# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 21:48:10 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: (7R,8R)-8-(2,4,5-trifluorophenyl)-6,7,8,9-tetrahydroimidazo[1,2-a:4,5-c']dipyridin-7-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1Cn2c(C[C@@H]1c3cc(F)c(F)cc3F)nc4cnccc24
#
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
 361  361  (7R,8R)-8-(2,4,5-trifluorophenyl)-6,7,8,9-tetrahydroimidazo[1,2-a:4,5-c']dipyridin-7-amine  ligand  36  23  .  2022-07-22  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_361
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
 361  F21   F  F     0  -0.304   4.3411  -1.9606   1.4658
 361  C5    C  CR6   0   0.409   3.8292  -1.0354   0.6485
 361  C6    C  CR6   0   0.405   4.6770  -0.3267  -0.1864
 361  F27   F  F     0  -0.299   5.9854  -0.5811  -0.1613
 361  C4    C  CR16  0  -0.444   2.4756  -0.7879   0.6360
 361  C3    C  CR6   0  -0.050   1.9289   0.1782  -0.2095
 361  C2    C  CR6   0   0.522   2.8103   0.8675  -1.0263
 361  F22   F  F     0  -0.301   2.3415   1.8051  -1.8607
 361  C1    C  CR16  0  -0.557   4.1745   0.6340  -1.0348
 361  C9    C  CH1   0  -0.356   0.4454   0.4438  -0.2192
 361  C14   C  CH1   0  -0.090  -0.0722   0.8641   1.1640
 361  N23   N  NH2   0  -0.796   0.6771   1.9978   1.6684
 361  C13   C  CH2   0  -0.279  -1.5287   1.2924   1.0365
 361  N12   N  NR5   0  -0.559  -2.2943   0.2942   0.3204
 361  C29   C  CR56  0   0.432  -3.6510   0.1676   0.2818
 361  C19   C  CR56  0   0.042  -3.8919  -0.8829  -0.6151
 361  N18   N  N     0  -0.486  -2.7056  -1.3674  -1.1081
 361  C11   C  CR5   0   0.481  -1.7864  -0.6436  -0.5323
 361  C10   C  CH2   0  -0.521  -0.3163  -0.7964  -0.7005
 361  C20   C  CR16  0  -0.131  -5.2108  -1.2526  -0.8571
 361  N21   N  N     0  -0.417  -6.2177  -0.6339  -0.2623
 361  C22   C  CR16  0  -0.096  -5.9617   0.3692   0.5886
 361  C23   C  CR16  0  -0.374  -4.6969   0.8292   0.9099
 361  H4    H  HCR6  0   0.298   1.8377  -1.3565   1.3022
 361  H1    H  HCR6  0   0.316   4.8310   1.1907  -1.6907
 361  H9    H  HCH1  0   0.281   0.2381   1.2675  -0.9069
 361  H14   H  HCH1  0   0.233  -0.0329  -0.0144   1.8269
 361  HN23  H  HNH2  0   0.357   0.3085   2.2698   2.5722
 361  HN2A  H  HNH2  0   0.358   1.6356   1.7231   1.8449
 361  H13   H  HCH2  0   0.279  -1.9713   1.4331   2.0242
 361  H13A  H  HCH2  0   0.265  -1.5787   2.2462   0.5052
 361  H10   H  HCH2  0   0.295  -0.0955  -1.0044  -1.7479
 361  H10A  H  HCH2  0   0.282   0.0028  -1.6792  -0.1369
 361  H20   H  HCR6  0   0.261  -5.4491  -2.0619  -1.5400
 361  H22   H  HCR6  0   0.260  -6.8273   0.8371   1.0432
 361  H23   H  HCR6  0   0.281  -4.5579   1.6463   1.6043

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
 361  F21  C5    single    1.336  0.020  1.336
 361  C5   C6    aromatic  1.385  0.020  1.385
 361  C5   C4    aromatic  1.376  0.020  1.376
 361  C6   F27   single    1.333  0.020  1.333
 361  C6   C1    aromatic  1.377  0.020  1.377
 361  C4   C3    aromatic  1.395  0.020  1.395
 361  C3   C2    aromatic  1.385  0.020  1.385
 361  C3   C9    single    1.507  0.020  1.507
 361  C2   F22   single    1.340  0.020  1.340
 361  C2   C1    aromatic  1.384  0.020  1.384
 361  C9   C14   single    1.536  0.020  1.536
 361  C9   C10   single    1.533  0.020  1.533
 361  C14  N23   single    1.450  0.020  1.450
 361  C14  C13   single    1.523  0.020  1.523
 361  C13  N12   single    1.447  0.020  1.447
 361  N12  C29   aromatic  1.363  0.020  1.363
 361  N12  C11   aromatic  1.365  0.020  1.365
 361  C29  C19   aromatic  1.402  0.020  1.402
 361  C29  C23   aromatic  1.388  0.020  1.388
 361  C19  N18   aromatic  1.373  0.020  1.373
 361  C19  C20   aromatic  1.391  0.020  1.391
 361  N18  C11   aromatic  1.304  0.020  1.304
 361  C11  C10   single    1.488  0.020  1.488
 361  C20  N21   aromatic  1.323  0.020  1.323
 361  N21  C22   aromatic  1.340  0.020  1.340
 361  C22  C23   aromatic  1.384  0.020  1.384
 361  C4   H4    single    0.930  0.020  1.080
 361  C1   H1    single    0.930  0.020  1.080
 361  C9   H9    single    0.970  0.020  1.090
 361  C14  H14   single    0.970  0.020  1.090
 361  N23  HN23  single    0.890  0.020  1.040
 361  N23  HN2A  single    0.890  0.020  1.040
 361  C13  H13   single    0.970  0.020  1.090
 361  C13  H13A  single    0.970  0.020  1.090
 361  C10  H10   single    0.970  0.020  1.090
 361  C10  H10A  single    0.970  0.020  1.090
 361  C20  H20   single    0.930  0.020  1.080
 361  C22  H22   single    0.930  0.020  1.080
 361  C23  H23   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
 361  C4    C5   C6    120.30  3.000
 361  C4    C5   F21   120.45  3.000
 361  C6    C5   F21   119.24  3.000
 361  C1    C6   F27   120.20  3.000
 361  C1    C6   C5    120.34  3.000
 361  F27   C6   C5    119.45  3.000
 361  H4    C4   C3    120.35  3.000
 361  H4    C4   C5    118.62  3.000
 361  C3    C4   C5    121.02  3.000
 361  C9    C3   C2    122.33  3.000
 361  C9    C3   C4    120.77  3.000
 361  C2    C3   C4    116.91  3.000
 361  C1    C2   F22   117.34  3.000
 361  C1    C2   C3    123.14  3.000
 361  F22   C2   C3    119.52  3.000
 361  H1    C1   C2    120.98  3.000
 361  H1    C1   C6    120.74  3.000
 361  C2    C1   C6    118.28  3.000
 361  H9    C9   C10   108.54  3.000
 361  H9    C9   C14   107.26  3.000
 361  C10   C9   C14   109.68  3.000
 361  H9    C9   C3    108.88  3.000
 361  C10   C9   C3    110.40  3.000
 361  C14   C9   C3    111.98  3.000
 361  H14   C14  C13   107.98  3.000
 361  H14   C14  N23   113.33  3.000
 361  C13   C14  N23   107.67  3.000
 361  H14   C14  C9    108.17  3.000
 361  C13   C14  C9    108.89  3.000
 361  N23   C14  C9    110.69  3.000
 361  HN2A  N23  HN23  105.17  3.000
 361  HN2A  N23  C14   109.75  3.000
 361  HN23  N23  C14   109.41  3.000
 361  H13A  C13  H13   107.99  3.000
 361  H13A  C13  N12   109.70  3.000
 361  H13   C13  N12   108.80  3.000
 361  H13A  C13  C14   109.25  3.000
 361  H13   C13  C14   110.38  3.000
 361  N12   C13  C14   110.68  3.000
 361  C11   N12  C29   106.79  3.000
 361  C11   N12  C13   125.86  3.000
 361  C29   N12  C13   127.19  3.000
 361  C23   C29  C19   121.14  3.000
 361  C23   C29  N12   133.87  3.000
 361  C19   C29  N12   104.99  3.000
 361  C20   C19  N18   131.53  3.000
 361  C20   C19  C29   118.25  3.000
 361  N18   C19  C29   110.22  3.000
 361  C11   N18  C19   104.75  3.000
 361  C10   C11  N18   126.14  3.000
 361  C10   C11  N12   120.58  3.000
 361  N18   C11  N12   113.25  3.000
 361  H10A  C10  H10   106.35  3.000
 361  H10A  C10  C11   108.22  3.000
 361  H10   C10  C11   109.16  3.000
 361  H10A  C10  C9    110.24  3.000
 361  H10   C10  C9    110.81  3.000
 361  C11   C10  C9    111.87  3.000
 361  H20   C20  N21   117.68  3.000
 361  H20   C20  C19   121.05  3.000
 361  N21   C20  C19   121.27  3.000
 361  C22   N21  C20   119.35  3.000
 361  H22   C22  C23   119.28  3.000
 361  H22   C22  N21   115.90  3.000
 361  C23   C22  N21   124.82  3.000
 361  H23   C23  C22   121.19  3.000
 361  H23   C23  C29   123.64  3.000
 361  C22   C23  C29   115.17  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
 361  CONST_01  C2   C1   C6   C5     0.00   0.0  0
 361  CONST_02  C2   C3   C4   C5     0.00   0.0  0
 361  CONST_03  C3   C4   C5   C6     0.00   0.0  0
 361  CONST_04  C3   C2   C1   C6     0.00   0.0  0
 361  CONST_05  C1   C6   C5   C4     0.00   0.0  0
 361  CONST_06  C1   C2   C3   C4     0.00   0.0  0
 361  CONST_07  N18  C19  C29  N12    0.00   0.0  0
 361  CONST_08  C20  C19  C29  N12  180.00   0.0  0
 361  CONST_09  C22  C23  C29  N12  180.00   0.0  0
 361  CONST_10  C19  N18  C11  N12    0.00   0.0  0
 361  CONST_11  N18  C11  N12  C29    0.00   0.0  0
 361  CONST_12  C11  N18  C19  C29    0.00   0.0  0
 361  CONST_13  N21  C20  C19  C29    0.00   0.0  0
 361  CONST_14  N21  C22  C23  C29    0.00   0.0  0
 361  CONST_15  C11  N12  C29  C19    0.00   0.0  0
 361  CONST_16  C22  C23  C29  C19    0.00   0.0  0
 361  CONST_17  C22  N21  C20  C19    0.00   0.0  0
 361  CONST_18  C23  C29  C19  N18  180.00   0.0  0
 361  CONST_19  N21  C20  C19  N18  180.00   0.0  0
 361  CONST_20  C23  C29  N12  C11  180.00   0.0  0
 361  CONST_21  C20  C19  N18  C11  180.00   0.0  0
 361  CONST_22  C23  C29  C19  C20    0.00   0.0  0
 361  CONST_23  C23  C22  N21  C20    0.00   0.0  0
 361  CONST_24  C9   C3   C4   C5   180.00   0.0  0
 361  CONST_25  C9   C3   C2   C1   180.00   0.0  0
 361  CONST_26  C1   C6   C5   F21  180.00   0.0  0
 361  CONST_27  C3   C4   C5   F21  180.00   0.0  0
 361  CONST_28  F22  C2   C1   C6   180.00   0.0  0
 361  CONST_29  C4   C5   C6   F27  180.00   0.0  0
 361  CONST_30  C2   C1   C6   F27  180.00   0.0  0
 361  CONST_31  F22  C2   C3   C4   180.00   0.0  0
 361  CONST_32  C9   C3   C2   F22    0.00   0.0  0
 361  CONST_33  H1   C1   C6   C5   180.00   0.0  0
 361  CONST_34  H4   C4   C5   C6   180.00   0.0  0
 361  CONST_35  H23  C23  C29  N12    0.00   0.0  0
 361  CONST_36  H20  C20  C19  C29  180.00   0.0  0
 361  CONST_37  H22  C22  C23  C29  180.00   0.0  0
 361  Var_01    N12  C11  C10  C9   -18.80  30.0  1
 361  Var_02    C29  N12  C13  C14  163.41  30.0  1

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
 361  chir_01  C9   C3   C14  C10  positiv
 361  chir_02  C14  N23  C9   C13  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
 361  plan-1  F21  0.020
 361  plan-1  C5   0.020
 361  plan-1  C6   0.020
 361  plan-1  F27  0.020
 361  plan-1  C4   0.020
 361  plan-1  C3   0.020
 361  plan-1  C2   0.020
 361  plan-1  F22  0.020
 361  plan-1  C1   0.020
 361  plan-1  C9   0.020
 361  plan-1  H4   0.020
 361  plan-1  H1   0.020
 361  plan-2  C13  0.020
 361  plan-2  N12  0.020
 361  plan-2  C29  0.020
 361  plan-2  C19  0.020
 361  plan-2  N18  0.020
 361  plan-2  C11  0.020
 361  plan-2  C10  0.020
 361  plan-2  C20  0.020
 361  plan-2  N21  0.020
 361  plan-2  C22  0.020
 361  plan-2  C23  0.020
 361  plan-2  H20  0.020
 361  plan-2  H22  0.020
 361  plan-2  H23  0.020

