# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 06:50:26 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 3-(3-{[(2S)-2,3-dihydroxypropyl]amino}phenyl)-4-(5-fluoro-1-methyl-1H-indol-3-yl)-1H-pyrrole-2,5-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(c2cc(F)ccc12)C3=C(C(=O)NC3=O)c4cccc(NC[C@H](O)CO)c4
#
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
 DFN  DFN  3-(3-{[(2S)-2,3-dihydroxypropyl]amino}phenyl)-4-(5-fluoro-1-methyl-1H-indol-3-yl)-1H-pyrrole-2,5-dione  ligand  50  30  .  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_DFN
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
 DFN  C28   C  CH3   0  -0.532  -2.2304   3.4150  -1.8324
 DFN  N22   N  NR5   0  -0.514  -2.5431   2.1390  -1.2340
 DFN  C48   C  CR15  0  -0.040  -1.6912   1.1059  -1.0745
 DFN  C21   C  CR56  0   0.362  -3.7703   1.7822  -0.7336
 DFN  C24   C  CR16  0  -0.286  -4.9412   2.5294  -0.6569
 DFN  C31   C  CR16  0  -0.438  -6.0451   1.9391  -0.0737
 DFN  C29   C  CR6   0   0.536  -5.9463   0.6368   0.4183
 DFN  F39   F  F     0  -0.326  -7.0402   0.1000   0.9948
 DFN  C20   C  CR56  0   0.067  -3.6812   0.4581  -0.2544
 DFN  C23   C  CR16  0  -0.562  -4.8035  -0.1214   0.3486
 DFN  C19   C  CR5   0  -0.041  -2.3282   0.0341  -0.4857
 DFN  C01   C  CR5   0  -0.047  -1.6873  -1.2202  -0.1839
 DFN  C02   C  CR5   0  -0.122  -0.4226  -1.4637   0.2127
 DFN  C03   C  CR5   0   0.574  -0.2317  -2.9408   0.2849
 DFN  O06   O  O     0  -0.396   0.7564  -3.5448   0.6188
 DFN  N04   N  NR15  0  -0.737  -1.4314  -3.5066  -0.0886
 DFN  C05   C  CR5   0   0.548  -2.3597  -2.5458  -0.4015
 DFN  O07   O  O     0  -0.391  -3.4785  -2.7459  -0.8006
 DFN  C08   C  CR6   0   0.043   0.6327  -0.5231   0.5935
 DFN  C09   C  CR16  0  -0.403   1.9024  -0.6414   0.0470
 DFN  C10   C  CR6   0   0.395   2.9298   0.2491   0.3954
 DFN  C11   C  CR16  0  -0.358   2.6473   1.2507   1.3314
 DFN  C12   C  CR16  0  -0.228   1.3742   1.3593   1.8767
 DFN  C13   C  CR16  0  -0.327   0.3612   0.4885   1.5196
 DFN  N15   N  NH1   0  -0.694   4.1579   0.1274  -0.2083
 DFN  C26   C  CH2   0  -0.294   5.3243   0.7819   0.3298
 DFN  C34   C  CH1   0  -0.035   6.5512   0.4496  -0.5123
 DFN  O41   O  OH1   0  -0.658   6.7268  -0.9441  -0.6537
 DFN  C40   C  CH2   0  -0.157   7.7761   1.1355   0.0664
 DFN  O45   O  OH1   0  -0.668   8.8729   0.9127  -0.7851
 DFN  H281  H  HCH3  0   0.261  -2.8763   3.6077  -2.6878
 DFN  H282  H  HCH3  0   0.261  -2.3535   4.2195  -1.1083
 DFN  H283  H  HCH3  0   0.271  -1.1985   3.4057  -2.1710
 DFN  H48   H  HCR5  0   0.300  -0.6693   1.1800  -1.4130
 DFN  H24   H  HCR6  0   0.281  -4.9988   3.5425  -1.0327
 DFN  H31   H  HCR6  0   0.277  -6.9794   2.4784   0.0085
 DFN  H23   H  HCR6  0   0.263  -4.7886  -1.1237   0.7532
 DFN  H04   H  HNR5  0   0.426  -1.6049  -4.5008  -0.1298
 DFN  H09   H  HCR6  0   0.254   2.1077  -1.4185  -0.6799
 DFN  H11   H  HCR6  0   0.266   3.4128   1.9496   1.6400
 DFN  H12   H  HCR6  0   0.254   1.1812   2.1394   2.6022
 DFN  H13   H  HCR6  0   0.245  -0.6251   0.5796   1.9547
 DFN  H15   H  HNH1  0   0.374   4.3474  -0.7882  -0.5883
 DFN  H261  H  HCH2  0   0.239   5.1806   1.8652   0.3141
 DFN  H262  H  HCH2  0   0.219   5.5053   0.5024   1.3799
 DFN  H34   H  HCH1  0   0.238   6.3833   0.8258  -1.5266
 DFN  H41   H  HOH1  0   0.447   6.9417  -1.3180   0.2088
 DFN  H401  H  HCH2  0   0.203   7.5553   2.2053   0.1754
 DFN  H402  H  HCH2  0   0.195   7.9614   0.7467   1.0785
 DFN  H45   H  HOH1  0   0.456   9.6341   1.3687  -0.4158

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
 DFN  C28  N22   single    1.444  0.020  1.444
 DFN  C28  H281  single    0.970  0.020  1.090
 DFN  C28  H282  single    0.970  0.020  1.090
 DFN  C28  H283  single    0.970  0.020  1.090
 DFN  N22  C48   aromatic  1.349  0.020  1.349
 DFN  N22  C21   aromatic  1.372  0.020  1.372
 DFN  C48  C19   aromatic  1.379  0.020  1.379
 DFN  C48  H48   single    0.930  0.020  1.080
 DFN  C21  C24   aromatic  1.391  0.020  1.391
 DFN  C21  C20   aromatic  1.411  0.020  1.411
 DFN  C24  C31   aromatic  1.381  0.020  1.381
 DFN  C24  H24   single    0.930  0.020  1.080
 DFN  C31  C29   aromatic  1.396  0.020  1.396
 DFN  C31  H31   single    0.930  0.020  1.080
 DFN  C29  F39   single    1.348  0.020  1.348
 DFN  C29  C23   aromatic  1.373  0.020  1.373
 DFN  C20  C23   aromatic  1.400  0.020  1.400
 DFN  C20  C19   aromatic  1.437  0.020  1.437
 DFN  C23  H23   single    0.930  0.020  1.080
 DFN  C19  C01   single    1.440  0.020  1.440
 DFN  C01  C02   double    1.348  0.020  1.348
 DFN  C01  C05   single    1.502  0.020  1.502
 DFN  C02  C03   single    1.491  0.020  1.491
 DFN  C02  C08   single    1.464  0.020  1.464
 DFN  C03  O06   double    1.205  0.020  1.205
 DFN  C03  N04   single    1.378  0.020  1.378
 DFN  N04  C05   single    1.372  0.020  1.372
 DFN  N04  H04   single    0.860  0.020  1.020
 DFN  C05  O07   double    1.205  0.020  1.205
 DFN  C08  C09   aromatic  1.387  0.020  1.387
 DFN  C08  C13   aromatic  1.398  0.020  1.398
 DFN  C09  C10   aromatic  1.403  0.020  1.403
 DFN  C09  H09   single    0.930  0.020  1.080
 DFN  C10  C11   aromatic  1.400  0.020  1.400
 DFN  C10  N15   single    1.374  0.020  1.374
 DFN  C11  C12   aromatic  1.389  0.020  1.389
 DFN  C11  H11   single    0.930  0.020  1.080
 DFN  C12  C13   aromatic  1.383  0.020  1.383
 DFN  C12  H12   single    0.930  0.020  1.080
 DFN  C13  H13   single    0.930  0.020  1.080
 DFN  N15  C26   single    1.442  0.020  1.442
 DFN  N15  H15   single    0.890  0.020  1.040
 DFN  C26  C34   single    1.525  0.020  1.525
 DFN  C26  H261  single    0.970  0.020  1.090
 DFN  C26  H262  single    0.970  0.020  1.090
 DFN  C34  O41   single    1.412  0.020  1.412
 DFN  C34  C40   single    1.518  0.020  1.518
 DFN  C34  H34   single    0.970  0.020  1.090
 DFN  O41  H41   single    0.850  0.020  0.980
 DFN  C40  O45   single    1.406  0.020  1.406
 DFN  C40  H401  single    0.970  0.020  1.090
 DFN  C40  H402  single    0.970  0.020  1.090
 DFN  O45  H45   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
 DFN  H283  C28  H282  108.72  3.000
 DFN  H283  C28  H281  108.68  3.000
 DFN  H282  C28  H281  108.93  3.000
 DFN  H283  C28  N22   109.11  3.000
 DFN  H282  C28  N22   110.65  3.000
 DFN  H281  C28  N22   110.70  3.000
 DFN  C21   N22  C48   108.82  3.000
 DFN  C21   N22  C28   125.07  3.000
 DFN  C48   N22  C28   126.11  3.000
 DFN  H48   C48  C19   128.67  3.000
 DFN  H48   C48  N22   120.57  3.000
 DFN  C19   C48  N22   110.74  3.000
 DFN  C20   C21  C24   122.58  3.000
 DFN  C20   C21  N22   108.14  3.000
 DFN  C24   C21  N22   129.28  3.000
 DFN  H24   C24  C31   120.29  3.000
 DFN  H24   C24  C21   121.90  3.000
 DFN  C31   C24  C21   117.80  3.000
 DFN  H31   C31  C29   119.97  3.000
 DFN  H31   C31  C24   120.61  3.000
 DFN  C29   C31  C24   119.42  3.000
 DFN  C23   C29  F39   118.50  3.000
 DFN  C23   C29  C31   123.80  3.000
 DFN  F39   C29  C31   117.71  3.000
 DFN  C19   C20  C23   134.62  3.000
 DFN  C19   C20  C21   106.36  3.000
 DFN  C23   C20  C21   118.96  3.000
 DFN  H23   C23  C20   122.28  3.000
 DFN  H23   C23  C29   120.29  3.000
 DFN  C20   C23  C29   117.42  3.000
 DFN  C01   C19  C20   129.96  3.000
 DFN  C01   C19  C48   124.11  3.000
 DFN  C20   C19  C48   105.93  3.000
 DFN  C05   C01  C02   107.65  3.000
 DFN  C05   C01  C19   122.60  3.000
 DFN  C02   C01  C19   129.54  3.000
 DFN  C08   C02  C03   122.11  3.000
 DFN  C08   C02  C01   129.56  3.000
 DFN  C03   C02  C01   108.27  3.000
 DFN  N04   C03  O06   125.66  3.000
 DFN  N04   C03  C02   106.39  3.000
 DFN  O06   C03  C02   127.94  3.000
 DFN  H04   N04  C05   124.32  3.000
 DFN  H04   N04  C03   124.39  3.000
 DFN  C05   N04  C03   111.30  3.000
 DFN  O07   C05  N04   125.98  3.000
 DFN  O07   C05  C01   127.61  3.000
 DFN  N04   C05  C01   106.38  3.000
 DFN  C13   C08  C09   120.02  3.000
 DFN  C13   C08  C02   119.81  3.000
 DFN  C09   C08  C02   120.16  3.000
 DFN  H09   C09  C10   118.87  3.000
 DFN  H09   C09  C08   119.91  3.000
 DFN  C10   C09  C08   121.20  3.000
 DFN  N15   C10  C11   122.53  3.000
 DFN  N15   C10  C09   119.28  3.000
 DFN  C11   C10  C09   118.18  3.000
 DFN  H11   C11  C12   119.08  3.000
 DFN  H11   C11  C10   120.69  3.000
 DFN  C12   C11  C10   120.23  3.000
 DFN  H12   C12  C13   119.75  3.000
 DFN  H12   C12  C11   118.87  3.000
 DFN  C13   C12  C11   121.38  3.000
 DFN  H13   C13  C12   120.73  3.000
 DFN  H13   C13  C08   120.29  3.000
 DFN  C12   C13  C08   118.98  3.000
 DFN  H15   N15  C26   113.60  3.000
 DFN  H15   N15  C10   114.44  3.000
 DFN  C26   N15  C10   121.26  3.000
 DFN  H262  C26  H261  106.66  3.000
 DFN  H262  C26  C34   109.81  3.000
 DFN  H261  C26  C34   108.29  3.000
 DFN  H262  C26  N15   111.94  3.000
 DFN  H261  C26  N15   109.77  3.000
 DFN  C34   C26  N15   110.24  3.000
 DFN  H34   C34  C40   108.76  3.000
 DFN  H34   C34  O41   105.40  3.000
 DFN  C40   C34  O41   112.57  3.000
 DFN  H34   C34  C26   108.26  3.000
 DFN  C40   C34  C26   109.89  3.000
 DFN  O41   C34  C26   111.74  3.000
 DFN  H41   O41  C34   108.72  3.000
 DFN  H402  C40  H401  106.68  3.000
 DFN  H402  C40  O45   111.70  3.000
 DFN  H401  C40  O45   111.80  3.000
 DFN  H402  C40  C34   109.08  3.000
 DFN  H401  C40  C34   108.41  3.000
 DFN  O45   C40  C34   109.08  3.000
 DFN  H45   O45  C40   108.05  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
 DFN  CONST_01  C20   C19  C48  N22     0.00   0.0  0
 DFN  CONST_02  C31   C24  C21  N22   180.00   0.0  0
 DFN  CONST_03  C23   C20  C21  N22   180.00   0.0  0
 DFN  CONST_04  C19   C20  C21  N22     0.00   0.0  0
 DFN  CONST_05  C24   C21  N22  C48   180.00   0.0  0
 DFN  CONST_06  C20   C21  N22  C48     0.00   0.0  0
 DFN  CONST_07  C21   C20  C19  C48     0.00   0.0  0
 DFN  CONST_08  C23   C20  C19  C48   180.00   0.0  0
 DFN  CONST_09  C19   C48  N22  C21     0.00   0.0  0
 DFN  CONST_10  C29   C31  C24  C21     0.00   0.0  0
 DFN  CONST_11  C29   C23  C20  C21     0.00   0.0  0
 DFN  CONST_12  C23   C20  C21  C24     0.00   0.0  0
 DFN  CONST_13  C19   C20  C21  C24   180.00   0.0  0
 DFN  CONST_14  C23   C29  C31  C24     0.00   0.0  0
 DFN  CONST_15  C20   C21  C24  C31     0.00   0.0  0
 DFN  CONST_16  C20   C23  C29  C31     0.00   0.0  0
 DFN  CONST_17  C19   C20  C23  C29   180.00   0.0  0
 DFN  CONST_18  C11   C10  C09  C08     0.00   0.0  0
 DFN  CONST_19  C11   C12  C13  C08     0.00   0.0  0
 DFN  CONST_20  C12   C13  C08  C09     0.00   0.0  0
 DFN  CONST_21  C12   C11  C10  C09     0.00   0.0  0
 DFN  CONST_22  C13   C08  C09  C10     0.00   0.0  0
 DFN  CONST_23  C13   C12  C11  C10     0.00   0.0  0
 DFN  CONST_24  C01   C19  C48  N22   180.00   0.0  0
 DFN  CONST_25  C01   C19  C20  C21   180.00   0.0  0
 DFN  CONST_26  C01   C19  C20  C23     0.00   0.0  0
 DFN  CONST_27  C10   C09  C08  C02   180.00   0.0  0
 DFN  CONST_28  C12   C13  C08  C02   180.00   0.0  0
 DFN  CONST_29  C05   N04  C03  C02     0.00   0.0  0
 DFN  CONST_30  C19   C48  N22  C28   180.00   0.0  0
 DFN  CONST_31  C24   C21  N22  C28     0.00   0.0  0
 DFN  CONST_32  C20   C21  N22  C28   180.00   0.0  0
 DFN  CONST_33  F39   C29  C31  C24   180.00   0.0  0
 DFN  CONST_34  C20   C23  C29  F39   180.00   0.0  0
 DFN  CONST_35  N15   C10  C09  C08   180.00   0.0  0
 DFN  CONST_36  N15   C10  C11  C12   180.00   0.0  0
 DFN  CONST_37  C05   N04  C03  O06   180.00   0.0  0
 DFN  CONST_38  H24   C24  C21  N22     0.00   0.0  0
 DFN  CONST_39  H48   C48  N22  C21   180.00   0.0  0
 DFN  CONST_40  H31   C31  C24  C21   180.00   0.0  0
 DFN  CONST_41  H23   C23  C20  C21   180.00   0.0  0
 DFN  CONST_42  H09   C09  C08  C02     0.00   0.0  0
 DFN  CONST_43  H13   C13  C08  C02     0.00   0.0  0
 DFN  CONST_44  H12   C12  C13  C08   180.00   0.0  0
 DFN  CONST_45  H11   C11  C10  C09   180.00   0.0  0
 DFN  CONST_46  H04   N04  C03  C02   180.00   0.0  0
 DFN  Var_01    C02   C01  C19  C48    34.80  30.0  2
 DFN  Var_02    C09   C08  C02  C01  -131.12  30.0  2
 DFN  Var_03    H281  C28  N22  C48   121.49  30.0  2
 DFN  Var_04    C34   C26  N15  C10   178.54  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 DFN  chir_01  C34  C26  O41  C40  positiv

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
 DFN  plan-1  C19  0.020
 DFN  plan-1  C01  0.020
 DFN  plan-1  C02  0.020
 DFN  plan-1  C03  0.020
 DFN  plan-1  O06  0.020
 DFN  plan-1  N04  0.020
 DFN  plan-1  C05  0.020
 DFN  plan-1  O07  0.020
 DFN  plan-1  C08  0.020
 DFN  plan-1  H04  0.020
 DFN  plan-2  C02  0.020
 DFN  plan-2  C08  0.020
 DFN  plan-2  C09  0.020
 DFN  plan-2  C10  0.020
 DFN  plan-2  C11  0.020
 DFN  plan-2  C12  0.020
 DFN  plan-2  C13  0.020
 DFN  plan-2  N15  0.020
 DFN  plan-2  H09  0.020
 DFN  plan-2  H11  0.020
 DFN  plan-2  H12  0.020
 DFN  plan-2  H13  0.020
 DFN  plan-3  C28  0.020
 DFN  plan-3  N22  0.020
 DFN  plan-3  C48  0.020
 DFN  plan-3  C21  0.020
 DFN  plan-3  C24  0.020
 DFN  plan-3  C31  0.020
 DFN  plan-3  C29  0.020
 DFN  plan-3  F39  0.020
 DFN  plan-3  C20  0.020
 DFN  plan-3  C23  0.020
 DFN  plan-3  C19  0.020
 DFN  plan-3  C01  0.020
 DFN  plan-3  H48  0.020
 DFN  plan-3  H24  0.020
 DFN  plan-3  H31  0.020
 DFN  plan-3  H23  0.020
 DFN  plan-4  C10  0.020
 DFN  plan-4  N15  0.020
 DFN  plan-4  C26  0.020
 DFN  plan-4  H15  0.020

