# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 15 00:45:52 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 6-[(7S)-7-phenyl-7H-[1,2,4]triazolo[3,4-b][1,3,4]thiadiazin-6-yl]-2H-1,4-benzoxazin-3(4H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1COc2ccc(cc2N1)C3=Nn4cnnc4S[C@H]3c5ccccc5
#
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
 LD1  LD1  6-[(7S)-7-phenyl-7H-[1,2,4]triazolo[3,4-b][1,3,4]thiadiazin-6-yl]-2H-1,4-benzoxazin-3(4H)-one  ligand  39  26  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_LD1
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
 LD1  C1    C  CR6   0   0.350  -3.5773   0.7752   0.2810
 LD1  C2    C  CR6   0   0.354  -3.2223  -0.5600   0.0658
 LD1  C3    C  CR16  0  -0.362  -1.8932  -0.9316   0.0874
 LD1  C4    C  CR6   0   0.055  -0.8995   0.0163   0.3454
 LD1  C5    C  CR16  0  -0.303  -1.2669   1.3420   0.5706
 LD1  C6    C  CR16  0  -0.341  -2.5987   1.7220   0.5240
 LD1  O7    O  O2    0  -0.467  -4.8769   1.1265   0.2992
 LD1  C8    C  CH2   0  -0.311  -5.7326   0.3599  -0.5307
 LD1  C9    C  C     0   0.486  -5.5158  -1.1337  -0.4066
 LD1  N10   N  NH1   0  -0.722  -4.2444  -1.4880  -0.1134
 LD1  O11   O  O     0  -0.451  -6.4075  -1.9326  -0.6068
 LD1  C12   C  CR6   0   0.312   0.5133  -0.3859   0.3427
 LD1  C13   C  CR16  0  -0.675   1.5211   0.5180   1.0175
 LD1  S14   S  S2    0   0.190   2.7696  -0.4809   1.9197
 LD1  C15   C  CR56  0   0.266   3.0932  -1.5491   0.6056
 LD1  N16   N  N     0  -0.311   2.0975  -1.8720  -0.2618
 LD1  N17   N  N     0  -0.239   0.8063  -1.4686  -0.2735
 LD1  N18   N  N     0  -0.318   4.1673  -2.2221   0.3212
 LD1  N19   N  N     0  -0.315   3.8785  -3.0074  -0.7566
 LD1  C20   C  CR15  0   0.100   2.6447  -2.7965  -1.0939
 LD1  C21   C  CR6   0   0.201   2.1627   1.5168   0.0876
 LD1  C22   C  CR16  0  -0.279   2.7138   2.6712   0.6432
 LD1  C23   C  CR16  0  -0.243   3.3261   3.6176  -0.1609
 LD1  C24   C  CR16  0  -0.258   3.3952   3.4237  -1.5360
 LD1  C25   C  CR16  0  -0.236   2.8448   2.2812  -2.0955
 LD1  C26   C  CR16  0  -0.290   2.2281   1.3317  -1.2892
 LD1  H3    H  HCR6  0   0.283  -1.6281  -1.9686  -0.0741
 LD1  H5    H  HCR6  0   0.263  -0.5234   2.1060   0.7539
 LD1  H6    H  HCR6  0   0.284  -2.8808   2.7529   0.6917
 LD1  H8    H  HCH2  0   0.289  -6.7537   0.5984  -0.2426
 LD1  H8A   H  HCH2  0   0.277  -5.5998   0.6382  -1.5838
 LD1  HN10  H  HNH1  0   0.420  -4.0183  -2.4734  -0.0863
 LD1  H13   H  HCR6  0   0.355   1.0225   1.0500   1.8285
 LD1  H20   H  HCR5  0   0.322   2.1058  -3.2425  -1.9140
 LD1  H22   H  HCR6  0   0.265   2.6646   2.8281   1.7145
 LD1  H23   H  HCR6  0   0.264   3.7459   4.5097   0.2847
 LD1  H24   H  HCR6  0   0.263   3.8719   4.1635  -2.1656
 LD1  H25   H  HCR6  0   0.264   2.8878   2.1235  -3.1651
 LD1  H26   H  HCR6  0   0.256   1.7927   0.4595  -1.7589

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
 LD1  C1   C2    aromatic  1.398  0.020  1.398
 LD1  C1   C6    aromatic  1.383  0.020  1.383
 LD1  C1   O7    single    1.346  0.020  1.346
 LD1  C2   C3    aromatic  1.380  0.020  1.380
 LD1  C2   N10   single    1.392  0.020  1.392
 LD1  C3   C4    aromatic  1.397  0.020  1.397
 LD1  C4   C5    aromatic  1.394  0.020  1.394
 LD1  C4   C12   single    1.469  0.020  1.469
 LD1  C5   C6    aromatic  1.386  0.020  1.386
 LD1  O7   C8    single    1.417  0.020  1.417
 LD1  C8   C9    single    1.514  0.020  1.514
 LD1  C9   N10   single    1.352  0.020  1.352
 LD1  C9   O11   double    1.214  0.020  1.214
 LD1  C12  C13   single    1.513  0.020  1.513
 LD1  C12  N17   double    1.280  0.020  1.280
 LD1  C13  S14   single    1.836  0.020  1.836
 LD1  C13  C21   single    1.508  0.020  1.508
 LD1  S14  C15   single    1.724  0.020  1.724
 LD1  C15  N16   aromatic  1.360  0.020  1.360
 LD1  C15  N18   aromatic  1.299  0.020  1.299
 LD1  N16  N17   single    1.353  0.020  1.353
 LD1  N16  C20   aromatic  1.359  0.020  1.359
 LD1  N18  N19   aromatic  1.365  0.020  1.365
 LD1  N19  C20   aromatic  1.296  0.020  1.296
 LD1  C21  C22   aromatic  1.395  0.020  1.395
 LD1  C21  C26   aromatic  1.391  0.020  1.391
 LD1  C22  C23   aromatic  1.385  0.020  1.385
 LD1  C23  C24   aromatic  1.390  0.020  1.390
 LD1  C24  C25   aromatic  1.386  0.020  1.386
 LD1  C25  C26   aromatic  1.390  0.020  1.390
 LD1  C3   H3    single    0.930  0.020  1.080
 LD1  C5   H5    single    0.930  0.020  1.080
 LD1  C6   H6    single    0.930  0.020  1.080
 LD1  C8   H8    single    0.970  0.020  1.090
 LD1  C8   H8A   single    0.970  0.020  1.090
 LD1  N10  HN10  single    0.860  0.020  1.020
 LD1  C13  H13   single    0.970  0.020  1.090
 LD1  C20  H20   single    0.930  0.020  1.080
 LD1  C22  H22   single    0.930  0.020  1.080
 LD1  C23  H23   single    0.930  0.020  1.080
 LD1  C24  H24   single    0.930  0.020  1.080
 LD1  C25  H25   single    0.930  0.020  1.080
 LD1  C26  H26   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
 LD1  O7    C1   C6   120.13  3.000
 LD1  O7    C1   C2   119.76  3.000
 LD1  C6    C1   C2   120.07  3.000
 LD1  N10   C2   C3   121.97  3.000
 LD1  N10   C2   C1   118.03  3.000
 LD1  C3    C2   C1   119.95  3.000
 LD1  H3    C3   C4   120.22  3.000
 LD1  H3    C3   C2   119.43  3.000
 LD1  C4    C3   C2   120.33  3.000
 LD1  C12   C4   C5   120.94  3.000
 LD1  C12   C4   C3   119.86  3.000
 LD1  C5    C4   C3   119.18  3.000
 LD1  H5    C5   C6   118.21  3.000
 LD1  H5    C5   C4   121.19  3.000
 LD1  C6    C5   C4   120.57  3.000
 LD1  H6    C6   C5   120.44  3.000
 LD1  H6    C6   C1   119.67  3.000
 LD1  C5    C6   C1   119.88  3.000
 LD1  C8    O7   C1   115.70  3.000
 LD1  H8A   C8   H8   108.20  3.000
 LD1  H8A   C8   C9   108.15  3.000
 LD1  H8    C8   C9   109.20  3.000
 LD1  H8A   C8   O7   110.59  3.000
 LD1  H8    C8   O7   107.05  3.000
 LD1  C9    C8   O7   113.52  3.000
 LD1  O11   C9   N10  123.65  3.000
 LD1  O11   C9   C8   122.04  3.000
 LD1  N10   C9   C8   114.26  3.000
 LD1  HN10  N10  C9   118.13  3.000
 LD1  HN10  N10  C2   118.81  3.000
 LD1  C9    N10  C2   122.93  3.000
 LD1  N17   C12  C13  124.60  3.000
 LD1  N17   C12  C4   116.92  3.000
 LD1  C13   C12  C4   118.45  3.000
 LD1  H13   C13  C21  109.27  3.000
 LD1  H13   C13  S14  102.17  3.000
 LD1  C21   C13  S14  111.96  3.000
 LD1  H13   C13  C12  108.59  3.000
 LD1  C21   C13  C12  113.84  3.000
 LD1  S14   C13  C12  110.32  3.000
 LD1  C15   S14  C13   95.18  3.000
 LD1  N18   C15  N16  110.05  3.000
 LD1  N18   C15  S14  130.02  3.000
 LD1  N16   C15  S14  119.73  3.000
 LD1  C20   N16  N17  125.59  3.000
 LD1  C20   N16  C15  104.91  3.000
 LD1  N17   N16  C15  129.33  3.000
 LD1  N16   N17  C12  117.82  3.000
 LD1  N19   N18  C15  107.23  3.000
 LD1  C20   N19  N18  108.25  3.000
 LD1  H20   C20  N19  127.33  3.000
 LD1  H20   C20  N16  123.09  3.000
 LD1  N19   C20  N16  109.56  3.000
 LD1  C26   C21  C22  119.07  3.000
 LD1  C26   C21  C13  122.85  3.000
 LD1  C22   C21  C13  118.08  3.000
 LD1  H22   C22  C23  119.68  3.000
 LD1  H22   C22  C21  119.71  3.000
 LD1  C23   C22  C21  120.61  3.000
 LD1  H23   C23  C24  120.20  3.000
 LD1  H23   C23  C22  119.73  3.000
 LD1  C24   C23  C22  120.07  3.000
 LD1  H24   C24  C25  120.23  3.000
 LD1  H24   C24  C23  120.13  3.000
 LD1  C25   C24  C23  119.63  3.000
 LD1  H25   C25  C26  119.44  3.000
 LD1  H25   C25  C24  120.23  3.000
 LD1  C26   C25  C24  120.33  3.000
 LD1  H26   C26  C25  118.51  3.000
 LD1  H26   C26  C21  121.20  3.000
 LD1  C25   C26  C21  120.28  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
 LD1  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 LD1  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 LD1  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 LD1  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 LD1  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 LD1  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 LD1  CONST_07  N19   C20  N16  C15     0.00   0.0  0
 LD1  CONST_08  C20   N19  N18  C15     0.00   0.0  0
 LD1  CONST_09  N19   N18  C15  N16     0.00   0.0  0
 LD1  CONST_10  N18   N19  C20  N16     0.00   0.0  0
 LD1  CONST_11  C20   N16  C15  N18     0.00   0.0  0
 LD1  CONST_12  C24   C23  C22  C21     0.00   0.0  0
 LD1  CONST_13  C24   C25  C26  C21     0.00   0.0  0
 LD1  CONST_14  C25   C26  C21  C22     0.00   0.0  0
 LD1  CONST_15  C25   C24  C23  C22     0.00   0.0  0
 LD1  CONST_16  C26   C21  C22  C23     0.00   0.0  0
 LD1  CONST_17  C26   C25  C24  C23     0.00   0.0  0
 LD1  CONST_18  C12   C4   C3   C2    180.00   0.0  0
 LD1  CONST_19  C12   C4   C5   C6    180.00   0.0  0
 LD1  CONST_20  C23   C22  C21  C13   180.00   0.0  0
 LD1  CONST_21  C25   C26  C21  C13   180.00   0.0  0
 LD1  CONST_22  C8    C9   N10  C2      0.00   0.0  0
 LD1  CONST_23  O11   C9   N10  C2    180.00   0.0  0
 LD1  CONST_24  H3    C3   C2   C1    180.00   0.0  0
 LD1  CONST_25  H5    C5   C6   C1    180.00   0.0  0
 LD1  CONST_26  H6    C6   C1   C2    180.00   0.0  0
 LD1  CONST_27  H22   C22  C21  C13     0.00   0.0  0
 LD1  CONST_28  H26   C26  C21  C13     0.00   0.0  0
 LD1  CONST_29  H20   C20  N16  C15   180.00   0.0  0
 LD1  CONST_30  H23   C23  C22  C21   180.00   0.0  0
 LD1  CONST_31  H25   C25  C26  C21   180.00   0.0  0
 LD1  CONST_32  H24   C24  C23  C22   180.00   0.0  0
 LD1  CONST_33  HN10  N10  C9   C8    180.00   0.0  0
 LD1  Var_01    C9    N10  C2   C1     16.28  30.0  1
 LD1  Var_02    C9    C8   O7   C1     46.62  30.0  1
 LD1  Var_03    C13   C12  C4   C3   -161.80  30.0  2
 LD1  Var_04    N10   C9   C8   O7    -30.95  30.0  1
 LD1  Var_05    C15   N16  N17  C12    21.58  30.0  1
 LD1  Var_06    N16   C15  S14  C13   -32.77  30.0  1

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
 LD1  chir_01  C13  C12  S14  C21  negativ

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
 LD1  plan-1  C13   0.020
 LD1  plan-1  C21   0.020
 LD1  plan-1  C22   0.020
 LD1  plan-1  C23   0.020
 LD1  plan-1  C24   0.020
 LD1  plan-1  C25   0.020
 LD1  plan-1  C26   0.020
 LD1  plan-1  H22   0.020
 LD1  plan-1  H23   0.020
 LD1  plan-1  H24   0.020
 LD1  plan-1  H25   0.020
 LD1  plan-1  H26   0.020
 LD1  plan-2  S14   0.020
 LD1  plan-2  C15   0.020
 LD1  plan-2  N16   0.020
 LD1  plan-2  N17   0.020
 LD1  plan-2  N18   0.020
 LD1  plan-2  N19   0.020
 LD1  plan-2  C20   0.020
 LD1  plan-2  H20   0.020
 LD1  plan-3  C1    0.020
 LD1  plan-3  C2    0.020
 LD1  plan-3  C3    0.020
 LD1  plan-3  C4    0.020
 LD1  plan-3  C5    0.020
 LD1  plan-3  C6    0.020
 LD1  plan-3  O7    0.020
 LD1  plan-3  N10   0.020
 LD1  plan-3  C12   0.020
 LD1  plan-3  H3    0.020
 LD1  plan-3  H5    0.020
 LD1  plan-3  H6    0.020
 LD1  plan-4  C2    0.020
 LD1  plan-4  C8    0.020
 LD1  plan-4  C9    0.020
 LD1  plan-4  N10   0.020
 LD1  plan-4  O11   0.020
 LD1  plan-4  HN10  0.020

