# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 04:09:48 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 6-[2-[5-[3-(dimethylamino)propyl]pyridin-3-yl]ethyl]-4-methyl-pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)CCCc1cncc(CCc2cc(C)cc(N)n2)c1
#
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
 W67  W67  6-[2-[5-[3-(dimethylamino)propyl]pyridin-3-yl]ethyl]-4-methyl-pyridin-2-amine  ligand  48  22  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_W67
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
 W67  N01   N  N     0  -0.487   3.1432  -1.0425  -0.6417
 W67  C02   C  CR6   0   0.443   4.3214  -1.6258  -0.8332
 W67  N02   N  NH2   0  -0.840   4.4396  -2.4467  -1.9161
 W67  C03   C  CR16  0  -0.447   5.4231  -1.3884   0.0084
 W67  C04   C  CR6   0   0.205   5.2858  -0.5064   1.0600
 W67  C05   C  CR16  0  -0.437   4.0425   0.1107   1.2442
 W67  C06   C  CR6   0   0.280   3.0081  -0.1913   0.3776
 W67  C07   C  CH3   0  -0.725   6.4321  -0.1973   1.9738
 W67  C08   C  CH2   0  -0.489   1.6542   0.4404   0.5353
 W67  C09   C  CH2   0  -0.511   1.2998   1.3588  -0.6421
 W67  N11   N  N     0  -0.398  -1.4513   3.7600   0.2603
 W67  C12   C  CR16  0  -0.117  -0.2594   3.2165   0.0533
 W67  C13   C  CR6   0   0.047  -0.0714   1.9452  -0.4811
 W67  C14   C  CR16  0  -0.239  -1.2124   1.2244  -0.8101
 W67  C15   C  CR6   0   0.057  -2.4745   1.7672  -0.5977
 W67  C16   C  CR16  0  -0.126  -2.5253   3.0473  -0.0556
 W67  C17   C  CH2   0  -0.509  -3.7259   0.9970  -0.9020
 W67  C18   C  CH2   0  -0.444  -3.9435  -0.1597   0.0759
 W67  C19   C  CH2   0  -0.253  -5.2234  -0.9195  -0.2416
 W67  C22   C  CH3   0  -0.519  -6.8710  -2.4777   0.4953
 W67  N20   N  NT    0  -0.408  -5.5310  -1.9739   0.7076
 W67  C21   C  CH3   0  -0.525  -4.5694  -3.0552   0.6659
 W67  H021  H  HNH2  0   0.389   5.1911  -3.1152  -1.9229
 W67  H022  H  HNH2  0   0.380   3.5820  -2.7771  -2.3263
 W67  H03   H  HCR6  0   0.254   6.3635  -1.8952  -0.1730
 W67  H05   H  HCR6  0   0.243   3.8874   0.8098   2.0564
 W67  H071  H  HCH3  0   0.254   6.8438   0.7886   1.7496
 W67  H072  H  HCH3  0   0.248   6.1106  -0.1788   3.0152
 W67  H073  H  HCH3  0   0.247   7.2368  -0.9239   1.8747
 W67  H081  H  HCH2  0   0.249   0.8973  -0.3455   0.6134
 W67  H082  H  HCH2  0   0.249   1.6176   1.0106   1.4659
 W67  H091  H  HCH2  0   0.251   2.0425   2.1567  -0.7146
 W67  H092  H  HCH2  0   0.253   1.3536   0.7855  -1.5698
 W67  H12   H  HCR6  0   0.251   0.6028   3.8214   0.3199
 W67  H14   H  HCR6  0   0.254  -1.1165   0.2307  -1.2373
 W67  H16   H  HCR6  0   0.251  -3.4884   3.5156   0.1270
 W67  H171  H  HCH2  0   0.243  -4.5857   1.6709  -0.8677
 W67  H172  H  HCH2  0   0.246  -3.6783   0.6033  -1.9217
 W67  H181  H  HCH2  0   0.234  -3.0769  -0.8240   0.0329
 W67  H182  H  HCH2  0   0.228  -3.9943   0.2267   1.0977
 W67  H191  H  HCH2  0   0.227  -6.0555  -0.2090  -0.2291
 W67  H192  H  HCH2  0   0.184  -5.1680  -1.3105  -1.2744
 W67  H221  H  HCH3  0   0.189  -7.0141  -2.9296  -0.4994
 W67  H222  H  HCH3  0   0.231  -7.1070  -3.2393   1.2403
 W67  H223  H  HCH3  0   0.231  -7.5986  -1.6715   0.6011
 W67  H211  H  HCH3  0   0.235  -3.5737  -2.7082   0.9407
 W67  H212  H  HCH3  0   0.233  -4.8517  -3.8268   1.3834
 W67  H213  H  HCH3  0   0.188  -4.4988  -3.5319  -0.3253

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
 W67  N02  C02   single    1.364  0.020  1.364
 W67  C02  C03   aromatic  1.407  0.020  1.407
 W67  C02  N01   aromatic  1.329  0.020  1.329
 W67  C03  C04   aromatic  1.379  0.020  1.379
 W67  C04  C05   aromatic  1.400  0.020  1.400
 W67  C04  C07   single    1.498  0.020  1.498
 W67  C05  C06   aromatic  1.383  0.020  1.383
 W67  N01  C06   aromatic  1.335  0.020  1.335
 W67  C06  C08   single    1.502  0.020  1.502
 W67  C08  C09   single    1.535  0.020  1.535
 W67  C09  C13   single    1.500  0.020  1.500
 W67  C13  C12   aromatic  1.392  0.020  1.392
 W67  C13  C14   aromatic  1.389  0.020  1.389
 W67  C12  N11   aromatic  1.326  0.020  1.326
 W67  N11  C16   aromatic  1.327  0.020  1.327
 W67  C16  C15   aromatic  1.391  0.020  1.391
 W67  C14  C15   aromatic  1.390  0.020  1.390
 W67  C15  C17   single    1.501  0.020  1.501
 W67  C17  C18   single    1.530  0.020  1.530
 W67  C18  C19   single    1.522  0.020  1.522
 W67  C19  N20   single    1.452  0.020  1.452
 W67  N20  C22   single    1.447  0.020  1.447
 W67  N20  C21   single    1.448  0.020  1.448
 W67  N02  H021  single    0.890  0.020  1.040
 W67  N02  H022  single    0.890  0.020  1.040
 W67  C03  H03   single    0.930  0.020  1.080
 W67  C05  H05   single    0.930  0.020  1.080
 W67  C07  H071  single    0.970  0.020  1.090
 W67  C07  H072  single    0.970  0.020  1.090
 W67  C07  H073  single    0.970  0.020  1.090
 W67  C08  H081  single    0.970  0.020  1.090
 W67  C08  H082  single    0.970  0.020  1.090
 W67  C09  H091  single    0.970  0.020  1.090
 W67  C09  H092  single    0.970  0.020  1.090
 W67  C12  H12   single    0.930  0.020  1.080
 W67  C14  H14   single    0.930  0.020  1.080
 W67  C16  H16   single    0.930  0.020  1.080
 W67  C17  H171  single    0.970  0.020  1.090
 W67  C17  H172  single    0.970  0.020  1.090
 W67  C18  H181  single    0.970  0.020  1.090
 W67  C18  H182  single    0.970  0.020  1.090
 W67  C19  H191  single    0.970  0.020  1.090
 W67  C19  H192  single    0.970  0.020  1.090
 W67  C22  H221  single    0.970  0.020  1.090
 W67  C22  H222  single    0.970  0.020  1.090
 W67  C22  H223  single    0.970  0.020  1.090
 W67  C21  H211  single    0.970  0.020  1.090
 W67  C21  H212  single    0.970  0.020  1.090
 W67  C21  H213  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
 W67  C06   N01  C02   118.68  3.000
 W67  C03   C02  N02   120.58  3.000
 W67  C03   C02  N01   122.29  3.000
 W67  N02   C02  N01   117.10  3.000
 W67  H022  N02  H021  114.57  3.000
 W67  H022  N02  C02   116.57  3.000
 W67  H021  N02  C02   118.04  3.000
 W67  H03   C03  C04   120.87  3.000
 W67  H03   C03  C02   120.04  3.000
 W67  C04   C03  C02   119.09  3.000
 W67  C07   C04  C05   120.55  3.000
 W67  C07   C04  C03   121.39  3.000
 W67  C05   C04  C03   118.06  3.000
 W67  H05   C05  C06   120.26  3.000
 W67  H05   C05  C04   120.69  3.000
 W67  C06   C05  C04   119.05  3.000
 W67  C08   C06  C05   121.10  3.000
 W67  C08   C06  N01   116.07  3.000
 W67  C05   C06  N01   122.83  3.000
 W67  H073  C07  H072  108.43  3.000
 W67  H073  C07  H071  107.77  3.000
 W67  H072  C07  H071  106.99  3.000
 W67  H073  C07  C04   111.86  3.000
 W67  H072  C07  C04   111.13  3.000
 W67  H071  C07  C04   110.47  3.000
 W67  H082  C08  H081  106.92  3.000
 W67  H082  C08  C09   109.48  3.000
 W67  H081  C08  C09   108.96  3.000
 W67  H082  C08  C06   109.83  3.000
 W67  H081  C08  C06   109.21  3.000
 W67  C09   C08  C06   112.29  3.000
 W67  H092  C09  H091  107.07  3.000
 W67  H092  C09  C13   109.97  3.000
 W67  H091  C09  C13   110.06  3.000
 W67  H092  C09  C08   109.04  3.000
 W67  H091  C09  C08   109.33  3.000
 W67  C13   C09  C08   111.27  3.000
 W67  C16   N11  C12   118.04  3.000
 W67  H12   C12  C13   119.71  3.000
 W67  H12   C12  N11   116.53  3.000
 W67  C13   C12  N11   123.76  3.000
 W67  C14   C13  C12   117.00  3.000
 W67  C14   C13  C09   121.51  3.000
 W67  C12   C13  C09   121.45  3.000
 W67  H14   C14  C15   119.84  3.000
 W67  H14   C14  C13   119.70  3.000
 W67  C15   C14  C13   120.46  3.000
 W67  C17   C15  C16   121.39  3.000
 W67  C17   C15  C14   121.71  3.000
 W67  C16   C15  C14   116.87  3.000
 W67  H16   C16  C15   119.64  3.000
 W67  H16   C16  N11   116.48  3.000
 W67  C15   C16  N11   123.87  3.000
 W67  H172  C17  H171  106.58  3.000
 W67  H172  C17  C18   109.26  3.000
 W67  H171  C17  C18   109.52  3.000
 W67  H172  C17  C15   109.72  3.000
 W67  H171  C17  C15   109.46  3.000
 W67  C18   C17  C15   112.14  3.000
 W67  H182  C18  H181  106.77  3.000
 W67  H182  C18  C19   109.41  3.000
 W67  H181  C18  C19   110.81  3.000
 W67  H182  C18  C17   109.67  3.000
 W67  H181  C18  C17   108.76  3.000
 W67  C19   C18  C17   111.32  3.000
 W67  H192  C19  H191  106.16  3.000
 W67  H192  C19  N20   111.38  3.000
 W67  H191  C19  N20   107.64  3.000
 W67  H192  C19  C18   109.22  3.000
 W67  H191  C19  C18   108.24  3.000
 W67  N20   C19  C18   113.85  3.000
 W67  H223  C22  H222  107.78  3.000
 W67  H223  C22  H221  107.70  3.000
 W67  H222  C22  H221  107.58  3.000
 W67  H223  C22  N20   110.24  3.000
 W67  H222  C22  N20   110.06  3.000
 W67  H221  C22  N20   113.29  3.000
 W67  C21   N20  C22   110.54  3.000
 W67  C21   N20  C19   112.52  3.000
 W67  C22   N20  C19   110.68  3.000
 W67  H213  C21  H212  107.59  3.000
 W67  H213  C21  H211  107.81  3.000
 W67  H212  C21  H211  107.21  3.000
 W67  H213  C21  N20   113.05  3.000
 W67  H212  C21  N20   109.73  3.000
 W67  H211  C21  N20   111.21  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
 W67  CONST_01  C04   C03  C02  N01     0.00   0.0  0
 W67  CONST_02  C04   C05  C06  N01     0.00   0.0  0
 W67  CONST_03  C05   C04  C03  C02     0.00   0.0  0
 W67  CONST_04  C05   C06  N01  C02     0.00   0.0  0
 W67  CONST_05  C06   N01  C02  C03     0.00   0.0  0
 W67  CONST_06  C06   C05  C04  C03     0.00   0.0  0
 W67  CONST_07  C14   C13  C12  N11     0.00   0.0  0
 W67  CONST_08  C14   C15  C16  N11     0.00   0.0  0
 W67  CONST_09  C15   C14  C13  C12     0.00   0.0  0
 W67  CONST_10  C15   C16  N11  C12     0.00   0.0  0
 W67  CONST_11  C16   N11  C12  C13     0.00   0.0  0
 W67  CONST_12  C16   C15  C14  C13     0.00   0.0  0
 W67  CONST_13  C07   C04  C03  C02   180.00   0.0  0
 W67  CONST_14  C08   C06  N01  C02   180.00   0.0  0
 W67  CONST_15  C04   C03  C02  N02   180.00   0.0  0
 W67  CONST_16  C06   N01  C02  N02   180.00   0.0  0
 W67  CONST_17  C08   C06  C05  C04   180.00   0.0  0
 W67  CONST_18  C07   C04  C05  C06   180.00   0.0  0
 W67  CONST_19  N11   C12  C13  C09   180.00   0.0  0
 W67  CONST_20  C15   C14  C13  C09   180.00   0.0  0
 W67  CONST_21  C17   C15  C16  N11   180.00   0.0  0
 W67  CONST_22  C17   C15  C14  C13   180.00   0.0  0
 W67  CONST_23  H03   C03  C02  N01   180.00   0.0  0
 W67  CONST_24  H05   C05  C06  N01   180.00   0.0  0
 W67  CONST_25  H14   C14  C13  C12   180.00   0.0  0
 W67  CONST_26  H16   C16  N11  C12   180.00   0.0  0
 W67  CONST_27  H12   C12  C13  C14   180.00   0.0  0
 W67  Var_01    C09   C08  C06  N01   -65.28  30.0  2
 W67  Var_02    C13   C09  C08  C06   178.33  30.0  3
 W67  Var_03    C12   C13  C09  C08    96.79  30.0  2
 W67  Var_04    C18   C17  C15  C14    70.23  30.0  2
 W67  Var_05    H071  C07  C04  C03   104.58  30.0  2
 W67  Var_06    C19   C18  C17  C15   179.46  30.0  3
 W67  Var_07    N20   C19  C18  C17  -176.07  30.0  3
 W67  Var_08    C22   N20  C19  C18   169.11  30.0  3
 W67  Var_09    H221  C22  N20  C19    61.92  30.0  3
 W67  Var_10    H211  C21  N20  C19    62.43  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
 W67  plan-1  N01   0.020
 W67  plan-1  C02   0.020
 W67  plan-1  N02   0.020
 W67  plan-1  C03   0.020
 W67  plan-1  C04   0.020
 W67  plan-1  C05   0.020
 W67  plan-1  C06   0.020
 W67  plan-1  C07   0.020
 W67  plan-1  C08   0.020
 W67  plan-1  H03   0.020
 W67  plan-1  H05   0.020
 W67  plan-2  C09   0.020
 W67  plan-2  N11   0.020
 W67  plan-2  C12   0.020
 W67  plan-2  C13   0.020
 W67  plan-2  C14   0.020
 W67  plan-2  C15   0.020
 W67  plan-2  C16   0.020
 W67  plan-2  C17   0.020
 W67  plan-2  H12   0.020
 W67  plan-2  H14   0.020
 W67  plan-2  H16   0.020
 W67  plan-3  C02   0.020
 W67  plan-3  N02   0.020
 W67  plan-3  H021  0.020
 W67  plan-3  H022  0.020

