# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 18:05:23 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 5-[(2-oxo-2,3-dihydro-1H-indol-1-yl)methyl]-1,3-benzodioxole-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1c(CN2C(=O)Cc3ccccc23)ccc4OCOc14
#
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
 IMV  IMV  '5-[(2-oxo-2,3-dihydro-1H-indol-1-yl)methyl]-1,3-benzodioxole-4-carboxylic acid'  ligand  36  23  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IMV
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
 IMV  O1    O  OH1   0  -0.589  -1.5839   2.7006   1.0511
 IMV  C2    C  C     0   0.509  -2.4415   1.9774   0.3467
 IMV  O3    O  O     0  -0.425  -3.5124   2.3941  -0.0191
 IMV  C4    C  CR6   0  -0.193  -1.9704   0.5965   0.0808
 IMV  C5    C  CR6   0   0.075  -0.6176   0.2054  -0.1135
 IMV  C6    C  CH2   0  -0.362   0.5046   1.2293  -0.0807
 IMV  N7    N  NR5   0  -0.596   1.7784   0.7034  -0.4916
 IMV  C8    C  CR5   0   0.520   2.2326   0.7334  -1.7830
 IMV  O9    O  O     0  -0.455   1.6177   1.1910  -2.7223
 IMV  C10   C  CH2   0  -0.611   3.6122   0.1028  -1.7973
 IMV  C11   C  CR56  0   0.007   3.8352  -0.2685  -0.3675
 IMV  C12   C  CR16  0  -0.326   4.8944  -0.8802   0.2682
 IMV  C13   C  CR16  0  -0.265   4.8170  -1.1092   1.6426
 IMV  C14   C  CR16  0  -0.264   3.6870  -0.7302   2.3541
 IMV  C15   C  CR16  0  -0.317   2.6075  -0.1149   1.7223
 IMV  C16   C  CR56  0   0.425   2.7089   0.1098   0.3623
 IMV  C17   C  CR16  0  -0.318  -0.3289  -1.1218  -0.3757
 IMV  C18   C  CR16  0  -0.322  -1.3139  -2.1162  -0.4469
 IMV  C19   C  CR56  0   0.302  -2.6078  -1.7207  -0.2617
 IMV  O20   O  O     0  -0.481  -3.7387  -2.4617  -0.2964
 IMV  C21   C  CH2   0   0.067  -4.7869  -1.6042   0.1265
 IMV  O22   O  O     0  -0.465  -4.2657  -0.2792   0.1054
 IMV  C23   C  CR56  0   0.332  -2.9307  -0.3922  -0.0219
 IMV  H6    H  HCH2  0   0.285   0.2683   2.0701  -0.7334
 IMV  H6A   H  HCH2  0   0.286   0.6225   1.6396   0.9218
 IMV  H10   H  HCH2  0   0.305   3.6191  -0.7562  -2.4729
 IMV  H10A  H  HCH2  0   0.305   4.3442   0.8167  -2.1828
 IMV  H12   H  HCR6  0   0.257   5.7730  -1.1816  -0.2884
 IMV  H13   H  HCR6  0   0.255   5.6414  -1.5869   2.1546
 IMV  H14   H  HCR6  0   0.260   3.6361  -0.9163   3.4189
 IMV  H15   H  HCR6  0   0.269   1.7292   0.1688   2.2877
 IMV  H17   H  HCR6  0   0.261   0.6937  -1.4272  -0.5434
 IMV  H18   H  HCR6  0   0.284  -1.0510  -3.1457  -0.6468
 IMV  H21   H  HCH2  0   0.252  -5.6285  -1.6764  -0.5614
 IMV  H21A  H  HCH2  0   0.241  -5.0956  -1.8613   1.1445
 IMV  H1    H  HOH1  0   0.490  -1.9280   3.5994   1.1689

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
 IMV  O1   C2    single    1.325  0.020  1.325
 IMV  C2   O3    double    1.206  0.020  1.206
 IMV  C2   C4    single    1.483  0.020  1.483
 IMV  C4   C5    aromatic  1.422  0.020  1.422
 IMV  C4   C23   aromatic  1.382  0.020  1.382
 IMV  C5   C6    single    1.520  0.020  1.520
 IMV  C5   C17   aromatic  1.383  0.020  1.383
 IMV  C6   N7    single    1.438  0.020  1.438
 IMV  N7   C8    single    1.369  0.020  1.369
 IMV  N7   C16   single    1.396  0.020  1.396
 IMV  C8   O9    double    1.212  0.020  1.212
 IMV  C8   C10   single    1.517  0.020  1.517
 IMV  C10  C11   single    1.494  0.020  1.494
 IMV  C11  C12   aromatic  1.379  0.020  1.379
 IMV  C11  C16   aromatic  1.394  0.020  1.394
 IMV  C12  C13   aromatic  1.395  0.020  1.395
 IMV  C13  C14   aromatic  1.388  0.020  1.388
 IMV  C14  C15   aromatic  1.394  0.020  1.394
 IMV  C15  C16   aromatic  1.382  0.020  1.382
 IMV  C17  C18   aromatic  1.401  0.020  1.401
 IMV  C18  C19   aromatic  1.366  0.020  1.366
 IMV  C19  O20   single    1.353  0.020  1.353
 IMV  C19  C23   aromatic  1.388  0.020  1.388
 IMV  O20  C21   single    1.419  0.020  1.419
 IMV  C21  O22   single    1.424  0.020  1.424
 IMV  O22  C23   single    1.346  0.020  1.346
 IMV  C6   H6    single    0.970  0.020  1.090
 IMV  C6   H6A   single    0.970  0.020  1.090
 IMV  C10  H10   single    0.970  0.020  1.090
 IMV  C10  H10A  single    0.970  0.020  1.090
 IMV  C12  H12   single    0.930  0.020  1.080
 IMV  C13  H13   single    0.930  0.020  1.080
 IMV  C14  H14   single    0.930  0.020  1.080
 IMV  C15  H15   single    0.930  0.020  1.080
 IMV  C17  H17   single    0.930  0.020  1.080
 IMV  C18  H18   single    0.930  0.020  1.080
 IMV  C21  H21   single    0.970  0.020  1.090
 IMV  C21  H21A  single    0.970  0.020  1.090
 IMV  O1   H1    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
 IMV  H1    O1   C2   109.93  3.000
 IMV  C4    C2   O3   123.33  3.000
 IMV  C4    C2   O1   113.45  3.000
 IMV  O3    C2   O1   123.20  3.000
 IMV  C23   C4   C5   117.01  3.000
 IMV  C23   C4   C2   117.30  3.000
 IMV  C5    C4   C2   125.66  3.000
 IMV  C17   C5   C6   119.77  3.000
 IMV  C17   C5   C4   119.24  3.000
 IMV  C6    C5   C4   120.96  3.000
 IMV  H6A   C6   H6   106.49  3.000
 IMV  H6A   C6   N7   107.74  3.000
 IMV  H6    C6   N7   107.64  3.000
 IMV  H6A   C6   C5   110.70  3.000
 IMV  H6    C6   C5   110.28  3.000
 IMV  N7    C6   C5   113.68  3.000
 IMV  C16   N7   C8   111.42  3.000
 IMV  C16   N7   C6   124.84  3.000
 IMV  C8    N7   C6   123.73  3.000
 IMV  C10   C8   O9   127.65  3.000
 IMV  C10   C8   N7   107.54  3.000
 IMV  O9    C8   N7   124.80  3.000
 IMV  H10A  C10  H10  106.93  3.000
 IMV  H10A  C10  C11  113.58  3.000
 IMV  H10   C10  C11  113.29  3.000
 IMV  H10A  C10  C8   109.94  3.000
 IMV  H10   C10  C8   109.77  3.000
 IMV  C11   C10  C8   103.30  3.000
 IMV  C16   C11  C12  119.98  3.000
 IMV  C16   C11  C10  108.24  3.000
 IMV  C12   C11  C10  131.78  3.000
 IMV  H12   C12  C13  120.37  3.000
 IMV  H12   C12  C11  120.66  3.000
 IMV  C13   C12  C11  118.96  3.000
 IMV  H13   C13  C14  119.89  3.000
 IMV  H13   C13  C12  119.76  3.000
 IMV  C14   C13  C12  120.35  3.000
 IMV  H14   C14  C15  119.04  3.000
 IMV  H14   C14  C13  119.72  3.000
 IMV  C15   C14  C13  121.24  3.000
 IMV  H15   C15  C16  122.07  3.000
 IMV  H15   C15  C14  120.49  3.000
 IMV  C16   C15  C14  117.44  3.000
 IMV  C15   C16  C11  122.02  3.000
 IMV  C15   C16  N7   128.49  3.000
 IMV  C11   C16  N7   109.50  3.000
 IMV  H17   C17  C18  117.18  3.000
 IMV  H17   C17  C5   119.88  3.000
 IMV  C18   C17  C5   122.94  3.000
 IMV  H18   C18  C19  122.09  3.000
 IMV  H18   C18  C17  120.94  3.000
 IMV  C19   C18  C17  116.97  3.000
 IMV  C23   C19  O20  109.53  3.000
 IMV  C23   C19  C18  121.41  3.000
 IMV  O20   C19  C18  129.06  3.000
 IMV  C21   O20  C19  106.20  3.000
 IMV  H21A  C21  H21  110.73  3.000
 IMV  H21A  C21  O22  109.61  3.000
 IMV  H21   C21  O22  109.58  3.000
 IMV  H21A  C21  O20  110.10  3.000
 IMV  H21   C21  O20  110.03  3.000
 IMV  O22   C21  O20  106.71  3.000
 IMV  C23   O22  C21  106.64  3.000
 IMV  O22   C23  C19  109.12  3.000
 IMV  O22   C23  C4   128.47  3.000
 IMV  C19   C23  C4   122.40  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
 IMV  CONST_01  C18  C17  C5   C4      0.00   0.0  0
 IMV  CONST_02  C18  C19  C23  C4      0.00   0.0  0
 IMV  CONST_03  C19  C23  C4   C5      0.00   0.0  0
 IMV  CONST_04  C19  C18  C17  C5      0.00   0.0  0
 IMV  CONST_05  C14  C13  C12  C11     0.00   0.0  0
 IMV  CONST_06  C14  C15  C16  C11     0.00   0.0  0
 IMV  CONST_07  C15  C16  C11  C12     0.00   0.0  0
 IMV  CONST_08  C15  C14  C13  C12     0.00   0.0  0
 IMV  CONST_09  C16  C11  C12  C13     0.00   0.0  0
 IMV  CONST_10  C16  C15  C14  C13     0.00   0.0  0
 IMV  CONST_11  C23  C4   C5   C17     0.00   0.0  0
 IMV  CONST_12  C23  C19  C18  C17     0.00   0.0  0
 IMV  CONST_13  C16  N7   C8   C10     0.00   0.0  0
 IMV  CONST_14  C17  C5   C4   C2    180.00   0.0  0
 IMV  CONST_15  C19  C23  C4   C2    180.00   0.0  0
 IMV  CONST_16  O22  C23  C4   C2      0.00   0.0  0
 IMV  CONST_17  C23  C4   C5   C6    180.00   0.0  0
 IMV  CONST_18  C18  C17  C5   C6    180.00   0.0  0
 IMV  CONST_19  C10  C8   N7   C6    180.00   0.0  0
 IMV  CONST_20  C16  N7   C8   O9    180.00   0.0  0
 IMV  CONST_21  H17  C17  C5   C4    180.00   0.0  0
 IMV  CONST_22  H18  C18  C17  C5    180.00   0.0  0
 IMV  CONST_23  H15  C15  C16  N7      0.00   0.0  0
 IMV  CONST_24  H12  C12  C11  C10     0.00   0.0  0
 IMV  CONST_25  H13  C13  C12  C11   180.00   0.0  0
 IMV  CONST_26  H14  C14  C13  C12   180.00   0.0  0
 IMV  CONST_27  O9   C8   N7   C6      0.00   0.0  0
 IMV  CONST_28  H1   O1   C2   C4    180.00   0.0  0
 IMV  Var_01    O22  C21  O20  C19    13.13  30.0  1
 IMV  Var_02    C23  C19  O20  C21    -8.51  30.0  1
 IMV  Var_03    N7   C6   C5   C4   -171.17  30.0  2
 IMV  Var_04    C8   N7   C6   C5     91.23  30.0  3
 IMV  Var_05    H10  C10  C8   N7    121.28  30.0  1
 IMV  Var_06    C5   C4   C2   O1    -32.98  30.0  2

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
 IMV  plan-1  C2   0.020
 IMV  plan-1  C4   0.020
 IMV  plan-1  C5   0.020
 IMV  plan-1  C6   0.020
 IMV  plan-1  C17  0.020
 IMV  plan-1  C18  0.020
 IMV  plan-1  C19  0.020
 IMV  plan-1  O20  0.020
 IMV  plan-1  O22  0.020
 IMV  plan-1  C23  0.020
 IMV  plan-1  H17  0.020
 IMV  plan-1  H18  0.020
 IMV  plan-2  C6   0.020
 IMV  plan-2  N7   0.020
 IMV  plan-2  C8   0.020
 IMV  plan-2  O9   0.020
 IMV  plan-2  C10  0.020
 IMV  plan-2  C11  0.020
 IMV  plan-2  C12  0.020
 IMV  plan-2  C13  0.020
 IMV  plan-2  C14  0.020
 IMV  plan-2  C15  0.020
 IMV  plan-2  C16  0.020
 IMV  plan-2  H12  0.020
 IMV  plan-2  H13  0.020
 IMV  plan-2  H14  0.020
 IMV  plan-2  H15  0.020
 IMV  plan-3  O1   0.020
 IMV  plan-3  C2   0.020
 IMV  plan-3  O3   0.020
 IMV  plan-3  C4   0.020
 IMV  plan-3  H1   0.020

