# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 10:56:19 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 6-{[(3R,4R)-4-{[5-(6-aminopyridin-2-yl)pentyl]oxy}pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(C[C@@H]2CNC[C@@H]2OCCCCCc3cccc(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
 HW0  HW0  6-{[(3R,4R)-4-{[5-(6-aminopyridin-2-yl)pentyl]oxy}pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine  ligand  58  27  .  2022-07-25  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_HW0
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
 HW0  N22  N  NH2   0  -0.836   7.4608   3.0617  -0.7603
 HW0  C22  C  CR6   0   0.428   7.4585   1.8481  -0.1332
 HW0  C23  C  CR16  0  -0.392   8.3704   1.5684   0.9000
 HW0  C24  C  CR16  0  -0.147   8.2870   0.3428   1.5213
 HW0  C25  C  CR16  0  -0.393   7.3172  -0.5743   1.1216
 HW0  N21  N  N     0  -0.476   6.5356   0.9719  -0.5170
 HW0  C26  C  CR6   0   0.265   6.4604  -0.2123   0.0933
 HW0  C14  C  CH2   0  -0.485   5.3696  -1.1302  -0.3781
 HW0  C13  C  CH2   0  -0.415   3.9874  -0.6689   0.0855
 HW0  C12  C  CH2   0  -0.429   2.8651  -1.5224  -0.4902
 HW0  C11  C  CH2   0  -0.462   1.4860  -1.0784  -0.0188
 HW0  C10  C  CH2   0  -0.126   0.3813  -1.8993  -0.6535
 HW0  O09  O  O2    0  -0.497  -0.8649  -1.4438  -0.1861
 HW0  C4'  C  CH1   0   0.020  -1.9761  -2.0594  -0.7996
 HW0  C5'  C  CH2   0  -0.309  -2.2800  -3.4508  -0.1973
 HW0  N1'  N  NH1   0  -0.600  -3.4173  -3.3038   0.7217
 HW0  C2'  C  CH2   0  -0.292  -3.6603  -1.8728   0.8648
 HW0  C3'  C  CH1   0  -0.277  -3.2333  -1.2554  -0.4662
 HW0  C08  C  CH2   0  -0.489  -3.0646   0.2602  -0.4663
 HW0  C06  C  CR6   0   0.282  -4.3717   0.9588  -0.2148
 HW0  N01  N  N     0  -0.485  -5.3053   0.8234  -1.1601
 HW0  C02  C  CR6   0   0.439  -6.4868   1.4016  -0.9788
 HW0  N02  N  NH2   0  -0.839  -7.3989   1.2841  -1.9886
 HW0  C03  C  CR16  0  -0.449  -6.7901   2.1485   0.1736
 HW0  C04  C  CR6   0   0.205  -5.8282   2.2895   1.1517
 HW0  C05  C  CR16  0  -0.435  -4.5852   1.6787   0.9467
 HW0  C07  C  CH3   0  -0.727  -6.0974   3.0671   2.4037
 HW0  H1   H  HNH2  0   0.379   6.9858   3.0992  -1.6474
 HW0  H2   H  HNH2  0   0.387   8.3129   3.5963  -0.7317
 HW0  H3   H  HCR6  0   0.262   9.1137   2.2990   1.1917
 HW0  H4   H  HCR6  0   0.262   8.9773   0.0953   2.3179
 HW0  H5   H  HCR6  0   0.249   7.2351  -1.5445   1.5924
 HW0  H6   H  HCH2  0   0.235   5.3864  -1.1681  -1.4712
 HW0  H7   H  HCH2  0   0.236   5.5569  -2.1450  -0.0200
 HW0  H8   H  HCH2  0   0.221   3.9447  -0.6909   1.1791
 HW0  H9   H  HCH2  0   0.222   3.8412   0.3743  -0.2095
 HW0  H10  H  HCH2  0   0.216   2.9105  -1.4806  -1.5839
 HW0  H11  H  HCH2  0   0.217   3.0246  -2.5712  -0.2190
 HW0  H12  H  HCH2  0   0.222   1.4249  -1.1643   1.0706
 HW0  H13  H  HCH2  0   0.221   1.3380  -0.0222  -0.2626
 HW0  H14  H  HCH2  0   0.192   0.4335  -1.8112  -1.7492
 HW0  H15  H  HCH2  0   0.191   0.5310  -2.9631  -0.4187
 HW0  H16  H  HCH1  0   0.223  -1.8110  -2.1158  -1.8842
 HW0  H17  H  HCH2  0   0.232  -2.5143  -4.1788  -0.9753
 HW0  H18  H  HCH2  0   0.223  -1.3981  -3.8286   0.3291
 HW0  H19  H  HNH1  0   0.348  -4.2328  -3.7196   0.2931
 HW0  H21  H  HCH2  0   0.237  -4.7058  -1.6860   1.1122
 HW0  H22  H  HCH2  0   0.211  -3.0579  -1.4596   1.6826
 HW0  H23  H  HCH1  0   0.243  -3.9895  -1.5153  -1.2154
 HW0  H24  H  HCH2  0   0.240  -2.3398   0.5589   0.2918
 HW0  H25  H  HCH2  0   0.243  -2.6678   0.5816  -1.4340
 HW0  H26  H  HNH2  0   0.378  -7.2392   0.5390  -2.6466
 HW0  H27  H  HNH2  0   0.387  -8.3679   1.4286  -1.7593
 HW0  H28  H  HCR6  0   0.253  -7.7664   2.6057   0.2820
 HW0  H29  H  HCR6  0   0.241  -3.8019   1.7630   1.6897
 HW0  H30  H  HCH3  0   0.252  -6.0706   2.4147   3.2781
 HW0  H31  H  HCH3  0   0.250  -5.3379   3.8349   2.5561
 HW0  H32  H  HCH3  0   0.246  -7.0715   3.5532   2.3764

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
 HW0  C24  C23  aromatic  1.377  0.020  1.377
 HW0  C24  C25  aromatic  1.393  0.020  1.393
 HW0  C23  C22  aromatic  1.406  0.020  1.406
 HW0  C25  C26  aromatic  1.387  0.020  1.387
 HW0  C22  N22  single    1.366  0.020  1.366
 HW0  C22  N21  aromatic  1.329  0.020  1.329
 HW0  C12  C13  single    1.523  0.020  1.523
 HW0  C12  C11  single    1.524  0.020  1.524
 HW0  C26  N21  aromatic  1.334  0.020  1.334
 HW0  C26  C14  single    1.501  0.020  1.501
 HW0  C14  C13  single    1.529  0.020  1.529
 HW0  C11  C10  single    1.516  0.020  1.516
 HW0  C10  O09  single    1.407  0.020  1.407
 HW0  O09  C4'  single    1.411  0.020  1.411
 HW0  C08  C06  single    1.503  0.020  1.503
 HW0  C08  C3'  single    1.525  0.020  1.525
 HW0  C4'  C3'  single    1.529  0.020  1.529
 HW0  C4'  C5'  single    1.546  0.020  1.546
 HW0  C06  N01  aromatic  1.335  0.020  1.335
 HW0  C06  C05  aromatic  1.383  0.020  1.383
 HW0  N01  C02  aromatic  1.328  0.020  1.328
 HW0  C05  C04  aromatic  1.400  0.020  1.400
 HW0  C3'  C2'  single    1.528  0.020  1.528
 HW0  C02  N02  single    1.366  0.020  1.366
 HW0  C02  C03  aromatic  1.406  0.020  1.406
 HW0  C5'  N1'  single    1.470  0.020  1.470
 HW0  C04  C03  aromatic  1.379  0.020  1.379
 HW0  C04  C07  single    1.498  0.020  1.498
 HW0  C2'  N1'  single    1.459  0.020  1.459
 HW0  N22  H1   single    0.890  0.020  1.040
 HW0  N22  H2   single    0.890  0.020  1.040
 HW0  C23  H3   single    0.930  0.020  1.080
 HW0  C24  H4   single    0.930  0.020  1.080
 HW0  C25  H5   single    0.930  0.020  1.080
 HW0  C14  H6   single    0.970  0.020  1.090
 HW0  C14  H7   single    0.970  0.020  1.090
 HW0  C13  H8   single    0.970  0.020  1.090
 HW0  C13  H9   single    0.970  0.020  1.090
 HW0  C12  H10  single    0.970  0.020  1.090
 HW0  C12  H11  single    0.970  0.020  1.090
 HW0  C11  H12  single    0.970  0.020  1.090
 HW0  C11  H13  single    0.970  0.020  1.090
 HW0  C10  H14  single    0.970  0.020  1.090
 HW0  C10  H15  single    0.970  0.020  1.090
 HW0  C4'  H16  single    0.970  0.020  1.090
 HW0  C5'  H17  single    0.970  0.020  1.090
 HW0  C5'  H18  single    0.970  0.020  1.090
 HW0  N1'  H19  single    0.890  0.020  1.040
 HW0  C2'  H21  single    0.970  0.020  1.090
 HW0  C2'  H22  single    0.970  0.020  1.090
 HW0  C3'  H23  single    0.970  0.020  1.090
 HW0  C08  H24  single    0.970  0.020  1.090
 HW0  C08  H25  single    0.970  0.020  1.090
 HW0  N02  H26  single    0.890  0.020  1.040
 HW0  N02  H27  single    0.890  0.020  1.040
 HW0  C03  H28  single    0.930  0.020  1.080
 HW0  C05  H29  single    0.930  0.020  1.080
 HW0  C07  H30  single    0.970  0.020  1.090
 HW0  C07  H31  single    0.970  0.020  1.090
 HW0  C07  H32  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
 HW0  H2   N22  H1   113.87  3.000
 HW0  H2   N22  C22  117.41  3.000
 HW0  H1   N22  C22  115.90  3.000
 HW0  N21  C22  C23  122.09  3.000
 HW0  N21  C22  N22  117.01  3.000
 HW0  C23  C22  N22  120.87  3.000
 HW0  H3   C23  C24  121.39  3.000
 HW0  H3   C23  C22  120.61  3.000
 HW0  C24  C23  C22  118.00  3.000
 HW0  H4   C24  C25  120.29  3.000
 HW0  H4   C24  C23  119.80  3.000
 HW0  C25  C24  C23  119.91  3.000
 HW0  H5   C25  C26  120.67  3.000
 HW0  H5   C25  C24  121.23  3.000
 HW0  C26  C25  C24  118.10  3.000
 HW0  C26  N21  C22  119.47  3.000
 HW0  C14  C26  N21  116.10  3.000
 HW0  C14  C26  C25  121.47  3.000
 HW0  N21  C26  C25  122.42  3.000
 HW0  H7   C14  H6   107.02  3.000
 HW0  H7   C14  C13  109.63  3.000
 HW0  H6   C14  C13  109.10  3.000
 HW0  H7   C14  C26  109.91  3.000
 HW0  H6   C14  C26  108.89  3.000
 HW0  C13  C14  C26  112.15  3.000
 HW0  H9   C13  H8   106.46  3.000
 HW0  H9   C13  C12  109.51  3.000
 HW0  H8   C13  C12  109.73  3.000
 HW0  H9   C13  C14  109.08  3.000
 HW0  H8   C13  C14  109.39  3.000
 HW0  C12  C13  C14  112.49  3.000
 HW0  H11  C12  H10  106.13  3.000
 HW0  H11  C12  C11  109.53  3.000
 HW0  H10  C12  C11  109.59  3.000
 HW0  H11  C12  C13  109.62  3.000
 HW0  H10  C12  C13  108.99  3.000
 HW0  C11  C12  C13  112.75  3.000
 HW0  H13  C11  H12  106.86  3.000
 HW0  H13  C11  C10  109.33  3.000
 HW0  H12  C11  C10  109.49  3.000
 HW0  H13  C11  C12  109.56  3.000
 HW0  H12  C11  C12  109.61  3.000
 HW0  C10  C11  C12  111.86  3.000
 HW0  H15  C10  H14  106.47  3.000
 HW0  H15  C10  O09  111.28  3.000
 HW0  H14  C10  O09  110.30  3.000
 HW0  H15  C10  C11  109.59  3.000
 HW0  H14  C10  C11  109.82  3.000
 HW0  O09  C10  C11  109.34  3.000
 HW0  C4'  O09  C10  114.33  3.000
 HW0  H16  C4'  C3'  111.45  3.000
 HW0  H16  C4'  C5'  111.59  3.000
 HW0  C3'  C4'  C5'  103.10  3.000
 HW0  H16  C4'  O09  109.47  3.000
 HW0  C5'  C4'  O09  112.22  3.000
 HW0  C3'  C4'  O09  108.87  3.000
 HW0  H18  C5'  H17  106.60  3.000
 HW0  H18  C5'  N1'  110.94  3.000
 HW0  H17  C5'  N1'  110.27  3.000
 HW0  H18  C5'  C4'  109.85  3.000
 HW0  H17  C5'  C4'  111.40  3.000
 HW0  N1'  C5'  C4'  107.80  3.000
 HW0  H19  N1'  C2'  108.11  3.000
 HW0  H19  N1'  C5'  108.55  3.000
 HW0  C2'  N1'  C5'  106.77  3.000
 HW0  H22  C2'  H21  107.03  3.000
 HW0  H22  C2'  C3'  110.11  3.000
 HW0  H21  C2'  C3'  113.35  3.000
 HW0  H22  C2'  N1'  110.57  3.000
 HW0  H21  C2'  N1'  110.49  3.000
 HW0  C3'  C2'  N1'  105.33  3.000
 HW0  H23  C3'  C08  108.18  3.000
 HW0  H23  C3'  C2'  107.87  3.000
 HW0  C08  C3'  C2'  115.62  3.000
 HW0  H23  C3'  C4'  107.08  3.000
 HW0  C2'  C3'  C4'  101.96  3.000
 HW0  C08  C3'  C4'  115.57  3.000
 HW0  H25  C08  H24  107.05  3.000
 HW0  H25  C08  C06  109.07  3.000
 HW0  H24  C08  C06  109.54  3.000
 HW0  H25  C08  C3'  109.39  3.000
 HW0  H24  C08  C3'  110.22  3.000
 HW0  C06  C08  C3'  111.45  3.000
 HW0  C05  C06  N01  122.64  3.000
 HW0  C05  C06  C08  121.10  3.000
 HW0  N01  C06  C08  116.25  3.000
 HW0  C02  N01  C06  118.77  3.000
 HW0  C03  C02  N02  120.49  3.000
 HW0  C03  C02  N01  122.34  3.000
 HW0  N02  C02  N01  117.12  3.000
 HW0  H27  N02  H26  114.08  3.000
 HW0  H27  N02  C02  117.54  3.000
 HW0  H26  N02  C02  116.16  3.000
 HW0  H28  C03  C04  120.95  3.000
 HW0  H28  C03  C02  120.03  3.000
 HW0  C04  C03  C02  119.02  3.000
 HW0  C07  C04  C05  120.55  3.000
 HW0  C07  C04  C03  121.37  3.000
 HW0  C05  C04  C03  118.08  3.000
 HW0  H29  C05  C04  120.51  3.000
 HW0  H29  C05  C06  120.34  3.000
 HW0  C04  C05  C06  119.15  3.000
 HW0  H32  C07  H31  108.19  3.000
 HW0  H32  C07  H30  107.99  3.000
 HW0  H31  C07  H30  106.97  3.000
 HW0  H32  C07  C04  111.80  3.000
 HW0  H31  C07  C04  110.92  3.000
 HW0  H30  C07  C04  110.79  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
 HW0  CONST_01  C25  C24  C23  C22     0.00   0.0  0
 HW0  CONST_02  C25  C26  N21  C22     0.00   0.0  0
 HW0  CONST_03  C26  C25  C24  C23     0.00   0.0  0
 HW0  CONST_04  C26  N21  C22  C23     0.00   0.0  0
 HW0  CONST_05  N21  C22  C23  C24     0.00   0.0  0
 HW0  CONST_06  N21  C26  C25  C24     0.00   0.0  0
 HW0  CONST_07  C03  C02  N01  C06     0.00   0.0  0
 HW0  CONST_08  C03  C04  C05  C06     0.00   0.0  0
 HW0  CONST_09  C04  C05  C06  N01     0.00   0.0  0
 HW0  CONST_10  C04  C03  C02  N01     0.00   0.0  0
 HW0  CONST_11  C05  C06  N01  C02     0.00   0.0  0
 HW0  CONST_12  C05  C04  C03  C02     0.00   0.0  0
 HW0  CONST_13  C24  C23  C22  N22   180.00   0.0  0
 HW0  CONST_14  C26  N21  C22  N22   180.00   0.0  0
 HW0  CONST_15  C14  C26  N21  C22   180.00   0.0  0
 HW0  CONST_16  C14  C26  C25  C24   180.00   0.0  0
 HW0  CONST_17  C02  N01  C06  C08   180.00   0.0  0
 HW0  CONST_18  C04  C05  C06  C08   180.00   0.0  0
 HW0  CONST_19  N02  C02  N01  C06   180.00   0.0  0
 HW0  CONST_20  C07  C04  C05  C06   180.00   0.0  0
 HW0  CONST_21  C07  C04  C03  C02   180.00   0.0  0
 HW0  CONST_22  C04  C03  C02  N02   180.00   0.0  0
 HW0  CONST_23  H4   C24  C23  C22   180.00   0.0  0
 HW0  CONST_24  H5   C25  C24  C23   180.00   0.0  0
 HW0  CONST_25  H3   C23  C24  C25   180.00   0.0  0
 HW0  CONST_26  H29  C05  C06  N01   180.00   0.0  0
 HW0  CONST_27  H28  C03  C02  N01   180.00   0.0  0
 HW0  Var_01    C2'  N1'  C5'  C4'    -9.16  30.0  1
 HW0  Var_02    C3'  C2'  N1'  C5'    30.36  30.0  1
 HW0  Var_03    N01  C06  C08  C3'   -65.97  30.0  2
 HW0  Var_04    C13  C14  C26  C25   105.84  30.0  2
 HW0  Var_05    H30  C07  C04  C03   115.17  30.0  2
 HW0  Var_06    C12  C13  C14  C26   174.90  30.0  3
 HW0  Var_07    H14  C10  O09  C4'    53.89  30.0  1
 HW0  Var_08    C11  C12  C13  C14   179.31  30.0  1
 HW0  Var_09    C10  C11  C12  C13   177.35  30.0  3
 HW0  Var_10    O09  C10  C11  C12  -179.83  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
 HW0  chir_01  C4'  O09  C3'  C5'  positiv
 HW0  chir_02  C3'  C08  C4'  C2'  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
 HW0  plan-1  N22  0.020
 HW0  plan-1  C22  0.020
 HW0  plan-1  C23  0.020
 HW0  plan-1  C24  0.020
 HW0  plan-1  C25  0.020
 HW0  plan-1  N21  0.020
 HW0  plan-1  C26  0.020
 HW0  plan-1  C14  0.020
 HW0  plan-1  H3   0.020
 HW0  plan-1  H4   0.020
 HW0  plan-1  H5   0.020
 HW0  plan-2  C08  0.020
 HW0  plan-2  C06  0.020
 HW0  plan-2  N01  0.020
 HW0  plan-2  C02  0.020
 HW0  plan-2  N02  0.020
 HW0  plan-2  C03  0.020
 HW0  plan-2  C04  0.020
 HW0  plan-2  C05  0.020
 HW0  plan-2  C07  0.020
 HW0  plan-2  H28  0.020
 HW0  plan-2  H29  0.020
 HW0  plan-3  N22  0.020
 HW0  plan-3  C22  0.020
 HW0  plan-3  H1   0.020
 HW0  plan-3  H2   0.020
 HW0  plan-4  C02  0.020
 HW0  plan-4  N02  0.020
 HW0  plan-4  H26  0.020
 HW0  plan-4  H27  0.020

