# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 09:30:36 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 1-[(2S)-2,3-dihydro-1,4-benzodioxin-2-ylmethyl]-3-hydroxythieno[3,2-d]pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ON1C(=O)N(C[C@H]2COc3ccccc3O2)c4ccsc4C1=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
 R3Z  R3Z  1-[(2S)-2,3-dihydro-1,4-benzodioxin-2-ylmethyl]-3-hydroxythieno[3,2-d]pyrimidine-2,4(1H,3H)-dione  ligand  35  23  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_R3Z
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
 R3Z  C1    C  CR16  0  -0.265   5.2172  -0.9747  -1.3185
 R3Z  C2    C  CR16  0  -0.267   4.1309  -1.8044  -1.5676
 R3Z  C3    C  CR16  0  -0.358   2.8812  -1.4797  -1.0623
 R3Z  C4    C  CR6   0   0.322   2.7128  -0.3337  -0.2966
 R3Z  C5    C  CR6   0   0.314   3.8086   0.4904  -0.0292
 R3Z  C6    C  CR16  0  -0.363   5.0563   0.1655  -0.5458
 R3Z  O7    O  O2    0  -0.478   3.6862   1.6106   0.7247
 R3Z  C8    C  CH2   0  -0.193   2.5015   1.6721   1.4964
 R3Z  C9    C  CH1   0  -0.024   1.3065   1.2818   0.6478
 R3Z  O10   O  O2    0  -0.483   1.4738  -0.0423   0.1703
 R3Z  C11   C  CH2   0  -0.368   0.0254   1.3130   1.4586
 R3Z  N12   N  NR6   0  -0.617  -1.1184   0.8172   0.7059
 R3Z  C13   C  CR56  0   0.486  -1.5243  -0.4913   0.8017
 R3Z  C14   C  CR15  0  -0.189  -0.9455  -1.5225   1.5907
 R3Z  C15   C  CR15  0  -0.444  -1.6312  -2.6899   1.4580
 R3Z  S16   S  S2    0   0.288  -2.9644  -2.5904   0.3941
 R3Z  C17   C  CR56  0  -0.439  -2.6235  -0.9337   0.1029
 R3Z  C18   C  CR6   0   0.587  -3.3715  -0.0823  -0.7581
 R3Z  O19   O  O     0  -0.465  -4.3576  -0.3605  -1.4201
 R3Z  N20   N  NR6   0  -0.318  -2.8551   1.1995  -0.7908
 R3Z  C21   C  CR6   0   0.740  -1.7641   1.7108  -0.1180
 R3Z  O22   O  O     0  -0.464  -1.4175   2.8627  -0.2506
 R3Z  O23   O  OH1   0  -0.525  -3.4804   2.1023  -1.5952
 R3Z  H1    H  HCR6  0   0.257   6.1938  -1.2173  -1.7158
 R3Z  H2    H  HCR6  0   0.257   4.2509  -2.6990  -2.1638
 R3Z  H3    H  HCR6  0   0.267   2.0229  -2.1108  -1.2577
 R3Z  H6    H  HCR6  0   0.267   5.8968   0.8154  -0.3355
 R3Z  H8    H  HCH2  0   0.242   2.5776   1.0078   2.3651
 R3Z  H8A   H  HCH2  0   0.267   2.4041   2.6970   1.8515
 R3Z  H9    H  HCH1  0   0.270   1.2310   1.9700  -0.2032
 R3Z  H11   H  HCH2  0   0.291   0.1239   0.7134   2.3624
 R3Z  H11A  H  HCH2  0   0.308  -0.1783   2.3323   1.7812
 R3Z  H14   H  HCR5  0   0.294  -0.0710  -1.4246   2.2138
 R3Z  H15   H  HCR5  0   0.320  -1.4032  -3.6258   1.9449
 R3Z  HO23  H  HOH1  0   0.485  -4.2432   1.6108  -1.9487

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
 R3Z  C1   C2    aromatic  1.389  0.020  1.389
 R3Z  C1   C6    aromatic  1.387  0.020  1.387
 R3Z  C2   C3    aromatic  1.387  0.020  1.387
 R3Z  C3   C4    aromatic  1.389  0.020  1.389
 R3Z  C4   C5    aromatic  1.397  0.020  1.397
 R3Z  C4   O10   single    1.356  0.020  1.356
 R3Z  C5   C6    aromatic  1.389  0.020  1.389
 R3Z  C5   O7    single    1.356  0.020  1.356
 R3Z  O7   C8    single    1.415  0.020  1.415
 R3Z  C8   C9    single    1.517  0.020  1.517
 R3Z  C9   O10   single    1.417  0.020  1.417
 R3Z  C9   C11   single    1.516  0.020  1.516
 R3Z  C11  N12   single    1.456  0.020  1.456
 R3Z  N12  C13   single    1.373  0.020  1.373
 R3Z  N12  C21   single    1.376  0.020  1.376
 R3Z  C13  C14   aromatic  1.422  0.020  1.422
 R3Z  C13  C17   aromatic  1.376  0.020  1.376
 R3Z  C14  C15   aromatic  1.360  0.020  1.360
 R3Z  C15  S16   aromatic  1.709  0.020  1.709
 R3Z  S16  C17   aromatic  1.716  0.020  1.716
 R3Z  C17  C18   single    1.423  0.020  1.423
 R3Z  C18  O19   double    1.220  0.020  1.220
 R3Z  C18  N20   single    1.382  0.020  1.382
 R3Z  N20  C21   single    1.380  0.020  1.380
 R3Z  N20  O23   single    1.361  0.020  1.361
 R3Z  C21  O22   double    1.210  0.020  1.210
 R3Z  C1   H1    single    0.930  0.020  1.080
 R3Z  C2   H2    single    0.930  0.020  1.080
 R3Z  C3   H3    single    0.930  0.020  1.080
 R3Z  C6   H6    single    0.930  0.020  1.080
 R3Z  C8   H8    single    0.970  0.020  1.090
 R3Z  C8   H8A   single    0.970  0.020  1.090
 R3Z  C9   H9    single    0.970  0.020  1.090
 R3Z  C11  H11   single    0.970  0.020  1.090
 R3Z  C11  H11A  single    0.970  0.020  1.090
 R3Z  C14  H14   single    0.930  0.020  1.080
 R3Z  C15  H15   single    0.930  0.020  1.080
 R3Z  O23  HO23  single    0.850  0.020  0.980

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
 R3Z  H1    C1   C6   119.59  3.000
 R3Z  H1    C1   C2   120.40  3.000
 R3Z  C6    C1   C2   120.01  3.000
 R3Z  H2    C2   C3   119.64  3.000
 R3Z  H2    C2   C1   120.39  3.000
 R3Z  C3    C2   C1   119.97  3.000
 R3Z  H3    C3   C4   118.97  3.000
 R3Z  H3    C3   C2   120.79  3.000
 R3Z  C4    C3   C2   120.23  3.000
 R3Z  O10   C4   C5   121.61  3.000
 R3Z  O10   C4   C3   118.56  3.000
 R3Z  C5    C4   C3   119.83  3.000
 R3Z  O7    C5   C6   118.77  3.000
 R3Z  O7    C5   C4   121.54  3.000
 R3Z  C6    C5   C4   119.70  3.000
 R3Z  H6    C6   C5   118.97  3.000
 R3Z  H6    C6   C1   120.77  3.000
 R3Z  C5    C6   C1   120.26  3.000
 R3Z  C8    O7   C5   114.50  3.000
 R3Z  H8A   C8   H8   108.55  3.000
 R3Z  H8A   C8   C9   110.74  3.000
 R3Z  H8    C8   C9   110.01  3.000
 R3Z  H8A   C8   O7   107.07  3.000
 R3Z  H8    C8   O7   110.35  3.000
 R3Z  C9    C8   O7   110.07  3.000
 R3Z  H9    C9   C11  110.10  3.000
 R3Z  H9    C9   O10  109.45  3.000
 R3Z  C11   C9   O10  107.40  3.000
 R3Z  H9    C9   C8   109.08  3.000
 R3Z  C11   C9   C8   111.17  3.000
 R3Z  O10   C9   C8   109.63  3.000
 R3Z  C9    O10  C4   115.13  3.000
 R3Z  H11A  C11  H11  106.65  3.000
 R3Z  H11A  C11  N12  108.97  3.000
 R3Z  H11   C11  N12  108.21  3.000
 R3Z  H11A  C11  C9   109.63  3.000
 R3Z  H11   C11  C9   110.85  3.000
 R3Z  N12   C11  C9   112.34  3.000
 R3Z  C21   N12  C13  121.45  3.000
 R3Z  C21   N12  C11  117.18  3.000
 R3Z  C13   N12  C11  121.36  3.000
 R3Z  C17   C13  C14  111.96  3.000
 R3Z  C17   C13  N12  120.47  3.000
 R3Z  C14   C13  N12  127.55  3.000
 R3Z  H14   C14  C15  122.89  3.000
 R3Z  H14   C14  C13  125.81  3.000
 R3Z  C15   C14  C13  111.29  3.000
 R3Z  H15   C15  S16  119.75  3.000
 R3Z  H15   C15  C14  126.41  3.000
 R3Z  S16   C15  C14  113.83  3.000
 R3Z  C17   S16  C15   90.39  3.000
 R3Z  C18   C17  S16  125.14  3.000
 R3Z  C18   C17  C13  122.34  3.000
 R3Z  S16   C17  C13  112.52  3.000
 R3Z  N20   C18  O19  120.04  3.000
 R3Z  N20   C18  C17  111.88  3.000
 R3Z  O19   C18  C17  128.08  3.000
 R3Z  O23   N20  C21  113.92  3.000
 R3Z  O23   N20  C18  117.22  3.000
 R3Z  C21   N20  C18  128.86  3.000
 R3Z  O22   C21  N20  121.72  3.000
 R3Z  O22   C21  N12  123.31  3.000
 R3Z  N20   C21  N12  114.97  3.000
 R3Z  HO23  O23  N20  103.86  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
 R3Z  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 R3Z  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 R3Z  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 R3Z  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 R3Z  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 R3Z  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 R3Z  CONST_07  S16  C15  C14  C13    0.00   0.0  0
 R3Z  CONST_08  C15  S16  C17  C13    0.00   0.0  0
 R3Z  CONST_09  S16  C17  C13  C14    0.00   0.0  0
 R3Z  CONST_10  C17  S16  C15  C14    0.00   0.0  0
 R3Z  CONST_11  C17  C13  C14  C15    0.00   0.0  0
 R3Z  CONST_12  C18  N20  C21  N12    0.00   0.0  0
 R3Z  CONST_13  N20  C21  N12  C13    0.00   0.0  0
 R3Z  CONST_14  C21  N20  C18  C17    0.00   0.0  0
 R3Z  CONST_15  N20  C21  N12  C11  180.00   0.0  0
 R3Z  CONST_16  O23  N20  C21  N12  180.00   0.0  0
 R3Z  CONST_17  O22  C21  N12  C13  180.00   0.0  0
 R3Z  CONST_18  O23  N20  C18  C17  180.00   0.0  0
 R3Z  CONST_19  O22  C21  N20  C18  180.00   0.0  0
 R3Z  CONST_20  C21  N20  C18  O19  180.00   0.0  0
 R3Z  CONST_21  H3   C3   C2   C1   180.00   0.0  0
 R3Z  CONST_22  H6   C6   C1   C2   180.00   0.0  0
 R3Z  CONST_23  H1   C1   C2   C3   180.00   0.0  0
 R3Z  CONST_24  H2   C2   C3   C4   180.00   0.0  0
 R3Z  CONST_25  H14  C14  C13  N12    0.00   0.0  0
 R3Z  CONST_26  H15  C15  C14  C13  180.00   0.0  0
 R3Z  CONST_27  O22  C21  N12  C11    0.00   0.0  0
 R3Z  CONST_28  O23  N20  C18  O19    0.00   0.0  0
 R3Z  CONST_29  O23  N20  C21  O22    0.00   0.0  0
 R3Z  Var_01    C9   C8   O7   C5   -45.88  30.0  1
 R3Z  Var_02    C13  N12  C11  C9    95.04  30.0  3

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
 R3Z  chir_01  C9  C8  O10  C11  negativ

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
 R3Z  plan-1  C11  0.020
 R3Z  plan-1  N12  0.020
 R3Z  plan-1  C13  0.020
 R3Z  plan-1  C14  0.020
 R3Z  plan-1  C15  0.020
 R3Z  plan-1  S16  0.020
 R3Z  plan-1  C17  0.020
 R3Z  plan-1  C18  0.020
 R3Z  plan-1  O19  0.020
 R3Z  plan-1  N20  0.020
 R3Z  plan-1  C21  0.020
 R3Z  plan-1  O22  0.020
 R3Z  plan-1  O23  0.020
 R3Z  plan-1  H14  0.020
 R3Z  plan-1  H15  0.020
 R3Z  plan-2  C1   0.020
 R3Z  plan-2  C2   0.020
 R3Z  plan-2  C3   0.020
 R3Z  plan-2  C4   0.020
 R3Z  plan-2  C5   0.020
 R3Z  plan-2  C6   0.020
 R3Z  plan-2  O7   0.020
 R3Z  plan-2  O10  0.020
 R3Z  plan-2  H1   0.020
 R3Z  plan-2  H2   0.020
 R3Z  plan-2  H3   0.020
 R3Z  plan-2  H6   0.020

