# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 08:56:55 2021
#   Inital geometry file: a 88 line input string
#   Ligand name: (2~{S},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)-~{N}-pentyl-pyrrolidine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCNC(=O)[C@H]1N[C@H](CO)[C@H](O)[C@@H]1O
#
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
 KFT  KFT  (2~{S},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)-~{N}-pentyl-pyrrolidine-2-carboxamide  ligand  39  17  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_KFT
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
 KFT  C1   C  CH3   0  -0.669  52.0641  -17.9452  -5.7566
 KFT  C2   C  CH2   0  -0.424  52.8999  -17.1382  -4.7709
 KFT  C3   C  CH2   0  -0.426  52.8729  -15.6326  -5.0180
 KFT  C4   C  CH2   0  -0.432  51.4866  -15.0077  -4.9095
 KFT  O4   O  OH1   0  -0.659  47.2814  -13.3244  -3.9071
 KFT  C5   C  CH2   0  -0.277  51.5431  -13.4887  -5.0215
 KFT  C6   C  C     0   0.509  49.5056  -12.6734  -6.1198
 KFT  C7   C  CH1   0  -0.172  48.0965  -12.1571  -5.8633
 KFT  C8   C  CH1   0  -0.113  46.1963  -12.4618  -7.2616
 KFT  C9   C  CH2   0  -0.147  45.1663  -11.6118  -7.9774
 KFT  N1   N  NH1   0  -0.622  50.2373  -12.8649  -5.0139
 KFT  O1   O  O     0  -0.493  49.9154  -12.9008  -7.2508
 KFT  N2   N  NH1   0  -0.634  47.4344  -11.7028  -7.0698
 KFT  O2   O  OH1   0  -0.676  43.9976  -12.3799  -8.1576
 KFT  C10  C  CH1   0   0.006  45.8257  -12.9174  -5.8577
 KFT  O3   O  OH1   0  -0.673  45.2654  -11.8540  -5.1307
 KFT  C11  C  CH1   0  -0.020  47.2061  -13.2846  -5.3068
 KFT  H1   H  HCH3  0   0.228  52.2043  -19.0161  -5.6049
 KFT  H2   H  HCH3  0   0.221  50.9978  -17.7416  -5.6512
 KFT  H3   H  HCH3  0   0.216  52.3416  -17.7195  -6.7883
 KFT  H4   H  HCH2  0   0.212  52.5590  -17.3422  -3.7515
 KFT  H5   H  HCH2  0   0.221  53.9377  -17.4793  -4.8164
 KFT  H6   H  HCH2  0   0.220  53.5439  -15.1464  -4.3024
 KFT  H7   H  HCH2  0   0.213  53.2843  -15.4207  -6.0110
 KFT  H8   H  HCH2  0   0.227  50.8340  -15.3985  -5.6943
 KFT  H9   H  HCH2  0   0.217  51.0284  -15.2830  -3.9539
 KFT  H11  H  HCH2  0   0.245  52.1154  -13.0734  -4.1902
 KFT  H12  H  HCH2  0   0.237  52.0588  -13.1971  -5.9368
 KFT  H13  H  HCH1  0   0.254  48.1516  -11.3546  -5.1154
 KFT  H14  H  HCH1  0   0.226  46.3626  -13.3695  -7.8601
 KFT  H15  H  HCH2  0   0.203  45.5916  -11.2955  -8.9395
 KFT  H16  H  HCH2  0   0.193  44.9782  -10.6999  -7.3996
 KFT  H17  H  HNH1  0   0.397  49.7951  -12.7184  -4.1200
 KFT  H18  H  HNH1  0   0.355  48.0472  -11.7995  -7.8686
 KFT  H20  H  HOH1  0   0.456  43.3676  -11.8565  -8.6603
 KFT  H21  H  HCH1  0   0.231  45.1571  -13.7876  -5.8760
 KFT  H22  H  HOH1  0   0.445  45.4184  -12.0301  -4.1949
 KFT  H23  H  HCH1  0   0.242  47.5047  -14.2438  -5.7496
 KFT  H10  H  HOH1  0   0.465  46.9867  -14.1897  -3.6053

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
 KFT  C9   O2   single  1.410  0.020  1.410
 KFT  C9   C8   single  1.515  0.020  1.515
 KFT  C1   C2   single  1.524  0.020  1.524
 KFT  N2   C8   single  1.465  0.020  1.465
 KFT  N2   C7   single  1.449  0.020  1.449
 KFT  O1   C6   double  1.224  0.020  1.224
 KFT  C8   C10  single  1.522  0.020  1.522
 KFT  C6   C7   single  1.522  0.020  1.522
 KFT  C6   N1   single  1.340  0.020  1.340
 KFT  C7   C11  single  1.541  0.020  1.541
 KFT  C2   C3   single  1.526  0.020  1.526
 KFT  O3   C10  single  1.405  0.020  1.405
 KFT  C10  C11  single  1.531  0.020  1.531
 KFT  C4   C3   single  1.524  0.020  1.524
 KFT  C4   C5   single  1.524  0.020  1.524
 KFT  C11  O4   single  1.402  0.020  1.402
 KFT  N1   C5   single  1.447  0.020  1.447
 KFT  C1   H1   single  0.970  0.020  1.090
 KFT  C1   H2   single  0.970  0.020  1.090
 KFT  C1   H3   single  0.970  0.020  1.090
 KFT  C2   H4   single  0.970  0.020  1.090
 KFT  C2   H5   single  0.970  0.020  1.090
 KFT  C3   H6   single  0.970  0.020  1.090
 KFT  C3   H7   single  0.970  0.020  1.090
 KFT  C4   H8   single  0.970  0.020  1.090
 KFT  C4   H9   single  0.970  0.020  1.090
 KFT  O4   H10  single  0.850  0.020  0.980
 KFT  C5   H11  single  0.970  0.020  1.090
 KFT  C5   H12  single  0.970  0.020  1.090
 KFT  C7   H13  single  0.970  0.020  1.090
 KFT  C8   H14  single  0.970  0.020  1.090
 KFT  C9   H15  single  0.970  0.020  1.090
 KFT  C9   H16  single  0.970  0.020  1.090
 KFT  N1   H17  single  0.860  0.020  1.020
 KFT  N2   H18  single  0.890  0.020  1.040
 KFT  O2   H20  single  0.850  0.020  0.980
 KFT  C10  H21  single  0.970  0.020  1.090
 KFT  O3   H22  single  0.850  0.020  0.980
 KFT  C11  H23  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
 KFT  H3   C1   H2   107.53  3.000
 KFT  H3   C1   H1   107.56  3.000
 KFT  H2   C1   H1   107.19  3.000
 KFT  H3   C1   C2   111.24  3.000
 KFT  H2   C1   C2   112.02  3.000
 KFT  H1   C1   C2   111.07  3.000
 KFT  H5   C2   H4   106.04  3.000
 KFT  H5   C2   C3   108.53  3.000
 KFT  H4   C2   C3   109.23  3.000
 KFT  H5   C2   C1   109.18  3.000
 KFT  H4   C2   C1   109.46  3.000
 KFT  C3   C2   C1   114.09  3.000
 KFT  H7   C3   H6   106.04  3.000
 KFT  H7   C3   C4   109.08  3.000
 KFT  H6   C3   C4   109.19  3.000
 KFT  H7   C3   C2   109.33  3.000
 KFT  H6   C3   C2   108.75  3.000
 KFT  C4   C3   C2   114.14  3.000
 KFT  H9   C4   H8   106.68  3.000
 KFT  H9   C4   C5   109.28  3.000
 KFT  H8   C4   C5   109.01  3.000
 KFT  H9   C4   C3   109.85  3.000
 KFT  H8   C4   C3   110.20  3.000
 KFT  C5   C4   C3   111.69  3.000
 KFT  H10  O4   C11  108.79  3.000
 KFT  H12  C5   H11  106.84  3.000
 KFT  H12  C5   N1   108.42  3.000
 KFT  H11  C5   N1   107.77  3.000
 KFT  H12  C5   C4   110.22  3.000
 KFT  H11  C5   C4   110.04  3.000
 KFT  N1   C5   C4   113.31  3.000
 KFT  O1   C6   N1   123.59  3.000
 KFT  N1   C6   C7   114.51  3.000
 KFT  O1   C6   C7   121.90  3.000
 KFT  H13  C7   C11  108.52  3.000
 KFT  H13  C7   N2   111.15  3.000
 KFT  C11  C7   N2   105.43  3.000
 KFT  H13  C7   C6   108.43  3.000
 KFT  C11  C7   C6   110.34  3.000
 KFT  N2   C7   C6   112.88  3.000
 KFT  H14  C8   C10  106.96  3.000
 KFT  H14  C8   N2   111.78  3.000
 KFT  C10  C8   N2   103.89  3.000
 KFT  H14  C8   C9   107.98  3.000
 KFT  C10  C8   C9   115.99  3.000
 KFT  N2   C8   C9   110.23  3.000
 KFT  H16  C9   H15  106.78  3.000
 KFT  H16  C9   O2   112.24  3.000
 KFT  H15  C9   O2   111.45  3.000
 KFT  H16  C9   C8   109.54  3.000
 KFT  H15  C9   C8   108.19  3.000
 KFT  O2   C9   C8   108.55  3.000
 KFT  H17  N1   C6   118.14  3.000
 KFT  H17  N1   C5   117.59  3.000
 KFT  C6   N1   C5   123.37  3.000
 KFT  H18  N2   C8   111.05  3.000
 KFT  H18  N2   C7   110.53  3.000
 KFT  C8   N2   C7   109.43  3.000
 KFT  H20  O2   C9   108.27  3.000
 KFT  H21  C10  C11  111.41  3.000
 KFT  H21  C10  O3   111.46  3.000
 KFT  C11  C10  O3   110.79  3.000
 KFT  H21  C10  C8   111.73  3.000
 KFT  C11  C10  C8   100.61  3.000
 KFT  O3   C10  C8   110.37  3.000
 KFT  H22  O3   C10  107.50  3.000
 KFT  H23  C11  C10  108.04  3.000
 KFT  H23  C11  C7   109.66  3.000
 KFT  C10  C11  C7   102.45  3.000
 KFT  H23  C11  O4   111.30  3.000
 KFT  C10  C11  O4   114.48  3.000
 KFT  C7   C11  O4   110.50  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
 KFT  CONST_01  C7   C6  N1  C5  180.00   0.0  0
 KFT  CONST_02  H17  N1  C6  C7    0.00   0.0  0
 KFT  CONST_03  O1   C6  N1  C5    0.00   0.0  0
 KFT  Var_01    C4   C3  C2  C1   61.10  30.0  3
 KFT  Var_02    C5   C4  C3  C2  174.07  30.0  2
 KFT  Var_03    N1   C5  C4  C3  176.05  30.0  3
 KFT  Var_04    C6   N1  C5  C4  -87.40  30.0  2
 KFT  Var_05    H1   C1  C2  C3  173.77  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
 KFT  chir_01  C7   N2  C6   C11  positiv
 KFT  chir_02  C8   N2  C10  C9   negativ
 KFT  chir_03  C10  O3  C8   C11  negativ
 KFT  chir_04  C11  O4  C10  C7   negativ

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
 KFT  plan-1  C5   0.020
 KFT  plan-1  C6   0.020
 KFT  plan-1  C7   0.020
 KFT  plan-1  N1   0.020
 KFT  plan-1  O1   0.020
 KFT  plan-1  H17  0.020

