# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 20:39:22 2020
#   Inital geometry file: a 154 line input string
#   Ligand name: 4-[2-(4-amino-2,5-dihydro-1,2,5-oxadiazol-3-yl)-6-{[(1S)-3-amino-1-phenylpropyl]oxy}-1-ethyl-1H-imidazo[4,5-c]pyridin-4-yl]-2-methylbut-3-yn-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCn1c2cc(O[C@@H](CCN)c3ccccc3)nc(C#CC(C)(C)O)c2nc1C4=C(N)NON4
#
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
 G98  G98  4-[2-(4-amino-2,5-dihydro-1,2,5-oxadiazol-3-yl)-6-{[(1S)-3-amino-1-phenylpropyl]oxy}-1-ethyl-1H-imidazo[4,5-c]pyridin-4-yl]-2-methylbut-3-yn-2-ol  ligand  63  34  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G98
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
 G98  N1    N  N     0  -0.486   1.0911  -0.4803  -0.1119
 G98  N3    N  N     0  -0.543  -2.5668  -0.1345   0.1551
 G98  C4    C  CR5   0   0.557  -3.0757   1.0770   0.0301
 G98  C5    C  CR56  0   0.091  -1.2203   0.0272   0.0258
 G98  C6    C  CR56  0   0.418  -0.9097   1.3828  -0.1980
 G98  C8    C  CH3   0  -0.662  -2.4240   4.1157   1.0918
 G98  C10   C  CR5   0   0.430  -5.3892   0.3782   0.5215
 G98  C13   C  CT    0   0.006  -0.9393  -4.8735   0.6458
 G98  C15   C  CH3   0  -0.656  -2.4369  -5.1210   0.4865
 G98  C17   C  CH2   0  -0.438   4.1298  -0.1032  -1.9024
 G98  C20   C  CR16  0  -0.314   5.5520   0.1124   1.2027
 G98  C21   C  CR16  0  -0.239   6.6362   0.6519   1.8841
 G98  C22   C  CR16  0  -0.268   7.0136   1.9676   1.6569
 G98  C24   C  CR16  0  -0.302   5.2227   2.1944   0.0610
 G98  O2    O  OH1   0  -0.654  -0.6075  -5.2339   1.9740
 G98  C14   C  CH3   0  -0.672  -0.1430  -5.7031  -0.3622
 G98  C12   C  CSP   0   0.046  -0.6579  -3.4422   0.4324
 G98  C3    C  CR6   0  -0.030  -0.1744  -0.8839   0.0602
 G98  C1    C  CR6   0   0.512   1.3534   0.7922  -0.3190
 G98  O3    O  O2    0  -0.506   2.6247   1.1906  -0.5020
 G98  C16   C  CH1   0  -0.053   3.6989   0.2478  -0.4815
 G98  C19   C  CR6   0   0.132   4.8365   0.8741   0.2852
 G98  C23   C  CR16  0  -0.240   6.3018   2.7370   0.7441
 G98  N7    N  NH2   0  -0.800   3.6531  -1.2086  -4.0229
 G98  C2    C  CR16  0  -0.469   0.3899   1.8077  -0.3714
 G98  N2    N  NR5   0  -0.577  -2.1108   2.0337  -0.2026
 G98  C9    C  CR5   0  -0.025  -4.4723   1.3102   0.1322
 G98  N5    N  NR15  0  -0.376  -6.6480   0.9900   0.6488
 G98  O1    O  O     0  -0.311  -6.3542   2.3705   0.5901
 G98  N4    N  NR15  0  -0.401  -5.1697   2.5336  -0.1511
 G98  H7    H  HCH2  0   0.269  -3.1262   3.7071  -0.9057
 G98  H7A   H  HCH2  0   0.267  -1.3939   3.8705  -0.7894
 G98  H8    H  HCH3  0   0.240  -3.3153   3.7470   1.5982
 G98  H8A   H  HCH3  0   0.233  -1.5577   3.9193   1.7237
 G98  H8B   H  HCH3  0   0.241  -2.5229   5.1955   0.9830
 G98  H15   H  HCH3  0   0.242  -3.0112  -4.5284   1.1986
 G98  H15A  H  HCH3  0   0.238  -2.7628  -4.8564  -0.5184
 G98  H15B  H  HCH3  0   0.243  -2.6601  -6.1762   0.6508
 G98  H17   H  HCH2  0   0.229   4.4432   0.8110  -2.4190
 G98  H17A  H  HCH2  0   0.235   5.0176  -0.7373  -1.8301
 G98  H20   H  HCR6  0   0.252   5.2592  -0.9141   1.3898
 G98  H21   H  HCR6  0   0.256   7.1797   0.0445   2.5960
 G98  H22   H  HCR6  0   0.256   7.8557   2.3928   2.1877
 G98  H24   H  HCR6  0   0.251   4.6837   2.8102  -0.6483
 G98  HO2   H  HOH1  0   0.452   0.3485  -5.1721   2.0794
 G98  H14   H  HCH3  0   0.239  -0.4069  -5.4354  -1.3847
 G98  H14A  H  HCH3  0   0.241   0.9299  -5.5452  -0.2404
 G98  H14B  H  HCH3  0   0.244  -0.3550  -6.7637  -0.2193
 G98  H16   H  HCH1  0   0.256   3.3813  -0.6615   0.0335
 G98  H23   H  HCR6  0   0.256   6.5882   3.7650   0.5631
 G98  H18   H  HCH2  0   0.219   2.7840  -1.7459  -2.2125
 G98  H18A  H  HCH2  0   0.198   2.1808  -0.2192  -2.8257
 G98  HN7   H  HNH2  0   0.347   2.9645  -1.7304  -4.5500
 G98  HN7A  H  HNH2  0   0.338   3.8275  -0.3708  -4.5653
 G98  H2    H  HCR6  0   0.281   0.6692   2.8389  -0.5404
 G98  HN6   H  HNH2  0   0.413  -4.3219  -1.2975   0.7016
 G98  HN6A  H  HNH2  0   0.408  -5.9096  -1.3803   1.3837
 G98  HN5   H  HNR5  0   0.395  -7.2682   0.7419  -0.1265
 G98  HN4   H  HNR5  0   0.368  -5.4464   2.5537  -1.1357
 G98  C7    C  CH2   0  -0.323  -2.2706   3.4768  -0.2758
 G98  C11   C  CSP   0   0.161  -0.4214  -2.2720   0.2659
 G98  C18   C  CH2   0  -0.281   3.0845  -0.8344  -2.7339
 G98  N6    N  NH2   0  -0.829  -5.2604  -0.9255   0.7628

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
 G98  N1   C3    aromatic  1.339  0.020  1.339
 G98  N1   C1    aromatic  1.316  0.020  1.316
 G98  N3   C4    aromatic  1.320  0.020  1.320
 G98  N3   C5    aromatic  1.362  0.020  1.362
 G98  C4   N2    aromatic  1.379  0.020  1.379
 G98  C4   C9    single    1.420  0.020  1.420
 G98  C5   C6    aromatic  1.409  0.020  1.409
 G98  C5   C3    aromatic  1.387  0.020  1.387
 G98  C6   C2    aromatic  1.378  0.020  1.378
 G98  C6   N2    aromatic  1.366  0.020  1.366
 G98  C7   C8    single    1.517  0.020  1.517
 G98  C7   N2    single    1.454  0.020  1.454
 G98  C10  C9    double    1.364  0.020  1.364
 G98  C10  N6    single    1.332  0.020  1.332
 G98  C10  N5    single    1.405  0.020  1.405
 G98  C13  C15   single    1.526  0.020  1.526
 G98  C13  O2    single    1.416  0.020  1.416
 G98  C13  C14   single    1.529  0.020  1.529
 G98  C13  C12   single    1.474  0.020  1.474
 G98  C17  C16   single    1.526  0.020  1.526
 G98  C17  C18   single    1.523  0.020  1.523
 G98  C20  C21   aromatic  1.390  0.020  1.390
 G98  C20  C19   aromatic  1.391  0.020  1.391
 G98  C21  C22   aromatic  1.387  0.020  1.387
 G98  C22  C23   aromatic  1.390  0.020  1.390
 G98  C24  C19   aromatic  1.394  0.020  1.394
 G98  C24  C23   aromatic  1.388  0.020  1.388
 G98  C12  C11   triple    1.205  0.020  1.205
 G98  C11  C3    single    1.425  0.020  1.425
 G98  C1   O3    single    1.345  0.020  1.345
 G98  C1   C2    aromatic  1.401  0.020  1.401
 G98  O3   C16   single    1.429  0.020  1.429
 G98  C16  C19   single    1.508  0.020  1.508
 G98  C18  N7    single    1.458  0.020  1.458
 G98  C9   N4    single    1.436  0.020  1.436
 G98  N5   O1    single    1.413  0.020  1.413
 G98  O1   N4    single    1.407  0.020  1.407
 G98  C7   H7    single    0.970  0.020  1.090
 G98  C7   H7A   single    0.970  0.020  1.090
 G98  C8   H8    single    0.970  0.020  1.090
 G98  C8   H8A   single    0.970  0.020  1.090
 G98  C8   H8B   single    0.970  0.020  1.090
 G98  C15  H15   single    0.970  0.020  1.090
 G98  C15  H15A  single    0.970  0.020  1.090
 G98  C15  H15B  single    0.970  0.020  1.090
 G98  C17  H17   single    0.970  0.020  1.090
 G98  C17  H17A  single    0.970  0.020  1.090
 G98  C20  H20   single    0.930  0.020  1.080
 G98  C21  H21   single    0.930  0.020  1.080
 G98  C22  H22   single    0.930  0.020  1.080
 G98  C24  H24   single    0.930  0.020  1.080
 G98  O2   HO2   single    0.850  0.020  0.980
 G98  C14  H14   single    0.970  0.020  1.090
 G98  C14  H14A  single    0.970  0.020  1.090
 G98  C14  H14B  single    0.970  0.020  1.090
 G98  C16  H16   single    0.970  0.020  1.090
 G98  C23  H23   single    0.930  0.020  1.080
 G98  C18  H18   single    0.970  0.020  1.090
 G98  C18  H18A  single    0.970  0.020  1.090
 G98  N7   HN7   single    0.890  0.020  1.040
 G98  N7   HN7A  single    0.890  0.020  1.040
 G98  C2   H2    single    0.930  0.020  1.080
 G98  N6   HN6   single    0.890  0.020  1.040
 G98  N6   HN6A  single    0.890  0.020  1.040
 G98  N5   HN5   single    0.890  0.020  1.040
 G98  N4   HN4   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
 G98  C1    N1   C3    120.00  3.000
 G98  C5    N3   C4    105.26  3.000
 G98  C9    C4   N2    125.92  3.000
 G98  C9    C4   N3    121.55  3.000
 G98  N2    C4   N3    112.52  3.000
 G98  C3    C5   C6    118.02  3.000
 G98  C3    C5   N3    131.66  3.000
 G98  C6    C5   N3    110.32  3.000
 G98  N2    C6   C2    132.98  3.000
 G98  N2    C6   C5    105.38  3.000
 G98  C2    C6   C5    121.64  3.000
 G98  H8B   C8   H8A   107.97  3.000
 G98  H8B   C8   H8    107.91  3.000
 G98  H8A   C8   H8    108.65  3.000
 G98  H8B   C8   C7    109.66  3.000
 G98  H8A   C8   C7    111.49  3.000
 G98  H8    C8   C7    111.05  3.000
 G98  N5    C10  N6    119.75  3.000
 G98  N5    C10  C9    109.30  3.000
 G98  N6    C10  C9    130.95  3.000
 G98  C12   C13  C14   109.38  3.000
 G98  C12   C13  O2    109.77  3.000
 G98  C14   C13  O2    110.99  3.000
 G98  C12   C13  C15   109.25  3.000
 G98  C14   C13  C15   110.74  3.000
 G98  O2    C13  C15   106.66  3.000
 G98  H15B  C15  H15A  108.23  3.000
 G98  H15B  C15  H15   108.64  3.000
 G98  H15A  C15  H15   108.24  3.000
 G98  H15B  C15  C13   109.99  3.000
 G98  H15A  C15  C13   110.52  3.000
 G98  H15   C15  C13   111.13  3.000
 G98  H17A  C17  H17   106.42  3.000
 G98  H17A  C17  C18   108.36  3.000
 G98  H17   C17  C18   109.85  3.000
 G98  H17A  C17  C16   107.52  3.000
 G98  H17   C17  C16   109.14  3.000
 G98  C18   C17  C16   115.16  3.000
 G98  H20   C20  C19   119.58  3.000
 G98  H20   C20  C21   119.60  3.000
 G98  C19   C20  C21   120.82  3.000
 G98  H21   C21  C22   120.22  3.000
 G98  H21   C21  C20   119.77  3.000
 G98  C22   C21  C20   120.00  3.000
 G98  H22   C22  C23   120.20  3.000
 G98  H22   C22  C21   120.25  3.000
 G98  C23   C22  C21   119.55  3.000
 G98  H24   C24  C23   119.15  3.000
 G98  H24   C24  C19   120.40  3.000
 G98  C23   C24  C19   120.44  3.000
 G98  HO2   O2   C13   108.59  3.000
 G98  H14B  C14  H14A  108.48  3.000
 G98  H14B  C14  H14   108.34  3.000
 G98  H14A  C14  H14   107.90  3.000
 G98  H14B  C14  C13   109.87  3.000
 G98  H14A  C14  C13   111.10  3.000
 G98  H14   C14  C13   111.06  3.000
 G98  C11   C12  C13   180.00  3.000
 G98  C11   C3   C5    120.84  3.000
 G98  C11   C3   N1    118.42  3.000
 G98  C5    C3   N1    120.74  3.000
 G98  C2    C1   O3    115.49  3.000
 G98  C2    C1   N1    124.75  3.000
 G98  O3    C1   N1    119.77  3.000
 G98  C16   O3   C1    120.87  3.000
 G98  H16   C16  C19   108.99  3.000
 G98  H16   C16  O3    109.71  3.000
 G98  C19   C16  O3    107.47  3.000
 G98  H16   C16  C17   109.25  3.000
 G98  C19   C16  C17   110.86  3.000
 G98  O3    C16  C17   110.52  3.000
 G98  C16   C19  C24   121.38  3.000
 G98  C16   C19  C20   119.74  3.000
 G98  C24   C19  C20   118.84  3.000
 G98  H23   C23  C24   119.66  3.000
 G98  H23   C23  C22   120.00  3.000
 G98  C24   C23  C22   120.34  3.000
 G98  HN7A  N7   HN7   105.34  3.000
 G98  HN7A  N7   C18   109.17  3.000
 G98  HN7   N7   C18   109.12  3.000
 G98  H2    C2   C1    121.29  3.000
 G98  H2    C2   C6    123.85  3.000
 G98  C1    C2   C6    114.85  3.000
 G98  C7    N2   C6    124.74  3.000
 G98  C7    N2   C4    128.35  3.000
 G98  C6    N2   C4    106.51  3.000
 G98  N4    C9   C10   108.17  3.000
 G98  N4    C9   C4    127.11  3.000
 G98  C10   C9   C4    124.72  3.000
 G98  HN5   N5   O1    109.36  3.000
 G98  HN5   N5   C10   111.63  3.000
 G98  O1    N5   C10   103.62  3.000
 G98  N4    O1   N5    108.08  3.000
 G98  HN4   N4   O1    106.35  3.000
 G98  HN4   N4   C9    109.75  3.000
 G98  O1    N4   C9    101.90  3.000
 G98  H7A   C7   H7    106.47  3.000
 G98  H7A   C7   N2    107.09  3.000
 G98  H7    C7   N2    109.03  3.000
 G98  H7A   C7   C8    110.73  3.000
 G98  H7    C7   C8    110.70  3.000
 G98  N2    C7   C8    112.56  3.000
 G98  C3    C11  C12   180.00  3.000
 G98  H18A  C18  H18   106.34  3.000
 G98  H18A  C18  N7    113.04  3.000
 G98  H18   C18  N7    108.38  3.000
 G98  H18A  C18  C17   109.99  3.000
 G98  H18   C18  C17   109.20  3.000
 G98  N7    C18  C17   109.77  3.000
 G98  HN6A  N6   HN6   118.00  3.000
 G98  HN6A  N6   C10   119.43  3.000
 G98  HN6   N6   C10   116.02  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
 G98  CONST_01  N3   C5   C3   N1    180.00   0.0  0
 G98  CONST_02  C6   C5   C3   N1      0.00   0.0  0
 G98  CONST_03  C6   C2   C1   N1      0.00   0.0  0
 G98  CONST_04  C6   N2   C4   N3      0.00   0.0  0
 G98  CONST_05  C2   C6   C5   N3    180.00   0.0  0
 G98  CONST_06  N2   C6   C5   N3      0.00   0.0  0
 G98  CONST_07  C6   C5   N3   C4      0.00   0.0  0
 G98  CONST_08  C3   C5   N3   C4    180.00   0.0  0
 G98  CONST_09  C5   C6   N2   C4      0.00   0.0  0
 G98  CONST_10  C2   C6   N2   C4    180.00   0.0  0
 G98  CONST_11  N2   C4   N3   C5      0.00   0.0  0
 G98  CONST_12  C1   C2   C6   C5      0.00   0.0  0
 G98  CONST_13  C1   N1   C3   C5      0.00   0.0  0
 G98  CONST_14  C23  C22  C21  C20     0.00   0.0  0
 G98  CONST_15  C23  C24  C19  C20     0.00   0.0  0
 G98  CONST_16  C24  C19  C20  C21     0.00   0.0  0
 G98  CONST_17  C24  C23  C22  C21     0.00   0.0  0
 G98  CONST_18  C19  C20  C21  C22     0.00   0.0  0
 G98  CONST_19  C19  C24  C23  C22     0.00   0.0  0
 G98  CONST_20  C2   C1   N1   C3      0.00   0.0  0
 G98  CONST_21  C2   C6   C5   C3      0.00   0.0  0
 G98  CONST_22  N2   C6   C5   C3    180.00   0.0  0
 G98  CONST_23  N2   C6   C2   C1    180.00   0.0  0
 G98  CONST_24  C9   C4   N3   C5    180.00   0.0  0
 G98  CONST_25  C9   C4   N2   C6    180.00   0.0  0
 G98  CONST_26  O1   N5   C10  C9      0.00   0.0  0
 G98  CONST_27  C7   N2   C4   N3    180.00   0.0  0
 G98  CONST_28  C11  C3   C5   N3      0.00   0.0  0
 G98  CONST_29  C7   N2   C6   C5    180.00   0.0  0
 G98  CONST_30  C11  C3   C5   C6    180.00   0.0  0
 G98  CONST_31  O3   C1   C2   C6    180.00   0.0  0
 G98  CONST_32  C9   C4   N2   C7      0.00   0.0  0
 G98  CONST_33  C2   C6   N2   C7      0.00   0.0  0
 G98  CONST_34  C16  C19  C20  C21   180.00   0.0  0
 G98  CONST_35  C1   N1   C3   C11   180.00   0.0  0
 G98  CONST_36  O3   C1   N1   C3    180.00   0.0  0
 G98  CONST_37  C23  C24  C19  C16   180.00   0.0  0
 G98  CONST_38  O1   N5   C10  N6    180.00   0.0  0
 G98  CONST_39  H2   C2   C1   N1    180.00   0.0  0
 G98  CONST_40  H22  C22  C21  C20   180.00   0.0  0
 G98  CONST_41  H24  C24  C19  C20   180.00   0.0  0
 G98  CONST_42  H23  C23  C22  C21   180.00   0.0  0
 G98  CONST_43  H20  C20  C21  C22   180.00   0.0  0
 G98  CONST_44  H21  C21  C20  C19   180.00   0.0  0
 G98  CONST_46  HN6  N6   C10  C9      0.00   0.0  0
 G98  Var_01    C10  C9   C4   N3      8.39  30.0  2
 G98  Var_02    C8   C7   N2   C4     76.53  30.0  3
 G98  Var_03    C2   C1   O3   C16  -179.52  30.0  2
 G98  Var_04    H8   C8   C7   N2    -61.80  30.0  3
 G98  Var_05    N7   C18  C17  C16  -175.31  30.0  3
 G98  Var_06    H14  C14  C13  C15    61.01  30.0  3
 G98  Var_07    HN7  N7   C18  C17   177.43  30.0  3
 G98  Var_08    H15  C15  C13  O2     59.44  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
 G98  chir_01  C16  C17  O3  C19  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
 G98  plan-1  C4    0.020
 G98  plan-1  C10   0.020
 G98  plan-1  C9    0.020
 G98  plan-1  N5    0.020
 G98  plan-1  O1    0.020
 G98  plan-1  N4    0.020
 G98  plan-1  HN6   0.020
 G98  plan-1  HN6A  0.020
 G98  plan-1  HN5   0.020
 G98  plan-1  HN4   0.020
 G98  plan-1  N6    0.020
 G98  plan-2  C20   0.020
 G98  plan-2  C21   0.020
 G98  plan-2  C22   0.020
 G98  plan-2  C24   0.020
 G98  plan-2  C16   0.020
 G98  plan-2  C19   0.020
 G98  plan-2  C23   0.020
 G98  plan-2  H20   0.020
 G98  plan-2  H21   0.020
 G98  plan-2  H22   0.020
 G98  plan-2  H24   0.020
 G98  plan-2  H23   0.020
 G98  plan-3  N1    0.020
 G98  plan-3  N3    0.020
 G98  plan-3  C4    0.020
 G98  plan-3  C5    0.020
 G98  plan-3  C6    0.020
 G98  plan-3  C12   0.020
 G98  plan-3  C3    0.020
 G98  plan-3  C1    0.020
 G98  plan-3  O3    0.020
 G98  plan-3  C2    0.020
 G98  plan-3  N2    0.020
 G98  plan-3  C9    0.020
 G98  plan-3  H2    0.020
 G98  plan-3  C7    0.020
 G98  plan-3  C11   0.020

