# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 15:42:23 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: 6-[5-({(3R,4R)-4-[(6-amino-4-methylpyridin-2-yl)methyl]pyrrolidin-3-yl}oxy)pentyl]-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(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
 HW1  HW1  6-[5-({(3R,4R)-4-[(6-amino-4-methylpyridin-2-yl)methyl]pyrrolidin-3-yl}oxy)pentyl]-4-methylpyridin-2-amine  ligand  61  28  .  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_HW1
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
 HW1  N02  N  NH2   0  -0.839  -7.8515  -1.2106   1.7904
 HW1  C02  C  CR6   0   0.438  -6.8960  -1.3554   0.8246
 HW1  C03  C  CR16  0  -0.449  -7.1573  -2.1143  -0.3301
 HW1  C04  C  CR6   0   0.205  -6.1541  -2.2827  -1.2614
 HW1  C07  C  CH3   0  -0.726  -6.3803  -3.0693  -2.5162
 HW1  C05  C  CR16  0  -0.434  -4.9125  -1.6877  -1.0077
 HW1  N01  N  N     0  -0.485  -5.7152  -0.7925   1.0520
 HW1  C06  C  CR6   0   0.282  -4.7414  -0.9549   0.1528
 HW1  C08  C  CH2   0  -0.489  -3.4374  -0.2711   0.4555
 HW1  C3'  C  CH1   0  -0.277  -3.5844   1.2461   0.4253
 HW1  C2'  C  CH2   0  -0.286  -3.9121   1.8492  -0.9399
 HW1  N1'  N  NH1   0  -0.604  -3.6466   3.2779  -0.8084
 HW1  C5'  C  CH2   0  -0.304  -2.6162   3.4353   0.2288
 HW1  C4'  C  CH1   0   0.017  -2.3424   2.0394   0.8276
 HW1  O09  O  O2    0  -0.496  -1.2066   1.4258   0.2585
 HW1  C10  C  CH2   0  -0.126   0.0173   1.8761   0.7862
 HW1  C11  C  CH2   0  -0.461   1.1517   1.0603   0.1988
 HW1  C12  C  CH2   0  -0.429   2.5060   1.5156   0.7281
 HW1  C13  C  CH2   0  -0.415   3.6597   0.6662   0.2117
 HW1  C14  C  CH2   0  -0.488   5.0160   1.1480   0.7280
 HW1  C26  C  CR6   0   0.274   6.1384   0.2460   0.3018
 HW1  N21  N  N     0  -0.484   6.2195  -0.9283   0.9312
 HW1  C22  C  CR6   0   0.440   7.1737  -1.7813   0.5733
 HW1  N22  N  NH2   0  -0.840   7.2606  -2.9455   1.2814
 HW1  C23  C  CR16  0  -0.446   8.0905  -1.4956  -0.4527
 HW1  C24  C  CR6   0   0.204   8.0100  -0.2814  -1.1041
 HW1  C25  C  CR16  0  -0.437   7.0074   0.6118  -0.7116
 HW1  C27  C  CH3   0  -0.726   8.9805   0.0834  -2.1855
 HW1  H1   H  HNH2  0   0.387  -8.8110  -1.3385   1.5151
 HW1  H2   H  HNH2  0   0.378  -7.7109  -0.4552   2.4410
 HW1  H3   H  HCR6  0   0.253  -8.1346  -2.5584  -0.4780
 HW1  H4   H  HCH3  0   0.252  -6.3447  -2.4182  -3.3914
 HW1  H5   H  HCH3  0   0.249  -5.6050  -3.8246  -2.6498
 HW1  H6   H  HCH3  0   0.246  -7.3469  -3.5708  -2.5106
 HW1  H7   H  HCR6  0   0.241  -4.0974  -1.7930  -1.7131
 HW1  H8   H  HCH2  0   0.243  -3.0911  -0.5838   1.4454
 HW1  H9   H  HCH2  0   0.240  -2.6822  -0.5910  -0.2634
 HW1  H10  H  HCH1  0   0.243  -4.3826   1.5283   1.1209
 HW1  H11  H  HCH2  0   0.209  -3.2704   1.4047  -1.7098
 HW1  H12  H  HCH2  0   0.236  -4.9439   1.6790  -1.2498
 HW1  H13  H  HNH1  0   0.349  -4.4934   3.7320  -0.4959
 HW1  H15  H  HCH2  0   0.223  -1.6956   3.8549  -0.1880
 HW1  H16  H  HCH2  0   0.230  -2.9543   4.1285   1.0011
 HW1  H17  H  HCH1  0   0.224  -2.2268   2.0844   1.9192
 HW1  H18  H  HCH2  0   0.191   0.1775   2.9416   0.5671
 HW1  H19  H  HCH2  0   0.192   0.0186   1.7798   1.8825
 HW1  H20  H  HCH2  0   0.221   1.0005   0.0033   0.4375
 HW1  H21  H  HCH2  0   0.222   1.1358   1.1448  -0.8922
 HW1  H22  H  HCH2  0   0.217   2.6709   2.5635   0.4563
 HW1  H23  H  HCH2  0   0.216   2.5012   1.4824   1.8230
 HW1  H24  H  HCH2  0   0.222   3.5110  -0.3753   0.5116
 HW1  H25  H  HCH2  0   0.221   3.6646   0.6756  -0.8830
 HW1  H26  H  HCH2  0   0.235   5.2008   2.1648   0.3740
 HW1  H27  H  HCH2  0   0.234   4.9886   1.1893   1.8207
 HW1  H28  H  HNH2  0   0.379   6.4357  -3.2226   1.7876
 HW1  H29  H  HNH2  0   0.387   7.7687  -3.7090   0.8679
 HW1  H30  H  HCR6  0   0.253   8.8464  -2.2230  -0.7244
 HW1  H31  H  HCR6  0   0.241   6.9058   1.5754  -1.1952
 HW1  H32  H  HCH3  0   0.254   9.7665   0.7301  -1.7902
 HW1  H33  H  HCH3  0   0.246   9.4613  -0.7972  -2.6088
 HW1  H34  H  HCH3  0   0.247   8.4904   0.6301  -2.9906

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
 HW1  C27  C24  single    1.498  0.020  1.498
 HW1  C24  C25  aromatic  1.399  0.020  1.399
 HW1  C24  C23  aromatic  1.380  0.020  1.380
 HW1  C25  C26  aromatic  1.384  0.020  1.384
 HW1  C23  C22  aromatic  1.405  0.020  1.405
 HW1  C26  C14  single    1.502  0.020  1.502
 HW1  C26  N21  aromatic  1.335  0.020  1.335
 HW1  C22  N21  aromatic  1.329  0.020  1.329
 HW1  C22  N22  single    1.365  0.020  1.365
 HW1  C14  C13  single    1.529  0.020  1.529
 HW1  C11  C12  single    1.524  0.020  1.524
 HW1  C11  C10  single    1.516  0.020  1.516
 HW1  C13  C12  single    1.523  0.020  1.523
 HW1  C10  O09  single    1.407  0.020  1.407
 HW1  O09  C4'  single    1.411  0.020  1.411
 HW1  C08  C3'  single    1.525  0.020  1.525
 HW1  C08  C06  single    1.503  0.020  1.503
 HW1  C4'  C3'  single    1.528  0.020  1.528
 HW1  C4'  C5'  single    1.543  0.020  1.543
 HW1  C3'  C2'  single    1.528  0.020  1.528
 HW1  C06  N01  aromatic  1.335  0.020  1.335
 HW1  C06  C05  aromatic  1.383  0.020  1.383
 HW1  N01  C02  aromatic  1.328  0.020  1.328
 HW1  C05  C04  aromatic  1.400  0.020  1.400
 HW1  C5'  N1'  single    1.470  0.020  1.470
 HW1  C02  N02  single    1.366  0.020  1.366
 HW1  C02  C03  aromatic  1.406  0.020  1.406
 HW1  C04  C03  aromatic  1.379  0.020  1.379
 HW1  C04  C07  single    1.498  0.020  1.498
 HW1  C2'  N1'  single    1.459  0.020  1.459
 HW1  N02  H1   single    0.890  0.020  1.040
 HW1  N02  H2   single    0.890  0.020  1.040
 HW1  C03  H3   single    0.930  0.020  1.080
 HW1  C07  H4   single    0.970  0.020  1.090
 HW1  C07  H5   single    0.970  0.020  1.090
 HW1  C07  H6   single    0.970  0.020  1.090
 HW1  C05  H7   single    0.930  0.020  1.080
 HW1  C08  H8   single    0.970  0.020  1.090
 HW1  C08  H9   single    0.970  0.020  1.090
 HW1  C3'  H10  single    0.970  0.020  1.090
 HW1  C2'  H11  single    0.970  0.020  1.090
 HW1  C2'  H12  single    0.970  0.020  1.090
 HW1  N1'  H13  single    0.890  0.020  1.040
 HW1  C5'  H15  single    0.970  0.020  1.090
 HW1  C5'  H16  single    0.970  0.020  1.090
 HW1  C4'  H17  single    0.970  0.020  1.090
 HW1  C10  H18  single    0.970  0.020  1.090
 HW1  C10  H19  single    0.970  0.020  1.090
 HW1  C11  H20  single    0.970  0.020  1.090
 HW1  C11  H21  single    0.970  0.020  1.090
 HW1  C12  H22  single    0.970  0.020  1.090
 HW1  C12  H23  single    0.970  0.020  1.090
 HW1  C13  H24  single    0.970  0.020  1.090
 HW1  C13  H25  single    0.970  0.020  1.090
 HW1  C14  H26  single    0.970  0.020  1.090
 HW1  C14  H27  single    0.970  0.020  1.090
 HW1  N22  H28  single    0.890  0.020  1.040
 HW1  N22  H29  single    0.890  0.020  1.040
 HW1  C23  H30  single    0.930  0.020  1.080
 HW1  C25  H31  single    0.930  0.020  1.080
 HW1  C27  H32  single    0.970  0.020  1.090
 HW1  C27  H33  single    0.970  0.020  1.090
 HW1  C27  H34  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
 HW1  H2   N02  H1   113.91  3.000
 HW1  H2   N02  C02  116.01  3.000
 HW1  H1   N02  C02  117.38  3.000
 HW1  N01  C02  C03  122.33  3.000
 HW1  C03  C02  N02  120.50  3.000
 HW1  N01  C02  N02  117.13  3.000
 HW1  H3   C03  C04  120.92  3.000
 HW1  H3   C03  C02  120.06  3.000
 HW1  C04  C03  C02  119.02  3.000
 HW1  C05  C04  C07  120.58  3.000
 HW1  C07  C04  C03  121.33  3.000
 HW1  C05  C04  C03  118.09  3.000
 HW1  H6   C07  H5   108.22  3.000
 HW1  H6   C07  H4   107.92  3.000
 HW1  H5   C07  H4   106.97  3.000
 HW1  H6   C07  C04  111.80  3.000
 HW1  H5   C07  C04  111.04  3.000
 HW1  H4   C07  C04  110.70  3.000
 HW1  H7   C05  C06  120.32  3.000
 HW1  H7   C05  C04  120.53  3.000
 HW1  C06  C05  C04  119.14  3.000
 HW1  C06  N01  C02  118.79  3.000
 HW1  C08  C06  N01  116.21  3.000
 HW1  N01  C06  C05  122.63  3.000
 HW1  C08  C06  C05  121.15  3.000
 HW1  H9   C08  H8   107.06  3.000
 HW1  H9   C08  C3'  110.22  3.000
 HW1  H8   C08  C3'  109.44  3.000
 HW1  H9   C08  C06  109.54  3.000
 HW1  H8   C08  C06  109.07  3.000
 HW1  C3'  C08  C06  111.41  3.000
 HW1  H10  C3'  C4'  106.94  3.000
 HW1  H10  C3'  C2'  108.02  3.000
 HW1  C4'  C3'  C2'  101.81  3.000
 HW1  H10  C3'  C08  108.30  3.000
 HW1  C2'  C3'  C08  115.54  3.000
 HW1  C4'  C3'  C08  115.66  3.000
 HW1  H12  C2'  H11  106.91  3.000
 HW1  H12  C2'  N1'  110.52  3.000
 HW1  H11  C2'  N1'  110.72  3.000
 HW1  H12  C2'  C3'  113.28  3.000
 HW1  H11  C2'  C3'  109.99  3.000
 HW1  N1'  C2'  C3'  105.48  3.000
 HW1  H13  N1'  C5'  108.73  3.000
 HW1  H13  N1'  C2'  108.38  3.000
 HW1  C5'  N1'  C2'  107.21  3.000
 HW1  H16  C5'  H15  106.65  3.000
 HW1  H16  C5'  C4'  110.78  3.000
 HW1  H15  C5'  C4'  110.21  3.000
 HW1  H16  C5'  N1'  110.48  3.000
 HW1  H15  C5'  N1'  111.22  3.000
 HW1  C4'  C5'  N1'  107.53  3.000
 HW1  H17  C4'  O09  109.51  3.000
 HW1  H17  C4'  C5'  111.54  3.000
 HW1  O09  C4'  C5'  112.31  3.000
 HW1  H17  C4'  C3'  111.62  3.000
 HW1  C5'  C4'  C3'  102.90  3.000
 HW1  O09  C4'  C3'  108.81  3.000
 HW1  C10  O09  C4'  114.20  3.000
 HW1  H19  C10  H18  106.45  3.000
 HW1  H19  C10  C11  109.76  3.000
 HW1  H18  C10  C11  109.59  3.000
 HW1  H19  C10  O09  110.28  3.000
 HW1  H18  C10  O09  111.23  3.000
 HW1  C11  C10  O09  109.48  3.000
 HW1  H21  C11  H20  106.86  3.000
 HW1  H21  C11  C12  109.64  3.000
 HW1  H20  C11  C12  109.61  3.000
 HW1  H21  C11  C10  109.51  3.000
 HW1  H20  C11  C10  109.39  3.000
 HW1  C12  C11  C10  111.70  3.000
 HW1  H23  C12  H22  106.12  3.000
 HW1  H23  C12  C13  108.99  3.000
 HW1  H22  C12  C13  109.61  3.000
 HW1  H23  C12  C11  109.53  3.000
 HW1  H22  C12  C11  109.48  3.000
 HW1  C13  C12  C11  112.89  3.000
 HW1  H25  C13  H24  106.44  3.000
 HW1  H25  C13  C14  109.33  3.000
 HW1  H24  C13  C14  109.14  3.000
 HW1  H25  C13  C12  109.73  3.000
 HW1  H24  C13  C12  109.57  3.000
 HW1  C14  C13  C12  112.44  3.000
 HW1  H27  C14  H26  107.03  3.000
 HW1  H27  C14  C26  108.96  3.000
 HW1  H26  C14  C26  109.92  3.000
 HW1  H27  C14  C13  109.09  3.000
 HW1  H26  C14  C13  109.50  3.000
 HW1  C26  C14  C13  112.20  3.000
 HW1  C25  C26  N21  122.65  3.000
 HW1  N21  C26  C14  116.10  3.000
 HW1  C25  C26  C14  121.22  3.000
 HW1  C22  N21  C26  118.77  3.000
 HW1  C23  C22  N22  120.69  3.000
 HW1  N22  C22  N21  116.96  3.000
 HW1  C23  C22  N21  122.31  3.000
 HW1  H29  N22  H28  114.31  3.000
 HW1  H29  N22  C22  117.78  3.000
 HW1  H28  N22  C22  116.31  3.000
 HW1  H30  C23  C24  120.85  3.000
 HW1  H30  C23  C22  120.11  3.000
 HW1  C24  C23  C22  119.03  3.000
 HW1  C27  C24  C25  120.75  3.000
 HW1  C25  C24  C23  118.11  3.000
 HW1  C27  C24  C23  121.13  3.000
 HW1  H31  C25  C24  120.67  3.000
 HW1  H31  C25  C26  120.21  3.000
 HW1  C24  C25  C26  119.12  3.000
 HW1  H34  C27  H33  108.49  3.000
 HW1  H34  C27  H32  107.11  3.000
 HW1  H33  C27  H32  107.57  3.000
 HW1  H34  C27  C24  111.35  3.000
 HW1  H33  C27  C24  111.70  3.000
 HW1  H32  C27  C24  110.44  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
 HW1  CONST_01  C05  C06  N01  C02    0.00   0.0  0
 HW1  CONST_02  C05  C04  C03  C02    0.00   0.0  0
 HW1  CONST_03  C06  N01  C02  C03    0.00   0.0  0
 HW1  CONST_04  C06  C05  C04  C03    0.00   0.0  0
 HW1  CONST_05  N01  C06  C05  C04    0.00   0.0  0
 HW1  CONST_06  N01  C02  C03  C04    0.00   0.0  0
 HW1  CONST_07  C23  C24  C25  C26    0.00   0.0  0
 HW1  CONST_08  C23  C22  N21  C26    0.00   0.0  0
 HW1  CONST_09  C24  C25  C26  N21    0.00   0.0  0
 HW1  CONST_10  C24  C23  C22  N21    0.00   0.0  0
 HW1  CONST_11  C25  C24  C23  C22    0.00   0.0  0
 HW1  CONST_12  C25  C26  N21  C22    0.00   0.0  0
 HW1  CONST_13  C06  N01  C02  N02  180.00   0.0  0
 HW1  CONST_14  C04  C03  C02  N02  180.00   0.0  0
 HW1  CONST_15  C08  C06  N01  C02  180.00   0.0  0
 HW1  CONST_16  C07  C04  C03  C02  180.00   0.0  0
 HW1  CONST_17  C08  C06  C05  C04  180.00   0.0  0
 HW1  CONST_18  C06  C05  C04  C07  180.00   0.0  0
 HW1  CONST_19  C24  C25  C26  C14  180.00   0.0  0
 HW1  CONST_20  C22  N21  C26  C14  180.00   0.0  0
 HW1  CONST_21  C27  C24  C25  C26  180.00   0.0  0
 HW1  CONST_22  N22  C22  N21  C26  180.00   0.0  0
 HW1  CONST_23  C27  C24  C23  C22  180.00   0.0  0
 HW1  CONST_24  C24  C23  C22  N22  180.00   0.0  0
 HW1  CONST_25  H7   C05  C04  C03  180.00   0.0  0
 HW1  CONST_26  H3   C03  C04  C05  180.00   0.0  0
 HW1  CONST_27  H31  C25  C26  N21  180.00   0.0  0
 HW1  CONST_28  H30  C23  C22  N21  180.00   0.0  0
 HW1  Var_01    C5'  N1'  C2'  C3'   27.41  30.0  1
 HW1  Var_02    C4'  C5'  N1'  C2'   -4.97  30.0  1
 HW1  Var_03    C3'  C08  C06  C05  112.89  30.0  2
 HW1  Var_04    C25  C26  C14  C13  104.41  30.0  2
 HW1  Var_05    H4   C07  C04  C03  112.71  30.0  2
 HW1  Var_06    H32  C27  C24  C23  -99.16  30.0  2
 HW1  Var_07    C11  C10  O09  C4'  174.70  30.0  1
 HW1  Var_08    C26  C14  C13  C12  175.63  30.0  1
 HW1  Var_09    C12  C11  C10  O09  179.48  30.0  1
 HW1  Var_10    C13  C12  C11  C10  176.97  30.0  3
 HW1  Var_11    C14  C13  C12  C11  178.92  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
 HW1  chir_01  C3'  C08  C4'  C2'  negativ
 HW1  chir_02  C4'  O09  C3'  C5'  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
 HW1  plan-1  N02  0.020
 HW1  plan-1  C02  0.020
 HW1  plan-1  C03  0.020
 HW1  plan-1  C04  0.020
 HW1  plan-1  C07  0.020
 HW1  plan-1  C05  0.020
 HW1  plan-1  N01  0.020
 HW1  plan-1  C06  0.020
 HW1  plan-1  C08  0.020
 HW1  plan-1  H3   0.020
 HW1  plan-1  H7   0.020
 HW1  plan-2  C14  0.020
 HW1  plan-2  C26  0.020
 HW1  plan-2  N21  0.020
 HW1  plan-2  C22  0.020
 HW1  plan-2  N22  0.020
 HW1  plan-2  C23  0.020
 HW1  plan-2  C24  0.020
 HW1  plan-2  C25  0.020
 HW1  plan-2  C27  0.020
 HW1  plan-2  H30  0.020
 HW1  plan-2  H31  0.020
 HW1  plan-3  N02  0.020
 HW1  plan-3  C02  0.020
 HW1  plan-3  H1   0.020
 HW1  plan-3  H2   0.020
 HW1  plan-4  C22  0.020
 HW1  plan-4  N22  0.020
 HW1  plan-4  H28  0.020
 HW1  plan-4  H29  0.020

