# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 07:57:53 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: (1R)-5-benzoyl-2,3-dihydro-1H-pyrrolizine-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1CCn2c1ccc2C(=O)c3ccccc3
#
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
 KTR  KTR  '(1R)-5-benzoyl-2,3-dihydro-1H-pyrrolizine-1-carboxylic acid'  ligand  32  19  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KTR
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
 KTR  O3   O  OH1   0  -0.588  -5.2733   0.6471   0.3464
 KTR  C4   C  CR15  0  -0.391  -1.1277   1.3772  -1.3553
 KTR  C5   C  CR55  0   0.453  -1.8691   0.3274  -0.8477
 KTR  C6   C  CH2   0  -0.274  -1.7244  -1.6970   0.3223
 KTR  N1   N  N     0  -0.496  -1.0404  -0.5748  -0.3006
 KTR  C7   C  CH2   0  -0.483  -3.1311  -1.5775  -0.2771
 KTR  C8   C  CR15  0  -0.539  -3.2889  -0.0837  -0.6748
 KTR  C9   C  C     0   0.574  -3.9526   0.6800   0.4500
 KTR  C10  C  CR6   0  -0.025   2.7214  -0.2726   0.1083
 KTR  C11  C  CR16  0  -0.288   2.8958   1.0269   0.5808
 KTR  C12  C  CR16  0  -0.244   4.1688   1.5741   0.6673
 KTR  C13  C  CR16  0  -0.251   5.2736   0.8336   0.2707
 KTR  C14  C  CR16  0  -0.246   5.1064  -0.4648  -0.1968
 KTR  C15  C  CR16  0  -0.275   3.8391  -1.0206  -0.2631
 KTR  O1   O  O     0  -0.422   1.2654  -2.0982   0.3910
 KTR  C2   C  CR5   0   0.237   0.2561  -0.1399  -0.3928
 KTR  C3   C  CR15  0  -0.363   0.2122   1.0803  -1.0673
 KTR  O2   O  O     0  -0.429  -3.3624   1.2114   1.3553
 KTR  H1   H  HOH1  0   0.484  -5.6810   1.0835   1.1100
 KTR  H2   H  HCR5  0   0.256  -1.5081   2.2469  -1.8661
 KTR  H3   H  HCH2  0   0.275  -1.2517  -2.6410   0.0702
 KTR  H4   H  HCH2  0   0.262  -1.7169  -1.5862   1.4077
 KTR  H5   H  HCH2  0   0.283  -3.1976  -2.1823  -1.1805
 KTR  H6   H  HCH2  0   0.277  -3.9008  -1.9271   0.4091
 KTR  H7   H  HCR5  0   0.317  -3.8788   0.0183  -1.5866
 KTR  H8   H  HCR6  0   0.272   2.0436   1.6065   0.9107
 KTR  H9   H  HCR6  0   0.263   4.2970   2.5784   1.0488
 KTR  H10  H  HCR6  0   0.264   6.2649   1.2634   0.3327
 KTR  H11  H  HCR6  0   0.262   5.9665  -1.0456  -0.5032
 KTR  H12  H  HCR6  0   0.262   3.7143  -2.0351  -0.6195
 KTR  H13  H  HCR5  0   0.270   1.0688   1.6726  -1.3479
 KTR  C1   C  C     0   0.302   1.3823  -0.9257   0.0637

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
 KTR  C12  C13  aromatic  1.388  0.020  1.388
 KTR  C12  C11  aromatic  1.388  0.020  1.388
 KTR  C13  C14  aromatic  1.390  0.020  1.390
 KTR  C11  C10  aromatic  1.394  0.020  1.394
 KTR  C14  C15  aromatic  1.385  0.020  1.385
 KTR  C3   C4   aromatic  1.402  0.020  1.402
 KTR  C3   C2   aromatic  1.395  0.020  1.395
 KTR  C10  C15  aromatic  1.395  0.020  1.395
 KTR  C10  C1   single    1.491  0.020  1.491
 KTR  C4   C5   aromatic  1.382  0.020  1.382
 KTR  C2   C1   single    1.447  0.020  1.447
 KTR  C2   N1   aromatic  1.371  0.020  1.371
 KTR  C1   O1   double    1.223  0.020  1.223
 KTR  C5   N1   aromatic  1.342  0.020  1.342
 KTR  C5   C8   single    1.488  0.020  1.488
 KTR  N1   C6   single    1.454  0.020  1.454
 KTR  O2   C9   double    1.204  0.020  1.204
 KTR  C8   C9   single    1.513  0.020  1.513
 KTR  C8   C7   single    1.554  0.020  1.554
 KTR  C9   O3   single    1.325  0.020  1.325
 KTR  C6   C7   single    1.534  0.020  1.534
 KTR  O3   H1   single    0.850  0.020  0.980
 KTR  C4   H2   single    0.930  0.020  1.080
 KTR  C6   H3   single    0.970  0.020  1.090
 KTR  C6   H4   single    0.970  0.020  1.090
 KTR  C7   H5   single    0.970  0.020  1.090
 KTR  C7   H6   single    0.970  0.020  1.090
 KTR  C8   H7   single    0.970  0.020  1.090
 KTR  C11  H8   single    0.930  0.020  1.080
 KTR  C12  H9   single    0.930  0.020  1.080
 KTR  C13  H10  single    0.930  0.020  1.080
 KTR  C14  H11  single    0.930  0.020  1.080
 KTR  C15  H12  single    0.930  0.020  1.080
 KTR  C3   H13  single    0.930  0.020  1.080

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
 KTR  H1   O3   C9   110.27  3.000
 KTR  H2   C4   C3   127.25  3.000
 KTR  H2   C4   C5   126.71  3.000
 KTR  C3   C4   C5   106.04  3.000
 KTR  C8   C5   N1   110.86  3.000
 KTR  C8   C5   C4   139.86  3.000
 KTR  N1   C5   C4   109.22  3.000
 KTR  H4   C6   H3   108.44  3.000
 KTR  H4   C6   C7   112.78  3.000
 KTR  H3   C6   C7   112.11  3.000
 KTR  H4   C6   N1   110.15  3.000
 KTR  H3   C6   N1   111.52  3.000
 KTR  C7   C6   N1   101.77  3.000
 KTR  C2   N1   C6   135.93  3.000
 KTR  C6   N1   C5   113.76  3.000
 KTR  C2   N1   C5   110.09  3.000
 KTR  H6   C7   H5   107.53  3.000
 KTR  H6   C7   C8   113.46  3.000
 KTR  H5   C7   C8   108.38  3.000
 KTR  H6   C7   C6   112.15  3.000
 KTR  H5   C7   C6   109.69  3.000
 KTR  C8   C7   C6   105.55  3.000
 KTR  H7   C8   C9   109.70  3.000
 KTR  H7   C8   C7   111.03  3.000
 KTR  C9   C8   C7   109.85  3.000
 KTR  H7   C8   C5   113.14  3.000
 KTR  C7   C8   C5   101.44  3.000
 KTR  C9   C8   C5   111.43  3.000
 KTR  O2   C9   C8   124.52  3.000
 KTR  C8   C9   O3   111.50  3.000
 KTR  O2   C9   O3   123.93  3.000
 KTR  C1   C10  C15  118.48  3.000
 KTR  C1   C10  C11  122.08  3.000
 KTR  C15  C10  C11  119.34  3.000
 KTR  H8   C11  C12  119.48  3.000
 KTR  H8   C11  C10  120.28  3.000
 KTR  C12  C11  C10  120.22  3.000
 KTR  H9   C12  C13  120.11  3.000
 KTR  H9   C12  C11  119.77  3.000
 KTR  C13  C12  C11  120.13  3.000
 KTR  H10  C13  C14  120.03  3.000
 KTR  H10  C13  C12  120.06  3.000
 KTR  C14  C13  C12  119.91  3.000
 KTR  H11  C14  C15  119.88  3.000
 KTR  H11  C14  C13  120.06  3.000
 KTR  C15  C14  C13  120.06  3.000
 KTR  H12  C15  C14  119.81  3.000
 KTR  H12  C15  C10  119.85  3.000
 KTR  C14  C15  C10  120.33  3.000
 KTR  C3   C2   C1   130.69  3.000
 KTR  C1   C2   N1   122.86  3.000
 KTR  C3   C2   N1   106.28  3.000
 KTR  H13  C3   C2   125.53  3.000
 KTR  H13  C3   C4   126.10  3.000
 KTR  C2   C3   C4   108.34  3.000
 KTR  C2   C1   O1   122.05  3.000
 KTR  O1   C1   C10  119.87  3.000
 KTR  C2   C1   C10  118.08  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
 KTR  CONST_01  N1   C2   C3   C4      0.00   0.0  0
 KTR  CONST_02  C2   N1   C5   C4      0.00   0.0  0
 KTR  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 KTR  CONST_04  C3   C2   N1   C5      0.00   0.0  0
 KTR  CONST_05  C3   C4   C5   N1      0.00   0.0  0
 KTR  CONST_06  C13  C12  C11  C10     0.00   0.0  0
 KTR  CONST_07  C13  C14  C15  C10     0.00   0.0  0
 KTR  CONST_08  C14  C13  C12  C11     0.00   0.0  0
 KTR  CONST_09  C14  C15  C10  C11     0.00   0.0  0
 KTR  CONST_10  C15  C14  C13  C12     0.00   0.0  0
 KTR  CONST_11  C15  C10  C11  C12     0.00   0.0  0
 KTR  CONST_12  C1   C2   C3   C4    180.00   0.0  0
 KTR  CONST_13  C1   C2   N1   C5    180.00   0.0  0
 KTR  CONST_14  C1   C2   N1   C6      0.00   0.0  0
 KTR  CONST_15  C1   C10  C11  C12   180.00   0.0  0
 KTR  CONST_16  C1   C10  C15  C14   180.00   0.0  0
 KTR  CONST_17  H13  C3   C4   C5    180.00   0.0  0
 KTR  CONST_18  H2   C4   C5   N1    180.00   0.0  0
 KTR  CONST_19  H9   C12  C11  C10   180.00   0.0  0
 KTR  CONST_20  H11  C14  C15  C10   180.00   0.0  0
 KTR  CONST_21  H10  C13  C12  C11   180.00   0.0  0
 KTR  CONST_22  H12  C15  C10  C11   180.00   0.0  0
 KTR  CONST_23  H8   C11  C12  C13   180.00   0.0  0
 KTR  CONST_24  H1   O3   C9   C8    180.00   0.0  0
 KTR  Var_01    C7   C6   N1   C5     16.19  30.0  1
 KTR  Var_02    C8   C7   C6   N1    -24.49  30.0  1
 KTR  Var_03    C10  C1   C2   N1   -170.74  30.0  2
 KTR  Var_04    C2   C1   C10  C11    42.41  30.0  2

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
 KTR  chir_01  C8  C5  C9  C7  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
 KTR  plan-1  C10  0.020
 KTR  plan-1  C11  0.020
 KTR  plan-1  C12  0.020
 KTR  plan-1  C13  0.020
 KTR  plan-1  C14  0.020
 KTR  plan-1  C15  0.020
 KTR  plan-1  H8   0.020
 KTR  plan-1  H9   0.020
 KTR  plan-1  H10  0.020
 KTR  plan-1  H11  0.020
 KTR  plan-1  H12  0.020
 KTR  plan-1  C1   0.020
 KTR  plan-2  C4   0.020
 KTR  plan-2  C5   0.020
 KTR  plan-2  C6   0.020
 KTR  plan-2  N1   0.020
 KTR  plan-2  C8   0.020
 KTR  plan-2  C2   0.020
 KTR  plan-2  C3   0.020
 KTR  plan-2  H2   0.020
 KTR  plan-2  H13  0.020
 KTR  plan-2  C1   0.020
 KTR  plan-3  C10  0.020
 KTR  plan-3  O1   0.020
 KTR  plan-3  C2   0.020
 KTR  plan-3  C1   0.020
 KTR  plan-4  O3   0.020
 KTR  plan-4  C8   0.020
 KTR  plan-4  C9   0.020
 KTR  plan-4  O2   0.020
 KTR  plan-4  H1   0.020

