# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 01:49:55 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 6-[2-[5-[2-methoxyethyl(methyl)amino]pyridin-3-yl]ethyl]-4-methyl-pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCN(C)c1cncc(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
 W30  W30  6-[2-[5-[2-methoxyethyl(methyl)amino]pyridin-3-yl]ethyl]-4-methyl-pyridin-2-amine  ligand  46  22  .  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_W30
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
 W30  C07   C  CH3   0  -0.726   6.8423   1.3155   0.0147
 W30  C06   C  CR6   0   0.278   3.2690   0.1290   0.3274
 W30  C05   C  CR16  0  -0.435   4.3629   0.9741   0.2894
 W30  C04   C  CR6   0   0.205   5.6319   0.4335   0.0510
 W30  C03   C  CR16  0  -0.446   5.7320  -0.9299  -0.1354
 W30  C02   C  CR6   0   0.440   4.5678  -1.7154  -0.0735
 W30  N02   N  NH2   0  -0.839   4.6376  -3.0734  -0.2007
 W30  N01   N  N     0  -0.485   3.3683  -1.1902   0.1505
 W30  C09   C  CH2   0  -0.516   1.0037   0.4820  -0.7063
 W30  C16   C  CR16  0  -0.165  -2.9104   1.9164  -0.0304
 W30  C15   C  CR6   0   0.332  -2.6196   0.6194   0.4441
 W30  C14   C  CR16  0  -0.322  -1.3217   0.1548   0.1834
 W30  C13   C  CR6   0   0.073  -0.4003   0.9574  -0.4738
 W30  C12   C  CR16  0  -0.166  -0.8079   2.2234  -0.8752
 W30  N11   N  N     0  -0.383  -2.0349   2.6799  -0.6586
 W30  C18   C  CH3   0  -0.536  -3.1834  -1.4809   1.5174
 W30  C19   C  CH2   0  -0.376  -4.9305   0.2427   1.1641
 W30  C20   C  CH2   0  -0.134  -5.6850  -0.0150  -0.1273
 W30  O21   O  O2    0  -0.477  -5.6756  -1.3919  -0.3996
 W30  C22   C  CH3   0  -0.393  -6.3297  -1.7086  -1.6011
 W30  H021  H  HNH2  0   0.387   5.4480  -3.4563  -0.6581
 W30  H022  H  HNH2  0   0.379   3.7768  -3.5416  -0.4321
 W30  H03   H  HCR6  0   0.255   6.6903  -1.3948  -0.3343
 W30  H071  H  HCH3  0   0.255   7.1347   1.6050   1.0257
 W30  H072  H  HCH3  0   0.247   7.6932   0.8163  -0.4459
 W30  H073  H  HCH3  0   0.248   6.6427   2.2345  -0.5367
 W30  H05   H  HCR6  0   0.243   4.2340   2.0399   0.4308
 W30  H081  H  HCH2  0   0.248   1.4181   0.1379   1.3818
 W30  H082  H  HCH2  0   0.248   1.9236   1.7202   0.8076
 W30  H091  H  HCH2  0   0.250   1.4475   1.0305  -1.5406
 W30  H092  H  HCH2  0   0.251   1.0021  -0.5736  -0.9855
 W30  H12   H  HCR6  0   0.242  -0.1218   2.8833  -1.3972
 W30  H14   H  HCR6  0   0.269  -1.0173  -0.8379   0.4891
 W30  H16   H  HCR6  0   0.255  -3.8940   2.3494   0.1063
 W30  H181  H  HCH3  0   0.234  -2.2854  -1.4909   2.1390
 W30  H182  H  HCH3  0   0.255  -3.9910  -1.9037   2.1088
 W30  H183  H  HCH3  0   0.228  -3.0134  -2.1439   0.6634
 W30  H191  H  HCH2  0   0.263  -5.4057  -0.3102   1.9754
 W30  H192  H  HCH2  0   0.257  -5.0378   1.2974   1.4267
 W30  H201  H  HCH2  0   0.208  -6.7118   0.3625  -0.0140
 W30  H202  H  HCH2  0   0.201  -5.2308   0.5471  -0.9564
 W30  H221  H  HCH3  0   0.203  -7.3876  -1.4199  -1.5836
 W30  H222  H  HCH3  0   0.204  -5.8634  -1.2198  -2.4650
 W30  H223  H  HCH3  0   0.233  -6.2710  -2.7872  -1.7437
 W30  C08   C  CH2   0  -0.487   1.8806   0.6624   0.5407
 W30  N17   N  NT    0  -0.502  -3.5334  -0.1337   1.1308

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
 W30  N02  C02   single    1.366  0.020  1.366
 W30  C02  C03   aromatic  1.406  0.020  1.406
 W30  C02  N01   aromatic  1.328  0.020  1.328
 W30  C03  C04   aromatic  1.380  0.020  1.380
 W30  C04  C07   single    1.498  0.020  1.498
 W30  C04  C05   aromatic  1.400  0.020  1.400
 W30  C05  C06   aromatic  1.383  0.020  1.383
 W30  N01  C06   aromatic  1.335  0.020  1.335
 W30  C06  C08   single    1.503  0.020  1.503
 W30  C08  C09   single    1.535  0.020  1.535
 W30  C09  C13   single    1.500  0.020  1.500
 W30  C13  C12   aromatic  1.389  0.020  1.389
 W30  C13  C14   aromatic  1.388  0.020  1.388
 W30  C12  N11   aromatic  1.327  0.020  1.327
 W30  C14  C15   aromatic  1.403  0.020  1.403
 W30  C15  C16   aromatic  1.411  0.020  1.411
 W30  C15  N17   single    1.369  0.020  1.369
 W30  C16  N11   aromatic  1.321  0.020  1.321
 W30  N17  C18   single    1.445  0.020  1.445
 W30  N17  C19   single    1.447  0.020  1.447
 W30  C19  C20   single    1.518  0.020  1.518
 W30  C20  O21   single    1.404  0.020  1.404
 W30  O21  C22   single    1.404  0.020  1.404
 W30  N02  H021  single    0.890  0.020  1.040
 W30  N02  H022  single    0.890  0.020  1.040
 W30  C03  H03   single    0.930  0.020  1.080
 W30  C07  H071  single    0.970  0.020  1.090
 W30  C07  H072  single    0.970  0.020  1.090
 W30  C07  H073  single    0.970  0.020  1.090
 W30  C05  H05   single    0.930  0.020  1.080
 W30  C08  H081  single    0.970  0.020  1.090
 W30  C08  H082  single    0.970  0.020  1.090
 W30  C09  H091  single    0.970  0.020  1.090
 W30  C09  H092  single    0.970  0.020  1.090
 W30  C12  H12   single    0.930  0.020  1.080
 W30  C14  H14   single    0.930  0.020  1.080
 W30  C16  H16   single    0.930  0.020  1.080
 W30  C18  H181  single    0.970  0.020  1.090
 W30  C18  H182  single    0.970  0.020  1.090
 W30  C18  H183  single    0.970  0.020  1.090
 W30  C19  H191  single    0.970  0.020  1.090
 W30  C19  H192  single    0.970  0.020  1.090
 W30  C20  H201  single    0.970  0.020  1.090
 W30  C20  H202  single    0.970  0.020  1.090
 W30  C22  H221  single    0.970  0.020  1.090
 W30  C22  H222  single    0.970  0.020  1.090
 W30  C22  H223  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
 W30  H073  C07  H072  108.40  3.000
 W30  H073  C07  H071  107.09  3.000
 W30  H072  C07  H071  107.70  3.000
 W30  H073  C07  C04   111.14  3.000
 W30  H072  C07  C04   111.82  3.000
 W30  H071  C07  C04   110.50  3.000
 W30  C08   C06  N01   116.01  3.000
 W30  C08   C06  C05   121.19  3.000
 W30  N01   C06  C05   122.79  3.000
 W30  H05   C05  C04   120.68  3.000
 W30  H05   C05  C06   120.25  3.000
 W30  C04   C05  C06   119.06  3.000
 W30  C03   C04  C05   118.06  3.000
 W30  C05   C04  C07   120.61  3.000
 W30  C03   C04  C07   121.33  3.000
 W30  H03   C03  C02   120.05  3.000
 W30  H03   C03  C04   120.86  3.000
 W30  C02   C03  C04   119.09  3.000
 W30  N01   C02  N02   117.07  3.000
 W30  N01   C02  C03   122.30  3.000
 W30  N02   C02  C03   120.61  3.000
 W30  H022  N02  H021  114.03  3.000
 W30  H022  N02  C02   116.11  3.000
 W30  H021  N02  C02   117.51  3.000
 W30  C02   N01  C06   118.71  3.000
 W30  H092  C09  H091  106.90  3.000
 W30  H092  C09  C13   110.15  3.000
 W30  H091  C09  C13   109.84  3.000
 W30  H092  C09  C08   108.79  3.000
 W30  H091  C09  C08   109.22  3.000
 W30  C13   C09  C08   111.80  3.000
 W30  H16   C16  N11   115.52  3.000
 W30  H16   C16  C15   120.80  3.000
 W30  N11   C16  C15   123.68  3.000
 W30  N17   C15  C14   121.91  3.000
 W30  N17   C15  C16   122.46  3.000
 W30  C14   C15  C16   115.63  3.000
 W30  H14   C14  C13   118.52  3.000
 W30  H14   C14  C15   120.76  3.000
 W30  C13   C14  C15   120.72  3.000
 W30  C12   C13  C14   117.98  3.000
 W30  C14   C13  C09   120.77  3.000
 W30  C12   C13  C09   121.23  3.000
 W30  H12   C12  N11   116.98  3.000
 W30  H12   C12  C13   120.49  3.000
 W30  N11   C12  C13   122.52  3.000
 W30  C12   N11  C16   119.46  3.000
 W30  H183  C18  H182  107.72  3.000
 W30  H183  C18  H181  108.11  3.000
 W30  H182  C18  H181  107.32  3.000
 W30  H183  C18  N17   113.19  3.000
 W30  H182  C18  N17   109.18  3.000
 W30  H181  C18  N17   111.11  3.000
 W30  H192  C19  H191  105.53  3.000
 W30  H192  C19  C20   108.64  3.000
 W30  H191  C19  C20   109.28  3.000
 W30  H192  C19  N17   110.58  3.000
 W30  H191  C19  N17   107.81  3.000
 W30  C20   C19  N17   114.59  3.000
 W30  H202  C20  H201  106.72  3.000
 W30  H202  C20  O21   110.63  3.000
 W30  H201  C20  O21   111.28  3.000
 W30  H202  C20  C19   110.44  3.000
 W30  H201  C20  C19   108.55  3.000
 W30  O21   C20  C19   109.17  3.000
 W30  C22   O21  C20   112.59  3.000
 W30  H223  C22  H222  108.37  3.000
 W30  H223  C22  H221  108.34  3.000
 W30  H222  C22  H221  107.78  3.000
 W30  H223  C22  O21   108.07  3.000
 W30  H222  C22  O21   112.05  3.000
 W30  H221  C22  O21   112.10  3.000
 W30  H082  C08  H081  107.06  3.000
 W30  H082  C08  C09   109.57  3.000
 W30  H081  C08  C09   109.07  3.000
 W30  H082  C08  C06   110.01  3.000
 W30  H081  C08  C06   109.24  3.000
 W30  C09   C08  C06   111.76  3.000
 W30  C19   N17  C18   118.05  3.000
 W30  C19   N17  C15   120.85  3.000
 W30  C18   N17  C15   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
 W30  CONST_01  C03   C04  C05  C06    0.00   0.0  0
 W30  CONST_02  C03   C02  N01  C06    0.00   0.0  0
 W30  CONST_03  C02   C03  C04  C05    0.00   0.0  0
 W30  CONST_04  C02   N01  C06  C05    0.00   0.0  0
 W30  CONST_05  N01   C02  C03  C04    0.00   0.0  0
 W30  CONST_06  N01   C06  C05  C04    0.00   0.0  0
 W30  CONST_07  C13   C14  C15  C16    0.00   0.0  0
 W30  CONST_08  C13   C12  N11  C16    0.00   0.0  0
 W30  CONST_09  C12   C13  C14  C15    0.00   0.0  0
 W30  CONST_10  C12   N11  C16  C15    0.00   0.0  0
 W30  CONST_11  N11   C12  C13  C14    0.00   0.0  0
 W30  CONST_12  N11   C16  C15  C14    0.00   0.0  0
 W30  CONST_13  C02   C03  C04  C07  180.00   0.0  0
 W30  CONST_14  C06   C05  C04  C07  180.00   0.0  0
 W30  CONST_15  N02   C02  N01  C06  180.00   0.0  0
 W30  CONST_16  N02   C02  C03  C04  180.00   0.0  0
 W30  CONST_17  C08   C06  C05  C04  180.00   0.0  0
 W30  CONST_18  C08   C06  N01  C02  180.00   0.0  0
 W30  CONST_19  N11   C12  C13  C09  180.00   0.0  0
 W30  CONST_20  C15   C14  C13  C09  180.00   0.0  0
 W30  CONST_21  N17   C15  C14  C13  180.00   0.0  0
 W30  CONST_22  N17   C15  C16  N11  180.00   0.0  0
 W30  CONST_23  H03   C03  C04  C05  180.00   0.0  0
 W30  CONST_24  H05   C05  C04  C03  180.00   0.0  0
 W30  CONST_25  H14   C14  C15  C16  180.00   0.0  0
 W30  CONST_26  H12   C12  N11  C16  180.00   0.0  0
 W30  CONST_27  H16   C16  C15  C14  180.00   0.0  0
 W30  CONST_28  C18   N17  C15  C16  180.00   0.0  0
 W30  CONST_29  C19   N17  C15  C16    0.00   0.0  0
 W30  CONST_30  C18   N17  C15  C14    0.00   0.0  0
 W30  CONST_31  C19   N17  C15  C14  180.00   0.0  0
 W30  Var_01    C13   C09  C08  C06  177.41  30.0  3
 W30  Var_02    C09   C08  C06  C05  112.92  30.0  2
 W30  Var_03    C12   C13  C09  C08   97.43  30.0  2
 W30  Var_04    H071  C07  C04  C05   75.96  30.0  2
 W30  Var_05    C20   C19  N17  C15   74.01  30.0  3
 W30  Var_06    H181  C18  N17  C15   57.92  30.0  3
 W30  Var_07    O21   C20  C19  N17   62.04  30.0  3
 W30  Var_08    H221  C22  O21  C20  -61.18  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
 W30  plan-1  C07   0.020
 W30  plan-1  C06   0.020
 W30  plan-1  C05   0.020
 W30  plan-1  C04   0.020
 W30  plan-1  C03   0.020
 W30  plan-1  C02   0.020
 W30  plan-1  N02   0.020
 W30  plan-1  N01   0.020
 W30  plan-1  H03   0.020
 W30  plan-1  H05   0.020
 W30  plan-1  C08   0.020
 W30  plan-2  C09   0.020
 W30  plan-2  C16   0.020
 W30  plan-2  C15   0.020
 W30  plan-2  C14   0.020
 W30  plan-2  C13   0.020
 W30  plan-2  C12   0.020
 W30  plan-2  N11   0.020
 W30  plan-2  H12   0.020
 W30  plan-2  H14   0.020
 W30  plan-2  H16   0.020
 W30  plan-2  N17   0.020
 W30  plan-3  C02   0.020
 W30  plan-3  N02   0.020
 W30  plan-3  H021  0.020
 W30  plan-3  H022  0.020
 W30  plan-4  C15   0.020
 W30  plan-4  C18   0.020
 W30  plan-4  C19   0.020
 W30  plan-4  N17   0.020

