# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 17:21:42 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 4-[(1R,2R)-2-{[(5-fluoro-1H-indol-2-yl)carbonyl]amino}-2,3-dihydro-1H-inden-1-yl]butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCC[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
 IPX  IPX  '4-[(1R,2R)-2-{[(5-fluoro-1H-indol-2-yl)carbonyl]amino}-2,3-dihydro-1H-inden-1-yl]butanoic acid'  ligand  48  28  .  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_IPX
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
 IPX  C1    C  CH1    0  -0.079   1.0085  -0.0138   1.2782
 IPX  C2    C  CR56   0   0.083  -4.9407  -0.3746   0.4024
 IPX  C3    C  CR56   0   0.338  -4.2753  -0.2091  -0.8316
 IPX  C4    C  CR16   0  -0.500  -6.3389  -0.4908   0.4270
 IPX  C5    C  CR16   0  -0.288  -4.9650  -0.1528  -2.0431
 IPX  C6    C  CR6    0   0.518  -6.9915  -0.4345  -0.7756
 IPX  C7    C  CR16   0  -0.429  -6.3379  -0.2682  -2.0033
 IPX  N8    N  NR15   0  -0.749  -2.9399  -0.1297  -0.5747
 IPX  C9    C  CR5    0   0.223  -2.7318  -0.2387   0.7767
 IPX  C10   C  CR15   0  -0.402  -3.9391  -0.3893   1.4085
 IPX  C12   C  C      0   0.549  -1.4201  -0.2063   1.4589
 IPX  O13   O  O      0  -0.489  -1.3714  -0.3200   2.6779
 IPX  N14   N  NH1    0  -0.663  -0.3226  -0.0651   0.6995
 IPX  C15   C  CH2    0  -0.494   1.3170   1.3780   1.8650
 IPX  C16   C  CR6    0   0.094   1.9091   2.1110   0.6948
 IPX  C17   C  CR6    0   0.134   2.3167   1.2078  -0.2841
 IPX  C18   C  CH1    0  -0.357   2.0683  -0.2077   0.1726
 IPX  C19   C  CR16   0  -0.327   2.0703   3.4744   0.5072
 IPX  C20   C  CR16   0  -0.260   2.6387   3.9298  -0.6788
 IPX  C21   C  CR16   0  -0.263   3.0357   3.0296  -1.6615
 IPX  C22   C  CR16   0  -0.322   2.8769   1.6604  -1.4688
 IPX  C23   C  CH2    0  -0.399   3.3246  -0.8713   0.7543
 IPX  C24   C  CH2    0  -0.414   4.4707  -1.0522  -0.2311
 IPX  C25   C  CH2    0  -0.580   5.6355  -1.7999   0.3991
 IPX  C26   C  C      0   0.411   6.8688  -2.0158  -0.4951
 IPX  O27   O  O      0  -0.609   6.8202  -1.6015  -1.6699
 IPX  O28   O  OC    -1  -0.634   7.8336  -2.6019   0.0414
 IPX  H1    H  HCH1   0   0.262   1.0804  -0.7952   2.0354
 IPX  H5    H  HCR6   0   0.276  -4.4483  -0.0228  -2.9847
 IPX  H7    H  HCR6   0   0.278  -6.9186  -0.2316  -2.9156
 IPX  HN8   H  HNR5   0   0.416  -2.2408  -0.0103  -1.2883
 IPX  H10   H  HCR5   0   0.260  -4.0862  -0.4957   2.4710
 IPX  HN14  H  HNH1   0   0.399  -0.4012   0.0653  -0.2956
 IPX  H15   H  HCH2   0   0.263   0.4343   1.8626   2.2827
 IPX  H15A  H  HCH2   0   0.258   2.0450   1.2916   2.6772
 IPX  H18   H  HCH1   0   0.255   1.6885  -0.8411  -0.6365
 IPX  H19   H  HCR6   0   0.246   1.7525   4.1799   1.2656
 IPX  H20   H  HCR6   0   0.252   2.7637   4.9926  -0.8427
 IPX  H21   H  HCR6   0   0.251   3.4665   3.3966  -2.5844
 IPX  H22   H  HCR6   0   0.249   3.1820   0.9629  -2.2396
 IPX  H23   H  HCH2   0   0.218   3.6735  -0.2917   1.6171
 IPX  H23A  H  HCH2   0   0.226   3.0324  -1.8513   1.1453
 IPX  H24   H  HCH2   0   0.204   4.1152  -1.5937  -1.1131
 IPX  H24A  H  HCH2   0   0.215   4.8127  -0.0791  -0.5895
 IPX  H25   H  HCH2   0   0.217   5.9570  -1.2764   1.3073
 IPX  H25A  H  HCH2   0   0.219   5.2940  -2.7819   0.7481
 IPX  F11   F  F      0  -0.326  -8.3350  -0.5445  -0.7965
 IPX  H4    H  HCR6   0   0.273  -6.8822  -0.6213   1.3542

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
 IPX  C1   N14   single    1.452  0.020  1.452
 IPX  C1   C15   single    1.542  0.020  1.542
 IPX  C1   C18   single    1.544  0.020  1.544
 IPX  C2   C3    aromatic  1.412  0.020  1.412
 IPX  C2   C4    aromatic  1.403  0.020  1.403
 IPX  C2   C10   aromatic  1.420  0.020  1.420
 IPX  C3   C5    aromatic  1.395  0.020  1.395
 IPX  C3   N8    aromatic  1.362  0.020  1.362
 IPX  C4   C6    aromatic  1.369  0.020  1.369
 IPX  C5   C7    aromatic  1.378  0.020  1.378
 IPX  C6   C7    aromatic  1.401  0.020  1.401
 IPX  C6   F11   single    1.348  0.020  1.348
 IPX  N8   C9    aromatic  1.372  0.020  1.372
 IPX  C9   C10   aromatic  1.371  0.020  1.371
 IPX  C9   C12   single    1.479  0.020  1.479
 IPX  C12  O13   double    1.225  0.020  1.225
 IPX  C12  N14   single    1.342  0.020  1.342
 IPX  C15  C16   single    1.502  0.020  1.502
 IPX  C16  C17   aromatic  1.393  0.020  1.393
 IPX  C16  C19   aromatic  1.386  0.020  1.386
 IPX  C17  C18   single    1.508  0.020  1.508
 IPX  C17  C22   aromatic  1.386  0.020  1.386
 IPX  C18  C23   single    1.535  0.020  1.535
 IPX  C19  C20   aromatic  1.392  0.020  1.392
 IPX  C20  C21   aromatic  1.391  0.020  1.391
 IPX  C21  C22   aromatic  1.392  0.020  1.392
 IPX  C23  C24   single    1.522  0.020  1.522
 IPX  C24  C25   single    1.521  0.020  1.521
 IPX  C25  C26   single    1.539  0.020  1.539
 IPX  C26  O27   deloc     1.247  0.020  1.247
 IPX  C26  O28   deloc     1.250  0.020  1.250
 IPX  C1   H1    single    0.970  0.020  1.090
 IPX  C4   H4    single    0.930  0.020  1.080
 IPX  C5   H5    single    0.930  0.020  1.080
 IPX  C7   H7    single    0.930  0.020  1.080
 IPX  N8   HN8   single    0.860  0.020  1.020
 IPX  C10  H10   single    0.930  0.020  1.080
 IPX  N14  HN14  single    0.860  0.020  1.020
 IPX  C15  H15   single    0.970  0.020  1.090
 IPX  C15  H15A  single    0.970  0.020  1.090
 IPX  C18  H18   single    0.970  0.020  1.090
 IPX  C19  H19   single    0.930  0.020  1.080
 IPX  C20  H20   single    0.930  0.020  1.080
 IPX  C21  H21   single    0.930  0.020  1.080
 IPX  C22  H22   single    0.930  0.020  1.080
 IPX  C23  H23   single    0.970  0.020  1.090
 IPX  C23  H23A  single    0.970  0.020  1.090
 IPX  C24  H24   single    0.970  0.020  1.090
 IPX  C24  H24A  single    0.970  0.020  1.090
 IPX  C25  H25   single    0.970  0.020  1.090
 IPX  C25  H25A  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
 IPX  H1    C1   C18  111.22  3.000
 IPX  H1    C1   C15  111.68  3.000
 IPX  C18   C1   C15  104.40  3.000
 IPX  H1    C1   N14  108.17  3.000
 IPX  C18   C1   N14  109.84  3.000
 IPX  C15   C1   N14  111.53  3.000
 IPX  C10   C2   C4   133.60  3.000
 IPX  C10   C2   C3   106.75  3.000
 IPX  C4    C2   C3   119.65  3.000
 IPX  N8    C3   C5   130.24  3.000
 IPX  N8    C3   C2   107.70  3.000
 IPX  C5    C3   C2   122.06  3.000
 IPX  H4    C4   C6   121.20  3.000
 IPX  H4    C4   C2   121.67  3.000
 IPX  C6    C4   C2   117.13  3.000
 IPX  H5    C5   C7   120.73  3.000
 IPX  H5    C5   C3   121.63  3.000
 IPX  C7    C5   C3   117.64  3.000
 IPX  F11   C6   C7   117.46  3.000
 IPX  F11   C6   C4   119.02  3.000
 IPX  C7    C6   C4   123.52  3.000
 IPX  H7    C7   C6   119.51  3.000
 IPX  H7    C7   C5   120.49  3.000
 IPX  C6    C7   C5   120.00  3.000
 IPX  HN8   N8   C9   127.07  3.000
 IPX  HN8   N8   C3   123.67  3.000
 IPX  C9    N8   C3   109.26  3.000
 IPX  C12   C9   C10  124.81  3.000
 IPX  C12   C9   N8   125.97  3.000
 IPX  C10   C9   N8   109.22  3.000
 IPX  H10   C10  C9   125.83  3.000
 IPX  H10   C10  C2   127.10  3.000
 IPX  C9    C10  C2   107.07  3.000
 IPX  N14   C12  O13  122.70  3.000
 IPX  N14   C12  C9   117.81  3.000
 IPX  O13   C12  C9   119.48  3.000
 IPX  HN14  N14  C12  120.61  3.000
 IPX  HN14  N14  C1   117.44  3.000
 IPX  C12   N14  C1   121.85  3.000
 IPX  H15A  C15  H15  106.83  3.000
 IPX  H15A  C15  C16  110.77  3.000
 IPX  H15   C15  C16  113.62  3.000
 IPX  H15A  C15  C1   110.14  3.000
 IPX  H15   C15  C1   112.65  3.000
 IPX  C16   C15  C1   102.87  3.000
 IPX  C19   C16  C17  120.58  3.000
 IPX  C19   C16  C15  129.15  3.000
 IPX  C17   C16  C15  110.27  3.000
 IPX  C22   C17  C18  129.18  3.000
 IPX  C22   C17  C16  120.47  3.000
 IPX  C18   C17  C16  110.34  3.000
 IPX  H18   C18  C23  108.28  3.000
 IPX  H18   C18  C17  112.10  3.000
 IPX  C23   C18  C17  112.68  3.000
 IPX  H18   C18  C1   111.32  3.000
 IPX  C23   C18  C1   110.17  3.000
 IPX  C17   C18  C1   102.25  3.000
 IPX  H19   C19  C20  120.21  3.000
 IPX  H19   C19  C16  120.78  3.000
 IPX  C20   C19  C16  119.00  3.000
 IPX  H20   C20  C21  119.71  3.000
 IPX  H20   C20  C19  119.83  3.000
 IPX  C21   C20  C19  120.46  3.000
 IPX  H21   C21  C22  119.80  3.000
 IPX  H21   C21  C20  119.77  3.000
 IPX  C22   C21  C20  120.43  3.000
 IPX  H22   C22  C21  120.18  3.000
 IPX  H22   C22  C17  120.77  3.000
 IPX  C21   C22  C17  119.05  3.000
 IPX  H23A  C23  H23  106.09  3.000
 IPX  H23A  C23  C24  109.01  3.000
 IPX  H23   C23  C24  109.43  3.000
 IPX  H23A  C23  C18  107.68  3.000
 IPX  H23   C23  C18  109.28  3.000
 IPX  C24   C23  C18  114.97  3.000
 IPX  H24A  C24  H24  106.15  3.000
 IPX  H24A  C24  C25  109.53  3.000
 IPX  H24   C24  C25  109.85  3.000
 IPX  H24A  C24  C23  110.02  3.000
 IPX  H24   C24  C23  109.63  3.000
 IPX  C25   C24  C23  111.52  3.000
 IPX  H25A  C25  H25  104.79  3.000
 IPX  H25A  C25  C26  107.99  3.000
 IPX  H25   C25  C26  108.26  3.000
 IPX  H25A  C25  C24  109.49  3.000
 IPX  H25   C25  C24  109.45  3.000
 IPX  C26   C25  C24  116.23  3.000
 IPX  O28   C26  O27  126.19  3.000
 IPX  O28   C26  C25  115.79  3.000
 IPX  O27   C26  C25  118.02  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
 IPX  CONST_01  C7    C5   C3   C2      0.00   0.0  0
 IPX  CONST_02  C9    N8   C3   C2      0.00   0.0  0
 IPX  CONST_03  C7    C6   C4   C2      0.00   0.0  0
 IPX  CONST_04  N8    C9   C10  C2      0.00   0.0  0
 IPX  CONST_05  C6    C4   C2   C3      0.00   0.0  0
 IPX  CONST_06  C9    C10  C2   C3      0.00   0.0  0
 IPX  CONST_07  C6    C7   C5   C3      0.00   0.0  0
 IPX  CONST_08  C10   C9   N8   C3      0.00   0.0  0
 IPX  CONST_09  C5    C3   C2   C4      0.00   0.0  0
 IPX  CONST_10  N8    C3   C2   C4    180.00   0.0  0
 IPX  CONST_11  C9    C10  C2   C4    180.00   0.0  0
 IPX  CONST_12  C5    C7   C6   C4      0.00   0.0  0
 IPX  CONST_13  C10   C2   C3   C5    180.00   0.0  0
 IPX  CONST_14  C9    N8   C3   C5    180.00   0.0  0
 IPX  CONST_15  C10   C2   C4   C6    180.00   0.0  0
 IPX  CONST_16  N8    C3   C5   C7    180.00   0.0  0
 IPX  CONST_17  C10   C2   C3   N8      0.00   0.0  0
 IPX  CONST_18  C21   C22  C17  C16     0.00   0.0  0
 IPX  CONST_19  C21   C20  C19  C16     0.00   0.0  0
 IPX  CONST_20  C20   C19  C16  C17     0.00   0.0  0
 IPX  CONST_21  C20   C21  C22  C17     0.00   0.0  0
 IPX  CONST_22  C22   C17  C16  C19     0.00   0.0  0
 IPX  CONST_23  C22   C21  C20  C19     0.00   0.0  0
 IPX  CONST_24  F11   C6   C4   C2    180.00   0.0  0
 IPX  CONST_25  C12   C9   C10  C2    180.00   0.0  0
 IPX  CONST_26  C12   C9   N8   C3    180.00   0.0  0
 IPX  CONST_27  F11   C6   C7   C5    180.00   0.0  0
 IPX  CONST_28  H5    C5   C3   C2    180.00   0.0  0
 IPX  CONST_29  HN8   N8   C3   C2    180.00   0.0  0
 IPX  CONST_30  H4    C4   C2   C3    180.00   0.0  0
 IPX  CONST_31  H10   C10  C2   C3    180.00   0.0  0
 IPX  CONST_32  H7    C7   C5   C3    180.00   0.0  0
 IPX  CONST_33  H19   C19  C16  C15     0.00   0.0  0
 IPX  CONST_34  H22   C22  C17  C16   180.00   0.0  0
 IPX  CONST_35  H20   C20  C19  C16   180.00   0.0  0
 IPX  CONST_36  H21   C21  C22  C17   180.00   0.0  0
 IPX  CONST_37  C9    C12  N14  C1    180.00   0.0  0
 IPX  CONST_38  O13   C12  N14  C1      0.00   0.0  0
 IPX  CONST_39  HN14  N14  C12  C9      0.00   0.0  0
 IPX  Var_01    C17   C16  C15  C1    -17.63  30.0  1
 IPX  Var_02    O13   C12  C9   N8   -179.72  30.0  2
 IPX  Var_03    C25   C24  C23  C18  -176.10  30.0  3
 IPX  Var_04    C26   C25  C24  C23  -178.69  30.0  3
 IPX  Var_05    O27   C26  C25  C24    -1.83  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
 IPX  chir_01  C1   N14  C15  C18  positiv
 IPX  chir_02  C18  C23  C17  C1   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
 IPX  plan-1  C2    0.020
 IPX  plan-1  C3    0.020
 IPX  plan-1  C4    0.020
 IPX  plan-1  C5    0.020
 IPX  plan-1  C6    0.020
 IPX  plan-1  C7    0.020
 IPX  plan-1  N8    0.020
 IPX  plan-1  C9    0.020
 IPX  plan-1  C10   0.020
 IPX  plan-1  C12   0.020
 IPX  plan-1  H5    0.020
 IPX  plan-1  H7    0.020
 IPX  plan-1  HN8   0.020
 IPX  plan-1  H10   0.020
 IPX  plan-1  F11   0.020
 IPX  plan-1  H4    0.020
 IPX  plan-2  C15   0.020
 IPX  plan-2  C16   0.020
 IPX  plan-2  C17   0.020
 IPX  plan-2  C18   0.020
 IPX  plan-2  C19   0.020
 IPX  plan-2  C20   0.020
 IPX  plan-2  C21   0.020
 IPX  plan-2  C22   0.020
 IPX  plan-2  H19   0.020
 IPX  plan-2  H20   0.020
 IPX  plan-2  H21   0.020
 IPX  plan-2  H22   0.020
 IPX  plan-3  C1    0.020
 IPX  plan-3  C9    0.020
 IPX  plan-3  C12   0.020
 IPX  plan-3  O13   0.020
 IPX  plan-3  N14   0.020
 IPX  plan-3  HN14  0.020
 IPX  plan-4  C25   0.020
 IPX  plan-4  C26   0.020
 IPX  plan-4  O27   0.020
 IPX  plan-4  O28   0.020

