# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 11:11:50 2022
#   Inital geometry file: a 127 line input string
#   Ligand name: (2S)-4-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)butane-1,2-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1OCCCOc2ccccc2CC[C@H](O)CO
#
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
 H6O  H6O  "(2S)-4-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)butane-1,2-diol"
  ligand  55  27  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_H6O
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
 H6O  C10   C  CR6   0   0.125  -5.3568   1.6016  -15.0271
 H6O  C13   C  CH2   0  -0.499  -4.4394  -1.1102  -12.7730
 H6O  C17   C  CR16  0  -0.377  -2.5416  -3.5014  -15.8068
 H6O  C20   C  CR16  0  -0.300   0.1098  -2.8517  -16.2266
 H6O  C21   C  CR6   0   0.034  -0.5909  -2.1738  -15.2380
 H6O  C22   C  CH2   0  -0.514   0.1014  -1.1445  -14.3867
 H6O  C24   C  CH1   0   0.012   1.2892  -0.7596  -12.1301
 H6O  C26   C  CH2   0  -0.186   2.6259  -0.3095  -12.7145
 H6O  C01   C  CH3   0  -0.669  -2.1274   1.2618  -16.3786
 H6O  C02   C  CH2   0  -0.505  -3.5779   0.8807  -16.6656
 H6O  C03   C  CR6   0   0.225  -4.5468   1.8819  -16.1070
 H6O  N04   N  N     0  -0.498  -4.5808   3.0743  -16.7157
 H6O  C05   C  CR6   0   0.507  -5.4291   3.9735  -16.2317
 H6O  N06   N  NH2   0  -0.825  -5.4203   5.2071  -16.8041
 H6O  N07   N  N     0  -0.500  -6.2740   3.7956  -15.2151
 H6O  C08   C  CR6   0   0.432  -6.2469   2.6156  -14.6090
 H6O  N09   N  NH2   0  -0.823  -7.0799   2.4174  -13.5672
 H6O  O11   O  O2    0  -0.495  -5.3551   0.3967  -14.3845
 H6O  C12   C  CH2   0  -0.173  -4.4551   0.3164  -13.2792
 H6O  C14   C  CH2   0  -0.193  -3.9392  -2.1217  -13.7835
 H6O  O15   O  O2    0  -0.476  -2.5860  -1.8187  -14.0745
 H6O  C16   C  CR6   0   0.356  -1.9405  -2.5084  -15.0375
 H6O  C18   C  CR16  0  -0.257  -1.8100  -4.1613  -16.7883
 H6O  C19   C  CR16  0  -0.268  -0.4818  -3.8398  -17.0058
 H6O  C23   C  CH2   0  -0.440   0.5162  -1.7168  -13.0277
 H6O  O25   O  OH1   0  -0.672   0.4729   0.3671  -11.8794
 H6O  H132  H  HCH2  0   0.248  -3.8215  -1.1485  -11.8725
 H6O  H131  H  HCH2  0   0.247  -5.4469  -1.4047  -12.4686
 H6O  H171  H  HCR6  0   0.274  -3.5769  -3.7751  -15.6561
 H6O  H201  H  HCR6  0   0.243   1.1508  -2.5953  -16.3884
 H6O  H221  H  HCH2  0   0.241   0.9848  -0.8000  -14.9287
 H6O  H222  H  HCH2  0   0.245  -0.5351  -0.2698  -14.2457
 H6O  H241  H  HCH1  0   0.209   1.5016  -1.2960  -11.1930
 H6O  H261  H  HCH2  0   0.196   2.4523   0.2704  -13.6303
 H6O  H262  H  HCH2  0   0.202   3.1043   0.3724  -11.9960
 H6O  H012  H  HCH3  0   0.234  -1.4474   0.5236  -16.8040
 H6O  H011  H  HCH3  0   0.229  -1.8843   2.2339  -16.8065
 H6O  H013  H  HCH3  0   0.232  -1.9349   1.3084  -15.3064
 H6O  H021  H  HCH2  0   0.247  -3.7285   0.8341  -17.7468
 H6O  H022  H  HCH2  0   0.250  -3.7841  -0.1152  -16.2751
 H6O  H062  H  HNH2  0   0.383  -5.0044   5.2825  -17.7169
 H6O  H061  H  HNH2  0   0.384  -6.2228   5.7928  -16.6473
 H6O  H092  H  HNH2  0   0.391  -7.8190   3.0857  -13.4266
 H6O  H091  H  HNH2  0   0.399  -7.2676   1.4787  -13.2585
 H6O  H121  H  HCH2  0   0.228  -3.4531   0.6314  -13.5862
 H6O  H122  H  HCH2  0   0.232  -4.7773   0.9910  -12.4785
 H6O  H142  H  HCH2  0   0.238  -4.0205  -3.1343  -13.3730
 H6O  H141  H  HCH2  0   0.227  -4.5491  -2.0879  -14.6917
 H6O  H181  H  HCR6  0   0.252  -2.2921  -4.9293  -17.3795
 H6O  H191  H  HCR6  0   0.245   0.0919  -4.3480  -17.7695
 H6O  H232  H  HCH2  0   0.237  -0.3725  -2.0489  -12.4851
 H6O  H231  H  HCH2  0   0.233   1.1271  -2.6084  -13.1835
 H6O  H251  H  HOH1  0   0.448   0.8985   0.9143  -11.2116
 H6O  H271  H  HOH1  0   0.454   4.2676  -1.1510  -13.3097
 H6O  O27   O  OH1   0  -0.668   3.4249  -1.4450  -12.9530

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
 H6O  C02  C01   single    1.527  0.020  1.527
 H6O  C03  C02   single    1.501  0.020  1.501
 H6O  N04  C03   aromatic  1.339  0.020  1.339
 H6O  C05  N04   aromatic  1.328  0.020  1.328
 H6O  N06  C05   single    1.360  0.020  1.360
 H6O  N07  C05   aromatic  1.334  0.020  1.334
 H6O  C08  N07   aromatic  1.327  0.020  1.327
 H6O  N09  C08   single    1.349  0.020  1.349
 H6O  C10  C08   aromatic  1.413  0.020  1.413
 H6O  O11  C10   single    1.366  0.020  1.366
 H6O  C12  O11   single    1.428  0.020  1.428
 H6O  C13  C12   single    1.514  0.020  1.514
 H6O  C14  C13   single    1.515  0.020  1.515
 H6O  O15  C14   single    1.417  0.020  1.417
 H6O  C16  O15   single    1.349  0.020  1.349
 H6O  C17  C16   aromatic  1.393  0.020  1.393
 H6O  C18  C17   aromatic  1.391  0.020  1.391
 H6O  C19  C18   aromatic  1.384  0.020  1.384
 H6O  C20  C19   aromatic  1.390  0.020  1.390
 H6O  C21  C20   aromatic  1.388  0.020  1.388
 H6O  C22  C21   single    1.504  0.020  1.504
 H6O  C23  C22   single    1.532  0.020  1.532
 H6O  C24  C23   single    1.523  0.020  1.523
 H6O  O25  C24   single    1.414  0.020  1.414
 H6O  C26  C24   single    1.527  0.020  1.527
 H6O  O27  C26   single    1.409  0.020  1.409
 H6O  C03  C10   aromatic  1.379  0.020  1.379
 H6O  C16  C21   aromatic  1.405  0.020  1.405
 H6O  C13  H132  single    0.970  0.020  1.090
 H6O  C13  H131  single    0.970  0.020  1.090
 H6O  C17  H171  single    0.930  0.020  1.080
 H6O  C20  H201  single    0.930  0.020  1.080
 H6O  C22  H221  single    0.970  0.020  1.090
 H6O  C22  H222  single    0.970  0.020  1.090
 H6O  C24  H241  single    0.970  0.020  1.090
 H6O  C26  H261  single    0.970  0.020  1.090
 H6O  C26  H262  single    0.970  0.020  1.090
 H6O  C01  H012  single    0.970  0.020  1.090
 H6O  C01  H011  single    0.970  0.020  1.090
 H6O  C01  H013  single    0.970  0.020  1.090
 H6O  C02  H021  single    0.970  0.020  1.090
 H6O  C02  H022  single    0.970  0.020  1.090
 H6O  N06  H062  single    0.890  0.020  1.040
 H6O  N06  H061  single    0.890  0.020  1.040
 H6O  N09  H092  single    0.890  0.020  1.040
 H6O  N09  H091  single    0.890  0.020  1.040
 H6O  C12  H121  single    0.970  0.020  1.090
 H6O  C12  H122  single    0.970  0.020  1.090
 H6O  C14  H142  single    0.970  0.020  1.090
 H6O  C14  H141  single    0.970  0.020  1.090
 H6O  C18  H181  single    0.930  0.020  1.080
 H6O  C19  H191  single    0.930  0.020  1.080
 H6O  C23  H232  single    0.970  0.020  1.090
 H6O  C23  H231  single    0.970  0.020  1.090
 H6O  O25  H251  single    0.850  0.020  0.980
 H6O  O27  H271  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
 H6O  O11   C10  C08   119.66  3.000
 H6O  O11   C10  C03   123.18  3.000
 H6O  C08   C10  C03   117.14  3.000
 H6O  H131  C13  H132  106.40  3.000
 H6O  H131  C13  C14   108.08  3.000
 H6O  H132  C13  C14   109.86  3.000
 H6O  H131  C13  C12   109.72  3.000
 H6O  H132  C13  C12   108.33  3.000
 H6O  C14   C13  C12   114.18  3.000
 H6O  H171  C17  C18   118.81  3.000
 H6O  H171  C17  C16   121.12  3.000
 H6O  C18   C17  C16   120.08  3.000
 H6O  H201  C20  C19   119.53  3.000
 H6O  H201  C20  C21   118.38  3.000
 H6O  C19   C20  C21   122.09  3.000
 H6O  C16   C21  C22   121.62  3.000
 H6O  C16   C21  C20   118.04  3.000
 H6O  C22   C21  C20   120.31  3.000
 H6O  H222  C22  H221  106.45  3.000
 H6O  H222  C22  C23   110.05  3.000
 H6O  H221  C22  C23   109.82  3.000
 H6O  H222  C22  C21   110.69  3.000
 H6O  H221  C22  C21   107.89  3.000
 H6O  C23   C22  C21   111.77  3.000
 H6O  H241  C24  O25   110.42  3.000
 H6O  H241  C24  C23   107.07  3.000
 H6O  O25   C24  C23   108.20  3.000
 H6O  H241  C24  C26   107.50  3.000
 H6O  O25   C24  C26   109.78  3.000
 H6O  C23   C24  C26   113.84  3.000
 H6O  H262  C26  H261  106.63  3.000
 H6O  H262  C26  O27   111.32  3.000
 H6O  H261  C26  O27   111.97  3.000
 H6O  H262  C26  C24   108.28  3.000
 H6O  H261  C26  C24   109.67  3.000
 H6O  O27   C26  C24   108.89  3.000
 H6O  H013  C01  H011  107.97  3.000
 H6O  H013  C01  H012  107.61  3.000
 H6O  H011  C01  H012  108.16  3.000
 H6O  H013  C01  C02   111.30  3.000
 H6O  H011  C01  C02   111.15  3.000
 H6O  H012  C01  C02   110.50  3.000
 H6O  H022  C02  H021  106.84  3.000
 H6O  H022  C02  C03   110.74  3.000
 H6O  H021  C02  C03   107.92  3.000
 H6O  H022  C02  C01   109.91  3.000
 H6O  H021  C02  C01   109.12  3.000
 H6O  C03   C02  C01   112.13  3.000
 H6O  N04   C03  C02   116.17  3.000
 H6O  N04   C03  C10   121.48  3.000
 H6O  C02   C03  C10   122.35  3.000
 H6O  C05   N04  C03   116.97  3.000
 H6O  N07   C05  N06   116.48  3.000
 H6O  N07   C05  N04   126.32  3.000
 H6O  N06   C05  N04   117.18  3.000
 H6O  H061  N06  H062  115.31  3.000
 H6O  H061  N06  C05   117.22  3.000
 H6O  H062  N06  C05   116.92  3.000
 H6O  C08   N07  C05   116.99  3.000
 H6O  N09   C08  N07   118.09  3.000
 H6O  N09   C08  C10   120.83  3.000
 H6O  N07   C08  C10   121.07  3.000
 H6O  H091  N09  H092  116.10  3.000
 H6O  H091  N09  C08   119.31  3.000
 H6O  H092  N09  C08   117.65  3.000
 H6O  C12   O11  C10   114.51  3.000
 H6O  H122  C12  H121  107.28  3.000
 H6O  H122  C12  O11   110.23  3.000
 H6O  H121  C12  O11   110.11  3.000
 H6O  H122  C12  C13   109.81  3.000
 H6O  H121  C12  C13   110.83  3.000
 H6O  O11   C12  C13   108.57  3.000
 H6O  H141  C14  H142  107.34  3.000
 H6O  H141  C14  O15   110.80  3.000
 H6O  H142  C14  O15   110.20  3.000
 H6O  H141  C14  C13   110.42  3.000
 H6O  H142  C14  C13   110.04  3.000
 H6O  O15   C14  C13   108.03  3.000
 H6O  C16   O15  C14   119.62  3.000
 H6O  O15   C16  C21   116.09  3.000
 H6O  C21   C16  C17   120.38  3.000
 H6O  O15   C16  C17   123.53  3.000
 H6O  H181  C18  C19   120.43  3.000
 H6O  H181  C18  C17   119.20  3.000
 H6O  C19   C18  C17   120.37  3.000
 H6O  H191  C19  C18   120.71  3.000
 H6O  H191  C19  C20   120.25  3.000
 H6O  C18   C19  C20   119.04  3.000
 H6O  H231  C23  H232  106.12  3.000
 H6O  H231  C23  C24   108.25  3.000
 H6O  H232  C23  C24   108.12  3.000
 H6O  H231  C23  C22   109.27  3.000
 H6O  H232  C23  C22   109.50  3.000
 H6O  C24   C23  C22   115.18  3.000
 H6O  H251  O25  C24   108.71  3.000
 H6O  H271  O27  C26   108.27  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
 H6O  CONST_01  C05   N07  C08  C10     0.00   0.0  0
 H6O  CONST_02  C05   N04  C03  C10     0.00   0.0  0
 H6O  CONST_03  C20   C21  C16  C17     0.00   0.0  0
 H6O  CONST_04  C20   C19  C18  C17     0.00   0.0  0
 H6O  CONST_05  C18   C19  C20  C21     0.00   0.0  0
 H6O  CONST_06  C18   C17  C16  C21     0.00   0.0  0
 H6O  CONST_07  N07   C05  N04  C03     0.00   0.0  0
 H6O  CONST_08  N07   C08  C10  C03     0.00   0.0  0
 H6O  CONST_09  C08   C10  C03  N04     0.00   0.0  0
 H6O  CONST_10  C08   N07  C05  N04     0.00   0.0  0
 H6O  CONST_11  C19   C18  C17  C16     0.00   0.0  0
 H6O  CONST_12  C19   C20  C21  C16     0.00   0.0  0
 H6O  CONST_13  C22   C21  C16  C17   180.00   0.0  0
 H6O  CONST_14  O15   C16  C21  C20   180.00   0.0  0
 H6O  CONST_15  C19   C20  C21  C22   180.00   0.0  0
 H6O  CONST_16  C05   N04  C03  C02   180.00   0.0  0
 H6O  CONST_17  C08   C10  C03  C02   180.00   0.0  0
 H6O  CONST_18  N06   C05  N04  C03   180.00   0.0  0
 H6O  CONST_19  N09   C08  C10  C03   180.00   0.0  0
 H6O  CONST_20  O11   C10  C03  N04   180.00   0.0  0
 H6O  CONST_21  N09   C08  N07  C05   180.00   0.0  0
 H6O  CONST_22  C08   N07  C05  N06   180.00   0.0  0
 H6O  CONST_23  O11   C10  C08  N07   180.00   0.0  0
 H6O  CONST_24  C18   C17  C16  O15   180.00   0.0  0
 H6O  CONST_25  H191  C19  C18  C17   180.00   0.0  0
 H6O  CONST_26  H181  C18  C19  C20   180.00   0.0  0
 H6O  CONST_27  H191  C19  C20  C21   180.00   0.0  0
 H6O  CONST_28  H171  C17  C16  C21   180.00   0.0  0
 H6O  CONST_29  H181  C18  C17  C16   180.00   0.0  0
 H6O  CONST_30  H201  C20  C21  C16   180.00   0.0  0
 H6O  CONST_31  H201  C20  C19  C18   180.00   0.0  0
 H6O  CONST_32  H171  C17  C18  C19   180.00   0.0  0
 H6O  CONST_33  H092  N09  C08  C10   180.00   0.0  0
 H6O  CONST_39  H092  N09  C08  N07     0.00   0.0  0
 H6O  Var_01    C01   C02  C03  C10  -109.40  30.0  2
 H6O  Var_02    C14   O15  C16  C17     1.69  30.0  2
 H6O  Var_03    C23   C22  C21  C20   -99.00  30.0  1
 H6O  Var_04    C14   O15  C16  C21  -178.22  30.0  2
 H6O  Var_05    N04   C03  C02  C01    70.40  30.0  1
 H6O  Var_06    C12   O11  C10  C03    91.54  30.0  1
 H6O  Var_07    C12   O11  C10  C08   -90.23  30.0  1
 H6O  Var_08    C23   C22  C21  C16    79.07  30.0  1
 H6O  Var_09    H021  C02  C03  C10   130.38  30.0  2
 H6O  Var_10    H022  C02  C03  C10    13.77  30.0  2
 H6O  Var_11    H221  C22  C21  C20    21.84  30.0  1
 H6O  Var_12    H222  C22  C21  C20   137.95  30.0  1
 H6O  Var_13    H021  C02  C03  N04   -49.81  30.0  2
 H6O  Var_14    H022  C02  C03  N04  -166.43  30.0  2
 H6O  Var_15    H221  C22  C21  C16  -160.09  30.0  1
 H6O  Var_16    H222  C22  C21  C16   -43.99  30.0  1
 H6O  Var_17    C13   C12  O11  C10  -173.37  30.0  1
 H6O  Var_18    C16   O15  C14  C13  -174.40  30.0  1
 H6O  Var_19    C24   C23  C22  C21   176.96  30.0  2
 H6O  Var_20    H121  C12  O11  C10   -51.88  30.0  1
 H6O  Var_21    H122  C12  O11  C10    66.30  30.0  1
 H6O  Var_22    H232  C23  C22  C21   -60.96  30.0  2
 H6O  Var_23    H231  C23  C22  C21    54.88  30.0  2
 H6O  Var_24    H012  C01  C02  C03  -179.42  30.0  3
 H6O  Var_25    H011  C01  C02  C03   -59.32  30.0  3
 H6O  Var_26    H013  C01  C02  C03    61.08  30.0  3
 H6O  Var_27    H142  C14  O15  C16    65.35  30.0  3
 H6O  Var_28    H141  C14  O15  C16   -53.31  30.0  3
 H6O  Var_29    C14   C13  C12  O11    62.36  30.0  1
 H6O  Var_30    O15   C14  C13  C12    63.50  30.0  2
 H6O  Var_31    H221  C22  C23  C24    57.24  30.0  3
 H6O  Var_32    H222  C22  C23  C24   -59.63  30.0  3
 H6O  Var_33    H132  C13  C12  O11  -174.89  30.0  1
 H6O  Var_34    H131  C13  C12  O11   -59.13  30.0  1
 H6O  Var_35    H142  C14  C13  C12  -176.14  30.0  2
 H6O  Var_36    H141  C14  C13  C12   -57.82  30.0  2
 H6O  Var_37    H121  C12  C13  C14   -58.70  30.0  3
 H6O  Var_38    H122  C12  C13  C14  -177.06  30.0  3
 H6O  Var_39    H132  C13  C14  O15   -58.41  30.0  3
 H6O  Var_40    H131  C13  C14  O15  -174.11  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
 H6O  chir_01  C24  C23  O25  C26  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
 H6O  plan-1  C17   0.020
 H6O  plan-1  C20   0.020
 H6O  plan-1  C21   0.020
 H6O  plan-1  C22   0.020
 H6O  plan-1  O15   0.020
 H6O  plan-1  C16   0.020
 H6O  plan-1  C18   0.020
 H6O  plan-1  C19   0.020
 H6O  plan-1  H171  0.020
 H6O  plan-1  H201  0.020
 H6O  plan-1  H181  0.020
 H6O  plan-1  H191  0.020
 H6O  plan-2  C10   0.020
 H6O  plan-2  C02   0.020
 H6O  plan-2  C03   0.020
 H6O  plan-2  N04   0.020
 H6O  plan-2  C05   0.020
 H6O  plan-2  N06   0.020
 H6O  plan-2  N07   0.020
 H6O  plan-2  C08   0.020
 H6O  plan-2  N09   0.020
 H6O  plan-2  O11   0.020
 H6O  plan-3  C05   0.020
 H6O  plan-3  N06   0.020
 H6O  plan-3  H062  0.020
 H6O  plan-3  H061  0.020
 H6O  plan-4  C08   0.020
 H6O  plan-4  N09   0.020
 H6O  plan-4  H092  0.020
 H6O  plan-4  H091  0.020

