# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 13:39:25 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: [(1R,2R)-2-{[(5-fluoro-1H-indol-2-yl)carbonyl]amino}-2,3-dihydro-1H-inden-1-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@H]1[C@@H](Cc2ccccc12)NC(=O)c3[nH]c4ccc(F)cc4c3
#
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
 IMX  IMX  '[(1R,2R)-2-{[(5-fluoro-1H-indol-2-yl)carbonyl]amino}-2,3-dihydro-1H-inden-1-yl]acetic acid'  ligand  42  26  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IMX
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
 IMX  C1    C  CH1    0  -0.099   1.7158  -0.9420   0.9586
 IMX  C2    C  CR56   0   0.079  -4.2055  -0.1416   0.4444
 IMX  C3    C  CR56   0   0.340  -3.5592   0.0975  -0.7881
 IMX  C4    C  CR16   0  -0.500  -5.5813   0.1033   0.5656
 IMX  C5    C  CR16   0  -0.287  -4.2502   0.5600  -1.9078
 IMX  C6    C  CR6    0   0.518  -6.2355   0.5607  -0.5477
 IMX  C7    C  CR16   0  -0.430  -5.6029   0.7916  -1.7754
 IMX  N8    N  NR15   0  -0.741  -2.2391  -0.2052  -0.6290
 IMX  C9    C  CR5    0   0.225  -2.0315  -0.6499   0.6514
 IMX  C10   C  CR15   0  -0.400  -3.2137  -0.6223   1.3420
 IMX  C12   C  C      0   0.528  -0.7195  -1.0569   1.1965
 IMX  O13   O  O      0  -0.486  -0.6594  -1.7336   2.2145
 IMX  N14   N  NH1    0  -0.652   0.3641  -0.6492   0.5138
 IMX  C15   C  CH2    0  -0.487   2.1842   0.0672   2.0251
 IMX  C16   C  C      0   0.087   2.7810   1.1692   1.1951
 IMX  C17   C  C      0   0.117   3.0559   0.7106  -0.0920
 IMX  C18   C  CH1    0  -0.314   2.6943  -0.7487  -0.2187
 IMX  C19   C  C1     0  -0.326   3.0643   2.4773   1.5548
 IMX  C20   C  C1     0  -0.262   3.6249   3.3309   0.6093
 IMX  C21   C  C1     0  -0.257   3.8981   2.8748  -0.6758
 IMX  C22   C  C1     0  -0.326   3.6185   1.5590  -1.0336
 IMX  C23   C  CH2    0  -0.562   3.9240  -1.6462  -0.0826
 IMX  C24   C  C      0   0.421   4.8953  -1.5782  -1.2760
 IMX  O26   O  OC    -1  -0.618   6.1010  -1.7737  -1.0251
 IMX  O25   O  O      0  -0.607   4.3957  -1.3769  -2.4019
 IMX  H1    H  HCH1   0   0.260   1.7313  -1.9661   1.3312
 IMX  H5    H  HCR6   0   0.276  -3.7499   0.7376  -2.8505
 IMX  H7    H  HCR6   0   0.278  -6.1813   1.1531  -2.6155
 IMX  HN8   H  HNR5   0   0.414  -1.5748  -0.2489  -1.3847
 IMX  H10   H  HCR5   0   0.261  -3.3478  -0.8908   2.3775
 IMX  HN14  H  HNH1   0   0.397   0.2617   0.0689  -0.1872
 IMX  H15   H  HCH2   0   0.260   1.3728   0.3962   2.6753
 IMX  H15A  H  HCH2   0   0.257   2.9424  -0.3868   2.6705
 IMX  H18   H  HCH1   0   0.248   2.2108  -0.9790  -1.1706
 IMX  H19   H  H      0   0.245   2.8476   2.8367   2.5540
 IMX  H20   H  H      0   0.250   3.8445   4.3577   0.8731
 IMX  H21   H  H      0   0.248   4.3286   3.5498  -1.4051
 IMX  H22   H  H      0   0.244   3.8382   1.2020  -2.0313
 IMX  H23   H  HCH2   0   0.217   4.4580  -1.4216   0.8445
 IMX  H23A  H  HCH2   0   0.240   3.5856  -2.6860   0.0062
 IMX  F11   F  F      0  -0.326  -7.5594   0.8039  -0.4726
 IMX  H4    H  HCR6   0   0.273  -6.1084  -0.0655   1.4959

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
 IMX  C1   N14   single    1.453  0.020  1.453
 IMX  C1   C15   single    1.541  0.020  1.541
 IMX  C1   C18   single    1.543  0.020  1.543
 IMX  C2   C3    aromatic  1.412  0.020  1.412
 IMX  C2   C4    aromatic  1.403  0.020  1.403
 IMX  C2   C10   aromatic  1.422  0.020  1.422
 IMX  C3   C5    aromatic  1.395  0.020  1.395
 IMX  C3   N8    aromatic  1.364  0.020  1.364
 IMX  C4   C6    aromatic  1.370  0.020  1.370
 IMX  C5   C7    aromatic  1.379  0.020  1.379
 IMX  C6   C7    aromatic  1.400  0.020  1.400
 IMX  C6   F11   single    1.348  0.020  1.348
 IMX  N8   C9    aromatic  1.371  0.020  1.371
 IMX  C9   C10   aromatic  1.369  0.020  1.369
 IMX  C9   C12   single    1.478  0.020  1.478
 IMX  C12  O13   double    1.224  0.020  1.224
 IMX  C12  N14   single    1.344  0.020  1.344
 IMX  C15  C16   single    1.503  0.020  1.503
 IMX  C16  C17   aromatic  1.394  0.020  1.394
 IMX  C16  C19   aromatic  1.386  0.020  1.386
 IMX  C17  C18   single    1.509  0.020  1.509
 IMX  C17  C22   aromatic  1.387  0.020  1.387
 IMX  C18  C23   single    1.528  0.020  1.528
 IMX  C19  C20   aromatic  1.392  0.020  1.392
 IMX  C20  C21   aromatic  1.391  0.020  1.391
 IMX  C21  C22   aromatic  1.392  0.020  1.392
 IMX  C23  C24   single    1.540  0.020  1.540
 IMX  C24  O25   deloc     1.248  0.020  1.248
 IMX  C24  O26   deloc     1.247  0.020  1.247
 IMX  C1   H1    single    0.970  0.020  1.090
 IMX  C4   H4    single    0.930  0.020  1.080
 IMX  C5   H5    single    0.930  0.020  1.080
 IMX  C7   H7    single    0.930  0.020  1.080
 IMX  N8   HN8   single    0.860  0.020  1.020
 IMX  C10  H10   single    0.930  0.020  1.080
 IMX  N14  HN14  single    0.860  0.020  1.020
 IMX  C15  H15   single    0.970  0.020  1.090
 IMX  C15  H15A  single    0.970  0.020  1.090
 IMX  C18  H18   single    0.970  0.020  1.090
 IMX  C19  H19   single    0.930  0.020  1.080
 IMX  C20  H20   single    0.930  0.020  1.080
 IMX  C21  H21   single    0.930  0.020  1.080
 IMX  C22  H22   single    0.930  0.020  1.080
 IMX  C23  H23   single    0.970  0.020  1.090
 IMX  C23  H23A  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
 IMX  H1    C1   C18  111.69  3.000
 IMX  H1    C1   C15  111.99  3.000
 IMX  C18   C1   C15  104.67  3.000
 IMX  H1    C1   N14  107.90  3.000
 IMX  C18   C1   N14  109.34  3.000
 IMX  C15   C1   N14  111.26  3.000
 IMX  C10   C2   C4   133.54  3.000
 IMX  C10   C2   C3   106.80  3.000
 IMX  C4    C2   C3   119.66  3.000
 IMX  N8    C3   C5   130.31  3.000
 IMX  N8    C3   C2   107.68  3.000
 IMX  C5    C3   C2   122.01  3.000
 IMX  H4    C4   C6   121.20  3.000
 IMX  H4    C4   C2   121.65  3.000
 IMX  C6    C4   C2   117.16  3.000
 IMX  H5    C5   C7   120.65  3.000
 IMX  H5    C5   C3   121.65  3.000
 IMX  C7    C5   C3   117.70  3.000
 IMX  F11   C6   C7   117.56  3.000
 IMX  F11   C6   C4   118.94  3.000
 IMX  C7    C6   C4   123.50  3.000
 IMX  H7    C7   C6   119.63  3.000
 IMX  H7    C7   C5   120.40  3.000
 IMX  C6    C7   C5   119.98  3.000
 IMX  HN8   N8   C9   125.93  3.000
 IMX  HN8   N8   C3   124.10  3.000
 IMX  C9    N8   C3   109.11  3.000
 IMX  C12   C9   C10  125.87  3.000
 IMX  C12   C9   N8   124.62  3.000
 IMX  C10   C9   N8   109.50  3.000
 IMX  H10   C10  C9   125.93  3.000
 IMX  H10   C10  C2   127.15  3.000
 IMX  C9    C10  C2   106.90  3.000
 IMX  N14   C12  O13  123.41  3.000
 IMX  N14   C12  C9   116.42  3.000
 IMX  O13   C12  C9   120.17  3.000
 IMX  HN14  N14  C12  119.14  3.000
 IMX  HN14  N14  C1   116.79  3.000
 IMX  C12   N14  C1   122.24  3.000
 IMX  H15A  C15  H15  106.80  3.000
 IMX  H15A  C15  C16  110.78  3.000
 IMX  H15   C15  C16  113.79  3.000
 IMX  H15A  C15  C1   110.30  3.000
 IMX  H15   C15  C1   112.58  3.000
 IMX  C16   C15  C1   102.63  3.000
 IMX  C19   C16  C17  120.65  3.000
 IMX  C19   C16  C15  129.04  3.000
 IMX  C17   C16  C15  110.31  3.000
 IMX  C22   C17  C18  129.20  3.000
 IMX  C22   C17  C16  120.39  3.000
 IMX  C18   C17  C16  110.39  3.000
 IMX  H18   C18  C23  108.06  3.000
 IMX  H18   C18  C17  112.53  3.000
 IMX  C23   C18  C17  111.57  3.000
 IMX  H18   C18  C1   110.97  3.000
 IMX  C23   C18  C1   111.64  3.000
 IMX  C17   C18  C1   102.07  3.000
 IMX  H19   C19  C20  120.23  3.000
 IMX  H19   C19  C16  120.76  3.000
 IMX  C20   C19  C16  119.01  3.000
 IMX  H20   C20  C21  119.76  3.000
 IMX  H20   C20  C19  119.86  3.000
 IMX  C21   C20  C19  120.38  3.000
 IMX  H21   C21  C22  119.73  3.000
 IMX  H21   C21  C20  119.73  3.000
 IMX  C22   C21  C20  120.54  3.000
 IMX  H22   C22  C21  120.54  3.000
 IMX  H22   C22  C17  120.43  3.000
 IMX  C21   C22  C17  119.03  3.000
 IMX  H23A  C23  H23  106.06  3.000
 IMX  H23A  C23  C24  107.40  3.000
 IMX  H23   C23  C24  109.88  3.000
 IMX  H23A  C23  C18  108.40  3.000
 IMX  H23   C23  C18  110.36  3.000
 IMX  C24   C23  C18  114.36  3.000
 IMX  O25   C24  O26  126.43  3.000
 IMX  O26   C24  C23  116.55  3.000
 IMX  O25   C24  C23  116.98  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
 IMX  CONST_01  C7    C5   C3   C2      0.00   0.0  0
 IMX  CONST_02  C9    N8   C3   C2      0.00   0.0  0
 IMX  CONST_03  C7    C6   C4   C2      0.00   0.0  0
 IMX  CONST_04  N8    C9   C10  C2      0.00   0.0  0
 IMX  CONST_05  C6    C4   C2   C3      0.00   0.0  0
 IMX  CONST_06  C9    C10  C2   C3      0.00   0.0  0
 IMX  CONST_07  C6    C7   C5   C3      0.00   0.0  0
 IMX  CONST_08  C10   C9   N8   C3      0.00   0.0  0
 IMX  CONST_09  C5    C3   C2   C4      0.00   0.0  0
 IMX  CONST_10  N8    C3   C2   C4    180.00   0.0  0
 IMX  CONST_11  C9    C10  C2   C4    180.00   0.0  0
 IMX  CONST_12  C5    C7   C6   C4      0.00   0.0  0
 IMX  CONST_13  C10   C2   C3   C5    180.00   0.0  0
 IMX  CONST_14  C9    N8   C3   C5    180.00   0.0  0
 IMX  CONST_15  C10   C2   C4   C6    180.00   0.0  0
 IMX  CONST_16  N8    C3   C5   C7    180.00   0.0  0
 IMX  CONST_17  C10   C2   C3   N8      0.00   0.0  0
 IMX  CONST_18  C21   C22  C17  C16     0.00   0.0  0
 IMX  CONST_19  C21   C20  C19  C16     0.00   0.0  0
 IMX  CONST_20  C20   C19  C16  C17     0.00   0.0  0
 IMX  CONST_21  C20   C21  C22  C17     0.00   0.0  0
 IMX  CONST_22  C22   C17  C16  C19     0.00   0.0  0
 IMX  CONST_23  C22   C21  C20  C19     0.00   0.0  0
 IMX  CONST_24  F11   C6   C4   C2    180.00   0.0  0
 IMX  CONST_25  C12   C9   C10  C2    180.00   0.0  0
 IMX  CONST_26  C12   C9   N8   C3    180.00   0.0  0
 IMX  CONST_27  F11   C6   C7   C5    180.00   0.0  0
 IMX  CONST_28  H5    C5   C3   C2    180.00   0.0  0
 IMX  CONST_29  HN8   N8   C3   C2    180.00   0.0  0
 IMX  CONST_30  H4    C4   C2   C3    180.00   0.0  0
 IMX  CONST_31  H10   C10  C2   C3    180.00   0.0  0
 IMX  CONST_32  H7    C7   C5   C3    180.00   0.0  0
 IMX  CONST_33  H19   C19  C16  C15     0.00   0.0  0
 IMX  CONST_34  H22   C22  C17  C16   180.00   0.0  0
 IMX  CONST_35  H20   C20  C19  C16   180.00   0.0  0
 IMX  CONST_36  H21   C21  C22  C17   180.00   0.0  0
 IMX  CONST_37  C9    C12  N14  C1    180.00   0.0  0
 IMX  CONST_38  O13   C12  N14  C1      0.00   0.0  0
 IMX  CONST_39  HN14  N14  C12  C9      0.00   0.0  0
 IMX  Var_01    C17   C16  C15  C1    -17.99  30.0  1
 IMX  Var_02    O13   C12  C9   N8   -162.34  30.0  2
 IMX  Var_03    O25   C24  C23  C18   -32.57  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
 IMX  chir_01  C1   N14  C15  C18  positiv
 IMX  chir_02  C18  C1   C17  C23  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
 IMX  plan-1  C2    0.020
 IMX  plan-1  C3    0.020
 IMX  plan-1  C4    0.020
 IMX  plan-1  C5    0.020
 IMX  plan-1  C6    0.020
 IMX  plan-1  C7    0.020
 IMX  plan-1  N8    0.020
 IMX  plan-1  C9    0.020
 IMX  plan-1  C10   0.020
 IMX  plan-1  C12   0.020
 IMX  plan-1  H5    0.020
 IMX  plan-1  H7    0.020
 IMX  plan-1  HN8   0.020
 IMX  plan-1  H10   0.020
 IMX  plan-1  F11   0.020
 IMX  plan-1  H4    0.020
 IMX  plan-2  C15   0.020
 IMX  plan-2  C16   0.020
 IMX  plan-2  C17   0.020
 IMX  plan-2  C18   0.020
 IMX  plan-2  C19   0.020
 IMX  plan-2  C20   0.020
 IMX  plan-2  C21   0.020
 IMX  plan-2  C22   0.020
 IMX  plan-2  H19   0.020
 IMX  plan-2  H20   0.020
 IMX  plan-2  H21   0.020
 IMX  plan-2  H22   0.020
 IMX  plan-3  C1    0.020
 IMX  plan-3  C9    0.020
 IMX  plan-3  C12   0.020
 IMX  plan-3  O13   0.020
 IMX  plan-3  N14   0.020
 IMX  plan-3  HN14  0.020
 IMX  plan-4  C23   0.020
 IMX  plan-4  C24   0.020
 IMX  plan-4  O26   0.020
 IMX  plan-4  O25   0.020

