# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 16:04:51 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: ethyl 5-{[(1R)-1-(ethoxycarbonyl)-2-oxopropyl]sulfanyl}-1,2-dihydro[1,2,3]triazolo[1,5-a]quinazoline-3-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)[C@H](SC1=NC2=C(NNN2c3ccccc13)C(=O)OCC)C(C)=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
 53A  53A  'ethyl 5-{[(1R)-1-(ethoxycarbonyl)-2-oxopropyl]sulfanyl}-1,2-dihydro[1,2,3]triazolo[1,5-a]quinazoline-3-carboxylate'  ligand  48  28  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_53A
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
 53A  N1    N  N     0  -0.506  -2.7291   0.6735  -0.0012
 53A  N3    N  NR15  0  -0.302  -3.9445   0.0380   0.2769
 53A  C4    C  CR6   0   0.078  -0.1879   1.4465  -0.1049
 53A  C5    C  CR66  0   0.007  -1.2245   2.4576  -0.2233
 53A  C6    C  CR66  0   0.477  -2.5583   2.0085  -0.1331
 53A  O2    O  O     0  -0.424   4.2383   1.9201  -0.1279
 53A  N4    N  NR15  0  -0.523  -3.6678  -1.2804  -0.2215
 53A  C10   C  C     0   0.440   2.1774  -0.3841   1.2380
 53A  C13   C  CH3   0  -0.778   1.9244   0.3646   2.5105
 53A  C7    C  CH1   0  -0.628   2.3477   0.4377  -0.0543
 53A  C9    C  C     0   0.637   3.8185   0.7955  -0.2169
 53A  O5    O  O2    0  -0.434   4.5403  -0.2747  -0.4432
 53A  C15   C  CH2   0  -0.187   5.9671  -0.1127  -0.5983
 53A  C19   C  CH3   0  -0.689   6.5522  -1.4727  -0.8814
 53A  S1    S  S2    0   0.141   1.4644   2.0146  -0.1029
 53A  N2    N  N     0  -0.440  -0.4092   0.1798   0.0202
 53A  C11   C  CR16  0  -0.316  -0.9826   3.8243  -0.3850
 53A  C16   C  CR16  0  -0.260  -2.0294   4.7210  -0.4395
 53A  C17   C  CR16  0  -0.238  -3.3422   4.2577  -0.3281
 53A  C12   C  CR16  0  -0.332  -3.6201   2.9153  -0.1716
 53A  C3    C  CR5   0  -0.115  -2.2588  -1.4774   0.0145
 53A  C1    C  CR56  0   0.552  -1.6945  -0.2405   0.0349
 53A  C8    C  C     0   0.562  -1.5988  -2.7548  -0.0066
 53A  O1    O  O     0  -0.459  -0.4048  -2.9308   0.1128
 53A  O4    O  O2    0  -0.481  -2.4832  -3.7440  -0.1693
 53A  C14   C  CH2   0  -0.172  -1.9862  -5.0867  -0.2072
 53A  C18   C  CH3   0  -0.688  -3.1633  -6.0088  -0.4175
 53A  HN3   H  HNR5  0   0.374  -3.9961  -0.0092   1.3017
 53A  HN4   H  HNR5  0   0.383  -4.2625  -1.9246   0.2846
 53A  H13   H  HCH3  0   0.266   2.5869   1.2265   2.5990
 53A  H13A  H  HCH3  0   0.279   0.9033   0.7473   2.5336
 53A  H13B  H  HCH3  0   0.275   2.0652  -0.2934   3.3649
 53A  H7    H  HCH1  0   0.367   2.0289  -0.1874  -0.8909
 53A  H15   H  HCH2  0   0.246   6.1621   0.5801  -1.4182
 53A  H15A  H  HCH2  0   0.247   6.3813   0.3143   0.3164
 53A  H19   H  HCH3  0   0.244   7.6290  -1.3725  -1.0137
 53A  H19A  H  HCH3  0   0.240   6.3795  -2.1646  -0.0576
 53A  H19B  H  HCH3  0   0.240   6.1421  -1.9040  -1.7943
 53A  H11   H  HCR6  0   0.273   0.0317   4.1937  -0.4694
 53A  H16   H  HCR6  0   0.271  -1.8335   5.7764  -0.5643
 53A  H17   H  HCR6  0   0.277  -4.1619   4.9626  -0.3667
 53A  H12   H  HCR6  0   0.285  -4.6383   2.5632  -0.0866
 53A  H14   H  HCH2  0   0.230  -1.2613  -5.1927  -1.0171
 53A  H14A  H  HCH2  0   0.230  -1.4766  -5.3206   0.7302
 53A  H18   H  HCH3  0   0.235  -3.8844  -5.9292   0.3957
 53A  H18A  H  HCH3  0   0.235  -3.6732  -5.8015  -1.3583
 53A  H18B  H  HCH3  0   0.238  -2.8083  -7.0386  -0.4503
 53A  O3    O  O     0  -0.356   2.3261  -1.5753   1.1838

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
 53A  N1   N3    single    1.399  0.020  1.399
 53A  N1   C6    single    1.352  0.020  1.352
 53A  N1   C1    single    1.381  0.020  1.381
 53A  N3   N4    single    1.436  0.020  1.436
 53A  C4   C5    single    1.453  0.020  1.453
 53A  C4   S1    single    1.747  0.020  1.747
 53A  C4   N2    double    1.292  0.020  1.292
 53A  C5   C6    aromatic  1.410  0.020  1.410
 53A  C5   C11   aromatic  1.397  0.020  1.397
 53A  C6   C12   aromatic  1.397  0.020  1.397
 53A  O2   C9    double    1.204  0.020  1.204
 53A  N4   C3    single    1.442  0.020  1.442
 53A  O3   C10   double    1.202  0.020  1.202
 53A  C10  C13   single    1.498  0.020  1.498
 53A  C10  C7    single    1.541  0.020  1.541
 53A  C7   C9    single    1.522  0.020  1.522
 53A  C7   S1    single    1.808  0.020  1.808
 53A  C9   O5    single    1.311  0.020  1.311
 53A  O5   C15   single    1.444  0.020  1.444
 53A  C15  C19   single    1.507  0.020  1.507
 53A  N2   C1    single    1.352  0.020  1.352
 53A  C11  C16   aromatic  1.379  0.020  1.379
 53A  C16  C17   aromatic  1.397  0.020  1.397
 53A  C17  C12   aromatic  1.380  0.020  1.380
 53A  C3   C1    double    1.360  0.020  1.360
 53A  C3   C8    single    1.438  0.020  1.438
 53A  C8   O1    double    1.213  0.020  1.213
 53A  C8   O4    single    1.337  0.020  1.337
 53A  O4   C14   single    1.432  0.020  1.432
 53A  C14  C18   single    1.510  0.020  1.510
 53A  N3   HN3   single    0.890  0.020  1.040
 53A  N4   HN4   single    0.890  0.020  1.040
 53A  C13  H13   single    0.970  0.020  1.090
 53A  C13  H13A  single    0.970  0.020  1.090
 53A  C13  H13B  single    0.970  0.020  1.090
 53A  C7   H7    single    0.970  0.020  1.090
 53A  C15  H15   single    0.970  0.020  1.090
 53A  C15  H15A  single    0.970  0.020  1.090
 53A  C19  H19   single    0.970  0.020  1.090
 53A  C19  H19A  single    0.970  0.020  1.090
 53A  C19  H19B  single    0.970  0.020  1.090
 53A  C11  H11   single    0.930  0.020  1.080
 53A  C16  H16   single    0.930  0.020  1.080
 53A  C17  H17   single    0.930  0.020  1.080
 53A  C12  H12   single    0.930  0.020  1.080
 53A  C14  H14   single    0.970  0.020  1.090
 53A  C14  H14A  single    0.970  0.020  1.090
 53A  C18  H18   single    0.970  0.020  1.090
 53A  C18  H18A  single    0.970  0.020  1.090
 53A  C18  H18B  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
 53A  C1    N1   C6    124.14  3.000
 53A  C1    N1   N3    110.18  3.000
 53A  C6    N1   N3    125.27  3.000
 53A  HN3   N3   N4    108.28  3.000
 53A  HN3   N3   N1    105.23  3.000
 53A  N4    N3   N1    100.40  3.000
 53A  N2    C4   S1    118.72  3.000
 53A  N2    C4   C5    124.61  3.000
 53A  S1    C4   C5    116.65  3.000
 53A  C11   C5   C6    118.86  3.000
 53A  C11   C5   C4    124.51  3.000
 53A  C6    C5   C4    116.61  3.000
 53A  C12   C6   C5    120.69  3.000
 53A  C12   C6   N1    123.19  3.000
 53A  C5    C6   N1    116.11  3.000
 53A  HN4   N4   C3    113.90  3.000
 53A  HN4   N4   N3    107.31  3.000
 53A  C3    N4   N3    104.88  3.000
 53A  C7    C10  C13   117.68  3.000
 53A  C7    C10  O3    118.50  3.000
 53A  C13   C10  O3    123.69  3.000
 53A  H13B  C13  H13A  108.47  3.000
 53A  H13B  C13  H13   109.61  3.000
 53A  H13A  C13  H13   106.84  3.000
 53A  H13B  C13  C10   110.07  3.000
 53A  H13A  C13  C10   110.58  3.000
 53A  H13   C13  C10   111.18  3.000
 53A  H7    C7   S1    109.64  3.000
 53A  H7    C7   C9    109.56  3.000
 53A  S1    C7   C9    105.32  3.000
 53A  H7    C7   C10   107.75  3.000
 53A  S1    C7   C10   115.70  3.000
 53A  C9    C7   C10   108.76  3.000
 53A  O5    C9   C7    111.02  3.000
 53A  O5    C9   O2    125.70  3.000
 53A  C7    C9   O2    123.27  3.000
 53A  C15   O5   C9    118.10  3.000
 53A  H15A  C15  H15   108.28  3.000
 53A  H15A  C15  C19   111.29  3.000
 53A  H15   C15  C19   111.25  3.000
 53A  H15A  C15  O5    109.20  3.000
 53A  H15   C15  O5    109.18  3.000
 53A  C19   C15  O5    107.60  3.000
 53A  H19B  C19  H19A  108.81  3.000
 53A  H19B  C19  H19   107.85  3.000
 53A  H19A  C19  H19   107.87  3.000
 53A  H19B  C19  C15   111.61  3.000
 53A  H19A  C19  C15   111.68  3.000
 53A  H19   C19  C15   108.87  3.000
 53A  C7    S1   C4    100.28  3.000
 53A  C1    N2   C4    117.94  3.000
 53A  H11   C11  C16   119.08  3.000
 53A  H11   C11  C5    120.32  3.000
 53A  C16   C11  C5    120.60  3.000
 53A  H16   C16  C17   120.24  3.000
 53A  H16   C16  C11   120.12  3.000
 53A  C17   C16  C11   119.64  3.000
 53A  H17   C17  C12   119.04  3.000
 53A  H17   C17  C16   119.56  3.000
 53A  C12   C17  C16   121.41  3.000
 53A  H12   C12  C17   121.04  3.000
 53A  H12   C12  C6    120.17  3.000
 53A  C17   C12  C6    118.79  3.000
 53A  C8    C3   C1    128.16  3.000
 53A  C8    C3   N4    124.57  3.000
 53A  C1    C3   N4    106.48  3.000
 53A  C3    C1   N2    132.61  3.000
 53A  C3    C1   N1    106.90  3.000
 53A  N2    C1   N1    120.40  3.000
 53A  O4    C8   O1    123.77  3.000
 53A  O4    C8   C3    110.82  3.000
 53A  O1    C8   C3    125.40  3.000
 53A  C14   O4   C8    117.87  3.000
 53A  H14A  C14  H14   107.81  3.000
 53A  H14A  C14  C18   110.64  3.000
 53A  H14   C14  C18   110.79  3.000
 53A  H14A  C14  O4    109.87  3.000
 53A  H14   C14  O4    109.93  3.000
 53A  C18   C14  O4    107.80  3.000
 53A  H18B  C18  H18A  107.83  3.000
 53A  H18B  C18  H18   107.88  3.000
 53A  H18A  C18  H18   108.70  3.000
 53A  H18B  C18  C14   109.11  3.000
 53A  H18A  C18  C14   111.64  3.000
 53A  H18   C18  C14   111.55  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
 53A  CONST_01  C17  C12  C6   C5      0.00   0.0  0
 53A  CONST_02  C17  C16  C11  C5      0.00   0.0  0
 53A  CONST_03  C16  C11  C5   C6      0.00   0.0  0
 53A  CONST_04  C16  C17  C12  C6      0.00   0.0  0
 53A  CONST_05  C12  C6   C5   C11     0.00   0.0  0
 53A  CONST_06  C12  C17  C16  C11     0.00   0.0  0
 53A  CONST_07  C4   N2   C1   N1      0.00   0.0  0
 53A  CONST_08  N2   C1   N1   N3    180.00   0.0  0
 53A  CONST_09  C3   C1   N1   N3      0.00   0.0  0
 53A  CONST_10  C3   C1   N2   C4    180.00   0.0  0
 53A  CONST_11  N2   C1   N1   C6      0.00   0.0  0
 53A  CONST_12  C3   C1   N1   C6    180.00   0.0  0
 53A  CONST_13  H12  C12  C6   N1      0.00   0.0  0
 53A  CONST_14  H11  C11  C5   C4      0.00   0.0  0
 53A  CONST_15  H16  C16  C11  C5    180.00   0.0  0
 53A  CONST_16  H17  C17  C12  C6    180.00   0.0  0
 53A  Var_01    O1   C8   C3   N4    175.49  30.0  2
 53A  Var_02    N2   C4   S1   C7      4.82  30.0  2
 53A  Var_03    C19  C15  O5   C9   -178.57  30.0  3
 53A  Var_04    C18  C14  O4   C8   -179.18  30.0  3
 53A  Var_05    H13  C13  C10  O3    131.24  30.0  3
 53A  Var_06    H19  C19  C15  O5    179.35  30.0  3
 53A  Var_07    H18  C18  C14  O4    -60.94  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
 53A  chir_01  C7  C10  C9  S1  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
 53A  plan-1  N1   0.020
 53A  plan-1  N3   0.020
 53A  plan-1  C4   0.020
 53A  plan-1  C5   0.020
 53A  plan-1  C6   0.020
 53A  plan-1  N4   0.020
 53A  plan-1  S1   0.020
 53A  plan-1  N2   0.020
 53A  plan-1  C11  0.020
 53A  plan-1  C16  0.020
 53A  plan-1  C17  0.020
 53A  plan-1  C12  0.020
 53A  plan-1  C3   0.020
 53A  plan-1  C1   0.020
 53A  plan-1  C8   0.020
 53A  plan-1  HN3  0.020
 53A  plan-1  HN4  0.020
 53A  plan-1  H11  0.020
 53A  plan-1  H16  0.020
 53A  plan-1  H17  0.020
 53A  plan-1  H12  0.020
 53A  plan-2  C10  0.020
 53A  plan-2  C13  0.020
 53A  plan-2  C7   0.020
 53A  plan-2  O3   0.020
 53A  plan-3  O2   0.020
 53A  plan-3  C7   0.020
 53A  plan-3  C9   0.020
 53A  plan-3  O5   0.020
 53A  plan-4  C3   0.020
 53A  plan-4  C8   0.020
 53A  plan-4  O1   0.020
 53A  plan-4  O4   0.020

