# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 23 12:42:35 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 6,6'-{[(2S)-3-aminopropane-1,2-diyl]bis(oxymethanediyl)}bis(4-methylpyridin-2-amine)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(COC[C@H](CN)OCc2cc(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
 1Q6  1Q6  6,6'-{[(2S)-3-aminopropane-1,2-diyl]bis(oxymethanediyl)}bis(4-methylpyridin-2-amine)  ligand  49  24  .  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_1Q6
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
 1Q6  N22  N  NH2   0  -0.839   5.0394  -2.4636   2.0163
 1Q6  C22  C  CR6   0   0.446   4.4348  -1.8232   0.9736
 1Q6  C23  C  CR16  0  -0.444   4.8009  -2.1118  -0.3539
 1Q6  C24  C  CR6   0   0.208   4.2062  -1.4091  -1.3794
 1Q6  C27  C  CH3   0  -0.727   4.5532  -1.6797  -2.8112
 1Q6  C25  C  CR16  0  -0.426   3.2586  -0.4283  -1.0550
 1Q6  N21  N  N     0  -0.492   3.5292  -0.9006   1.2715
 1Q6  C26  C  CR6   0   0.198   2.9599  -0.2183   0.2758
 1Q6  C28  C  CH2   0  -0.165   1.9642   0.8114   0.7382
 1Q6  O29  O  O2    0  -0.490   1.3216   1.4044  -0.3513
 1Q6  C11  C  CH1   0   0.018   0.6818   2.6339  -0.0869
 1Q6  C12  C  CH2   0  -0.302   0.2556   3.2082  -1.4284
 1Q6  N13  N  NH2   0  -0.804   1.4152   3.4716  -2.2664
 1Q6  C10  C  CH2   0  -0.175  -0.4761   2.4966   0.8876
 1Q6  O09  O  O2    0  -0.477  -1.4016   1.5621   0.3995
 1Q6  C08  C  CH2   0  -0.153  -2.5009   1.3922   1.2437
 1Q6  C06  C  CR6   0   0.190  -3.4001   0.3004   0.7344
 1Q6  C05  C  CR16  0  -0.423  -3.0822  -0.4741  -0.3628
 1Q6  N01  N  N     0  -0.492  -4.5160   0.1399   1.4482
 1Q6  C02  C  CR6   0   0.444  -5.3690  -0.8105   1.0885
 1Q6  N02  N  NH2   0  -0.838  -6.5230  -0.9189   1.8116
 1Q6  C03  C  CR16  0  -0.443  -5.1330  -1.6490  -0.0158
 1Q6  C04  C  CR6   0   0.208  -3.9774  -1.4810  -0.7485
 1Q6  C07  C  CH3   0  -0.727  -3.6770  -2.3468  -1.9334
 1Q6  H1   H  HNH2  0   0.388   5.4842  -3.3457   1.8256
 1Q6  H2   H  HNH2  0   0.380   4.5584  -2.4276   2.9000
 1Q6  H3   H  HCR6  0   0.255   5.5394  -2.8776  -0.5583
 1Q6  H4   H  HCH3  0   0.252   3.6752  -2.0128  -3.3667
 1Q6  H5   H  HCH3  0   0.251   4.9149  -0.7748  -3.3015
 1Q6  H6   H  HCH3  0   0.247   5.3222  -2.4452  -2.9037
 1Q6  H7   H  HCR6  0   0.249   2.7773   0.1442  -1.8352
 1Q6  H8   H  HCH2  0   0.225   1.2523   0.3190   1.4139
 1Q6  H9   H  HCH2  0   0.224   2.4977   1.5598   1.3421
 1Q6  H10  H  HCH1  0   0.214   1.3947   3.3356   0.3754
 1Q6  H11  H  HCH2  0   0.207  -0.4861   2.5426  -1.8893
 1Q6  H12  H  HCH2  0   0.223  -0.2501   4.1572  -1.2362
 1Q6  H13  H  HNH2  0   0.342   1.8281   2.5938  -2.5536
 1Q6  H14  H  HNH2  0   0.349   1.1134   3.9230  -3.1200
 1Q6  H16  H  HCH2  0   0.220  -0.1072   2.1949   1.8790
 1Q6  H17  H  HCH2  0   0.218  -0.9357   3.4868   1.0204
 1Q6  H18  H  HCH2  0   0.220  -2.1804   1.1326   2.2642
 1Q6  H19  H  HCH2  0   0.221  -3.0840   2.3206   1.3340
 1Q6  H20  H  HCR6  0   0.250  -2.1621  -0.3180  -0.9082
 1Q6  H21  H  HNH2  0   0.379  -6.5070  -0.4995   2.7270
 1Q6  H22  H  HNH2  0   0.388  -7.0067  -1.8009   1.7782
 1Q6  H23  H  HCR6  0   0.255  -5.8532  -2.4141  -0.2806
 1Q6  H24  H  HCH3  0   0.252  -3.6268  -1.7499  -2.8455
 1Q6  H25  H  HCH3  0   0.251  -2.7092  -2.8375  -1.8220
 1Q6  H26  H  HCH3  0   0.246  -4.4351  -3.1155  -2.0738

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
 1Q6  C07  C04  single    1.498  0.020  1.498
 1Q6  C04  C03  aromatic  1.379  0.020  1.379
 1Q6  C04  C05  aromatic  1.401  0.020  1.401
 1Q6  C03  C02  aromatic  1.407  0.020  1.407
 1Q6  C05  C06  aromatic  1.380  0.020  1.380
 1Q6  C02  N02  single    1.366  0.020  1.366
 1Q6  C02  N01  aromatic  1.327  0.020  1.327
 1Q6  N13  C12  single    1.455  0.020  1.455
 1Q6  C12  C11  single    1.520  0.020  1.520
 1Q6  C06  N01  aromatic  1.334  0.020  1.334
 1Q6  C06  C08  single    1.503  0.020  1.503
 1Q6  C10  O09  single    1.403  0.020  1.403
 1Q6  C10  C11  single    1.520  0.020  1.520
 1Q6  O09  C08  single    1.396  0.020  1.396
 1Q6  C11  O29  single    1.411  0.020  1.411
 1Q6  O29  C28  single    1.397  0.020  1.397
 1Q6  C27  C24  single    1.498  0.020  1.498
 1Q6  C25  C24  aromatic  1.402  0.020  1.402
 1Q6  C25  C26  aromatic  1.380  0.020  1.380
 1Q6  C28  C26  single    1.505  0.020  1.505
 1Q6  C24  C23  aromatic  1.378  0.020  1.378
 1Q6  C26  N21  aromatic  1.335  0.020  1.335
 1Q6  C23  C22  aromatic  1.407  0.020  1.407
 1Q6  N21  C22  aromatic  1.327  0.020  1.327
 1Q6  C22  N22  single    1.365  0.020  1.365
 1Q6  N22  H1   single    0.890  0.020  1.040
 1Q6  N22  H2   single    0.890  0.020  1.040
 1Q6  C23  H3   single    0.930  0.020  1.080
 1Q6  C27  H4   single    0.970  0.020  1.090
 1Q6  C27  H5   single    0.970  0.020  1.090
 1Q6  C27  H6   single    0.970  0.020  1.090
 1Q6  C25  H7   single    0.930  0.020  1.080
 1Q6  C28  H8   single    0.970  0.020  1.090
 1Q6  C28  H9   single    0.970  0.020  1.090
 1Q6  C11  H10  single    0.970  0.020  1.090
 1Q6  C12  H11  single    0.970  0.020  1.090
 1Q6  C12  H12  single    0.970  0.020  1.090
 1Q6  N13  H13  single    0.890  0.020  1.040
 1Q6  N13  H14  single    0.890  0.020  1.040
 1Q6  C10  H16  single    0.970  0.020  1.090
 1Q6  C10  H17  single    0.970  0.020  1.090
 1Q6  C08  H18  single    0.970  0.020  1.090
 1Q6  C08  H19  single    0.970  0.020  1.090
 1Q6  C05  H20  single    0.930  0.020  1.080
 1Q6  N02  H21  single    0.890  0.020  1.040
 1Q6  N02  H22  single    0.890  0.020  1.040
 1Q6  C03  H23  single    0.930  0.020  1.080
 1Q6  C07  H24  single    0.970  0.020  1.090
 1Q6  C07  H25  single    0.970  0.020  1.090
 1Q6  C07  H26  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
 1Q6  H2   N22  H1   114.14  3.000
 1Q6  H2   N22  C22  116.24  3.000
 1Q6  H1   N22  C22  117.54  3.000
 1Q6  N21  C22  C23  122.15  3.000
 1Q6  N21  C22  N22  117.20  3.000
 1Q6  C23  C22  N22  120.62  3.000
 1Q6  H3   C23  C24  120.94  3.000
 1Q6  H3   C23  C22  120.03  3.000
 1Q6  C24  C23  C22  119.03  3.000
 1Q6  C25  C24  C27  120.28  3.000
 1Q6  C25  C24  C23  118.44  3.000
 1Q6  C27  C24  C23  121.28  3.000
 1Q6  H6   C27  H5   108.11  3.000
 1Q6  H6   C27  H4   108.08  3.000
 1Q6  H5   C27  H4   106.94  3.000
 1Q6  H6   C27  C24  111.83  3.000
 1Q6  H5   C27  C24  110.88  3.000
 1Q6  H4   C27  C24  110.81  3.000
 1Q6  H7   C25  C26  121.28  3.000
 1Q6  H7   C25  C24  120.30  3.000
 1Q6  C26  C25  C24  118.42  3.000
 1Q6  C26  N21  C22  118.63  3.000
 1Q6  C28  C26  N21  113.75  3.000
 1Q6  N21  C26  C25  123.33  3.000
 1Q6  C28  C26  C25  122.92  3.000
 1Q6  H9   C28  H8   106.36  3.000
 1Q6  H9   C28  O29  111.26  3.000
 1Q6  H8   C28  O29  111.85  3.000
 1Q6  H9   C28  C26  108.26  3.000
 1Q6  H8   C28  C26  108.13  3.000
 1Q6  O29  C28  C26  110.80  3.000
 1Q6  C11  O29  C28  115.62  3.000
 1Q6  H10  C11  C10  106.35  3.000
 1Q6  H10  C11  C12  108.12  3.000
 1Q6  C10  C11  C12  112.73  3.000
 1Q6  H10  C11  O29  109.88  3.000
 1Q6  C10  C11  O29  112.76  3.000
 1Q6  C12  C11  O29  106.91  3.000
 1Q6  H12  C12  H11  106.72  3.000
 1Q6  H12  C12  N13  108.25  3.000
 1Q6  H11  C12  N13  113.98  3.000
 1Q6  H12  C12  C11  107.62  3.000
 1Q6  H11  C12  C11  109.32  3.000
 1Q6  N13  C12  C11  110.69  3.000
 1Q6  H14  N13  H13  105.63  3.000
 1Q6  H14  N13  C12  109.21  3.000
 1Q6  H13  N13  C12  109.38  3.000
 1Q6  H17  C10  H16  106.16  3.000
 1Q6  H17  C10  O09  111.47  3.000
 1Q6  H16  C10  O09  110.62  3.000
 1Q6  H17  C10  C11  108.33  3.000
 1Q6  H16  C10  C11  110.32  3.000
 1Q6  O09  C10  C11  109.86  3.000
 1Q6  C08  O09  C10  112.96  3.000
 1Q6  H19  C08  H18  106.10  3.000
 1Q6  H19  C08  C06  108.89  3.000
 1Q6  H18  C08  C06  108.48  3.000
 1Q6  H19  C08  O09  111.36  3.000
 1Q6  H18  C08  O09  111.09  3.000
 1Q6  C06  C08  O09  110.76  3.000
 1Q6  N01  C06  C05  123.39  3.000
 1Q6  N01  C06  C08  113.97  3.000
 1Q6  C05  C06  C08  122.63  3.000
 1Q6  H20  C05  C04  120.57  3.000
 1Q6  H20  C05  C06  121.07  3.000
 1Q6  C04  C05  C06  118.35  3.000
 1Q6  C02  N01  C06  118.61  3.000
 1Q6  C03  C02  N02  120.66  3.000
 1Q6  N02  C02  N01  117.16  3.000
 1Q6  C03  C02  N01  122.14  3.000
 1Q6  H22  N02  H21  113.75  3.000
 1Q6  H22  N02  C02  117.26  3.000
 1Q6  H21  N02  C02  115.76  3.000
 1Q6  H23  C03  C04  120.88  3.000
 1Q6  H23  C03  C02  120.08  3.000
 1Q6  C04  C03  C02  119.03  3.000
 1Q6  C07  C04  C03  121.21  3.000
 1Q6  C03  C04  C05  118.47  3.000
 1Q6  C07  C04  C05  120.32  3.000
 1Q6  H26  C07  H25  108.26  3.000
 1Q6  H26  C07  H24  108.09  3.000
 1Q6  H25  C07  H24  106.89  3.000
 1Q6  H26  C07  C04  111.74  3.000
 1Q6  H25  C07  C04  110.93  3.000
 1Q6  H24  C07  C04  110.75  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
 1Q6  CONST_01  C25  C24  C23  C22     0.00   0.0  0
 1Q6  CONST_02  C25  C26  N21  C22     0.00   0.0  0
 1Q6  CONST_03  C26  C25  C24  C23     0.00   0.0  0
 1Q6  CONST_04  C26  N21  C22  C23     0.00   0.0  0
 1Q6  CONST_05  N21  C26  C25  C24     0.00   0.0  0
 1Q6  CONST_06  N21  C22  C23  C24     0.00   0.0  0
 1Q6  CONST_07  C03  C04  C05  C06     0.00   0.0  0
 1Q6  CONST_08  C03  C02  N01  C06     0.00   0.0  0
 1Q6  CONST_09  C02  C03  C04  C05     0.00   0.0  0
 1Q6  CONST_10  C02  N01  C06  C05     0.00   0.0  0
 1Q6  CONST_11  C04  C03  C02  N01     0.00   0.0  0
 1Q6  CONST_12  C04  C05  C06  N01     0.00   0.0  0
 1Q6  CONST_13  C24  C23  C22  N22   180.00   0.0  0
 1Q6  CONST_14  C26  N21  C22  N22   180.00   0.0  0
 1Q6  CONST_15  C27  C24  C23  C22   180.00   0.0  0
 1Q6  CONST_16  C28  C26  N21  C22   180.00   0.0  0
 1Q6  CONST_17  C28  C26  C25  C24   180.00   0.0  0
 1Q6  CONST_18  C26  C25  C24  C27   180.00   0.0  0
 1Q6  CONST_19  C04  C05  C06  C08   180.00   0.0  0
 1Q6  CONST_20  C02  N01  C06  C08   180.00   0.0  0
 1Q6  CONST_21  C07  C04  C05  C06   180.00   0.0  0
 1Q6  CONST_22  N02  C02  N01  C06   180.00   0.0  0
 1Q6  CONST_23  C07  C04  C03  C02   180.00   0.0  0
 1Q6  CONST_24  C04  C03  C02  N02   180.00   0.0  0
 1Q6  CONST_25  H7   C25  C24  C23   180.00   0.0  0
 1Q6  CONST_26  H3   C23  C24  C25   180.00   0.0  0
 1Q6  CONST_27  H23  C03  C04  C05   180.00   0.0  0
 1Q6  CONST_28  H20  C05  C06  N01   180.00   0.0  0
 1Q6  Var_01    O29  C28  C26  C25     5.58  30.0  2
 1Q6  Var_02    C05  C06  C08  O09     4.84  30.0  2
 1Q6  Var_03    H4   C27  C24  C23   118.89  30.0  2
 1Q6  Var_04    H24  C07  C04  C05   -62.62  30.0  2
 1Q6  Var_05    C06  C08  O09  C10  -175.21  30.0  3
 1Q6  Var_06    H13  N13  C12  C11    69.52  30.0  3
 1Q6  Var_07    H16  C10  O09  C08    58.40  30.0  1

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
 1Q6  chir_01  C11  C12  C10  O29  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
 1Q6  plan-1  N22  0.020
 1Q6  plan-1  C22  0.020
 1Q6  plan-1  C23  0.020
 1Q6  plan-1  C24  0.020
 1Q6  plan-1  C27  0.020
 1Q6  plan-1  C25  0.020
 1Q6  plan-1  N21  0.020
 1Q6  plan-1  C26  0.020
 1Q6  plan-1  C28  0.020
 1Q6  plan-1  H3   0.020
 1Q6  plan-1  H7   0.020
 1Q6  plan-2  C08  0.020
 1Q6  plan-2  C06  0.020
 1Q6  plan-2  C05  0.020
 1Q6  plan-2  N01  0.020
 1Q6  plan-2  C02  0.020
 1Q6  plan-2  N02  0.020
 1Q6  plan-2  C03  0.020
 1Q6  plan-2  C04  0.020
 1Q6  plan-2  C07  0.020
 1Q6  plan-2  H20  0.020
 1Q6  plan-2  H23  0.020
 1Q6  plan-3  N22  0.020
 1Q6  plan-3  C22  0.020
 1Q6  plan-3  H1   0.020
 1Q6  plan-3  H2   0.020
 1Q6  plan-4  C02  0.020
 1Q6  plan-4  N02  0.020
 1Q6  plan-4  H21  0.020
 1Q6  plan-4  H22  0.020

