# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 11:18:55 2022
#   Inital geometry file: a 102 line input string
#   Ligand name: (2S)-4-(4-fluorobenzyl)-N-(3-sulfanylpropyl)piperazine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(CN2CCN[C@@H](C2)C(=O)NCCCS)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
 F1K  F1K  (2S)-4-(4-fluorobenzyl)-N-(3-sulfanylpropyl)piperazine-2-carboxamide  ligand  43  21  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_F1K
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
 F1K  C24   C  CR16  0  -0.296  -4.7366   0.2576   1.4447
 F1K  C23   C  CR16  0  -0.398  -5.9589   0.7187   0.9699
 F1K  C22   C  CR6   0   0.509  -5.9738   1.4622  -0.1919
 F1K  C20   C  CR16  0  -0.262  -3.6080   1.2901  -0.3948
 F1K  C12   C  CH2   0  -0.551   6.5598   0.8534   0.2110
 F1K  C11   C  CH2   0  -0.474   5.0862   0.8426  -0.1621
 F1K  C10   C  CH2   0  -0.231   4.4443  -0.4884   0.1999
 F1K  C7    C  C     0   0.533   2.2234  -1.5153   0.0660
 F1K  C4    C  CH2   0  -0.252  -0.0468  -0.7521   0.7249
 F1K  C5    C  CH1   0  -0.202   0.7964  -1.3065  -0.4233
 F1K  C2    C  CH2   0  -0.275  -1.9816  -1.8073  -0.1861
 F1K  C1    C  CH2   0  -0.304  -1.1420  -2.3694  -1.3156
 F1K  F25   F  F     0  -0.319  -7.1503   1.9102  -0.6645
 F1K  C21   C  CR16  0  -0.398  -4.8160   1.7573  -0.8886
 F1K  C19   C  CR6   0   0.076  -3.5504   0.5388   0.7777
 F1K  C18   C  CH2   0  -0.324  -2.2250   0.0632   1.3127
 F1K  N3    N  NT    0  -0.423  -1.4136  -0.5583   0.2868
 F1K  N6    N  NH1   0  -0.600   0.2246  -2.5591  -0.8635
 F1K  O9    O  O     0  -0.490   2.5682  -2.5087   0.6879
 F1K  N8    N  NH1   0  -0.644   3.0558  -0.5012  -0.2081
 F1K  S13   S  S2    0  -0.253   7.2713   2.4721  -0.2354
 F1K  H24   H  HCR6  0   0.260  -4.7162  -0.3361   2.3508
 F1K  H23   H  HCR6  0   0.277  -6.8797   0.4956   1.4927
 F1K  H20   H  HCR6  0   0.256  -2.6949   1.5039  -0.9355
 F1K  H12   H  HCH2  0   0.269   6.6854   0.6869   1.2809
 F1K  H12A  H  HCH2  0   0.269   7.0922   0.0657  -0.3223
 F1K  H11   H  HCH2  0   0.250   4.5652   1.6535   0.3539
 F1K  H11A  H  HCH2  0   0.248   4.9795   1.0213  -1.2361
 F1K  H10   H  HCH2  0   0.235   4.9866  -1.3059  -0.2850
 F1K  H10A  H  HCH2  0   0.239   4.5144  -0.6548   1.2777
 F1K  H4    H  HCH2  0   0.201   0.0197  -1.4438   1.5819
 F1K  H4A   H  HCH2  0   0.245   0.3645   0.2093   1.0427
 F1K  H5    H  HCH1  0   0.227   0.7966  -0.5461  -1.2232
 F1K  H2    H  HCH2  0   0.242  -2.9950  -1.6291  -0.5501
 F1K  H2A   H  HCH2  0   0.194  -2.0508  -2.5520   0.6258
 F1K  H1    H  HCH2  0   0.239  -1.5509  -3.3327  -1.6246
 F1K  H1A   H  HCH2  0   0.197  -1.2129  -1.6889  -2.1781
 F1K  H21   H  HCR6  0   0.276  -4.8574   2.3410  -1.7992
 F1K  H18   H  HCH2  0   0.253  -1.6707   0.9232   1.7015
 F1K  H18A  H  HCH2  0   0.215  -2.3955  -0.6078   2.1711
 F1K  HN6   H  HNH1  0   0.355   0.7797  -2.9498  -1.6143
 F1K  HN8   H  HNH1  0   0.403   2.7226   0.2578  -0.7810
 F1K  HS13  H  HSH1  0   0.225   8.5219   2.2354   0.1741

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
 F1K  C24  C23   aromatic  1.390  0.020  1.390
 F1K  C24  C19   aromatic  1.390  0.020  1.390
 F1K  C23  C22   aromatic  1.379  0.020  1.379
 F1K  C22  F25   single    1.345  0.020  1.345
 F1K  C22  C21   aromatic  1.383  0.020  1.383
 F1K  C20  C21   aromatic  1.386  0.020  1.386
 F1K  C20  C19   aromatic  1.394  0.020  1.394
 F1K  C12  C11   single    1.520  0.020  1.520
 F1K  C12  S13   single    1.824  0.020  1.824
 F1K  C11  C10   single    1.521  0.020  1.521
 F1K  C10  N8    single    1.447  0.020  1.447
 F1K  C7   C5    single    1.523  0.020  1.523
 F1K  C7   O9    double    1.222  0.020  1.222
 F1K  C7   N8    single    1.340  0.020  1.340
 F1K  C4   C5    single    1.529  0.020  1.529
 F1K  C4   N3    single    1.448  0.020  1.448
 F1K  C5   N6    single    1.446  0.020  1.446
 F1K  C2   C1    single    1.516  0.020  1.516
 F1K  C2   N3    single    1.451  0.020  1.451
 F1K  C1   N6    single    1.452  0.020  1.452
 F1K  C19  C18   single    1.506  0.020  1.506
 F1K  C18  N3    single    1.448  0.020  1.448
 F1K  C24  H24   single    0.930  0.020  1.080
 F1K  C23  H23   single    0.930  0.020  1.080
 F1K  C20  H20   single    0.930  0.020  1.080
 F1K  C12  H12   single    0.970  0.020  1.090
 F1K  C12  H12A  single    0.970  0.020  1.090
 F1K  C11  H11   single    0.970  0.020  1.090
 F1K  C11  H11A  single    0.970  0.020  1.090
 F1K  C10  H10   single    0.970  0.020  1.090
 F1K  C10  H10A  single    0.970  0.020  1.090
 F1K  C4   H4    single    0.970  0.020  1.090
 F1K  C4   H4A   single    0.970  0.020  1.090
 F1K  C5   H5    single    0.970  0.020  1.090
 F1K  C2   H2    single    0.970  0.020  1.090
 F1K  C2   H2A   single    0.970  0.020  1.090
 F1K  C1   H1    single    0.970  0.020  1.090
 F1K  C1   H1A   single    0.970  0.020  1.090
 F1K  C21  H21   single    0.930  0.020  1.080
 F1K  C18  H18   single    0.970  0.020  1.090
 F1K  C18  H18A  single    0.970  0.020  1.090
 F1K  N6   HN6   single    0.890  0.020  1.040
 F1K  N8   HN8   single    0.860  0.020  1.020
 F1K  S13  HS13  single    1.200  0.020  1.300

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
 F1K  H24   C24  C19  119.76  3.000
 F1K  H24   C24  C23  118.95  3.000
 F1K  C19   C24  C23  121.30  3.000
 F1K  H23   C23  C22  120.58  3.000
 F1K  H23   C23  C24  120.99  3.000
 F1K  C22   C23  C24  118.43  3.000
 F1K  C21   C22  F25  118.96  3.000
 F1K  C21   C22  C23  122.02  3.000
 F1K  F25   C22  C23  119.02  3.000
 F1K  H20   C20  C19  119.46  3.000
 F1K  H20   C20  C21  119.38  3.000
 F1K  C19   C20  C21  121.16  3.000
 F1K  H12A  C12  H12  108.27  3.000
 F1K  H12A  C12  S13  109.33  3.000
 F1K  H12   C12  S13  109.32  3.000
 F1K  H12A  C12  C11  110.38  3.000
 F1K  H12   C12  C11  110.59  3.000
 F1K  S13   C12  C11  108.93  3.000
 F1K  H11A  C11  H11  107.20  3.000
 F1K  H11A  C11  C10  109.59  3.000
 F1K  H11   C11  C10  109.61  3.000
 F1K  H11A  C11  C12  109.53  3.000
 F1K  H11   C11  C12  109.93  3.000
 F1K  C10   C11  C12  110.90  3.000
 F1K  H10A  C10  H10  106.95  3.000
 F1K  H10A  C10  N8   109.77  3.000
 F1K  H10   C10  N8   110.12  3.000
 F1K  H10A  C10  C11  109.92  3.000
 F1K  H10   C10  C11  109.82  3.000
 F1K  N8    C10  C11  110.20  3.000
 F1K  N8    C7   O9   122.96  3.000
 F1K  N8    C7   C5   114.36  3.000
 F1K  O9    C7   C5   122.65  3.000
 F1K  H4A   C4   H4   107.64  3.000
 F1K  H4A   C4   N3   108.99  3.000
 F1K  H4    C4   N3   112.07  3.000
 F1K  H4A   C4   C5   109.26  3.000
 F1K  H4    C4   C5   108.83  3.000
 F1K  N3    C4   C5   109.99  3.000
 F1K  H5    C5   N6   112.11  3.000
 F1K  H5    C5   C4   107.13  3.000
 F1K  N6    C5   C4   108.96  3.000
 F1K  H5    C5   C7   109.10  3.000
 F1K  N6    C5   C7   110.47  3.000
 F1K  C4    C5   C7   108.98  3.000
 F1K  H2A   C2   H2   107.29  3.000
 F1K  H2A   C2   N3   111.43  3.000
 F1K  H2    C2   N3   109.36  3.000
 F1K  H2A   C2   C1   109.44  3.000
 F1K  H2    C2   C1   109.05  3.000
 F1K  N3    C2   C1   110.20  3.000
 F1K  H1A   C1   H1   107.44  3.000
 F1K  H1A   C1   N6   112.67  3.000
 F1K  H1    C1   N6   109.00  3.000
 F1K  H1A   C1   C2   108.60  3.000
 F1K  H1    C1   C2   109.32  3.000
 F1K  N6    C1   C2   109.75  3.000
 F1K  H21   C21  C20  120.98  3.000
 F1K  H21   C21  C22  120.46  3.000
 F1K  C20   C21  C22  118.56  3.000
 F1K  C18   C19  C20  120.35  3.000
 F1K  C18   C19  C24  121.11  3.000
 F1K  C20   C19  C24  118.53  3.000
 F1K  H18A  C18  H18  106.25  3.000
 F1K  H18A  C18  N3   112.14  3.000
 F1K  H18   C18  N3   107.77  3.000
 F1K  H18A  C18  C19  109.42  3.000
 F1K  H18   C18  C19  108.89  3.000
 F1K  N3    C18  C19  112.14  3.000
 F1K  C18   N3   C2   112.39  3.000
 F1K  C18   N3   C4   111.83  3.000
 F1K  C2    N3   C4   110.65  3.000
 F1K  HN6   N6   C1   109.61  3.000
 F1K  HN6   N6   C5   110.08  3.000
 F1K  C1    N6   C5   110.73  3.000
 F1K  HN8   N8   C7   118.74  3.000
 F1K  HN8   N8   C10  118.09  3.000
 F1K  C7    N8   C10  123.01  3.000
 F1K  HS13  S13  C12   97.63  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
 F1K  CONST_01  C21  C22  C23  C24     0.00   0.0  0
 F1K  CONST_02  C21  C20  C19  C24     0.00   0.0  0
 F1K  CONST_03  C20  C19  C24  C23     0.00   0.0  0
 F1K  CONST_04  C20  C21  C22  C23     0.00   0.0  0
 F1K  CONST_05  C19  C24  C23  C22     0.00   0.0  0
 F1K  CONST_06  C19  C20  C21  C22     0.00   0.0  0
 F1K  CONST_07  F25  C22  C23  C24   180.00   0.0  0
 F1K  CONST_08  C18  C19  C24  C23   180.00   0.0  0
 F1K  CONST_09  F25  C22  C21  C20   180.00   0.0  0
 F1K  CONST_10  C18  C19  C20  C21   180.00   0.0  0
 F1K  CONST_11  H20  C20  C19  C24   180.00   0.0  0
 F1K  CONST_12  H21  C21  C22  C23   180.00   0.0  0
 F1K  CONST_13  H24  C24  C23  C22   180.00   0.0  0
 F1K  CONST_14  H23  C23  C22  C21   180.00   0.0  0
 F1K  CONST_15  C5   C7   N8   C10   180.00   0.0  0
 F1K  CONST_16  HN8  N8   C7   C5      0.00   0.0  0
 F1K  CONST_17  O9   C7   N8   C10     0.00   0.0  0
 F1K  Var_01    C1   C2   N3   C4    -57.74  30.0  1
 F1K  Var_02    C2   N3   C4   C5     58.34  30.0  1
 F1K  Var_03    C2   C1   N6   C5    -59.35  30.0  1
 F1K  Var_04    N6   C1   C2   N3     57.55  30.0  1
 F1K  Var_05    N3   C18  C19  C24   132.60  30.0  2
 F1K  Var_06    C19  C18  N3   C4    167.63  30.0  1
 F1K  Var_07    N8   C10  C11  C12  -177.81  30.0  3
 F1K  Var_08    C7   N8   C10  C11  -175.43  30.0  3
 F1K  Var_09    S13  C12  C11  C10  -179.65  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
 F1K  chir_01  C5  C7  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
 F1K  plan-1  C24  0.020
 F1K  plan-1  C23  0.020
 F1K  plan-1  C22  0.020
 F1K  plan-1  C20  0.020
 F1K  plan-1  F25  0.020
 F1K  plan-1  C21  0.020
 F1K  plan-1  C19  0.020
 F1K  plan-1  C18  0.020
 F1K  plan-1  H24  0.020
 F1K  plan-1  H23  0.020
 F1K  plan-1  H20  0.020
 F1K  plan-1  H21  0.020
 F1K  plan-2  C10  0.020
 F1K  plan-2  C7   0.020
 F1K  plan-2  C5   0.020
 F1K  plan-2  O9   0.020
 F1K  plan-2  N8   0.020
 F1K  plan-2  HN8  0.020

