# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 10:47:40 2022
#   Inital geometry file: a 128 line input string
#   Ligand name: (2R)-3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)-2-methylpropanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1OCCCOc2ccccc2C[C@H](C)C(N)=O
#
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
 GI6  GI6  "(2R)-3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)-2-methylpropanamide"
  ligand  54  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 PERFECT
;

data_comp_GI6
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
 GI6  C10   C  CR6   0   0.123  -27.8271  10.1193  -25.6725
 GI6  C13   C  CH2   0  -0.497  -28.7686   6.6050  -25.5816
 GI6  C17   C  CR16  0  -0.379  -29.6173   3.6343  -28.5598
 GI6  C20   C  CR16  0  -0.285  -31.6937   4.2713  -30.2600
 GI6  C21   C  CR6   0   0.016  -31.3528   5.1752  -29.2610
 GI6  C22   C  CH2   0  -0.493  -32.1076   6.4737  -29.1617
 GI6  C24   C  CH3   0  -0.657  -30.2351   7.9831  -30.0068
 GI6  C01   C  CH3   0  -0.669  -31.1762  10.9163  -26.3688
 GI6  C02   C  CH2   0  -0.495  -30.1832  10.8922  -25.2100
 GI6  C03   C  CR6   0   0.222  -28.7740  11.1205  -25.6725
 GI6  C05   C  CR6   0   0.507  -27.2416  12.5768  -26.5080
 GI6  C08   C  CR6   0   0.436  -26.5282  10.4603  -26.1104
 GI6  C12   C  CH2   0  -0.154  -28.4737   7.9328  -26.2510
 GI6  C14   C  CH2   0  -0.203  -28.9126   5.4613  -26.5604
 GI6  C16   C  CR6   0   0.352  -30.2986   4.8405  -28.3976
 GI6  C18   C  CR16  0  -0.254  -29.9804   2.7559  -29.5724
 GI6  C19   C  CR16  0  -0.268  -31.0220   3.0682  -30.4295
 GI6  C23   C  CH1   0  -0.362  -31.6605   7.4850  -30.2315
 GI6  C25   C  C     0   0.532  -32.6131   8.6685  -30.2450
 GI6  N04   N  N     0  -0.498  -28.4830  12.3590  -26.0905
 GI6  N06   N  NH2   0  -0.825  -26.9570  13.8163  -26.9887
 GI6  N07   N  N     0  -0.500  -26.2473  11.6880  -26.5278
 GI6  N09   N  NH2   0  -0.823  -25.5431   9.5396  -26.1341
 GI6  N26   N  NH2   0  -0.802  -33.1588   8.9592  -31.4356
 GI6  O11   O  O2    0  -0.497  -28.0828   8.8519  -25.2327
 GI6  O15   O  O2    0  -0.471  -29.9994   5.7322  -27.4289
 GI6  O27   O  O     0  -0.490  -32.8521   9.3137  -29.2329
 GI6  H132  H  HCH2  0   0.247  -27.9375   6.3478  -24.9194
 GI6  H131  H  HCH2  0   0.245  -29.6613   6.6832  -24.9559
 GI6  H171  H  HCR6  0   0.276  -28.8020   3.3614  -27.9039
 GI6  H201  H  HCR6  0   0.245  -32.5131   4.5219  -30.9251
 GI6  H221  H  HCH2  0   0.255  -33.1708   6.2611  -29.3045
 GI6  H222  H  HCH2  0   0.250  -32.0103   6.9208  -28.1730
 GI6  H242  H  HCH3  0   0.238  -29.9353   8.6828  -30.7879
 GI6  H241  H  HCH3  0   0.235  -30.1419   8.4878  -29.0449
 GI6  H243  H  HCH3  0   0.239  -29.5304   7.1520  -30.0222
 GI6  H013  H  HCH3  0   0.233  -32.1959  10.8004  -26.0017
 GI6  H011  H  HCH3  0   0.226  -31.1214  11.8578  -26.9148
 GI6  H012  H  HCH3  0   0.231  -30.9850  10.1071  -27.0743
 GI6  H021  H  HCH2  0   0.246  -30.4363  11.6858  -24.5028
 GI6  H022  H  HCH2  0   0.243  -30.2635   9.9485  -24.6714
 GI6  H121  H  HCH2  0   0.232  -29.3534   8.3125  -26.7796
 GI6  H122  H  HCH2  0   0.216  -27.6712   7.8155  -26.9903
 GI6  H141  H  HCH2  0   0.225  -27.9868   5.3422  -27.1358
 GI6  H142  H  HCH2  0   0.240  -29.0818   4.5295  -26.0101
 GI6  H181  H  HCR6  0   0.253  -29.4402   1.8242  -29.6810
 GI6  H191  H  HCR6  0   0.247  -31.3132   2.3858  -31.2170
 GI6  H231  H  HCH1  0   0.254  -31.6981   6.9837  -31.2038
 GI6  H062  H  HNH2  0   0.384  -27.5913  14.5578  -26.7446
 GI6  H061  H  HNH2  0   0.384  -25.9876  14.0781  -27.0461
 GI6  H091  H  HNH2  0   0.391  -24.6008   9.8662  -26.2686
 GI6  H092  H  HNH2  0   0.399  -25.6450   8.6951  -25.5972
 GI6  H262  H  HNH2  0   0.396  -33.7854   9.7421  -31.5328
 GI6  H261  H  HNH2  0   0.405  -32.9630   8.4183  -32.2598

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
 GI6  C02  C01   single    1.526  0.020  1.526
 GI6  C03  C02   single    1.501  0.020  1.501
 GI6  N04  C03   aromatic  1.339  0.020  1.339
 GI6  C05  N04   aromatic  1.328  0.020  1.328
 GI6  N06  C05   single    1.360  0.020  1.360
 GI6  N07  C05   aromatic  1.334  0.020  1.334
 GI6  C08  N07   aromatic  1.327  0.020  1.327
 GI6  N09  C08   single    1.349  0.020  1.349
 GI6  C10  C08   aromatic  1.413  0.020  1.413
 GI6  O11  C10   single    1.366  0.020  1.366
 GI6  C12  O11   single    1.426  0.020  1.426
 GI6  C13  C12   single    1.516  0.020  1.516
 GI6  C14  C13   single    1.512  0.020  1.512
 GI6  O15  C14   single    1.417  0.020  1.417
 GI6  C16  O15   single    1.350  0.020  1.350
 GI6  C17  C16   aromatic  1.395  0.020  1.395
 GI6  C18  C17   aromatic  1.389  0.020  1.389
 GI6  C19  C18   aromatic  1.385  0.020  1.385
 GI6  C20  C19   aromatic  1.388  0.020  1.388
 GI6  C21  C20   aromatic  1.390  0.020  1.390
 GI6  C22  C21   single    1.505  0.020  1.505
 GI6  C23  C22   single    1.539  0.020  1.539
 GI6  C24  C23   single    1.527  0.020  1.527
 GI6  C25  C23   single    1.519  0.020  1.519
 GI6  N26  C25   single    1.342  0.020  1.342
 GI6  O27  C25   double    1.224  0.020  1.224
 GI6  C03  C10   aromatic  1.378  0.020  1.378
 GI6  C16  C21   aromatic  1.403  0.020  1.403
 GI6  C13  H132  single    0.970  0.020  1.090
 GI6  C13  H131  single    0.970  0.020  1.090
 GI6  C17  H171  single    0.930  0.020  1.080
 GI6  C20  H201  single    0.930  0.020  1.080
 GI6  C22  H221  single    0.970  0.020  1.090
 GI6  C22  H222  single    0.970  0.020  1.090
 GI6  C24  H242  single    0.970  0.020  1.090
 GI6  C24  H241  single    0.970  0.020  1.090
 GI6  C24  H243  single    0.970  0.020  1.090
 GI6  C01  H013  single    0.970  0.020  1.090
 GI6  C01  H011  single    0.970  0.020  1.090
 GI6  C01  H012  single    0.970  0.020  1.090
 GI6  C02  H021  single    0.970  0.020  1.090
 GI6  C02  H022  single    0.970  0.020  1.090
 GI6  C12  H121  single    0.970  0.020  1.090
 GI6  C12  H122  single    0.970  0.020  1.090
 GI6  C14  H141  single    0.970  0.020  1.090
 GI6  C14  H142  single    0.970  0.020  1.090
 GI6  C18  H181  single    0.930  0.020  1.080
 GI6  C19  H191  single    0.930  0.020  1.080
 GI6  C23  H231  single    0.970  0.020  1.090
 GI6  N06  H062  single    0.890  0.020  1.040
 GI6  N06  H061  single    0.890  0.020  1.040
 GI6  N09  H091  single    0.890  0.020  1.040
 GI6  N09  H092  single    0.890  0.020  1.040
 GI6  N26  H262  single    0.860  0.020  1.020
 GI6  N26  H261  single    0.860  0.020  1.020

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
 GI6  O11   C10  C08   119.74  3.000
 GI6  O11   C10  C03   123.07  3.000
 GI6  C08   C10  C03   117.16  3.000
 GI6  H131  C13  H132  106.92  3.000
 GI6  H131  C13  C14   110.30  3.000
 GI6  H132  C13  C14   106.65  3.000
 GI6  H131  C13  C12   110.42  3.000
 GI6  H132  C13  C12   109.00  3.000
 GI6  C14   C13  C12   113.27  3.000
 GI6  H171  C17  C18   118.67  3.000
 GI6  H171  C17  C16   121.07  3.000
 GI6  C18   C17  C16   120.27  3.000
 GI6  H201  C20  C19   119.40  3.000
 GI6  H201  C20  C21   118.41  3.000
 GI6  C19   C20  C21   122.19  3.000
 GI6  C16   C21  C22   122.81  3.000
 GI6  C16   C21  C20   118.13  3.000
 GI6  C22   C21  C20   119.04  3.000
 GI6  H222  C22  H221  106.57  3.000
 GI6  H222  C22  C23   109.59  3.000
 GI6  H221  C22  C23   108.63  3.000
 GI6  H222  C22  C21   111.66  3.000
 GI6  H221  C22  C21   108.13  3.000
 GI6  C23   C22  C21   112.05  3.000
 GI6  H243  C24  H241  108.08  3.000
 GI6  H243  C24  H242  107.54  3.000
 GI6  H241  C24  H242  108.15  3.000
 GI6  H243  C24  C23   110.66  3.000
 GI6  H241  C24  C23   111.15  3.000
 GI6  H242  C24  C23   111.13  3.000
 GI6  H012  C01  H011  107.94  3.000
 GI6  H012  C01  H013  107.64  3.000
 GI6  H011  C01  H013  107.91  3.000
 GI6  H012  C01  C02   111.44  3.000
 GI6  H011  C01  C02   111.18  3.000
 GI6  H013  C01  C02   110.57  3.000
 GI6  H022  C02  H021  106.98  3.000
 GI6  H022  C02  C03   110.69  3.000
 GI6  H021  C02  C03   107.85  3.000
 GI6  H022  C02  C01   109.93  3.000
 GI6  H021  C02  C01   109.22  3.000
 GI6  C03   C02  C01   112.00  3.000
 GI6  N04   C03  C02   116.17  3.000
 GI6  N04   C03  C10   121.51  3.000
 GI6  C02   C03  C10   122.32  3.000
 GI6  N07   C05  N06   116.50  3.000
 GI6  N07   C05  N04   126.32  3.000
 GI6  N06   C05  N04   117.17  3.000
 GI6  N09   C08  N07   118.13  3.000
 GI6  N09   C08  C10   120.82  3.000
 GI6  N07   C08  C10   121.04  3.000
 GI6  H122  C12  H121  107.43  3.000
 GI6  H122  C12  O11   110.45  3.000
 GI6  H121  C12  O11   109.97  3.000
 GI6  H122  C12  C13   110.25  3.000
 GI6  H121  C12  C13   111.15  3.000
 GI6  O11   C12  C13   107.61  3.000
 GI6  H142  C14  H141  107.55  3.000
 GI6  H142  C14  O15   110.61  3.000
 GI6  H141  C14  O15   110.28  3.000
 GI6  H142  C14  C13   109.44  3.000
 GI6  H141  C14  C13   109.96  3.000
 GI6  O15   C14  C13   108.97  3.000
 GI6  O15   C16  C21   116.77  3.000
 GI6  C21   C16  C17   120.11  3.000
 GI6  O15   C16  C17   123.11  3.000
 GI6  H181  C18  C19   120.49  3.000
 GI6  H181  C18  C17   119.15  3.000
 GI6  C19   C18  C17   120.36  3.000
 GI6  H191  C19  C18   120.72  3.000
 GI6  H191  C19  C20   120.35  3.000
 GI6  C18   C19  C20   118.93  3.000
 GI6  H231  C23  C25   109.11  3.000
 GI6  H231  C23  C24   108.20  3.000
 GI6  C25   C23  C24   109.42  3.000
 GI6  H231  C23  C22   107.86  3.000
 GI6  C25   C23  C22   109.63  3.000
 GI6  C24   C23  C22   112.55  3.000
 GI6  O27   C25  N26   122.70  3.000
 GI6  O27   C25  C23   121.73  3.000
 GI6  N26   C25  C23   115.57  3.000
 GI6  C05   N04  C03   116.94  3.000
 GI6  H061  N06  H062  115.45  3.000
 GI6  H061  N06  C05   117.34  3.000
 GI6  H062  N06  C05   117.02  3.000
 GI6  C08   N07  C05   117.01  3.000
 GI6  H092  N09  H091  116.02  3.000
 GI6  H092  N09  C08   119.33  3.000
 GI6  H091  N09  C08   117.70  3.000
 GI6  H261  N26  H262  117.40  3.000
 GI6  H261  N26  C25   122.13  3.000
 GI6  H262  N26  C25   120.47  3.000
 GI6  C12   O11  C10   114.80  3.000
 GI6  C16   O15  C14   118.90  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
 GI6  CONST_01  C05   N07  C08  C10     0.00   0.0  0
 GI6  CONST_02  C05   N04  C03  C10     0.00   0.0  0
 GI6  CONST_03  C20   C21  C16  C17     0.00   0.0  0
 GI6  CONST_04  C20   C19  C18  C17     0.00   0.0  0
 GI6  CONST_05  C18   C19  C20  C21     0.00   0.0  0
 GI6  CONST_06  C18   C17  C16  C21     0.00   0.0  0
 GI6  CONST_07  N07   C05  N04  C03     0.00   0.0  0
 GI6  CONST_08  N07   C08  C10  C03     0.00   0.0  0
 GI6  CONST_09  N04   C05  N07  C08     0.00   0.0  0
 GI6  CONST_10  N04   C03  C10  C08     0.00   0.0  0
 GI6  CONST_11  C19   C18  C17  C16     0.00   0.0  0
 GI6  CONST_12  C19   C20  C21  C16     0.00   0.0  0
 GI6  CONST_13  C22   C21  C16  C17   180.00   0.0  0
 GI6  CONST_14  O15   C16  C21  C20   180.00   0.0  0
 GI6  CONST_15  C19   C20  C21  C22   180.00   0.0  0
 GI6  CONST_16  C05   N04  C03  C02   180.00   0.0  0
 GI6  CONST_17  C08   C10  C03  C02   180.00   0.0  0
 GI6  CONST_18  N06   C05  N04  C03   180.00   0.0  0
 GI6  CONST_19  N09   C08  C10  C03   180.00   0.0  0
 GI6  CONST_20  N09   C08  N07  C05   180.00   0.0  0
 GI6  CONST_21  N06   C05  N07  C08   180.00   0.0  0
 GI6  CONST_22  O15   C16  C17  C18   180.00   0.0  0
 GI6  CONST_23  O11   C10  C03  N04   180.00   0.0  0
 GI6  CONST_24  O11   C10  C08  N07   180.00   0.0  0
 GI6  CONST_25  H191  C19  C18  C17   180.00   0.0  0
 GI6  CONST_26  H181  C18  C19  C20   180.00   0.0  0
 GI6  CONST_27  H191  C19  C20  C21   180.00   0.0  0
 GI6  CONST_28  H171  C17  C16  C21   180.00   0.0  0
 GI6  CONST_29  H181  C18  C17  C16   180.00   0.0  0
 GI6  CONST_30  H201  C20  C21  C16   180.00   0.0  0
 GI6  CONST_31  H201  C20  C19  C18   180.00   0.0  0
 GI6  CONST_32  H171  C17  C18  C19   180.00   0.0  0
 GI6  CONST_33  H091  N09  C08  C10   180.00   0.0  0
 GI6  CONST_39  H091  N09  C08  N07     0.00   0.0  0
 GI6  CONST_41  H262  N26  C25  C23   180.00   0.0  0
 GI6  CONST_42  H261  N26  C25  C23     0.00   0.0  0
 GI6  CONST_43  H262  N26  C25  O27     0.00   0.0  0
 GI6  CONST_44  H261  N26  C25  O27   180.00   0.0  0
 GI6  Var_01    C01   C02  C03  C10  -109.24  30.0  2
 GI6  Var_02    C14   O15  C16  C17     2.33  30.0  2
 GI6  Var_03    C23   C22  C21  C20   -76.92  30.0  2
 GI6  Var_04    C14   O15  C16  C21  -177.84  30.0  2
 GI6  Var_05    N04   C03  C02  C01    70.68  30.0  2
 GI6  Var_06    C12   O11  C10  C03    93.85  30.0  1
 GI6  Var_07    C12   O11  C10  C08   -88.41  30.0  1
 GI6  Var_08    C23   C22  C21  C16   102.07  30.0  2
 GI6  Var_09    H021  C02  C03  C10   130.56  30.0  2
 GI6  Var_10    H022  C02  C03  C10    13.84  30.0  2
 GI6  Var_11    H221  C22  C21  C20    42.77  30.0  2
 GI6  Var_12    H222  C22  C21  C20   159.70  30.0  2
 GI6  Var_13    H221  C22  C21  C16  -138.24  30.0  2
 GI6  Var_14    H222  C22  C21  C16   -21.31  30.0  2
 GI6  Var_15    H021  C02  C03  N04   -49.53  30.0  2
 GI6  Var_16    H022  C02  C03  N04  -166.25  30.0  2
 GI6  Var_17    C13   C12  O11  C10  -177.76  30.0  2
 GI6  Var_18    C16   O15  C14  C13   179.32  30.0  2
 GI6  Var_19    H121  C12  O11  C10   -56.55  30.0  2
 GI6  Var_20    H122  C12  O11  C10    61.85  30.0  2
 GI6  Var_21    H013  C01  C02  C03  -177.04  30.0  3
 GI6  Var_22    H011  C01  C02  C03   -57.19  30.0  3
 GI6  Var_23    H012  C01  C02  C03    63.28  30.0  3
 GI6  Var_24    H141  C14  O15  C16    58.53  30.0  3
 GI6  Var_25    H142  C14  O15  C16   -60.32  30.0  3
 GI6  Var_26    O15   C14  C13  C12   -61.29  30.0  3
 GI6  Var_27    O11   C12  C13  C14  -167.87  30.0  3
 GI6  Var_28    H141  C14  C13  C12    59.70  30.0  3
 GI6  Var_29    H142  C14  C13  C12   177.63  30.0  3
 GI6  Var_30    H121  C12  C13  C14    71.67  30.0  3
 GI6  Var_31    H122  C12  C13  C14   -47.35  30.0  3
 GI6  Var_32    H132  C13  C12  O11   -49.31  30.0  1
 GI6  Var_33    H131  C13  C12  O11    67.86  30.0  1
 GI6  Var_34    H132  C13  C14  O15   178.80  30.0  3
 GI6  Var_35    H131  C13  C14  O15    63.05  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
 GI6  chir_01  C23  C22  C24  C25  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
 GI6  plan-1  C17   0.020
 GI6  plan-1  C20   0.020
 GI6  plan-1  C21   0.020
 GI6  plan-1  C22   0.020
 GI6  plan-1  C16   0.020
 GI6  plan-1  C18   0.020
 GI6  plan-1  C19   0.020
 GI6  plan-1  O15   0.020
 GI6  plan-1  H171  0.020
 GI6  plan-1  H201  0.020
 GI6  plan-1  H181  0.020
 GI6  plan-1  H191  0.020
 GI6  plan-2  C10   0.020
 GI6  plan-2  C02   0.020
 GI6  plan-2  C03   0.020
 GI6  plan-2  C05   0.020
 GI6  plan-2  C08   0.020
 GI6  plan-2  N04   0.020
 GI6  plan-2  N06   0.020
 GI6  plan-2  N07   0.020
 GI6  plan-2  N09   0.020
 GI6  plan-2  O11   0.020
 GI6  plan-3  C23   0.020
 GI6  plan-3  C25   0.020
 GI6  plan-3  N26   0.020
 GI6  plan-3  O27   0.020
 GI6  plan-3  H262  0.020
 GI6  plan-3  H261  0.020
 GI6  plan-4  C05   0.020
 GI6  plan-4  N06   0.020
 GI6  plan-4  H062  0.020
 GI6  plan-4  H061  0.020
 GI6  plan-5  C08   0.020
 GI6  plan-5  N09   0.020
 GI6  plan-5  H091  0.020
 GI6  plan-5  H092  0.020

