# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 02:12:18 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: (1S,3aS,4R,8aS,8bR)-4-[4-(diaminomethyl)phenyl]-1-(difluoromethyl)-2-(4-fluorobenzyl)octahydropyrrolo[3,4-a]pyrrolizin-3(2H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(N)c1ccc(cc1)[C@H]2[C@@H]3[C@H]([C@@H]4CCCN24)[C@@H](C(F)F)N(Cc5ccc(F)cc5)C3=O
#
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
 F25  F25  (1S,3aS,4R,8aS,8bR)-4-[4-(diaminomethyl)phenyl]-1-(difluoromethyl)-2-(4-fluorobenzyl)octahydropyrrolo[3,4-a]pyrrolizin-3(2H)-one  ligand  59  32  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_F25
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
 F25  O21   O  O     0  -0.465   0.6300  -0.8325   2.1914
 F25  C20   C  CR5   0   0.597  -0.3910  -0.9836   1.5520
 F25  N19   N  NR5   0  -0.465  -1.4527  -0.1350   1.5749
 F25  C23   C  CH2   0  -0.424  -1.3776   1.1989   2.1395
 F25  C24   C  CR6   0   0.125  -1.0455   2.2149   1.0756
 F25  C32   C  CR16  0  -0.289  -2.0217   3.0690   0.5761
 F25  C31   C  CR16  0  -0.400  -1.7369   3.9717  -0.4416
 F25  C30   C  CR6   0   0.520  -0.4550   4.0031  -0.9499
 F25  F29   F  F     0  -0.316  -0.1650   4.8695  -1.9348
 F25  C26   C  CR16  0  -0.402   0.5449   3.1731  -0.4758
 F25  C25   C  CR16  0  -0.273   0.2404   2.2816   0.5400
 F25  C17   C  CR15  0  -0.222  -2.6001  -0.6068   0.8384
 F25  C16   C  CR15  0  -0.310  -2.0214  -1.7096  -0.0510
 F25  C15   C  CH1   0  -0.059  -1.5598  -1.1898  -1.4174
 F25  N11   N  NT    0  -0.435  -0.4020  -2.0061  -1.7619
 F25  C12   C  CH2   0  -0.281  -0.8681  -3.0636  -2.6469
 F25  C13   C  CH2   0  -0.458  -1.8434  -2.3195  -3.5457
 F25  C14   C  CH2   0  -0.472  -2.5614  -1.3775  -2.5686
 F25  C10   C  CH1   0  -0.128   0.2837  -2.4169  -0.5479
 F25  C7    C  CR6   0   0.151   1.6298  -1.7485  -0.3976
 F25  C8    C  CR16  0  -0.271   2.6410  -2.3602   0.3361
 F25  C9    C  CR16  0  -0.302   3.8745  -1.7507   0.4923
 F25  C4    C  CR6   0   0.084   4.1318  -0.4981  -0.0611
 F25  C5    C  CR16  0  -0.284   3.1175   0.1160  -0.7864
 F25  C6    C  CR16  0  -0.295   1.8878  -0.5062  -0.9596
 F25  C3    C  CH1   0  -0.018   5.4720   0.1689   0.1952
 F25  N1    N  NH2   0  -0.778   5.5520   0.7930   1.5078
 F25  N2    N  NH2   0  -0.795   5.7312   1.1981  -0.7900
 F25  C22   C  CR15  0  -0.414  -0.7211  -2.1379   0.6259
 F25  C18   C  CH1   0   0.589  -3.6576  -1.1606   1.7773
 F25  F33   F  F     0  -0.338  -4.1314  -0.1894   2.6079
 F25  F32   F  F     0  -0.339  -4.7242  -1.5937   1.0494
 F25  H231  H  HCH2  0   0.276  -2.3227   1.4525   2.6159
 F25  H232  H  HCH2  0   0.281  -0.6220   1.1943   2.9247
 F25  H25   H  HCR6  0   0.266  -3.0255   3.0354   0.9826
 F25  H26   H  HCR6  0   0.280  -2.5006   4.6326  -0.8299
 F25  H28   H  HCR6  0   0.275   1.5438   3.2254  -0.8896
 F25  H29   H  HCR6  0   0.271   1.0178   1.6274   0.9139
 F25  H17   H  HCR5  0   0.289  -3.0461   0.2015   0.2461
 F25  H16   H  HCR5  0   0.285  -2.7173  -2.5401  -0.1787
 F25  H15   H  HCH1  0   0.239  -1.2576  -0.1388  -1.3139
 F25  H121  H  HCH2  0   0.201  -1.3857  -3.8734  -2.1088
 F25  H122  H  HCH2  0   0.237  -0.0375  -3.5144  -3.1933
 F25  H131  H  HCH2  0   0.239  -2.5251  -2.9904  -4.0677
 F25  H132  H  HCH2  0   0.234  -1.2957  -1.7463  -4.2955
 F25  H142  H  HCH2  0   0.249  -2.8383  -0.4311  -3.0289
 F25  H141  H  HCH2  0   0.238  -3.4825  -1.8334  -2.2012
 F25  H10   H  HCH1  0   0.258   0.4513  -3.4975  -0.5809
 F25  H8    H  HCR6  0   0.235   2.4684  -3.3367   0.7749
 F25  H9    H  HCR6  0   0.239   4.6522  -2.2594   1.0523
 F25  H5    H  HCR6  0   0.242   3.2914   1.0882  -1.2304
 F25  H6    H  HCR6  0   0.241   1.1245  -0.0085  -1.5438
 F25  H33   H  HCH1  0   0.211   6.2355  -0.6234   0.1921
 F25  H12   H  HNH2  0   0.337   4.7134   1.3377   1.6752
 F25  HN1   H  HNH2  0   0.347   5.5732   0.0779   2.2238
 F25  H23   H  HNH2  0   0.349   6.6342   1.6115  -0.5940
 F25  HN2   H  HNH2  0   0.345   5.7941   0.7887  -1.7139
 F25  H22   H  HCR5  0   0.308  -0.8333  -3.0394   1.2331
 F25  H18   H  HCH1  0   0.194  -3.2912  -1.9856   2.3914

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
 F25  O21  C20   double    1.214  0.020  1.214
 F25  C20  N19   single    1.359  0.020  1.359
 F25  C20  C22   single    1.516  0.020  1.516
 F25  N19  C23   single    1.450  0.020  1.450
 F25  N19  C17   single    1.443  0.020  1.443
 F25  C23  C24   single    1.508  0.020  1.508
 F25  C23  H231  single    0.970  0.020  1.090
 F25  C23  H232  single    0.970  0.020  1.090
 F25  C24  C32   aromatic  1.390  0.020  1.390
 F25  C24  C25   aromatic  1.395  0.020  1.395
 F25  C32  C31   aromatic  1.390  0.020  1.390
 F25  C32  H25   single    0.930  0.020  1.080
 F25  C31  C30   aromatic  1.379  0.020  1.379
 F25  C31  H26   single    0.930  0.020  1.080
 F25  C30  F29   single    1.343  0.020  1.343
 F25  C30  C26   aromatic  1.383  0.020  1.383
 F25  C26  C25   aromatic  1.385  0.020  1.385
 F25  C26  H28   single    0.930  0.020  1.080
 F25  C25  H29   single    0.930  0.020  1.080
 F25  C17  C16   single    1.530  0.020  1.530
 F25  C17  C18   single    1.519  0.020  1.519
 F25  C17  H17   single    0.970  0.020  1.090
 F25  C16  C15   single    1.533  0.020  1.533
 F25  C16  C22   single    1.527  0.020  1.527
 F25  C16  H16   single    0.970  0.020  1.090
 F25  C15  N11   single    1.458  0.020  1.458
 F25  C15  C14   single    1.537  0.020  1.537
 F25  C15  H15   single    0.970  0.020  1.090
 F25  N11  C12   single    1.456  0.020  1.456
 F25  N11  C10   single    1.454  0.020  1.454
 F25  C12  C13   single    1.521  0.020  1.521
 F25  C12  H121  single    0.970  0.020  1.090
 F25  C12  H122  single    0.970  0.020  1.090
 F25  C13  C14   single    1.535  0.020  1.535
 F25  C13  H131  single    0.970  0.020  1.090
 F25  C13  H132  single    0.970  0.020  1.090
 F25  C14  H142  single    0.970  0.020  1.090
 F25  C14  H141  single    0.970  0.020  1.090
 F25  C10  C7    single    1.510  0.020  1.510
 F25  C10  C22   single    1.570  0.020  1.570
 F25  C10  H10   single    0.970  0.020  1.090
 F25  C7   C8    aromatic  1.391  0.020  1.391
 F25  C7   C6    aromatic  1.388  0.020  1.388
 F25  C8   C9    aromatic  1.385  0.020  1.385
 F25  C8   H8    single    0.930  0.020  1.080
 F25  C9   C4    aromatic  1.393  0.020  1.393
 F25  C9   H9    single    0.930  0.020  1.080
 F25  C4   C5    aromatic  1.390  0.020  1.390
 F25  C4   C3    single    1.519  0.020  1.519
 F25  C5   C6    aromatic  1.389  0.020  1.389
 F25  C5   H5    single    0.930  0.020  1.080
 F25  C6   H6    single    0.930  0.020  1.080
 F25  C3   N1    single    1.456  0.020  1.456
 F25  C3   N2    single    1.448  0.020  1.448
 F25  C3   H33   single    0.970  0.020  1.090
 F25  N1   H12   single    0.890  0.020  1.040
 F25  N1   HN1   single    0.890  0.020  1.040
 F25  N2   H23   single    0.890  0.020  1.040
 F25  N2   HN2   single    0.890  0.020  1.040
 F25  C22  H22   single    0.970  0.020  1.090
 F25  C18  F33   single    1.363  0.020  1.363
 F25  C18  F32   single    1.362  0.020  1.362
 F25  C18  H18   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
 F25  C22   C20  N19   108.39  3.000
 F25  C22   C20  O21   126.83  3.000
 F25  N19   C20  O21   124.77  3.000
 F25  C17   N19  C23   122.73  3.000
 F25  C17   N19  C20   114.11  3.000
 F25  C23   N19  C20   122.70  3.000
 F25  H232  C23  H231  106.72  3.000
 F25  H232  C23  C24   111.01  3.000
 F25  H231  C23  C24   110.06  3.000
 F25  H232  C23  N19   108.21  3.000
 F25  H231  C23  N19   109.86  3.000
 F25  C24   C23  N19   110.88  3.000
 F25  C25   C24  C32   118.70  3.000
 F25  C25   C24  C23   120.41  3.000
 F25  C32   C24  C23   120.85  3.000
 F25  H25   C32  C31   118.99  3.000
 F25  H25   C32  C24   119.79  3.000
 F25  C31   C32  C24   121.22  3.000
 F25  H26   C31  C30   120.65  3.000
 F25  H26   C31  C32   120.99  3.000
 F25  C30   C31  C32   118.37  3.000
 F25  C26   C30  F29   118.83  3.000
 F25  C26   C30  C31   122.12  3.000
 F25  F29   C30  C31   119.04  3.000
 F25  H28   C26  C25   120.94  3.000
 F25  H28   C26  C30   120.46  3.000
 F25  C25   C26  C30   118.59  3.000
 F25  H29   C25  C26   118.96  3.000
 F25  H29   C25  C24   120.04  3.000
 F25  C26   C25  C24   121.00  3.000
 F25  H17   C17  C18   108.62  3.000
 F25  H17   C17  C16   111.77  3.000
 F25  C18   C17  C16   111.09  3.000
 F25  H17   C17  N19   110.98  3.000
 F25  C18   C17  N19   110.95  3.000
 F25  C16   C17  N19   103.39  3.000
 F25  H16   C16  C22   112.43  3.000
 F25  H16   C16  C15   110.23  3.000
 F25  C22   C16  C15   103.52  3.000
 F25  H16   C16  C17   112.04  3.000
 F25  C22   C16  C17   105.45  3.000
 F25  C15   C16  C17   112.80  3.000
 F25  H15   C15  C14   111.51  3.000
 F25  H15   C15  N11   109.84  3.000
 F25  C14   C15  N11   105.79  3.000
 F25  H15   C15  C16   108.86  3.000
 F25  C14   C15  C16   115.46  3.000
 F25  N11   C15  C16   105.06  3.000
 F25  C10   N11  C12   116.97  3.000
 F25  C10   N11  C15   109.61  3.000
 F25  C12   N11  C15   107.23  3.000
 F25  H122  C12  H121  107.37  3.000
 F25  H122  C12  C13   113.22  3.000
 F25  H121  C12  C13   110.31  3.000
 F25  H122  C12  N11   111.15  3.000
 F25  H121  C12  N11   112.80  3.000
 F25  C13   C12  N11   102.07  3.000
 F25  H132  C13  H131  107.95  3.000
 F25  H132  C13  C14   110.47  3.000
 F25  H131  C13  C14   112.96  3.000
 F25  H132  C13  C12   109.95  3.000
 F25  H131  C13  C12   112.53  3.000
 F25  C14   C13  C12   102.95  3.000
 F25  H141  C14  H142  106.91  3.000
 F25  H141  C14  C13   110.64  3.000
 F25  H142  C14  C13   112.55  3.000
 F25  H141  C14  C15   110.41  3.000
 F25  H142  C14  C15   112.10  3.000
 F25  C13   C14  C15   104.29  3.000
 F25  H10   C10  C22   107.22  3.000
 F25  H10   C10  C7    107.67  3.000
 F25  C22   C10  C7    114.66  3.000
 F25  H10   C10  N11   109.04  3.000
 F25  C22   C10  N11   105.80  3.000
 F25  C7    C10  N11   112.24  3.000
 F25  C6    C7   C8    118.17  3.000
 F25  C6    C7   C10   121.44  3.000
 F25  C8    C7   C10   120.38  3.000
 F25  H8    C8   C9    119.50  3.000
 F25  H8    C8   C7    119.59  3.000
 F25  C9    C8   C7    120.90  3.000
 F25  H9    C9   C4    119.61  3.000
 F25  H9    C9   C8    119.37  3.000
 F25  C4    C9   C8    121.02  3.000
 F25  C3    C4   C5    122.54  3.000
 F25  C3    C4   C9    119.38  3.000
 F25  C5    C4   C9    118.02  3.000
 F25  H5    C5   C6    119.56  3.000
 F25  H5    C5   C4    119.56  3.000
 F25  C6    C5   C4    120.87  3.000
 F25  H6    C6   C5    119.06  3.000
 F25  H6    C6   C7    119.94  3.000
 F25  C5    C6   C7    121.01  3.000
 F25  H33   C3   N2    112.69  3.000
 F25  H33   C3   N1    105.85  3.000
 F25  N2    C3   N1    107.39  3.000
 F25  H33   C3   C4    107.19  3.000
 F25  N2    C3   C4    110.81  3.000
 F25  N1    C3   C4    112.89  3.000
 F25  HN1   N1   H12   106.26  3.000
 F25  HN1   N1   C3    109.64  3.000
 F25  H12   N1   C3    109.49  3.000
 F25  HN2   N2   H23   106.64  3.000
 F25  HN2   N2   C3    110.15  3.000
 F25  H23   N2   C3    108.55  3.000
 F25  H22   C22  C10   109.55  3.000
 F25  H22   C22  C16   112.97  3.000
 F25  C10   C22  C16   105.26  3.000
 F25  H22   C22  C20   108.12  3.000
 F25  C10   C22  C20   116.91  3.000
 F25  C16   C22  C20   104.04  3.000
 F25  H18   C18  F32   108.85  3.000
 F25  H18   C18  F33   108.20  3.000
 F25  F32   C18  F33   106.27  3.000
 F25  H18   C18  C17   112.92  3.000
 F25  F32   C18  C17   109.33  3.000
 F25  F33   C18  C17   111.04  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
 F25  CONST_01  C30  C31  C32  C24     0.00   0.0  0
 F25  CONST_02  C30  C26  C25  C24     0.00   0.0  0
 F25  CONST_03  C26  C25  C24  C32     0.00   0.0  0
 F25  CONST_04  C26  C30  C31  C32     0.00   0.0  0
 F25  CONST_05  C25  C24  C32  C31     0.00   0.0  0
 F25  CONST_06  C25  C26  C30  C31     0.00   0.0  0
 F25  CONST_07  C4   C9   C8   C7      0.00   0.0  0
 F25  CONST_08  C4   C5   C6   C7      0.00   0.0  0
 F25  CONST_09  C5   C6   C7   C8      0.00   0.0  0
 F25  CONST_10  C5   C4   C9   C8      0.00   0.0  0
 F25  CONST_11  C6   C7   C8   C9      0.00   0.0  0
 F25  CONST_12  C6   C5   C4   C9      0.00   0.0  0
 F25  CONST_13  C9   C8   C7   C10   180.00   0.0  0
 F25  CONST_14  C5   C6   C7   C10   180.00   0.0  0
 F25  CONST_15  C22  C20  N19  C17     0.00   0.0  0
 F25  CONST_16  C31  C32  C24  C23   180.00   0.0  0
 F25  CONST_17  C26  C25  C24  C23   180.00   0.0  0
 F25  CONST_18  F29  C30  C31  C32   180.00   0.0  0
 F25  CONST_19  C25  C26  C30  F29   180.00   0.0  0
 F25  CONST_20  C3   C4   C9   C8    180.00   0.0  0
 F25  CONST_21  C3   C4   C5   C6    180.00   0.0  0
 F25  CONST_22  C17  N19  C20  O21   180.00   0.0  0
 F25  CONST_23  C22  C20  N19  C23   180.00   0.0  0
 F25  CONST_24  H26  C31  C32  C24   180.00   0.0  0
 F25  CONST_25  H28  C26  C25  C24   180.00   0.0  0
 F25  CONST_26  H29  C25  C24  C32   180.00   0.0  0
 F25  CONST_27  H25  C32  C31  C30   180.00   0.0  0
 F25  CONST_28  H8   C8   C7   C10     0.00   0.0  0
 F25  CONST_29  H6   C6   C7   C10     0.00   0.0  0
 F25  CONST_30  H9   C9   C8   C7    180.00   0.0  0
 F25  CONST_31  H5   C5   C6   C7    180.00   0.0  0
 F25  CONST_32  C23  N19  C20  O21     0.00   0.0  0
 F25  Var_01    C13  C12  N11  C15    40.93  30.0  1
 F25  Var_02    C12  C13  C14  C15    25.01  30.0  1
 F25  Var_03    C14  C13  C12  N11   -40.02  30.0  1
 F25  Var_04    C24  C23  N19  C20    93.22  30.0  3
 F25  Var_05    C32  C24  C23  N19   104.89  30.0  2
 F25  Var_06    N1   C3   C4   C9    -78.98  30.0  2
 F25  Var_07    H12  N1   C3   C4    -46.67  30.0  3
 F25  Var_08    H23  N2   C3   C4   -179.37  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
 F25  chir_01  C17  N19  C16  C18  negativ
 F25  chir_02  C16  C17  C15  C22  negativ
 F25  chir_03  C15  N11  C16  C14  positiv
 F25  chir_04  C10  N11  C22  C7   positiv
 F25  chir_05  C22  C10  C16  C20  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
 F25  plan-1  C23  0.020
 F25  plan-1  C24  0.020
 F25  plan-1  C32  0.020
 F25  plan-1  C31  0.020
 F25  plan-1  C30  0.020
 F25  plan-1  F29  0.020
 F25  plan-1  C26  0.020
 F25  plan-1  C25  0.020
 F25  plan-1  H25  0.020
 F25  plan-1  H26  0.020
 F25  plan-1  H28  0.020
 F25  plan-1  H29  0.020
 F25  plan-2  C10  0.020
 F25  plan-2  C7   0.020
 F25  plan-2  C8   0.020
 F25  plan-2  C9   0.020
 F25  plan-2  C4   0.020
 F25  plan-2  C5   0.020
 F25  plan-2  C6   0.020
 F25  plan-2  C3   0.020
 F25  plan-2  H8   0.020
 F25  plan-2  H9   0.020
 F25  plan-2  H5   0.020
 F25  plan-2  H6   0.020
 F25  plan-3  O21  0.020
 F25  plan-3  C20  0.020
 F25  plan-3  N19  0.020
 F25  plan-3  C23  0.020
 F25  plan-3  C17  0.020
 F25  plan-3  C22  0.020

