# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 15:33:02 2021
#   Inital geometry file: a 126 line input string
#   Ligand name: (1S,3S,4S)-3-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-4-(1,1,3,3,3-pentafluoroprop-1-en-2-yl)cyclopentane-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(C=N[C@H]2C[C@H](C[C@H]2C(=C(F)F)C(F)(F)F)C(O)=O)c1O
#
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
 IF1  IF1  '(1S,3S,4S)-3-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-4-(1,1,3,3,3-pentafluoroprop-1-en-2-yl)cyclopentane-1-carboxylic acid'  ligand  50  32  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_IF1
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
 IF1  C01  C  C     0   0.549  -17.7103   -6.9637  -4.2647
 IF1  C02  C  CT    0   1.069  -21.2610   -6.9462  -0.5008
 IF1  C03  C  C     0   0.801  -20.5224   -5.0897   0.9038
 IF1  C04  C  CR6   0   0.269  -19.1289   -8.6745   3.0649
 IF1  C05  C  CR6   0   0.128  -19.3202   -9.4198   4.2438
 IF1  C07  C  CR16  0  -0.143  -17.5638  -10.7893   3.7277
 IF1  C08  C  CR6   0   0.004  -17.3046  -10.1312   2.5409
 IF1  C09  C  CR6   0   0.059  -18.1031   -9.0337   2.1892
 IF1  C12  C  CH2   0  -0.298  -16.1653  -10.5837   1.6825
 IF1  C18  C  C1    0  -0.073  -17.8634   -8.3422   0.9099
 IF1  C20  C  CH1   0  -0.073  -17.8373   -6.4873  -0.5197
 IF1  C21  C  CH2   0  -0.483  -17.4578   -7.3274  -1.7408
 IF1  C22  C  CH1   0  -0.385  -17.7789   -6.3676  -2.8860
 IF1  C23  C  CH2   0  -0.432  -19.1763   -5.8584  -2.5042
 IF1  C24  C  CH1   0  -0.332  -19.0666   -5.6207  -0.9845
 IF1  C25  C  C     0  -0.474  -20.3167   -5.8422  -0.1648
 IF1  F28  F  F     0  -0.318  -22.0346   -6.6386  -1.5589
 IF1  F29  F  F     0  -0.308  -20.5976   -8.0645  -0.8314
 IF1  F30  F  F     0  -0.296  -22.0971   -7.2775   0.4840
 IF1  F31  F  F     0  -0.258  -19.7003   -4.1437   1.2859
 IF1  F32  F  F     0  -0.254  -21.5313   -5.1399   1.7335
 IF1  N06  N  N     0  -0.402  -18.5477  -10.4471   4.5500
 IF1  O10  O  OH1   0  -0.593  -19.9231   -7.6400   2.7625
 IF1  O13  O  O2    0  -0.578  -15.1964   -9.5255   1.6409
 IF1  O15  O  O     0  -0.700  -14.6201   -9.4689  -0.9174
 IF1  O16  O  OH1   0  -0.730  -13.3095   -8.1728   0.9250
 IF1  O17  O  OH1   0  -0.738  -13.1835  -10.7077   0.8647
 IF1  O26  O  OH1   0  -0.591  -18.4441   -8.0641  -4.3855
 IF1  O27  O  O     0  -0.444  -17.0711   -6.4987  -5.1766
 IF1  P14  P  P     0   1.459  -14.1132   -9.4712   0.4700
 IF1  H1   H  HCR6  0   0.262  -16.9499  -11.6318   4.0295
 IF1  H2   H  HCH3  0   0.275  -20.4066   -9.7273   6.0484
 IF1  H3   H  HCH3  0   0.263  -20.3072   -8.0341   5.5739
 IF1  H4   H  HCH3  0   0.260  -21.4070   -9.1279   4.7341
 IF1  H5   H  HCH2  0   0.263  -16.5063  -10.8311   0.6732
 IF1  H6   H  HCH2  0   0.276  -15.7121  -11.4816   2.1065
 IF1  H7   H  H     0   0.238  -17.4869   -8.9815   0.1069
 IF1  H8   H  HCH1  0   0.266  -17.0206   -5.7792  -0.3453
 IF1  H9   H  HCH2  0   0.243  -18.0836   -8.2195  -1.8144
 IF1  H10  H  HCH2  0   0.272  -16.4169   -7.6508  -1.7227
 IF1  H11  H  HCH1  0   0.277  -17.0713   -5.5346  -2.8669
 IF1  H12  H  HCH2  0   0.272  -19.4545   -4.9467  -3.0319
 IF1  H13  H  HCH2  0   0.249  -19.9082   -6.6191  -2.7665
 IF1  H14  H  HCH1  0   0.289  -18.7883   -4.5759  -0.8561
 IF1  H15  H  HOH1  0   0.484  -20.6712   -7.5922   3.3684
 IF1  H16  H  HOH1  0   0.504  -13.1971   -7.5158   0.2258
 IF1  H17  H  HOH1  0   0.500  -12.5860  -10.9968   0.1621
 IF1  H18  H  HOH1  0   0.483  -18.3888   -8.4019  -5.2918
 IF1  N19  N  N     0  -0.320  -18.0763   -7.1099   0.7506
 IF1  C11  C  CH3   0  -0.789  -20.4185   -9.0532   5.1957

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
 IF1  O27  C01  double    1.207  0.020  1.207
 IF1  O26  C01  single    1.328  0.020  1.328
 IF1  C01  C22  single    1.504  0.020  1.504
 IF1  C22  C23  single    1.535  0.020  1.535
 IF1  C22  C21  single    1.528  0.020  1.528
 IF1  C23  C24  single    1.542  0.020  1.542
 IF1  F28  C02  single    1.346  0.020  1.346
 IF1  C21  C20  single    1.530  0.020  1.530
 IF1  F29  C02  single    1.342  0.020  1.342
 IF1  C02  C25  single    1.491  0.020  1.491
 IF1  C02  F30  single    1.334  0.020  1.334
 IF1  C24  C20  single    1.574  0.020  1.574
 IF1  C24  C25  single    1.511  0.020  1.511
 IF1  C20  N19  single    1.435  0.020  1.435
 IF1  C25  C03  double    1.323  0.020  1.323
 IF1  O15  P14  double    1.477  0.020  1.477
 IF1  O17  P14  single    1.597  0.020  1.597
 IF1  N19  C18  double    1.261  0.020  1.261
 IF1  C03  F32  single    1.307  0.020  1.307
 IF1  C03  F31  single    1.310  0.020  1.310
 IF1  P14  O16  single    1.593  0.020  1.593
 IF1  P14  O13  single    1.596  0.020  1.596
 IF1  C18  C09  single    1.474  0.020  1.474
 IF1  C12  O13  single    1.435  0.020  1.435
 IF1  C12  C08  single    1.496  0.020  1.496
 IF1  C09  C08  aromatic  1.402  0.020  1.402
 IF1  C09  C04  aromatic  1.396  0.020  1.396
 IF1  C08  C07  aromatic  1.382  0.020  1.382
 IF1  O10  C04  single    1.339  0.020  1.339
 IF1  C04  C05  aromatic  1.408  0.020  1.408
 IF1  C07  N06  aromatic  1.327  0.020  1.327
 IF1  C05  N06  aromatic  1.321  0.020  1.321
 IF1  C05  C11  single    1.499  0.020  1.499
 IF1  C07  H1   single    0.930  0.020  1.080
 IF1  C11  H2   single    0.970  0.020  1.090
 IF1  C11  H3   single    0.970  0.020  1.090
 IF1  C11  H4   single    0.970  0.020  1.090
 IF1  C12  H5   single    0.970  0.020  1.090
 IF1  C12  H6   single    0.970  0.020  1.090
 IF1  C18  H7   single    0.930  0.020  1.080
 IF1  C20  H8   single    0.970  0.020  1.090
 IF1  C21  H9   single    0.970  0.020  1.090
 IF1  C21  H10  single    0.970  0.020  1.090
 IF1  C22  H11  single    0.970  0.020  1.090
 IF1  C23  H12  single    0.970  0.020  1.090
 IF1  C23  H13  single    0.970  0.020  1.090
 IF1  C24  H14  single    0.970  0.020  1.090
 IF1  O10  H15  single    0.850  0.020  0.980
 IF1  O16  H16  single    0.850  0.020  0.980
 IF1  O17  H17  single    0.850  0.020  0.980
 IF1  O26  H18  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
 IF1  O27  C01  O26  122.89  3.000
 IF1  O26  C01  C22  112.75  3.000
 IF1  O27  C01  C22  124.35  3.000
 IF1  F30  C02  F29  106.55  3.000
 IF1  F30  C02  F28  106.08  3.000
 IF1  F29  C02  F28  106.32  3.000
 IF1  F30  C02  C25  114.49  3.000
 IF1  F29  C02  C25  111.07  3.000
 IF1  F28  C02  C25  111.83  3.000
 IF1  F32  C03  F31  109.08  3.000
 IF1  F31  C03  C25  123.27  3.000
 IF1  F32  C03  C25  127.65  3.000
 IF1  O10  C04  C09  119.54  3.000
 IF1  O10  C04  C05  121.17  3.000
 IF1  C09  C04  C05  119.28  3.000
 IF1  N06  C05  C11  118.12  3.000
 IF1  C11  C05  C04  120.13  3.000
 IF1  N06  C05  C04  121.75  3.000
 IF1  H1   C07  N06  116.56  3.000
 IF1  H1   C07  C08  120.17  3.000
 IF1  N06  C07  C08  123.27  3.000
 IF1  C12  C08  C09  121.76  3.000
 IF1  C09  C08  C07  118.78  3.000
 IF1  C12  C08  C07  119.44  3.000
 IF1  C18  C09  C08  119.50  3.000
 IF1  C08  C09  C04  117.55  3.000
 IF1  C18  C09  C04  122.92  3.000
 IF1  H6   C12  H5   107.56  3.000
 IF1  H6   C12  O13  109.72  3.000
 IF1  H5   C12  O13  110.52  3.000
 IF1  H6   C12  C08  110.00  3.000
 IF1  H5   C12  C08  111.12  3.000
 IF1  O13  C12  C08  107.92  3.000
 IF1  H7   C18  N19  122.48  3.000
 IF1  H7   C18  C09  114.78  3.000
 IF1  N19  C18  C09  122.74  3.000
 IF1  H8   C20  N19  105.30  3.000
 IF1  H8   C20  C24  105.87  3.000
 IF1  N19  C20  C24  111.73  3.000
 IF1  H8   C20  C21  107.28  3.000
 IF1  N19  C20  C21  120.65  3.000
 IF1  C24  C20  C21  105.09  3.000
 IF1  H10  C21  H9   107.81  3.000
 IF1  H10  C21  C22  113.54  3.000
 IF1  H9   C21  C22  110.01  3.000
 IF1  H10  C21  C20  112.74  3.000
 IF1  H9   C21  C20  111.11  3.000
 IF1  C22  C21  C20  101.60  3.000
 IF1  H11  C22  C23  109.40  3.000
 IF1  H11  C22  C21  109.24  3.000
 IF1  C23  C22  C21  102.31  3.000
 IF1  H11  C22  C01  106.77  3.000
 IF1  C21  C22  C01  115.37  3.000
 IF1  C23  C22  C01  113.64  3.000
 IF1  H13  C23  H12  107.26  3.000
 IF1  H13  C23  C24  113.16  3.000
 IF1  H12  C23  C24  111.50  3.000
 IF1  H13  C23  C22  108.69  3.000
 IF1  H12  C23  C22  112.92  3.000
 IF1  C24  C23  C22  103.38  3.000
 IF1  H14  C24  C25  106.75  3.000
 IF1  H14  C24  C23  106.39  3.000
 IF1  C25  C24  C23  116.94  3.000
 IF1  H14  C24  C20  107.08  3.000
 IF1  C25  C24  C20  113.90  3.000
 IF1  C23  C24  C20  105.17  3.000
 IF1  C24  C25  C03  118.90  3.000
 IF1  C03  C25  C02  120.31  3.000
 IF1  C24  C25  C02  120.67  3.000
 IF1  C07  N06  C05  119.36  3.000
 IF1  H15  O10  C04  110.90  3.000
 IF1  P14  O13  C12  120.30  3.000
 IF1  H16  O16  P14  113.97  3.000
 IF1  H17  O17  P14  114.32  3.000
 IF1  H18  O26  C01  110.03  3.000
 IF1  O17  P14  O16  105.47  3.000
 IF1  O16  P14  O15  116.10  3.000
 IF1  O17  P14  O15  115.67  3.000
 IF1  O16  P14  O13   99.24  3.000
 IF1  O17  P14  O13  100.81  3.000
 IF1  O15  P14  O13  117.15  3.000
 IF1  C20  N19  C18  120.52  3.000
 IF1  H4   C11  H3   107.57  3.000
 IF1  H4   C11  H2   107.38  3.000
 IF1  H3   C11  H2   107.81  3.000
 IF1  H4   C11  C05  112.18  3.000
 IF1  H3   C11  C05  111.92  3.000
 IF1  H2   C11  C05  109.78  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
 IF1  CONST_01  C07  C08  C09  C04     0.00   0.0  0
 IF1  CONST_02  C07  N06  C05  C04     0.00   0.0  0
 IF1  CONST_03  C08  C09  C04  C05     0.00   0.0  0
 IF1  CONST_04  C08  C07  N06  C05     0.00   0.0  0
 IF1  CONST_05  N06  C07  C08  C09     0.00   0.0  0
 IF1  CONST_06  N06  C05  C04  C09     0.00   0.0  0
 IF1  CONST_07  C12  C08  C09  C04   180.00   0.0  0
 IF1  CONST_08  C18  C09  C04  C05   180.00   0.0  0
 IF1  CONST_09  C18  C09  C08  C07   180.00   0.0  0
 IF1  CONST_10  C11  C05  N06  C07   180.00   0.0  0
 IF1  CONST_11  O10  C04  C09  C08   180.00   0.0  0
 IF1  CONST_12  C11  C05  C04  C09   180.00   0.0  0
 IF1  CONST_13  N06  C07  C08  C12   180.00   0.0  0
 IF1  CONST_14  O10  C04  C05  N06   180.00   0.0  0
 IF1  CONST_15  H1   C07  N06  C05   180.00   0.0  0
 IF1  CONST_16  H18  O26  C01  C22   180.00   0.0  0
 IF1  Var_01    N19  C18  C09  C04    33.29  30.0  1
 IF1  Var_02    O13  C12  C08  C07  -115.09  30.0  2
 IF1  Var_03    H2   C11  C05  C04  -179.34  30.0  2
 IF1  Var_04    F32  C03  C25  C24  -179.50   0.0  2
 IF1  Var_05    F28  C02  C25  C24   -77.41  30.0  3
 IF1  Var_06    O15  P14  O13  C12    55.65  30.0  1

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
 IF1  chir_01  C20  C21  C24  N19  negativ
 IF1  chir_02  C22  C21  C23  C01  positiv
 IF1  chir_03  C24  C23  C20  C25  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
 IF1  plan-1  C04  0.020
 IF1  plan-1  C05  0.020
 IF1  plan-1  C07  0.020
 IF1  plan-1  C08  0.020
 IF1  plan-1  C09  0.020
 IF1  plan-1  C12  0.020
 IF1  plan-1  C18  0.020
 IF1  plan-1  N06  0.020
 IF1  plan-1  O10  0.020
 IF1  plan-1  H1   0.020
 IF1  plan-1  C11  0.020
 IF1  plan-2  C01  0.020
 IF1  plan-2  C22  0.020
 IF1  plan-2  O26  0.020
 IF1  plan-2  O27  0.020
 IF1  plan-2  H18  0.020
 IF1  plan-3  C02  0.020
 IF1  plan-3  C03  0.020
 IF1  plan-3  C24  0.020
 IF1  plan-3  C25  0.020
 IF1  plan-3  F31  0.020
 IF1  plan-3  F32  0.020
 IF1  plan-4  C09  0.020
 IF1  plan-4  C18  0.020
 IF1  plan-4  C20  0.020
 IF1  plan-4  H7   0.020
 IF1  plan-4  N19  0.020

