# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 20:46:20 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 6-({[(3R,5S)-5-{[(6-amino-4-methylpyridin-2-yl)methoxy]methyl}pyrrolidin-3-yl]oxy}methyl)-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(COC[C@@H]2C[C@H](CN2)OCc3cc(C)cc(N)n3)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
 QJ8  QJ8  6-({[(3R,5S)-5-{[(6-amino-4-methylpyridin-2-yl)methoxy]methyl}pyrrolidin-3-yl]oxy}methyl)-4-methylpyridin-2-amine  ligand  53  26  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QJ8
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
 QJ8  N22  N  NH2   0  -0.839  -8.3670   0.1143   1.8588
 QJ8  C22  C  CR6   0   0.445  -7.4233  -0.0875   0.8929
 QJ8  C23  C  CR16  0  -0.444  -7.7924  -0.5382  -0.3876
 QJ8  C24  C  CR6   0   0.208  -6.8186  -0.6829  -1.3523
 QJ8  C27  C  CH3   0  -0.726  -7.1566  -1.1542  -2.7331
 QJ8  C25  C  CR16  0  -0.425  -5.4937  -0.3725  -1.0161
 QJ8  N21  N  N     0  -0.492  -6.1658   0.1994   1.2047
 QJ8  C26  C  CR6   0   0.195  -5.2268   0.0601   0.2669
 QJ8  C12  C  CH2   0  -0.168  -3.8435   0.4217   0.7330
 QJ8  O11  O  O2    0  -0.494  -2.9081   0.2113  -0.2862
 QJ8  C4'  C  CH1   0   0.083  -1.6148   0.6579   0.0326
 QJ8  C5'  C  CH2   0  -0.319  -0.8972  -0.1558   1.1125
 QJ8  N1'  N  NH1   0  -0.613   0.4886   0.1452   0.8189
 QJ8  C3'  C  CH2   0  -0.512  -0.6896   0.5221  -1.1844
 QJ8  C2'  C  CH1   0  -0.099   0.6348  -0.0230  -0.6221
 QJ8  C10  C  CH2   0  -0.127   1.8382   0.7200  -1.1537
 QJ8  O09  O  O2    0  -0.489   2.9995   0.1905  -0.5623
 QJ8  C08  C  CH2   0  -0.158   4.1734   0.7878  -1.0287
 QJ8  C06  C  CR6   0   0.194   5.3745   0.2529  -0.2990
 QJ8  N01  N  N     0  -0.493   6.5394   0.6787  -0.7912
 QJ8  C02  C  CR6   0   0.447   7.6607   0.2786  -0.2050
 QJ8  N02  N  NH2   0  -0.839   8.8364   0.6896  -0.7634
 QJ8  C03  C  CR16  0  -0.446   7.6569  -0.5710   0.9163
 QJ8  C04  C  CR6   0   0.207   6.4511  -1.0080   1.4218
 QJ8  C05  C  CR16  0  -0.429   5.2717  -0.5850   0.7930
 QJ8  C07  C  CH3   0  -0.736   6.3893  -1.9163   2.6116
 QJ8  H1   H  HNH2  0   0.388  -9.2397  -0.3781   1.7642
 QJ8  H2   H  HNH2  0   0.379  -8.0266   0.1626   2.8054
 QJ8  H3   H  HCR6  0   0.256  -8.8287  -0.7652  -0.6071
 QJ8  H4   H  HCH3  0   0.252  -6.9011  -0.3944  -3.4734
 QJ8  H5   H  HCH3  0   0.251  -6.5898  -2.0502  -2.9902
 QJ8  H6   H  HCH3  0   0.246  -8.2163  -1.3821  -2.8352
 QJ8  H7   H  HCR6  0   0.249  -4.7056  -0.4736  -1.7488
 QJ8  H8   H  HCH2  0   0.223  -3.8445   1.4733   1.0567
 QJ8  H9   H  HCH2  0   0.225  -3.6108  -0.1732   1.6272
 QJ8  H10  H  HCH1  0   0.215  -1.6556   1.7073   0.3554
 QJ8  H11  H  HCH2  0   0.236  -1.1565   0.1409   2.1304
 QJ8  H12  H  HCH2  0   0.200  -1.1567  -1.2203   0.9924
 QJ8  H13  H  HNH1  0   0.351   1.1251  -0.4459   1.3357
 QJ8  H15  H  HCH2  0   0.251  -1.1191  -0.1696  -1.9096
 QJ8  H16  H  HCH2  0   0.246  -0.5575   1.4814  -1.6893
 QJ8  H17  H  HCH1  0   0.220   0.7309  -1.0842  -0.8990
 QJ8  H18  H  HCH2  0   0.203   1.8810   0.6244  -2.2487
 QJ8  H19  H  HCH2  0   0.197   1.7382   1.7913  -0.9248
 QJ8  H20  H  HCH2  0   0.221   4.3043   0.6171  -2.1071
 QJ8  H21  H  HCH2  0   0.221   4.1420   1.8799  -0.8946
 QJ8  H22  H  HNH2  0   0.380   8.7864   1.4980  -1.3614
 QJ8  H23  H  HNH2  0   0.387   9.6625   0.6529  -0.1903
 QJ8  H24  H  HCR6  0   0.254   8.5925  -0.8708   1.3731
 QJ8  H25  H  HCR6  0   0.254   4.3083  -0.9031   1.1658
 QJ8  H26  H  HCH3  0   0.255   5.7604  -1.4901   3.3944
 QJ8  H27  H  HCH3  0   0.258   5.9512  -2.8778   2.3388
 QJ8  H28  H  HCH3  0   0.249   7.3771  -2.1004   3.0316

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
 QJ8  C07  C04  single    1.498  0.020  1.498
 QJ8  C04  C03  aromatic  1.378  0.020  1.378
 QJ8  C04  C05  aromatic  1.402  0.020  1.402
 QJ8  C03  C02  aromatic  1.407  0.020  1.407
 QJ8  C05  C06  aromatic  1.380  0.020  1.380
 QJ8  C02  N02  single    1.365  0.020  1.365
 QJ8  C02  N01  aromatic  1.327  0.020  1.327
 QJ8  C06  N01  aromatic  1.334  0.020  1.334
 QJ8  C06  C08  single    1.504  0.020  1.504
 QJ8  O09  C08  single    1.397  0.020  1.397
 QJ8  O09  C10  single    1.407  0.020  1.407
 QJ8  C3'  C2'  single    1.539  0.020  1.539
 QJ8  C3'  C4'  single    1.535  0.020  1.535
 QJ8  C10  C2'  single    1.511  0.020  1.511
 QJ8  C2'  N1'  single    1.458  0.020  1.458
 QJ8  C4'  O11  single    1.405  0.020  1.405
 QJ8  C4'  C5'  single    1.531  0.020  1.531
 QJ8  O11  C12  single    1.399  0.020  1.399
 QJ8  C12  C26  single    1.504  0.020  1.504
 QJ8  C25  C26  aromatic  1.380  0.020  1.380
 QJ8  C25  C24  aromatic  1.402  0.020  1.402
 QJ8  C26  N21  aromatic  1.334  0.020  1.334
 QJ8  C27  C24  single    1.498  0.020  1.498
 QJ8  C24  C23  aromatic  1.378  0.020  1.378
 QJ8  N21  C22  aromatic  1.327  0.020  1.327
 QJ8  C23  C22  aromatic  1.407  0.020  1.407
 QJ8  C22  N22  single    1.365  0.020  1.365
 QJ8  N1'  C5'  single    1.448  0.020  1.448
 QJ8  N22  H1   single    0.890  0.020  1.040
 QJ8  N22  H2   single    0.890  0.020  1.040
 QJ8  C23  H3   single    0.930  0.020  1.080
 QJ8  C27  H4   single    0.970  0.020  1.090
 QJ8  C27  H5   single    0.970  0.020  1.090
 QJ8  C27  H6   single    0.970  0.020  1.090
 QJ8  C25  H7   single    0.930  0.020  1.080
 QJ8  C12  H8   single    0.970  0.020  1.090
 QJ8  C12  H9   single    0.970  0.020  1.090
 QJ8  C4'  H10  single    0.970  0.020  1.090
 QJ8  C5'  H11  single    0.970  0.020  1.090
 QJ8  C5'  H12  single    0.970  0.020  1.090
 QJ8  N1'  H13  single    0.890  0.020  1.040
 QJ8  C3'  H15  single    0.970  0.020  1.090
 QJ8  C3'  H16  single    0.970  0.020  1.090
 QJ8  C2'  H17  single    0.970  0.020  1.090
 QJ8  C10  H18  single    0.970  0.020  1.090
 QJ8  C10  H19  single    0.970  0.020  1.090
 QJ8  C08  H20  single    0.970  0.020  1.090
 QJ8  C08  H21  single    0.970  0.020  1.090
 QJ8  N02  H22  single    0.890  0.020  1.040
 QJ8  N02  H23  single    0.890  0.020  1.040
 QJ8  C03  H24  single    0.930  0.020  1.080
 QJ8  C05  H25  single    0.930  0.020  1.080
 QJ8  C07  H26  single    0.970  0.020  1.090
 QJ8  C07  H27  single    0.970  0.020  1.090
 QJ8  C07  H28  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
 QJ8  H2   N22  H1   113.89  3.000
 QJ8  H2   N22  C22  116.00  3.000
 QJ8  H1   N22  C22  117.42  3.000
 QJ8  N21  C22  C23  122.13  3.000
 QJ8  C23  C22  N22  120.66  3.000
 QJ8  N21  C22  N22  117.18  3.000
 QJ8  H3   C23  C24  120.80  3.000
 QJ8  H3   C23  C22  120.17  3.000
 QJ8  C24  C23  C22  119.03  3.000
 QJ8  C25  C24  C27  120.27  3.000
 QJ8  C27  C24  C23  121.26  3.000
 QJ8  C25  C24  C23  118.47  3.000
 QJ8  H6   C27  H5   108.16  3.000
 QJ8  H6   C27  H4   108.07  3.000
 QJ8  H5   C27  H4   106.88  3.000
 QJ8  H6   C27  C24  111.83  3.000
 QJ8  H5   C27  C24  111.01  3.000
 QJ8  H4   C27  C24  110.70  3.000
 QJ8  H7   C25  C26  121.23  3.000
 QJ8  H7   C25  C24  120.39  3.000
 QJ8  C26  C25  C24  118.37  3.000
 QJ8  C26  N21  C22  118.63  3.000
 QJ8  C12  C26  N21  113.85  3.000
 QJ8  N21  C26  C25  123.37  3.000
 QJ8  C12  C26  C25  122.78  3.000
 QJ8  H9   C12  H8   106.15  3.000
 QJ8  H9   C12  O11  111.70  3.000
 QJ8  H8   C12  O11  111.01  3.000
 QJ8  H9   C12  C26  108.48  3.000
 QJ8  H8   C12  C26  108.67  3.000
 QJ8  O11  C12  C26  110.67  3.000
 QJ8  C4'  O11  C12  113.72  3.000
 QJ8  H10  C4'  C3'  109.87  3.000
 QJ8  H10  C4'  C5'  108.53  3.000
 QJ8  C3'  C4'  C5'  103.29  3.000
 QJ8  H10  C4'  O11  109.64  3.000
 QJ8  C5'  C4'  O11  115.00  3.000
 QJ8  C3'  C4'  O11  110.30  3.000
 QJ8  H12  C5'  H11  107.95  3.000
 QJ8  H12  C5'  N1'  113.82  3.000
 QJ8  H11  C5'  N1'  111.09  3.000
 QJ8  H12  C5'  C4'  109.03  3.000
 QJ8  H11  C5'  C4'  113.71  3.000
 QJ8  N1'  C5'  C4'  101.24  3.000
 QJ8  H13  N1'  C2'  112.00  3.000
 QJ8  H13  N1'  C5'  112.17  3.000
 QJ8  C2'  N1'  C5'  105.81  3.000
 QJ8  H16  C3'  H15  107.31  3.000
 QJ8  H16  C3'  C2'  112.08  3.000
 QJ8  H15  C3'  C2'  110.94  3.000
 QJ8  H16  C3'  C4'  111.21  3.000
 QJ8  H15  C3'  C4'  110.25  3.000
 QJ8  C2'  C3'  C4'  105.10  3.000
 QJ8  H17  C2'  C10  108.42  3.000
 QJ8  H17  C2'  C3'  108.95  3.000
 QJ8  C10  C2'  C3'  112.51  3.000
 QJ8  H17  C2'  N1'  111.62  3.000
 QJ8  C10  C2'  N1'  111.77  3.000
 QJ8  C3'  C2'  N1'  103.53  3.000
 QJ8  H19  C10  H18  107.18  3.000
 QJ8  H19  C10  O09  110.74  3.000
 QJ8  H18  C10  O09  110.72  3.000
 QJ8  H19  C10  C2'  109.47  3.000
 QJ8  H18  C10  C2'  109.78  3.000
 QJ8  O09  C10  C2'  108.94  3.000
 QJ8  C08  O09  C10  113.10  3.000
 QJ8  H21  C08  H20  106.07  3.000
 QJ8  H21  C08  C06  108.46  3.000
 QJ8  H20  C08  C06  109.00  3.000
 QJ8  H21  C08  O09  111.07  3.000
 QJ8  H20  C08  O09  111.16  3.000
 QJ8  C06  C08  O09  110.92  3.000
 QJ8  C05  C06  N01  123.40  3.000
 QJ8  N01  C06  C08  113.88  3.000
 QJ8  C05  C06  C08  122.71  3.000
 QJ8  C02  N01  C06  118.59  3.000
 QJ8  C03  C02  N02  120.68  3.000
 QJ8  N02  C02  N01  117.15  3.000
 QJ8  C03  C02  N01  122.13  3.000
 QJ8  H23  N02  H22  114.10  3.000
 QJ8  H23  N02  C02  117.60  3.000
 QJ8  H22  N02  C02  116.23  3.000
 QJ8  H24  C03  C04  120.87  3.000
 QJ8  H24  C03  C02  120.05  3.000
 QJ8  C04  C03  C02  119.08  3.000
 QJ8  C07  C04  C05  120.29  3.000
 QJ8  C05  C04  C03  118.41  3.000
 QJ8  C07  C04  C03  121.30  3.000
 QJ8  H25  C05  C04  120.42  3.000
 QJ8  H25  C05  C06  121.19  3.000
 QJ8  C04  C05  C06  118.39  3.000
 QJ8  H28  C07  H27  108.15  3.000
 QJ8  H28  C07  H26  108.19  3.000
 QJ8  H27  C07  H26  106.99  3.000
 QJ8  H28  C07  C04  111.80  3.000
 QJ8  H27  C07  C04  110.62  3.000
 QJ8  H26  C07  C04  110.91  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
 QJ8  CONST_01  C25  C26  N21  C22    0.00   0.0  0
 QJ8  CONST_02  C25  C24  C23  C22    0.00   0.0  0
 QJ8  CONST_03  C26  C25  C24  C23    0.00   0.0  0
 QJ8  CONST_04  C26  N21  C22  C23    0.00   0.0  0
 QJ8  CONST_05  N21  C26  C25  C24    0.00   0.0  0
 QJ8  CONST_06  N21  C22  C23  C24    0.00   0.0  0
 QJ8  CONST_07  C03  C04  C05  C06    0.00   0.0  0
 QJ8  CONST_08  C03  C02  N01  C06    0.00   0.0  0
 QJ8  CONST_09  C04  C03  C02  N01    0.00   0.0  0
 QJ8  CONST_10  C04  C05  C06  N01    0.00   0.0  0
 QJ8  CONST_11  C05  C04  C03  C02    0.00   0.0  0
 QJ8  CONST_12  C05  C06  N01  C02    0.00   0.0  0
 QJ8  CONST_13  C26  N21  C22  N22  180.00   0.0  0
 QJ8  CONST_14  C24  C23  C22  N22  180.00   0.0  0
 QJ8  CONST_15  C12  C26  N21  C22  180.00   0.0  0
 QJ8  CONST_16  C27  C24  C23  C22  180.00   0.0  0
 QJ8  CONST_17  C12  C26  C25  C24  180.00   0.0  0
 QJ8  CONST_18  C26  C25  C24  C27  180.00   0.0  0
 QJ8  CONST_19  C04  C05  C06  C08  180.00   0.0  0
 QJ8  CONST_20  C02  N01  C06  C08  180.00   0.0  0
 QJ8  CONST_21  C07  C04  C05  C06  180.00   0.0  0
 QJ8  CONST_22  N02  C02  N01  C06  180.00   0.0  0
 QJ8  CONST_23  C07  C04  C03  C02  180.00   0.0  0
 QJ8  CONST_24  C04  C03  C02  N02  180.00   0.0  0
 QJ8  CONST_25  H7   C25  C24  C23  180.00   0.0  0
 QJ8  CONST_26  H3   C23  C24  C25  180.00   0.0  0
 QJ8  CONST_27  H24  C03  C02  N01  180.00   0.0  0
 QJ8  CONST_28  H25  C05  C06  N01  180.00   0.0  0
 QJ8  Var_01    C2'  N1'  C5'  C4'  -47.14  30.0  1
 QJ8  Var_02    O11  C12  C26  C25   -2.03  30.0  2
 QJ8  Var_03    C05  C06  C08  O09   -7.60  30.0  2
 QJ8  Var_04    H4   C27  C24  C23  118.68  30.0  2
 QJ8  Var_05    H26  C07  C04  C03  125.03  30.0  2
 QJ8  Var_06    C06  C08  O09  C10  176.14  30.0  3
 QJ8  Var_07    H18  C10  O09  C08   57.16  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
 QJ8  chir_01  C4'  C3'  O11  C5'  negativ
 QJ8  chir_02  C2'  N1'  C3'  C10  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
 QJ8  plan-1  N22  0.020
 QJ8  plan-1  C22  0.020
 QJ8  plan-1  C23  0.020
 QJ8  plan-1  C24  0.020
 QJ8  plan-1  C27  0.020
 QJ8  plan-1  C25  0.020
 QJ8  plan-1  N21  0.020
 QJ8  plan-1  C26  0.020
 QJ8  plan-1  C12  0.020
 QJ8  plan-1  H3   0.020
 QJ8  plan-1  H7   0.020
 QJ8  plan-2  C08  0.020
 QJ8  plan-2  C06  0.020
 QJ8  plan-2  N01  0.020
 QJ8  plan-2  C02  0.020
 QJ8  plan-2  N02  0.020
 QJ8  plan-2  C03  0.020
 QJ8  plan-2  C04  0.020
 QJ8  plan-2  C05  0.020
 QJ8  plan-2  C07  0.020
 QJ8  plan-2  H24  0.020
 QJ8  plan-2  H25  0.020
 QJ8  plan-3  N22  0.020
 QJ8  plan-3  C22  0.020
 QJ8  plan-3  H1   0.020
 QJ8  plan-3  H2   0.020
 QJ8  plan-4  C02  0.020
 QJ8  plan-4  N02  0.020
 QJ8  plan-4  H22  0.020
 QJ8  plan-4  H23  0.020

