# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 21:17:51 2021
#   Inital geometry file: a 99 line input string
#   Ligand name: 5-[(E)-(2-oxo-2,3-dihydro-1H-inden-1-ylidene)methyl]-1,3-benzodioxole-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1c2OCOc2ccc1\C=C/3C(=O)Cc4ccccc/34
#
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
 ZT2  ZT2  '5-[(E)-(2-oxo-2,3-dihydro-1H-inden-1-ylidene)methyl]-1,3-benzodioxole-4-carboxylic acid'  ligand  35  23  .  2022-03-29  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ZT2
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
 ZT2  C1    C  CR16  0  -0.250   -7.8236  25.9881  11.5883
 ZT2  C2    C  CR16  0  -0.260   -8.9674  25.6157  10.8885
 ZT2  C3    C  CR16  0  -0.336   -6.8792  25.0420  11.9586
 ZT2  C4    C  CR16  0  -0.309   -3.6891  24.2231  12.0237
 ZT2  C5    C  CR16  0  -0.300   -9.1843  24.2828  10.5621
 ZT2  C6    C  CR16  0  -0.318   -2.7142  25.1845  12.3085
 ZT2  C7    C  CR6   0   0.124   -7.0837  23.7056  11.6233
 ZT2  C8    C  CR6   0   0.028   -4.1739  23.3511  12.9859
 ZT2  C9    C  CR6   0  -0.208   -3.6660  23.3996  14.3121
 ZT2  C10   C  CR6   0   0.031   -8.2464  23.3352  10.9344
 ZT2  C11   C  CR56  0   0.312   -2.2436  25.2262  13.5920
 ZT2  C12   C  CR56  0   0.340   -2.7001  24.3534  14.5748
 ZT2  C13   C  C     0  -0.003   -6.2890  22.5099  11.9174
 ZT2  C14   C  C     0   0.344   -7.0533  21.3429  11.3905
 ZT2  C15   C  C1    0  -0.288   -5.1250  22.3180  12.5558
 ZT2  C16   C  C     0   0.525   -4.2064  22.4971  15.3500
 ZT2  C17   C  CH2   0  -0.613   -8.3079  21.8560  10.7141
 ZT2  C18   C  CH2   0   0.068   -1.2744  25.7864  15.5096
 ZT2  O19   O  OH1   0  -0.585   -3.4884  22.4924  16.4615
 ZT2  O20   O  O     0  -0.394   -6.7258  20.1823  11.4771
 ZT2  O21   O  O     0  -0.428   -5.2027  21.8306  15.2016
 ZT2  O22   O  O     0  -0.476   -1.3113  26.0483  14.1152
 ZT2  O23   O  O     0  -0.461   -2.0651  24.6224  15.7277
 ZT2  H1    H  HCR6  0   0.259   -7.6662  27.0270  11.8475
 ZT2  H2    H  HCR6  0   0.259   -9.6929  26.3664  10.6028
 ZT2  H3    H  HCR6  0   0.254   -5.9995  25.3544  12.5026
 ZT2  H5    H  HCR6  0   0.256  -10.0797  23.9892  10.0281
 ZT2  H6    H  HCR6  0   0.289   -2.3493  25.8551  11.5429
 ZT2  H15   H  H     0   0.279   -4.8182  21.2871  12.7046
 ZT2  H171  H  HCH2  0   0.296   -9.1959  21.3953  11.1552
 ZT2  H172  H  HCH2  0   0.298   -8.3023  21.5799   9.6556
 ZT2  H19   H  HOH1  0   0.489   -3.8935  21.8940  17.1073
 ZT2  H181  H  HCH2  0   0.253   -0.2493  25.5960  15.8267
 ZT2  H182  H  HCH2  0   0.246   -1.7002  26.6294  16.0612
 ZT2  H4    H  HCR6  0   0.278   -4.0657  24.1530  11.0124

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
 ZT2  C1   C2    aromatic  1.392  0.020  1.392
 ZT2  C1   C3    aromatic  1.387  0.020  1.387
 ZT2  C2   C5    aromatic  1.389  0.020  1.389
 ZT2  C3   C7    aromatic  1.393  0.020  1.393
 ZT2  C4   C6    aromatic  1.399  0.020  1.399
 ZT2  C4   C8    aromatic  1.386  0.020  1.386
 ZT2  C5   C10   aromatic  1.384  0.020  1.384
 ZT2  C6   C11   aromatic  1.368  0.020  1.368
 ZT2  C7   C10   aromatic  1.401  0.020  1.401
 ZT2  C7   C13   single    1.466  0.020  1.466
 ZT2  C8   C9    aromatic  1.421  0.020  1.421
 ZT2  C8   C15   single    1.469  0.020  1.469
 ZT2  C9   C12   aromatic  1.383  0.020  1.383
 ZT2  C9   C16   single    1.478  0.020  1.478
 ZT2  C10  C17   single    1.497  0.020  1.497
 ZT2  C11  C12   aromatic  1.391  0.020  1.391
 ZT2  C11  O22   single    1.349  0.020  1.349
 ZT2  C12  O23   single    1.343  0.020  1.343
 ZT2  C13  C14   single    1.491  0.020  1.491
 ZT2  C13  C15   double    1.341  0.020  1.341
 ZT2  C14  C17   single    1.515  0.020  1.515
 ZT2  C14  O20   double    1.209  0.020  1.209
 ZT2  C16  O19   single    1.323  0.020  1.323
 ZT2  C16  O21   double    1.208  0.020  1.208
 ZT2  C18  O22   single    1.419  0.020  1.419
 ZT2  C18  O23   single    1.424  0.020  1.424
 ZT2  C1   H1    single    0.930  0.020  1.080
 ZT2  C2   H2    single    0.930  0.020  1.080
 ZT2  C3   H3    single    0.930  0.020  1.080
 ZT2  C5   H5    single    0.930  0.020  1.080
 ZT2  C4   H4    single    0.930  0.020  1.080
 ZT2  C6   H6    single    0.930  0.020  1.080
 ZT2  C15  H15   single    0.930  0.020  1.080
 ZT2  C17  H171  single    0.970  0.020  1.090
 ZT2  C17  H172  single    0.970  0.020  1.090
 ZT2  O19  H19   single    0.850  0.020  0.980
 ZT2  C18  H181  single    0.970  0.020  1.090
 ZT2  C18  H182  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
 ZT2  H1    C1   C3    119.46  3.000
 ZT2  H1    C1   C2    119.79  3.000
 ZT2  C3    C1   C2    120.75  3.000
 ZT2  H2    C2   C5    119.92  3.000
 ZT2  H2    C2   C1    119.87  3.000
 ZT2  C5    C2   C1    120.21  3.000
 ZT2  H3    C3   C7    121.21  3.000
 ZT2  H3    C3   C1    119.44  3.000
 ZT2  C7    C3   C1    119.35  3.000
 ZT2  H4    C4   C8    119.12  3.000
 ZT2  H4    C4   C6    118.54  3.000
 ZT2  C8    C4   C6    122.34  3.000
 ZT2  H5    C5   C10   120.47  3.000
 ZT2  H5    C5   C2    120.34  3.000
 ZT2  C10   C5   C2    119.19  3.000
 ZT2  H6    C6   C11   121.98  3.000
 ZT2  H6    C6   C4    121.16  3.000
 ZT2  C11   C6   C4    116.86  3.000
 ZT2  C13   C7   C10   109.45  3.000
 ZT2  C13   C7   C3    130.91  3.000
 ZT2  C10   C7   C3    119.59  3.000
 ZT2  C15   C8   C9    121.93  3.000
 ZT2  C15   C8   C4    117.76  3.000
 ZT2  C9    C8   C4    120.09  3.000
 ZT2  C16   C9   C12   122.91  3.000
 ZT2  C16   C9   C8    120.26  3.000
 ZT2  C12   C9   C8    116.78  3.000
 ZT2  C17   C10  C7    111.57  3.000
 ZT2  C17   C10  C5    127.52  3.000
 ZT2  C7    C10  C5    120.90  3.000
 ZT2  O22   C11  C12   109.59  3.000
 ZT2  O22   C11  C6    128.35  3.000
 ZT2  C12   C11  C6    122.07  3.000
 ZT2  O23   C12  C11   108.99  3.000
 ZT2  O23   C12  C9    129.16  3.000
 ZT2  C11   C12  C9    121.85  3.000
 ZT2  C15   C13  C14   120.06  3.000
 ZT2  C15   C13  C7    133.06  3.000
 ZT2  C14   C13  C7    106.84  3.000
 ZT2  O20   C14  C17   125.56  3.000
 ZT2  O20   C14  C13   125.95  3.000
 ZT2  C17   C14  C13   108.49  3.000
 ZT2  H15   C15  C13   116.50  3.000
 ZT2  H15   C15  C8    116.41  3.000
 ZT2  C13   C15  C8    126.92  3.000
 ZT2  O21   C16  O19   123.29  3.000
 ZT2  O21   C16  C9    123.53  3.000
 ZT2  O19   C16  C9    113.19  3.000
 ZT2  H172  C17  H171  106.74  3.000
 ZT2  H172  C17  C14   110.02  3.000
 ZT2  H171  C17  C14   110.48  3.000
 ZT2  H172  C17  C10   113.05  3.000
 ZT2  H171  C17  C10   112.98  3.000
 ZT2  C14   C17  C10   103.59  3.000
 ZT2  H182  C18  H181  110.74  3.000
 ZT2  H182  C18  O23   109.67  3.000
 ZT2  H181  C18  O23   109.57  3.000
 ZT2  H182  C18  O22   110.07  3.000
 ZT2  H181  C18  O22   110.03  3.000
 ZT2  O23   C18  O22   106.67  3.000
 ZT2  H19   O19  C16   109.58  3.000
 ZT2  C18   O22  C11   106.65  3.000
 ZT2  C18   O23  C12   107.14  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
 ZT2  CONST_01  C10  C5   C2   C1      0.00   0.0  0
 ZT2  CONST_02  C10  C7   C3   C1      0.00   0.0  0
 ZT2  CONST_03  C7   C3   C1   C2      0.00   0.0  0
 ZT2  CONST_04  C7   C10  C5   C2      0.00   0.0  0
 ZT2  CONST_05  C5   C2   C1   C3      0.00   0.0  0
 ZT2  CONST_06  C5   C10  C7   C3      0.00   0.0  0
 ZT2  CONST_07  C12  C11  C6   C4      0.00   0.0  0
 ZT2  CONST_08  C12  C9   C8   C4      0.00   0.0  0
 ZT2  CONST_09  C9   C8   C4   C6      0.00   0.0  0
 ZT2  CONST_10  C9   C12  C11  C6      0.00   0.0  0
 ZT2  CONST_11  C11  C6   C4   C8      0.00   0.0  0
 ZT2  CONST_12  C11  C12  C9   C8      0.00   0.0  0
 ZT2  CONST_13  C16  C9   C8   C4    180.00   0.0  0
 ZT2  CONST_14  C15  C8   C4   C6    180.00   0.0  0
 ZT2  CONST_15  C16  C9   C12  C11   180.00   0.0  0
 ZT2  CONST_16  C15  C8   C9   C12   180.00   0.0  0
 ZT2  CONST_17  O23  C12  C9   C16     0.00   0.0  0
 ZT2  CONST_18  H5   C5   C2   C1    180.00   0.0  0
 ZT2  CONST_19  H3   C3   C1   C2    180.00   0.0  0
 ZT2  CONST_20  H2   C2   C1   C3    180.00   0.0  0
 ZT2  CONST_21  H1   C1   C2   C5    180.00   0.0  0
 ZT2  CONST_22  H6   C6   C4   C8    180.00   0.0  0
 ZT2  CONST_23  H4   C4   C8   C9    180.00   0.0  0
 ZT2  CONST_24  H19  O19  C16  C9    180.00   0.0  0
 ZT2  Var_01    C14  C13  C7   C3    175.86  30.0  1
 ZT2  Var_02    C14  C17  C10  C5   -177.17  30.0  1
 ZT2  Var_03    C17  C14  C13  C7      2.36  30.0  1
 ZT2  Var_04    C13  C14  C17  C10    -2.40  30.0  1
 ZT2  Var_05    O23  C18  O22  C11     9.57  30.0  1
 ZT2  Var_06    O22  C18  O23  C12    -9.43  30.0  1
 ZT2  Var_07    C8   C15  C13  C7    -10.59   0.0  2
 ZT2  Var_08    C13  C15  C8   C4    -55.90  30.0  2
 ZT2  Var_09    O19  C16  C9   C8    169.00  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
 ZT2  plan-1  C1   0.020
 ZT2  plan-1  C2   0.020
 ZT2  plan-1  C3   0.020
 ZT2  plan-1  C5   0.020
 ZT2  plan-1  C7   0.020
 ZT2  plan-1  C10  0.020
 ZT2  plan-1  C13  0.020
 ZT2  plan-1  C17  0.020
 ZT2  plan-1  H1   0.020
 ZT2  plan-1  H2   0.020
 ZT2  plan-1  H3   0.020
 ZT2  plan-1  H5   0.020
 ZT2  plan-2  C4   0.020
 ZT2  plan-2  C6   0.020
 ZT2  plan-2  C8   0.020
 ZT2  plan-2  C9   0.020
 ZT2  plan-2  C11  0.020
 ZT2  plan-2  C12  0.020
 ZT2  plan-2  C15  0.020
 ZT2  plan-2  C16  0.020
 ZT2  plan-2  O22  0.020
 ZT2  plan-2  O23  0.020
 ZT2  plan-2  H6   0.020
 ZT2  plan-2  H4   0.020
 ZT2  plan-3  C13  0.020
 ZT2  plan-3  C14  0.020
 ZT2  plan-3  C17  0.020
 ZT2  plan-3  O20  0.020
 ZT2  plan-4  C9   0.020
 ZT2  plan-4  C16  0.020
 ZT2  plan-4  O19  0.020
 ZT2  plan-4  O21  0.020
 ZT2  plan-4  H19  0.020
 ZT2  plan-5  C7   0.020
 ZT2  plan-5  C8   0.020
 ZT2  plan-5  C13  0.020
 ZT2  plan-5  C14  0.020
 ZT2  plan-5  C15  0.020
 ZT2  plan-5  H15  0.020

