# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 23 03:42:17 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 1-{2-fluoro-4-[3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl]benzyl}pyrrolidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cc(ccc1CN2CCCC2=O)n3nc(c4CCCCc34)C(F)(F)F
#
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
 1NF  1NF  1-{2-fluoro-4-[3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl]benzyl}pyrrolidin-2-one  ligand  46  27  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1NF
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
 1NF  C1    C  CR6   0   0.556  -2.1827  -0.8941  -0.0790
 1NF  F1    F  F     0  -0.302  -2.9867  -1.6531   0.6769
 1NF  N1    N  NT    0  -0.457  -4.9744   0.4273  -0.3103
 1NF  C2    C  CR16  0  -0.439  -0.8354  -0.8821   0.2167
 1NF  N2    N  NR5   0  -0.471   1.3876  -0.0767  -0.3032
 1NF  C3    C  CR6   0   0.337   0.0025  -0.1007  -0.5680
 1NF  N3    N  N     0  -0.285   2.0381   1.0828  -0.3393
 1NF  C4    C  CR16  0  -0.277  -0.5104   0.6610  -1.6085
 1NF  C5    C  CR16  0  -0.285  -1.8730   0.6320  -1.8596
 1NF  C6    C  CR6   0  -0.100  -2.7412  -0.1512  -1.1077
 1NF  C7    C  CH2   0  -0.364  -4.2214  -0.1766  -1.3793
 1NF  C8    C  CH2   0  -0.257  -4.8565   1.8411  -0.0100
 1NF  C9    C  CH2   0  -0.479  -5.5853   1.9706   1.3282
 1NF  C10   C  CH2   0  -0.584  -6.5834   0.8180   1.3053
 1NF  C11   C  C     0   0.541  -5.9562  -0.1971   0.3739
 1NF  C12   C  CR5   0  -0.045   3.2947   0.7724  -0.1067
 1NF  C13   C  CR5   0  -0.170   3.4780  -0.6084   0.0820
 1NF  C14   C  CH2   0  -0.507   4.6912  -1.4441   0.3295
 1NF  C15   C  CH2   0  -0.454   4.2693  -2.8613   0.7212
 1NF  C16   C  CH2   0  -0.448   3.1519  -3.3888  -0.1771
 1NF  C17   C  CH2   0  -0.517   1.8667  -2.5744  -0.0051
 1NF  C18   C  CR5   0   0.437   2.2149  -1.1284  -0.0589
 1NF  C19   C  CT    0   1.068   4.3364   1.8269  -0.0373
 1NF  H2    H  HCR6  0   0.297  -0.4623  -1.4538   1.0557
 1NF  H4    H  HCR6  0   0.280   0.1457   1.2667  -2.2173
 1NF  H5    H  HCR6  0   0.276  -2.2734   1.2251  -2.6723
 1NF  H7    H  HCH2  0   0.280  -4.5752  -1.1990  -1.5133
 1NF  H7A   H  HCH2  0   0.272  -4.4197   0.3532  -2.3154
 1NF  H8    H  HCH2  0   0.251  -3.8095   2.1406   0.0546
 1NF  H8A   H  HCH2  0   0.241  -5.3270   2.4398  -0.7970
 1NF  H9    H  HCH2  0   0.251  -4.8773   1.8370   2.1468
 1NF  H9A   H  HCH2  0   0.257  -6.0525   2.9459   1.4464
 1NF  H10   H  HCH2  0   0.273  -6.7854   0.3832   2.2834
 1NF  H10A  H  HCH2  0   0.273  -7.5444   1.1181   0.8775
 1NF  H14   H  HCH2  0   0.247   5.3094  -1.4750  -0.5727
 1NF  H14A  H  HCH2  0   0.250   5.3145  -1.0059   1.1119
 1NF  H15   H  HCH2  0   0.245   5.1332  -3.5258   0.6749
 1NF  H15A  H  HCH2  0   0.230   3.9246  -2.8651   1.7597
 1NF  H16   H  HCH2  0   0.234   3.4715  -3.3510  -1.2223
 1NF  H16A  H  HCH2  0   0.248   2.9446  -4.4344   0.0540
 1NF  H17   H  HCH2  0   0.271   1.1330  -2.8333  -0.7718
 1NF  H17A  H  HCH2  0   0.262   1.4120  -2.8195   0.9593
 1NF  O1    O  O     0  -0.500  -6.2931  -1.3612   0.2354
 1NF  F2    F  F     0  -0.304   3.8702   3.0264  -0.3807
 1NF  F3    F  F     0  -0.315   5.3680   1.5456  -0.8465
 1NF  F4    F  F     0  -0.316   4.8463   1.9334   1.1997

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
 1NF  C1   F1    single    1.339  0.020  1.339
 1NF  C1   C2    aromatic  1.379  0.020  1.379
 1NF  C1   C6    aromatic  1.386  0.020  1.386
 1NF  N1   C7    single    1.440  0.020  1.440
 1NF  N1   C8    single    1.450  0.020  1.450
 1NF  N1   C11   single    1.350  0.020  1.350
 1NF  O1   C11   double    1.220  0.020  1.220
 1NF  C2   C3    aromatic  1.389  0.020  1.389
 1NF  F2   C19   single    1.332  0.020  1.332
 1NF  N2   C3    single    1.410  0.020  1.410
 1NF  N2   N3    aromatic  1.330  0.020  1.330
 1NF  N2   C18   aromatic  1.360  0.020  1.360
 1NF  C3   C4    aromatic  1.388  0.020  1.388
 1NF  F3   C19   single    1.341  0.020  1.341
 1NF  N3   C12   aromatic  1.315  0.020  1.315
 1NF  C4   C5    aromatic  1.386  0.020  1.386
 1NF  F4   C19   single    1.342  0.020  1.342
 1NF  C5   C6    aromatic  1.390  0.020  1.390
 1NF  C6   C7    single    1.505  0.020  1.505
 1NF  C8   C9    single    1.529  0.020  1.529
 1NF  C9   C10   single    1.525  0.020  1.525
 1NF  C10  C11   single    1.514  0.020  1.514
 1NF  C12  C13   aromatic  1.406  0.020  1.406
 1NF  C12  C19   single    1.484  0.020  1.484
 1NF  C13  C14   single    1.494  0.020  1.494
 1NF  C13  C18   aromatic  1.373  0.020  1.373
 1NF  C14  C15   single    1.530  0.020  1.530
 1NF  C15  C16   single    1.528  0.020  1.528
 1NF  C16  C17   single    1.531  0.020  1.531
 1NF  C17  C18   single    1.488  0.020  1.488
 1NF  C2   H2    single    0.930  0.020  1.080
 1NF  C4   H4    single    0.930  0.020  1.080
 1NF  C5   H5    single    0.930  0.020  1.080
 1NF  C7   H7    single    0.970  0.020  1.090
 1NF  C7   H7A   single    0.970  0.020  1.090
 1NF  C8   H8    single    0.970  0.020  1.090
 1NF  C8   H8A   single    0.970  0.020  1.090
 1NF  C9   H9    single    0.970  0.020  1.090
 1NF  C9   H9A   single    0.970  0.020  1.090
 1NF  C10  H10   single    0.970  0.020  1.090
 1NF  C10  H10A  single    0.970  0.020  1.090
 1NF  C14  H14   single    0.970  0.020  1.090
 1NF  C14  H14A  single    0.970  0.020  1.090
 1NF  C15  H15   single    0.970  0.020  1.090
 1NF  C15  H15A  single    0.970  0.020  1.090
 1NF  C16  H16   single    0.970  0.020  1.090
 1NF  C16  H16A  single    0.970  0.020  1.090
 1NF  C17  H17   single    0.970  0.020  1.090
 1NF  C17  H17A  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
 1NF  C6    C1   C2   123.22  3.000
 1NF  C6    C1   F1   118.73  3.000
 1NF  C2    C1   F1   118.05  3.000
 1NF  C11   N1   C8   113.90  3.000
 1NF  C11   N1   C7   124.23  3.000
 1NF  C8    N1   C7   121.33  3.000
 1NF  H2    C2   C3   121.84  3.000
 1NF  H2    C2   C1   119.91  3.000
 1NF  C3    C2   C1   118.24  3.000
 1NF  C18   N2   N3   112.42  3.000
 1NF  C18   N2   C3   128.16  3.000
 1NF  N3    N2   C3   119.35  3.000
 1NF  C4    C3   N2   119.63  3.000
 1NF  C4    C3   C2   120.63  3.000
 1NF  N2    C3   C2   119.74  3.000
 1NF  C12   N3   N2   104.88  3.000
 1NF  H4    C4   C5   120.44  3.000
 1NF  H4    C4   C3   120.37  3.000
 1NF  C5    C4   C3   119.20  3.000
 1NF  H5    C5   C6   118.92  3.000
 1NF  H5    C5   C4   119.22  3.000
 1NF  C6    C5   C4   121.86  3.000
 1NF  C7    C6   C5   121.74  3.000
 1NF  C7    C6   C1   121.40  3.000
 1NF  C5    C6   C1   116.85  3.000
 1NF  H7A   C7   H7   106.87  3.000
 1NF  H7A   C7   C6   108.94  3.000
 1NF  H7    C7   C6   110.93  3.000
 1NF  H7A   C7   N1   109.72  3.000
 1NF  H7    C7   N1   108.35  3.000
 1NF  C6    C7   N1   111.91  3.000
 1NF  H8A   C8   H8   107.75  3.000
 1NF  H8A   C8   C9   112.21  3.000
 1NF  H8    C8   C9   112.48  3.000
 1NF  H8A   C8   N1   110.44  3.000
 1NF  H8    C8   N1   110.97  3.000
 1NF  C9    C8   N1   103.00  3.000
 1NF  H9A   C9   H9   107.88  3.000
 1NF  H9A   C9   C10  113.47  3.000
 1NF  H9    C9   C10  110.10  3.000
 1NF  H9A   C9   C8   112.06  3.000
 1NF  H9    C9   C8   109.70  3.000
 1NF  C10   C9   C8   103.58  3.000
 1NF  H10A  C10  H10  107.32  3.000
 1NF  H10A  C10  C11  107.90  3.000
 1NF  H10   C10  C11  111.21  3.000
 1NF  H10A  C10  C9   111.93  3.000
 1NF  H10   C10  C9   114.18  3.000
 1NF  C11   C10  C9   104.18  3.000
 1NF  C10   C11  O1   126.54  3.000
 1NF  C10   C11  N1   107.64  3.000
 1NF  O1    C11  N1   125.80  3.000
 1NF  C19   C12  C13  126.89  3.000
 1NF  C19   C12  N3   120.75  3.000
 1NF  C13   C12  N3   112.35  3.000
 1NF  C18   C13  C14  123.52  3.000
 1NF  C18   C13  C12  103.78  3.000
 1NF  C14   C13  C12  132.66  3.000
 1NF  H14A  C14  H14  106.24  3.000
 1NF  H14A  C14  C15  110.23  3.000
 1NF  H14   C14  C15  109.93  3.000
 1NF  H14A  C14  C13  110.96  3.000
 1NF  H14   C14  C13  109.76  3.000
 1NF  C15   C14  C13  109.67  3.000
 1NF  H15A  C15  H15  106.71  3.000
 1NF  H15A  C15  C16  109.06  3.000
 1NF  H15   C15  C16  110.12  3.000
 1NF  H15A  C15  C14  109.46  3.000
 1NF  H15   C15  C14  109.57  3.000
 1NF  C16   C15  C14  111.78  3.000
 1NF  H16A  C16  H16  106.92  3.000
 1NF  H16A  C16  C17  109.06  3.000
 1NF  H16   C16  C17  109.53  3.000
 1NF  H16A  C16  C15  110.21  3.000
 1NF  H16   C16  C15  109.65  3.000
 1NF  C17   C16  C15  111.36  3.000
 1NF  H17A  C17  H17  106.65  3.000
 1NF  H17A  C17  C18  110.29  3.000
 1NF  H17   C17  C18  111.23  3.000
 1NF  H17A  C17  C16  109.19  3.000
 1NF  H17   C17  C16  111.03  3.000
 1NF  C18   C17  C16  108.44  3.000
 1NF  C17   C18  C13  125.41  3.000
 1NF  C17   C18  N2   127.98  3.000
 1NF  C13   C18  N2   106.56  3.000
 1NF  C12   C19  F4   111.48  3.000
 1NF  C12   C19  F3   111.27  3.000
 1NF  F4    C19  F3   106.30  3.000
 1NF  C12   C19  F2   112.47  3.000
 1NF  F4    C19  F2   107.41  3.000
 1NF  F3    C19  F2   107.61  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
 1NF  CONST_01  N2   C3   C2   C1   180.00   0.0  0
 1NF  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 1NF  CONST_03  C4   C5   C6   C1     0.00   0.0  0
 1NF  CONST_04  C5   C6   C1   C2     0.00   0.0  0
 1NF  CONST_07  C5   C4   C3   C2     0.00   0.0  0
 1NF  CONST_08  C5   C4   C3   N2   180.00   0.0  0
 1NF  CONST_09  C13  C12  N3   N2     0.00   0.0  0
 1NF  CONST_10  C12  C13  C18  N2     0.00   0.0  0
 1NF  CONST_11  C6   C1   C2   C3     0.00   0.0  0
 1NF  CONST_12  C12  N3   N2   C3   180.00   0.0  0
 1NF  CONST_13  C13  C18  N2   C3   180.00   0.0  0
 1NF  CONST_14  C6   C5   C4   C3     0.00   0.0  0
 1NF  CONST_16  C13  C18  N2   N3     0.00   0.0  0
 1NF  CONST_17  C18  C13  C12  N3     0.00   0.0  0
 1NF  CONST_19  C18  N2   N3   C12    0.00   0.0  0
 1NF  CONST_20  C17  C18  N2   C3     0.00   0.0  0
 1NF  CONST_21  C10  C11  N1   C8     0.00   0.0  0
 1NF  CONST_22  C3   C2   C1   F1   180.00   0.0  0
 1NF  CONST_23  C5   C6   C1   F1   180.00   0.0  0
 1NF  CONST_24  C7   C6   C1   C2   180.00   0.0  0
 1NF  CONST_25  C19  C12  N3   N2   180.00   0.0  0
 1NF  CONST_26  C7   C6   C5   C4   180.00   0.0  0
 1NF  CONST_27  C19  C12  C13  C14    0.00   0.0  0
 1NF  CONST_28  C19  C12  C13  C18  180.00   0.0  0
 1NF  CONST_29  C8   N1   C11  O1   180.00   0.0  0
 1NF  CONST_30  C10  C11  N1   C7   180.00   0.0  0
 1NF  CONST_31  H5   C5   C6   C1   180.00   0.0  0
 1NF  CONST_32  H4   C4   C3   C2   180.00   0.0  0
 1NF  CONST_33  H2   C2   C3   N2     0.00   0.0  0
 1NF  CONST_34  C7   N1   C11  O1     0.00   0.0  0
 1NF  Var_01    C10  C9   C8   N1   -26.71  30.0  1
 1NF  Var_02    C9   C10  C11  N1   -15.02  30.0  1
 1NF  Var_03    C16  C17  C18  N2   160.97  30.0  1
 1NF  Var_04    C11  C10  C9   C8    25.57  30.0  1
 1NF  Var_05    C11  N1   C8   C9    19.01  30.0  1
 1NF  Var_06    C15  C14  C13  C12  169.28  30.0  1
 1NF  Var_07    C16  C15  C14  C13   44.54  30.0  1
 1NF  Var_08    C17  C16  C15  C14  -64.85  30.0  1
 1NF  Var_09    C18  C17  C16  C15   47.18  30.0  1
 1NF  Var_10    N1   C7   C6   C1    66.96  30.0  2
 1NF  Var_11    C8   N1   C7   C6    65.57  30.0  1
 1NF  Var_12    N3   C12  C19  F2    -7.12  30.0  3

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
 1NF  plan-1  C1   0.020
 1NF  plan-1  F1   0.020
 1NF  plan-1  C2   0.020
 1NF  plan-1  N2   0.020
 1NF  plan-1  C3   0.020
 1NF  plan-1  C4   0.020
 1NF  plan-1  C5   0.020
 1NF  plan-1  C6   0.020
 1NF  plan-1  C7   0.020
 1NF  plan-1  H2   0.020
 1NF  plan-1  H4   0.020
 1NF  plan-1  H5   0.020
 1NF  plan-2  N2   0.020
 1NF  plan-2  C3   0.020
 1NF  plan-2  N3   0.020
 1NF  plan-2  C12  0.020
 1NF  plan-2  C13  0.020
 1NF  plan-2  C14  0.020
 1NF  plan-2  C17  0.020
 1NF  plan-2  C18  0.020
 1NF  plan-2  C19  0.020
 1NF  plan-3  N1   0.020
 1NF  plan-3  C7   0.020
 1NF  plan-3  C8   0.020
 1NF  plan-3  C10  0.020
 1NF  plan-3  C11  0.020
 1NF  plan-3  O1   0.020

