# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 02:22:07 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 4-methyl-6-[2-[5-[3-(methylamino)propyl]pyridin-3-yl]ethyl]pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCCCc1cncc(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
 W66  W66  4-methyl-6-[2-[5-[3-(methylamino)propyl]pyridin-3-yl]ethyl]pyridin-2-amine  ligand  45  21  .  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_W66
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
 W66  C07   C  CH3   0  -0.724   4.5888   3.5883  -0.2750
 W66  C06   C  CR6   0   0.279   2.7952   0.3141   0.3201
 W66  C05   C  CR16  0  -0.440   3.0046   1.6646   0.1016
 W66  C04   C  CR6   0   0.203   4.3118   2.1291  -0.0778
 W66  C03   C  CR16  0  -0.443   5.3397   1.2081  -0.0392
 W66  C02   C  CR6   0   0.439   5.0359  -0.1448   0.1859
 W66  N02   N  NH2   0  -0.838   6.0216  -1.0906   0.1869
 W66  N01   N  N     0  -0.485   3.7901  -0.5728   0.3641
 W66  C09   C  CH2   0  -0.514   1.0060  -1.1633  -0.6569
 W66  C16   C  CR16  0  -0.124  -2.8476  -2.7515   0.0171
 W66  C15   C  CR6   0   0.056  -2.7759  -1.5003  -0.5861
 W66  C14   C  CR16  0  -0.239  -1.5053  -0.9886  -0.8241
 W66  C13   C  CR6   0   0.048  -0.3762  -1.7124  -0.4626
 W66  C12   C  CR16  0  -0.116  -0.5849  -2.9528   0.1338
 W66  N11   N  N     0  -0.398  -1.7851  -3.4655   0.3679
 W66  C18   C  CH2   0  -0.438  -4.2447   0.4392   0.0438
 W66  N20   N  NH1   0  -0.593  -5.7131   2.3128   0.6396
 W66  C19   C  CH2   0  -0.254  -5.5105   1.2145  -0.2844
 W66  C21   C  CH3   0  -0.518  -6.9171   3.0658   0.3545
 W66  H021  H  HNH2  0   0.387   6.9620  -0.7804   0.3656
 W66  H022  H  HNH2  0   0.379   5.7903  -1.9675   0.6246
 W66  H03   H  HCR6  0   0.254   6.3686   1.5170  -0.1817
 W66  H071  H  HCH3  0   0.255   4.7575   4.0757   0.6875
 W66  H072  H  HCH3  0   0.247   5.4788   3.7505  -0.8817
 W66  H073  H  HCH3  0   0.247   3.7500   4.0944  -0.7512
 W66  H05   H  HCR6  0   0.245   2.1671   2.3501   0.0738
 W66  H081  H  HCH2  0   0.250   1.3655  -0.8017   1.4372
 W66  H082  H  HCH2  0   0.248   0.6900   0.5775   0.5830
 W66  H091  H  HCH2  0   0.253   1.0535  -0.6059  -1.5958
 W66  H092  H  HCH2  0   0.252   1.7295  -1.9773  -0.7314
 W66  H14   H  HCR6  0   0.254  -1.3940  -0.0188  -1.2996
 W66  H12   H  HCR6  0   0.251   0.2672  -3.5591   0.4285
 W66  H16   H  HCR6  0   0.251  -3.8180  -3.1955   0.2204
 W66  H171  H  HCH2  0   0.245  -3.9431  -0.3363  -1.9433
 W66  H172  H  HCH2  0   0.243  -4.8804  -1.3902  -0.9019
 W66  H181  H  HCH2  0   0.226  -4.3057   0.0494   1.0652
 W66  H182  H  HCH2  0   0.228  -3.3877   1.1179   0.0178
 W66  H191  H  HCH2  0   0.215  -5.4289   1.6281  -1.2953
 W66  H192  H  HCH2  0   0.186  -6.3672   0.5204  -0.3084
 W66  H20   H  HNH1  0   0.340  -5.7794   1.9378   1.5782
 W66  H211  H  HCH3  0   0.230  -7.0602   3.8381   1.1105
 W66  H212  H  HCH3  0   0.220  -6.8233   3.5659  -0.6116
 W66  H213  H  HCH3  0   0.191  -7.8323   2.4573   0.3181
 W66  C08   C  CH2   0  -0.488   1.4101  -0.2391   0.5003
 W66  C17   C  CH2   0  -0.512  -4.0147  -0.7235  -0.9229

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
 W66  N02  C02   single    1.366  0.020  1.366
 W66  C02  C03   aromatic  1.405  0.020  1.405
 W66  C02  N01   aromatic  1.329  0.020  1.329
 W66  C03  C04   aromatic  1.381  0.020  1.381
 W66  C04  C07   single    1.498  0.020  1.498
 W66  C04  C05   aromatic  1.399  0.020  1.399
 W66  C05  C06   aromatic  1.384  0.020  1.384
 W66  N01  C06   aromatic  1.334  0.020  1.334
 W66  C06  C08   single    1.502  0.020  1.502
 W66  C08  C09   single    1.535  0.020  1.535
 W66  C09  C13   single    1.500  0.020  1.500
 W66  C13  C14   aromatic  1.389  0.020  1.389
 W66  C13  C12   aromatic  1.392  0.020  1.392
 W66  C14  C15   aromatic  1.390  0.020  1.390
 W66  C12  N11   aromatic  1.326  0.020  1.326
 W66  N11  C16   aromatic  1.327  0.020  1.327
 W66  C16  C15   aromatic  1.391  0.020  1.391
 W66  C15  C17   single    1.501  0.020  1.501
 W66  C17  C18   single    1.529  0.020  1.529
 W66  C18  C19   single    1.520  0.020  1.520
 W66  C19  N20   single    1.449  0.020  1.449
 W66  N20  C21   single    1.448  0.020  1.448
 W66  N02  H021  single    0.890  0.020  1.040
 W66  N02  H022  single    0.890  0.020  1.040
 W66  C03  H03   single    0.930  0.020  1.080
 W66  C07  H071  single    0.970  0.020  1.090
 W66  C07  H072  single    0.970  0.020  1.090
 W66  C07  H073  single    0.970  0.020  1.090
 W66  C05  H05   single    0.930  0.020  1.080
 W66  C08  H081  single    0.970  0.020  1.090
 W66  C08  H082  single    0.970  0.020  1.090
 W66  C09  H091  single    0.970  0.020  1.090
 W66  C09  H092  single    0.970  0.020  1.090
 W66  C14  H14   single    0.930  0.020  1.080
 W66  C12  H12   single    0.930  0.020  1.080
 W66  C16  H16   single    0.930  0.020  1.080
 W66  C17  H171  single    0.970  0.020  1.090
 W66  C17  H172  single    0.970  0.020  1.090
 W66  C18  H181  single    0.970  0.020  1.090
 W66  C18  H182  single    0.970  0.020  1.090
 W66  C19  H191  single    0.970  0.020  1.090
 W66  C19  H192  single    0.970  0.020  1.090
 W66  N20  H20   single    0.890  0.020  1.040
 W66  C21  H211  single    0.970  0.020  1.090
 W66  C21  H212  single    0.970  0.020  1.090
 W66  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
 W66  H073  C07  H072  108.46  3.000
 W66  H073  C07  H071  107.27  3.000
 W66  H072  C07  H071  107.35  3.000
 W66  H073  C07  C04   111.57  3.000
 W66  H072  C07  C04   111.68  3.000
 W66  H071  C07  C04   110.32  3.000
 W66  C08   C06  N01   116.04  3.000
 W66  C08   C06  C05   121.18  3.000
 W66  N01   C06  C05   122.77  3.000
 W66  H05   C05  C04   120.62  3.000
 W66  H05   C05  C06   120.32  3.000
 W66  C04   C05  C06   119.05  3.000
 W66  C03   C04  C05   118.08  3.000
 W66  C05   C04  C07   120.86  3.000
 W66  C03   C04  C07   121.05  3.000
 W66  H03   C03  C02   120.07  3.000
 W66  H03   C03  C04   120.86  3.000
 W66  C02   C03  C04   119.07  3.000
 W66  N01   C02  N02   116.94  3.000
 W66  N01   C02  C03   122.30  3.000
 W66  N02   C02  C03   120.73  3.000
 W66  H022  N02  H021  113.95  3.000
 W66  H022  N02  C02   115.95  3.000
 W66  H021  N02  C02   117.45  3.000
 W66  C02   N01  C06   118.73  3.000
 W66  H092  C09  H091  107.03  3.000
 W66  H092  C09  C13   110.28  3.000
 W66  H091  C09  C13   109.76  3.000
 W66  H092  C09  C08   109.02  3.000
 W66  H091  C09  C08   109.22  3.000
 W66  C13   C09  C08   111.42  3.000
 W66  H16   C16  N11   116.47  3.000
 W66  H16   C16  C15   119.66  3.000
 W66  N11   C16  C15   123.87  3.000
 W66  C17   C15  C14   121.71  3.000
 W66  C17   C15  C16   121.36  3.000
 W66  C14   C15  C16   116.90  3.000
 W66  H14   C14  C13   119.74  3.000
 W66  H14   C14  C15   119.82  3.000
 W66  C13   C14  C15   120.44  3.000
 W66  C12   C13  C14   117.00  3.000
 W66  C12   C13  C09   121.32  3.000
 W66  C14   C13  C09   121.64  3.000
 W66  H12   C12  N11   116.50  3.000
 W66  H12   C12  C13   119.73  3.000
 W66  N11   C12  C13   123.77  3.000
 W66  C12   N11  C16   118.03  3.000
 W66  H182  C18  H181  106.67  3.000
 W66  H182  C18  C19   109.33  3.000
 W66  H181  C18  C19   109.66  3.000
 W66  H182  C18  C17   109.82  3.000
 W66  H181  C18  C17   109.10  3.000
 W66  C19   C18  C17   112.11  3.000
 W66  H20   N20  C21   108.69  3.000
 W66  H20   N20  C19   108.62  3.000
 W66  C21   N20  C19   112.62  3.000
 W66  H192  C19  H191  105.99  3.000
 W66  H192  C19  N20   112.47  3.000
 W66  H191  C19  N20   108.21  3.000
 W66  H192  C19  C18   109.31  3.000
 W66  H191  C19  C18   109.26  3.000
 W66  N20   C19  C18   111.42  3.000
 W66  H213  C21  H212  107.20  3.000
 W66  H213  C21  H211  107.80  3.000
 W66  H212  C21  H211  107.48  3.000
 W66  H213  C21  N20   114.25  3.000
 W66  H212  C21  N20   109.93  3.000
 W66  H211  C21  N20   109.93  3.000
 W66  H082  C08  H081  107.04  3.000
 W66  H082  C08  C09   109.49  3.000
 W66  H081  C08  C09   108.99  3.000
 W66  H082  C08  C06   109.98  3.000
 W66  H081  C08  C06   109.26  3.000
 W66  C09   C08  C06   111.96  3.000
 W66  H172  C17  H171  106.60  3.000
 W66  H172  C17  C18   109.43  3.000
 W66  H171  C17  C18   109.29  3.000
 W66  H172  C17  C15   109.50  3.000
 W66  H171  C17  C15   109.79  3.000
 W66  C18   C17  C15   112.08  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
 W66  CONST_01  C03   C04  C05  C06     0.00   0.0  0
 W66  CONST_02  C03   C02  N01  C06     0.00   0.0  0
 W66  CONST_03  C02   C03  C04  C05     0.00   0.0  0
 W66  CONST_04  C02   N01  C06  C05     0.00   0.0  0
 W66  CONST_05  N01   C02  C03  C04     0.00   0.0  0
 W66  CONST_06  N01   C06  C05  C04     0.00   0.0  0
 W66  CONST_07  C13   C12  N11  C16     0.00   0.0  0
 W66  CONST_08  C13   C14  C15  C16     0.00   0.0  0
 W66  CONST_09  C12   C13  C14  C15     0.00   0.0  0
 W66  CONST_10  C12   N11  C16  C15     0.00   0.0  0
 W66  CONST_11  N11   C12  C13  C14     0.00   0.0  0
 W66  CONST_12  N11   C16  C15  C14     0.00   0.0  0
 W66  CONST_13  C02   C03  C04  C07   180.00   0.0  0
 W66  CONST_14  C06   C05  C04  C07   180.00   0.0  0
 W66  CONST_15  N02   C02  N01  C06   180.00   0.0  0
 W66  CONST_16  N02   C02  C03  C04   180.00   0.0  0
 W66  CONST_17  C08   C06  C05  C04   180.00   0.0  0
 W66  CONST_18  C08   C06  N01  C02   180.00   0.0  0
 W66  CONST_19  C15   C14  C13  C09   180.00   0.0  0
 W66  CONST_20  N11   C12  C13  C09   180.00   0.0  0
 W66  CONST_21  C17   C15  C14  C13   180.00   0.0  0
 W66  CONST_22  C17   C15  C16  N11   180.00   0.0  0
 W66  CONST_23  H03   C03  C04  C05   180.00   0.0  0
 W66  CONST_24  H05   C05  C04  C03   180.00   0.0  0
 W66  CONST_25  H12   C12  N11  C16   180.00   0.0  0
 W66  CONST_26  H14   C14  C15  C16   180.00   0.0  0
 W66  CONST_27  H16   C16  C15  C14   180.00   0.0  0
 W66  Var_01    C13   C09  C08  C06   179.80  30.0  3
 W66  Var_02    C09   C08  C06  C05   113.37  30.0  2
 W66  Var_03    C14   C13  C09  C08    83.10  30.0  2
 W66  Var_04    C18   C17  C15  C16   105.12  30.0  2
 W66  Var_05    H071  C07  C04  C05    90.10  30.0  2
 W66  Var_06    C19   C18  C17  C15  -179.16  30.0  3
 W66  Var_07    N20   C19  C18  C17  -179.95  30.0  3
 W66  Var_08    C21   N20  C19  C18  -179.71  30.0  3
 W66  Var_09    H211  C21  N20  C19   176.39  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
 W66  plan-1  C07   0.020
 W66  plan-1  C06   0.020
 W66  plan-1  C05   0.020
 W66  plan-1  C04   0.020
 W66  plan-1  C03   0.020
 W66  plan-1  C02   0.020
 W66  plan-1  N02   0.020
 W66  plan-1  N01   0.020
 W66  plan-1  H03   0.020
 W66  plan-1  H05   0.020
 W66  plan-1  C08   0.020
 W66  plan-2  C09   0.020
 W66  plan-2  C16   0.020
 W66  plan-2  C15   0.020
 W66  plan-2  C14   0.020
 W66  plan-2  C13   0.020
 W66  plan-2  C12   0.020
 W66  plan-2  N11   0.020
 W66  plan-2  H14   0.020
 W66  plan-2  H12   0.020
 W66  plan-2  H16   0.020
 W66  plan-2  C17   0.020
 W66  plan-3  C02   0.020
 W66  plan-3  N02   0.020
 W66  plan-3  H021  0.020
 W66  plan-3  H022  0.020

