# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 22:01:50 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: N-{3-[5-oxo-7-(piperazin-1-yl)-5H-[1,3,4]thiadiazolo[3,2-a]pyrimidin-2-yl]phenyl}glycinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC(=O)Nc1cccc(c1)C2=NN3C(=O)C=C(N=C3S2)N4CCNCC4
#
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
 RC2  RC2  N-{3-[5-oxo-7-(piperazin-1-yl)-5H-[1,3,4]thiadiazolo[3,2-a]pyrimidin-2-yl]phenyl}glycinamide  ligand  46  27  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RC2
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
 RC2  C     C  C     0   0.529  -5.3167   1.9144   0.0543
 RC2  N     N  NH2   0  -0.789  -6.4056   4.0998   0.2093
 RC2  O     O  O     0  -0.456  -4.2334   2.4465   0.1880
 RC2  S     S  S2    0   0.221  -0.1839   0.4936   0.3131
 RC2  C01   C  CH2   0  -0.312   6.9168   0.6107  -0.8043
 RC2  N01   N  NH1   0  -0.750  -5.4947   0.5715  -0.0888
 RC2  C02   C  CH2   0  -0.317   5.6218   2.5778  -0.3749
 RC2  N02   N  NH1   0  -0.579   6.9566   2.0421  -0.5723
 RC2  C03   C  CR56  0   0.380   1.3974  -0.2125   0.2192
 RC2  N03   N  NT    0  -0.500   4.7904   0.4062   0.3783
 RC2  C04   C  CR6   0   0.562   2.4033  -2.3829  -0.1434
 RC2  N04   N  N     0  -0.414   1.2624  -1.5392  -0.0221
 RC2  C05   C  CH2   0  -0.324   4.8134   1.8302   0.6802
 RC2  N05   N  N     0  -0.521   2.5008   0.4258   0.3543
 RC2  C06   C  CR16  0  -0.224  -4.1456  -2.8228  -0.3157
 RC2  N06   N  N     0  -0.203   0.0149  -2.0222  -0.1436
 RC2  C07   C  CR16  0  -0.593   3.6137  -1.6741   0.0073
 RC2  C08   C  CR5   0   0.081  -0.8568  -1.0947   0.0016
 RC2  C09   C  CH2   0  -0.322   6.1199  -0.1625   0.2452
 RC2  C10   C  CR6   0   0.121  -2.2975  -1.3222  -0.0832
 RC2  C11   C  CR16  0  -0.298  -2.7790  -2.6214  -0.2251
 RC2  C12   C  CH2   0  -0.419  -6.6226   2.6888   0.0047
 RC2  C13   C  CR16  0  -0.344  -5.0230  -1.7538  -0.2666
 RC2  C14   C  CR6   0   0.416  -4.5470  -0.4481  -0.1231
 RC2  C15   C  CR16  0  -0.403  -3.1718  -0.2385  -0.0308
 RC2  C16   C  CR6   0   0.591   3.6544  -0.2985   0.2425
 RC2  HN    H  HNH2  0   0.349  -5.9752   4.5069  -0.6104
 RC2  HNA   H  HNH2  0   0.358  -7.3016   4.5564   0.3117
 RC2  H01   H  HCH2  0   0.230   6.4745   0.4268  -1.7884
 RC2  H01A  H  HCH2  0   0.248   7.9361   0.2224  -0.8336
 RC2  HN01  H  HNH1  0   0.419  -6.4503   0.2615  -0.1906
 RC2  H02   H  HCH2  0   0.246   5.6951   3.6289  -0.0907
 RC2  H02A  H  HCH2  0   0.228   5.0841   2.5388  -1.3278
 RC2  HN02  H  HNH1  0   0.345   7.5161   2.2307   0.2518
 RC2  H05   H  HCH2  0   0.238   5.2723   1.9701   1.6659
 RC2  H05A  H  HCH2  0   0.278   3.7995   2.2132   0.7316
 RC2  H06   H  HCR6  0   0.272  -4.5357  -3.8255  -0.4260
 RC2  H07   H  HCR6  0   0.276   4.5105  -2.2675  -0.0700
 RC2  H09   H  HCH2  0   0.269   6.0748  -1.2110  -0.0327
 RC2  H09A  H  HCH2  0   0.246   6.6284  -0.1063   1.2145
 RC2  H11   H  HCR6  0   0.270  -2.0983  -3.4601  -0.2611
 RC2  H12   H  HCH2  0   0.246  -7.1231   2.4276  -0.9394
 RC2  H12A  H  HCH2  0   0.271  -7.2712   2.3073   0.7982
 RC2  H13   H  HCR6  0   0.282  -6.0896  -1.9303  -0.3408
 RC2  H15   H  HCR6  0   0.280  -2.7967   0.7682   0.0732
 RC2  O01   O  O     0  -0.487   2.2387  -3.5741  -0.3523

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
 RC2  C    O     double    1.214  0.020  1.214
 RC2  C    N01   single    1.362  0.020  1.362
 RC2  C    C12   single    1.519  0.020  1.519
 RC2  N    C12   single    1.442  0.020  1.442
 RC2  S    C03   single    1.734  0.020  1.734
 RC2  S    C08   single    1.753  0.020  1.753
 RC2  C01  N02   single    1.451  0.020  1.451
 RC2  C01  C09   single    1.528  0.020  1.528
 RC2  N01  C14   single    1.392  0.020  1.392
 RC2  O01  C04   double    1.221  0.020  1.221
 RC2  C02  N02   single    1.452  0.020  1.452
 RC2  C02  C05   single    1.525  0.020  1.525
 RC2  C03  N04   single    1.355  0.020  1.355
 RC2  C03  N05   double    1.282  0.020  1.282
 RC2  N03  C05   single    1.456  0.020  1.456
 RC2  N03  C09   single    1.452  0.020  1.452
 RC2  N03  C16   single    1.344  0.020  1.344
 RC2  C04  N04   single    1.424  0.020  1.424
 RC2  C04  C07   single    1.411  0.020  1.411
 RC2  N04  N06   single    1.343  0.020  1.343
 RC2  N05  C16   single    1.367  0.020  1.367
 RC2  C06  C11   aromatic  1.384  0.020  1.384
 RC2  C06  C13   aromatic  1.384  0.020  1.384
 RC2  N06  C08   double    1.281  0.020  1.281
 RC2  C07  C16   double    1.396  0.020  1.396
 RC2  C08  C10   single    1.461  0.020  1.461
 RC2  C10  C11   aromatic  1.393  0.020  1.393
 RC2  C10  C15   aromatic  1.393  0.020  1.393
 RC2  C13  C14   aromatic  1.397  0.020  1.397
 RC2  C14  C15   aromatic  1.394  0.020  1.394
 RC2  N    HN    single    0.890  0.020  1.040
 RC2  N    HNA   single    0.890  0.020  1.040
 RC2  C01  H01   single    0.970  0.020  1.090
 RC2  C01  H01A  single    0.970  0.020  1.090
 RC2  N01  HN01  single    0.860  0.020  1.020
 RC2  C02  H02   single    0.970  0.020  1.090
 RC2  C02  H02A  single    0.970  0.020  1.090
 RC2  N02  HN02  single    0.890  0.020  1.040
 RC2  C05  H05   single    0.970  0.020  1.090
 RC2  C05  H05A  single    0.970  0.020  1.090
 RC2  C06  H06   single    0.930  0.020  1.080
 RC2  C07  H07   single    0.930  0.020  1.080
 RC2  C09  H09   single    0.970  0.020  1.090
 RC2  C09  H09A  single    0.970  0.020  1.090
 RC2  C11  H11   single    0.930  0.020  1.080
 RC2  C12  H12   single    0.970  0.020  1.090
 RC2  C12  H12A  single    0.970  0.020  1.090
 RC2  C13  H13   single    0.930  0.020  1.080
 RC2  C15  H15   single    0.930  0.020  1.080

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
 RC2  C12   C    N01  112.75  3.000
 RC2  C12   C    O    123.17  3.000
 RC2  N01   C    O    124.07  3.000
 RC2  HNA   N    HN   106.11  3.000
 RC2  HNA   N    C12  108.84  3.000
 RC2  HN    N    C12  110.05  3.000
 RC2  C08   S    C03   88.36  3.000
 RC2  H01A  C01  H01  107.08  3.000
 RC2  H01A  C01  C09  109.00  3.000
 RC2  H01   C01  C09  108.77  3.000
 RC2  H01A  C01  N02  109.26  3.000
 RC2  H01   C01  N02  108.71  3.000
 RC2  C09   C01  N02  113.81  3.000
 RC2  HN01  N01  C14  114.64  3.000
 RC2  HN01  N01  C    115.91  3.000
 RC2  C14   N01  C    129.46  3.000
 RC2  H02A  C02  H02  107.10  3.000
 RC2  H02A  C02  C05  108.93  3.000
 RC2  H02   C02  C05  109.12  3.000
 RC2  H02A  C02  N02  108.67  3.000
 RC2  H02   C02  N02  109.21  3.000
 RC2  C05   C02  N02  113.61  3.000
 RC2  HN02  N02  C02  109.16  3.000
 RC2  HN02  N02  C01  109.19  3.000
 RC2  C02   N02  C01  111.14  3.000
 RC2  N05   C03  N04  126.30  3.000
 RC2  N05   C03  S    125.19  3.000
 RC2  N04   C03  S    108.51  3.000
 RC2  C16   N03  C09  124.01  3.000
 RC2  C16   N03  C05  123.18  3.000
 RC2  C09   N03  C05  112.80  3.000
 RC2  C07   C04  N04  112.37  3.000
 RC2  C07   C04  O01  128.64  3.000
 RC2  N04   C04  O01  118.99  3.000
 RC2  N06   N04  C04  121.55  3.000
 RC2  N06   N04  C03  117.43  3.000
 RC2  C04   N04  C03  121.02  3.000
 RC2  H05A  C05  H05  107.67  3.000
 RC2  H05A  C05  N03  109.90  3.000
 RC2  H05   C05  N03  108.53  3.000
 RC2  H05A  C05  C02  110.80  3.000
 RC2  H05   C05  C02  109.73  3.000
 RC2  N03   C05  C02  110.15  3.000
 RC2  C16   N05  C03  117.00  3.000
 RC2  H06   C06  C13  119.41  3.000
 RC2  H06   C06  C11  119.84  3.000
 RC2  C13   C06  C11  120.75  3.000
 RC2  C08   N06  N04  111.18  3.000
 RC2  H07   C07  C16  122.01  3.000
 RC2  H07   C07  C04  115.43  3.000
 RC2  C16   C07  C04  122.55  3.000
 RC2  C10   C08  N06  123.48  3.000
 RC2  C10   C08  S    122.00  3.000
 RC2  N06   C08  S    114.52  3.000
 RC2  H09A  C09  H09  107.17  3.000
 RC2  H09A  C09  N03  108.88  3.000
 RC2  H09   C09  N03  111.32  3.000
 RC2  H09A  C09  C01  109.85  3.000
 RC2  H09   C09  C01  109.54  3.000
 RC2  N03   C09  C01  110.02  3.000
 RC2  C15   C10  C11  120.82  3.000
 RC2  C15   C10  C08  119.70  3.000
 RC2  C11   C10  C08  119.48  3.000
 RC2  H11   C11  C10  120.63  3.000
 RC2  H11   C11  C06  120.45  3.000
 RC2  C10   C11  C06  118.92  3.000
 RC2  H12A  C12  H12  105.67  3.000
 RC2  H12A  C12  N    109.13  3.000
 RC2  H12   C12  N    114.99  3.000
 RC2  H12A  C12  C    107.96  3.000
 RC2  H12   C12  C    107.34  3.000
 RC2  N     C12  C    111.39  3.000
 RC2  H13   C13  C14  119.64  3.000
 RC2  H13   C13  C06  119.73  3.000
 RC2  C14   C13  C06  120.63  3.000
 RC2  C15   C14  C13  118.91  3.000
 RC2  C15   C14  N01  124.03  3.000
 RC2  C13   C14  N01  117.06  3.000
 RC2  H15   C15  C14  119.31  3.000
 RC2  H15   C15  C10  120.72  3.000
 RC2  C14   C15  C10  119.97  3.000
 RC2  C07   C16  N05  120.75  3.000
 RC2  C07   C16  N03  123.95  3.000
 RC2  N05   C16  N03  115.30  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
 RC2  CONST_01  C15   C10  C11  C06     0.00   0.0  0
 RC2  CONST_02  C15   C14  C13  C06     0.00   0.0  0
 RC2  CONST_03  C13   C06  C11  C10     0.00   0.0  0
 RC2  CONST_04  C13   C14  C15  C10     0.00   0.0  0
 RC2  CONST_05  C14   C13  C06  C11     0.00   0.0  0
 RC2  CONST_06  C14   C15  C10  C11     0.00   0.0  0
 RC2  CONST_07  C08   C10  C11  C06   180.00   0.0  0
 RC2  CONST_08  C14   C15  C10  C08   180.00   0.0  0
 RC2  CONST_09  C04   N04  C03  S     180.00   0.0  0
 RC2  CONST_10  N06   N04  C03  S       0.00   0.0  0
 RC2  CONST_11  C16   N05  C03  S     180.00   0.0  0
 RC2  CONST_12  C07   C04  N04  C03     0.00   0.0  0
 RC2  CONST_13  N03   C16  N05  C03   180.00   0.0  0
 RC2  CONST_14  C07   C16  N05  C03     0.00   0.0  0
 RC2  CONST_15  N05   C03  N04  C04     0.00   0.0  0
 RC2  CONST_16  C16   N05  C03  N04     0.00   0.0  0
 RC2  CONST_17  N05   C16  N03  C05     0.00   0.0  0
 RC2  CONST_18  C07   C16  N03  C05   180.00   0.0  0
 RC2  CONST_19  N06   N04  C03  N05   180.00   0.0  0
 RC2  CONST_20  C09   N03  C16  N05   180.00   0.0  0
 RC2  CONST_21  C07   C04  N04  N06   180.00   0.0  0
 RC2  CONST_22  C09   N03  C16  C07     0.00   0.0  0
 RC2  CONST_23  C06   C13  C14  N01   180.00   0.0  0
 RC2  CONST_24  C10   C15  C14  N01   180.00   0.0  0
 RC2  CONST_25  C03   N04  C04  O01   180.00   0.0  0
 RC2  CONST_26  N06   N04  C04  O01     0.00   0.0  0
 RC2  CONST_27  H11   C11  C10  C08     0.00   0.0  0
 RC2  CONST_28  H15   C15  C10  C08     0.00   0.0  0
 RC2  CONST_29  H06   C06  C11  C10   180.00   0.0  0
 RC2  CONST_30  H13   C13  C06  C11   180.00   0.0  0
 RC2  CONST_31  C13   C14  N01  C     180.00   0.0  0
 RC2  CONST_32  C15   C14  N01  C       0.00   0.0  0
 RC2  CONST_33  HN01  N01  C14  C13     0.00   0.0  0
 RC2  CONST_34  C14   N01  C    O       0.00   0.0  0
 RC2  CONST_35  C14   N01  C    C12   180.00   0.0  0
 RC2  Var_01    C11   C10  C08  S    -174.84  30.0  2
 RC2  Var_02    C05   C02  N02  C01    51.50  30.0  1
 RC2  Var_03    C05   N03  C09  C01   -55.27  30.0  1
 RC2  Var_04    C09   C01  N02  C02   -51.45  30.0  1
 RC2  Var_05    C09   N03  C05  C02    55.50  30.0  1
 RC2  Var_06    N03   C09  C01  N02    53.27  30.0  1
 RC2  Var_07    N03   C05  C02  N02   -53.43  30.0  1
 RC2  Var_08    O     C    C12  N      -3.18  30.0  1
 RC2  Var_09    HN    N    C12  C      72.76  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
 RC2  plan-1  N01   0.020
 RC2  plan-1  C06   0.020
 RC2  plan-1  C08   0.020
 RC2  plan-1  C10   0.020
 RC2  plan-1  C11   0.020
 RC2  plan-1  C13   0.020
 RC2  plan-1  C14   0.020
 RC2  plan-1  C15   0.020
 RC2  plan-1  H06   0.020
 RC2  plan-1  H11   0.020
 RC2  plan-1  H13   0.020
 RC2  plan-1  H15   0.020
 RC2  plan-2  S     0.020
 RC2  plan-2  C03   0.020
 RC2  plan-2  N03   0.020
 RC2  plan-2  C04   0.020
 RC2  plan-2  N04   0.020
 RC2  plan-2  C05   0.020
 RC2  plan-2  N05   0.020
 RC2  plan-2  N06   0.020
 RC2  plan-2  C07   0.020
 RC2  plan-2  C08   0.020
 RC2  plan-2  C09   0.020
 RC2  plan-2  C10   0.020
 RC2  plan-2  C16   0.020
 RC2  plan-2  H07   0.020
 RC2  plan-2  O01   0.020
 RC2  plan-3  C     0.020
 RC2  plan-3  O     0.020
 RC2  plan-3  N01   0.020
 RC2  plan-3  C12   0.020
 RC2  plan-3  C14   0.020
 RC2  plan-3  HN01  0.020

