# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 15:26:42 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: (2S)-4-(4-fluorobenzyl)-N-(2-sulfanylethyl)piperazine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(CN2CCN[C@@H](C2)C(=O)NCCS)cc1
#
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
 F1J  F1J  (2S)-4-(4-fluorobenzyl)-N-(2-sulfanylethyl)piperazine-2-carboxamide  ligand  40  20  .  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_F1J
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
 F1J  C15   C  C     0   0.528   2.7892   0.9881   0.4788
 F1J  C12   C  CR16  0  -0.397  -5.4092  -0.8424  -1.1535
 F1J  C13   C  CR16  0  -0.296  -4.0787  -0.6623  -1.5122
 F1J  C11   C  CR6   0   0.508  -5.7122  -1.0123   0.1817
 F1J  C10   C  CR16  0  -0.397  -4.7360  -1.0072   1.1610
 F1J  C9    C  CR16  0  -0.265  -3.4146  -0.8307   0.7800
 F1J  C8    C  CR6   0   0.074  -3.0674  -0.6590  -0.5585
 F1J  C7    C  CH2   0  -0.318  -1.6239  -0.5125  -0.9641
 F1J  C4    C  CH2   0  -0.253   0.5428   0.2434  -0.2764
 F1J  C5    C  CH1   0  -0.202   1.2925   1.1124   0.7367
 F1J  C2    C  CH2   0  -0.276  -1.3050   1.7534  -0.2099
 F1J  C1    C  CH2   0  -0.303  -0.5626   2.6115   0.7944
 F1J  O17   O  O     0  -0.479   3.4159   1.7982  -0.1840
 F1J  N16   N  NH1   0  -0.631   3.3524  -0.1053   1.0234
 F1J  C18   C  CH2   0  -0.279   4.7283  -0.4780   0.8005
 F1J  C19   C  CH2   0  -0.552   4.9018  -1.2372  -0.5103
 F1J  S20   S  S2    0  -0.259   6.6615  -1.6793  -0.6942
 F1J  N6    N  NH1   0  -0.601   0.8674   2.4827   0.5835
 F1J  N3    N  NT    0  -0.424  -0.8873   0.3691  -0.0836
 F1J  H12   H  HCR6  0   0.277  -6.1918  -0.8422  -1.9006
 F1J  H13   H  HCR6  0   0.260  -3.8315  -0.5195  -2.5574
 F1J  H10   H  HCR6  0   0.276  -5.0025  -1.1392   2.2016
 F1J  H9    H  HCR6  0   0.257  -2.6405  -0.8141   1.5362
 F1J  H7    H  HCH2  0   0.254  -1.1470  -1.4971  -0.9285
 F1J  H7A   H  HCH2  0   0.216  -1.5716  -0.1877  -2.0165
 F1J  H4    H  HCH2  0   0.203   0.8538   0.5368  -1.2939
 F1J  H4A   H  HCH2  0   0.242   0.8240  -0.8031  -0.1369
 F1J  H5    H  HCH1  0   0.233   1.0697   0.7099   1.7401
 F1J  H2    H  HCH2  0   0.241  -2.3773   1.8275  -0.0198
 F1J  H2A   H  HCH2  0   0.196  -1.1239   2.1357  -1.2292
 F1J  H1    H  HCH2  0   0.239  -0.8475   3.6563   0.6604
 F1J  H1A   H  HCH2  0   0.197  -0.8729   2.3127   1.8075
 F1J  HN16  H  HNH1  0   0.405   2.7790  -0.7315   1.5651
 F1J  H18   H  HCH2  0   0.253   5.3512   0.4171   0.8031
 F1J  H18A  H  HCH2  0   0.264   5.0467  -1.0983   1.6382
 F1J  H19   H  HCH2  0   0.271   4.2935  -2.1411  -0.5018
 F1J  H19A  H  HCH2  0   0.273   4.5926  -0.6155  -1.3494
 F1J  HS20  H  HSH1  0   0.229   6.5582  -2.3086  -1.8690
 F1J  HN6   H  HNH1  0   0.355   1.3643   3.0785   1.2330
 F1J  F14   F  F     0  -0.319  -6.9960  -1.1831   0.5438

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
 F1J  C15  C5    single    1.524  0.020  1.524
 F1J  C15  O17   double    1.220  0.020  1.220
 F1J  C15  N16   single    1.345  0.020  1.345
 F1J  C12  C13   aromatic  1.390  0.020  1.390
 F1J  C12  C11   aromatic  1.380  0.020  1.380
 F1J  C13  C8    aromatic  1.390  0.020  1.390
 F1J  C11  C10   aromatic  1.383  0.020  1.383
 F1J  C11  F14   single    1.345  0.020  1.345
 F1J  C10  C9    aromatic  1.386  0.020  1.386
 F1J  C9   C8    aromatic  1.393  0.020  1.393
 F1J  C8   C7    single    1.507  0.020  1.507
 F1J  C7   N3    single    1.447  0.020  1.447
 F1J  C4   C5    single    1.531  0.020  1.531
 F1J  C4   N3    single    1.448  0.020  1.448
 F1J  C5   N6    single    1.443  0.020  1.443
 F1J  C2   C1    single    1.515  0.020  1.515
 F1J  C2   N3    single    1.451  0.020  1.451
 F1J  C1   N6    single    1.451  0.020  1.451
 F1J  N16  C18   single    1.443  0.020  1.443
 F1J  C18  C19   single    1.525  0.020  1.525
 F1J  C19  S20   single    1.824  0.020  1.824
 F1J  C12  H12   single    0.930  0.020  1.080
 F1J  C13  H13   single    0.930  0.020  1.080
 F1J  C10  H10   single    0.930  0.020  1.080
 F1J  C9   H9    single    0.930  0.020  1.080
 F1J  C7   H7    single    0.970  0.020  1.090
 F1J  C7   H7A   single    0.970  0.020  1.090
 F1J  C4   H4    single    0.970  0.020  1.090
 F1J  C4   H4A   single    0.970  0.020  1.090
 F1J  C5   H5    single    0.970  0.020  1.090
 F1J  C2   H2    single    0.970  0.020  1.090
 F1J  C2   H2A   single    0.970  0.020  1.090
 F1J  C1   H1    single    0.970  0.020  1.090
 F1J  C1   H1A   single    0.970  0.020  1.090
 F1J  N16  HN16  single    0.860  0.020  1.020
 F1J  C18  H18   single    0.970  0.020  1.090
 F1J  C18  H18A  single    0.970  0.020  1.090
 F1J  C19  H19   single    0.970  0.020  1.090
 F1J  C19  H19A  single    0.970  0.020  1.090
 F1J  S20  HS20  single    1.200  0.020  1.300
 F1J  N6   HN6   single    0.890  0.020  1.040

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
 F1J  N16   C15  O17  123.00  3.000
 F1J  N16   C15  C5   114.15  3.000
 F1J  O17   C15  C5   122.84  3.000
 F1J  H12   C12  C11  120.62  3.000
 F1J  H12   C12  C13  120.95  3.000
 F1J  C11   C12  C13  118.43  3.000
 F1J  H13   C13  C8   119.71  3.000
 F1J  H13   C13  C12  118.98  3.000
 F1J  C8    C13  C12  121.31  3.000
 F1J  F14   C11  C10  118.93  3.000
 F1J  F14   C11  C12  119.07  3.000
 F1J  C10   C11  C12  122.00  3.000
 F1J  H10   C10  C9   120.96  3.000
 F1J  H10   C10  C11  120.44  3.000
 F1J  C9    C10  C11  118.60  3.000
 F1J  H9    C9   C8   119.41  3.000
 F1J  H9    C9   C10  119.45  3.000
 F1J  C8    C9   C10  121.14  3.000
 F1J  C7    C8   C9   120.62  3.000
 F1J  C7    C8   C13  120.84  3.000
 F1J  C9    C8   C13  118.52  3.000
 F1J  H7A   C7   H7   105.98  3.000
 F1J  H7A   C7   N3   112.15  3.000
 F1J  H7    C7   N3   107.84  3.000
 F1J  H7A   C7   C8   109.33  3.000
 F1J  H7    C7   C8   108.74  3.000
 F1J  N3    C7   C8   112.53  3.000
 F1J  H4A   C4   H4   107.44  3.000
 F1J  H4A   C4   N3   108.68  3.000
 F1J  H4    C4   N3   112.20  3.000
 F1J  H4A   C4   C5   109.46  3.000
 F1J  H4    C4   C5   108.74  3.000
 F1J  N3    C4   C5   110.25  3.000
 F1J  H5    C5   N6   112.54  3.000
 F1J  H5    C5   C4   107.20  3.000
 F1J  N6    C5   C4   108.94  3.000
 F1J  H5    C5   C15  108.80  3.000
 F1J  N6    C5   C15  110.42  3.000
 F1J  C4    C5   C15  108.82  3.000
 F1J  H2A   C2   H2   107.37  3.000
 F1J  H2A   C2   N3   111.31  3.000
 F1J  H2    C2   N3   109.41  3.000
 F1J  H2A   C2   C1   109.61  3.000
 F1J  H2    C2   C1   109.11  3.000
 F1J  N3    C2   C1   109.96  3.000
 F1J  H1A   C1   H1   107.42  3.000
 F1J  H1A   C1   N6   112.79  3.000
 F1J  H1    C1   N6   108.93  3.000
 F1J  H1A   C1   C2   108.55  3.000
 F1J  H1    C1   C2   109.45  3.000
 F1J  N6    C1   C2   109.65  3.000
 F1J  HN16  N16  C18  117.74  3.000
 F1J  HN16  N16  C15  119.00  3.000
 F1J  C18   N16  C15  123.14  3.000
 F1J  H18A  C18  H18  107.37  3.000
 F1J  H18A  C18  C19  110.13  3.000
 F1J  H18   C18  C19  110.23  3.000
 F1J  H18A  C18  N16  107.87  3.000
 F1J  H18   C18  N16  109.41  3.000
 F1J  C19   C18  N16  111.71  3.000
 F1J  H19A  C19  H19  108.73  3.000
 F1J  H19A  C19  S20  109.55  3.000
 F1J  H19   C19  S20  109.78  3.000
 F1J  H19A  C19  C18  110.23  3.000
 F1J  H19   C19  C18  110.05  3.000
 F1J  S20   C19  C18  108.49  3.000
 F1J  HS20  S20  C19   97.36  3.000
 F1J  HN6   N6   C1   109.78  3.000
 F1J  HN6   N6   C5   110.27  3.000
 F1J  C1    N6   C5   111.05  3.000
 F1J  C2    N3   C4   110.81  3.000
 F1J  C2    N3   C7   112.42  3.000
 F1J  C4    N3   C7   111.63  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
 F1J  CONST_01  C9    C8   C13  C12     0.00   0.0  0
 F1J  CONST_02  C9    C10  C11  C12     0.00   0.0  0
 F1J  CONST_03  C10   C11  C12  C13     0.00   0.0  0
 F1J  CONST_04  C10   C9   C8   C13     0.00   0.0  0
 F1J  CONST_05  C8    C13  C12  C11     0.00   0.0  0
 F1J  CONST_06  C8    C9   C10  C11     0.00   0.0  0
 F1J  CONST_07  C7    C8   C13  C12   180.00   0.0  0
 F1J  CONST_08  F14   C11  C12  C13   180.00   0.0  0
 F1J  CONST_09  C7    C8   C9   C10   180.00   0.0  0
 F1J  CONST_10  F14   C11  C10  C9    180.00   0.0  0
 F1J  CONST_11  H10   C10  C11  C12   180.00   0.0  0
 F1J  CONST_12  H9    C9   C8   C13   180.00   0.0  0
 F1J  CONST_13  H13   C13  C12  C11   180.00   0.0  0
 F1J  CONST_14  H12   C12  C11  C10   180.00   0.0  0
 F1J  CONST_15  C18   N16  C15  C5    180.00   0.0  0
 F1J  CONST_16  HN16  N16  C15  C5      0.00   0.0  0
 F1J  CONST_17  C18   N16  C15  O17     0.00   0.0  0
 F1J  Var_01    C1    C2   N3   C4    -57.84  30.0  1
 F1J  Var_02    C2    N3   C4   C5     57.91  30.0  1
 F1J  Var_03    C2    C1   N6   C5    -59.67  30.0  1
 F1J  Var_04    N3    C2   C1   N6     57.90  30.0  1
 F1J  Var_05    N3    C7   C8   C13   138.35  30.0  2
 F1J  Var_06    C4    N3   C7   C8    165.73  30.0  3
 F1J  Var_07    C19   C18  N16  C15   -82.77  30.0  3
 F1J  Var_08    S20   C19  C18  N16  -179.38  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
 F1J  chir_01  C5  C15  C4  N6  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
 F1J  plan-1  C12   0.020
 F1J  plan-1  C13   0.020
 F1J  plan-1  C11   0.020
 F1J  plan-1  C10   0.020
 F1J  plan-1  C9    0.020
 F1J  plan-1  C8    0.020
 F1J  plan-1  C7    0.020
 F1J  plan-1  H12   0.020
 F1J  plan-1  H13   0.020
 F1J  plan-1  H10   0.020
 F1J  plan-1  H9    0.020
 F1J  plan-1  F14   0.020
 F1J  plan-2  C15   0.020
 F1J  plan-2  C5    0.020
 F1J  plan-2  O17   0.020
 F1J  plan-2  N16   0.020
 F1J  plan-2  C18   0.020
 F1J  plan-2  HN16  0.020

