# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 12:19:46 2022
#   Inital geometry file: a 104 line input string
#   Ligand name: 3-{4-methyl-2-[(Z)-(2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]-1H-pyrrol-3-yl}propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c[nH]c(\C=C2/C(=O)Nc3ccccc23)c1CCC(O)=O
#
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
 SU1  SU1  '3-{4-methyl-2-[(Z)-(2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]-1H-pyrrol-3-yl}propanoic acid'  ligand  37  22  .  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_SU1
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
 SU1  N1    N  NR15   0  -0.761   1.2803  -0.4498  -3.8230
 SU1  C2    C  CR5    0   0.526   1.6667  -0.3852  -2.5156
 SU1  O2    O  O      0  -0.498   2.8192  -0.5796  -2.1333
 SU1  C3    C  CR5    0  -0.071   0.4558  -0.0504  -1.7431
 SU1  C4    C  CR16   0  -0.381  -1.9721   0.3521  -2.6072
 SU1  C5    C  CR16   0  -0.261  -2.7504   0.3846  -3.7604
 SU1  C6    C  CR16   0  -0.278  -2.1845   0.1326  -5.0067
 SU1  C7    C  CR16   0  -0.301  -0.8286  -0.1600  -5.1344
 SU1  C8    C  CR56   0   0.376  -0.0708  -0.1890  -3.9798
 SU1  C9    C  CR56   0   0.077  -0.6205   0.0630  -2.7157
 SU1  C10   C  C1     0  -0.373   0.3226   0.1277  -0.3973
 SU1  N1'   N  NR15   0  -0.677   2.5845  -0.2080   0.5568
 SU1  C2'   C  CR5    0   0.318   1.2442   0.0620   0.6691
 SU1  C3'   C  CR5    0   0.030   0.9722   0.2637   2.0330
 SU1  C4'   C  CR5    0  -0.031   2.1852   0.1012   2.7235
 SU1  C5'   C  CR15   0  -0.056   3.1521  -0.1865   1.7698
 SU1  C11   C  CH3    0  -0.748   2.4002   0.2182   4.1963
 SU1  C12   C  CH2    0  -0.538  -0.3546   0.5383   2.6612
 SU1  C13   C  CH2    0  -0.578  -1.0044  -0.7331   3.2053
 SU1  C14   C  C      0   0.414  -2.3637  -0.5359   3.9005
 SU1  O3    O  O      0  -0.606  -2.8458   0.6132   3.9233
 SU1  O4    O  OC    -1  -0.629  -2.8769  -1.5651   4.3872
 SU1  HN1   H  HNR5   0   0.410   1.9179  -0.6592  -4.5756
 SU1  H4    H  HCR6   0   0.249  -2.4236   0.5522  -1.6428
 SU1  H5    H  HCR6   0   0.253  -3.8066   0.6070  -3.6865
 SU1  H6    H  HCR6   0   0.256  -2.8050   0.1647  -5.8926
 SU1  H7    H  HCR6   0   0.265  -0.3889  -0.3574  -6.1033
 SU1  H101  H  H      0   0.258  -0.6823   0.3713  -0.0662
 SU1  H5'1  H  HCR5   0   0.279   4.2075  -0.3707   1.8990
 SU1  H111  H  HCH3   0   0.238   2.1110   1.2026   4.5705
 SU1  H112  H  HCH3   0   0.238   1.8121  -0.5159   4.7502
 SU1  H113  H  HCH3   0   0.245   3.4467   0.0623   4.4569
 SU1  H121  H  HCH2   0   0.234  -0.2219   1.2572   3.4741
 SU1  H122  H  HCH2   0   0.232  -1.0297   1.0196   1.9508
 SU1  H131  H  HCH2   0   0.229  -1.1354  -1.4526   2.3893
 SU1  H132  H  HCH2   0   0.230  -0.3246  -1.2256   3.9091
 SU1  HN1'  H  HNR5   0   0.428   3.0295  -0.3961  -0.3398

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
 SU1  N1   C2    single    1.365  0.020  1.365
 SU1  N1   C8    single    1.385  0.020  1.385
 SU1  N1   HN1   single    0.860  0.020  1.020
 SU1  C2   O2    double    1.230  0.020  1.230
 SU1  C2   C3    single    1.475  0.020  1.475
 SU1  C3   C9    single    1.455  0.020  1.455
 SU1  C3   C10   double    1.364  0.020  1.364
 SU1  C4   C5    aromatic  1.392  0.020  1.392
 SU1  C4   C9    aromatic  1.386  0.020  1.386
 SU1  C4   H4    single    0.930  0.020  1.080
 SU1  C5   C6    aromatic  1.392  0.020  1.392
 SU1  C5   H5    single    0.930  0.020  1.080
 SU1  C6   C7    aromatic  1.393  0.020  1.393
 SU1  C6   H6    single    0.930  0.020  1.080
 SU1  C7   C8    aromatic  1.381  0.020  1.381
 SU1  C7   H7    single    0.930  0.020  1.080
 SU1  C8   C9    aromatic  1.401  0.020  1.401
 SU1  C10  C2'   single    1.411  0.020  1.411
 SU1  C10  H101  single    0.930  0.020  1.080
 SU1  N1'  C2'   aromatic  1.372  0.020  1.372
 SU1  N1'  C5'   aromatic  1.339  0.020  1.339
 SU1  N1'  HN1'  single    0.860  0.020  1.020
 SU1  C2'  C3'   aromatic  1.405  0.020  1.405
 SU1  C3'  C4'   aromatic  1.405  0.020  1.405
 SU1  C3'  C12   single    1.493  0.020  1.493
 SU1  C4'  C5'   aromatic  1.388  0.020  1.388
 SU1  C4'  C11   single    1.493  0.020  1.493
 SU1  C5'  H5'1  single    0.930  0.020  1.080
 SU1  C11  H111  single    0.970  0.020  1.090
 SU1  C11  H112  single    0.970  0.020  1.090
 SU1  C11  H113  single    0.970  0.020  1.090
 SU1  C12  C13   single    1.528  0.020  1.528
 SU1  C12  H121  single    0.970  0.020  1.090
 SU1  C12  H122  single    0.970  0.020  1.090
 SU1  C13  C14   single    1.539  0.020  1.539
 SU1  C13  H131  single    0.970  0.020  1.090
 SU1  C13  H132  single    0.970  0.020  1.090
 SU1  C14  O3    deloc     1.246  0.020  1.246
 SU1  C14  O4    deloc     1.249  0.020  1.249

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
 SU1  HN1   N1   C8    124.85  3.000
 SU1  HN1   N1   C2    123.08  3.000
 SU1  C8    N1   C2    112.07  3.000
 SU1  C3    C2   O2    129.98  3.000
 SU1  C3    C2   N1    106.26  3.000
 SU1  O2    C2   N1    123.76  3.000
 SU1  C10   C3   C9    125.24  3.000
 SU1  C10   C3   C2    128.80  3.000
 SU1  C9    C3   C2    105.96  3.000
 SU1  H4    C4   C9    120.96  3.000
 SU1  H4    C4   C5    120.02  3.000
 SU1  C9    C4   C5    119.03  3.000
 SU1  H5    C5   C6    119.69  3.000
 SU1  H5    C5   C4    119.62  3.000
 SU1  C6    C5   C4    120.69  3.000
 SU1  H6    C6   C7    119.30  3.000
 SU1  H6    C6   C5    119.64  3.000
 SU1  C7    C6   C5    121.06  3.000
 SU1  H7    C7   C8    121.44  3.000
 SU1  H7    C7   C6    121.06  3.000
 SU1  C8    C7   C6    117.50  3.000
 SU1  C9    C8   C7    122.34  3.000
 SU1  C9    C8   N1    108.32  3.000
 SU1  C7    C8   N1    129.33  3.000
 SU1  C8    C9   C4    119.37  3.000
 SU1  C8    C9   C3    107.38  3.000
 SU1  C4    C9   C3    133.24  3.000
 SU1  H101  C10  C2'   112.61  3.000
 SU1  H101  C10  C3    114.87  3.000
 SU1  C2'   C10  C3    132.52  3.000
 SU1  HN1'  N1'  C5'   127.96  3.000
 SU1  HN1'  N1'  C2'   122.36  3.000
 SU1  C5'   N1'  C2'   109.68  3.000
 SU1  C3'   C2'  N1'   107.26  3.000
 SU1  C3'   C2'  C10   126.90  3.000
 SU1  N1'   C2'  C10   125.83  3.000
 SU1  C12   C3'  C4'   125.55  3.000
 SU1  C12   C3'  C2'   127.34  3.000
 SU1  C4'   C3'  C2'   107.05  3.000
 SU1  C11   C4'  C5'   126.42  3.000
 SU1  C11   C4'  C3'   126.87  3.000
 SU1  C5'   C4'  C3'   106.72  3.000
 SU1  H5'1  C5'  C4'   129.37  3.000
 SU1  H5'1  C5'  N1'   121.34  3.000
 SU1  C4'   C5'  N1'   109.29  3.000
 SU1  H113  C11  H112  107.44  3.000
 SU1  H113  C11  H111  107.54  3.000
 SU1  H112  C11  H111  106.83  3.000
 SU1  H113  C11  C4'   111.29  3.000
 SU1  H112  C11  C4'   111.73  3.000
 SU1  H111  C11  C4'   111.75  3.000
 SU1  H122  C12  H121  105.60  3.000
 SU1  H122  C12  C13   109.61  3.000
 SU1  H121  C12  C13   109.52  3.000
 SU1  H122  C12  C3'   110.89  3.000
 SU1  H121  C12  C3'   109.01  3.000
 SU1  C13   C12  C3'   112.00  3.000
 SU1  H132  C13  H131  104.92  3.000
 SU1  H132  C13  C14   108.39  3.000
 SU1  H131  C13  C14   108.35  3.000
 SU1  H132  C13  C12   109.81  3.000
 SU1  H131  C13  C12   109.39  3.000
 SU1  C14   C13  C12   115.45  3.000
 SU1  O4    C14  O3    126.42  3.000
 SU1  O4    C14  C13   115.68  3.000
 SU1  O3    C14  C13   117.90  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
 SU1  CONST_01  C7    C6   C5   C4     0.00   0.0  0
 SU1  CONST_02  C7    C8   C9   C4     0.00   0.0  0
 SU1  CONST_03  C8    C9   C4   C5     0.00   0.0  0
 SU1  CONST_04  C8    C7   C6   C5     0.00   0.0  0
 SU1  CONST_05  C9    C4   C5   C6     0.00   0.0  0
 SU1  CONST_06  C9    C8   C7   C6     0.00   0.0  0
 SU1  CONST_07  C4'   C3'  C2'  N1'    0.00   0.0  0
 SU1  CONST_08  C3'   C4'  C5'  N1'    0.00   0.0  0
 SU1  CONST_09  C4'   C5'  N1'  C2'    0.00   0.0  0
 SU1  CONST_10  C5'   C4'  C3'  C2'    0.00   0.0  0
 SU1  CONST_11  C5'   N1'  C2'  C3'    0.00   0.0  0
 SU1  CONST_12  C8    N1   C2   C3     0.00   0.0  0
 SU1  CONST_13  C5'   N1'  C2'  C10  180.00   0.0  0
 SU1  CONST_14  C4'   C3'  C2'  C10  180.00   0.0  0
 SU1  CONST_15  C12   C3'  C2'  N1'  180.00   0.0  0
 SU1  CONST_16  C11   C4'  C5'  N1'  180.00   0.0  0
 SU1  CONST_17  C11   C4'  C3'  C2'  180.00   0.0  0
 SU1  CONST_18  C12   C3'  C4'  C5'  180.00   0.0  0
 SU1  CONST_19  C8    N1   C2   O2   180.00   0.0  0
 SU1  CONST_20  H7    C7   C8   N1     0.00   0.0  0
 SU1  CONST_21  H4    C4   C9   C3     0.00   0.0  0
 SU1  CONST_22  H6    C6   C5   C4   180.00   0.0  0
 SU1  CONST_23  H5    C5   C6   C7   180.00   0.0  0
 SU1  CONST_24  H5'1  C5'  N1'  C2'  180.00   0.0  0
 SU1  CONST_25  HN1'  N1'  C2'  C3'  180.00   0.0  0
 SU1  CONST_26  HN1   N1   C2   C3   180.00   0.0  0
 SU1  Var_01    C2'   C10  C3   C2     0.20   0.0  2
 SU1  Var_02    N1'   C2'  C10  C3     0.63  30.0  2
 SU1  Var_03    C13   C12  C3'  C2'   96.33  30.0  2
 SU1  Var_04    H111  C11  C4'  C3'  -58.63  30.0  2
 SU1  Var_05    C14   C13  C12  C3'  178.64  30.0  3
 SU1  Var_06    O3    C14  C13  C12    2.56  30.0  3

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
 SU1  plan-1  C10   0.020
 SU1  plan-1  N1'   0.020
 SU1  plan-1  C2'   0.020
 SU1  plan-1  C3'   0.020
 SU1  plan-1  C4'   0.020
 SU1  plan-1  C5'   0.020
 SU1  plan-1  C11   0.020
 SU1  plan-1  C12   0.020
 SU1  plan-1  H5'1  0.020
 SU1  plan-1  HN1'  0.020
 SU1  plan-2  N1    0.020
 SU1  plan-2  C2    0.020
 SU1  plan-2  O2    0.020
 SU1  plan-2  C3    0.020
 SU1  plan-2  C4    0.020
 SU1  plan-2  C5    0.020
 SU1  plan-2  C6    0.020
 SU1  plan-2  C7    0.020
 SU1  plan-2  C8    0.020
 SU1  plan-2  C9    0.020
 SU1  plan-2  C10   0.020
 SU1  plan-2  C2'   0.020
 SU1  plan-2  HN1   0.020
 SU1  plan-2  H4    0.020
 SU1  plan-2  H5    0.020
 SU1  plan-2  H6    0.020
 SU1  plan-2  H7    0.020
 SU1  plan-2  H101  0.020
 SU1  plan-3  C13   0.020
 SU1  plan-3  C14   0.020
 SU1  plan-3  O3    0.020
 SU1  plan-3  O4    0.020

