# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 11:48:41 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 1,3-dimethyl-2,4,7-trioxo-1,2,3,4,7,8-hexahydropteridine-6-carbaldehyde
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N(C)C2=C(N=C(C=O)C(=O)N2)C1=O
#
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
 B59  B59  1,3-dimethyl-2,4,7-trioxo-1,2,3,4,7,8-hexahydropteridine-6-carbaldehyde  ligand  25  17  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_B59
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
 B59  O17   O  O     0  -0.428   0.8433  -2.7166  -0.0478
 B59  C1    C  CR6   0   0.575   1.0095  -1.5181  -0.0350
 B59  N2    N  NR6   0  -0.599   2.2778  -0.9479  -0.0383
 B59  C16   C  CH3   0  -0.530   3.4485  -1.8210  -0.0591
 B59  C6    C  CR66  0  -0.068  -0.0830  -0.5593  -0.0147
 B59  C5    C  CR66  0   0.793   0.1921   0.8046  -0.0046
 B59  N4    N  NR6   0  -0.608   1.4533   1.2743  -0.0109
 B59  C14   C  CH3   0  -0.596   1.7034   2.7134   0.0033
 B59  C3    C  CR6   0   0.782   2.5447   0.4009  -0.0302
 B59  O15   O  O     0  -0.446   3.6748   0.8244  -0.0390
 B59  N7    N  N     0  -0.310  -1.3343  -1.0092  -0.0074
 B59  C8    C  CR6   0  -0.077  -2.3433  -0.1917   0.0086
 B59  C11   C  C1    0   0.139  -3.7069  -0.7579   0.0150
 B59  O12   O  O     0  -0.373  -3.9233  -1.9458   0.0072
 B59  C9    C  CR6   0   0.545  -2.1797   1.2547   0.0191
 B59  O13   O  O     0  -0.429  -3.0679   2.0808   0.0329
 B59  N10   N  NR16  0  -0.726  -0.8439   1.6542   0.0121
 B59  H16   H  HCH3  0   0.274   3.1122  -2.8499  -0.0483
 B59  H16A  H  HCH3  0   0.265   4.0354  -1.6501  -0.9586
 B59  H16B  H  HCH3  0   0.264   4.0707  -1.6436   0.8147
 B59  H14   H  HCH3  0   0.285   1.2913   3.1610   0.9066
 B59  H14A  H  HCH3  0   0.308   2.7716   2.8833  -0.0051
 B59  H14B  H  HCH3  0   0.285   1.2741   3.1827  -0.8808
 B59  H11   H  H     0   0.211  -4.5272  -0.0259   0.0281
 B59  HN10  H  HNR6  0   0.462  -0.6883   2.6567   0.0188

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
 B59  O17  C1    double  1.210  0.020  1.210
 B59  C1   N2    single  1.391  0.020  1.391
 B59  C1   C6    single  1.454  0.020  1.454
 B59  N2   C16   single  1.461  0.020  1.461
 B59  N2   C3    single  1.375  0.020  1.375
 B59  C6   C5    double  1.391  0.020  1.391
 B59  C6   N7    single  1.330  0.020  1.330
 B59  C5   N4    single  1.346  0.020  1.346
 B59  C5   N10   single  1.340  0.020  1.340
 B59  N4   C14   single  1.461  0.020  1.461
 B59  N4   C3    single  1.398  0.020  1.398
 B59  C3   O15   double  1.207  0.020  1.207
 B59  N7   C8    double  1.299  0.020  1.299
 B59  C8   C11   single  1.477  0.020  1.477
 B59  C8   C9    single  1.456  0.020  1.456
 B59  C11  O12   double  1.208  0.020  1.208
 B59  C9   O13   double  1.213  0.020  1.213
 B59  C9   N10   single  1.394  0.020  1.394
 B59  C16  H16   single  0.970  0.020  1.090
 B59  C16  H16A  single  0.970  0.020  1.090
 B59  C16  H16B  single  0.970  0.020  1.090
 B59  C14  H14   single  0.970  0.020  1.090
 B59  C14  H14A  single  0.970  0.020  1.090
 B59  C14  H14B  single  0.970  0.020  1.090
 B59  C11  H11   single  0.930  0.020  1.080
 B59  N10  HN10  single  0.860  0.020  1.020

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
 B59  C6    C1   N2    114.52  3.000
 B59  C6    C1   O17   123.38  3.000
 B59  N2    C1   O17   122.10  3.000
 B59  C3    N2   C16   115.52  3.000
 B59  C3    N2   C1    125.40  3.000
 B59  C16   N2   C1    119.08  3.000
 B59  H16B  C16  H16A  109.28  3.000
 B59  H16B  C16  H16   108.96  3.000
 B59  H16A  C16  H16   108.98  3.000
 B59  H16B  C16  N2    110.47  3.000
 B59  H16A  C16  N2    110.51  3.000
 B59  H16   C16  N2    108.60  3.000
 B59  N7    C6   C5    121.17  3.000
 B59  N7    C6   C1    118.96  3.000
 B59  C5    C6   C1    119.87  3.000
 B59  N10   C5   N4    120.23  3.000
 B59  N10   C5   C6    117.95  3.000
 B59  N4    C5   C6    121.82  3.000
 B59  C3    N4   C14   118.81  3.000
 B59  C3    N4   C5    120.91  3.000
 B59  C14   N4   C5    120.27  3.000
 B59  H14B  C14  H14A  108.38  3.000
 B59  H14B  C14  H14   110.30  3.000
 B59  H14A  C14  H14   108.39  3.000
 B59  H14B  C14  N4    110.44  3.000
 B59  H14A  C14  N4    108.89  3.000
 B59  H14   C14  N4    110.38  3.000
 B59  O15   C3   N4    120.79  3.000
 B59  O15   C3   N2    121.73  3.000
 B59  N4    C3   N2    117.47  3.000
 B59  C8    N7   C6    121.21  3.000
 B59  C9    C8   C11   119.00  3.000
 B59  C9    C8   N7    122.56  3.000
 B59  C11   C8   N7    118.44  3.000
 B59  H11   C11  O12   121.42  3.000
 B59  H11   C11  C8    115.71  3.000
 B59  O12   C11  C8    122.87  3.000
 B59  N10   C9   O13   120.43  3.000
 B59  N10   C9   C8    113.10  3.000
 B59  O13   C9   C8    126.48  3.000
 B59  HN10  N10  C9    115.47  3.000
 B59  HN10  N10  C5    120.53  3.000
 B59  C9    N10  C5    124.00  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
 B59  CONST_01  N4    C3   N2   C1     0.00   0.0  0
 B59  CONST_02  C5    N4   C3   N2     0.00   0.0  0
 B59  CONST_03  C3    N2   C1   C6     0.00   0.0  0
 B59  CONST_04  C3    N4   C5   C6     0.00   0.0  0
 B59  CONST_05  C9    N10  C5   C6     0.00   0.0  0
 B59  CONST_06  C8    C9   N10  C5     0.00   0.0  0
 B59  CONST_07  C9    N10  C5   N4   180.00   0.0  0
 B59  CONST_08  N10   C5   N4   C3   180.00   0.0  0
 B59  CONST_09  C3    N2   C1   O17  180.00   0.0  0
 B59  CONST_10  O15   C3   N2   C1   180.00   0.0  0
 B59  CONST_11  C14   N4   C3   N2   180.00   0.0  0
 B59  CONST_12  C6    C1   N2   C16  180.00   0.0  0
 B59  CONST_13  N4    C3   N2   C16  180.00   0.0  0
 B59  CONST_14  C14   N4   C5   C6   180.00   0.0  0
 B59  CONST_15  O15   C3   N4   C5   180.00   0.0  0
 B59  CONST_16  O13   C9   N10  C5   180.00   0.0  0
 B59  CONST_17  N10   C5   N4   C14    0.00   0.0  0
 B59  CONST_18  HN10  N10  C5   C6   180.00   0.0  0
 B59  CONST_19  C16   N2   C1   O17    0.00   0.0  0
 B59  CONST_20  O15   C3   N2   C16    0.00   0.0  0
 B59  CONST_21  O15   C3   N4   C14    0.00   0.0  0
 B59  Var_01    O12   C11  C8   N7     0.06  30.0  2
 B59  Var_02    H16   C16  N2   C1    -1.17  30.0  3
 B59  Var_03    H14   C14  N4   C5    61.16  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
 B59  plan-1  O17   0.020
 B59  plan-1  C1    0.020
 B59  plan-1  N2    0.020
 B59  plan-1  C16   0.020
 B59  plan-1  C6    0.020
 B59  plan-1  C5    0.020
 B59  plan-1  N4    0.020
 B59  plan-1  C14   0.020
 B59  plan-1  C3    0.020
 B59  plan-1  O15   0.020
 B59  plan-1  N7    0.020
 B59  plan-1  C8    0.020
 B59  plan-1  C11   0.020
 B59  plan-1  C9    0.020
 B59  plan-1  O13   0.020
 B59  plan-1  N10   0.020
 B59  plan-1  HN10  0.020
 B59  plan-2  C8    0.020
 B59  plan-2  C11   0.020
 B59  plan-2  O12   0.020
 B59  plan-2  H11   0.020

