# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 18:46:11 2022
#   Inital geometry file: a 114 line input string
#   Ligand name: 3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}pyridin-3-yl)prop-2-yn-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1OCCCOc2ncccc2C#CCO
#
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
 HVR  HVR  "3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}pyridin-3-yl)prop-2-yn-1-ol"
  ligand  46  25  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HVR
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
 HVR  C01   C  CH3   0  -0.673   5.2331   3.7250  15.1173
 HVR  C02   C  CH2   0  -0.504   6.4674   3.2477  15.8806
 HVR  C03   C  CR6   0   0.227   7.6683   4.0913  15.5658
 HVR  C05   C  CR6   0   0.507   8.6622   6.1318  15.7173
 HVR  C08   C  CR6   0   0.433   9.8055   4.5203  14.6055
 HVR  C10   C  CR6   0   0.128   8.7487   3.6158  14.8557
 HVR  C12   C  CH2   0  -0.172   8.2245   2.0456  13.1778
 HVR  C13   C  CH2   0  -0.505   8.6787   0.6832  12.6953
 HVR  C14   C  CH2   0  -0.177   8.5136  -0.4404  13.6974
 HVR  C16   C  CR6   0   0.511   6.7558  -1.4151  14.9577
 HVR  C18   C  CR16  0  -0.053   7.2206  -3.1522  16.3529
 HVR  C19   C  CR16  0  -0.344   5.9131  -3.2476  16.7851
 HVR  C20   C  CR16  0  -0.177   4.9865  -2.3597  16.2539
 HVR  C21   C  CR6   0  -0.276   5.3912  -1.4146  15.3211
 HVR  C22   C  CSP   0   0.252   4.4798  -0.4832  14.7551
 HVR  C23   C  CSP   0  -0.037   3.6854   0.2984  14.2976
 HVR  C24   C  CH2   0  -0.347   2.7219   1.2325  13.7288
 HVR  N04   N  N     0  -0.499   7.6237   5.3565  16.0040
 HVR  N06   N  NH2   0  -0.825   8.5976   7.4287  16.1202
 HVR  N07   N  N     0  -0.501   9.7549   5.7722  15.0421
 HVR  N09   N  NH2   0  -0.823  10.8844   4.1352  13.8965
 HVR  N17   N  N     0  -0.457   7.6330  -2.2559  15.4575
 HVR  O11   O  O2    0  -0.498   8.8686   2.3282  14.4170
 HVR  O15   O  O2    0  -0.463   7.1352  -0.5120  14.0613
 HVR  O25   O  OH1   0  -0.658   2.0382   1.8828  14.7756
 HVR  H012  H  HCH3  0   0.238   4.3579   3.1371  15.3903
 HVR  H011  H  HCH3  0   0.228   5.0183   4.7702  15.3374
 HVR  H013  H  HCH3  0   0.224   5.3744   3.6311  14.0395
 HVR  H021  H  HCH2  0   0.249   6.2761   3.3190  16.9542
 HVR  H022  H  HCH2  0   0.243   6.6576   2.1966  15.6634
 HVR  H121  H  HCH2  0   0.228   7.1374   2.0731  13.3049
 HVR  H122  H  HCH2  0   0.234   8.4830   2.8030  12.4300
 HVR  H132  H  HCH2  0   0.248   8.1350   0.4501  11.7764
 HVR  H131  H  HCH2  0   0.248   9.7374   0.7209  12.4257
 HVR  H142  H  HCH2  0   0.241   8.8348  -1.3852  13.2524
 HVR  H141  H  HCH2  0   0.233   9.1272  -0.2706  14.5841
 HVR  H181  H  HCR6  0   0.269   7.9786  -3.8241  16.7385
 HVR  H191  H  HCR6  0   0.272   5.6240  -3.9914  17.5133
 HVR  H201  H  HCR6  0   0.274   3.9492  -2.3945  16.5600
 HVR  H241  H  HCH2  0   0.241   3.2619   1.9392  13.0869
 HVR  H242  H  HCH2  0   0.244   2.0362   0.6772  13.0757
 HVR  H062  H  HNH2  0   0.383   7.9265   7.6518  16.8353
 HVR  H061  H  HNH2  0   0.384   9.4603   7.9444  16.1597
 HVR  H092  H  HNH2  0   0.391  11.6886   4.7397  13.8928
 HVR  H091  H  HNH2  0   0.398  11.0599   3.1546  13.7594
 HVR  H251  H  HOH1  0   0.461   1.4705   2.5527  14.3805

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
 HVR  C02  C01   single    1.528  0.020  1.528
 HVR  C03  C02   single    1.501  0.020  1.501
 HVR  N04  C03   aromatic  1.340  0.020  1.340
 HVR  C05  N04   aromatic  1.327  0.020  1.327
 HVR  N06  C05   single    1.360  0.020  1.360
 HVR  N07  C05   aromatic  1.334  0.020  1.334
 HVR  C08  N07   aromatic  1.327  0.020  1.327
 HVR  N09  C08   single    1.347  0.020  1.347
 HVR  C10  C08   aromatic  1.413  0.020  1.413
 HVR  O11  C10   single    1.366  0.020  1.366
 HVR  C12  O11   single    1.425  0.020  1.425
 HVR  C13  C12   single    1.515  0.020  1.515
 HVR  C14  C13   single    1.515  0.020  1.515
 HVR  O15  C14   single    1.427  0.020  1.427
 HVR  C16  O15   single    1.328  0.020  1.328
 HVR  N17  C16   aromatic  1.314  0.020  1.314
 HVR  C18  N17   aromatic  1.332  0.020  1.332
 HVR  C19  C18   aromatic  1.380  0.020  1.380
 HVR  C20  C19   aromatic  1.389  0.020  1.389
 HVR  C21  C20   aromatic  1.388  0.020  1.388
 HVR  C22  C21   single    1.421  0.020  1.421
 HVR  C23  C22   triple    1.205  0.020  1.205
 HVR  C24  C23   single    1.458  0.020  1.458
 HVR  O25  C24   single    1.409  0.020  1.409
 HVR  C03  C10   aromatic  1.378  0.020  1.378
 HVR  C16  C21   aromatic  1.412  0.020  1.412
 HVR  C01  H012  single    0.970  0.020  1.090
 HVR  C01  H011  single    0.970  0.020  1.090
 HVR  C01  H013  single    0.970  0.020  1.090
 HVR  C02  H021  single    0.970  0.020  1.090
 HVR  C02  H022  single    0.970  0.020  1.090
 HVR  C12  H121  single    0.970  0.020  1.090
 HVR  C12  H122  single    0.970  0.020  1.090
 HVR  C13  H132  single    0.970  0.020  1.090
 HVR  C13  H131  single    0.970  0.020  1.090
 HVR  C14  H142  single    0.970  0.020  1.090
 HVR  C14  H141  single    0.970  0.020  1.090
 HVR  C18  H181  single    0.930  0.020  1.080
 HVR  C19  H191  single    0.930  0.020  1.080
 HVR  C20  H201  single    0.930  0.020  1.080
 HVR  C24  H241  single    0.970  0.020  1.090
 HVR  C24  H242  single    0.970  0.020  1.090
 HVR  N06  H062  single    0.890  0.020  1.040
 HVR  N06  H061  single    0.890  0.020  1.040
 HVR  N09  H092  single    0.890  0.020  1.040
 HVR  N09  H091  single    0.890  0.020  1.040
 HVR  O25  H251  single    0.850  0.020  0.980

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
 HVR  H013  C01  H011  107.92  3.000
 HVR  H013  C01  H012  107.77  3.000
 HVR  H011  C01  H012  107.98  3.000
 HVR  H013  C01  C02   111.23  3.000
 HVR  H011  C01  C02   110.98  3.000
 HVR  H012  C01  C02   110.82  3.000
 HVR  H022  C02  H021  106.81  3.000
 HVR  H022  C02  C03   111.13  3.000
 HVR  H021  C02  C03   108.02  3.000
 HVR  H022  C02  C01   110.04  3.000
 HVR  H021  C02  C01   109.21  3.000
 HVR  C03   C02  C01   111.47  3.000
 HVR  N04   C03  C10   121.38  3.000
 HVR  C10   C03  C02   122.80  3.000
 HVR  N04   C03  C02   115.82  3.000
 HVR  N07   C05  N06   116.49  3.000
 HVR  N07   C05  N04   126.35  3.000
 HVR  N06   C05  N04   117.14  3.000
 HVR  N09   C08  N07   118.26  3.000
 HVR  N09   C08  C10   120.60  3.000
 HVR  N07   C08  C10   121.14  3.000
 HVR  O11   C10  C08   118.75  3.000
 HVR  O11   C10  C03   124.05  3.000
 HVR  C08   C10  C03   117.18  3.000
 HVR  H122  C12  H121  107.23  3.000
 HVR  H122  C12  O11   110.48  3.000
 HVR  H121  C12  O11   110.05  3.000
 HVR  H122  C12  C13   109.49  3.000
 HVR  H121  C12  C13   110.93  3.000
 HVR  O11   C12  C13   108.65  3.000
 HVR  H131  C13  H132  106.37  3.000
 HVR  H131  C13  C14   107.11  3.000
 HVR  H132  C13  C14   110.11  3.000
 HVR  H131  C13  C12   109.75  3.000
 HVR  H132  C13  C12   108.09  3.000
 HVR  C14   C13  C12   115.07  3.000
 HVR  H141  C14  H142  107.46  3.000
 HVR  H141  C14  O15   110.09  3.000
 HVR  H142  C14  O15   110.14  3.000
 HVR  H141  C14  C13   111.15  3.000
 HVR  H142  C14  C13   109.87  3.000
 HVR  O15   C14  C13   108.13  3.000
 HVR  O15   C16  N17   120.09  3.000
 HVR  N17   C16  C21   123.19  3.000
 HVR  O15   C16  C21   116.72  3.000
 HVR  H181  C18  N17   116.08  3.000
 HVR  H181  C18  C19   120.55  3.000
 HVR  N17   C18  C19   123.37  3.000
 HVR  H191  C19  C20   121.29  3.000
 HVR  H191  C19  C18   120.80  3.000
 HVR  C20   C19  C18   117.90  3.000
 HVR  H201  C20  C21   119.44  3.000
 HVR  H201  C20  C19   120.71  3.000
 HVR  C21   C20  C19   119.85  3.000
 HVR  C22   C21  C20   121.80  3.000
 HVR  C22   C21  C16   121.17  3.000
 HVR  C20   C21  C16   117.02  3.000
 HVR  C23   C22  C21   180.00  3.000
 HVR  C24   C23  C22   180.00  3.000
 HVR  H242  C24  H241  106.57  3.000
 HVR  H242  C24  O25   111.86  3.000
 HVR  H241  C24  O25   112.10  3.000
 HVR  H242  C24  C23   108.71  3.000
 HVR  H241  C24  C23   108.42  3.000
 HVR  O25   C24  C23   109.06  3.000
 HVR  C05   N04  C03   117.06  3.000
 HVR  H061  N06  H062  115.51  3.000
 HVR  H061  N06  C05   117.39  3.000
 HVR  H062  N06  C05   117.00  3.000
 HVR  C08   N07  C05   116.88  3.000
 HVR  H091  N09  H092  116.48  3.000
 HVR  H091  N09  C08   119.36  3.000
 HVR  H092  N09  C08   118.05  3.000
 HVR  C18   N17  C16   118.66  3.000
 HVR  C12   O11  C10   115.26  3.000
 HVR  C16   O15  C14   118.82  3.000
 HVR  H251  O25  C24   107.59  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
 HVR  CONST_01  N07   C05  N04  C03     0.00   0.0  0
 HVR  CONST_02  N07   C08  C10  C03     0.00   0.0  0
 HVR  CONST_03  C10   C03  N04  C05     0.00   0.0  0
 HVR  CONST_04  C10   C08  N07  C05     0.00   0.0  0
 HVR  CONST_05  N04   C05  N07  C08     0.00   0.0  0
 HVR  CONST_06  N04   C03  C10  C08     0.00   0.0  0
 HVR  CONST_07  C19   C18  N17  C16     0.00   0.0  0
 HVR  CONST_08  C19   C20  C21  C16     0.00   0.0  0
 HVR  CONST_09  C21   C16  N17  C18     0.00   0.0  0
 HVR  CONST_10  C21   C20  C19  C18     0.00   0.0  0
 HVR  CONST_11  N17   C18  C19  C20     0.00   0.0  0
 HVR  CONST_12  N17   C16  C21  C20     0.00   0.0  0
 HVR  CONST_13  C05   N04  C03  C02   180.00   0.0  0
 HVR  CONST_14  C08   C10  C03  C02   180.00   0.0  0
 HVR  CONST_15  N06   C05  N04  C03   180.00   0.0  0
 HVR  CONST_16  N09   C08  C10  C03   180.00   0.0  0
 HVR  CONST_17  N09   C08  N07  C05   180.00   0.0  0
 HVR  CONST_18  N06   C05  N07  C08   180.00   0.0  0
 HVR  CONST_19  O15   C16  N17  C18   180.00   0.0  0
 HVR  CONST_20  C22   C21  C20  C19   180.00   0.0  0
 HVR  CONST_21  O15   C16  C21  C20   180.00   0.0  0
 HVR  CONST_22  N17   C16  C21  C22   180.00   0.0  0
 HVR  CONST_23  O11   C10  C03  N04   180.00   0.0  0
 HVR  CONST_24  O11   C10  C08  N07   180.00   0.0  0
 HVR  CONST_25  H181  C18  N17  C16   180.00   0.0  0
 HVR  CONST_26  H201  C20  C21  C16   180.00   0.0  0
 HVR  CONST_27  H201  C20  C19  C18   180.00   0.0  0
 HVR  CONST_28  H181  C18  C19  C20   180.00   0.0  0
 HVR  CONST_29  H191  C19  C20  C21   180.00   0.0  0
 HVR  CONST_30  H191  C19  C18  N17   180.00   0.0  0
 HVR  CONST_31  H092  N09  C08  C10   180.00   0.0  0
 HVR  CONST_37  H092  N09  C08  N07     0.00   0.0  0
 HVR  Var_01    N04   C03  C02  C01    67.70  30.0  2
 HVR  Var_02    C10   C03  C02  C01  -111.42  30.0  2
 HVR  Var_03    C12   O11  C10  C03    84.13  30.0  3
 HVR  Var_04    C12   O11  C10  C08   -97.66  30.0  3
 HVR  Var_05    N17   C16  O15  C14    -2.49  30.0  2
 HVR  Var_06    C21   C16  O15  C14   177.75  30.0  2
 HVR  Var_07    H021  C02  C03  C10   128.59  30.0  2
 HVR  Var_08    H022  C02  C03  C10    11.73  30.0  2
 HVR  Var_09    H021  C02  C03  N04   -52.29  30.0  2
 HVR  Var_10    H022  C02  C03  N04  -169.16  30.0  2
 HVR  Var_11    C13   C12  O11  C10   168.64  30.0  2
 HVR  Var_12    C16   O15  C14  C13  -178.65  30.0  1
 HVR  Var_13    C24   C23  C22  C21  -108.75  30.0  2
 HVR  Var_14    H012  C01  C02  C03  -177.22  30.0  3
 HVR  Var_15    H011  C01  C02  C03   -57.25  30.0  3
 HVR  Var_16    H013  C01  C02  C03    62.91  30.0  3
 HVR  Var_17    H121  C12  O11  C10   -69.72  30.0  2
 HVR  Var_18    H122  C12  O11  C10    48.51  30.0  2
 HVR  Var_19    H142  C14  O15  C16    61.29  30.0  3
 HVR  Var_20    H141  C14  O15  C16   -57.04  30.0  3
 HVR  Var_21    O15   C14  C13  C12    57.90  30.0  2
 HVR  Var_22    O11   C12  C13  C14    53.16  30.0  3
 HVR  Var_23    O25   C24  C23  C22   148.90  30.0  1
 HVR  Var_24    H142  C14  C13  C12   178.14  30.0  2
 HVR  Var_25    H141  C14  C13  C12   -63.05  30.0  2
 HVR  Var_26    H121  C12  C13  C14   -67.94  30.0  3
 HVR  Var_27    H122  C12  C13  C14   173.91  30.0  3
 HVR  Var_28    H241  C24  C23  C22   -88.78  30.0  1
 HVR  Var_29    H242  C24  C23  C22    26.71  30.0  1
 HVR  Var_30    H132  C13  C12  O11   176.68  30.0  2
 HVR  Var_31    H131  C13  C12  O11   -67.71  30.0  2
 HVR  Var_32    H132  C13  C14  O15   -64.53  30.0  3
 HVR  Var_33    H131  C13  C14  O15  -179.79  30.0  3

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
 HVR  plan-1  C02   0.020
 HVR  plan-1  C03   0.020
 HVR  plan-1  C05   0.020
 HVR  plan-1  C08   0.020
 HVR  plan-1  C10   0.020
 HVR  plan-1  N04   0.020
 HVR  plan-1  N06   0.020
 HVR  plan-1  N07   0.020
 HVR  plan-1  N09   0.020
 HVR  plan-1  O11   0.020
 HVR  plan-2  C16   0.020
 HVR  plan-2  C18   0.020
 HVR  plan-2  C19   0.020
 HVR  plan-2  C20   0.020
 HVR  plan-2  C21   0.020
 HVR  plan-2  C22   0.020
 HVR  plan-2  C23   0.020
 HVR  plan-2  N17   0.020
 HVR  plan-2  O15   0.020
 HVR  plan-2  H181  0.020
 HVR  plan-2  H191  0.020
 HVR  plan-2  H201  0.020
 HVR  plan-3  C05   0.020
 HVR  plan-3  N06   0.020
 HVR  plan-3  H062  0.020
 HVR  plan-3  H061  0.020
 HVR  plan-4  C08   0.020
 HVR  plan-4  N09   0.020
 HVR  plan-4  H092  0.020
 HVR  plan-4  H091  0.020

