# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 08:53:52 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: (2S,4E)-N-methyl-5-(5-phenoxypyridin-3-yl)pent-4-en-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@@H](C)C/C=C/c1cncc(Oc2ccccc2)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
 7LB  7LB  (2S,4E)-N-methyl-5-(5-phenoxypyridin-3-yl)pent-4-en-2-amine  ligand  40  20  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7LB
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
 7LB  C4   C  CH3   0  -0.518  -6.3066   0.2423   1.3378
 7LB  C5   C  CH2   0  -0.493  -3.6177  -1.0439  -0.9512
 7LB  C6   C  C1    0  -0.182  -2.6468   0.0615  -0.7040
 7LB  C11  C  CR16  0  -0.143   1.5568   2.8680   0.0473
 7LB  C7   C  C1    0  -0.310  -1.3255  -0.1133  -0.6301
 7LB  C8   C  CR6   0   0.078  -0.3212   0.9263  -0.3931
 7LB  C9   C  CR16  0  -0.309   1.0130   0.5556  -0.2207
 7LB  C10  C  CR6   0   0.303   1.9646   1.5376   0.0019
 7LB  C13  C  CR16  0  -0.142  -0.6186   2.2896  -0.3374
 7LB  N3   N  NH1   0  -0.584  -5.4528   0.0939   0.1783
 7LB  C1   C  CH3   0  -0.669  -5.5553  -2.3955  -0.1039
 7LB  C15  C  CR6   0   0.294   3.7390   0.0033   0.1989
 7LB  C16  C  CR16  0  -0.300   4.1889  -0.5777  -0.9767
 7LB  C17  C  CR16  0  -0.254   4.6850  -1.8743  -0.9431
 7LB  C18  C  CR16  0  -0.254   4.7228  -2.5797   0.2525
 7LB  C19  C  CR16  0  -0.254   4.2659  -1.9842   1.4213
 7LB  C2   C  CH1   0  -0.082  -4.7008  -1.1495   0.1298
 7LB  C20  C  CR16  0  -0.298   3.7672  -0.6887   1.3999
 7LB  N12  N  N     0  -0.379   0.2936   3.2247  -0.1214
 7LB  O14  O  O2    0  -0.511   3.2885   1.3034   0.1787
 7LB  H41  H  HCH3  0   0.231  -6.8226   1.2016   1.2890
 7LB  H42  H  HCH3  0   0.194  -7.0716  -0.5350   1.4622
 7LB  H43  H  HCH3  0   0.221  -5.6980   0.2475   2.2442
 7LB  H51  H  HCH2  0   0.235  -4.1135  -0.8833  -1.9173
 7LB  H52  H  HCH2  0   0.242  -3.0892  -1.9973  -1.0308
 7LB  H6   H  H     0   0.249  -3.0809   1.0469  -0.5689
 7LB  H9L  H  HCR6  0   0.272   2.2840   3.6538   0.2228
 7LB  H7   H  H     0   0.244  -0.9275  -1.1175  -0.7515
 7LB  H9   H  HCR6  0   0.286   1.2836  -0.4928  -0.2590
 7LB  H9M  H  HCR6  0   0.255  -1.6345   2.6399  -0.4792
 7LB  H32  H  HNH1  0   0.337  -6.0076   0.1804  -0.6659
 7LB  H11  H  HCH3  0   0.226  -4.9501  -3.3027  -0.0663
 7LB  H12  H  HCH3  0   0.232  -6.3406  -2.4951   0.6467
 7LB  H13  H  HCH3  0   0.216  -6.0334  -2.3573  -1.0861
 7LB  H16  H  HCR6  0   0.275   4.1568  -0.0212  -1.9050
 7LB  H17  H  HCR6  0   0.266   5.0397  -2.3326  -1.8567
 7LB  H18  H  HCR6  0   0.262   5.1124  -3.5888   0.2750
 7LB  H19  H  HCR6  0   0.266   4.2984  -2.5282   2.3561
 7LB  H2   H  HCH1  0   0.224  -4.1982  -1.2528   1.0987
 7LB  H20  H  HCR6  0   0.276   3.4149  -0.2178   2.3090

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
 7LB  C17  C18  aromatic  1.389  0.020  1.389
 7LB  C17  C16  aromatic  1.389  0.020  1.389
 7LB  C18  C19  aromatic  1.389  0.020  1.389
 7LB  C16  C15  aromatic  1.386  0.020  1.386
 7LB  C19  C20  aromatic  1.388  0.020  1.388
 7LB  C20  C15  aromatic  1.386  0.020  1.386
 7LB  C15  O14  single    1.376  0.020  1.376
 7LB  O14  C10  single    1.356  0.020  1.356
 7LB  C10  C9   aromatic  1.385  0.020  1.385
 7LB  C10  C11  aromatic  1.392  0.020  1.392
 7LB  C9   C8   aromatic  1.395  0.020  1.395
 7LB  C7   C8   single    1.465  0.020  1.465
 7LB  C7   C6   double    1.335  0.020  1.335
 7LB  C4   N3   single    1.448  0.020  1.448
 7LB  C2   N3   single    1.454  0.020  1.454
 7LB  C2   C1   single    1.529  0.020  1.529
 7LB  C2   C5   single    1.534  0.020  1.534
 7LB  C8   C13  aromatic  1.396  0.020  1.396
 7LB  C11  N12  aromatic  1.323  0.020  1.323
 7LB  C5   C6   single    1.492  0.020  1.492
 7LB  C13  N12  aromatic  1.324  0.020  1.324
 7LB  C4   H41  single    0.970  0.020  1.090
 7LB  C4   H42  single    0.970  0.020  1.090
 7LB  C4   H43  single    0.970  0.020  1.090
 7LB  C5   H51  single    0.970  0.020  1.090
 7LB  C5   H52  single    0.970  0.020  1.090
 7LB  C6   H6   single    0.930  0.020  1.080
 7LB  C11  H9L  single    0.930  0.020  1.080
 7LB  C7   H7   single    0.930  0.020  1.080
 7LB  C9   H9   single    0.930  0.020  1.080
 7LB  C13  H9M  single    0.930  0.020  1.080
 7LB  N3   H32  single    0.890  0.020  1.040
 7LB  C1   H11  single    0.970  0.020  1.090
 7LB  C1   H12  single    0.970  0.020  1.090
 7LB  C1   H13  single    0.970  0.020  1.090
 7LB  C16  H16  single    0.930  0.020  1.080
 7LB  C17  H17  single    0.930  0.020  1.080
 7LB  C18  H18  single    0.930  0.020  1.080
 7LB  C19  H19  single    0.930  0.020  1.080
 7LB  C2   H2   single    0.970  0.020  1.090
 7LB  C20  H20  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
 7LB  H43  C4   H42  107.32  3.000
 7LB  H43  C4   H41  107.27  3.000
 7LB  H42  C4   H41  107.36  3.000
 7LB  H43  C4   N3   109.67  3.000
 7LB  H42  C4   N3   115.42  3.000
 7LB  H41  C4   N3   109.48  3.000
 7LB  H52  C5   H51  106.37  3.000
 7LB  H52  C5   C2   109.43  3.000
 7LB  H51  C5   C2   108.14  3.000
 7LB  H52  C5   C6   110.11  3.000
 7LB  H51  C5   C6   109.35  3.000
 7LB  C2   C5   C6   113.19  3.000
 7LB  H6   C6   C7   120.53  3.000
 7LB  H6   C6   C5   115.66  3.000
 7LB  C7   C6   C5   123.81  3.000
 7LB  H9L  C11  N12  117.72  3.000
 7LB  H9L  C11  C10  120.07  3.000
 7LB  N12  C11  C10  122.21  3.000
 7LB  H7   C7   C8   115.00  3.000
 7LB  H7   C7   C6   118.50  3.000
 7LB  C8   C7   C6   126.49  3.000
 7LB  C13  C8   C9   117.26  3.000
 7LB  C13  C8   C7   123.59  3.000
 7LB  C9   C8   C7   119.14  3.000
 7LB  H9   C9   C10  121.33  3.000
 7LB  H9   C9   C8   119.45  3.000
 7LB  C10  C9   C8   119.22  3.000
 7LB  O14  C10  C9   124.69  3.000
 7LB  C9   C10  C11  118.78  3.000
 7LB  O14  C10  C11  116.53  3.000
 7LB  H9M  C13  N12  116.03  3.000
 7LB  H9M  C13  C8   120.66  3.000
 7LB  N12  C13  C8   123.31  3.000
 7LB  H32  N3   C2   109.16  3.000
 7LB  H32  N3   C4   109.59  3.000
 7LB  C2   N3   C4   114.81  3.000
 7LB  H13  C1   H12  107.85  3.000
 7LB  H13  C1   H11  107.62  3.000
 7LB  H12  C1   H11  107.44  3.000
 7LB  H13  C1   C2   110.69  3.000
 7LB  H12  C1   C2   111.82  3.000
 7LB  H11  C1   C2   111.24  3.000
 7LB  O14  C15  C20  119.40  3.000
 7LB  O14  C15  C16  119.32  3.000
 7LB  C20  C15  C16  121.25  3.000
 7LB  H16  C16  C17  120.74  3.000
 7LB  H16  C16  C15  120.13  3.000
 7LB  C17  C16  C15  119.12  3.000
 7LB  H17  C17  C18  120.19  3.000
 7LB  H17  C17  C16  119.48  3.000
 7LB  C18  C17  C16  120.32  3.000
 7LB  H18  C18  C19  120.05  3.000
 7LB  H18  C18  C17  120.10  3.000
 7LB  C19  C18  C17  119.85  3.000
 7LB  H19  C19  C20  119.55  3.000
 7LB  H19  C19  C18  120.10  3.000
 7LB  C20  C19  C18  120.35  3.000
 7LB  H2   C2   C1   108.33  3.000
 7LB  H2   C2   N3   106.75  3.000
 7LB  C1   C2   N3   114.39  3.000
 7LB  H2   C2   C5   107.79  3.000
 7LB  C1   C2   C5   110.07  3.000
 7LB  N3   C2   C5   109.26  3.000
 7LB  H20  C20  C19  120.65  3.000
 7LB  H20  C20  C15  120.24  3.000
 7LB  C19  C20  C15  119.10  3.000
 7LB  C13  N12  C11  119.21  3.000
 7LB  C15  O14  C10  118.99  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
 7LB  CONST_01  C8   C9   C10  C11    0.00   0.0  0
 7LB  CONST_02  C8   C13  N12  C11    0.00   0.0  0
 7LB  CONST_03  N12  C11  C10  C9     0.00   0.0  0
 7LB  CONST_04  N12  C13  C8   C9     0.00   0.0  0
 7LB  CONST_05  C13  C8   C9   C10    0.00   0.0  0
 7LB  CONST_06  C13  N12  C11  C10    0.00   0.0  0
 7LB  CONST_07  C18  C17  C16  C15    0.00   0.0  0
 7LB  CONST_08  C18  C19  C20  C15    0.00   0.0  0
 7LB  CONST_09  C19  C18  C17  C16    0.00   0.0  0
 7LB  CONST_10  C19  C20  C15  C16    0.00   0.0  0
 7LB  CONST_11  C20  C19  C18  C17    0.00   0.0  0
 7LB  CONST_12  C20  C15  C16  C17    0.00   0.0  0
 7LB  CONST_13  C10  C9   C8   C7   180.00   0.0  0
 7LB  CONST_14  N12  C13  C8   C7   180.00   0.0  0
 7LB  CONST_15  O14  C10  C9   C8   180.00   0.0  0
 7LB  CONST_16  O14  C15  C16  C17  180.00   0.0  0
 7LB  CONST_17  O14  C15  C20  C19  180.00   0.0  0
 7LB  CONST_18  O14  C10  C11  N12  180.00   0.0  0
 7LB  CONST_19  H9   C9   C10  C11  180.00   0.0  0
 7LB  CONST_20  H9M  C13  N12  C11  180.00   0.0  0
 7LB  CONST_21  H9L  C11  C10  C9   180.00   0.0  0
 7LB  CONST_22  H17  C17  C16  C15  180.00   0.0  0
 7LB  CONST_23  H19  C19  C20  C15  180.00   0.0  0
 7LB  CONST_24  H18  C18  C17  C16  180.00   0.0  0
 7LB  CONST_25  H20  C20  C15  C16  180.00   0.0  0
 7LB  CONST_26  H16  C16  C17  C18  180.00   0.0  0
 7LB  Var_01    C16  C15  O14  C10   93.10  30.0  2
 7LB  Var_02    C9   C8   C7   C6   174.07  30.0  2
 7LB  Var_03    C8   C7   C6   C5   179.88   0.0  2
 7LB  Var_04    C2   C5   C6   C7   124.43  30.0  2
 7LB  Var_05    H41  C4   N3   C2   179.71  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
 7LB  chir_01  C2  N3  C1  C5  negativ

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
 7LB  plan-1  C11  0.020
 7LB  plan-1  C7   0.020
 7LB  plan-1  C8   0.020
 7LB  plan-1  C9   0.020
 7LB  plan-1  C10  0.020
 7LB  plan-1  C13  0.020
 7LB  plan-1  N12  0.020
 7LB  plan-1  O14  0.020
 7LB  plan-1  H9L  0.020
 7LB  plan-1  H9   0.020
 7LB  plan-1  H9M  0.020
 7LB  plan-2  C15  0.020
 7LB  plan-2  C16  0.020
 7LB  plan-2  C17  0.020
 7LB  plan-2  C18  0.020
 7LB  plan-2  C19  0.020
 7LB  plan-2  C20  0.020
 7LB  plan-2  O14  0.020
 7LB  plan-2  H16  0.020
 7LB  plan-2  H17  0.020
 7LB  plan-2  H18  0.020
 7LB  plan-2  H19  0.020
 7LB  plan-2  H20  0.020
 7LB  plan-3  C5   0.020
 7LB  plan-3  C6   0.020
 7LB  plan-3  C7   0.020
 7LB  plan-3  C8   0.020
 7LB  plan-3  H6   0.020
 7LB  plan-3  H7   0.020

