# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 17:26:22 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: 1,3-dimethyl-1H-pyrrolo[3,4-d]pyrimidine-2,4(3H,6H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N(C)c2c[nH]cc2C1=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
 X0Y  X0Y  1,3-dimethyl-1H-pyrrolo[3,4-d]pyrimidine-2,4(3H,6H)-dione  ligand  22  13  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_X0Y
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
 X0Y  C01   C  CR6   0   0.548  60.7744   1.4253  -3.2116
 X0Y  C02   C  CR56  0  -0.204  62.1924   1.2220  -3.2812
 X0Y  C03   C  CR15  0  -0.023  63.1220   1.5263  -4.2575
 X0Y  C05   C  CR15  0  -0.083  64.2107   0.5341  -2.5621
 X0Y  C06   C  CR56  0   0.274  62.8844   0.6010  -2.2224
 X0Y  C08   C  CR6   0   0.707  60.8738   0.3537  -0.9615
 X0Y  N04   N  NR15  0  -0.573  64.3129   1.1069  -3.8057
 X0Y  N07   N  NR6   0  -0.593  62.2216   0.1802  -1.0911
 X0Y  N09   N  NR6   0  -0.598  60.2023   0.9687  -2.0258
 X0Y  O11   O  O     0  -0.488  60.2708  -0.0068   0.0329
 X0Y  O13   O  O     0  -0.455  60.0917   1.9409  -4.0776
 X0Y  H031  H  HCR5  0   0.295  63.0070   2.0038  -5.2160
 X0Y  H051  H  HCR5  0   0.295  65.0697   0.1394  -2.0475
 X0Y  H102  H  HCH3  0   0.267  58.4290   0.7853  -0.9426
 X0Y  H101  H  HCH3  0   0.249  58.5024   2.2052  -1.9863
 X0Y  H103  H  HCH3  0   0.249  58.2393   0.6026  -2.6878
 X0Y  H121  H  HCH3  0   0.274  62.3538  -0.7361   0.7800
 X0Y  H122  H  HCH3  0   0.252  63.4867  -1.3483  -0.4324
 X0Y  H123  H  HCH3  0   0.252  63.7621   0.2307   0.3225
 X0Y  H1    H  HNR5  0   0.425  65.1790   1.2050  -4.3116
 X0Y  C10   C  CH3   0  -0.528  58.7606   1.1511  -1.9053
 X0Y  C12   C  CH3   0  -0.541  62.9970  -0.4542  -0.0448

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
 X0Y  C03  N04   aromatic  1.341  0.020  1.341
 X0Y  C03  C02   aromatic  1.382  0.020  1.382
 X0Y  O13  C01   double    1.217  0.020  1.217
 X0Y  N04  C05   aromatic  1.373  0.020  1.373
 X0Y  C02  C01   single    1.434  0.020  1.434
 X0Y  C02  C06   aromatic  1.409  0.020  1.409
 X0Y  C01  N09   single    1.394  0.020  1.394
 X0Y  C05  C06   aromatic  1.371  0.020  1.371
 X0Y  C06  N07   single    1.377  0.020  1.377
 X0Y  N09  C10   single    1.458  0.020  1.458
 X0Y  N09  C08   single    1.401  0.020  1.401
 X0Y  N07  C08   single    1.365  0.020  1.365
 X0Y  N07  C12   single    1.449  0.020  1.449
 X0Y  C08  O11   double    1.218  0.020  1.218
 X0Y  C03  H031  single    0.930  0.020  1.080
 X0Y  C05  H051  single    0.930  0.020  1.080
 X0Y  C10  H102  single    0.970  0.020  1.090
 X0Y  C10  H101  single    0.970  0.020  1.090
 X0Y  C10  H103  single    0.970  0.020  1.090
 X0Y  C12  H121  single    0.970  0.020  1.090
 X0Y  C12  H122  single    0.970  0.020  1.090
 X0Y  C12  H123  single    0.970  0.020  1.090
 X0Y  N04  H1    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
 X0Y  O13   C01  N09   120.92  3.000
 X0Y  N09   C01  C02   113.63  3.000
 X0Y  O13   C01  C02   125.45  3.000
 X0Y  C06   C02  C03   107.31  3.000
 X0Y  C06   C02  C01   120.76  3.000
 X0Y  C03   C02  C01   131.92  3.000
 X0Y  H031  C03  N04   122.23  3.000
 X0Y  H031  C03  C02   130.88  3.000
 X0Y  N04   C03  C02   106.89  3.000
 X0Y  H051  C05  N04   121.78  3.000
 X0Y  H051  C05  C06   132.19  3.000
 X0Y  N04   C05  C06   106.03  3.000
 X0Y  N07   C06  C05   130.87  3.000
 X0Y  N07   C06  C02   121.04  3.000
 X0Y  C05   C06  C02   108.08  3.000
 X0Y  O11   C08  N09   120.87  3.000
 X0Y  O11   C08  N07   121.93  3.000
 X0Y  N09   C08  N07   117.20  3.000
 X0Y  H1    N04  C05   124.00  3.000
 X0Y  H1    N04  C03   124.31  3.000
 X0Y  C05   N04  C03   111.68  3.000
 X0Y  C12   N07  C08   121.04  3.000
 X0Y  C12   N07  C06   118.01  3.000
 X0Y  C08   N07  C06   120.95  3.000
 X0Y  C10   N09  C08   117.79  3.000
 X0Y  C08   N09  C01   126.41  3.000
 X0Y  C10   N09  C01   115.80  3.000
 X0Y  H103  C10  H101  108.72  3.000
 X0Y  H103  C10  H102  108.81  3.000
 X0Y  H101  C10  H102  108.72  3.000
 X0Y  H103  C10  N09   110.56  3.000
 X0Y  H101  C10  N09   110.46  3.000
 X0Y  H102  C10  N09   109.53  3.000
 X0Y  H123  C12  H122  108.63  3.000
 X0Y  H123  C12  H121  108.88  3.000
 X0Y  H122  C12  H121  108.89  3.000
 X0Y  H123  C12  N07   110.11  3.000
 X0Y  H122  C12  N07   110.04  3.000
 X0Y  H121  C12  N07   110.25  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
 X0Y  CONST_01  C05   N04  C03  C02     0.00   0.0  0
 X0Y  CONST_02  N04   C05  C06  C02     0.00   0.0  0
 X0Y  CONST_03  C06   C05  N04  C03     0.00   0.0  0
 X0Y  CONST_04  C05   C06  C02  C03     0.00   0.0  0
 X0Y  CONST_05  N04   C03  C02  C06     0.00   0.0  0
 X0Y  CONST_06  N07   C08  N09  C01     0.00   0.0  0
 X0Y  CONST_07  C08   N09  C01  C02     0.00   0.0  0
 X0Y  CONST_08  N09   C08  N07  C06     0.00   0.0  0
 X0Y  CONST_09  O11   C08  N09  C01   180.00   0.0  0
 X0Y  CONST_10  C10   N09  C01  C02   180.00   0.0  0
 X0Y  CONST_11  O11   C08  N07  C06   180.00   0.0  0
 X0Y  CONST_12  O13   C01  N09  C08   180.00   0.0  0
 X0Y  CONST_13  N07   C08  N09  C10   180.00   0.0  0
 X0Y  CONST_14  N09   C08  N07  C12   180.00   0.0  0
 X0Y  CONST_15  H031  C03  C02  C01     0.00   0.0  0
 X0Y  CONST_16  H1    N04  C03  C02   180.00   0.0  0
 X0Y  CONST_17  H051  C05  C06  C02   180.00   0.0  0
 X0Y  CONST_18  O13   C01  N09  C10     0.00   0.0  0
 X0Y  CONST_19  O11   C08  N09  C10     0.00   0.0  0
 X0Y  CONST_20  O11   C08  N07  C12     0.00   0.0  0
 X0Y  Var_01    H102  C10  N09  C01  -178.64  30.0  3
 X0Y  Var_02    H121  C12  N07  C06  -179.83  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
 X0Y  plan-1  C01   0.020
 X0Y  plan-1  C02   0.020
 X0Y  plan-1  C03   0.020
 X0Y  plan-1  C05   0.020
 X0Y  plan-1  C06   0.020
 X0Y  plan-1  C08   0.020
 X0Y  plan-1  N04   0.020
 X0Y  plan-1  N07   0.020
 X0Y  plan-1  N09   0.020
 X0Y  plan-1  O11   0.020
 X0Y  plan-1  O13   0.020
 X0Y  plan-1  H031  0.020
 X0Y  plan-1  H051  0.020
 X0Y  plan-1  H1    0.020
 X0Y  plan-1  C10   0.020
 X0Y  plan-1  C12   0.020

