# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 22:40:45 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 8-(2-ethenyl-6-ethyl-4-methylphenyl)tetrahydro-7H-pyrazolo[1,2-d][1,4,5]oxadiazepine-7,9(8H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1cc(C)cc(C=C)c1C2C(=O)N3CCOCCN3C2=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
 GY3  GY3  8-(2-ethenyl-6-ethyl-4-methylphenyl)tetrahydro-7H-pyrazolo[1,2-d][1,4,5]oxadiazepine-7,9(8H)-dione  ligand  45  23  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GY3
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
 GY3  O1    O  O2    0  -0.469  -4.6137  -0.6810   0.0440
 GY3  C2    C  CH2   0  -0.185  -3.9668  -0.6179  -1.2000
 GY3  C3    C  CH2   0  -0.357  -3.2360   0.6927  -1.4669
 GY3  N4    N  NR5   0  -0.323  -1.9704   0.8109  -0.7853
 GY3  C5    C  CR5   0   0.602  -0.7435   0.8007  -1.3451
 GY3  C6    C  CR15  0  -0.785   0.2466   0.9784  -0.2103
 GY3  C7    C  CR5   0   0.631  -0.6157   0.8780   1.0328
 GY3  N8    N  NR5   0  -0.321  -1.8976   0.8700   0.6114
 GY3  C9    C  CH2   0  -0.358  -3.0676   0.6417   1.4251
 GY3  C10   C  CH2   0  -0.187  -3.7616  -0.6902   1.1610
 GY3  O11   O  O     0  -0.454  -0.4992   0.7073  -2.5314
 GY3  O12   O  O     0  -0.455  -0.2438   0.8503   2.1880
 GY3  C19   C  CR6   0   0.135   1.4612   0.0927  -0.2258
 GY3  C20   C  CR6   0   0.113   2.7445   0.6414  -0.3179
 GY3  C21   C  CR16  0  -0.374   3.8485  -0.2082  -0.2927
 GY3  C22   C  CR6   0   0.132   3.7211  -1.5846  -0.1654
 GY3  C23   C  CR16  0  -0.376   2.4394  -2.1127  -0.0720
 GY3  C24   C  CR6   0   0.090   1.3118  -1.2971  -0.0995
 GY3  C25   C  C1    0  -0.286  -0.0176  -1.9258   0.0048
 GY3  C26   C  C2    0  -0.494  -0.3378  -2.8511   0.9047
 GY3  C27   C  CH3   0  -0.724   4.9268  -2.4762  -0.1153
 GY3  C28   C  CH2   0  -0.546   2.9940   2.1264  -0.3831
 GY3  C29   C  CH3   0  -0.656   2.9318   2.7820   0.9968
 GY3  H2    H  HCH2  0   0.216  -3.2673  -1.4560  -1.3288
 GY3  H2A   H  HCH2  0   0.259  -4.7452  -0.7229  -1.9568
 GY3  H3    H  HCH2  0   0.291  -3.0031   0.7487  -2.5291
 GY3  H3A   H  HCH2  0   0.281  -3.8739   1.5483  -1.2341
 GY3  H6    H  HCR5  0   0.369   0.5467   2.0311  -0.2728
 GY3  H9    H  HCH2  0   0.289  -2.7130   0.6583   2.4544
 GY3  H9A   H  HCH2  0   0.279  -3.7741   1.4673   1.3156
 GY3  H10   H  HCH2  0   0.260  -4.3910  -0.9116   2.0239
 GY3  H10A  H  HCH2  0   0.216  -3.0085  -1.4865   1.0853
 GY3  H21   H  HCR6  0   0.241   4.8396   0.2243  -0.3804
 GY3  H23   H  HCR6  0   0.247   2.3081  -3.1860   0.0002
 GY3  H25   H  H     0   0.260  -0.7708  -1.6420  -0.7236
 GY3  H26   H  H     0   0.249  -1.3202  -3.3045   0.9116
 GY3  H26A  H  H     0   0.250   0.3579  -3.1829   1.6655
 GY3  H27   H  HCH3  0   0.251   5.2556  -2.6273   0.9150
 GY3  H27A  H  HCH3  0   0.245   4.7139  -3.4594  -0.5342
 GY3  H27B  H  HCH3  0   0.245   5.7655  -2.0482  -0.6632
 GY3  H28   H  HCH2  0   0.258   3.9836   2.2972  -0.8102
 GY3  H28A  H  HCH2  0   0.248   2.2934   2.6158  -1.0635
 GY3  H29   H  HCH3  0   0.225   1.9588   2.6445   1.4700
 GY3  H29A  H  HCH3  0   0.231   3.6805   2.3505   1.6618
 GY3  H29B  H  HCH3  0   0.236   3.1223   3.8529   0.9257

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
 GY3  C2   O1    single    1.404  0.020  1.404
 GY3  O1   C10   single    1.405  0.020  1.405
 GY3  C3   C2    single    1.524  0.020  1.524
 GY3  C2   H2    single    0.970  0.020  1.090
 GY3  C2   H2A   single    0.970  0.020  1.090
 GY3  N4   C3    single    1.442  0.020  1.442
 GY3  C3   H3    single    0.970  0.020  1.090
 GY3  C3   H3A   single    0.970  0.020  1.090
 GY3  C5   N4    single    1.349  0.020  1.349
 GY3  N4   N8    single    1.400  0.020  1.400
 GY3  O11  C5    double    1.215  0.020  1.215
 GY3  C6   C5    single    1.516  0.020  1.516
 GY3  C19  C6    single    1.503  0.020  1.503
 GY3  C6   C7    single    1.516  0.020  1.516
 GY3  C6   H6    single    0.970  0.020  1.090
 GY3  O12  C7    double    1.214  0.020  1.214
 GY3  C7   N8    single    1.349  0.020  1.349
 GY3  N8   C9    single    1.443  0.020  1.443
 GY3  C9   C10   single    1.525  0.020  1.525
 GY3  C9   H9    single    0.970  0.020  1.090
 GY3  C9   H9A   single    0.970  0.020  1.090
 GY3  C10  H10   single    0.970  0.020  1.090
 GY3  C10  H10A  single    0.970  0.020  1.090
 GY3  C24  C19   aromatic  1.404  0.020  1.404
 GY3  C19  C20   aromatic  1.399  0.020  1.399
 GY3  C21  C20   aromatic  1.393  0.020  1.393
 GY3  C20  C28   single    1.507  0.020  1.507
 GY3  C22  C21   aromatic  1.388  0.020  1.388
 GY3  C21  H21   single    0.930  0.020  1.080
 GY3  C27  C22   single    1.500  0.020  1.500
 GY3  C23  C22   aromatic  1.389  0.020  1.389
 GY3  C23  C24   aromatic  1.392  0.020  1.392
 GY3  C23  H23   single    0.930  0.020  1.080
 GY3  C25  C24   single    1.474  0.020  1.474
 GY3  C26  C25   double    1.330  0.020  1.330
 GY3  C25  H25   single    0.930  0.020  1.080
 GY3  C26  H26   single    0.930  0.020  1.080
 GY3  C26  H26A  single    0.930  0.020  1.080
 GY3  C27  H27   single    0.970  0.020  1.090
 GY3  C27  H27A  single    0.970  0.020  1.090
 GY3  C27  H27B  single    0.970  0.020  1.090
 GY3  C28  C29   single    1.529  0.020  1.529
 GY3  C28  H28   single    0.970  0.020  1.090
 GY3  C28  H28A  single    0.970  0.020  1.090
 GY3  C29  H29   single    0.970  0.020  1.090
 GY3  C29  H29A  single    0.970  0.020  1.090
 GY3  C29  H29B  single    0.970  0.020  1.090

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
 GY3  C10   O1   C2    115.18  3.000
 GY3  H2A   C2   H2    107.43  3.000
 GY3  H2A   C2   C3    107.67  3.000
 GY3  H2    C2   C3    109.27  3.000
 GY3  H2A   C2   O1    106.36  3.000
 GY3  H2    C2   O1    111.27  3.000
 GY3  C3    C2   O1    114.51  3.000
 GY3  H3A   C3   H3    107.01  3.000
 GY3  H3A   C3   N4    110.34  3.000
 GY3  H3    C3   N4    105.62  3.000
 GY3  H3A   C3   C2    110.87  3.000
 GY3  H3    C3   C2    108.51  3.000
 GY3  N4    C3   C2    114.11  3.000
 GY3  N8    N4   C5    111.54  3.000
 GY3  N8    N4   C3    121.37  3.000
 GY3  C5    N4   C3    126.98  3.000
 GY3  O11   C5   C6    127.48  3.000
 GY3  C6    C5   N4    106.41  3.000
 GY3  O11   C5   N4    126.08  3.000
 GY3  H6    C6   C19   110.11  3.000
 GY3  H6    C6   C7    105.42  3.000
 GY3  C19   C6   C7    115.40  3.000
 GY3  H6    C6   C5    104.39  3.000
 GY3  C7    C6   C5    103.56  3.000
 GY3  C19   C6   C5    116.79  3.000
 GY3  O12   C7   N8    126.02  3.000
 GY3  N8    C7   C6    106.54  3.000
 GY3  O12   C7   C6    127.41  3.000
 GY3  C9    N8   C7    126.51  3.000
 GY3  C9    N8   N4    120.91  3.000
 GY3  C7    N8   N4    111.18  3.000
 GY3  H9A   C9   H9    107.09  3.000
 GY3  H9A   C9   C10   110.39  3.000
 GY3  H9    C9   C10   108.98  3.000
 GY3  H9A   C9   N8    110.38  3.000
 GY3  H9    C9   N8    105.46  3.000
 GY3  C10   C9   N8    114.17  3.000
 GY3  H10A  C10  H10   107.64  3.000
 GY3  H10A  C10  C9    109.45  3.000
 GY3  H10   C10  C9    107.63  3.000
 GY3  H10A  C10  O1    111.45  3.000
 GY3  H10   C10  O1    106.28  3.000
 GY3  C9    C10  O1    114.08  3.000
 GY3  C24   C19  C20   119.47  3.000
 GY3  C20   C19  C6    120.73  3.000
 GY3  C24   C19  C6    119.77  3.000
 GY3  C28   C20  C21   118.06  3.000
 GY3  C28   C20  C19   122.76  3.000
 GY3  C21   C20  C19   119.12  3.000
 GY3  H21   C21  C22   119.12  3.000
 GY3  H21   C21  C20   118.64  3.000
 GY3  C22   C21  C20   122.24  3.000
 GY3  C27   C22  C23   120.88  3.000
 GY3  C23   C22  C21   117.89  3.000
 GY3  C27   C22  C21   121.23  3.000
 GY3  H23   C23  C24   118.92  3.000
 GY3  H23   C23  C22   119.51  3.000
 GY3  C24   C23  C22   121.55  3.000
 GY3  C25   C24  C23   118.64  3.000
 GY3  C25   C24  C19   121.64  3.000
 GY3  C23   C24  C19   119.72  3.000
 GY3  H25   C25  C26   117.96  3.000
 GY3  H25   C25  C24   117.82  3.000
 GY3  C26   C25  C24   124.18  3.000
 GY3  H26A  C26  H26   116.76  3.000
 GY3  H26A  C26  C25   122.27  3.000
 GY3  H26   C26  C25   120.97  3.000
 GY3  H27B  C27  H27A  108.15  3.000
 GY3  H27B  C27  H27   107.28  3.000
 GY3  H27A  C27  H27   107.26  3.000
 GY3  H27B  C27  C22   111.62  3.000
 GY3  H27A  C27  C22   111.49  3.000
 GY3  H27   C27  C22   110.84  3.000
 GY3  H28A  C28  H28   105.53  3.000
 GY3  H28A  C28  C29   110.11  3.000
 GY3  H28   C28  C29   108.84  3.000
 GY3  H28A  C28  C20   111.23  3.000
 GY3  H28   C28  C20   108.74  3.000
 GY3  C29   C28  C20   112.13  3.000
 GY3  H29B  C29  H29A  107.97  3.000
 GY3  H29B  C29  H29   107.94  3.000
 GY3  H29A  C29  H29   107.34  3.000
 GY3  H29B  C29  C28   110.81  3.000
 GY3  H29A  C29  C28   110.66  3.000
 GY3  H29   C29  C28   111.95  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
 GY3  CONST_01  C22   C23  C24  C19     0.00   0.0  0
 GY3  CONST_02  C22   C21  C20  C19     0.00   0.0  0
 GY3  CONST_03  C23   C24  C19  C20     0.00   0.0  0
 GY3  CONST_04  C23   C22  C21  C20     0.00   0.0  0
 GY3  CONST_05  C24   C19  C20  C21     0.00   0.0  0
 GY3  CONST_06  C24   C23  C22  C21     0.00   0.0  0
 GY3  CONST_07  C23   C24  C19  C6    180.00   0.0  0
 GY3  CONST_08  C21   C20  C19  C6    180.00   0.0  0
 GY3  CONST_09  C25   C24  C19  C6      0.00   0.0  0
 GY3  CONST_10  C28   C20  C19  C6      0.00   0.0  0
 GY3  CONST_11  C25   C24  C19  C20   180.00   0.0  0
 GY3  CONST_12  C27   C22  C21  C20   180.00   0.0  0
 GY3  CONST_13  C28   C20  C21  C22   180.00   0.0  0
 GY3  CONST_14  C25   C24  C23  C22   180.00   0.0  0
 GY3  CONST_15  C28   C20  C19  C24   180.00   0.0  0
 GY3  CONST_16  C27   C22  C23  C24   180.00   0.0  0
 GY3  CONST_17  H23   C23  C24  C19   180.00   0.0  0
 GY3  CONST_18  H21   C21  C20  C19   180.00   0.0  0
 GY3  CONST_19  H26   C26  C25  C24   180.00   0.0  0
 GY3  CONST_20  H26A  C26  C25  C24     0.00   0.0  0
 GY3  Var_01    C26   C25  C24  C19  -133.06  30.0  2
 GY3  Var_02    C29   C28  C20  C19    80.21  30.0  2
 GY3  Var_03    H27   C27  C22  C21    90.84  30.0  2
 GY3  Var_04    H29   C29  C28  C20   -59.86  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
 GY3  chir_01  C6  C5  C19  C7  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
 GY3  plan-1  C6    0.020
 GY3  plan-1  C19   0.020
 GY3  plan-1  C20   0.020
 GY3  plan-1  C21   0.020
 GY3  plan-1  C22   0.020
 GY3  plan-1  C23   0.020
 GY3  plan-1  C24   0.020
 GY3  plan-1  C25   0.020
 GY3  plan-1  C27   0.020
 GY3  plan-1  C28   0.020
 GY3  plan-1  H21   0.020
 GY3  plan-1  H23   0.020
 GY3  plan-2  C3    0.020
 GY3  plan-2  N4    0.020
 GY3  plan-2  C5    0.020
 GY3  plan-2  C6    0.020
 GY3  plan-2  C7    0.020
 GY3  plan-2  N8    0.020
 GY3  plan-2  C9    0.020
 GY3  plan-2  O11   0.020
 GY3  plan-2  O12   0.020
 GY3  plan-3  C24   0.020
 GY3  plan-3  C25   0.020
 GY3  plan-3  C26   0.020
 GY3  plan-3  H25   0.020
 GY3  plan-3  H26   0.020
 GY3  plan-3  H26A  0.020

