# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 20:45:43 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: (3Z)-4-[(3R,4S,5R)-4-amino-3,5-dihydroxyhex-1-yn-1-yl]-5-fluoro-3-[(3-methoxy-1H-pyrrol-2-yl)methylidene]-1,3-dihydro-2H-indol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc[nH]c1/C=C/2C(=O)Nc3ccc(F)c(C#C[C@@H](O)[C@@H](N)[C@@H](C)O)c/23
#
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
 FMD  FMD  (3Z)-4-[(3R,4S,5R)-4-amino-3,5-dihydroxyhex-1-yn-1-yl]-5-fluoro-3-[(3-methoxy-1H-pyrrol-2-yl)methylidene]-1,3-dihydro-2H-indol-2-one  ligand  48  28  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FMD
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
 FMD  F17   F  F     0  -0.302  -4.2772  -0.9768   1.4675
 FMD  C1    C  CR6   0   0.496  -3.9503  -0.6058   0.2199
 FMD  C2    C  CR6   0  -0.358  -2.5936  -0.4406  -0.0683
 FMD  C18   C  CSP   0   0.138  -1.6244  -0.6794   0.9410
 FMD  C19   C  CSP   0   0.070  -0.7804  -0.8832   1.7776
 FMD  C20   C  CH1   0  -0.151   0.3251  -1.1717   2.6975
 FMD  O27   O  OH1   0  -0.653   1.2918  -1.9811   2.0697
 FMD  C23   C  CH1   0  -0.153   0.9084   0.1357   3.2693
 FMD  N28   N  NH2   0  -0.789  -0.1718   0.8585   3.9090
 FMD  C24   C  CH1   0   0.015   2.1308  -0.1453   4.1623
 FMD  O26   O  OH1   0  -0.666   1.7923  -0.9824   5.2510
 FMD  C25   C  CH3   0  -0.699   2.7962   1.1423   4.6234
 FMD  C3    C  CR56  0   0.132  -2.2620  -0.0532  -1.3723
 FMD  C4    C  CR56  0   0.351  -3.2896   0.1356  -2.3104
 FMD  N9    N  NR15  0  -0.763  -2.7189   0.4959  -3.5175
 FMD  C8    C  CR5   0   0.537  -1.3598   0.5566  -3.4396
 FMD  O10   O  O     0  -0.501  -0.6306   0.8509  -4.3852
 FMD  C5    C  CR16  0  -0.285  -4.6227  -0.0331  -2.0033
 FMD  C6    C  CR16  0  -0.452  -4.9536  -0.4110  -0.7037
 FMD  C7    C  CR5   0  -0.140  -1.0078   0.2141  -2.0508
 FMD  C11   C  C1    0  -0.348   0.2430   0.1748  -1.4929
 FMD  C12   C  CR5   0   0.270   1.5216   0.4058  -2.0159
 FMD  C13   C  CR5   0   0.285   2.7417   0.3369  -1.3103
 FMD  O21   O  O2    0  -0.476   2.8021   0.0266  -0.0115
 FMD  C22   C  CH3   0  -0.440   4.0925   0.0484   0.5823
 FMD  C14   C  CR15  0  -0.462   3.7798   0.6407  -2.1953
 FMD  C15   C  CR15  0   0.012   3.1748   0.8870  -3.4227
 FMD  N16   N  NR15  0  -0.668   1.8555   0.7464  -3.3080
 FMD  H20   H  HCH1  0   0.269  -0.0648  -1.7643   3.5316
 FMD  H27   H  HOH1  0   0.443   1.6449  -1.5104   1.3051
 FMD  H23   H  HCH1  0   0.235   1.2530   0.7437   2.4239
 FMD  H281  H  HNH2  0   0.339  -0.4612   0.4009   4.7650
 FMD  H282  H  HNH2  0   0.361   0.1133   1.7967   4.1552
 FMD  H24   H  HCH1  0   0.224   2.8588  -0.7129   3.5767
 FMD  H26   H  HOH1  0   0.441   1.3345  -0.4560   5.9144
 FMD  H251  H  HCH3  0   0.247   3.6739   0.9242   5.2319
 FMD  H252  H  HCH3  0   0.232   3.1235   1.7406   3.7715
 FMD  H253  H  HCH3  0   0.221   2.1190   1.7584   5.2197
 FMD  HN9   H  HNR5  0   0.413  -3.2354   0.6948  -4.3602
 FMD  HC5   H  HCR6  0   0.281  -5.3966   0.1196  -2.7431
 FMD  HC6   H  HCR6  0   0.284  -5.9867  -0.5547  -0.4176
 FMD  H11   H  H     0   0.255   0.2639  -0.0777  -0.4415
 FMD  H221  H  HCH3  0   0.255   3.9639  -0.2257   1.6262
 FMD  H222  H  HCH3  0   0.243   4.7613  -0.6730   0.1090
 FMD  H223  H  HCH3  0   0.245   4.5368   1.0441   0.5283
 FMD  H14   H  HCR5  0   0.284   4.8380   0.6824  -1.9973
 FMD  H15   H  HCR5  0   0.294   3.6310   1.1542  -4.3618
 FMD  H16   H  HNR5  0   0.436   1.1427   0.8702  -4.0265

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
 FMD  F17  C1    single    1.342  0.020  1.342
 FMD  C1   C2    aromatic  1.397  0.020  1.397
 FMD  C1   C6    aromatic  1.378  0.020  1.378
 FMD  C2   C18   single    1.419  0.020  1.419
 FMD  C2   C3    aromatic  1.400  0.020  1.400
 FMD  C18  C19   triple    1.206  0.020  1.206
 FMD  C19  C20   single    1.467  0.020  1.467
 FMD  C20  O27   single    1.408  0.020  1.408
 FMD  C20  C23   single    1.542  0.020  1.542
 FMD  C20  H20   single    0.970  0.020  1.090
 FMD  O27  H27   single    0.850  0.020  0.980
 FMD  C23  N28   single    1.449  0.020  1.449
 FMD  C23  C24   single    1.540  0.020  1.540
 FMD  C23  H23   single    0.970  0.020  1.090
 FMD  N28  H281  single    0.890  0.020  1.040
 FMD  N28  H282  single    0.890  0.020  1.040
 FMD  C24  O26   single    1.414  0.020  1.414
 FMD  C24  C25   single    1.521  0.020  1.521
 FMD  C24  H24   single    0.970  0.020  1.090
 FMD  O26  H26   single    0.850  0.020  0.980
 FMD  C25  H251  single    0.970  0.020  1.090
 FMD  C25  H252  single    0.970  0.020  1.090
 FMD  C25  H253  single    0.970  0.020  1.090
 FMD  C3   C4    aromatic  1.404  0.020  1.404
 FMD  C3   C7    single    1.451  0.020  1.451
 FMD  C4   N9    single    1.383  0.020  1.383
 FMD  C4   C5    aromatic  1.378  0.020  1.378
 FMD  N9   C8    single    1.363  0.020  1.363
 FMD  N9   HN9   single    0.860  0.020  1.020
 FMD  C8   O10   double    1.230  0.020  1.230
 FMD  C8   C7    single    1.473  0.020  1.473
 FMD  C5   C6    aromatic  1.393  0.020  1.393
 FMD  C5   HC5   single    0.930  0.020  1.080
 FMD  C6   HC6   single    0.930  0.020  1.080
 FMD  C7   C11   double    1.370  0.020  1.370
 FMD  C11  C12   single    1.401  0.020  1.401
 FMD  C11  H11   single    0.930  0.020  1.080
 FMD  C12  C13   aromatic  1.411  0.020  1.411
 FMD  C12  N16   aromatic  1.377  0.020  1.377
 FMD  C13  O21   single    1.337  0.020  1.337
 FMD  C13  C14   aromatic  1.397  0.020  1.397
 FMD  O21  C22   single    1.421  0.020  1.421
 FMD  C22  H221  single    0.970  0.020  1.090
 FMD  C22  H222  single    0.970  0.020  1.090
 FMD  C22  H223  single    0.970  0.020  1.090
 FMD  C14  C15   aromatic  1.390  0.020  1.390
 FMD  C14  H14   single    0.930  0.020  1.080
 FMD  C15  N16   aromatic  1.332  0.020  1.332
 FMD  C15  H15   single    0.930  0.020  1.080
 FMD  N16  H16   single    0.860  0.020  1.020

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
 FMD  C6    C1   C2    123.53  3.000
 FMD  C6    C1   F17   119.01  3.000
 FMD  C2    C1   F17   117.46  3.000
 FMD  C3    C2   C18   123.17  3.000
 FMD  C3    C2   C1    117.06  3.000
 FMD  C18   C2   C1    119.77  3.000
 FMD  C19   C18  C2    180.00  3.000
 FMD  C20   C19  C18   180.00  3.000
 FMD  H20   C20  C23   108.13  3.000
 FMD  H20   C20  O27   105.84  3.000
 FMD  C23   C20  O27   113.14  3.000
 FMD  H20   C20  C19   108.41  3.000
 FMD  C23   C20  C19   110.55  3.000
 FMD  O27   C20  C19   110.54  3.000
 FMD  H27   O27  C20   108.91  3.000
 FMD  H23   C23  C24   107.38  3.000
 FMD  H23   C23  N28   107.34  3.000
 FMD  C24   C23  N28   115.27  3.000
 FMD  H23   C23  C20   107.64  3.000
 FMD  C24   C23  C20   111.15  3.000
 FMD  N28   C23  C20   107.75  3.000
 FMD  H282  N28  H281  107.10  3.000
 FMD  H282  N28  C23   111.12  3.000
 FMD  H281  N28  C23   111.15  3.000
 FMD  H24   C24  C25   108.10  3.000
 FMD  H24   C24  O26   105.32  3.000
 FMD  C25   C24  O26   111.86  3.000
 FMD  H24   C24  C23   108.23  3.000
 FMD  C25   C24  C23   111.64  3.000
 FMD  O26   C24  C23   111.37  3.000
 FMD  H26   O26  C24   108.70  3.000
 FMD  H253  C25  H252  107.63  3.000
 FMD  H253  C25  H251  107.90  3.000
 FMD  H252  C25  H251  107.70  3.000
 FMD  H253  C25  C24   111.82  3.000
 FMD  H252  C25  C24   111.02  3.000
 FMD  H251  C25  C24   110.62  3.000
 FMD  C7    C3   C4    107.18  3.000
 FMD  C7    C3   C2    133.73  3.000
 FMD  C4    C3   C2    119.09  3.000
 FMD  C5    C4   N9    128.71  3.000
 FMD  C5    C4   C3    122.85  3.000
 FMD  N9    C4   C3    108.43  3.000
 FMD  HN9   N9   C8    123.36  3.000
 FMD  HN9   N9   C4    124.72  3.000
 FMD  C8    N9   C4    111.92  3.000
 FMD  C7    C8   O10   129.70  3.000
 FMD  C7    C8   N9    106.37  3.000
 FMD  O10   C8   N9    123.92  3.000
 FMD  HC5   C5   C6    120.43  3.000
 FMD  HC5   C5   C4    121.50  3.000
 FMD  C6    C5   C4    118.08  3.000
 FMD  HC6   C6   C5    120.64  3.000
 FMD  HC6   C6   C1    119.97  3.000
 FMD  C5    C6   C1    119.39  3.000
 FMD  C11   C7   C8    127.49  3.000
 FMD  C11   C7   C3    126.41  3.000
 FMD  C8    C7   C3    106.09  3.000
 FMD  H11   C11  C12   112.57  3.000
 FMD  H11   C11  C7    114.84  3.000
 FMD  C12   C11  C7    132.58  3.000
 FMD  N16   C12  C13   105.76  3.000
 FMD  N16   C12  C11   127.76  3.000
 FMD  C13   C12  C11   126.48  3.000
 FMD  C14   C13  O21   129.22  3.000
 FMD  C14   C13  C12   108.36  3.000
 FMD  O21   C13  C12   122.42  3.000
 FMD  C22   O21  C13   116.33  3.000
 FMD  H223  C22  H222  109.39  3.000
 FMD  H223  C22  H221  109.00  3.000
 FMD  H222  C22  H221  108.80  3.000
 FMD  H223  C22  O21   111.28  3.000
 FMD  H222  C22  O21   111.42  3.000
 FMD  H221  C22  O21   106.87  3.000
 FMD  H14   C14  C15   125.64  3.000
 FMD  H14   C14  C13   128.43  3.000
 FMD  C15   C14  C13   105.92  3.000
 FMD  H15   C15  N16   121.37  3.000
 FMD  H15   C15  C14   128.98  3.000
 FMD  N16   C15  C14   109.65  3.000
 FMD  H16   N16  C15   128.25  3.000
 FMD  H16   N16  C12   121.44  3.000
 FMD  C15   N16  C12   110.30  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
 FMD  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 FMD  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 FMD  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 FMD  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 FMD  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 FMD  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 FMD  CONST_07  C15   C14  C13  C12     0.00   0.0  0
 FMD  CONST_08  C14   C15  N16  C12     0.00   0.0  0
 FMD  CONST_09  C15   N16  C12  C13     0.00   0.0  0
 FMD  CONST_10  N16   C15  C14  C13     0.00   0.0  0
 FMD  CONST_11  N16   C12  C13  C14     0.00   0.0  0
 FMD  CONST_12  C7    C8   N9   C4      0.00   0.0  0
 FMD  CONST_13  C3    C2   C1   F17   180.00   0.0  0
 FMD  CONST_14  C5    C6   C1   F17   180.00   0.0  0
 FMD  CONST_15  C6    C1   C2   C18   180.00   0.0  0
 FMD  CONST_16  C4    C3   C2   C18   180.00   0.0  0
 FMD  CONST_17  C7    C3   C2   C18     0.00   0.0  0
 FMD  CONST_18  C14   C13  C12  C11   180.00   0.0  0
 FMD  CONST_19  C15   N16  C12  C11   180.00   0.0  0
 FMD  CONST_20  N16   C12  C13  O21   180.00   0.0  0
 FMD  CONST_21  C15   C14  C13  O21   180.00   0.0  0
 FMD  CONST_22  O10   C8   N9   C4    180.00   0.0  0
 FMD  CONST_23  HC5   C5   C6   C1    180.00   0.0  0
 FMD  CONST_24  HC6   C6   C1   C2    180.00   0.0  0
 FMD  CONST_25  H14   C14  C13  C12   180.00   0.0  0
 FMD  CONST_26  H15   C15  N16  C12   180.00   0.0  0
 FMD  CONST_27  H16   N16  C12  C13   180.00   0.0  0
 FMD  CONST_28  HN9   N9   C8   C7    180.00   0.0  0
 FMD  Var_01    C12   C11  C7   C3   -179.98  30.0  2
 FMD  Var_02    C13   C12  C11  C7    179.53  30.0  2
 FMD  Var_03    C14   C13  O21  C22     2.43  30.0  2
 FMD  Var_04    H221  C22  O21  C13  -179.91  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
 FMD  chir_01  C20  C19  O27  C23  negativ
 FMD  chir_02  C23  N28  C20  C24  positiv
 FMD  chir_03  C24  O26  C23  C25  negativ

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
 FMD  plan-1  C11  0.020
 FMD  plan-1  C12  0.020
 FMD  plan-1  C13  0.020
 FMD  plan-1  O21  0.020
 FMD  plan-1  C14  0.020
 FMD  plan-1  C15  0.020
 FMD  plan-1  N16  0.020
 FMD  plan-1  H14  0.020
 FMD  plan-1  H15  0.020
 FMD  plan-1  H16  0.020
 FMD  plan-2  F17  0.020
 FMD  plan-2  C1   0.020
 FMD  plan-2  C2   0.020
 FMD  plan-2  C18  0.020
 FMD  plan-2  C19  0.020
 FMD  plan-2  C3   0.020
 FMD  plan-2  C4   0.020
 FMD  plan-2  N9   0.020
 FMD  plan-2  C8   0.020
 FMD  plan-2  O10  0.020
 FMD  plan-2  C5   0.020
 FMD  plan-2  C6   0.020
 FMD  plan-2  C7   0.020
 FMD  plan-2  C11  0.020
 FMD  plan-2  HN9  0.020
 FMD  plan-2  HC5  0.020
 FMD  plan-2  HC6  0.020

