# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 03:44:52 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 5-[(6-chloro-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)Cc3ccc(Cl)cc23)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
 CD9  CD9  '5-[(6-chloro-2-oxo-2,3-dihydro-1H-indol-1-yl)methyl]-1,3-benzodioxole-4-carboxylic acid'  ligand  36  24  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CD9
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
 CD9  C1    C   CR16  0  -0.228   4.4514   0.8025   0.6425
 CD9  C2    C   CR6   0  -0.049   3.3785   1.3948  -0.0032
 CD9  C3    C   CR16  0  -0.269   2.2300   0.6890  -0.3497
 CD9  C4    C   CR56  0   0.432   2.2094  -0.6532  -0.0235
 CD9  C5    C   CR56  0   0.019   3.2703  -1.2795   0.6291
 CD9  C6    C   CR16  0  -0.333   4.3919  -0.5541   0.9623
 CD9  C7    C   CH2   0  -0.612   2.9080  -2.7128   0.8361
 CD9  C8    C   CR5   0   0.521   1.5248  -2.8148   0.2210
 CD9  O9    O   O     0  -0.449   0.8205  -3.7972   0.1477
 CD9  N10   N   NR5   0  -0.601   1.1916  -1.5718  -0.2561
 CD9  C11   C   CH2   0  -0.357  -0.0276  -1.2701  -0.9620
 CD9  C12   C   CR6   0   0.053  -1.0661  -0.5699  -0.1031
 CD9  C13   C   CR16  0  -0.314  -0.8231  -0.4054   1.2474
 CD9  C14   C   CR16  0  -0.318  -1.7225   0.2312   2.1116
 CD9  C15   C   CR56  0   0.308  -2.8782   0.7036   1.5620
 CD9  C16   C   CR56  0   0.340  -3.1566   0.5567   0.2079
 CD9  C17   C   CR6   0  -0.217  -2.2836  -0.0803  -0.6622
 CD9  C18   C   C     0   0.546  -2.6162  -0.2562  -2.0940
 CD9  O19   O   OH1   0  -0.588  -3.7543   0.3266  -2.4395
 CD9  O20   O   O     0  -0.437  -1.9372  -0.8678  -2.8854
 CD9  O21   O   O     0  -0.461  -4.3634   1.0937  -0.0443
 CD9  C22   C   CH2   0   0.069  -4.7991   1.7320   1.1509
 CD9  O23   O   O     0  -0.480  -3.9066   1.3295   2.1753
 CD9  CL24  CL  CL    0  -0.126   3.4567   3.0824  -0.3945
 CD9  H1    H   HCR6  0   0.279   5.3248   1.3850   0.8997
 CD9  H3    H   HCR6  0   0.289   1.4010   1.1793  -0.8414
 CD9  H6    H   HCR6  0   0.268   5.2265  -1.0228   1.4672
 CD9  H17   H   HCH2  0   0.309   3.5890  -3.4096   0.3417
 CD9  H27   H   HCH2  0   0.308   2.8666  -2.9987   1.8900
 CD9  H111  H   HCH2  0   0.277   0.2336  -0.6627  -1.8287
 CD9  H211  H   HCH2  0   0.293  -0.4217  -2.2073  -1.3520
 CD9  H13   H   HCR6  0   0.260   0.0938  -0.7769   1.6799
 CD9  H14   H   HCR6  0   0.285  -1.5036   0.3361   3.1652
 CD9  H122  H   HCH2  0   0.242  -4.7602   2.8177   1.0210
 CD9  H222  H   HCH2  0   0.251  -5.8126   1.4094   1.3885
 CD9  HO19  H   HOH1  0   0.487  -3.9181   0.1739  -3.3825

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
 CD9  O23   C22   single    1.417  0.020  1.417
 CD9  O23   C15   single    1.351  0.020  1.351
 CD9  C22   O21   single    1.423  0.020  1.423
 CD9  C15   C14   aromatic  1.364  0.020  1.364
 CD9  C15   C16   aromatic  1.390  0.020  1.390
 CD9  O21   C16   single    1.345  0.020  1.345
 CD9  C14   C13   aromatic  1.400  0.020  1.400
 CD9  C16   C17   aromatic  1.387  0.020  1.387
 CD9  C13   C12   aromatic  1.382  0.020  1.382
 CD9  C17   C12   aromatic  1.426  0.020  1.426
 CD9  C17   C18   single    1.480  0.020  1.480
 CD9  O19   C18   single    1.324  0.020  1.324
 CD9  C12   C11   single    1.519  0.020  1.519
 CD9  C18   O20   double    1.209  0.020  1.209
 CD9  C11   N10   single    1.441  0.020  1.441
 CD9  O9    C8    double    1.211  0.020  1.211
 CD9  N10   C8    single    1.372  0.020  1.372
 CD9  N10   C4    single    1.391  0.020  1.391
 CD9  C8    C7    single    1.517  0.020  1.517
 CD9  C3    C4    aromatic  1.381  0.020  1.381
 CD9  C3    C2    aromatic  1.392  0.020  1.392
 CD9  C4    C5    aromatic  1.394  0.020  1.394
 CD9  CL24  C2    single    1.734  0.020  1.734
 CD9  C2    C1    aromatic  1.385  0.020  1.385
 CD9  C7    C5    single    1.493  0.020  1.493
 CD9  C5    C6    aromatic  1.377  0.020  1.377
 CD9  C1    C6    aromatic  1.395  0.020  1.395
 CD9  C1    H1    single    0.930  0.020  1.080
 CD9  C3    H3    single    0.930  0.020  1.080
 CD9  C6    H6    single    0.930  0.020  1.080
 CD9  C7    H17   single    0.970  0.020  1.090
 CD9  C7    H27   single    0.970  0.020  1.090
 CD9  C11   H111  single    0.970  0.020  1.090
 CD9  C11   H211  single    0.970  0.020  1.090
 CD9  C13   H13   single    0.930  0.020  1.080
 CD9  C14   H14   single    0.930  0.020  1.080
 CD9  C22   H122  single    0.970  0.020  1.090
 CD9  C22   H222  single    0.970  0.020  1.090
 CD9  O19   HO19  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
 CD9  H1    C1   C6    120.26  3.000
 CD9  H1    C1   C2    120.42  3.000
 CD9  C6    C1   C2    119.32  3.000
 CD9  CL24  C2   C3    118.32  3.000
 CD9  CL24  C2   C1    119.10  3.000
 CD9  C3    C2   C1    122.57  3.000
 CD9  H3    C3   C4    122.44  3.000
 CD9  H3    C3   C2    121.06  3.000
 CD9  C4    C3   C2    116.50  3.000
 CD9  N10   C4   C5    109.79  3.000
 CD9  C5    C4   C3    122.39  3.000
 CD9  N10   C4   C3    127.82  3.000
 CD9  C7    C5   C6    132.07  3.000
 CD9  C6    C5   C4    119.77  3.000
 CD9  C7    C5   C4    108.15  3.000
 CD9  H6    C6   C5    120.87  3.000
 CD9  H6    C6   C1    119.69  3.000
 CD9  C5    C6   C1    119.45  3.000
 CD9  H27   C7   H17   107.04  3.000
 CD9  H27   C7   C8    109.81  3.000
 CD9  H17   C7   C8    110.00  3.000
 CD9  H27   C7   C5    113.21  3.000
 CD9  H17   C7   C5    113.47  3.000
 CD9  C8    C7   C5    103.27  3.000
 CD9  N10   C8   O9    124.92  3.000
 CD9  N10   C8   C7    107.54  3.000
 CD9  O9    C8   C7    127.54  3.000
 CD9  C11   N10  C8    124.43  3.000
 CD9  C8    N10  C4    111.25  3.000
 CD9  C11   N10  C4    124.26  3.000
 CD9  H211  C11  H111  106.36  3.000
 CD9  H211  C11  C12   110.60  3.000
 CD9  H111  C11  C12   110.89  3.000
 CD9  H211  C11  N10   107.55  3.000
 CD9  H111  C11  N10   107.66  3.000
 CD9  C12   C11  N10   113.46  3.000
 CD9  C17   C12  C13   119.49  3.000
 CD9  C17   C12  C11   121.35  3.000
 CD9  C13   C12  C11   119.17  3.000
 CD9  H13   C13  C14   117.05  3.000
 CD9  H13   C13  C12   119.98  3.000
 CD9  C14   C13  C12   122.97  3.000
 CD9  H14   C14  C15   122.04  3.000
 CD9  H14   C14  C13   121.03  3.000
 CD9  C15   C14  C13   116.94  3.000
 CD9  O23   C15  C16   109.80  3.000
 CD9  C16   C15  C14   121.70  3.000
 CD9  O23   C15  C14   128.49  3.000
 CD9  O21   C16  C17   129.08  3.000
 CD9  C17   C16  C15   122.23  3.000
 CD9  O21   C16  C15   108.67  3.000
 CD9  C18   C17  C16   121.31  3.000
 CD9  C18   C17  C12   122.01  3.000
 CD9  C16   C17  C12   116.67  3.000
 CD9  O20   C18  O19   122.30  3.000
 CD9  O20   C18  C17   124.55  3.000
 CD9  O19   C18  C17   113.15  3.000
 CD9  HO19  O19  C18   109.26  3.000
 CD9  C22   O21  C16   107.24  3.000
 CD9  H222  C22  H122  110.65  3.000
 CD9  H222  C22  O23   110.12  3.000
 CD9  H122  C22  O23   110.20  3.000
 CD9  H222  C22  O21   109.57  3.000
 CD9  H122  C22  O21   109.54  3.000
 CD9  O23   C22  O21   106.67  3.000
 CD9  C22   O23  C15   106.43  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
 CD9  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 CD9  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 CD9  CONST_03  C5    C4   C3   C2      0.00   0.0  0
 CD9  CONST_04  C5    C6   C1   C2      0.00   0.0  0
 CD9  CONST_05  C6    C5   C4   C3      0.00   0.0  0
 CD9  CONST_06  C6    C1   C2   C3      0.00   0.0  0
 CD9  CONST_07  C15   C14  C13  C12     0.00   0.0  0
 CD9  CONST_08  C15   C16  C17  C12     0.00   0.0  0
 CD9  CONST_09  C16   C15  C14  C13     0.00   0.0  0
 CD9  CONST_10  C16   C17  C12  C13     0.00   0.0  0
 CD9  CONST_11  C17   C16  C15  C14     0.00   0.0  0
 CD9  CONST_12  C17   C12  C13  C14     0.00   0.0  0
 CD9  CONST_13  C7    C8   N10  C4      0.00   0.0  0
 CD9  CONST_14  CL24  C2   C3   C4    180.00   0.0  0
 CD9  CONST_15  CL24  C2   C1   C6    180.00   0.0  0
 CD9  CONST_16  C14   C13  C12  C11   180.00   0.0  0
 CD9  CONST_17  C16   C17  C12  C11   180.00   0.0  0
 CD9  CONST_18  C18   C17  C12  C13   180.00   0.0  0
 CD9  CONST_19  C18   C17  C16  C15   180.00   0.0  0
 CD9  CONST_20  O21   C16  C17  C18     0.00   0.0  0
 CD9  CONST_21  O9    C8   N10  C4    180.00   0.0  0
 CD9  CONST_22  C11   N10  C8   C7    180.00   0.0  0
 CD9  CONST_23  H3    C3   C2   C1    180.00   0.0  0
 CD9  CONST_24  H6    C6   C1   C2    180.00   0.0  0
 CD9  CONST_25  H1    C1   C2   C3    180.00   0.0  0
 CD9  CONST_26  H14   C14  C13  C12   180.00   0.0  0
 CD9  CONST_27  H13   C13  C14  C15   180.00   0.0  0
 CD9  CONST_28  C11   N10  C8   O9      0.00   0.0  0
 CD9  CONST_29  HO19  O19  C18  C17   180.00   0.0  0
 CD9  Var_01    O21   C22  O23  C15    10.63  30.0  1
 CD9  Var_02    O23   C22  O21  C16   -10.63  30.0  1
 CD9  Var_03    C12   C11  N10  C4    -80.68  30.0  2
 CD9  Var_04    C13   C12  C11  N10    -6.01  30.0  3
 CD9  Var_05    H17   C7   C5   C4    119.18  30.0  1
 CD9  Var_06    O19   C18  C17  C12  -176.63  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
 CD9  plan-1  C11   0.020
 CD9  plan-1  C12   0.020
 CD9  plan-1  C13   0.020
 CD9  plan-1  C14   0.020
 CD9  plan-1  C15   0.020
 CD9  plan-1  C16   0.020
 CD9  plan-1  C17   0.020
 CD9  plan-1  C18   0.020
 CD9  plan-1  O21   0.020
 CD9  plan-1  O23   0.020
 CD9  plan-1  H13   0.020
 CD9  plan-1  H14   0.020
 CD9  plan-2  C1    0.020
 CD9  plan-2  C2    0.020
 CD9  plan-2  C3    0.020
 CD9  plan-2  C4    0.020
 CD9  plan-2  C5    0.020
 CD9  plan-2  C6    0.020
 CD9  plan-2  C7    0.020
 CD9  plan-2  C8    0.020
 CD9  plan-2  O9    0.020
 CD9  plan-2  N10   0.020
 CD9  plan-2  C11   0.020
 CD9  plan-2  CL24  0.020
 CD9  plan-2  H1    0.020
 CD9  plan-2  H3    0.020
 CD9  plan-2  H6    0.020
 CD9  plan-3  C17   0.020
 CD9  plan-3  C18   0.020
 CD9  plan-3  O19   0.020
 CD9  plan-3  O20   0.020
 CD9  plan-3  HO19  0.020

