# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 07:58:43 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: (3S)-1-{[4-(1,3-benzodioxol-5-ylmethyl)piperazin-1-yl]methyl}-3-hydroxy-1,3-dihydro-2H-indol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1C(=O)N(CN2CCN(CC2)Cc3ccc4OCOc4c3)c5ccccc15
#
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
 1VL  1VL  (3S)-1-{[4-(1,3-benzodioxol-5-ylmethyl)piperazin-1-yl]methyl}-3-hydroxy-1,3-dihydro-2H-indol-2-one  ligand  51  28  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1VL
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
 1VL  O10  O  O     0  -0.448  -3.6732   2.3326   1.5054
 1VL  C8   C  CR5   0   0.517  -4.0703   1.3457   0.9281
 1VL  C7   C  CR15  0  -0.115  -5.4176   0.6447   1.1574
 1VL  O11  O  OH1   0  -0.646  -6.5037   1.5190   1.0642
 1VL  N9   N  NR5   0  -0.610  -3.4027   0.6711  -0.0530
 1VL  C5   C  CR56  0   0.434  -4.1958  -0.3542  -0.5811
 1VL  C4   C  CR16  0  -0.310  -3.9018  -1.2368  -1.6035
 1VL  C3   C  CR16  0  -0.256  -4.8857  -2.1554  -1.9663
 1VL  C2   C  CR16  0  -0.269  -6.1172  -2.1890  -1.3267
 1VL  C1   C  CR16  0  -0.311  -6.3904  -1.2991  -0.2882
 1VL  C6   C  CR56  0  -0.019  -5.4227  -0.3893   0.0779
 1VL  C12  C  CH2   0  -0.150  -2.0945   1.0620  -0.5176
 1VL  N13  N  NT    0  -0.417  -1.0510   0.6018   0.3618
 1VL  C14  C  CH2   0  -0.310  -0.8977  -0.8443   0.3506
 1VL  C15  C  CH2   0  -0.325   0.1761  -1.2559   1.3510
 1VL  N16  N  NT    0  -0.408   1.4577  -0.6092   1.1359
 1VL  C17  C  CH2   0  -0.323   1.2750   0.8311   1.0684
 1VL  C18  C  CH2   0  -0.298   0.2112   1.2608   0.0655
 1VL  H1   H  HCR5  0   0.272  -5.3662   0.1589   2.1430
 1VL  H2   H  HOH1  0   0.464  -6.5373   2.0496   1.8671
 1VL  H3   H  HCR6  0   0.268  -2.9502  -1.2252  -2.1176
 1VL  H4   H  HCR6  0   0.263  -4.6804  -2.8539  -2.7670
 1VL  H5   H  HCR6  0   0.257  -6.8650  -2.9081  -1.6328
 1VL  H6   H  HCR6  0   0.260  -7.3456  -1.3238   0.2206
 1VL  H7   H  HCH2  0   0.238  -1.9797   0.6997  -1.5493
 1VL  H8   H  HCH2  0   0.267  -2.0576   2.1518  -0.5590
 1VL  H10  H  HCH2  0   0.248  -1.8407  -1.3143   0.6393
 1VL  H11  H  HCH2  0   0.202  -0.6490  -1.2179  -0.6590
 1VL  H12  H  HCH2  0   0.234  -0.1726  -0.9961   2.3561
 1VL  H13  H  HCH2  0   0.243   0.3081  -2.3394   1.3254
 1VL  H16  H  HCH2  0   0.233   0.9861   1.1912   2.0608
 1VL  H17  H  HCH2  0   0.245   2.2251   1.3079   0.8205
 1VL  H18  H  HCH2  0   0.201   0.5508   1.0489  -0.9630
 1VL  H19  H  HCH2  0   0.245   0.0733   2.3428   0.1348
 1VL  C19  C  CH2   0  -0.331   2.2209  -1.1539   0.0293
 1VL  C20  C  CR6   0   0.077   3.6769  -0.7581   0.0924
 1VL  C21  C  CR16  0  -0.298   4.3667  -0.7776   1.2984
 1VL  C22  C  CR16  0  -0.329   5.7255  -0.4540   1.3792
 1VL  C23  C  CR56  0   0.282   6.3561  -0.1172   0.2063
 1VL  C24  C  CR56  0   0.313   5.6776  -0.0931  -0.9996
 1VL  C25  C  CR16  0  -0.402   4.3423  -0.4015  -1.0898
 1VL  O27  O  O     0  -0.489   6.5240   0.3018  -1.9840
 1VL  O28  O  O     0  -0.488   7.6449   0.2611   0.0062
 1VL  C26  C  CH2   0   0.069   7.8211   0.3159  -1.4027
 1VL  H9   H  HCH2  0   0.252   2.1445  -2.2442   0.0851
 1VL  H14  H  HCH2  0   0.218   1.8308  -0.8797  -0.9622
 1VL  H15  H  HCR6  0   0.246   3.8350  -1.0431   2.2023
 1VL  H20  H  HCR6  0   0.269   6.2502  -0.4657   2.3252
 1VL  H21  H  HCR6  0   0.264   3.8172  -0.3686  -2.0368
 1VL  H22  H  HCH2  0   0.230   8.3896  -0.5577  -1.7414
 1VL  H23  H  HCH2  0   0.244   8.3377   1.2360  -1.6753

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
 1VL  C2   C1   aromatic  1.395  0.020  1.395
 1VL  C2   C3   aromatic  1.388  0.020  1.388
 1VL  C1   C6   aromatic  1.378  0.020  1.378
 1VL  C3   C4   aromatic  1.394  0.020  1.394
 1VL  C6   C7   single    1.495  0.020  1.495
 1VL  C6   C5   aromatic  1.393  0.020  1.393
 1VL  O11  C7   single    1.397  0.020  1.397
 1VL  C4   C5   aromatic  1.382  0.020  1.382
 1VL  C7   C8   single    1.536  0.020  1.536
 1VL  C5   N9   single    1.400  0.020  1.400
 1VL  C8   N9   single    1.365  0.020  1.365
 1VL  C8   O10  double    1.210  0.020  1.210
 1VL  N9   C12  single    1.442  0.020  1.442
 1VL  C14  N13  single    1.454  0.020  1.454
 1VL  C14  C15  single    1.524  0.020  1.524
 1VL  C12  N13  single    1.440  0.020  1.440
 1VL  N13  C18  single    1.454  0.020  1.454
 1VL  C15  N16  single    1.451  0.020  1.451
 1VL  N16  C17  single    1.453  0.020  1.453
 1VL  C18  C17  single    1.524  0.020  1.524
 1VL  C7   H1   single    0.970  0.020  1.090
 1VL  O11  H2   single    0.850  0.020  0.980
 1VL  C4   H3   single    0.930  0.020  1.080
 1VL  C3   H4   single    0.930  0.020  1.080
 1VL  C2   H5   single    0.930  0.020  1.080
 1VL  C1   H6   single    0.930  0.020  1.080
 1VL  C12  H7   single    0.970  0.020  1.090
 1VL  C12  H8   single    0.970  0.020  1.090
 1VL  C14  H10  single    0.970  0.020  1.090
 1VL  C14  H11  single    0.970  0.020  1.090
 1VL  C15  H12  single    0.970  0.020  1.090
 1VL  C15  H13  single    0.970  0.020  1.090
 1VL  C17  H16  single    0.970  0.020  1.090
 1VL  C17  H17  single    0.970  0.020  1.090
 1VL  C18  H18  single    0.970  0.020  1.090
 1VL  C18  H19  single    0.970  0.020  1.090
 1VL  N16  C19  single    1.450  0.020  1.450
 1VL  C19  C20  single    1.510  0.020  1.510
 1VL  C20  C21  aromatic  1.389  0.020  1.389
 1VL  C21  C22  aromatic  1.399  0.020  1.399
 1VL  C22  C23  aromatic  1.374  0.020  1.374
 1VL  C23  C24  aromatic  1.384  0.020  1.384
 1VL  C24  C25  aromatic  1.373  0.020  1.373
 1VL  C25  C20  aromatic  1.403  0.020  1.403
 1VL  C24  O27  single    1.357  0.020  1.357
 1VL  C23  O28  single    1.358  0.020  1.358
 1VL  O27  C26  single    1.421  0.020  1.421
 1VL  O28  C26  single    1.421  0.020  1.421
 1VL  C19  H9   single    0.970  0.020  1.090
 1VL  C19  H14  single    0.970  0.020  1.090
 1VL  C21  H15  single    0.930  0.020  1.080
 1VL  C22  H20  single    0.930  0.020  1.080
 1VL  C25  H21  single    0.930  0.020  1.080
 1VL  C26  H22  single    0.970  0.020  1.090
 1VL  C26  H23  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
 1VL  N9   C8   C7   108.10  3.000
 1VL  N9   C8   O10  125.83  3.000
 1VL  C7   C8   O10  126.07  3.000
 1VL  H1   C7   C6   109.98  3.000
 1VL  H1   C7   O11  111.86  3.000
 1VL  C6   C7   O11  112.46  3.000
 1VL  H1   C7   C8   107.12  3.000
 1VL  O11  C7   C8   112.72  3.000
 1VL  C6   C7   C8   102.17  3.000
 1VL  H2   O11  C7   108.44  3.000
 1VL  C12  N9   C5   126.22  3.000
 1VL  C12  N9   C8   122.76  3.000
 1VL  C5   N9   C8   110.86  3.000
 1VL  C6   C5   C4   121.40  3.000
 1VL  C4   C5   N9   128.78  3.000
 1VL  C6   C5   N9   109.81  3.000
 1VL  H3   C4   C3   120.28  3.000
 1VL  H3   C4   C5   122.13  3.000
 1VL  C3   C4   C5   117.59  3.000
 1VL  H4   C3   C2   119.58  3.000
 1VL  H4   C3   C4   118.94  3.000
 1VL  C2   C3   C4   121.48  3.000
 1VL  H5   C2   C1   119.96  3.000
 1VL  H5   C2   C3   119.94  3.000
 1VL  C1   C2   C3   120.10  3.000
 1VL  H6   C1   C6   120.66  3.000
 1VL  H6   C1   C2   120.55  3.000
 1VL  C6   C1   C2   118.79  3.000
 1VL  C1   C6   C5   120.63  3.000
 1VL  C5   C6   C7   108.73  3.000
 1VL  C1   C6   C7   130.62  3.000
 1VL  H8   C12  H7   106.85  3.000
 1VL  H8   C12  N13  108.53  3.000
 1VL  H7   C12  N13  113.08  3.000
 1VL  H8   C12  N9   108.28  3.000
 1VL  H7   C12  N9   107.92  3.000
 1VL  N13  C12  N9   111.96  3.000
 1VL  C18  N13  C14  110.95  3.000
 1VL  C18  N13  C12  111.08  3.000
 1VL  C14  N13  C12  112.92  3.000
 1VL  H11  C14  H10  106.87  3.000
 1VL  H11  C14  C15  110.48  3.000
 1VL  H10  C14  C15  108.57  3.000
 1VL  H11  C14  N13  111.53  3.000
 1VL  H10  C14  N13  109.56  3.000
 1VL  C15  C14  N13  109.74  3.000
 1VL  H13  C15  H12  107.18  3.000
 1VL  H13  C15  N16  109.39  3.000
 1VL  H12  C15  N16  108.14  3.000
 1VL  H13  C15  C14  109.74  3.000
 1VL  H12  C15  C14  108.30  3.000
 1VL  N16  C15  C14  113.86  3.000
 1VL  C19  N16  C17  113.76  3.000
 1VL  C19  N16  C15  114.22  3.000
 1VL  C17  N16  C15  109.72  3.000
 1VL  H17  C17  H16  106.98  3.000
 1VL  H17  C17  C18  109.57  3.000
 1VL  H16  C17  C18  108.64  3.000
 1VL  H17  C17  N16  109.51  3.000
 1VL  H16  C17  N16  108.49  3.000
 1VL  C18  C17  N16  113.43  3.000
 1VL  H19  C18  H18  106.74  3.000
 1VL  H19  C18  C17  108.99  3.000
 1VL  H18  C18  C17  110.14  3.000
 1VL  H19  C18  N13  109.03  3.000
 1VL  H18  C18  N13  111.71  3.000
 1VL  C17  C18  N13  110.12  3.000
 1VL  H14  C19  H9   105.64  3.000
 1VL  H14  C19  C20  108.31  3.000
 1VL  H9   C19  C20  109.04  3.000
 1VL  H14  C19  N16  114.04  3.000
 1VL  H9   C19  N16  107.37  3.000
 1VL  C20  C19  N16  112.15  3.000
 1VL  C25  C20  C21  119.97  3.000
 1VL  C25  C20  C19  119.26  3.000
 1VL  C21  C20  C19  120.75  3.000
 1VL  H15  C21  C22  119.07  3.000
 1VL  H15  C21  C20  118.99  3.000
 1VL  C22  C21  C20  121.94  3.000
 1VL  H20  C22  C23  121.78  3.000
 1VL  H20  C22  C21  121.27  3.000
 1VL  C23  C22  C21  116.95  3.000
 1VL  O28  C23  C24  109.39  3.000
 1VL  O28  C23  C22  129.04  3.000
 1VL  C24  C23  C22  121.55  3.000
 1VL  O27  C24  C25  128.62  3.000
 1VL  O27  C24  C23  109.35  3.000
 1VL  C25  C24  C23  122.01  3.000
 1VL  H21  C25  C24  121.46  3.000
 1VL  H21  C25  C20  120.97  3.000
 1VL  C24  C25  C20  117.58  3.000
 1VL  C26  O27  C24  105.98  3.000
 1VL  C26  O28  C23  105.93  3.000
 1VL  H23  C26  H22  110.47  3.000
 1VL  H23  C26  O28  109.84  3.000
 1VL  H22  C26  O28  109.88  3.000
 1VL  H23  C26  O27  109.79  3.000
 1VL  H22  C26  O27  109.82  3.000
 1VL  O28  C26  O27  106.98  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
 1VL  CONST_01  C2   C1   C6   C5      0.00   0.0  0
 1VL  CONST_02  C2   C3   C4   C5      0.00   0.0  0
 1VL  CONST_03  C1   C2   C3   C4      0.00   0.0  0
 1VL  CONST_04  C1   C6   C5   C4      0.00   0.0  0
 1VL  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 1VL  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 1VL  CONST_07  C23  C22  C21  C20     0.00   0.0  0
 1VL  CONST_08  C23  C24  C25  C20     0.00   0.0  0
 1VL  CONST_09  C24  C25  C20  C21     0.00   0.0  0
 1VL  CONST_10  C24  C23  C22  C21     0.00   0.0  0
 1VL  CONST_11  C25  C20  C21  C22     0.00   0.0  0
 1VL  CONST_12  C25  C24  C23  C22     0.00   0.0  0
 1VL  CONST_13  C5   N9   C8   C7      0.00   0.0  0
 1VL  CONST_14  C22  C21  C20  C19   180.00   0.0  0
 1VL  CONST_15  C24  C25  C20  C19   180.00   0.0  0
 1VL  CONST_16  C5   N9   C8   O10   180.00   0.0  0
 1VL  CONST_17  C12  N9   C8   C7    180.00   0.0  0
 1VL  CONST_18  H6   C1   C6   C7      0.00   0.0  0
 1VL  CONST_19  H3   C4   C5   N9      0.00   0.0  0
 1VL  CONST_20  H4   C3   C4   C5    180.00   0.0  0
 1VL  CONST_21  H5   C2   C3   C4    180.00   0.0  0
 1VL  CONST_22  H20  C22  C21  C20   180.00   0.0  0
 1VL  CONST_23  H21  C25  C20  C21   180.00   0.0  0
 1VL  CONST_24  H15  C21  C22  C23   180.00   0.0  0
 1VL  CONST_25  C12  N9   C8   O10     0.00   0.0  0
 1VL  Var_01    N16  C15  C14  N13   -55.67  30.0  1
 1VL  Var_02    N16  C17  C18  N13    55.64  30.0  1
 1VL  Var_03    C17  C18  N13  C14   -57.44  30.0  1
 1VL  Var_04    C17  N16  C15  C14    52.59  30.0  1
 1VL  Var_05    C18  N13  C14  C15    57.21  30.0  1
 1VL  Var_06    C18  C17  N16  C15   -52.36  30.0  1
 1VL  Var_07    O27  C26  O28  C23    14.93  30.0  1
 1VL  Var_08    O28  C26  O27  C24   -14.97  30.0  1
 1VL  Var_09    N13  C12  N9   C8     80.48  30.0  3
 1VL  Var_10    C14  N13  C12  N9     68.21  30.0  3
 1VL  Var_11    C20  C19  N16  C15  -162.86  30.0  3
 1VL  Var_12    C21  C20  C19  N16    42.33  30.0  2

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
 1VL  chir_01  C7  C6  O11  C8  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
 1VL  plan-1  C19  0.020
 1VL  plan-1  C20  0.020
 1VL  plan-1  C21  0.020
 1VL  plan-1  C22  0.020
 1VL  plan-1  C23  0.020
 1VL  plan-1  C24  0.020
 1VL  plan-1  C25  0.020
 1VL  plan-1  O27  0.020
 1VL  plan-1  O28  0.020
 1VL  plan-1  H15  0.020
 1VL  plan-1  H20  0.020
 1VL  plan-1  H21  0.020
 1VL  plan-2  O10  0.020
 1VL  plan-2  C8   0.020
 1VL  plan-2  C7   0.020
 1VL  plan-2  N9   0.020
 1VL  plan-2  C5   0.020
 1VL  plan-2  C4   0.020
 1VL  plan-2  C3   0.020
 1VL  plan-2  C2   0.020
 1VL  plan-2  C1   0.020
 1VL  plan-2  C6   0.020
 1VL  plan-2  C12  0.020
 1VL  plan-2  H3   0.020
 1VL  plan-2  H4   0.020
 1VL  plan-2  H5   0.020
 1VL  plan-2  H6   0.020

