# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 07:48:26 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: N'-[3-[2-(6-azanyl-4-methyl-pyridin-2-yl)ethyl]-5-fluoranyl-phenyl]-N'-cyclopropyl-N-methyl-ethane-1,2-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCCN(C1CC1)c2cc(F)cc(CCc3cc(C)cc(N)n3)c2
#
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
 S90  S90  N'-[3-[2-(6-azanyl-4-methyl-pyridin-2-yl)ethyl]-5-fluoranyl-phenyl]-N'-cyclopropyl-N-methyl-ethane-1,2-diamine  ligand  52  25  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_S90
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
 S90  F13   F  F     0  -0.325   1.8928  -3.7028  -0.1992
 S90  C13   C  CR6   0   0.569   1.5336  -2.4052  -0.1624
 S90  C14   C  CR16  0  -0.549   2.5168  -1.4798   0.1163
 S90  C15   C  CR6   0   0.428   2.1814  -0.1154   0.1582
 S90  N17   N  NT    0  -0.516   3.1288   0.8430   0.4231
 S90  C21   C  CH1   0  -0.118   2.7315   2.2087   0.5399
 S90  C23   C  CH2   0  -0.483   2.3683   2.9845  -0.6901
 S90  C22   C  CH2   0  -0.510   3.6457   3.2762   0.0305
 S90  C17   C  CH2   0  -0.343   4.4418   0.4707   0.9143
 S90  C18   C  CH2   0  -0.270   5.4297   0.1352  -0.2004
 S90  N18   N  NH1   0  -0.594   6.7129  -0.2277   0.3597
 S90  C19   C  CH3   0  -0.516   7.6699  -0.6349  -0.6488
 S90  C12   C  CR16  0  -0.517   0.2182  -2.0774  -0.4095
 S90  C11   C  CR6   0   0.167  -0.1243  -0.7270  -0.3635
 S90  C16   C  CR16  0  -0.427   0.8370   0.2316  -0.0789
 S90  C09   C  CH2   0  -0.513  -1.5545  -0.3167  -0.5777
 S90  C08   C  CH2   0  -0.489  -2.3982  -0.5013   0.6913
 S90  C06   C  CR6   0   0.276  -3.8244  -0.0846   0.4715
 S90  N01   N  N     0  -0.485  -4.0335   1.2228   0.2987
 S90  C02   C  CR6   0   0.440  -5.2711   1.6456   0.0673
 S90  N02   N  NH2   0  -0.839  -5.4543   2.9935  -0.0544
 S90  C03   C  CR16  0  -0.448  -6.3652   0.7647  -0.0056
 S90  C04   C  CR6   0   0.205  -6.1508  -0.5862   0.1719
 S90  C07   C  CH3   0  -0.727  -7.2753  -1.5734   0.0997
 S90  C05   C  CR16  0  -0.432  -4.8420  -1.0191   0.4187
 S90  H14   H  HCR6  0   0.275   3.5241  -1.8350   0.2804
 S90  H12   H  HCR6  0   0.257  -0.5168  -2.8414  -0.6303
 S90  H16   H  HCR6  0   0.264   0.5288   1.2673  -0.0432
 S90  H21   H  HCH1  0   0.259   2.1715   2.4568   1.4410
 S90  H171  H  HCH2  0   0.264   4.8288   1.3063   1.4998
 S90  H172  H  HCH2  0   0.243   4.3690  -0.3754   1.6046
 S90  H231  H  HCH2  0   0.257   2.4370   2.4646  -1.6373
 S90  H232  H  HCH2  0   0.256   1.5522   3.6921  -0.6211
 S90  H221  H  HCH2  0   0.260   3.7199   4.1840   0.6147
 S90  H222  H  HCH2  0   0.257   4.5700   2.9789  -0.4484
 S90  H181  H  HCH2  0   0.225   5.0552  -0.7131  -0.7799
 S90  H182  H  HCH2  0   0.200   5.4874   0.9799  -0.9056
 S90  H18   H  HNH1  0   0.344   7.0879   0.5675   0.8623
 S90  H191  H  HCH3  0   0.222   7.3492  -1.5713  -1.1098
 S90  H192  H  HCH3  0   0.194   7.8103   0.0970  -1.4568
 S90  H193  H  HCH3  0   0.232   8.6408  -0.8120  -0.1863
 S90  H091  H  HCH2  0   0.249  -1.6030   0.7291  -0.8865
 S90  H092  H  HCH2  0   0.249  -1.9916  -0.9093  -1.3857
 S90  H081  H  HCH2  0   0.247  -2.3605  -1.5457   1.0074
 S90  H082  H  HCH2  0   0.248  -1.9635   0.0952   1.4980
 S90  H05   H  HCR6  0   0.243  -4.6264  -2.0706   0.5623
 S90  H021  H  HNH2  0   0.379  -4.6334   3.5322  -0.2778
 S90  H022  H  HNH2  0   0.387  -6.2890   3.3080  -0.5201
 S90  H03   H  HCR6  0   0.255  -7.3590   1.1489  -0.2023
 S90  H071  H  HCH3  0   0.252  -7.1216  -2.2745  -0.7219
 S90  H072  H  HCH3  0   0.251  -7.3328  -2.1633   1.0154
 S90  H073  H  HCH3  0   0.247  -8.2364  -1.0843  -0.0500

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
 S90  F13  C13   single    1.347  0.020  1.347
 S90  C13  C14   aromatic  1.379  0.020  1.379
 S90  C13  C12   aromatic  1.378  0.020  1.378
 S90  C14  C15   aromatic  1.406  0.020  1.406
 S90  C15  N17   single    1.373  0.020  1.373
 S90  C15  C16   aromatic  1.409  0.020  1.409
 S90  N17  C21   single    1.427  0.020  1.427
 S90  N17  C17   single    1.450  0.020  1.450
 S90  C21  C23   single    1.499  0.020  1.499
 S90  C21  C22   single    1.495  0.020  1.495
 S90  C23  C22   single    1.495  0.020  1.495
 S90  C17  C18   single    1.527  0.020  1.527
 S90  C18  N18   single    1.446  0.020  1.446
 S90  N18  C19   single    1.449  0.020  1.449
 S90  C12  C11   aromatic  1.394  0.020  1.394
 S90  C11  C16   aromatic  1.387  0.020  1.387
 S90  C11  C09   single    1.503  0.020  1.503
 S90  C09  C08   single    1.535  0.020  1.535
 S90  C08  C06   single    1.502  0.020  1.502
 S90  C06  N01   aromatic  1.335  0.020  1.335
 S90  C06  C05   aromatic  1.383  0.020  1.383
 S90  N01  C02   aromatic  1.328  0.020  1.328
 S90  C02  N02   single    1.366  0.020  1.366
 S90  C02  C03   aromatic  1.407  0.020  1.407
 S90  C03  C04   aromatic  1.379  0.020  1.379
 S90  C04  C07   single    1.498  0.020  1.498
 S90  C04  C05   aromatic  1.400  0.020  1.400
 S90  C14  H14   single    0.930  0.020  1.080
 S90  C12  H12   single    0.930  0.020  1.080
 S90  C16  H16   single    0.930  0.020  1.080
 S90  C21  H21   single    0.970  0.020  1.090
 S90  C17  H171  single    0.970  0.020  1.090
 S90  C17  H172  single    0.970  0.020  1.090
 S90  C23  H231  single    0.970  0.020  1.090
 S90  C23  H232  single    0.970  0.020  1.090
 S90  C22  H221  single    0.970  0.020  1.090
 S90  C22  H222  single    0.970  0.020  1.090
 S90  C18  H181  single    0.970  0.020  1.090
 S90  C18  H182  single    0.970  0.020  1.090
 S90  N18  H18   single    0.890  0.020  1.040
 S90  C19  H191  single    0.970  0.020  1.090
 S90  C19  H192  single    0.970  0.020  1.090
 S90  C19  H193  single    0.970  0.020  1.090
 S90  C09  H091  single    0.970  0.020  1.090
 S90  C09  H092  single    0.970  0.020  1.090
 S90  C08  H081  single    0.970  0.020  1.090
 S90  C08  H082  single    0.970  0.020  1.090
 S90  C05  H05   single    0.930  0.020  1.080
 S90  N02  H021  single    0.890  0.020  1.040
 S90  N02  H022  single    0.890  0.020  1.040
 S90  C03  H03   single    0.930  0.020  1.080
 S90  C07  H071  single    0.970  0.020  1.090
 S90  C07  H072  single    0.970  0.020  1.090
 S90  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
 S90  C12   C13  C14   123.87  3.000
 S90  C12   C13  F13   118.61  3.000
 S90  C14   C13  F13   117.52  3.000
 S90  H14   C14  C15   122.48  3.000
 S90  H14   C14  C13   118.35  3.000
 S90  C15   C14  C13   119.17  3.000
 S90  C16   C15  N17   121.26  3.000
 S90  C16   C15  C14   117.51  3.000
 S90  N17   C15  C14   121.23  3.000
 S90  C17   N17  C21   118.03  3.000
 S90  C17   N17  C15   120.71  3.000
 S90  C21   N17  C15   119.44  3.000
 S90  H21   C21  C22   115.70  3.000
 S90  H21   C21  C23   115.87  3.000
 S90  C22   C21  C23    59.93  3.000
 S90  H21   C21  N17   115.38  3.000
 S90  C22   C21  N17   119.02  3.000
 S90  C23   C21  N17   119.71  3.000
 S90  H232  C23  H231  114.68  3.000
 S90  H232  C23  C22   119.07  3.000
 S90  H231  C23  C22   117.45  3.000
 S90  H232  C23  C21   117.96  3.000
 S90  H231  C23  C21   117.00  3.000
 S90  C22   C23  C21    59.90  3.000
 S90  H222  C22  H221  114.25  3.000
 S90  H222  C22  C23   117.56  3.000
 S90  H221  C22  C23   118.84  3.000
 S90  H222  C22  C21   118.48  3.000
 S90  H221  C22  C21   117.19  3.000
 S90  C23   C22  C21    60.17  3.000
 S90  H172  C17  H171  106.09  3.000
 S90  H172  C17  C18   109.49  3.000
 S90  H171  C17  C18   109.30  3.000
 S90  H172  C17  N17   110.60  3.000
 S90  H171  C17  N17   107.83  3.000
 S90  C18   C17  N17   113.26  3.000
 S90  H182  C18  H181  105.87  3.000
 S90  H182  C18  N18   113.19  3.000
 S90  H181  C18  N18   108.33  3.000
 S90  H182  C18  C17   109.43  3.000
 S90  H181  C18  C17   109.62  3.000
 S90  N18   C18  C17   110.27  3.000
 S90  H18   N18  C19   108.75  3.000
 S90  H18   N18  C18   108.89  3.000
 S90  C19   N18  C18   112.77  3.000
 S90  H193  C19  H192  107.84  3.000
 S90  H193  C19  H191  107.55  3.000
 S90  H192  C19  H191  107.35  3.000
 S90  H193  C19  N18   109.80  3.000
 S90  H192  C19  N18   114.14  3.000
 S90  H191  C19  N18   109.93  3.000
 S90  H12   C12  C11   121.56  3.000
 S90  H12   C12  C13   121.11  3.000
 S90  C11   C12  C13   117.33  3.000
 S90  C09   C11  C16   120.00  3.000
 S90  C09   C11  C12   119.57  3.000
 S90  C16   C11  C12   120.39  3.000
 S90  H16   C16  C11   118.11  3.000
 S90  H16   C16  C15   120.17  3.000
 S90  C11   C16  C15   121.72  3.000
 S90  H092  C09  H091  107.01  3.000
 S90  H092  C09  C08   109.03  3.000
 S90  H091  C09  C08   108.95  3.000
 S90  H092  C09  C11   109.74  3.000
 S90  H091  C09  C11   110.13  3.000
 S90  C08   C09  C11   111.86  3.000
 S90  H082  C08  H081  107.13  3.000
 S90  H082  C08  C06   109.52  3.000
 S90  H081  C08  C06   109.91  3.000
 S90  H082  C08  C09   109.01  3.000
 S90  H081  C08  C09   109.60  3.000
 S90  C06   C08  C09   111.56  3.000
 S90  C05   C06  N01   122.80  3.000
 S90  C05   C06  C08   121.12  3.000
 S90  N01   C06  C08   116.06  3.000
 S90  C02   N01  C06   118.70  3.000
 S90  C03   C02  N02   120.61  3.000
 S90  C03   C02  N01   122.31  3.000
 S90  N02   C02  N01   117.05  3.000
 S90  H022  N02  H021  113.97  3.000
 S90  H022  N02  C02   117.45  3.000
 S90  H021  N02  C02   116.00  3.000
 S90  H03   C03  C04   120.88  3.000
 S90  H03   C03  C02   120.06  3.000
 S90  C04   C03  C02   119.07  3.000
 S90  C05   C04  C07   120.42  3.000
 S90  C05   C04  C03   118.08  3.000
 S90  C07   C04  C03   121.50  3.000
 S90  H073  C07  H072  108.17  3.000
 S90  H073  C07  H071  108.03  3.000
 S90  H072  C07  H071  106.98  3.000
 S90  H073  C07  C04   111.92  3.000
 S90  H072  C07  C04   110.83  3.000
 S90  H071  C07  C04   110.74  3.000
 S90  H05   C05  C04   120.64  3.000
 S90  H05   C05  C06   120.31  3.000
 S90  C04   C05  C06   119.05  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
 S90  CONST_01  C16   C15  C14  C13     0.00   0.0  0
 S90  CONST_02  C16   C11  C12  C13     0.00   0.0  0
 S90  CONST_03  C11   C12  C13  C14     0.00   0.0  0
 S90  CONST_04  C11   C16  C15  C14     0.00   0.0  0
 S90  CONST_05  C12   C13  C14  C15     0.00   0.0  0
 S90  CONST_06  C12   C11  C16  C15     0.00   0.0  0
 S90  CONST_07  C03   C02  N01  C06     0.00   0.0  0
 S90  CONST_08  C03   C04  C05  C06     0.00   0.0  0
 S90  CONST_09  C04   C05  C06  N01     0.00   0.0  0
 S90  CONST_10  C04   C03  C02  N01     0.00   0.0  0
 S90  CONST_11  C05   C06  N01  C02     0.00   0.0  0
 S90  CONST_12  C05   C04  C03  C02     0.00   0.0  0
 S90  CONST_13  C15   C14  C13  F13   180.00   0.0  0
 S90  CONST_14  C11   C12  C13  F13   180.00   0.0  0
 S90  CONST_15  N17   C15  C14  C13   180.00   0.0  0
 S90  CONST_16  C09   C11  C12  C13   180.00   0.0  0
 S90  CONST_17  C09   C11  C16  C15   180.00   0.0  0
 S90  CONST_18  C11   C16  C15  N17   180.00   0.0  0
 S90  CONST_19  C02   N01  C06  C08   180.00   0.0  0
 S90  CONST_20  C04   C05  C06  C08   180.00   0.0  0
 S90  CONST_21  N02   C02  N01  C06   180.00   0.0  0
 S90  CONST_22  C07   C04  C05  C06   180.00   0.0  0
 S90  CONST_23  C07   C04  C03  C02   180.00   0.0  0
 S90  CONST_24  C04   C03  C02  N02   180.00   0.0  0
 S90  CONST_25  C21   N17  C15  C14   180.00   0.0  0
 S90  CONST_26  C16   C15  N17  C21     0.00   0.0  0
 S90  CONST_27  H12   C12  C13  C14   180.00   0.0  0
 S90  CONST_28  H16   C16  C15  C14   180.00   0.0  0
 S90  CONST_29  H14   C14  C13  C12   180.00   0.0  0
 S90  CONST_30  H05   C05  C06  N01   180.00   0.0  0
 S90  CONST_31  H03   C03  C02  N01   180.00   0.0  0
 S90  CONST_32  C17   N17  C15  C14     0.00   0.0  0
 S90  CONST_33  C16   C15  N17  C17   180.00   0.0  0
 S90  Var_01    C23   C21  N17  C15   -74.04  30.0  3
 S90  Var_02    C22   C23  C21  N17  -108.37  30.0  1
 S90  Var_03    H221  C22  C23  C21  -106.59  30.0  1
 S90  Var_04    C08   C09  C11  C12    80.16  30.0  2
 S90  Var_05    C06   C08  C09  C11   179.78  30.0  3
 S90  Var_06    N01   C06  C08  C09   -68.95  30.0  2
 S90  Var_07    H071  C07  C04  C03   117.60  30.0  2
 S90  Var_08    C18   C17  N17  C15    86.41  30.0  3
 S90  Var_09    N18   C18  C17  N17  -179.92  30.0  3
 S90  Var_10    C19   N18  C18  C17   176.52  30.0  3
 S90  Var_11    H191  C19  N18  C18   -66.85  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
 S90  chir_01  C21  N17  C23  C22  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
 S90  plan-1  F13   0.020
 S90  plan-1  C13   0.020
 S90  plan-1  C14   0.020
 S90  plan-1  C15   0.020
 S90  plan-1  N17   0.020
 S90  plan-1  C12   0.020
 S90  plan-1  C11   0.020
 S90  plan-1  C16   0.020
 S90  plan-1  C09   0.020
 S90  plan-1  H14   0.020
 S90  plan-1  H12   0.020
 S90  plan-1  H16   0.020
 S90  plan-2  C08   0.020
 S90  plan-2  C06   0.020
 S90  plan-2  N01   0.020
 S90  plan-2  C02   0.020
 S90  plan-2  N02   0.020
 S90  plan-2  C03   0.020
 S90  plan-2  C04   0.020
 S90  plan-2  C07   0.020
 S90  plan-2  C05   0.020
 S90  plan-2  H05   0.020
 S90  plan-2  H03   0.020
 S90  plan-3  C15   0.020
 S90  plan-3  N17   0.020
 S90  plan-3  C21   0.020
 S90  plan-3  C17   0.020
 S90  plan-4  C02   0.020
 S90  plan-4  N02   0.020
 S90  plan-4  H021  0.020
 S90  plan-4  H022  0.020

