000
 H2B  H9    C9   C6    108.58  3.000
 H2B  C10   C9   C6    112.75  3.000
 H2B  O9    C9   C6    108.91  3.000
 H2B  H9O1  O9   C9    109.07  3.000
 H2B  H10   C10  O10   110.64  3.000
 H2B  H10   C10  C11   108.29  3.000
 H2B  O10   C10  C11   107.30  3.000
 H2B  H10   C10  C9    107.85  3.000
 H2B  O10   C10  C9    111.21  3.000
 H2B  C11   C10  C9    111.54  3.000
 H2B  H111  C11  H112  108.24  3.000
 H2B  H111  C11  H113  107.51  3.000
 H2B  H112  C11  H113  108.12  3.000
 H2B  H111  C11  C10   111.84  3.000
 H2B  H112  C11  C10   111.14  3.000
 H2B  H113  C11  C10   109.85  3.000
 H2B  H1O1  O10  C10   107.03  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
 H2B  CONST_01  C4   N3   C2   N1     0.00   0.0  0
 H2B  CONST_02  C7   N8   C8A  N1   180.00   0.0  0
 H2B  CONST_03  C4A  C8A  N1   C2     0.00   0.0  0
 H2B  CONST_04  N8   C8A  N1   C2   180.00   0.0  0
 H2B  CONST_05  C8A  N1   C2   N3     0.00   0.0  0
 H2B  CONST_06  C7   N8   C8A  C4A    0.00   0.0  0
 H2B  CONST_07  C8A  N1   C2   N2   180.00   0.0  0
 H2B  CONST_08  C4   N3   C2   N2   180.00   0.0  0
 H2B  CONST_09  H8   N8   C8A  N1     0.00   0.0  0
 H2B  CONST_10  H22  N2   C2   N1   180.00   0.0  0
 H2B  CONST_11  H21  N2   C2   N1     0.00   0.0  0
 H2B  Var_01    C6   C7   N8   C8A  -38.26  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 H2B  chir_01  C6   N5   C7  C9   positiv
 H2B  chir_02  C9   O9   C6  C10  positiv
 H2B  chir_03  C10  O10  C9  C11  positiv

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
 H2B  plan-1  N1   0.020
 H2B  plan-1  C2   0.020
 H2B  plan-1  N2   0.020
 H2B  plan-1  N3   0.020
 H2B  plan-1  C4   0.020
 H2B  plan-1  O4   0.020
 H2B  plan-1  C4A  0.020
 H2B  plan-1  C8A  0.020
 H2B  plan-1  N5   0.020
 H2B  plan-1  N8   0.020
 H2B  plan-1  C7   0.020
 H2B  plan-1  H22  0.020
 H2B  plan-1  H21  0.020
 H2B  plan-1  H8   0.020

