# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 17 20:53:18 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 6-[4-({[2-(3-fluorophenyl)ethyl]amino}methyl)phenyl]-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(c1)c2ccc(CNCCc3cccc(F)c3)cc2
#
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
 0GD  0GD  6-[4-({[2-(3-fluorophenyl)ethyl]amino}methyl)phenyl]-4-methylpyridin-2-amine  ligand  47  25  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0GD
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
 0GD  C08   C  CH3   0  -0.727  -7.2263   2.2170  -1.5692
 0GD  C04   C  CR6   0   0.208  -6.6241   1.0997  -0.7735
 0GD  C05   C  CR16  0  -0.427  -5.2392   1.0320  -0.5884
 0GD  C03   C  CR16  0  -0.443  -7.4079   0.1082  -0.2221
 0GD  C02   C  CR6   0   0.452  -6.7863  -0.9315   0.4923
 0GD  N07   N  NH2   0  -0.841  -7.5296  -1.9109   1.0841
 0GD  N01   N  N     0  -0.494  -5.4719  -0.9845   0.6640
 0GD  C06   C  CR6   0   0.247  -4.7090  -0.0207   0.1413
 0GD  C09   C  CR6   0   0.055  -3.2515  -0.1497   0.3689
 0GD  C10   C  CR16  0  -0.272  -2.6920  -1.3911   0.6691
 0GD  C11   C  CR16  0  -0.297  -1.3264  -1.5267   0.8674
 0GD  C14   C  CR16  0  -0.309  -2.3960   0.9518   0.2929
 0GD  C13   C  CR16  0  -0.273  -1.0336   0.8146   0.5000
 0GD  C12   C  CR6   0   0.069  -0.4754  -0.4287   0.7910
 0GD  C15   C  CH2   0  -0.309   1.0018  -0.5753   1.0373
 0GD  N16   N  NH1   0  -0.597   1.7822   0.1878   0.0840
 0GD  C17   C  CH2   0  -0.246   3.2092   0.0766   0.3081
 0GD  C18   C  CH2   0  -0.530   3.9821   0.9264  -0.6978
 0GD  C19   C  CR6   0   0.138   5.4645   0.8218  -0.4800
 0GD  C20   C  CR16  0  -0.463   6.1830  -0.2267  -1.0505
 0GD  C21   C  CR6   0   0.538   7.5372  -0.3329  -0.8025
 0GD  F25   F  F     0  -0.319   8.2155  -1.3499  -1.3628
 0GD  C22   C  CR16  0  -0.426   8.2198   0.5645  -0.0043
 0GD  C23   C  CR16  0  -0.224   7.4991   1.6077   0.5612
 0GD  C24   C  CR16  0  -0.321   6.1367   1.7361   0.3280
 0GD  H081  H  HCH3  0   0.254  -6.9407   2.1388  -2.6196
 0GD  H082  H  HCH3  0   0.248  -8.3136   2.2102  -1.5161
 0GD  H083  H  HCH3  0   0.251  -6.8732   3.1851  -1.2134
 0GD  H05   H  HCR6  0   0.249  -4.6018   1.7843  -1.0336
 0GD  H03   H  HCR6  0   0.259  -8.4850   0.1213  -0.3384
 0GD  H071  H  HNH2  0   0.389  -8.4565  -2.0730   0.7278
 0GD  H072  H  HNH2  0   0.380  -7.0349  -2.7494   1.3407
 0GD  H10   H  HCR6  0   0.248  -3.3320  -2.2606   0.7343
 0GD  H14   H  HCR6  0   0.248  -2.7911   1.9385   0.0884
 0GD  H11   H  HCR6  0   0.248  -0.9181  -2.5071   1.0837
 0GD  H13   H  HCR6  0   0.248  -0.3938   1.6855   0.4376
 0GD  H151  H  HCH2  0   0.241   1.2375  -0.1990   2.0389
 0GD  H152  H  HCH2  0   0.214   1.2614  -1.6450   1.0505
 0GD  H16   H  HNH1  0   0.344   1.5683  -0.1397  -0.8513
 0GD  H171  H  HCH2  0   0.227   3.4291   0.4286   1.3205
 0GD  H172  H  HCH2  0   0.200   3.5686  -0.9635   0.2585
 0GD  H181  H  HCH2  0   0.247   3.7326   0.5990  -1.7110
 0GD  H182  H  HCH2  0   0.248   3.6598   1.9661  -0.6077
 0GD  H20   H  HCR6  0   0.270   5.6900  -0.9531  -1.6861
 0GD  H24   H  HCR6  0   0.253   5.5906   2.5578   0.7746
 0GD  H22   H  HCR6  0   0.277   9.2823   0.4540   0.1687
 0GD  H23   H  HCR6  0   0.266   8.0100   2.3275   1.1872

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
 0GD  C08  C04   single    1.498  0.020  1.498
 0GD  C04  C05   aromatic  1.399  0.020  1.399
 0GD  C04  C03   aromatic  1.379  0.020  1.379
 0GD  C05  C06   aromatic  1.386  0.020  1.386
 0GD  C03  C02   aromatic  1.406  0.020  1.406
 0GD  C02  N07   single    1.364  0.020  1.364
 0GD  C02  N01   aromatic  1.327  0.020  1.327
 0GD  N01  C06   aromatic  1.336  0.020  1.336
 0GD  C06  C09   single    1.481  0.020  1.481
 0GD  C09  C10   aromatic  1.394  0.020  1.394
 0GD  C09  C14   aromatic  1.397  0.020  1.397
 0GD  C10  C11   aromatic  1.387  0.020  1.387
 0GD  C11  C12   aromatic  1.391  0.020  1.391
 0GD  C14  C13   aromatic  1.385  0.020  1.385
 0GD  C13  C12   aromatic  1.393  0.020  1.393
 0GD  C12  C15   single    1.505  0.020  1.505
 0GD  C15  N16   single    1.449  0.020  1.449
 0GD  N16  C17   single    1.449  0.020  1.449
 0GD  C17  C18   single    1.527  0.020  1.527
 0GD  C18  C19   single    1.502  0.020  1.502
 0GD  C19  C20   aromatic  1.393  0.020  1.393
 0GD  C19  C24   aromatic  1.393  0.020  1.393
 0GD  C20  C21   aromatic  1.381  0.020  1.381
 0GD  C21  F25   single    1.345  0.020  1.345
 0GD  C21  C22   aromatic  1.381  0.020  1.381
 0GD  C22  C23   aromatic  1.388  0.020  1.388
 0GD  C23  C24   aromatic  1.388  0.020  1.388
 0GD  C08  H081  single    0.970  0.020  1.090
 0GD  C08  H082  single    0.970  0.020  1.090
 0GD  C08  H083  single    0.970  0.020  1.090
 0GD  C05  H05   single    0.930  0.020  1.080
 0GD  C03  H03   single    0.930  0.020  1.080
 0GD  N07  H071  single    0.890  0.020  1.040
 0GD  N07  H072  single    0.890  0.020  1.040
 0GD  C10  H10   single    0.930  0.020  1.080
 0GD  C14  H14   single    0.930  0.020  1.080
 0GD  C11  H11   single    0.930  0.020  1.080
 0GD  C13  H13   single    0.930  0.020  1.080
 0GD  C15  H151  single    0.970  0.020  1.090
 0GD  C15  H152  single    0.970  0.020  1.090
 0GD  N16  H16   single    0.890  0.020  1.040
 0GD  C17  H171  single    0.970  0.020  1.090
 0GD  C17  H172  single    0.970  0.020  1.090
 0GD  C18  H181  single    0.970  0.020  1.090
 0GD  C18  H182  single    0.970  0.020  1.090
 0GD  C20  H20   single    0.930  0.020  1.080
 0GD  C24  H24   single    0.930  0.020  1.080
 0GD  C22  H22   single    0.930  0.020  1.080
 0GD  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
 0GD  H083  C08  H082  108.24  3.000
 0GD  H083  C08  H081  107.04  3.000
 0GD  H082  C08  H081  107.93  3.000
 0GD  H083  C08  C04   111.02  3.000
 0GD  H082  C08  C04   111.78  3.000
 0GD  H081  C08  C04   110.65  3.000
 0GD  C03   C04  C05   118.36  3.000
 0GD  C03   C04  C08   121.34  3.000
 0GD  C05   C04  C08   120.29  3.000
 0GD  H05   C05  C06   121.29  3.000
 0GD  H05   C05  C04   119.68  3.000
 0GD  C06   C05  C04   119.02  3.000
 0GD  H03   C03  C02   120.19  3.000
 0GD  H03   C03  C04   120.90  3.000
 0GD  C02   C03  C04   118.91  3.000
 0GD  N01   C02  N07   117.06  3.000
 0GD  N01   C02  C03   122.22  3.000
 0GD  N07   C02  C03   120.68  3.000
 0GD  H072  N07  H071  114.13  3.000
 0GD  H072  N07  C02   116.14  3.000
 0GD  H071  N07  C02   117.64  3.000
 0GD  C06   N01  C02   119.11  3.000
 0GD  C09   C06  N01   116.05  3.000
 0GD  C09   C06  C05   121.56  3.000
 0GD  N01   C06  C05   122.38  3.000
 0GD  C14   C09  C10   117.91  3.000
 0GD  C14   C09  C06   121.72  3.000
 0GD  C10   C09  C06   120.37  3.000
 0GD  H10   C10  C11   119.70  3.000
 0GD  H10   C10  C09   119.42  3.000
 0GD  C11   C10  C09   120.87  3.000
 0GD  H11   C11  C12   119.63  3.000
 0GD  H11   C11  C10   119.21  3.000
 0GD  C12   C11  C10   121.16  3.000
 0GD  H14   C14  C13   118.54  3.000
 0GD  H14   C14  C09   120.37  3.000
 0GD  C13   C14  C09   121.08  3.000
 0GD  H13   C13  C12   119.55  3.000
 0GD  H13   C13  C14   119.55  3.000
 0GD  C12   C13  C14   120.91  3.000
 0GD  C15   C12  C13   120.95  3.000
 0GD  C15   C12  C11   120.97  3.000
 0GD  C13   C12  C11   118.07  3.000
 0GD  H152  C15  H151  105.79  3.000
 0GD  H152  C15  N16   113.12  3.000
 0GD  H151  C15  N16   107.74  3.000
 0GD  H152  C15  C12   109.15  3.000
 0GD  H151  C15  C12   109.11  3.000
 0GD  N16   C15  C12   111.69  3.000
 0GD  H16   N16  C17   109.01  3.000
 0GD  H16   N16  C15   108.85  3.000
 0GD  C17   N16  C15   112.84  3.000
 0GD  H172  C17  H171  106.25  3.000
 0GD  H172  C17  C18   109.31  3.000
 0GD  H171  C17  C18   109.19  3.000
 0GD  H172  C17  N16   112.76  3.000
 0GD  H171  C17  N16   108.44  3.000
 0GD  C18   C17  N16   110.73  3.000
 0GD  H182  C18  H181  107.10  3.000
 0GD  H182  C18  C19   110.22  3.000
 0GD  H181  C18  C19   109.79  3.000
 0GD  H182  C18  C17   109.03  3.000
 0GD  H181  C18  C17   109.16  3.000
 0GD  C19   C18  C17   111.43  3.000
 0GD  C24   C19  C20   118.86  3.000
 0GD  C24   C19  C18   120.97  3.000
 0GD  C20   C19  C18   120.14  3.000
 0GD  H20   C20  C21   119.99  3.000
 0GD  H20   C20  C19   120.66  3.000
 0GD  C21   C20  C19   119.35  3.000
 0GD  C22   C21  F25   118.87  3.000
 0GD  C22   C21  C20   122.57  3.000
 0GD  F25   C21  C20   118.56  3.000
 0GD  H22   C22  C23   121.41  3.000
 0GD  H22   C22  C21   120.74  3.000
 0GD  C23   C22  C21   117.84  3.000
 0GD  H23   C23  C24   119.94  3.000
 0GD  H23   C23  C22   119.37  3.000
 0GD  C24   C23  C22   120.70  3.000
 0GD  H24   C24  C23   119.72  3.000
 0GD  H24   C24  C19   119.60  3.000
 0GD  C23   C24  C19   120.68  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
 0GD  CONST_01  N01   C06  C05  C04     0.00   0.0  0
 0GD  CONST_02  C09   C06  C05  C04   180.00   0.0  0
 0GD  CONST_03  N01   C02  C03  C04     0.00   0.0  0
 0GD  CONST_04  C02   C03  C04  C05     0.00   0.0  0
 0GD  CONST_05  C02   N01  C06  C05     0.00   0.0  0
 0GD  CONST_08  C06   C05  C04  C03     0.00   0.0  0
 0GD  CONST_09  C06   N01  C02  C03     0.00   0.0  0
 0GD  CONST_10  C09   C06  N01  C02   180.00   0.0  0
 0GD  CONST_13  C11   C10  C09  C06   180.00   0.0  0
 0GD  CONST_14  C13   C14  C09  C06   180.00   0.0  0
 0GD  CONST_15  C12   C11  C10  C09     0.00   0.0  0
 0GD  CONST_16  C12   C13  C14  C09     0.00   0.0  0
 0GD  CONST_17  C13   C14  C09  C10     0.00   0.0  0
 0GD  CONST_18  C13   C12  C11  C10     0.00   0.0  0
 0GD  CONST_19  C14   C09  C10  C11     0.00   0.0  0
 0GD  CONST_20  C14   C13  C12  C11     0.00   0.0  0
 0GD  CONST_21  C22   C21  C20  C19     0.00   0.0  0
 0GD  CONST_22  C22   C23  C24  C19     0.00   0.0  0
 0GD  CONST_23  C23   C24  C19  C20     0.00   0.0  0
 0GD  CONST_24  C23   C22  C21  C20     0.00   0.0  0
 0GD  CONST_25  C24   C19  C20  C21     0.00   0.0  0
 0GD  CONST_26  C24   C23  C22  C21     0.00   0.0  0
 0GD  CONST_27  C06   C05  C04  C08   180.00   0.0  0
 0GD  CONST_28  C02   C03  C04  C08   180.00   0.0  0
 0GD  CONST_29  N07   C02  C03  C04   180.00   0.0  0
 0GD  CONST_30  C06   N01  C02  N07   180.00   0.0  0
 0GD  CONST_31  C15   C12  C11  C10   180.00   0.0  0
 0GD  CONST_32  C15   C12  C13  C14   180.00   0.0  0
 0GD  CONST_33  C21   C20  C19  C18   180.00   0.0  0
 0GD  CONST_34  C23   C24  C19  C18   180.00   0.0  0
 0GD  CONST_35  F25   C21  C20  C19   180.00   0.0  0
 0GD  CONST_36  C23   C22  C21  F25   180.00   0.0  0
 0GD  CONST_37  H03   C03  C04  C05   180.00   0.0  0
 0GD  CONST_38  H05   C05  C04  C03   180.00   0.0  0
 0GD  CONST_39  H10   C10  C09  C06     0.00   0.0  0
 0GD  CONST_40  H14   C14  C09  C06     0.00   0.0  0
 0GD  CONST_41  H11   C11  C10  C09   180.00   0.0  0
 0GD  CONST_42  H13   C13  C14  C09   180.00   0.0  0
 0GD  CONST_43  H23   C23  C24  C19   180.00   0.0  0
 0GD  CONST_44  H24   C24  C19  C20   180.00   0.0  0
 0GD  CONST_45  H22   C22  C21  C20   180.00   0.0  0
 0GD  CONST_46  H20   C20  C21  C22   180.00   0.0  0
 0GD  Var_01    N16   C15  C12  C11   137.87  30.0  2
 0GD  Var_02    C20   C19  C18  C17    84.91  30.0  2
 0GD  Var_03    H081  C08  C04  C05    67.20  30.0  2
 0GD  Var_04    C17   N16  C15  C12   179.34  30.0  3
 0GD  Var_05    C19   C18  C17  N16  -179.96  30.0  3
 0GD  Var_06    C18   C17  N16  C15  -178.51  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
 0GD  plan-1  C08   0.020
 0GD  plan-1  C04   0.020
 0GD  plan-1  C05   0.020
 0GD  plan-1  C03   0.020
 0GD  plan-1  C02   0.020
 0GD  plan-1  N07   0.020
 0GD  plan-1  N01   0.020
 0GD  plan-1  C06   0.020
 0GD  plan-1  C09   0.020
 0GD  plan-1  H05   0.020
 0GD  plan-1  H03   0.020
 0GD  plan-2  C06   0.020
 0GD  plan-2  C09   0.020
 0GD  plan-2  C10   0.020
 0GD  plan-2  C11   0.020
 0GD  plan-2  C14   0.020
 0GD  plan-2  C13   0.020
 0GD  plan-2  C12   0.020
 0GD  plan-2  C15   0.020
 0GD  plan-2  H10   0.020
 0GD  plan-2  H14   0.020
 0GD  plan-2  H11   0.020
 0GD  plan-2  H13   0.020
 0GD  plan-3  C18   0.020
 0GD  plan-3  C19   0.020
 0GD  plan-3  C20   0.020
 0GD  plan-3  C21   0.020
 0GD  plan-3  F25   0.020
 0GD  plan-3  C22   0.020
 0GD  plan-3  C23   0.020
 0GD  plan-3  C24   0.020
 0GD  plan-3  H20   0.020
 0GD  plan-3  H24   0.020
 0GD  plan-3  H22   0.020
 0GD  plan-3  H23   0.020
 0GD  plan-4  C02   0.020
 0GD  plan-4  N07   0.020
 0GD  plan-4  H071  0.020
 0GD  plan-4  H072  0.020

