# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 12:58:24 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: (6R)-2-amino-6-methyl-5,6,7,8-tetrahydropteridin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CNC2=C(N1)C(=O)NC(=N2)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
 B62  B62  (6R)-2-amino-6-methyl-5,6,7,8-tetrahydropteridin-4(3H)-one  ligand  24  13  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_B62
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
 B62  O12   O  O     0  -0.517   0.8967  -2.6530  -0.0581
 B62  C1    C  CR6   0   0.481   0.8788  -1.4243  -0.0076
 B62  N2    N  NR16  0  -0.712   2.0786  -0.7223  -0.1775
 B62  C6    C  CR6   0  -0.074  -0.2415  -0.5926   0.2311
 B62  N7    N  NH1   0  -0.646  -1.5253  -1.1799   0.3740
 B62  C8    C  CH1   0  -0.162  -2.6113  -0.2593   0.0693
 B62  C11   C  CH3   0  -0.644  -2.7566  -0.0827  -1.4360
 B62  C9    C  CH2   0  -0.271  -2.4059   1.0788   0.7888
 B62  N10   N  NH1   0  -0.655  -1.1077   1.6024   0.4442
 B62  C5    C  CR6   0   0.508  -0.0581   0.7848   0.2463
 B62  N4    N  N     0  -0.529   1.1329   1.3957   0.0291
 B62  C3    C  CR6   0   0.668   2.1660   0.6270  -0.1734
 B62  N13   N  NH2   0  -0.829   3.3700   1.1744  -0.4300
 B62  HN2   H  HNR6  0   0.414   2.9049  -1.2778  -0.3536
 B62  HN7   H  HNH1  0   0.356  -1.6488  -1.5753   1.2977
 B62  H8    H  HCH1  0   0.247  -3.5303  -0.7033   0.4570
 B62  H11   H  HCH3  0   0.232  -2.9958  -1.0362  -1.9068
 B62  H11A  H  HCH3  0   0.225  -3.5578   0.6201  -1.6677
 B62  H11B  H  HCH3  0   0.228  -1.8418   0.2938  -1.8954
 B62  H9    H  HCH2  0   0.245  -3.1675   1.8043   0.5007
 B62  H9A   H  HCH2  0   0.236  -2.4992   0.9231   1.8700
 B62  HN10  H  HNH1  0   0.388  -0.9367   2.5934   0.4713
 B62  HN13  H  HNH2  0   0.407   4.2067   0.6262  -0.3206
 B62  HN1A  H  HNH2  0   0.405   3.4685   2.1581  -0.2430

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
 B62  O12  C1    double  1.230  0.020  1.230
 B62  C1   N2    single  1.401  0.020  1.401
 B62  C1   C6    single  1.416  0.020  1.416
 B62  N2   C3    single  1.352  0.020  1.352
 B62  C6   N7    single  1.419  0.020  1.419
 B62  C6   C5    double  1.390  0.020  1.390
 B62  N7   C8    single  1.456  0.020  1.456
 B62  C8   C11   single  1.523  0.020  1.523
 B62  C8   C9    single  1.533  0.020  1.533
 B62  C9   N10   single  1.442  0.020  1.442
 B62  N10  C5    single  1.345  0.020  1.345
 B62  C5   N4    single  1.356  0.020  1.356
 B62  N4   C3    double  1.304  0.020  1.304
 B62  C3   N13   single  1.347  0.020  1.347
 B62  N2   HN2   single  0.860  0.020  1.020
 B62  N7   HN7   single  0.890  0.020  1.040
 B62  C8   H8    single  0.970  0.020  1.090
 B62  C11  H11   single  0.970  0.020  1.090
 B62  C11  H11A  single  0.970  0.020  1.090
 B62  C11  H11B  single  0.970  0.020  1.090
 B62  C9   H9    single  0.970  0.020  1.090
 B62  C9   H9A   single  0.970  0.020  1.090
 B62  N10  HN10  single  0.860  0.020  1.020
 B62  N13  HN13  single  0.890  0.020  1.040
 B62  N13  HN1A  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
 B62  C6    C1   N2    113.83  3.000
 B62  C6    C1   O12   127.27  3.000
 B62  N2    C1   O12   118.90  3.000
 B62  HN2   N2   C3    119.74  3.000
 B62  HN2   N2   C1    116.48  3.000
 B62  C3    N2   C1    123.72  3.000
 B62  C5    C6   N7    121.91  3.000
 B62  C5    C6   C1    118.67  3.000
 B62  N7    C6   C1    119.33  3.000
 B62  HN7   N7   C8    110.30  3.000
 B62  HN7   N7   C6    111.34  3.000
 B62  C8    N7   C6    113.08  3.000
 B62  H8    C8   C9    107.52  3.000
 B62  H8    C8   C11   108.54  3.000
 B62  C9    C8   C11   112.06  3.000
 B62  H8    C8   N7    107.24  3.000
 B62  C9    C8   N7    110.72  3.000
 B62  C11   C8   N7    110.57  3.000
 B62  H11B  C11  H11A  107.71  3.000
 B62  H11B  C11  H11   107.70  3.000
 B62  H11A  C11  H11   108.10  3.000
 B62  H11B  C11  C8    112.12  3.000
 B62  H11A  C11  C8    110.79  3.000
 B62  H11   C11  C8    110.27  3.000
 B62  H9A   C9   H9    107.20  3.000
 B62  H9A   C9   N10   111.34  3.000
 B62  H9    C9   N10   108.92  3.000
 B62  H9A   C9   C8    109.11  3.000
 B62  H9    C9   C8    111.29  3.000
 B62  N10   C9   C8    108.99  3.000
 B62  HN10  N10  C5    118.04  3.000
 B62  HN10  N10  C9    120.29  3.000
 B62  C5    N10  C9    121.14  3.000
 B62  N4    C5   N10   115.79  3.000
 B62  N4    C5   C6    124.11  3.000
 B62  N10   C5   C6    120.07  3.000
 B62  C3    N4   C5    117.08  3.000
 B62  N13   C3   N4    119.89  3.000
 B62  N13   C3   N2    117.55  3.000
 B62  N4    C3   N2    122.53  3.000
 B62  HN1A  N13  HN13  115.53  3.000
 B62  HN1A  N13  C3    116.70  3.000
 B62  HN13  N13  C3    120.07  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
 B62  CONST_01  N4    C3   N2   C1      0.00   0.0  0
 B62  CONST_02  C5    N4   C3   N2      0.00   0.0  0
 B62  CONST_03  C3    N2   C1   C6      0.00   0.0  0
 B62  CONST_04  C9    N10  C5   C6      0.00   0.0  0
 B62  CONST_05  C3    N4   C5   C6      0.00   0.0  0
 B62  CONST_06  N4    C5   N10  C9    180.00   0.0  0
 B62  CONST_07  C3    N4   C5   N10   180.00   0.0  0
 B62  CONST_08  C3    N2   C1   O12   180.00   0.0  0
 B62  CONST_09  N13   C3   N2   C1    180.00   0.0  0
 B62  CONST_10  N13   C3   N4   C5    180.00   0.0  0
 B62  CONST_11  HN2   N2   C1   C6    180.00   0.0  0
 B62  CONST_12  HN10  N10  C5   C6    180.00   0.0  0
 B62  CONST_14  HN1A  N13  C3   N2    180.00   0.0  0
 B62  Var_01    C8    N7   C6   C1   -156.33  30.0  1
 B62  Var_02    C5    N10  C9   C8    -34.95  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
 B62  chir_01  C8  N7  C11  C9  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
 B62  plan-1  O12   0.020
 B62  plan-1  C1    0.020
 B62  plan-1  N2    0.020
 B62  plan-1  C6    0.020
 B62  plan-1  N7    0.020
 B62  plan-1  C9    0.020
 B62  plan-1  N10   0.020
 B62  plan-1  C5    0.020
 B62  plan-1  N4    0.020
 B62  plan-1  C3    0.020
 B62  plan-1  N13   0.020
 B62  plan-1  HN2   0.020
 B62  plan-1  HN10  0.020
 B62  plan-1  HN13  0.020
 B62  plan-1  HN1A  0.020
 B62  plan-2  C6    0.020
 B62  plan-2  N7    0.020
 B62  plan-2  C8    0.020
 B62  plan-2  HN7   0.020

