# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 18:37:41 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 5-[(E)-(2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]-1,3-benzodioxole-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1c(ccc2OCOc12)\C=C3\C(=O)Nc4ccccc34
#
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
 RVN  RVN  '5-[(E)-(2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]-1,3-benzodioxole-4-carboxylic acid'  ligand  33  23  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RVN
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
 RVN  O1    O  O      0  -0.462   3.0635  -2.6473   1.0449
 RVN  C2    C  CR5    0   0.512   3.0157  -1.5117   0.6071
 RVN  C4    C  C1     0  -0.256   0.5891  -1.1147   0.6766
 RVN  C5    C  CR6    0   0.006  -0.6493  -0.3278   0.7071
 RVN  C6    C  CR16   0  -0.309  -0.6616   0.8264   1.4829
 RVN  C7    C  CR16   0  -0.338  -1.8131   1.6009   1.6406
 RVN  C8    C  CR6    0   0.298  -2.9389   1.1593   0.9956
 RVN  O9    O  O2     0  -0.483  -4.1705   1.7184   0.9894
 RVN  C10   C  CH2    0   0.065  -4.9180   1.0007   0.0181
 RVN  O11   O  O2     0  -0.469  -4.1947  -0.1858  -0.2621
 RVN  C12   C  CR6    0   0.295  -2.9469  -0.0046   0.2352
 RVN  C13   C  CR6    0  -0.229  -1.8231  -0.7849   0.0608
 RVN  C14   C  C      0   0.404  -1.8251  -2.0317  -0.8039
 RVN  O15   O  O      0  -0.578  -2.9325  -2.5162  -1.0914
 RVN  O16   O  OC    -1  -0.570  -0.7036  -2.4517  -1.1488
 RVN  C17   C  CR5    0   0.041   2.3126   0.6079  -0.1548
 RVN  C18   C  CR5    0   0.371   3.7078   0.4830  -0.2523
 RVN  N19   N  NR15   0  -0.772   4.0896  -0.7649   0.2143
 RVN  C20   C  C1     0  -0.305   4.5078   1.4870  -0.7628
 RVN  C21   C  C1     0  -0.271   3.8824   2.6512  -1.2011
 RVN  C22   C  C1     0  -0.261   2.5010   2.7902  -1.1322
 RVN  C23   C  C1     0  -0.372   1.7092   1.7712  -0.6092
 RVN  C3    C  CR5    0  -0.043   1.8185  -0.6492   0.4019
 RVN  H19   H  HNR5   0   0.409   5.0418  -1.0944   0.2509
 RVN  H4    H  H      0   0.271   0.5247  -2.1451   1.0067
 RVN  H6    H  HCR6   0   0.265   0.2437   1.1330   1.9907
 RVN  H7    H  HCR6   0   0.276  -1.8122   2.4970   2.2458
 RVN  H101  H  HCH2   0   0.245  -5.9001   0.7500   0.4179
 RVN  H102  H  HCH2   0   0.231  -5.0169   1.6028  -0.8923
 RVN  H23   H  H      0   0.255   0.6364   1.8966  -0.5618
 RVN  H20   H  H      0   0.265   5.5821   1.3720  -0.8269
 RVN  H21   H  H      0   0.257   4.4832   3.4557  -1.6047
 RVN  H22   H  H      0   0.253   2.0346   3.6992  -1.4878

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
 RVN  O1   C2    double    1.218  0.020  1.218
 RVN  C2   N19   single    1.366  0.020  1.366
 RVN  C2   C3    single    1.490  0.020  1.490
 RVN  C4   C5    single    1.468  0.020  1.468
 RVN  C4   C3    double    1.343  0.020  1.343
 RVN  C5   C6    aromatic  1.391  0.020  1.391
 RVN  C5   C13   aromatic  1.416  0.020  1.416
 RVN  C6   C7    aromatic  1.397  0.020  1.397
 RVN  C7   C8    aromatic  1.371  0.020  1.371
 RVN  C8   O9    single    1.353  0.020  1.353
 RVN  C8   C12   aromatic  1.390  0.020  1.390
 RVN  O9   C10   single    1.420  0.020  1.420
 RVN  C10  O11   single    1.418  0.020  1.418
 RVN  O11  C12   single    1.355  0.020  1.355
 RVN  C12  C13   aromatic  1.379  0.020  1.379
 RVN  C13  C14   single    1.517  0.020  1.517
 RVN  C14  O15   deloc     1.242  0.020  1.242
 RVN  C14  O16   deloc     1.246  0.020  1.246
 RVN  C17  C18   aromatic  1.404  0.020  1.404
 RVN  C17  C23   aromatic  1.387  0.020  1.387
 RVN  C17  C3    single    1.461  0.020  1.461
 RVN  C18  N19   single    1.386  0.020  1.386
 RVN  C18  C20   aromatic  1.382  0.020  1.382
 RVN  C20  C21   aromatic  1.392  0.020  1.392
 RVN  C21  C22   aromatic  1.390  0.020  1.390
 RVN  C22  C23   aromatic  1.392  0.020  1.392
 RVN  N19  H19   single    0.860  0.020  1.020
 RVN  C4   H4    single    0.930  0.020  1.080
 RVN  C6   H6    single    0.930  0.020  1.080
 RVN  C7   H7    single    0.930  0.020  1.080
 RVN  C10  H101  single    0.970  0.020  1.090
 RVN  C10  H102  single    0.970  0.020  1.090
 RVN  C23  H23   single    0.930  0.020  1.080
 RVN  C20  H20   single    0.930  0.020  1.080
 RVN  C21  H21   single    0.930  0.020  1.080
 RVN  C22  H22   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
 RVN  C3    C2   N19   106.01  3.000
 RVN  C3    C2   O1    128.38  3.000
 RVN  N19   C2   O1    125.61  3.000
 RVN  H4    C4   C3    116.50  3.000
 RVN  H4    C4   C5    116.95  3.000
 RVN  C3    C4   C5    126.23  3.000
 RVN  C13   C5   C6    121.01  3.000
 RVN  C13   C5   C4    121.14  3.000
 RVN  C6    C5   C4    117.65  3.000
 RVN  H6    C6   C7    118.66  3.000
 RVN  H6    C6   C5    119.30  3.000
 RVN  C7    C6   C5    122.04  3.000
 RVN  H7    C7   C8    122.07  3.000
 RVN  H7    C7   C6    121.47  3.000
 RVN  C8    C7   C6    116.45  3.000
 RVN  C12   C8   O9    109.78  3.000
 RVN  C12   C8   C7    122.13  3.000
 RVN  O9    C8   C7    128.09  3.000
 RVN  C10   O9   C8    105.87  3.000
 RVN  H102  C10  H101  110.48  3.000
 RVN  H102  C10  O11   109.98  3.000
 RVN  H101  C10  O11   109.87  3.000
 RVN  H102  C10  O9    109.75  3.000
 RVN  H101  C10  O9    109.85  3.000
 RVN  O11   C10  O9    106.83  3.000
 RVN  C12   O11  C10   106.58  3.000
 RVN  C13   C12  O11   128.91  3.000
 RVN  C13   C12  C8    122.56  3.000
 RVN  O11   C12  C8    108.53  3.000
 RVN  C14   C13  C12   122.40  3.000
 RVN  C14   C13  C5    121.78  3.000
 RVN  C12   C13  C5    115.80  3.000
 RVN  O16   C14  O15   127.35  3.000
 RVN  O16   C14  C13   115.68  3.000
 RVN  O15   C14  C13   116.97  3.000
 RVN  C3    C17  C23   134.38  3.000
 RVN  C3    C17  C18   106.61  3.000
 RVN  C23   C17  C18   118.96  3.000
 RVN  C20   C18  N19   128.26  3.000
 RVN  C20   C18  C17   122.44  3.000
 RVN  N19   C18  C17   109.30  3.000
 RVN  H19   N19  C18   124.52  3.000
 RVN  H19   N19  C2    123.61  3.000
 RVN  C18   N19  C2    111.87  3.000
 RVN  H20   C20  C21   121.07  3.000
 RVN  H20   C20  C18   121.30  3.000
 RVN  C21   C20  C18   117.63  3.000
 RVN  H21   C21  C22   119.72  3.000
 RVN  H21   C21  C20   119.31  3.000
 RVN  C22   C21  C20   120.96  3.000
 RVN  H22   C22  C23   119.55  3.000
 RVN  H22   C22  C21   119.75  3.000
 RVN  C23   C22  C21   120.70  3.000
 RVN  H23   C23  C22   119.73  3.000
 RVN  H23   C23  C17   120.97  3.000
 RVN  C22   C23  C17   119.30  3.000
 RVN  C17   C3   C4    133.30  3.000
 RVN  C17   C3   C2    106.19  3.000
 RVN  C4    C3   C2    120.46  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
 RVN  CONST_01  C8   C7   C6   C5      0.00   0.0  0
 RVN  CONST_02  C8   C12  C13  C5      0.00   0.0  0
 RVN  CONST_03  C12  C13  C5   C6      0.00   0.0  0
 RVN  CONST_04  C12  C8   C7   C6      0.00   0.0  0
 RVN  CONST_05  C13  C5   C6   C7      0.00   0.0  0
 RVN  CONST_06  C13  C12  C8   C7      0.00   0.0  0
 RVN  CONST_07  C21  C20  C18  C17     0.00   0.0  0
 RVN  CONST_08  C21  C22  C23  C17     0.00   0.0  0
 RVN  CONST_09  C22  C23  C17  C18     0.00   0.0  0
 RVN  CONST_10  C22  C21  C20  C18     0.00   0.0  0
 RVN  CONST_11  C23  C17  C18  C20     0.00   0.0  0
 RVN  CONST_12  C23  C22  C21  C20     0.00   0.0  0
 RVN  CONST_13  C3   C2   N19  C18     0.00   0.0  0
 RVN  CONST_14  C7   C6   C5   C4    180.00   0.0  0
 RVN  CONST_15  C12  C13  C5   C4    180.00   0.0  0
 RVN  CONST_16  C14  C13  C5   C6    180.00   0.0  0
 RVN  CONST_17  C14  C13  C12  C8    180.00   0.0  0
 RVN  CONST_18  C14  C13  C12  O11     0.00   0.0  0
 RVN  CONST_19  C18  N19  C2   O1    180.00   0.0  0
 RVN  CONST_20  H7   C7   C6   C5    180.00   0.0  0
 RVN  CONST_21  H6   C6   C7   C8    180.00   0.0  0
 RVN  CONST_22  H20  C20  C18  C17   180.00   0.0  0
 RVN  CONST_23  H22  C22  C23  C17   180.00   0.0  0
 RVN  CONST_24  H23  C23  C17  C18   180.00   0.0  0
 RVN  CONST_25  H21  C21  C20  C18   180.00   0.0  0
 RVN  CONST_26  H19  N19  C2   C3    180.00   0.0  0
 RVN  Var_01    O11  C10  O9   C8     15.10  30.0  1
 RVN  Var_02    C12  C8   O9   C10    -9.56  30.0  1
 RVN  Var_03    C13  C12  O11  C10  -170.28  30.0  1
 RVN  Var_04    C5   C4   C3   C2    170.66  30.0  2
 RVN  Var_05    C3   C4   C5   C6    -52.03  30.0  2
 RVN  Var_06    O15  C14  C13  C5    164.94  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
 RVN  plan-1  O1   0.020
 RVN  plan-1  C2   0.020
 RVN  plan-1  C4   0.020
 RVN  plan-1  C17  0.020
 RVN  plan-1  C18  0.020
 RVN  plan-1  N19  0.020
 RVN  plan-1  C20  0.020
 RVN  plan-1  C21  0.020
 RVN  plan-1  C22  0.020
 RVN  plan-1  C23  0.020
 RVN  plan-1  C3   0.020
 RVN  plan-1  H19  0.020
 RVN  plan-1  H23  0.020
 RVN  plan-1  H20  0.020
 RVN  plan-1  H21  0.020
 RVN  plan-1  H22  0.020
 RVN  plan-2  C4   0.020
 RVN  plan-2  C5   0.020
 RVN  plan-2  C6   0.020
 RVN  plan-2  C7   0.020
 RVN  plan-2  C8   0.020
 RVN  plan-2  O9   0.020
 RVN  plan-2  O11  0.020
 RVN  plan-2  C12  0.020
 RVN  plan-2  C13  0.020
 RVN  plan-2  C14  0.020
 RVN  plan-2  H6   0.020
 RVN  plan-2  H7   0.020
 RVN  plan-3  C13  0.020
 RVN  plan-3  C14  0.020
 RVN  plan-3  O15  0.020
 RVN  plan-3  O16  0.020

