# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 05:29:00 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: N-{3-[(1S,4S,6S)-2-amino-4-methyl-3-azabicyclo[4.1.0]hept-2-en-4-yl]-4-fluorophenyl}-5-chloropyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]1(C[C@@H]2C[C@@H]2C(=N1)N)c3cc(NC(=O)c4ccc(Cl)cn4)ccc3F
#
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
 8T3  8T3  N-{3-[(1S,4S,6S)-2-amino-4-methyl-3-azabicyclo[4.1.0]hept-2-en-4-yl]-4-fluorophenyl}-5-chloropyridine-2-carboxamide  ligand  44  26  .  2022-07-24  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_8T3
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
 8T3  CL    CL  CL    0  -0.095  -6.7665   2.4544  -0.0152
 8T3  C21   C   CR6   0  -0.109  -5.5329   1.2573   0.0538
 8T3  C20   C   CR16  0  -0.021  -4.2066   1.6253  -0.1431
 8T3  N10   N   N     0  -0.439  -3.2301   0.7400  -0.0973
 8T3  C25   C   CR16  0  -0.090  -5.8455  -0.0673   0.3043
 8T3  C18   C   CR16  0  -0.299  -4.8099  -0.9857   0.3487
 8T3  C12   C   CR6   0   0.130  -3.5148  -0.5347   0.1402
 8T3  C8    C   C     0   0.538  -2.3693  -1.5053   0.1841
 8T3  O16   O   O     0  -0.460  -2.5596  -2.6903   0.4052
 8T3  N11   N   NH1   0  -0.761  -1.1744  -0.9281  -0.0357
 8T3  C15   C   CR6   0   0.423   0.0993  -1.5039  -0.0580
 8T3  C22   C   CR16  0  -0.317   0.3513  -2.8684   0.0558
 8T3  C19   C   CR16  0  -0.394   1.6664  -3.3078   0.0213
 8T3  C13   C   CR6   0   0.500   2.7006  -2.4091  -0.1299
 8T3  F23   F   F     0  -0.318   3.9520  -2.9143  -0.1515
 8T3  C14   C   CR16  0  -0.432   1.1695  -0.6215  -0.2159
 8T3  C7    C   CR6   0  -0.061   2.4933  -1.0384  -0.2610
 8T3  C2    C   CT    0   0.035   3.6287  -0.0258  -0.4276
 8T3  C24   C   CH3   0  -0.646   4.4075  -0.3328  -1.7183
 8T3  C9    C   CH2   0  -0.448   4.5495  -0.0779   0.8095
 8T3  C4    C   CH1   0  -0.244   5.5948   1.0177   0.7569
 8T3  C6    C   CH2   0  -0.474   5.4242   2.2366   1.6054
 8T3  C3    C   CH1   0  -0.364   5.1504   2.2976   0.1270
 8T3  C5    C   C     0   0.428   3.7413   2.3253  -0.3430
 8T3  N1    N   N     0  -0.437   3.0273   1.2904  -0.5629
 8T3  N17   N   NH2   0  -0.819   3.2402   3.5697  -0.5844
 8T3  H20   H   HCR6  0   0.296  -3.9404   2.6585  -0.3316
 8T3  H25   H   HCR6  0   0.304  -6.8697  -0.3760   0.4634
 8T3  H18   H   HCR6  0   0.290  -5.0087  -2.0300   0.5396
 8T3  H11   H   HNH1  0   0.422  -1.2137   0.0719  -0.1936
 8T3  H22   H   HCR6  0   0.284  -0.4414  -3.5883   0.1705
 8T3  H14   H   HCR6  0   0.276   0.9795   0.4390  -0.3167
 8T3  H19   H   HCR6  0   0.276   1.8855  -4.3639   0.1132
 8T3  H241  H   HCH3  0   0.232   3.7439  -0.2719  -2.5818
 8T3  H242  H   HCH3  0   0.240   5.2033   0.4001  -1.8549
 8T3  H243  H   HCH3  0   0.231   4.8646  -1.3202  -1.7071
 8T3  H91C  H   HCH2  0   0.241   3.9232   0.0322   1.6991
 8T3  H92C  H   HCH2  0   0.249   5.0414  -1.0454   0.8926
 8T3  H4    H   HCH1  0   0.265   6.6099   0.7050   0.5457
 8T3  H61C  H   HCH2  0   0.253   4.5821   2.2696   2.2868
 8T3  H62C  H   HCH2  0   0.262   6.3103   2.7472   1.9611
 8T3  H3    H   HCH1  0   0.291   5.8507   2.8624  -0.4781
 8T3  H171  H   HNH2  0   0.388   3.6539   4.3401  -0.0850
 8T3  H172  H   HNH2  0   0.376   2.2414   3.6428  -0.7020

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
 8T3  CL   C21   single    1.720  0.020  1.720
 8T3  C21  C20   aromatic  1.390  0.020  1.390
 8T3  C21  C25   aromatic  1.384  0.020  1.384
 8T3  C20  N10   aromatic  1.319  0.020  1.319
 8T3  N10  C12   aromatic  1.328  0.020  1.328
 8T3  C25  C18   aromatic  1.385  0.020  1.385
 8T3  C18  C12   aromatic  1.387  0.020  1.387
 8T3  C12  C8    single    1.502  0.020  1.502
 8T3  C8   O16   double    1.220  0.020  1.220
 8T3  C8   N11   single    1.345  0.020  1.345
 8T3  N11  C15   single    1.398  0.020  1.398
 8T3  C15  C22   aromatic  1.392  0.020  1.392
 8T3  C15  C14   aromatic  1.396  0.020  1.396
 8T3  C22  C19   aromatic  1.387  0.020  1.387
 8T3  C19  C13   aromatic  1.378  0.020  1.378
 8T3  C13  F23   single    1.350  0.020  1.350
 8T3  C13  C7    aromatic  1.392  0.020  1.392
 8T3  C14  C7    aromatic  1.389  0.020  1.389
 8T3  C7   C2    single    1.530  0.020  1.530
 8T3  C2   C24   single    1.538  0.020  1.538
 8T3  C2   C9    single    1.543  0.020  1.543
 8T3  C2   N1    single    1.453  0.020  1.453
 8T3  C9   C4    single    1.515  0.020  1.515
 8T3  C4   C6    single    1.495  0.020  1.495
 8T3  C4   C3    single    1.494  0.020  1.494
 8T3  C6   C3    single    1.505  0.020  1.505
 8T3  C3   C5    single    1.486  0.020  1.486
 8T3  C5   N1    double    1.276  0.020  1.276
 8T3  C5   N17   single    1.363  0.020  1.363
 8T3  C20  H20   single    0.930  0.020  1.080
 8T3  C25  H25   single    0.930  0.020  1.080
 8T3  C18  H18   single    0.930  0.020  1.080
 8T3  N11  H11   single    0.860  0.020  1.020
 8T3  C22  H22   single    0.930  0.020  1.080
 8T3  C14  H14   single    0.930  0.020  1.080
 8T3  C19  H19   single    0.930  0.020  1.080
 8T3  C24  H241  single    0.970  0.020  1.090
 8T3  C24  H242  single    0.970  0.020  1.090
 8T3  C24  H243  single    0.970  0.020  1.090
 8T3  C9   H91C  single    0.970  0.020  1.090
 8T3  C9   H92C  single    0.970  0.020  1.090
 8T3  C4   H4    single    0.970  0.020  1.090
 8T3  C6   H61C  single    0.970  0.020  1.090
 8T3  C6   H62C  single    0.970  0.020  1.090
 8T3  C3   H3    single    0.970  0.020  1.090
 8T3  N17  H171  single    0.890  0.020  1.040
 8T3  N17  H172  single    0.890  0.020  1.040

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
 8T3  C25   C21  C20   119.64  3.000
 8T3  C25   C21  CL    120.75  3.000
 8T3  C20   C21  CL    119.61  3.000
 8T3  H20   C20  N10   117.66  3.000
 8T3  H20   C20  C21   120.76  3.000
 8T3  N10   C20  C21   121.58  3.000
 8T3  C12   N10  C20   119.47  3.000
 8T3  H25   C25  C18   120.94  3.000
 8T3  H25   C25  C21   120.92  3.000
 8T3  C18   C25  C21   118.14  3.000
 8T3  H18   C18  C12   120.84  3.000
 8T3  H18   C18  C25   120.61  3.000
 8T3  C12   C18  C25   118.54  3.000
 8T3  C8    C12  C18   119.84  3.000
 8T3  C8    C12  N10   117.52  3.000
 8T3  C18   C12  N10   122.63  3.000
 8T3  N11   C8   O16   125.79  3.000
 8T3  N11   C8   C12   113.29  3.000
 8T3  O16   C8   C12   120.91  3.000
 8T3  H11   N11  C15   116.07  3.000
 8T3  H11   N11  C8    114.49  3.000
 8T3  C15   N11  C8    129.44  3.000
 8T3  C14   C15  C22   119.33  3.000
 8T3  C14   C15  N11   116.10  3.000
 8T3  C22   C15  N11   124.56  3.000
 8T3  H22   C22  C19   119.26  3.000
 8T3  H22   C22  C15   122.04  3.000
 8T3  C19   C22  C15   118.69  3.000
 8T3  H19   C19  C13   119.57  3.000
 8T3  H19   C19  C22   119.93  3.000
 8T3  C13   C19  C22   120.50  3.000
 8T3  C7    C13  F23   120.33  3.000
 8T3  C7    C13  C19   122.71  3.000
 8T3  F23   C13  C19   116.96  3.000
 8T3  H14   C14  C7    117.29  3.000
 8T3  H14   C14  C15   119.70  3.000
 8T3  C7    C14  C15   123.01  3.000
 8T3  C2    C7   C14   120.81  3.000
 8T3  C2    C7   C13   123.44  3.000
 8T3  C14   C7   C13   115.75  3.000
 8T3  N1    C2   C9    110.62  3.000
 8T3  N1    C2   C24   108.19  3.000
 8T3  C9    C2   C24   111.33  3.000
 8T3  N1    C2   C7    107.59  3.000
 8T3  C9    C2   C7    109.46  3.000
 8T3  C24   C2   C7    109.57  3.000
 8T3  H243  C24  H242  107.74  3.000
 8T3  H243  C24  H241  108.33  3.000
 8T3  H242  C24  H241  107.90  3.000
 8T3  H243  C24  C2    112.65  3.000
 8T3  H242  C24  C2    109.90  3.000
 8T3  H241  C24  C2    110.18  3.000
 8T3  H92C  C9   H91C  106.63  3.000
 8T3  H92C  C9   C4    109.48  3.000
 8T3  H91C  C9   C4    110.52  3.000
 8T3  H92C  C9   C2    111.16  3.000
 8T3  H91C  C9   C2    107.89  3.000
 8T3  C4    C9   C2    111.07  3.000
 8T3  H4    C4   C3    116.35  3.000
 8T3  H4    C4   C6    116.94  3.000
 8T3  C3    C4   C6     60.45  3.000
 8T3  H4    C4   C9    116.40  3.000
 8T3  C3    C4   C9    115.39  3.000
 8T3  C6    C4   C9    119.42  3.000
 8T3  H62C  C6   H61C  114.52  3.000
 8T3  H62C  C6   C3    116.91  3.000
 8T3  H61C  C6   C3    118.36  3.000
 8T3  H62C  C6   C4    118.53  3.000
 8T3  H61C  C6   C4    118.05  3.000
 8T3  C3    C6   C4     59.74  3.000
 8T3  H3    C3   C5    115.24  3.000
 8T3  H3    C3   C6    116.86  3.000
 8T3  C5    C3   C6    118.95  3.000
 8T3  H3    C3   C4    119.30  3.000
 8T3  C5    C3   C4    115.56  3.000
 8T3  C6    C3   C4     59.80  3.000
 8T3  N17   C5   N1    120.27  3.000
 8T3  N17   C5   C3    114.95  3.000
 8T3  N1    C5   C3    124.74  3.000
 8T3  C5    N1   C2    119.13  3.000
 8T3  H172  N17  H171  114.17  3.000
 8T3  H172  N17  C5    116.80  3.000
 8T3  H171  N17  C5    117.35  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
 8T3  CONST_01  C12   N10  C20  C21     0.00   0.0  0
 8T3  CONST_02  C12   C18  C25  C21     0.00   0.0  0
 8T3  CONST_03  C18   C25  C21  C20     0.00   0.0  0
 8T3  CONST_04  C18   C12  N10  C20     0.00   0.0  0
 8T3  CONST_05  C25   C21  C20  N10     0.00   0.0  0
 8T3  CONST_06  C25   C18  C12  N10     0.00   0.0  0
 8T3  CONST_07  C13   C19  C22  C15     0.00   0.0  0
 8T3  CONST_08  C13   C7   C14  C15     0.00   0.0  0
 8T3  CONST_09  C7    C14  C15  C22     0.00   0.0  0
 8T3  CONST_10  C7    C13  C19  C22     0.00   0.0  0
 8T3  CONST_11  C14   C15  C22  C19     0.00   0.0  0
 8T3  CONST_12  C14   C7   C13  C19     0.00   0.0  0
 8T3  CONST_13  C2    C7   C14  C15   180.00   0.0  0
 8T3  CONST_14  C2    C7   C13  C19   180.00   0.0  0
 8T3  CONST_15  C3    C5   N1   C2      0.00   0.0  0
 8T3  CONST_16  N10   C20  C21  CL    180.00   0.0  0
 8T3  CONST_17  C18   C25  C21  CL    180.00   0.0  0
 8T3  CONST_18  C8    C12  N10  C20   180.00   0.0  0
 8T3  CONST_19  C8    C12  C18  C25   180.00   0.0  0
 8T3  CONST_20  C19   C22  C15  N11   180.00   0.0  0
 8T3  CONST_21  C7    C14  C15  N11   180.00   0.0  0
 8T3  CONST_22  F23   C13  C19  C22   180.00   0.0  0
 8T3  CONST_23  C14   C7   C13  F23   180.00   0.0  0
 8T3  CONST_24  C2    C7   C13  F23     0.00   0.0  0
 8T3  CONST_25  N17   C5   N1   C2    180.00   0.0  0
 8T3  CONST_26  H18   C18  C25  C21   180.00   0.0  0
 8T3  CONST_27  H25   C25  C21  C20   180.00   0.0  0
 8T3  CONST_28  H20   C20  C21  C25   180.00   0.0  0
 8T3  CONST_29  H19   C19  C22  C15   180.00   0.0  0
 8T3  CONST_30  H14   C14  C15  C22   180.00   0.0  0
 8T3  CONST_31  H22   C22  C19  C13   180.00   0.0  0
 8T3  CONST_32  C15   N11  C8   C12   180.00   0.0  0
 8T3  CONST_33  C22   C15  N11  C8      0.00   0.0  0
 8T3  CONST_34  C14   C15  N11  C8    180.00   0.0  0
 8T3  CONST_35  H11   N11  C15  C22   180.00   0.0  0
 8T3  CONST_37  H172  N17  C5   C3    180.00   0.0  0
 8T3  CONST_38  C15   N11  C8   O16     0.00   0.0  0
 8T3  Var_01    C6    C4   C9   C2    103.00  30.0  1
 8T3  Var_02    C3    C6   C4   C9   -104.26  30.0  1
 8T3  Var_03    N1    C5   C3   C4    -18.87  30.0  1
 8T3  Var_04    O16   C8   C12  N10   179.58  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
 8T3  chir_01  C2  C7  C9  N1  positiv
 8T3  chir_02  C4  C9  C6  C3  both
 8T3  chir_03  C3  C4  C6  C5  both

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
 8T3  plan-1  CL    0.020
 8T3  plan-1  C21   0.020
 8T3  plan-1  C20   0.020
 8T3  plan-1  N10   0.020
 8T3  plan-1  C25   0.020
 8T3  plan-1  C18   0.020
 8T3  plan-1  C12   0.020
 8T3  plan-1  C8    0.020
 8T3  plan-1  H20   0.020
 8T3  plan-1  H25   0.020
 8T3  plan-1  H18   0.020
 8T3  plan-2  N11   0.020
 8T3  plan-2  C15   0.020
 8T3  plan-2  C22   0.020
 8T3  plan-2  C19   0.020
 8T3  plan-2  C13   0.020
 8T3  plan-2  F23   0.020
 8T3  plan-2  C14   0.020
 8T3  plan-2  C7    0.020
 8T3  plan-2  C2    0.020
 8T3  plan-2  H22   0.020
 8T3  plan-2  H14   0.020
 8T3  plan-2  H19   0.020
 8T3  plan-3  C12   0.020
 8T3  plan-3  C8    0.020
 8T3  plan-3  O16   0.020
 8T3  plan-3  N11   0.020
 8T3  plan-3  C15   0.020
 8T3  plan-3  H11   0.020
 8T3  plan-4  C2    0.020
 8T3  plan-4  C3    0.020
 8T3  plan-4  C5    0.020
 8T3  plan-4  N1    0.020
 8T3  plan-4  N17   0.020
 8T3  plan-4  H171  0.020
 8T3  plan-4  H172  0.020

