# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 04:03:59 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: N'-[3-[2-(6-azanyl-4-methyl-pyridin-2-yl)ethyl]-5-(trifluoromethyl)phenyl]-N,N'-dimethyl-ethane-1,2-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCCN(C)c1cc(CCc2cc(C)cc(N)n2)cc(c1)C(F)(F)F
#
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
 S84  S84  N'-[3-[2-(6-azanyl-4-methyl-pyridin-2-yl)ethyl]-5-(trifluoromethyl)phenyl]-N,N'-dimethyl-ethane-1,2-diamine  ligand  51  26  .  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_S84
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
 S84  F20   F  F     0  -0.304  -3.6481  -2.8547   0.0226
 S84  C17   C  CT    0   1.047  -2.3180  -2.8540   0.1585
 S84  F18   F  F     0  -0.315  -2.0446  -3.5081   1.2971
 S84  F19   F  F     0  -0.318  -1.8284  -3.6108  -0.8373
 S84  C13   C  CR6   0  -0.152  -1.7217  -1.4807   0.1481
 S84  C14   C  CR16  0  -0.423  -2.5040  -0.3837  -0.1655
 S84  C15   C  CR6   0   0.453  -1.9375   0.9060  -0.1978
 S84  N22   N  NT    0  -0.514  -2.6738   2.0070  -0.5325
 S84  C21   C  CH3   0  -0.547  -2.1034   3.3266  -0.3912
 S84  C23   C  CH2   0  -0.353  -4.0538   1.9043  -0.9479
 S84  C24   C  CH2   0  -0.265  -5.0461   1.9261   0.2096
 S84  N25   N  NH1   0  -0.594  -6.4001   1.8189  -0.2900
 S84  C26   C  CH3   0  -0.516  -7.3886   1.8019   0.7686
 S84  C12   C  CR16  0  -0.394  -0.3694  -1.3541   0.4446
 S84  C11   C  CR6   0   0.174   0.2038  -0.0888   0.4328
 S84  C16   C  CR16  0  -0.422  -0.5735   1.0188   0.1216
 S84  C09   C  CH2   0  -0.515   1.6743   0.0845   0.6881
 S84  C08   C  CH2   0  -0.489   2.4846  -0.0567  -0.6079
 S84  C06   C  CR6   0   0.282   3.9535   0.1688  -0.3877
 S84  N01   N  N     0  -0.487   4.3023   1.3889   0.0278
 S84  C02   C  CR6   0   0.440   5.5858   1.6439   0.2526
 S84  N02   N  NH2   0  -0.839   5.9109   2.9155   0.6302
 S84  C03   C  CR16  0  -0.448   6.5874   0.6744   0.0678
 S84  C04   C  CR6   0   0.206   6.2295  -0.5872  -0.3590
 S84  C07   C  CH3   0  -0.726   7.2545  -1.6620  -0.5551
 S84  C05   C  CR16  0  -0.437   4.8727  -0.8435  -0.5932
 S84  H14   H  HCR6  0   0.272  -3.5556  -0.5191  -0.3694
 S84  H12   H  HCR6  0   0.253   0.2367  -2.2188   0.6867
 S84  H16   H  HCR6  0   0.265  -0.0921   1.9881   0.1209
 S84  H211  H  HCH3  0   0.237  -1.2740   3.4975  -1.0837
 S84  H212  H  HCH3  0   0.261  -2.8686   4.0681  -0.6066
 S84  H213  H  HCH3  0   0.238  -1.7396   3.5122   0.6226
 S84  H231  H  HCH2  0   0.259  -4.2635   2.7404  -1.6196
 S84  H232  H  HCH2  0   0.248  -4.2009   1.0038  -1.5479
 S84  H241  H  HCH2  0   0.222  -4.8571   1.0783   0.8763
 S84  H242  H  HCH2  0   0.199  -4.8796   2.8325   0.8150
 S84  H25   H  HNH1  0   0.344  -6.5876   2.6061  -0.8989
 S84  H261  H  HCH3  0   0.222  -7.2762   0.8957   1.3670
 S84  H262  H  HCH3  0   0.194  -7.3262   2.6582   1.4540
 S84  H263  H  HCH3  0   0.231  -8.3903   1.7888   0.3390
 S84  H091  H  HCH2  0   0.250   1.8668   1.0684   1.1190
 S84  H092  H  HCH2  0   0.250   2.0203  -0.6571   1.4121
 S84  H081  H  HCH2  0   0.248   2.3198  -1.0475  -1.0351
 S84  H082  H  HCH2  0   0.249   2.1140   0.6687  -1.3382
 S84  H05   H  HCR6  0   0.244   4.5443  -1.8191  -0.9293
 S84  H021  H  HNH2  0   0.379   5.1568   3.4746   0.9947
 S84  H022  H  HNH2  0   0.388   6.7869   3.0480   1.1071
 S84  H03   H  HCR6  0   0.255   7.6247   0.9230   0.2576
 S84  H071  H  HCH3  0   0.253   7.1231  -2.4552   0.1826
 S84  H072  H  HCH3  0   0.250   7.1597  -2.1217  -1.5394
 S84  H073  H  HCH3  0   0.246   8.2676  -1.2754  -0.4556

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
 S84  F20  C17   single    1.337  0.020  1.337
 S84  C17  F18   single    1.341  0.020  1.341
 S84  C17  F19   single    1.343  0.020  1.343
 S84  C17  C13   single    1.497  0.020  1.497
 S84  C13  C14   aromatic  1.383  0.020  1.383
 S84  C13  C12   aromatic  1.390  0.020  1.390
 S84  C14  C15   aromatic  1.409  0.020  1.409
 S84  C15  N22   single    1.366  0.020  1.366
 S84  C15  C16   aromatic  1.405  0.020  1.405
 S84  N22  C21   single    1.445  0.020  1.445
 S84  N22  C23   single    1.445  0.020  1.445
 S84  C23  C24   single    1.525  0.020  1.525
 S84  C24  N25   single    1.447  0.020  1.447
 S84  N25  C26   single    1.449  0.020  1.449
 S84  C12  C11   aromatic  1.389  0.020  1.389
 S84  C11  C16   aromatic  1.388  0.020  1.388
 S84  C11  C09   single    1.503  0.020  1.503
 S84  C09  C08   single    1.535  0.020  1.535
 S84  C08  C06   single    1.502  0.020  1.502
 S84  C06  N01   aromatic  1.335  0.020  1.335
 S84  C06  C05   aromatic  1.383  0.020  1.383
 S84  N01  C02   aromatic  1.328  0.020  1.328
 S84  C02  N02   single    1.366  0.020  1.366
 S84  C02  C03   aromatic  1.406  0.020  1.406
 S84  C03  C04   aromatic  1.379  0.020  1.379
 S84  C04  C07   single    1.498  0.020  1.498
 S84  C04  C05   aromatic  1.400  0.020  1.400
 S84  C14  H14   single    0.930  0.020  1.080
 S84  C12  H12   single    0.930  0.020  1.080
 S84  C16  H16   single    0.930  0.020  1.080
 S84  C21  H211  single    0.970  0.020  1.090
 S84  C21  H212  single    0.970  0.020  1.090
 S84  C21  H213  single    0.970  0.020  1.090
 S84  C23  H231  single    0.970  0.020  1.090
 S84  C23  H232  single    0.970  0.020  1.090
 S84  C24  H241  single    0.970  0.020  1.090
 S84  C24  H242  single    0.970  0.020  1.090
 S84  N25  H25   single    0.890  0.020  1.040
 S84  C26  H261  single    0.970  0.020  1.090
 S84  C26  H262  single    0.970  0.020  1.090
 S84  C26  H263  single    0.970  0.020  1.090
 S84  C09  H091  single    0.970  0.020  1.090
 S84  C09  H092  single    0.970  0.020  1.090
 S84  C08  H081  single    0.970  0.020  1.090
 S84  C08  H082  single    0.970  0.020  1.090
 S84  C05  H05   single    0.930  0.020  1.080
 S84  N02  H021  single    0.890  0.020  1.040
 S84  N02  H022  single    0.890  0.020  1.040
 S84  C03  H03   single    0.930  0.020  1.080
 S84  C07  H071  single    0.970  0.020  1.090
 S84  C07  H072  single    0.970  0.020  1.090
 S84  C07  H073  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
 S84  C13   C17  F19   111.50  3.000
 S84  C13   C17  F18   111.85  3.000
 S84  F19   C17  F18   106.27  3.000
 S84  C13   C17  F20   113.33  3.000
 S84  F19   C17  F20   106.68  3.000
 S84  F18   C17  F20   106.79  3.000
 S84  C12   C13  C14   121.75  3.000
 S84  C12   C13  C17   117.99  3.000
 S84  C14   C13  C17   120.25  3.000
 S84  H14   C14  C15   120.13  3.000
 S84  H14   C14  C13   119.61  3.000
 S84  C15   C14  C13   120.25  3.000
 S84  C16   C15  N22   120.94  3.000
 S84  C16   C15  C14   117.28  3.000
 S84  N22   C15  C14   121.78  3.000
 S84  C23   N22  C21   118.05  3.000
 S84  C23   N22  C15   121.87  3.000
 S84  C21   N22  C15   119.96  3.000
 S84  H213  C21  H212  107.59  3.000
 S84  H213  C21  H211  107.96  3.000
 S84  H212  C21  H211  107.56  3.000
 S84  H213  C21  N22   112.16  3.000
 S84  H212  C21  N22   109.01  3.000
 S84  H211  C21  N22   112.35  3.000
 S84  H232  C23  H231  105.51  3.000
 S84  H232  C23  C24   109.95  3.000
 S84  H231  C23  C24   109.32  3.000
 S84  H232  C23  N22   110.19  3.000
 S84  H231  C23  N22   107.80  3.000
 S84  C24   C23  N22   113.72  3.000
 S84  H242  C24  H241  106.03  3.000
 S84  H242  C24  N25   113.06  3.000
 S84  H241  C24  N25   108.32  3.000
 S84  H242  C24  C23   109.28  3.000
 S84  H241  C24  C23   109.81  3.000
 S84  N25   C24  C23   110.22  3.000
 S84  H25   N25  C26   108.79  3.000
 S84  H25   N25  C24   108.86  3.000
 S84  C26   N25  C24   112.77  3.000
 S84  H263  C26  H262  107.90  3.000
 S84  H263  C26  H261  107.50  3.000
 S84  H262  C26  H261  107.41  3.000
 S84  H263  C26  N25   109.84  3.000
 S84  H262  C26  N25   114.08  3.000
 S84  H261  C26  N25   109.88  3.000
 S84  H12   C12  C11   119.87  3.000
 S84  H12   C12  C13   121.28  3.000
 S84  C11   C12  C13   118.85  3.000
 S84  C09   C11  C16   119.60  3.000
 S84  C09   C11  C12   120.49  3.000
 S84  C16   C11  C12   119.83  3.000
 S84  H16   C16  C11   117.75  3.000
 S84  H16   C16  C15   120.23  3.000
 S84  C11   C16  C15   122.03  3.000
 S84  H092  C09  H091  107.12  3.000
 S84  H092  C09  C08   109.26  3.000
 S84  H091  C09  C08   108.86  3.000
 S84  H092  C09  C11   110.13  3.000
 S84  H091  C09  C11   110.10  3.000
 S84  C08   C09  C11   111.26  3.000
 S84  H082  C08  H081  106.83  3.000
 S84  H082  C08  C06   109.24  3.000
 S84  H081  C08  C06   109.95  3.000
 S84  H082  C08  C09   108.90  3.000
 S84  H081  C08  C09   109.52  3.000
 S84  C06   C08  C09   112.25  3.000
 S84  C05   C06  N01   122.79  3.000
 S84  C05   C06  C08   121.22  3.000
 S84  N01   C06  C08   115.98  3.000
 S84  C02   N01  C06   118.73  3.000
 S84  C03   C02  N02   120.58  3.000
 S84  C03   C02  N01   122.27  3.000
 S84  N02   C02  N01   117.11  3.000
 S84  H022  N02  H021  114.03  3.000
 S84  H022  N02  C02   117.45  3.000
 S84  H021  N02  C02   116.03  3.000
 S84  H03   C03  C04   120.84  3.000
 S84  H03   C03  C02   120.05  3.000
 S84  C04   C03  C02   119.11  3.000
 S84  C05   C04  C07   120.64  3.000
 S84  C05   C04  C03   118.08  3.000
 S84  C07   C04  C03   121.28  3.000
 S84  H073  C07  H072  108.24  3.000
 S84  H073  C07  H071  107.96  3.000
 S84  H072  C07  H071  107.05  3.000
 S84  H073  C07  C04   111.71  3.000
 S84  H072  C07  C04   111.18  3.000
 S84  H071  C07  C04   110.53  3.000
 S84  H05   C05  C04   120.70  3.000
 S84  H05   C05  C06   120.27  3.000
 S84  C04   C05  C06   119.02  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
 S84  CONST_01  C16   C15  C14  C13     0.00   0.0  0
 S84  CONST_02  C16   C11  C12  C13     0.00   0.0  0
 S84  CONST_03  C11   C12  C13  C14     0.00   0.0  0
 S84  CONST_04  C11   C16  C15  C14     0.00   0.0  0
 S84  CONST_05  C12   C13  C14  C15     0.00   0.0  0
 S84  CONST_06  C12   C11  C16  C15     0.00   0.0  0
 S84  CONST_07  C03   C02  N01  C06     0.00   0.0  0
 S84  CONST_08  C03   C04  C05  C06     0.00   0.0  0
 S84  CONST_09  C04   C05  C06  N01     0.00   0.0  0
 S84  CONST_10  C04   C03  C02  N01     0.00   0.0  0
 S84  CONST_11  C05   C06  N01  C02     0.00   0.0  0
 S84  CONST_12  C05   C04  C03  C02     0.00   0.0  0
 S84  CONST_13  C15   C14  C13  C17   180.00   0.0  0
 S84  CONST_14  C11   C12  C13  C17   180.00   0.0  0
 S84  CONST_15  N22   C15  C14  C13   180.00   0.0  0
 S84  CONST_16  C09   C11  C12  C13   180.00   0.0  0
 S84  CONST_17  C09   C11  C16  C15   180.00   0.0  0
 S84  CONST_18  C11   C16  C15  N22   180.00   0.0  0
 S84  CONST_19  C02   N01  C06  C08   180.00   0.0  0
 S84  CONST_20  C04   C05  C06  C08   180.00   0.0  0
 S84  CONST_21  N02   C02  N01  C06   180.00   0.0  0
 S84  CONST_22  C07   C04  C05  C06   180.00   0.0  0
 S84  CONST_23  C07   C04  C03  C02   180.00   0.0  0
 S84  CONST_24  C04   C03  C02  N02   180.00   0.0  0
 S84  CONST_25  H12   C12  C13  C14   180.00   0.0  0
 S84  CONST_26  H16   C16  C15  C14   180.00   0.0  0
 S84  CONST_27  H14   C14  C13  C12   180.00   0.0  0
 S84  CONST_28  H05   C05  C06  N01   180.00   0.0  0
 S84  CONST_29  H03   C03  C02  N01   180.00   0.0  0
 S84  CONST_30  C21   N22  C15  C14   180.00   0.0  0
 S84  CONST_31  C23   N22  C15  C14     0.00   0.0  0
 S84  CONST_32  C16   C15  N22  C21     0.00   0.0  0
 S84  CONST_33  C16   C15  N22  C23   180.00   0.0  0
 S84  Var_01    C14   C13  C17  F20    -8.45  30.0  2
 S84  Var_02    C08   C09  C11  C12    86.95  30.0  2
 S84  Var_03    C06   C08  C09  C11   177.65  30.0  3
 S84  Var_04    N01   C06  C08  C09   -63.23  30.0  2
 S84  Var_05    H071  C07  C04  C03   112.40  30.0  2
 S84  Var_06    C24   C23  N22  C15    87.34  30.0  3
 S84  Var_07    H211  C21  N22  C15    66.65  30.0  3
 S84  Var_08    N25   C24  C23  N22  -179.98  30.0  3
 S84  Var_09    C26   N25  C24  C23   178.61  30.0  3
 S84  Var_10    H261  C26  N25  C24   -65.78  30.0  3

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
 S84  plan-1  C17   0.020
 S84  plan-1  C13   0.020
 S84  plan-1  C14   0.020
 S84  plan-1  C15   0.020
 S84  plan-1  N22   0.020
 S84  plan-1  C12   0.020
 S84  plan-1  C11   0.020
 S84  plan-1  C16   0.020
 S84  plan-1  C09   0.020
 S84  plan-1  H14   0.020
 S84  plan-1  H12   0.020
 S84  plan-1  H16   0.020
 S84  plan-2  C08   0.020
 S84  plan-2  C06   0.020
 S84  plan-2  N01   0.020
 S84  plan-2  C02   0.020
 S84  plan-2  N02   0.020
 S84  plan-2  C03   0.020
 S84  plan-2  C04   0.020
 S84  plan-2  C07   0.020
 S84  plan-2  C05   0.020
 S84  plan-2  H05   0.020
 S84  plan-2  H03   0.020
 S84  plan-3  C15   0.020
 S84  plan-3  N22   0.020
 S84  plan-3  C21   0.020
 S84  plan-3  C23   0.020
 S84  plan-4  C02   0.020
 S84  plan-4  N02   0.020
 S84  plan-4  H021  0.020
 S84  plan-4  H022  0.020

