# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 06:41:33 2022
#   Inital geometry file: a 122 line input string
#   Ligand name: 3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1OCCCOc2ccccc2CCC(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
 GWL  GWL  "3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)propanamide"
  ligand  51  26  .  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_GWL
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
 GWL  C01   C  CR6   0   0.225   4.1177  -2.6428  30.7821
 GWL  C02   C  CH2   0  -0.504   5.0757  -1.5325  31.1015
 GWL  C03   C  CH3   0  -0.669   6.4161  -1.7165  30.3951
 GWL  C04   C  CR6   0   0.125   2.9961  -2.4497  30.0039
 GWL  O05   O  O2    0  -0.494   2.6603  -1.2363  29.4747
 GWL  C06   C  CH2   0  -0.173   3.1085  -1.0251  28.1342
 GWL  C07   C  CH2   0  -0.498   2.8954   0.4311  27.7756
 GWL  C08   C  CH2   0  -0.195   3.7202   1.4001  28.5979
 GWL  O09   O  O2    0  -0.474   5.0872   1.1598  28.3111
 GWL  C10   C  CR6   0   0.361   6.0434   1.7863  29.0242
 GWL  C11   C  CR16  0  -0.379   5.7781   2.6973  30.0426
 GWL  C12   C  CR16  0  -0.254   6.8289   3.2822  30.7414
 GWL  C13   C  CR6   0   0.022   7.3680   1.4659  28.6857
 GWL  C14   C  CH2   0  -0.516   7.6750   0.5266  27.5533
 GWL  C15   C  CH2   0  -0.549   7.5033   1.1708  26.1682
 GWL  C16   C  C     0   0.488   8.3518   2.4149  26.0074
 GWL  O17   O  O     0  -0.481   7.8725   3.5386  25.9745
 GWL  N18   N  NH2   0  -0.792   9.6751   2.1883  25.9285
 GWL  C19   C  CR16  0  -0.288   8.3936   2.0633  29.4050
 GWL  C20   C  CR16  0  -0.270   8.1399   2.9662  30.4321
 GWL  C21   C  CR6   0   0.431   2.1655  -3.5711  29.7837
 GWL  N22   N  N     0  -0.500   2.4726  -4.7605  30.2851
 GWL  C23   C  CR6   0   0.508   3.5899  -4.8424  31.0094
 GWL  N24   N  NH2   0  -0.825   3.8755  -6.0575  31.5463
 GWL  N25   N  N     0  -0.498   4.4185  -3.8444  31.2912
 GWL  N26   N  NH2   0  -0.822   1.0482  -3.4688  29.0338
 GWL  H021  H  HCH2  0   0.246   5.2358  -1.5260  32.1824
 GWL  H022  H  HCH2  0   0.251   4.6485  -0.5651  30.8405
 GWL  H031  H  HCH3  0   0.234   7.0962  -0.9020  30.6436
 GWL  H033  H  HCH3  0   0.228   6.8889  -2.6542  30.6857
 GWL  H032  H  HCH3  0   0.231   6.2915  -1.7244  29.3121
 GWL  H061  H  HCH2  0   0.227   4.1640  -1.3004  28.0420
 GWL  H062  H  HCH2  0   0.231   2.5464  -1.6610  27.4417
 GWL  H072  H  HCH2  0   0.248   3.1217   0.5607  26.7145
 GWL  H071  H  HCH2  0   0.248   1.8409   0.6906  27.8984
 GWL  H082  H  HCH2  0   0.240   3.4549   2.4317  28.3423
 GWL  H081  H  HCH2  0   0.228   3.5174   1.2632  29.6646
 GWL  H111  H  HCR6  0   0.275   4.7632   2.9653  30.3033
 GWL  H121  H  HCR6  0   0.253   6.6077   3.9873  31.5323
 GWL  H142  H  HCH2  0   0.262   7.0353  -0.3562  27.5937
 GWL  H141  H  HCH2  0   0.251   8.6986   0.1632  27.6622
 GWL  H151  H  HCH2  0   0.262   7.7718   0.4364  25.4042
 GWL  H152  H  HCH2  0   0.258   6.4614   1.4429  26.0069
 GWL  H181  H  HNH2  0   0.396  10.3216   2.9557  25.8467
 GWL  H182  H  HNH2  0   0.405  10.0579   1.2588  25.9349
 GWL  H191  H  HCR6  0   0.246   9.4176   1.8140  29.1522
 GWL  H201  H  HCR6  0   0.247   8.9590   3.4155  30.9776
 GWL  H241  H  HNH2  0   0.384   3.4228  -6.8606  31.1444
 GWL  H242  H  HNH2  0   0.384   4.8143  -6.2064  31.8747
 GWL  H261  H  HNH2  0   0.391   0.3966  -4.2351  29.0661
 GWL  H262  H  HNH2  0   0.399   0.6492  -2.5600  28.8698

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
 GWL  C03  C02   single    1.526  0.020  1.526
 GWL  C02  C01   single    1.501  0.020  1.501
 GWL  C04  C01   aromatic  1.379  0.020  1.379
 GWL  C06  O05   single    1.429  0.020  1.429
 GWL  C07  C06   single    1.515  0.020  1.515
 GWL  C08  C07   single    1.515  0.020  1.515
 GWL  O09  C08   single    1.417  0.020  1.417
 GWL  C10  O09   single    1.347  0.020  1.347
 GWL  C12  C11   aromatic  1.391  0.020  1.391
 GWL  C11  C10   aromatic  1.392  0.020  1.392
 GWL  C13  C10   aromatic  1.404  0.020  1.404
 GWL  C15  C14   single    1.537  0.020  1.537
 GWL  C16  C15   single    1.514  0.020  1.514
 GWL  O17  C16   double    1.222  0.020  1.222
 GWL  N18  C16   single    1.345  0.020  1.345
 GWL  C14  C13   single    1.503  0.020  1.503
 GWL  C19  C13   aromatic  1.388  0.020  1.388
 GWL  C20  C19   aromatic  1.391  0.020  1.391
 GWL  O05  C04   single    1.366  0.020  1.366
 GWL  C21  C04   aromatic  1.413  0.020  1.413
 GWL  C23  N22   aromatic  1.334  0.020  1.334
 GWL  N24  C23   single    1.359  0.020  1.359
 GWL  N25  C23   aromatic  1.327  0.020  1.327
 GWL  N22  C21   aromatic  1.327  0.020  1.327
 GWL  N26  C21   single    1.350  0.020  1.350
 GWL  C01  N25   aromatic  1.339  0.020  1.339
 GWL  C12  C20   aromatic  1.384  0.020  1.384
 GWL  C02  H021  single    0.970  0.020  1.090
 GWL  C02  H022  single    0.970  0.020  1.090
 GWL  C03  H031  single    0.970  0.020  1.090
 GWL  C03  H033  single    0.970  0.020  1.090
 GWL  C03  H032  single    0.970  0.020  1.090
 GWL  C06  H061  single    0.970  0.020  1.090
 GWL  C06  H062  single    0.970  0.020  1.090
 GWL  C07  H072  single    0.970  0.020  1.090
 GWL  C07  H071  single    0.970  0.020  1.090
 GWL  C08  H082  single    0.970  0.020  1.090
 GWL  C08  H081  single    0.970  0.020  1.090
 GWL  C11  H111  single    0.930  0.020  1.080
 GWL  C12  H121  single    0.930  0.020  1.080
 GWL  C14  H142  single    0.970  0.020  1.090
 GWL  C14  H141  single    0.970  0.020  1.090
 GWL  C15  H151  single    0.970  0.020  1.090
 GWL  C15  H152  single    0.970  0.020  1.090
 GWL  N18  H181  single    0.860  0.020  1.020
 GWL  N18  H182  single    0.860  0.020  1.020
 GWL  C19  H191  single    0.930  0.020  1.080
 GWL  C20  H201  single    0.930  0.020  1.080
 GWL  N24  H241  single    0.890  0.020  1.040
 GWL  N24  H242  single    0.890  0.020  1.040
 GWL  N26  H261  single    0.890  0.020  1.040
 GWL  N26  H262  single    0.890  0.020  1.040

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
 GWL  N25   C01  C04   121.53  3.000
 GWL  N25   C01  C02   116.07  3.000
 GWL  C04   C01  C02   122.40  3.000
 GWL  H022  C02  H021  106.82  3.000
 GWL  H022  C02  C03   109.91  3.000
 GWL  H021  C02  C03   109.26  3.000
 GWL  H022  C02  C01   110.83  3.000
 GWL  H021  C02  C01   107.96  3.000
 GWL  C03   C02  C01   111.89  3.000
 GWL  H032  C03  H033  107.95  3.000
 GWL  H032  C03  H031  107.66  3.000
 GWL  H033  C03  H031  108.16  3.000
 GWL  H032  C03  C02   111.12  3.000
 GWL  H033  C03  C02   111.18  3.000
 GWL  H031  C03  C02   110.63  3.000
 GWL  C21   C04  O05   120.02  3.000
 GWL  C21   C04  C01   117.07  3.000
 GWL  O05   C04  C01   122.90  3.000
 GWL  C06   O05  C04   114.69  3.000
 GWL  H062  C06  H061  107.19  3.000
 GWL  H062  C06  C07   109.65  3.000
 GWL  H061  C06  C07   110.94  3.000
 GWL  H062  C06  O05   110.26  3.000
 GWL  H061  C06  O05   110.14  3.000
 GWL  C07   C06  O05   108.66  3.000
 GWL  H071  C07  H072  106.30  3.000
 GWL  H071  C07  C08   108.20  3.000
 GWL  H072  C07  C08   109.78  3.000
 GWL  H071  C07  C06   109.72  3.000
 GWL  H072  C07  C06   108.35  3.000
 GWL  C08   C07  C06   114.19  3.000
 GWL  H081  C08  H082  107.48  3.000
 GWL  H081  C08  O09   110.78  3.000
 GWL  H082  C08  O09   110.24  3.000
 GWL  H081  C08  C07   110.38  3.000
 GWL  H082  C08  C07   110.11  3.000
 GWL  O09   C08  C07   107.87  3.000
 GWL  C10   O09  C08   119.91  3.000
 GWL  C13   C10  C11   120.37  3.000
 GWL  C13   C10  O09   115.83  3.000
 GWL  C11   C10  O09   123.80  3.000
 GWL  H111  C11  C12   118.92  3.000
 GWL  H111  C11  C10   121.16  3.000
 GWL  C12   C11  C10   119.92  3.000
 GWL  H121  C12  C20   120.39  3.000
 GWL  H121  C12  C11   119.12  3.000
 GWL  C20   C12  C11   120.50  3.000
 GWL  C19   C13  C14   120.57  3.000
 GWL  C19   C13  C10   118.29  3.000
 GWL  C14   C13  C10   121.13  3.000
 GWL  H141  C14  H142  106.07  3.000
 GWL  H141  C14  C15   109.52  3.000
 GWL  H142  C14  C15   107.88  3.000
 GWL  H141  C14  C13   108.93  3.000
 GWL  H142  C14  C13   110.98  3.000
 GWL  C15   C14  C13   113.22  3.000
 GWL  H152  C15  H151  107.42  3.000
 GWL  H152  C15  C16   108.36  3.000
 GWL  H151  C15  C16   109.88  3.000
 GWL  H152  C15  C14   110.18  3.000
 GWL  H151  C15  C14   108.71  3.000
 GWL  C16   C15  C14   112.17  3.000
 GWL  N18   C16  O17   122.63  3.000
 GWL  N18   C16  C15   114.77  3.000
 GWL  O17   C16  C15   122.58  3.000
 GWL  H182  N18  H181  117.43  3.000
 GWL  H182  N18  C16   122.02  3.000
 GWL  H181  N18  C16   120.54  3.000
 GWL  H191  C19  C20   119.60  3.000
 GWL  H191  C19  C13   118.58  3.000
 GWL  C20   C19  C13   121.83  3.000
 GWL  H201  C20  C19   120.26  3.000
 GWL  H201  C20  C12   120.65  3.000
 GWL  C19   C20  C12   119.09  3.000
 GWL  N26   C21  N22   118.01  3.000
 GWL  N26   C21  C04   120.87  3.000
 GWL  N22   C21  C04   121.10  3.000
 GWL  C23   N22  C21   117.01  3.000
 GWL  N25   C23  N24   117.21  3.000
 GWL  N25   C23  N22   126.30  3.000
 GWL  N24   C23  N22   116.45  3.000
 GWL  H242  N24  H241  115.63  3.000
 GWL  H242  N24  C23   117.23  3.000
 GWL  H241  N24  C23   117.49  3.000
 GWL  C23   N25  C01   116.97  3.000
 GWL  H262  N26  H261  115.86  3.000
 GWL  H262  N26  C21   119.18  3.000
 GWL  H261  N26  C21   117.42  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
 GWL  CONST_01  N22   C21  C04  C01     0.00   0.0  0
 GWL  CONST_02  N22   C23  N25  C01     0.00   0.0  0
 GWL  CONST_03  C23   N25  C01  C04     0.00   0.0  0
 GWL  CONST_04  C23   N22  C21  C04     0.00   0.0  0
 GWL  CONST_05  C20   C12  C11  C10     0.00   0.0  0
 GWL  CONST_06  C20   C19  C13  C10     0.00   0.0  0
 GWL  CONST_07  C19   C20  C12  C11     0.00   0.0  0
 GWL  CONST_08  C19   C13  C10  C11     0.00   0.0  0
 GWL  CONST_09  C13   C10  C11  C12     0.00   0.0  0
 GWL  CONST_10  C13   C19  C20  C12     0.00   0.0  0
 GWL  CONST_11  N25   C01  C04  C21     0.00   0.0  0
 GWL  CONST_12  N25   C23  N22  C21     0.00   0.0  0
 GWL  CONST_13  N26   C21  C04  C01   180.00   0.0  0
 GWL  CONST_14  N24   C23  N25  C01   180.00   0.0  0
 GWL  CONST_15  C21   C04  C01  C02   180.00   0.0  0
 GWL  CONST_16  C23   N25  C01  C02   180.00   0.0  0
 GWL  CONST_17  N25   C01  C04  O05   180.00   0.0  0
 GWL  CONST_18  N22   C21  C04  O05   180.00   0.0  0
 GWL  CONST_19  C12   C11  C10  O09   180.00   0.0  0
 GWL  CONST_20  C19   C13  C10  O09   180.00   0.0  0
 GWL  CONST_21  C14   C13  C10  C11   180.00   0.0  0
 GWL  CONST_22  C20   C19  C13  C14   180.00   0.0  0
 GWL  CONST_23  N24   C23  N22  C21   180.00   0.0  0
 GWL  CONST_24  N26   C21  N22  C23   180.00   0.0  0
 GWL  CONST_25  H121  C12  C11  C10   180.00   0.0  0
 GWL  CONST_26  H191  C19  C13  C10   180.00   0.0  0
 GWL  CONST_27  H201  C20  C12  C11   180.00   0.0  0
 GWL  CONST_28  H191  C19  C20  C12   180.00   0.0  0
 GWL  CONST_29  H111  C11  C10  C13   180.00   0.0  0
 GWL  CONST_30  H201  C20  C19  C13   180.00   0.0  0
 GWL  CONST_31  H121  C12  C20  C19   180.00   0.0  0
 GWL  CONST_32  H111  C11  C12  C20   180.00   0.0  0
 GWL  CONST_33  H261  N26  C21  C04   180.00   0.0  0
 GWL  CONST_37  H261  N26  C21  N22     0.00   0.0  0
 GWL  CONST_41  H181  N18  C16  C15   180.00   0.0  0
 GWL  CONST_42  H182  N18  C16  C15     0.00   0.0  0
 GWL  CONST_43  H181  N18  C16  O17     0.00   0.0  0
 GWL  CONST_44  H182  N18  C16  O17   180.00   0.0  0
 GWL  Var_01    C06   O05  C04  C01    95.12  30.0  2
 GWL  Var_02    C04   C01  C02  C03  -110.19  30.0  2
 GWL  Var_03    N25   C01  C02  C03    69.40  30.0  2
 GWL  Var_04    C21   C04  O05  C06   -86.10  30.0  2
 GWL  Var_05    C11   C10  O09  C08    -1.02  30.0  2
 GWL  Var_06    C13   C10  O09  C08   178.80  30.0  2
 GWL  Var_07    C15   C14  C13  C10    76.21  30.0  2
 GWL  Var_08    C19   C13  C14  C15  -102.30  30.0  2
 GWL  Var_09    H021  C02  C01  C04   129.55  30.0  1
 GWL  Var_10    H022  C02  C01  C04    12.88  30.0  1
 GWL  Var_11    H142  C14  C13  C10   -45.28  30.0  2
 GWL  Var_12    H141  C14  C13  C10  -161.69  30.0  2
 GWL  Var_13    H142  C14  C13  C19   136.21  30.0  2
 GWL  Var_14    H141  C14  C13  C19    19.80  30.0  2
 GWL  Var_15    H021  C02  C01  N25   -50.87  30.0  1
 GWL  Var_16    H022  C02  C01  N25  -167.54  30.0  1
 GWL  Var_17    C07   C06  O05  C04  -169.64  30.0  2
 GWL  Var_18    C10   O09  C08  C07  -172.53  30.0  1
 GWL  Var_19    C16   C15  C14  C13    56.66  30.0  2
 GWL  Var_20    H031  C03  C02  C01  -179.81  30.0  3
 GWL  Var_21    H033  C03  C02  C01   -59.61  30.0  3
 GWL  Var_22    H032  C03  C02  C01    60.66  30.0  3
 GWL  Var_23    H061  C06  O05  C04   -47.93  30.0  2
 GWL  Var_24    H062  C06  O05  C04    70.16  30.0  2
 GWL  Var_25    H082  C08  O09  C10    67.21  30.0  3
 GWL  Var_26    H081  C08  O09  C10   -51.62  30.0  3
 GWL  Var_27    H151  C15  C14  C13   178.38  30.0  2
 GWL  Var_28    H152  C15  C14  C13   -64.15  30.0  2
 GWL  Var_29    C08   C07  C06  O05    64.28  30.0  1
 GWL  Var_30    O09   C08  C07  C06    64.31  30.0  2
 GWL  Var_31    O17   C16  C15  C14  -108.70  30.0  1
 GWL  Var_32    N18   C16  C15  C14    70.13  30.0  1
 GWL  Var_33    H072  C07  C06  O05  -173.04  30.0  1
 GWL  Var_34    H071  C07  C06  O05   -57.37  30.0  1
 GWL  Var_35    H082  C08  C07  C06  -175.36  30.0  2
 GWL  Var_36    H081  C08  C07  C06   -56.85  30.0  2
 GWL  Var_37    H061  C06  C07  C08   -56.93  30.0  3
 GWL  Var_38    H062  C06  C07  C08  -175.14  30.0  3
 GWL  Var_39    H072  C07  C08  O09   -57.59  30.0  3
 GWL  Var_40    H071  C07  C08  O09  -173.21  30.0  3
 GWL  Var_41    H142  C14  C15  C16   179.87  30.0  3
 GWL  Var_42    H141  C14  C15  C16   -65.11  30.0  3
 GWL  Var_43    H151  C15  C16  O17   130.26  30.0  3
 GWL  Var_44    H152  C15  C16  O17    13.16  30.0  3
 GWL  Var_45    H151  C15  C16  N18   -50.91  30.0  3
 GWL  Var_46    H152  C15  C16  N18  -168.01  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
 GWL  plan-1  C01   0.020
 GWL  plan-1  C02   0.020
 GWL  plan-1  C04   0.020
 GWL  plan-1  O05   0.020
 GWL  plan-1  C21   0.020
 GWL  plan-1  N22   0.020
 GWL  plan-1  C23   0.020
 GWL  plan-1  N24   0.020
 GWL  plan-1  N25   0.020
 GWL  plan-1  N26   0.020
 GWL  plan-2  O09   0.020
 GWL  plan-2  C10   0.020
 GWL  plan-2  C11   0.020
 GWL  plan-2  C12   0.020
 GWL  plan-2  C13   0.020
 GWL  plan-2  C14   0.020
 GWL  plan-2  C19   0.020
 GWL  plan-2  C20   0.020
 GWL  plan-2  H111  0.020
 GWL  plan-2  H121  0.020
 GWL  plan-2  H191  0.020
 GWL  plan-2  H201  0.020
 GWL  plan-3  C15   0.020
 GWL  plan-3  C16   0.020
 GWL  plan-3  O17   0.020
 GWL  plan-3  N18   0.020
 GWL  plan-3  H181  0.020
 GWL  plan-3  H182  0.020
 GWL  plan-4  C23   0.020
 GWL  plan-4  N24   0.020
 GWL  plan-4  H241  0.020
 GWL  plan-4  H242  0.020
 GWL  plan-5  C21   0.020
 GWL  plan-5  N26   0.020
 GWL  plan-5  H261  0.020
 GWL  plan-5  H262  0.020

