# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 10:24:13 2021
#   Inital geometry file: a 82 line input string
#   Ligand name: 1-{2-[(propan-2-yl)oxy]ethyl}-2-sulfanylidene-1,2,3,5-tetrahydro-4H-pyrrolo[3,2-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)OCCN1C(=S)NC(=O)c2[nH]ccc12
#
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
 W4Y  W4Y  1-{2-[(propan-2-yl)oxy]ethyl}-2-sulfanylidene-1,2,3,5-tetrahydro-4H-pyrrolo[3,2-d]pyrimidin-4-one  ligand  32  17  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_W4Y
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
 W4Y  C10   C  CR6   0   0.531  -44.6932  -29.3262   5.7728
 W4Y  N12   N  NR16  0  -0.691  -43.4849  -29.6320   5.1539
 W4Y  C13   C  CR6   0   0.376  -43.2219  -29.8533   3.8333
 W4Y  C17   C  CR15  0  -0.383  -46.7473  -29.2501   2.7959
 W4Y  C01   C  CH3   0  -0.670  -45.7921  -25.8864   0.1359
 W4Y  C02   C  CH1   0   0.051  -44.5208  -26.7026  -0.0021
 W4Y  C03   C  CH3   0  -0.686  -43.2803  -25.8457   0.2096
 W4Y  C05   C  CH2   0  -0.137  -43.6372  -28.7639   0.7925
 W4Y  C08   C  CR56  0   0.316  -45.5162  -29.4228   3.4575
 W4Y  C09   C  CR56  0   0.146  -45.7344  -29.2321   4.8096
 W4Y  C16   C  CR15  0  -0.004  -47.6661  -28.9623   3.7840
 W4Y  N07   N  NR6   0  -0.526  -44.2623  -29.7517   2.9788
 W4Y  N15   N  NR15  0  -0.640  -47.0543  -28.9508   4.9844
 W4Y  O04   O  O2    0  -0.479  -44.6094  -27.7641   0.9324
 W4Y  O11   O  O     0  -0.459  -44.7708  -29.1720   6.9781
 W4Y  S14   S  S1    0  -0.370  -41.6596  -30.2384   3.3703
 W4Y  H121  H  HNR6  0   0.429  -42.6821  -29.7179   5.7640
 W4Y  H171  H  HCR5  0   0.273  -46.9508  -29.2967   1.7405
 W4Y  H012  H  HCH3  0   0.233  -46.6780  -26.5059  -0.0074
 W4Y  H013  H  HCH3  0   0.223  -45.8542  -25.4235   1.1227
 W4Y  H011  H  HCH3  0   0.226  -45.8125  -25.0911  -0.6090
 W4Y  H021  H  HCH1  0   0.197  -44.4802  -27.1271  -1.0172
 W4Y  H033  H  HCH3  0   0.235  -42.3574  -26.4157   0.0938
 W4Y  H032  H  HCH3  0   0.232  -43.2549  -25.0371  -0.5218
 W4Y  H031  H  HCH3  0   0.223  -43.2812  -25.3989   1.2060
 W4Y  H051  H  HCH2  0   0.216  -43.5033  -29.0520  -0.2597
 W4Y  H052  H  HCH2  0   0.212  -42.6577  -28.4434   1.1657
 W4Y  H061  H  HCH2  0   0.276  -45.0370  -30.3594   1.1596
 W4Y  H062  H  HCH2  0   0.284  -43.3535  -30.7881   1.4224
 W4Y  H161  H  HCR5  0   0.298  -48.7205  -28.7596   3.6954
 W4Y  H151  H  HNR5  0   0.427  -47.5002  -28.7614   5.8678
 W4Y  C06   C  CH2   0  -0.360  -44.0876  -29.9950   1.5491

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
 W4Y  C02  C03   single    1.522  0.020  1.522
 W4Y  C02  C01   single    1.517  0.020  1.517
 W4Y  C02  O04   single    1.417  0.020  1.417
 W4Y  O04  C05   single    1.402  0.020  1.402
 W4Y  C05  C06   single    1.514  0.020  1.514
 W4Y  C06  N07   single    1.461  0.020  1.461
 W4Y  C17  C08   aromatic  1.408  0.020  1.408
 W4Y  C17  C16   aromatic  1.380  0.020  1.380
 W4Y  N07  C08   single    1.382  0.020  1.382
 W4Y  N07  C13   single    1.350  0.020  1.350
 W4Y  S14  C13   double    1.674  0.020  1.674
 W4Y  C08  C09   aromatic  1.383  0.020  1.383
 W4Y  C16  N15   aromatic  1.347  0.020  1.347
 W4Y  C13  N12   single    1.365  0.020  1.365
 W4Y  C09  N15   aromatic  1.361  0.020  1.361
 W4Y  C09  C10   single    1.421  0.020  1.421
 W4Y  N12  C10   single    1.392  0.020  1.392
 W4Y  C10  O11   double    1.218  0.020  1.218
 W4Y  N12  H121  single    0.860  0.020  1.020
 W4Y  C17  H171  single    0.930  0.020  1.080
 W4Y  C01  H012  single    0.970  0.020  1.090
 W4Y  C01  H013  single    0.970  0.020  1.090
 W4Y  C01  H011  single    0.970  0.020  1.090
 W4Y  C02  H021  single    0.970  0.020  1.090
 W4Y  C03  H033  single    0.970  0.020  1.090
 W4Y  C03  H032  single    0.970  0.020  1.090
 W4Y  C03  H031  single    0.970  0.020  1.090
 W4Y  C05  H051  single    0.970  0.020  1.090
 W4Y  C05  H052  single    0.970  0.020  1.090
 W4Y  C06  H061  single    0.970  0.020  1.090
 W4Y  C06  H062  single    0.970  0.020  1.090
 W4Y  C16  H161  single    0.930  0.020  1.080
 W4Y  N15  H151  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
 W4Y  O11   C10  C09   128.01  3.000
 W4Y  O11   C10  N12   121.56  3.000
 W4Y  C09   C10  N12   110.43  3.000
 W4Y  H121  N12  C13   114.63  3.000
 W4Y  H121  N12  C10   116.06  3.000
 W4Y  C13   N12  C10   129.31  3.000
 W4Y  S14   C13  N07   124.15  3.000
 W4Y  S14   C13  N12   119.00  3.000
 W4Y  N07   C13  N12   116.85  3.000
 W4Y  H171  C17  C16   125.85  3.000
 W4Y  H171  C17  C08   128.38  3.000
 W4Y  C16   C17  C08   105.74  3.000
 W4Y  H011  C01  H013  107.89  3.000
 W4Y  H011  C01  H012  108.02  3.000
 W4Y  H013  C01  H012  108.27  3.000
 W4Y  H011  C01  C02   110.25  3.000
 W4Y  H013  C01  C02   110.98  3.000
 W4Y  H012  C01  C02   111.30  3.000
 W4Y  H021  C02  O04   108.75  3.000
 W4Y  H021  C02  C03   108.37  3.000
 W4Y  O04   C02  C03   112.39  3.000
 W4Y  H021  C02  C01   108.80  3.000
 W4Y  O04   C02  C01   106.89  3.000
 W4Y  C03   C02  C01   111.55  3.000
 W4Y  H031  C03  H032  107.98  3.000
 W4Y  H031  C03  H033  108.14  3.000
 W4Y  H032  C03  H033  107.25  3.000
 W4Y  H031  C03  C02   110.88  3.000
 W4Y  H032  C03  C02   110.06  3.000
 W4Y  H033  C03  C02   112.36  3.000
 W4Y  H052  C05  H051  107.08  3.000
 W4Y  H052  C05  O04   112.17  3.000
 W4Y  H051  C05  O04   111.54  3.000
 W4Y  H052  C05  C06   109.48  3.000
 W4Y  H051  C05  C06   107.55  3.000
 W4Y  O04   C05  C06   108.90  3.000
 W4Y  N07   C08  C09   120.97  3.000
 W4Y  C09   C08  C17   107.73  3.000
 W4Y  N07   C08  C17   131.28  3.000
 W4Y  N15   C09  C08   107.89  3.000
 W4Y  N15   C09  C10   129.57  3.000
 W4Y  C08   C09  C10   122.54  3.000
 W4Y  H161  C16  N15   121.07  3.000
 W4Y  H161  C16  C17   129.20  3.000
 W4Y  N15   C16  C17   109.72  3.000
 W4Y  C08   N07  C06   119.16  3.000
 W4Y  C08   N07  C13   119.86  3.000
 W4Y  C06   N07  C13   120.98  3.000
 W4Y  H151  N15  C16   125.58  3.000
 W4Y  H151  N15  C09   125.50  3.000
 W4Y  C16   N15  C09   108.92  3.000
 W4Y  C05   O04  C02   115.16  3.000
 W4Y  H062  C06  H061  107.62  3.000
 W4Y  H062  C06  N07   108.43  3.000
 W4Y  H061  C06  N07   107.55  3.000
 W4Y  H062  C06  C05   109.51  3.000
 W4Y  H061  C06  C05   110.66  3.000
 W4Y  N07   C06  C05   112.91  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
 W4Y  CONST_01  N15   C09  C08  C17     0.00   0.0  0
 W4Y  CONST_02  C09   N15  C16  C17     0.00   0.0  0
 W4Y  CONST_03  N15   C16  C17  C08     0.00   0.0  0
 W4Y  CONST_04  C16   N15  C09  C08     0.00   0.0  0
 W4Y  CONST_05  C16   C17  C08  C09     0.00   0.0  0
 W4Y  CONST_06  N07   C13  N12  C10     0.00   0.0  0
 W4Y  CONST_07  C08   N07  C13  N12     0.00   0.0  0
 W4Y  CONST_08  C09   C10  N12  C13     0.00   0.0  0
 W4Y  CONST_09  S14   C13  N12  C10   180.00   0.0  0
 W4Y  CONST_10  C06   N07  C13  N12   180.00   0.0  0
 W4Y  CONST_11  O11   C10  N12  C13   180.00   0.0  0
 W4Y  CONST_12  S14   C13  N07  C08   180.00   0.0  0
 W4Y  CONST_13  H151  N15  C09  C10     0.00   0.0  0
 W4Y  CONST_14  H161  C16  C17  C08   180.00   0.0  0
 W4Y  CONST_15  H171  C17  C08  C09   180.00   0.0  0
 W4Y  CONST_16  H121  N12  C10  C09   180.00   0.0  0
 W4Y  CONST_17  S14   C13  N07  C06     0.00   0.0  0
 W4Y  Var_01    C05   C06  N07  C13   -86.22  30.0  2
 W4Y  Var_02    O04   C05  C06  N07   -60.76  30.0  2
 W4Y  Var_03    C06   C05  O04  C02  -163.22  30.0  3
 W4Y  Var_04    H033  C03  C02  C01  -178.87  30.0  3
 W4Y  Var_05    H012  C01  C02  C03  -179.48  30.0  3
 W4Y  Var_06    H021  C02  O04  C05    51.86  30.0  1

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
 W4Y  plan-1  C10   0.020
 W4Y  plan-1  N12   0.020
 W4Y  plan-1  C13   0.020
 W4Y  plan-1  C17   0.020
 W4Y  plan-1  C08   0.020
 W4Y  plan-1  C09   0.020
 W4Y  plan-1  C16   0.020
 W4Y  plan-1  N07   0.020
 W4Y  plan-1  N15   0.020
 W4Y  plan-1  O11   0.020
 W4Y  plan-1  S14   0.020
 W4Y  plan-1  H121  0.020
 W4Y  plan-1  H171  0.020
 W4Y  plan-1  H161  0.020
 W4Y  plan-1  H151  0.020
 W4Y  plan-1  C06   0.020

