# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 07:06:36 2022
#   Inital geometry file: a 114 line input string
#   Ligand name: (3R)-1-[3-(2-fluorophenyl)propanoyl]-N-(pyridin-2-yl)pyrrolidine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccccc1CCC(=O)N2CC[C@H](C2)C(=O)Nc3ccccn3
#
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
 L7C  L7C  "(3R)-1-[3-(2-fluorophenyl)propanoyl]-N-(pyridin-2-yl)pyrrolidine-3-carboxamide"
  ligand  45  25  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L7C
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
 L7C  F    F  F     0  -0.313  -64.8241  18.2028  13.0182
 L7C  C17  C  CR6   0   0.507  -65.4416  17.5944  14.0470
 L7C  C18  C  CR16  0  -0.400  -64.9271  16.3904  14.4917
 L7C  C16  C  CR16  0  -0.254  -65.5468  15.7510  15.5550
 L7C  C14  C  CR16  0  -0.253  -66.6592  16.3267  16.1550
 L7C  C15  C  CR16  0  -0.284  -67.1511  17.5333  15.6811
 L7C  C13  C  CR6   0  -0.071  -66.5553  18.1977  14.6105
 L7C  C12  C  CH2   0  -0.514  -67.1345  19.4815  14.0847
 L7C  C11  C  CH2   0  -0.568  -68.4087  19.2512  13.2566
 L7C  C10  C  C     0   0.530  -68.2043  18.3153  12.0843
 L7C  O1   O  O     0  -0.500  -68.5601  17.1429  12.1407
 L7C  N2   N  NT    0  -0.451  -67.6169  18.8097  10.9803
 L7C  C8   C  CH2   0  -0.281  -67.1734  20.1767  10.7527
 L7C  C7   C  CH2   0  -0.457  -67.1011  20.2676   9.2364
 L7C  C9   C  CH2   0  -0.242  -67.4027  17.9572   9.8169
 L7C  C6   C  CH1   0  -0.468  -66.6903  18.8485   8.8013
 L7C  C5   C  C     0   0.590  -65.1824  18.7078   8.8588
 L7C  O    O  O     0  -0.447  -64.5892  18.4430   9.8866
 L7C  N1   N  NH1   0  -0.718  -64.5692  18.9459   7.6676
 L7C  C1   C  CR6   0   0.480  -63.2114  19.0039   7.3632
 L7C  N    N  N     0  -0.448  -62.9820  19.2502   6.0786
 L7C  C2   C  CR16  0  -0.371  -62.1833  18.8321   8.2931
 L7C  C4   C  CR16  0  -0.148  -60.8812  18.9258   7.8335
 L7C  C3   C  CR16  0  -0.336  -60.6325  19.1824   6.4925
 L7C  C    C  CR16  0  -0.063  -61.7273  19.3367   5.6595
 L7C  H1   H  HCR6  0   0.274  -64.0578  15.9621  14.0093
 L7C  H2   H  HCR6  0   0.264  -65.1551  14.8086  15.9142
 L7C  H3   H  HCR6  0   0.257  -67.1428  15.8367  16.9895
 L7C  H4   H  HCR6  0   0.260  -68.0200  17.9787  16.1521
 L7C  H5   H  HCH2  0   0.265  -66.3978  20.0356  13.5042
 L7C  H6   H  HCH2  0   0.270  -67.4026  20.1230  14.9261
 L7C  H7   H  HCH2  0   0.267  -68.7972  20.2175  12.9287
 L7C  H8   H  HCH2  0   0.268  -69.1708  18.8027  13.8945
 L7C  H9   H  HCH2  0   0.244  -66.1957  20.3606  11.2053
 L7C  H10  H  HCH2  0   0.262  -67.8710  20.9052  11.1641
 L7C  H11  H  HCH2  0   0.268  -66.4194  21.0452   8.8926
 L7C  H12  H  HCH2  0   0.267  -68.0870  20.4886   8.8250
 L7C  H13  H  HCH2  0   0.253  -68.3603  17.6238   9.4106
 L7C  H14  H  HCH2  0   0.254  -66.8301  17.0664  10.0766
 L7C  H15  H  HCH1  0   0.298  -67.0477  18.6430   7.7912
 L7C  H16  H  HNH1  0   0.411  -65.1601  19.1192   6.8664
 L7C  H17  H  HCR6  0   0.288  -62.3884  18.6324   9.3313
 L7C  H18  H  HCR6  0   0.274  -60.0618  18.7991   8.5291
 L7C  H19  H  HCR6  0   0.268  -59.6269  19.2609   6.1046
 L7C  H20  H  HCR6  0   0.265  -61.5909  19.5381   4.6028

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
 L7C  C    N    aromatic  1.326  0.020  1.326
 L7C  C    C3   aromatic  1.384  0.020  1.384
 L7C  N    C1   aromatic  1.328  0.020  1.328
 L7C  C3   C4   aromatic  1.388  0.020  1.388
 L7C  C1   N1   single    1.393  0.020  1.393
 L7C  C1   C2   aromatic  1.397  0.020  1.397
 L7C  N1   C5   single    1.361  0.020  1.361
 L7C  C4   C2   aromatic  1.384  0.020  1.384
 L7C  C6   C5   single    1.515  0.020  1.515
 L7C  C6   C7   single    1.540  0.020  1.540
 L7C  C6   C9   single    1.528  0.020  1.528
 L7C  C5   O    double    1.216  0.020  1.216
 L7C  C7   C8   single    1.521  0.020  1.521
 L7C  C9   N2   single    1.458  0.020  1.458
 L7C  N2   C8   single    1.455  0.020  1.455
 L7C  N2   C10  single    1.345  0.020  1.345
 L7C  O1   C10  double    1.226  0.020  1.226
 L7C  C10  C11  single    1.514  0.020  1.514
 L7C  C11  C12  single    1.537  0.020  1.537
 L7C  F    C17  single    1.345  0.020  1.345
 L7C  C12  C13  single    1.503  0.020  1.503
 L7C  C17  C13  aromatic  1.386  0.020  1.386
 L7C  C17  C18  aromatic  1.383  0.020  1.383
 L7C  C13  C15  aromatic  1.394  0.020  1.394
 L7C  C18  C16  aromatic  1.387  0.020  1.387
 L7C  C15  C14  aromatic  1.387  0.020  1.387
 L7C  C16  C14  aromatic  1.389  0.020  1.389
 L7C  C18  H1   single    0.930  0.020  1.080
 L7C  C16  H2   single    0.930  0.020  1.080
 L7C  C14  H3   single    0.930  0.020  1.080
 L7C  C15  H4   single    0.930  0.020  1.080
 L7C  C12  H5   single    0.970  0.020  1.090
 L7C  C12  H6   single    0.970  0.020  1.090
 L7C  C11  H7   single    0.970  0.020  1.090
 L7C  C11  H8   single    0.970  0.020  1.090
 L7C  C8   H9   single    0.970  0.020  1.090
 L7C  C8   H10  single    0.970  0.020  1.090
 L7C  C7   H11  single    0.970  0.020  1.090
 L7C  C7   H12  single    0.970  0.020  1.090
 L7C  C9   H13  single    0.970  0.020  1.090
 L7C  C9   H14  single    0.970  0.020  1.090
 L7C  C6   H15  single    0.970  0.020  1.090
 L7C  N1   H16  single    0.860  0.020  1.020
 L7C  C2   H17  single    0.930  0.020  1.080
 L7C  C4   H18  single    0.930  0.020  1.080
 L7C  C3   H19  single    0.930  0.020  1.080
 L7C  C    H20  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
 L7C  C13  C17  C18  123.17  3.000
 L7C  C18  C17  F    117.96  3.000
 L7C  C13  C17  F    118.87  3.000
 L7C  H1   C18  C16  121.21  3.000
 L7C  H1   C18  C17  119.99  3.000
 L7C  C16  C18  C17  118.80  3.000
 L7C  H2   C16  C14  120.50  3.000
 L7C  H2   C16  C18  119.63  3.000
 L7C  C14  C16  C18  119.87  3.000
 L7C  H3   C14  C15  119.95  3.000
 L7C  H3   C14  C16  120.24  3.000
 L7C  C15  C14  C16  119.82  3.000
 L7C  H4   C15  C13  118.72  3.000
 L7C  H4   C15  C14  119.57  3.000
 L7C  C13  C15  C14  121.71  3.000
 L7C  C12  C13  C15  120.73  3.000
 L7C  C15  C13  C17  116.63  3.000
 L7C  C12  C13  C17  122.61  3.000
 L7C  H6   C12  H5   106.14  3.000
 L7C  H6   C12  C11  107.44  3.000
 L7C  H5   C12  C11  110.47  3.000
 L7C  H6   C12  C13  109.09  3.000
 L7C  H5   C12  C13  111.11  3.000
 L7C  C11  C12  C13  112.33  3.000
 L7C  H8   C11  H7   106.92  3.000
 L7C  H8   C11  C10  107.04  3.000
 L7C  H7   C11  C10  111.26  3.000
 L7C  H8   C11  C12  109.02  3.000
 L7C  H7   C11  C12  108.92  3.000
 L7C  C10  C11  C12  113.44  3.000
 L7C  N2   C10  O1   121.06  3.000
 L7C  O1   C10  C11  121.08  3.000
 L7C  N2   C10  C11  117.86  3.000
 L7C  C9   N2   C8   112.31  3.000
 L7C  C8   N2   C10  127.37  3.000
 L7C  C9   N2   C10  120.28  3.000
 L7C  H10  C8   H9   107.69  3.000
 L7C  H10  C8   C7   111.53  3.000
 L7C  H9   C8   C7   111.12  3.000
 L7C  H10  C8   N2   111.96  3.000
 L7C  H9   C8   N2   111.47  3.000
 L7C  C7   C8   N2   103.10  3.000
 L7C  H12  C7   H11  107.57  3.000
 L7C  H12  C7   C6   108.74  3.000
 L7C  H11  C7   C6   113.67  3.000
 L7C  H12  C7   C8   110.19  3.000
 L7C  H11  C7   C8   112.77  3.000
 L7C  C6   C7   C8   103.85  3.000
 L7C  H14  C9   H13  107.43  3.000
 L7C  H14  C9   C6   112.96  3.000
 L7C  H13  C9   C6   109.86  3.000
 L7C  H14  C9   N2   111.40  3.000
 L7C  H13  C9   N2   110.27  3.000
 L7C  C6   C9   N2   104.94  3.000
 L7C  H15  C6   C5   110.10  3.000
 L7C  H15  C6   C9   110.66  3.000
 L7C  C5   C6   C9   112.62  3.000
 L7C  H15  C6   C7   110.35  3.000
 L7C  C9   C6   C7   103.02  3.000
 L7C  C5   C6   C7   109.89  3.000
 L7C  N1   C5   O    123.93  3.000
 L7C  O    C5   C6   122.53  3.000
 L7C  N1   C5   C6   113.51  3.000
 L7C  H16  N1   C1   112.94  3.000
 L7C  H16  N1   C5   117.42  3.000
 L7C  C1   N1   C5   129.64  3.000
 L7C  C2   C1   N    122.66  3.000
 L7C  C2   C1   N1   124.54  3.000
 L7C  N    C1   N1   112.80  3.000
 L7C  C    N    C1   118.78  3.000
 L7C  H17  C2   C4   120.79  3.000
 L7C  H17  C2   C1   121.62  3.000
 L7C  C4   C2   C1   117.58  3.000
 L7C  H18  C4   C3   120.47  3.000
 L7C  H18  C4   C2   119.40  3.000
 L7C  C3   C4   C2   120.13  3.000
 L7C  H19  C3   C    120.79  3.000
 L7C  H19  C3   C4   121.80  3.000
 L7C  C    C3   C4   117.41  3.000
 L7C  H20  C    C3   120.51  3.000
 L7C  H20  C    N    116.05  3.000
 L7C  C3   C    N    123.44  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
 L7C  CONST_01  C14  C15  C13  C17     0.00   0.0  0
 L7C  CONST_02  C14  C16  C18  C17     0.00   0.0  0
 L7C  CONST_03  C15  C13  C17  C18     0.00   0.0  0
 L7C  CONST_04  C15  C14  C16  C18     0.00   0.0  0
 L7C  CONST_05  C13  C17  C18  C16     0.00   0.0  0
 L7C  CONST_06  C13  C15  C14  C16     0.00   0.0  0
 L7C  CONST_07  C3   C    N    C1      0.00   0.0  0
 L7C  CONST_08  C3   C4   C2   C1      0.00   0.0  0
 L7C  CONST_09  C4   C3   C    N       0.00   0.0  0
 L7C  CONST_10  C4   C2   C1   N       0.00   0.0  0
 L7C  CONST_11  C    N    C1   C2      0.00   0.0  0
 L7C  CONST_12  C    C3   C4   C2      0.00   0.0  0
 L7C  CONST_13  C15  C13  C17  F     180.00   0.0  0
 L7C  CONST_14  C16  C18  C17  F     180.00   0.0  0
 L7C  CONST_15  C12  C13  C17  C18   180.00   0.0  0
 L7C  CONST_16  C12  C13  C15  C14   180.00   0.0  0
 L7C  CONST_17  C    N    C1   N1    180.00   0.0  0
 L7C  CONST_18  C4   C2   C1   N1    180.00   0.0  0
 L7C  CONST_19  H4   C15  C13  C17   180.00   0.0  0
 L7C  CONST_20  H2   C16  C18  C17   180.00   0.0  0
 L7C  CONST_21  H3   C14  C16  C18   180.00   0.0  0
 L7C  CONST_22  H4   C15  C14  C16   180.00   0.0  0
 L7C  CONST_23  H1   C18  C16  C14   180.00   0.0  0
 L7C  CONST_24  H2   C16  C14  C15   180.00   0.0  0
 L7C  CONST_25  H1   C18  C17  C13   180.00   0.0  0
 L7C  CONST_26  H3   C14  C15  C13   180.00   0.0  0
 L7C  CONST_27  H20  C    N    C1    180.00   0.0  0
 L7C  CONST_28  H18  C4   C2   C1    180.00   0.0  0
 L7C  CONST_29  H19  C3   C    N     180.00   0.0  0
 L7C  CONST_30  H17  C2   C1   N     180.00   0.0  0
 L7C  CONST_31  H19  C3   C4   C2    180.00   0.0  0
 L7C  CONST_32  H20  C    C3   C4    180.00   0.0  0
 L7C  CONST_33  H17  C2   C4   C3    180.00   0.0  0
 L7C  CONST_34  H18  C4   C3   C     180.00   0.0  0
 L7C  CONST_35  C9   N2   C10  C11   180.00   0.0  0
 L7C  CONST_36  C8   N2   C10  C11     0.00   0.0  0
 L7C  CONST_37  C9   N2   C10  O1      0.00   0.0  0
 L7C  CONST_38  C8   N2   C10  O1    180.00   0.0  0
 L7C  CONST_39  C1   N1   C5   C6    180.00   0.0  0
 L7C  CONST_40  N    C1   N1   C5    180.00   0.0  0
 L7C  CONST_41  C2   C1   N1   C5      0.00   0.0  0
 L7C  CONST_42  H16  N1   C1   N       0.00   0.0  0
 L7C  CONST_43  H16  N1   C1   C2    180.00   0.0  0
 L7C  CONST_44  C1   N1   C5   O       0.00   0.0  0
 L7C  CONST_45  H16  N1   C5   C6      0.00   0.0  0
 L7C  CONST_46  H16  N1   C5   O     180.00   0.0  0
 L7C  Var_01    C6   C7   C8   N2    -32.86  30.0  1
 L7C  Var_02    C6   C9   N2   C8      3.43  30.0  1
 L7C  Var_03    C9   N2   C8   C7     18.68  30.0  1
 L7C  Var_04    C6   C9   N2   C10  -178.49  30.0  1
 L7C  Var_05    C7   C8   N2   C10  -159.24  30.0  1
 L7C  Var_06    H11  C7   C8   N2   -156.35  30.0  1
 L7C  Var_07    H12  C7   C8   N2     83.44  30.0  1
 L7C  Var_08    H13  C9   N2   C8   -114.82  30.0  1
 L7C  Var_09    H14  C9   N2   C8    125.99  30.0  1
 L7C  Var_10    H9   C8   N2   C9   -100.60  30.0  1
 L7C  Var_11    H10  C8   N2   C9    138.68  30.0  1
 L7C  Var_12    H9   C8   C7   C6     86.66  30.0  1
 L7C  Var_13    H10  C8   C7   C6   -153.16  30.0  1
 L7C  Var_14    C11  C12  C13  C17   103.14  30.0  2
 L7C  Var_15    C11  C12  C13  C15   -74.98  30.0  2
 L7C  Var_16    H5   C12  C13  C17   -21.19  30.0  2
 L7C  Var_17    H6   C12  C13  C17  -137.86  30.0  2
 L7C  Var_18    H5   C12  C13  C15   160.70  30.0  2
 L7C  Var_19    H6   C12  C13  C15    44.03  30.0  2
 L7C  Var_20    H13  C9   N2   C10    63.26  30.0  1
 L7C  Var_21    H14  C9   N2   C10   -55.92  30.0  1
 L7C  Var_22    H9   C8   N2   C10    81.48  30.0  1
 L7C  Var_23    H10  C8   N2   C10   -39.24  30.0  1
 L7C  Var_24    C10  C11  C12  C13   -57.15  30.0  1
 L7C  Var_25    N2   C10  C11  C12   -78.57  30.0  2
 L7C  Var_26    H7   C11  C12  C13   178.34  30.0  1
 L7C  Var_27    H8   C11  C12  C13    62.01  30.0  1
 L7C  Var_28    H7   C11  C10  N2     44.66  30.0  3
 L7C  Var_29    H8   C11  C10  N2    161.14  30.0  3
 L7C  Var_30    O1   C10  C11  C12   101.27  30.0  2
 L7C  Var_31    H5   C12  C11  C10    67.52  30.0  3
 L7C  Var_32    H6   C12  C11  C10  -177.12  30.0  3
 L7C  Var_33    H7   C11  C10  O1   -135.50  30.0  3
 L7C  Var_34    H8   C11  C10  O1    -19.02  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
 L7C  chir_01  C6  C5  C7  C9  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
 L7C  plan-1  F    0.020
 L7C  plan-1  C17  0.020
 L7C  plan-1  C18  0.020
 L7C  plan-1  C16  0.020
 L7C  plan-1  C14  0.020
 L7C  plan-1  C15  0.020
 L7C  plan-1  C13  0.020
 L7C  plan-1  C12  0.020
 L7C  plan-1  H1   0.020
 L7C  plan-1  H2   0.020
 L7C  plan-1  H3   0.020
 L7C  plan-1  H4   0.020
 L7C  plan-2  N1   0.020
 L7C  plan-2  C1   0.020
 L7C  plan-2  N    0.020
 L7C  plan-2  C2   0.020
 L7C  plan-2  C4   0.020
 L7C  plan-2  C3   0.020
 L7C  plan-2  C    0.020
 L7C  plan-2  H17  0.020
 L7C  plan-2  H18  0.020
 L7C  plan-2  H19  0.020
 L7C  plan-2  H20  0.020
 L7C  plan-3  C6   0.020
 L7C  plan-3  C5   0.020
 L7C  plan-3  O    0.020
 L7C  plan-3  N1   0.020
 L7C  plan-3  C1   0.020
 L7C  plan-3  H16  0.020
 L7C  plan-4  C11  0.020
 L7C  plan-4  C10  0.020
 L7C  plan-4  O1   0.020
 L7C  plan-4  N2   0.020
 L7C  plan-4  C8   0.020
 L7C  plan-4  C9   0.020

