# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 22:40:28 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 1-methyl-3-(2-methylpropyl)-3,9-dihydro-1H-purine-2,6-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CN1C(=O)N(C)C(=O)c2nc[nH]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
 IBM  IBM  1-methyl-3-(2-methylpropyl)-3,9-dihydro-1H-purine-2,6-dione  ligand  30  16  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IBM
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
 IBM  N9    N  NR15  0  -0.651  -2.2549  -0.1275  -0.0289
 IBM  C8    C  CR15  0   0.099  -2.8593   0.2477  -1.2010
 IBM  N7    N  N     0  -0.426  -2.0072   0.4234  -2.1615
 IBM  C5    C  CR56  0  -0.062  -0.7855   0.1520  -1.6026
 IBM  C4    C  CR56  0   0.642  -0.9326  -0.1886  -0.2845
 IBM  N3    N  NR6   0  -0.594   0.0835  -0.5219   0.5502
 IBM  C2    C  CR6   0   0.762   1.3659  -0.5270   0.0400
 IBM  N1    N  NR6   0  -0.610   1.5248  -0.1936  -1.2979
 IBM  C6    C  CR6   0   0.532   0.5124   0.1717  -2.2009
 IBM  O6    O  OC    0  -0.460   0.7574   0.4615  -3.3561
 IBM  O2    O  OC    0  -0.484   2.3228  -0.8143   0.7303
 IBM  C10   C  CH3   0  -0.529   2.9017  -0.2337  -1.7795
 IBM  C11   C  CH2   0  -0.331  -0.1693  -0.8238   1.9561
 IBM  C12   C  CH1   0  -0.259  -0.4585   0.4137   2.8075
 IBM  C13   C  CH3   0  -0.655  -0.7615  -0.0377   4.2322
 IBM  C14   C  CH3   0  -0.653   0.6861   1.4183   2.7757
 IBM  HN9   H  HNR5  0   0.439  -2.7309  -0.3224   0.8394
 IBM  H8    H  HCR5  0   0.295  -3.9290   0.3693  -1.2628
 IBM  H101  H  HCH3  0   0.267   2.9093   0.0066  -2.8356
 IBM  H102  H  HCH3  0   0.255   3.5175   0.4911  -1.2507
 IBM  H103  H  HCH3  0   0.255   3.3254  -1.2260  -1.6431
 IBM  H111  H  HCH2  0   0.281   0.6999  -1.3514   2.3422
 IBM  H112  H  HCH2  0   0.273  -1.0066  -1.5240   2.0025
 IBM  H12   H  HCH1  0   0.231  -1.3558   0.9082   2.4186
 IBM  H131  H  HCH3  0   0.238  -1.0292   0.8146   4.8572
 IBM  H132  H  HCH3  0   0.233  -1.5936  -0.7432   4.2634
 IBM  H133  H  HCH3  0   0.223   0.1064  -0.5219   4.6848
 IBM  H141  H  HCH3  0   0.223   1.6135   0.9720   3.1387
 IBM  H142  H  HCH3  0   0.230   0.8684   1.8053   1.7722
 IBM  H143  H  HCH3  0   0.237   0.4545   2.2734   3.4117

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
 IBM  N9   C8    aromatic  1.371  0.020  1.371
 IBM  N9   C4    aromatic  1.348  0.020  1.348
 IBM  N9   HN9   single    0.860  0.020  1.020
 IBM  C8   N7    aromatic  1.296  0.020  1.296
 IBM  C8   H8    single    0.930  0.020  1.080
 IBM  N7   C5    aromatic  1.371  0.020  1.371
 IBM  C5   C4    aromatic  1.369  0.020  1.369
 IBM  C5   C6    aromatic  1.429  0.020  1.429
 IBM  C4   N3    aromatic  1.357  0.020  1.357
 IBM  N3   C2    aromatic  1.380  0.020  1.380
 IBM  N3   C11   single    1.460  0.020  1.460
 IBM  C2   N1    aromatic  1.388  0.020  1.388
 IBM  C2   O2    double    1.214  0.020  1.214
 IBM  N1   C6    aromatic  1.405  0.020  1.405
 IBM  N1   C10   single    1.459  0.020  1.459
 IBM  C6   O6    double    1.216  0.020  1.216
 IBM  C10  H101  single    0.970  0.020  1.090
 IBM  C10  H102  single    0.970  0.020  1.090
 IBM  C10  H103  single    0.970  0.020  1.090
 IBM  C11  C12   single    1.530  0.020  1.530
 IBM  C11  H111  single    0.970  0.020  1.090
 IBM  C11  H112  single    0.970  0.020  1.090
 IBM  C12  C13   single    1.525  0.020  1.525
 IBM  C12  C14   single    1.523  0.020  1.523
 IBM  C12  H12   single    0.970  0.020  1.090
 IBM  C13  H131  single    0.970  0.020  1.090
 IBM  C13  H132  single    0.970  0.020  1.090
 IBM  C13  H133  single    0.970  0.020  1.090
 IBM  C14  H141  single    0.970  0.020  1.090
 IBM  C14  H142  single    0.970  0.020  1.090
 IBM  C14  H143  single    0.970  0.020  1.090

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
 IBM  HN9   N9   C4    128.10  3.000
 IBM  HN9   N9   C8    125.48  3.000
 IBM  C4    N9   C8    106.42  3.000
 IBM  H8    C8   N7    126.48  3.000
 IBM  H8    C8   N9    121.13  3.000
 IBM  N7    C8   N9    112.38  3.000
 IBM  C5    N7   C8    104.89  3.000
 IBM  C6    C5   C4    120.26  3.000
 IBM  C6    C5   N7    129.49  3.000
 IBM  C4    C5   N7    110.25  3.000
 IBM  N3    C4   C5    124.96  3.000
 IBM  N3    C4   N9    128.98  3.000
 IBM  C5    C4   N9    106.06  3.000
 IBM  C11   N3   C2    121.07  3.000
 IBM  C11   N3   C4    120.91  3.000
 IBM  C2    N3   C4    117.99  3.000
 IBM  O2    C2   N1    120.96  3.000
 IBM  O2    C2   N3    121.53  3.000
 IBM  N1    C2   N3    117.51  3.000
 IBM  C10   N1   C6    118.35  3.000
 IBM  C10   N1   C2    114.81  3.000
 IBM  C6    N1   C2    126.83  3.000
 IBM  O6    C6   N1    121.83  3.000
 IBM  O6    C6   C5    125.74  3.000
 IBM  N1    C6   C5    112.44  3.000
 IBM  H103  C10  H102  109.05  3.000
 IBM  H103  C10  H101  108.79  3.000
 IBM  H102  C10  H101  108.79  3.000
 IBM  H103  C10  N1    110.56  3.000
 IBM  H102  C10  N1    110.81  3.000
 IBM  H101  C10  N1    108.80  3.000
 IBM  H112  C11  H111  106.65  3.000
 IBM  H112  C11  C12   110.49  3.000
 IBM  H111  C11  C12   110.24  3.000
 IBM  H112  C11  N3    107.83  3.000
 IBM  H111  C11  N3    107.68  3.000
 IBM  C12   C11  N3    113.67  3.000
 IBM  H12   C12  C14   108.08  3.000
 IBM  H12   C12  C13   107.60  3.000
 IBM  C14   C12  C13   111.35  3.000
 IBM  H12   C12  C11   108.80  3.000
 IBM  C14   C12  C11   112.33  3.000
 IBM  C13   C12  C11   108.55  3.000
 IBM  H133  C13  H132  107.90  3.000
 IBM  H133  C13  H131  107.71  3.000
 IBM  H132  C13  H131  107.56  3.000
 IBM  H133  C13  C12   111.13  3.000
 IBM  H132  C13  C12   111.69  3.000
 IBM  H131  C13  C12   110.67  3.000
 IBM  H143  C14  H142  107.09  3.000
 IBM  H143  C14  H141  107.88  3.000
 IBM  H142  C14  H141  108.00  3.000
 IBM  H143  C14  C12   110.20  3.000
 IBM  H142  C14  C12   112.26  3.000
 IBM  H141  C14  C12   111.22  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
 IBM  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 IBM  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 IBM  CONST_03  C6    C5   C4   N9    180.00   0.0  0
 IBM  CONST_04  C2    N3   C4   N9    180.00   0.0  0
 IBM  CONST_05  C5    C4   N9   C8      0.00   0.0  0
 IBM  CONST_06  N3    C4   N9   C8    180.00   0.0  0
 IBM  CONST_07  C4    C5   N7   C8      0.00   0.0  0
 IBM  CONST_08  C6    C5   N7   C8    180.00   0.0  0
 IBM  CONST_09  C4    N9   C8   N7      0.00   0.0  0
 IBM  CONST_10  N3    C4   C5   N7    180.00   0.0  0
 IBM  CONST_11  N1    C6   C5   N7    180.00   0.0  0
 IBM  CONST_12  C2    N3   C4   C5      0.00   0.0  0
 IBM  CONST_13  C2    N1   C6   C5      0.00   0.0  0
 IBM  CONST_14  N1    C6   C5   C4      0.00   0.0  0
 IBM  CONST_15  N1    C2   N3   C4      0.00   0.0  0
 IBM  CONST_16  C6    C5   C4   N3      0.00   0.0  0
 IBM  CONST_17  C6    N1   C2   N3      0.00   0.0  0
 IBM  CONST_18  C11   N3   C4   N9      0.00   0.0  0
 IBM  CONST_19  O6    C6   C5   N7      0.00   0.0  0
 IBM  CONST_20  C11   N3   C4   C5    180.00   0.0  0
 IBM  CONST_21  C10   N1   C6   C5    180.00   0.0  0
 IBM  CONST_22  O6    C6   C5   C4    180.00   0.0  0
 IBM  CONST_23  O2    C2   N3   C4    180.00   0.0  0
 IBM  CONST_24  C10   N1   C2   N3    180.00   0.0  0
 IBM  CONST_25  O6    C6   N1   C2    180.00   0.0  0
 IBM  CONST_26  C11   N3   C2   N1    180.00   0.0  0
 IBM  CONST_27  O2    C2   N1   C6    180.00   0.0  0
 IBM  CONST_28  HN9   N9   C8   N7    180.00   0.0  0
 IBM  CONST_29  H8    C8   N7   C5    180.00   0.0  0
 IBM  CONST_30  C10   N1   C6   O6      0.00   0.0  0
 IBM  CONST_31  C11   N3   C2   O2      0.00   0.0  0
 IBM  CONST_32  C10   N1   C2   O2      0.00   0.0  0
 IBM  Var_01    C12   C11  N3   C4    -74.95  30.0  2
 IBM  Var_02    H101  C10  N1   C2    178.01  30.0  2
 IBM  Var_03    C13   C12  C11  N3    177.65  30.0  3
 IBM  Var_04    H131  C13  C12  C11  -176.76  30.0  3
 IBM  Var_05    H141  C14  C12  C11   -59.03  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
 IBM  plan-1  N9   0.020
 IBM  plan-1  C8   0.020
 IBM  plan-1  N7   0.020
 IBM  plan-1  C5   0.020
 IBM  plan-1  C4   0.020
 IBM  plan-1  N3   0.020
 IBM  plan-1  C2   0.020
 IBM  plan-1  N1   0.020
 IBM  plan-1  C6   0.020
 IBM  plan-1  O6   0.020
 IBM  plan-1  O2   0.020
 IBM  plan-1  C10  0.020
 IBM  plan-1  C11  0.020
 IBM  plan-1  HN9  0.020
 IBM  plan-1  H8   0.020

