# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 15:14:30 2022
#   Inital geometry file: a 92 line input string
#   Ligand name: 8-bromo-2-{[(3S)-3-hydroxypyrrolidin-1-yl]methyl}[1]benzofuro[3,2-d]pyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1CCN(C1)CC2=Nc3c(oc4ccc(Br)cc34)C(=O)N2
#
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
 WUL  WUL  8-bromo-2-{[(3S)-3-hydroxypyrrolidin-1-yl]methyl}[1]benzofuro[3,2-d]pyrimidin-4(3H)-one  ligand  36  22  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WUL
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
 WUL  C14   C   CH1   0   0.012  -4.8264   2.7719  -0.0096
 WUL  N3    N   NT    0  -0.425  -3.7022   0.7388   0.1607
 WUL  O3    O   OH1   0  -0.672  -3.9632   3.5230   0.8167
 WUL  C13   C   CH2   0  -0.511  -4.2220   2.4770  -1.3823
 WUL  N1    N   N     0  -0.431  -1.2737  -0.5928   0.2598
 WUL  C12   C   CH2   0  -0.251  -3.3195   1.2576  -1.1536
 WUL  N2    N   NR16  0  -0.706  -2.3405  -2.6587   0.0604
 WUL  C5    C   CH2   0  -0.354  -3.7153  -0.6811   0.2895
 WUL  C3    C   CR6   0   0.497  -2.3493  -1.3037   0.1981
 WUL  C2    C   CR56  0   0.166  -0.1201  -1.3019   0.1708
 WUL  C7    C   CR56  0   0.027   1.2435  -0.8482   0.1761
 WUL  C11   C   CR16  0  -0.293   1.8610   0.3966   0.2643
 WUL  C10   C   CR6   0  -0.116   3.2409   0.4196   0.2211
 WUL  C9    C   CR16  0  -0.217   4.0012  -0.7517   0.0960
 WUL  C8    C   CR16  0  -0.308   3.3913  -1.9900   0.0082
 WUL  O2    O   O     0  -0.453   1.2263  -3.1107  -0.0288
 WUL  C6    C   CR56  0   0.363   2.0086  -2.0098   0.0499
 WUL  C1    C   CR56  0   0.153  -0.0467  -2.6601   0.0439
 WUL  C4    C   CR6   0   0.491  -1.2157  -3.4855  -0.0218
 WUL  C15   C   CH2   0  -0.277  -4.9445   1.3755   0.5666
 WUL  H3    H   HOH1  0   0.448  -3.8120   4.3744   0.3953
 WUL  H14   H   HCH1  0   0.224  -5.8082   3.2520  -0.0969
 WUL  H151  H   HCH2  0   0.252  -5.0545   1.3699   1.6545
 WUL  H152  H   HCH2  0   0.198  -5.8374   0.8901   0.1406
 WUL  H131  H   HCH2  0   0.234  -5.0257   2.2325  -2.0789
 WUL  H132  H   HCH2  0   0.245  -3.6882   3.3312  -1.8021
 WUL  H121  H   HCH2  0   0.235  -2.2601   1.5160  -1.1636
 WUL  H122  H   HCH2  0   0.199  -3.4731   0.5131  -1.9456
 WUL  H51C  H   HCH2  0   0.276  -4.1276  -0.9487   1.2689
 WUL  H52C  H   HCH2  0   0.210  -4.3686  -1.1753  -0.4545
 WUL  H2    H   HNR6  0   0.405  -3.2288  -3.1397   0.0031
 WUL  H11   H   HCR6  0   0.262   1.2731   1.2988   0.3617
 WUL  H9    H   HCR6  0   0.270   5.0804  -0.6977   0.0645
 WUL  H8    H   HCR6  0   0.268   3.9774  -2.8925  -0.0918
 WUL  BR1   BR  BR    0  -0.024   4.1399   2.0734   0.3299
 WUL  O1    O   O     0  -0.395  -1.2945  -4.6867  -0.1356

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
 WUL  O3   C14   single    1.411  0.020  1.411
 WUL  C14  C15   single    1.515  0.020  1.515
 WUL  C14  C13   single    1.529  0.020  1.529
 WUL  C15  N3    single    1.454  0.020  1.454
 WUL  C13  C12   single    1.534  0.020  1.534
 WUL  C12  N3    single    1.464  0.020  1.464
 WUL  N3   C5    single    1.426  0.020  1.426
 WUL  C5   C3    single    1.504  0.020  1.504
 WUL  C3   N1    double    1.291  0.020  1.291
 WUL  C3   N2    single    1.362  0.020  1.362
 WUL  N1   C2    single    1.357  0.020  1.357
 WUL  C2   C7    aromatic  1.437  0.020  1.437
 WUL  C2   C1    aromatic  1.366  0.020  1.366
 WUL  C7   C11   aromatic  1.392  0.020  1.392
 WUL  C7   C6    aromatic  1.397  0.020  1.397
 WUL  C11  C10   aromatic  1.381  0.020  1.381
 WUL  C10  BR1   single    1.886  0.020  1.886
 WUL  C10  C9    aromatic  1.402  0.020  1.402
 WUL  C9   C8    aromatic  1.383  0.020  1.383
 WUL  C8   C6    aromatic  1.383  0.020  1.383
 WUL  C6   O2    aromatic  1.353  0.020  1.353
 WUL  O2   C1    aromatic  1.352  0.020  1.352
 WUL  C1   C4    single    1.432  0.020  1.432
 WUL  C4   O1    double    1.209  0.020  1.209
 WUL  C4   N2    single    1.398  0.020  1.398
 WUL  O3   H3    single    0.850  0.020  0.980
 WUL  C14  H14   single    0.970  0.020  1.090
 WUL  C15  H151  single    0.970  0.020  1.090
 WUL  C15  H152  single    0.970  0.020  1.090
 WUL  C13  H131  single    0.970  0.020  1.090
 WUL  C13  H132  single    0.970  0.020  1.090
 WUL  C12  H121  single    0.970  0.020  1.090
 WUL  C12  H122  single    0.970  0.020  1.090
 WUL  C5   H51C  single    0.970  0.020  1.090
 WUL  C5   H52C  single    0.970  0.020  1.090
 WUL  N2   H2    single    0.860  0.020  1.020
 WUL  C11  H11   single    0.930  0.020  1.080
 WUL  C9   H9    single    0.930  0.020  1.080
 WUL  C8   H8    single    0.930  0.020  1.080

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
 WUL  H14   C14  C15   111.35  3.000
 WUL  H14   C14  C13   111.54  3.000
 WUL  C15   C14  C13   101.22  3.000
 WUL  H14   C14  O3    111.17  3.000
 WUL  C13   C14  O3    112.74  3.000
 WUL  C15   C14  O3    108.39  3.000
 WUL  C15   N3   C5    113.77  3.000
 WUL  C5    N3   C12   115.88  3.000
 WUL  C15   N3   C12   108.59  3.000
 WUL  H3    O3   C14   108.09  3.000
 WUL  H132  C13  H131  106.86  3.000
 WUL  H132  C13  C12   113.06  3.000
 WUL  H131  C13  C12   110.51  3.000
 WUL  H132  C13  C14   112.82  3.000
 WUL  H131  C13  C14   108.98  3.000
 WUL  C12   C13  C14   104.60  3.000
 WUL  C2    N1   C3    114.67  3.000
 WUL  H122  C12  H121  106.86  3.000
 WUL  H122  C12  C13   110.43  3.000
 WUL  H121  C12  C13   112.44  3.000
 WUL  H122  C12  N3    111.76  3.000
 WUL  H121  C12  N3    110.26  3.000
 WUL  C13   C12  N3    105.17  3.000
 WUL  H2    N2   C4    114.95  3.000
 WUL  H2    N2   C3    118.23  3.000
 WUL  C4    N2   C3    126.82  3.000
 WUL  H52C  C5   H51C  105.65  3.000
 WUL  H52C  C5   C3    108.09  3.000
 WUL  H51C  C5   C3    107.15  3.000
 WUL  H52C  C5   N3    112.92  3.000
 WUL  H51C  C5   N3    109.11  3.000
 WUL  C3    C5   N3    113.48  3.000
 WUL  C5    C3   N2    115.08  3.000
 WUL  N2    C3   N1    123.19  3.000
 WUL  C5    C3   N1    121.73  3.000
 WUL  C1    C2   C7    105.27  3.000
 WUL  C1    C2   N1    124.84  3.000
 WUL  C7    C2   N1    129.89  3.000
 WUL  C6    C7   C11   120.42  3.000
 WUL  C6    C7   C2    104.88  3.000
 WUL  C11   C7   C2    134.70  3.000
 WUL  H11   C11  C10   122.16  3.000
 WUL  H11   C11  C7    120.70  3.000
 WUL  C10   C11  C7    117.14  3.000
 WUL  C9    C10  C11   122.06  3.000
 WUL  C9    C10  BR1   118.65  3.000
 WUL  C11   C10  BR1   119.29  3.000
 WUL  H9    C9   C8    118.89  3.000
 WUL  H9    C9   C10   120.15  3.000
 WUL  C8    C9   C10   120.97  3.000
 WUL  H8    C8   C6    122.20  3.000
 WUL  H8    C8   C9    120.96  3.000
 WUL  C6    C8   C9    116.85  3.000
 WUL  C1    O2   C6    105.67  3.000
 WUL  O2    C6   C8    126.01  3.000
 WUL  O2    C6   C7    111.42  3.000
 WUL  C8    C6   C7    122.57  3.000
 WUL  C4    C1   O2    125.01  3.000
 WUL  C4    C1   C2    122.23  3.000
 WUL  O2    C1   C2    112.75  3.000
 WUL  C1    C4   N2    108.24  3.000
 WUL  N2    C4   O1    122.71  3.000
 WUL  C1    C4   O1    129.04  3.000
 WUL  H152  C15  H151  107.51  3.000
 WUL  H152  C15  N3    113.05  3.000
 WUL  H151  C15  N3    111.19  3.000
 WUL  H152  C15  C14   108.79  3.000
 WUL  H151  C15  C14   113.01  3.000
 WUL  N3    C15  C14   103.35  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
 WUL  CONST_01  C10  C11  C7   C2   180.00   0.0  0
 WUL  CONST_02  C8   C6   C7   C2   180.00   0.0  0
 WUL  CONST_03  O2   C6   C7   C2     0.00   0.0  0
 WUL  CONST_04  C6   O2   C1   C2     0.00   0.0  0
 WUL  CONST_05  O2   C1   C2   C7     0.00   0.0  0
 WUL  CONST_06  C9   C10  C11  C7     0.00   0.0  0
 WUL  CONST_07  C9   C8   C6   C7     0.00   0.0  0
 WUL  CONST_08  C1   O2   C6   C7     0.00   0.0  0
 WUL  CONST_09  C1   C2   C7   C11  180.00   0.0  0
 WUL  CONST_10  C8   C6   C7   C11    0.00   0.0  0
 WUL  CONST_11  O2   C6   C7   C11  180.00   0.0  0
 WUL  CONST_12  C8   C9   C10  C11    0.00   0.0  0
 WUL  CONST_13  C6   C7   C11  C10    0.00   0.0  0
 WUL  CONST_14  C6   C8   C9   C10    0.00   0.0  0
 WUL  CONST_15  O2   C6   C8   C9   180.00   0.0  0
 WUL  CONST_16  C1   O2   C6   C8   180.00   0.0  0
 WUL  CONST_17  C1   C2   C7   C6     0.00   0.0  0
 WUL  CONST_18  C4   N2   C3   N1     0.00   0.0  0
 WUL  CONST_19  C2   N1   C3   N2     0.00   0.0  0
 WUL  CONST_20  C1   C4   N2   C3     0.00   0.0  0
 WUL  CONST_21  BR1  C10  C11  C7   180.00   0.0  0
 WUL  CONST_22  C8   C9   C10  BR1  180.00   0.0  0
 WUL  CONST_23  C3   N2   C4   O1   180.00   0.0  0
 WUL  CONST_24  C2   N1   C3   C5   180.00   0.0  0
 WUL  CONST_25  C4   N2   C3   C5   180.00   0.0  0
 WUL  CONST_26  H11  C11  C7   C2     0.00   0.0  0
 WUL  CONST_27  H8   C8   C6   C7   180.00   0.0  0
 WUL  CONST_28  H9   C9   C10  C11  180.00   0.0  0
 WUL  CONST_29  H2   N2   C3   N1   180.00   0.0  0
 WUL  Var_01    C12  N3   C15  C14  -34.28  30.0  1
 WUL  Var_02    N3   C12  C13  C14   13.75  30.0  1
 WUL  Var_03    C15  N3   C12  C13   12.63  30.0  1
 WUL  Var_04    N1   C3   C5   N3    12.58  30.0  3
 WUL  Var_05    C3   C5   N3   C12   67.25  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
 WUL  chir_01  C14  O3  C15  C13  positiv

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
 WUL  plan-1  N1   0.020
 WUL  plan-1  N2   0.020
 WUL  plan-1  C5   0.020
 WUL  plan-1  C3   0.020
 WUL  plan-1  C2   0.020
 WUL  plan-1  C7   0.020
 WUL  plan-1  C11  0.020
 WUL  plan-1  C10  0.020
 WUL  plan-1  C9   0.020
 WUL  plan-1  C8   0.020
 WUL  plan-1  O2   0.020
 WUL  plan-1  C6   0.020
 WUL  plan-1  C1   0.020
 WUL  plan-1  C4   0.020
 WUL  plan-1  H2   0.020
 WUL  plan-1  H11  0.020
 WUL  plan-1  H9   0.020
 WUL  plan-1  H8   0.020
 WUL  plan-1  BR1  0.020
 WUL  plan-1  O1   0.020

