# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 22:10:51 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: 4-methyl-6-{[(3R,4R)-4-{[5-(4-methylpyridin-2-yl)pentyl]oxy}pyrrolidin-3-yl]methyl}pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccnc(CCCCCO[C@H]2CNC[C@H]2Cc3cc(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
 HW9  HW9  4-methyl-6-{[(3R,4R)-4-{[5-(4-methylpyridin-2-yl)pentyl]oxy}pyrrolidin-3-yl]methyl}pyridin-2-amine  ligand  59  27  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HW9
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
 HW9  N02  N  NH2   0  -0.839  -6.7148  -2.2054   2.1760
 HW9  C02  C  CR6   0   0.437  -6.1438  -1.9079   0.9708
 HW9  C03  C  CR16  0  -0.449  -6.7513  -2.3182  -0.2290
 HW9  C04  C  CR6   0   0.205  -6.1244  -2.0391  -1.4258
 HW9  C05  C  CR16  0  -0.433  -4.8994  -1.3632  -1.3855
 HW9  C07  C  CH3   0  -0.726  -6.7358  -2.4308  -2.7362
 HW9  N01  N  N     0  -0.485  -4.9837  -1.2625   0.9954
 HW9  C06  C  CR6   0   0.282  -4.3716  -0.9968  -0.1611
 HW9  C08  C  CH2   0  -0.490  -3.0686  -0.2537  -0.0675
 HW9  C4'  C  CH1   0  -0.305  -3.2800   1.1747   0.4316
 HW9  C3'  C  CH1   0   0.068  -1.9860   2.0146   0.5890
 HW9  C2'  C  CH2   0  -0.352  -2.2378   3.2541  -0.2965
 HW9  N1'  N  NH1   0  -0.585  -3.6795   3.3935  -0.4236
 HW9  C5'  C  CH2   0  -0.306  -4.1511   2.0184  -0.5181
 HW9  O09  O  O2    0  -0.492  -0.8486   1.2723   0.2319
 HW9  C10  C  CH2   0  -0.121   0.3737   1.9294   0.4755
 HW9  C11  C  CH2   0  -0.459   1.5051   0.9270   0.3555
 HW9  C12  C  CH2   0  -0.429   2.8718   1.5760   0.5372
 HW9  C13  C  CH2   0  -0.416   4.0076   0.5638   0.4641
 HW9  C14  C  CH2   0  -0.489   5.3858   1.2045   0.6353
 HW9  C26  C  CR6   0   0.265   6.4820   0.1811   0.5615
 HW9  N21  N  N     0  -0.431   6.6323  -0.6202   1.6142
 HW9  C22  C  CR16  0  -0.077   7.5649  -1.5641   1.5506
 HW9  C23  C  CR16  0  -0.371   8.3869  -1.7630   0.4553
 HW9  C24  C  CR6   0   0.195   8.2459  -0.9313  -0.6529
 HW9  C25  C  CR16  0  -0.400   7.2689   0.0543  -0.5806
 HW9  C27  C  CH3   0  -0.724   9.1195  -1.0871  -1.8591
 HW9  H1   H  HNH2  0   0.387  -7.7004  -2.4082   2.1837
 HW9  H2   H  HNH2  0   0.378  -6.4053  -1.6529   2.9590
 HW9  H3   H  HCR6  0   0.253  -7.6969  -2.8470  -0.2058
 HW9  H4   H  HCR6  0   0.241  -4.3695  -1.1291  -2.3004
 HW9  H5   H  HCH3  0   0.253  -7.1056  -1.5505  -3.2653
 HW9  H6   H  HCH3  0   0.249  -6.0015  -2.9082  -3.3854
 HW9  H7   H  HCH3  0   0.246  -7.5718  -3.1157  -2.6046
 HW9  H8   H  HCH2  0   0.247  -2.4002  -0.7929   0.6082
 HW9  H9   H  HCH2  0   0.235  -2.5903  -0.2357  -1.0490
 HW9  H10  H  HCH1  0   0.247  -3.7757   1.1204   1.4042
 HW9  H11  H  HCH1  0   0.208  -1.8893   2.3348   1.6366
 HW9  H12  H  HCH2  0   0.243  -1.7888   4.1679   0.0939
 HW9  H13  H  HCH2  0   0.224  -1.8095   3.0695  -1.2887
 HW9  H14  H  HNH1  0   0.344  -4.0474   3.8080   0.4249
 HW9  H16  H  HCH2  0   0.219  -4.0151   1.6724  -1.5497
 HW9  H17  H  HCH2  0   0.241  -5.2160   1.9508  -0.2949
 HW9  H18  H  HCH2  0   0.196   0.5277   2.7527  -0.2358
 HW9  H19  H  HCH2  0   0.191   0.3766   2.3755   1.4809
 HW9  H20  H  HCH2  0   0.221   1.3700   0.1403   1.1041
 HW9  H21  H  HCH2  0   0.222   1.4600   0.4424  -0.6250
 HW9  H22  H  HCH2  0   0.218   3.0186   2.3429  -0.2302
 HW9  H23  H  HCH2  0   0.217   2.9092   2.0951   1.5011
 HW9  H24  H  HCH2  0   0.223   3.8704  -0.1986   1.2362
 HW9  H25  H  HCH2  0   0.222   3.9704   0.0408  -0.4970
 HW9  H26  H  HCH2  0   0.237   5.5353   1.9638  -0.1359
 HW9  H27  H  HCH2  0   0.240   5.4297   1.7158   1.6011
 HW9  H28  H  HCR6  0   0.255   7.6654  -2.2005   2.4236
 HW9  H29  H  HCR6  0   0.258   9.1247  -2.5552   0.4687
 HW9  H30  H  HCR6  0   0.254   7.1120   0.7299  -1.4130
 HW9  H31  H  HCH3  0   0.257  10.1365  -0.7557  -1.6425
 HW9  H32  H  HCH3  0   0.252   9.1821  -2.1309  -2.1675
 HW9  H33  H  HCH3  0   0.249   8.7508  -0.5032  -2.7008

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
 HW9  C27  C24  single    1.497  0.020  1.497
 HW9  C24  C25  aromatic  1.390  0.020  1.390
 HW9  C24  C23  aromatic  1.393  0.020  1.393
 HW9  C25  C26  aromatic  1.393  0.020  1.393
 HW9  C23  C22  aromatic  1.384  0.020  1.384
 HW9  C26  C14  single    1.501  0.020  1.501
 HW9  C26  N21  aromatic  1.331  0.020  1.331
 HW9  C22  N21  aromatic  1.328  0.020  1.328
 HW9  C14  C13  single    1.529  0.020  1.529
 HW9  C12  C13  single    1.523  0.020  1.523
 HW9  C12  C11  single    1.524  0.020  1.524
 HW9  C11  C10  single    1.516  0.020  1.516
 HW9  C10  O09  single    1.409  0.020  1.409
 HW9  O09  C3'  single    1.404  0.020  1.404
 HW9  C3'  C4'  single    1.551  0.020  1.551
 HW9  C3'  C2'  single    1.544  0.020  1.544
 HW9  C08  C4'  single    1.528  0.020  1.528
 HW9  C08  C06  single    1.503  0.020  1.503
 HW9  C4'  C5'  single    1.540  0.020  1.540
 HW9  C06  N01  aromatic  1.335  0.020  1.335
 HW9  C06  C05  aromatic  1.383  0.020  1.383
 HW9  N01  C02  aromatic  1.328  0.020  1.328
 HW9  C2'  N1'  single    1.454  0.020  1.454
 HW9  C05  C04  aromatic  1.400  0.020  1.400
 HW9  C02  N02  single    1.366  0.020  1.366
 HW9  C02  C03  aromatic  1.406  0.020  1.406
 HW9  C04  C03  aromatic  1.380  0.020  1.380
 HW9  C04  C07  single    1.498  0.020  1.498
 HW9  C5'  N1'  single    1.457  0.020  1.457
 HW9  N02  H1   single    0.890  0.020  1.040
 HW9  N02  H2   single    0.890  0.020  1.040
 HW9  C03  H3   single    0.930  0.020  1.080
 HW9  C05  H4   single    0.930  0.020  1.080
 HW9  C07  H5   single    0.970  0.020  1.090
 HW9  C07  H6   single    0.970  0.020  1.090
 HW9  C07  H7   single    0.970  0.020  1.090
 HW9  C08  H8   single    0.970  0.020  1.090
 HW9  C08  H9   single    0.970  0.020  1.090
 HW9  C4'  H10  single    0.970  0.020  1.090
 HW9  C3'  H11  single    0.970  0.020  1.090
 HW9  C2'  H12  single    0.970  0.020  1.090
 HW9  C2'  H13  single    0.970  0.020  1.090
 HW9  N1'  H14  single    0.890  0.020  1.040
 HW9  C5'  H16  single    0.970  0.020  1.090
 HW9  C5'  H17  single    0.970  0.020  1.090
 HW9  C10  H18  single    0.970  0.020  1.090
 HW9  C10  H19  single    0.970  0.020  1.090
 HW9  C11  H20  single    0.970  0.020  1.090
 HW9  C11  H21  single    0.970  0.020  1.090
 HW9  C12  H22  single    0.970  0.020  1.090
 HW9  C12  H23  single    0.970  0.020  1.090
 HW9  C13  H24  single    0.970  0.020  1.090
 HW9  C13  H25  single    0.970  0.020  1.090
 HW9  C14  H26  single    0.970  0.020  1.090
 HW9  C14  H27  single    0.970  0.020  1.090
 HW9  C22  H28  single    0.930  0.020  1.080
 HW9  C23  H29  single    0.930  0.020  1.080
 HW9  C25  H30  single    0.930  0.020  1.080
 HW9  C27  H31  single    0.970  0.020  1.090
 HW9  C27  H32  single    0.970  0.020  1.090
 HW9  C27  H33  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
 HW9  H2   N02  H1   113.93  3.000
 HW9  H2   N02  C02  115.97  3.000
 HW9  H1   N02  C02  117.38  3.000
 HW9  N01  C02  C03  122.35  3.000
 HW9  C03  C02  N02  120.57  3.000
 HW9  N01  C02  N02  117.04  3.000
 HW9  H3   C03  C04  120.92  3.000
 HW9  H3   C03  C02  120.07  3.000
 HW9  C04  C03  C02  119.01  3.000
 HW9  C07  C04  C05  120.57  3.000
 HW9  C07  C04  C03  121.36  3.000
 HW9  C05  C04  C03  118.07  3.000
 HW9  H4   C05  C06  120.27  3.000
 HW9  H4   C05  C04  120.56  3.000
 HW9  C06  C05  C04  119.17  3.000
 HW9  H7   C07  H6   108.28  3.000
 HW9  H7   C07  H5   107.81  3.000
 HW9  H6   C07  H5   107.02  3.000
 HW9  H7   C07  C04  111.84  3.000
 HW9  H6   C07  C04  111.13  3.000
 HW9  H5   C07  C04  110.57  3.000
 HW9  C06  N01  C02  118.76  3.000
 HW9  C08  C06  N01  116.22  3.000
 HW9  N01  C06  C05  122.64  3.000
 HW9  C08  C06  C05  121.14  3.000
 HW9  H9   C08  H8   107.22  3.000
 HW9  H9   C08  C4'  109.81  3.000
 HW9  H8   C08  C4'  110.12  3.000
 HW9  H9   C08  C06  109.38  3.000
 HW9  H8   C08  C06  108.96  3.000
 HW9  C4'  C08  C06  111.26  3.000
 HW9  H10  C4'  C5'  108.63  3.000
 HW9  H10  C4'  C3'  108.37  3.000
 HW9  C5'  C4'  C3'  103.75  3.000
 HW9  H10  C4'  C08  107.88  3.000
 HW9  C5'  C4'  C08  112.89  3.000
 HW9  C3'  C4'  C08  115.09  3.000
 HW9  H11  C3'  O09  108.96  3.000
 HW9  H11  C3'  C2'  109.09  3.000
 HW9  O09  C3'  C2'  114.24  3.000
 HW9  H11  C3'  C4'  109.13  3.000
 HW9  C2'  C3'  C4'  103.92  3.000
 HW9  O09  C3'  C4'  111.33  3.000
 HW9  H13  C2'  H12  107.71  3.000
 HW9  H13  C2'  N1'  108.93  3.000
 HW9  H12  C2'  N1'  111.05  3.000
 HW9  H13  C2'  C3'  108.67  3.000
 HW9  H12  C2'  C3'  113.60  3.000
 HW9  N1'  C2'  C3'  106.79  3.000
 HW9  H14  N1'  C5'  108.84  3.000
 HW9  H14  N1'  C2'  109.02  3.000
 HW9  C5'  N1'  C2'  103.66  3.000
 HW9  H17  C5'  H16  107.11  3.000
 HW9  H17  C5'  N1'  111.19  3.000
 HW9  H16  C5'  N1'  108.58  3.000
 HW9  H17  C5'  C4'  113.09  3.000
 HW9  H16  C5'  C4'  109.70  3.000
 HW9  N1'  C5'  C4'  107.10  3.000
 HW9  C10  O09  C3'  114.34  3.000
 HW9  H19  C10  H18  106.70  3.000
 HW9  H19  C10  C11  109.79  3.000
 HW9  H18  C10  C11  109.85  3.000
 HW9  H19  C10  O09  110.46  3.000
 HW9  H18  C10  O09  111.04  3.000
 HW9  C11  C10  O09  108.99  3.000
 HW9  H21  C11  H20  106.82  3.000
 HW9  H21  C11  C12  109.41  3.000
 HW9  H20  C11  C12  109.60  3.000
 HW9  H21  C11  C10  109.44  3.000
 HW9  H20  C11  C10  109.20  3.000
 HW9  C12  C11  C10  112.22  3.000
 HW9  H23  C12  H22  106.28  3.000
 HW9  H23  C12  C13  109.37  3.000
 HW9  H22  C12  C13  109.38  3.000
 HW9  H23  C12  C11  109.72  3.000
 HW9  H22  C12  C11  109.57  3.000
 HW9  C13  C12  C11  112.33  3.000
 HW9  H25  C13  H24  106.41  3.000
 HW9  H25  C13  C14  109.20  3.000
 HW9  H24  C13  C14  109.03  3.000
 HW9  H25  C13  C12  109.53  3.000
 HW9  H24  C13  C12  109.62  3.000
 HW9  C14  C13  C12  112.84  3.000
 HW9  H27  C14  H26  107.03  3.000
 HW9  H27  C14  C26  109.43  3.000
 HW9  H26  C14  C26  109.82  3.000
 HW9  H27  C14  C13  109.32  3.000
 HW9  H26  C14  C13  109.60  3.000
 HW9  C26  C14  C13  111.52  3.000
 HW9  C25  C26  N21  121.99  3.000
 HW9  N21  C26  C14  116.99  3.000
 HW9  C25  C26  C14  120.99  3.000
 HW9  C22  N21  C26  117.97  3.000
 HW9  H28  C22  C23  119.83  3.000
 HW9  H28  C22  N21  116.32  3.000
 HW9  C23  C22  N21  123.85  3.000
 HW9  H29  C23  C24  121.05  3.000
 HW9  H29  C23  C22  120.01  3.000
 HW9  C24  C23  C22  118.93  3.000
 HW9  C27  C24  C25  121.73  3.000
 HW9  C25  C24  C23  116.95  3.000
 HW9  C27  C24  C23  121.31  3.000
 HW9  H30  C25  C24  120.27  3.000
 HW9  H30  C25  C26  119.43  3.000
 HW9  C24  C25  C26  120.30  3.000
 HW9  H33  C27  H32  108.32  3.000
 HW9  H33  C27  H31  107.82  3.000
 HW9  H32  C27  H31  107.06  3.000
 HW9  H33  C27  C24  111.67  3.000
 HW9  H32  C27  C24  111.16  3.000
 HW9  H31  C27  C24  110.62  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
 HW9  CONST_01  C05  C06  N01  C02    0.00   0.0  0
 HW9  CONST_02  C05  C04  C03  C02    0.00   0.0  0
 HW9  CONST_03  C06  N01  C02  C03    0.00   0.0  0
 HW9  CONST_04  C06  C05  C04  C03    0.00   0.0  0
 HW9  CONST_05  N01  C06  C05  C04    0.00   0.0  0
 HW9  CONST_06  N01  C02  C03  C04    0.00   0.0  0
 HW9  CONST_07  C23  C24  C25  C26    0.00   0.0  0
 HW9  CONST_08  C23  C22  N21  C26    0.00   0.0  0
 HW9  CONST_09  C24  C25  C26  N21    0.00   0.0  0
 HW9  CONST_10  C24  C23  C22  N21    0.00   0.0  0
 HW9  CONST_11  C25  C24  C23  C22    0.00   0.0  0
 HW9  CONST_12  C25  C26  N21  C22    0.00   0.0  0
 HW9  CONST_13  C06  N01  C02  N02  180.00   0.0  0
 HW9  CONST_14  C04  C03  C02  N02  180.00   0.0  0
 HW9  CONST_15  C08  C06  N01  C02  180.00   0.0  0
 HW9  CONST_16  C07  C04  C03  C02  180.00   0.0  0
 HW9  CONST_17  C08  C06  C05  C04  180.00   0.0  0
 HW9  CONST_18  C06  C05  C04  C07  180.00   0.0  0
 HW9  CONST_19  C24  C25  C26  C14  180.00   0.0  0
 HW9  CONST_20  C22  N21  C26  C14  180.00   0.0  0
 HW9  CONST_21  C27  C24  C25  C26  180.00   0.0  0
 HW9  CONST_22  C27  C24  C23  C22  180.00   0.0  0
 HW9  CONST_23  H4   C05  C04  C03  180.00   0.0  0
 HW9  CONST_24  H3   C03  C04  C05  180.00   0.0  0
 HW9  CONST_25  H28  C22  N21  C26  180.00   0.0  0
 HW9  CONST_26  H30  C25  C26  N21  180.00   0.0  0
 HW9  CONST_27  H29  C23  C22  N21  180.00   0.0  0
 HW9  Var_01    C2'  N1'  C5'  C4'   37.53  30.0  1
 HW9  Var_02    C5'  N1'  C2'  C3'  -37.71  30.0  1
 HW9  Var_03    C4'  C08  C06  C05  111.84  30.0  2
 HW9  Var_04    C25  C26  C14  C13  103.81  30.0  2
 HW9  Var_05    H5   C07  C04  C03  107.98  30.0  2
 HW9  Var_06    H31  C27  C24  C23  -71.48  30.0  2
 HW9  Var_07    C11  C10  O09  C3'  167.09  30.0  1
 HW9  Var_08    C26  C14  C13  C12  179.87  30.0  1
 HW9  Var_09    C12  C11  C10  O09  177.14  30.0  1
 HW9  Var_10    C13  C12  C11  C10  178.06  30.0  1
 HW9  Var_11    C14  C13  C12  C11  179.59  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
 HW9  chir_01  C4'  C3'  C08  C5'  positiv
 HW9  chir_02  C3'  O09  C4'  C2'  positiv

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
 HW9  plan-1  N02  0.020
 HW9  plan-1  C02  0.020
 HW9  plan-1  C03  0.020
 HW9  plan-1  C04  0.020
 HW9  plan-1  C05  0.020
 HW9  plan-1  C07  0.020
 HW9  plan-1  N01  0.020
 HW9  plan-1  C06  0.020
 HW9  plan-1  C08  0.020
 HW9  plan-1  H3   0.020
 HW9  plan-1  H4   0.020
 HW9  plan-2  C14  0.020
 HW9  plan-2  C26  0.020
 HW9  plan-2  N21  0.020
 HW9  plan-2  C22  0.020
 HW9  plan-2  C23  0.020
 HW9  plan-2  C24  0.020
 HW9  plan-2  C25  0.020
 HW9  plan-2  C27  0.020
 HW9  plan-2  H28  0.020
 HW9  plan-2  H29  0.020
 HW9  plan-2  H30  0.020
 HW9  plan-3  N02  0.020
 HW9  plan-3  C02  0.020
 HW9  plan-3  H1   0.020
 HW9  plan-3  H2   0.020

