# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 06:40:21 2021
#   Inital geometry file: a 92 line input string
#   Ligand name: 1-[(2~{R})-2-oxidanylpropyl]-3-[[(2~{R})-oxiran-2-yl]methyl]-5-[[(2~{S})-oxiran-2-yl]methyl]-1,3,5-triazinane-2,4,6-trione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)CN1C(=O)N(C[C@H]2CO2)C(=O)N(C[C@@H]3CO3)C1=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
 S7H  S7H  1-[(2~{R})-2-oxidanylpropyl]-3-[[(2~{R})-oxiran-2-yl]methyl]-5-[[(2~{S})-oxiran-2-yl]methyl]-1,3,5-triazinane-2,4,6-trione  ligand  38  21  .  2022-07-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_S7H
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
 S7H  N10   N  NR6   0  -0.598   7.6026  -1.5052  23.6518
 S7H  C11   C  CH2   0  -0.345   6.7199  -2.0300  24.6865
 S7H  C12   C  CH1   0   0.023   6.0655  -0.9439  25.5019
 S7H  C13   C  CH2   0  -0.230   5.6682   0.3512  24.9665
 S7H  C18   C  CH2   0  -0.343  11.0997  -0.4323  23.3204
 S7H  C19   C  CH1   0   0.025  11.2717   0.9648  23.8599
 S7H  C20   C  CH2   0  -0.231  10.4401   2.1001  23.4831
 S7H  C02   C  CR6   0   0.775   9.2851  -0.5153  21.7058
 S7H  C04   C  CH2   0  -0.351   7.4146  -0.5088  20.1172
 S7H  C05   C  CH1   0   0.031   7.1458  -1.7252  19.2219
 S7H  C06   C  CH3   0  -0.666   8.2177  -2.7895  19.3368
 S7H  C08   C  CR6   0   0.783   7.1000  -1.3273  22.3919
 S7H  C15   C  CR6   0   0.789   8.9245  -1.2679  24.0038
 S7H  N03   N  NR6   0  -0.602   7.9564  -0.8025  21.4518
 S7H  N17   N  NR6   0  -0.604   9.7158  -0.7498  22.9879
 S7H  O01   O  O     0  -0.471  10.0226  -0.0796  20.8510
 S7H  O07   O  OH1   0  -0.675   5.8669  -2.2843  19.3950
 S7H  O09   O  O     0  -0.473   5.9530  -1.6130  22.1112
 S7H  O14   O  O2    0  -0.434   6.8184   0.2107  25.7808
 S7H  O16   O  O     0  -0.387   9.3588  -1.5367  25.0863
 S7H  O21   O  O2    0  -0.428  10.2885   1.4573  24.7350
 S7H  H112  H  HCH2  0   0.281   5.9551  -2.6460  24.2207
 S7H  H111  H  HCH2  0   0.286   7.3051  -2.6758  25.3369
 S7H  H121  H  HCH1  0   0.246   5.4938  -1.3464  26.3377
 S7H  H131  H  HCH2  0   0.219   5.8445   0.6077  23.9256
 S7H  H132  H  HCH2  0   0.230   4.8242   0.8725  25.4105
 S7H  H181  H  HCH2  0   0.288  11.4447  -1.1538  24.0573
 S7H  H182  H  HCH2  0   0.273  11.7169  -0.5560  22.4345
 S7H  H191  H  HCH1  0   0.243  12.3027   1.1653  24.1511
 S7H  H202  H  HCH2  0   0.229  10.8683   3.0989  23.5017
 S7H  H201  H  HCH2  0   0.216   9.6166   1.9895  22.7834
 S7H  H041  H  HCH2  0   0.275   8.1425   0.1266  19.6247
 S7H  H042  H  HCH2  0   0.277   6.5083   0.0867  20.2302
 S7H  H051  H  HCH1  0   0.233   7.1637  -1.3288  18.2022
 S7H  H061  H  HCH3  0   0.220   9.2128  -2.3827  19.1511
 S7H  H062  H  HCH3  0   0.211   8.2267  -3.2622  20.3210
 S7H  H2    H  HCH3  0   0.246   8.0425  -3.5739  18.6016
 S7H  H1    H  HOH1  0   0.440   5.6792  -2.2789  20.3429

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
 S7H  C05  C06   single  1.515  0.020  1.515
 S7H  C05  O07   single  1.406  0.020  1.406
 S7H  C05  C04   single  1.534  0.020  1.534
 S7H  C04  N03   single  1.470  0.020  1.470
 S7H  O01  C02   double  1.210  0.020  1.210
 S7H  N03  C02   single  1.383  0.020  1.383
 S7H  N03  C08   single  1.376  0.020  1.376
 S7H  C02  N17   single  1.373  0.020  1.373
 S7H  O09  C08   double  1.215  0.020  1.215
 S7H  C08  N10   single  1.368  0.020  1.368
 S7H  N17  C18   single  1.458  0.020  1.458
 S7H  N17  C15   single  1.388  0.020  1.388
 S7H  C18  C19   single  1.507  0.020  1.507
 S7H  N10  C15   single  1.388  0.020  1.388
 S7H  N10  C11   single  1.458  0.020  1.458
 S7H  C20  C19   single  1.457  0.020  1.457
 S7H  C20  O21   single  1.415  0.020  1.415
 S7H  C15  O16   double  1.197  0.020  1.197
 S7H  C19  O21   single  1.405  0.020  1.405
 S7H  C11  C12   single  1.508  0.020  1.508
 S7H  C13  C12   single  1.457  0.020  1.457
 S7H  C13  O14   single  1.416  0.020  1.416
 S7H  C12  O14   single  1.406  0.020  1.406
 S7H  C11  H112  single  0.970  0.020  1.090
 S7H  C11  H111  single  0.970  0.020  1.090
 S7H  C12  H121  single  0.970  0.020  1.090
 S7H  C13  H131  single  0.970  0.020  1.090
 S7H  C13  H132  single  0.970  0.020  1.090
 S7H  C18  H181  single  0.970  0.020  1.090
 S7H  C18  H182  single  0.970  0.020  1.090
 S7H  C19  H191  single  0.970  0.020  1.090
 S7H  C20  H202  single  0.970  0.020  1.090
 S7H  C20  H201  single  0.970  0.020  1.090
 S7H  C04  H041  single  0.970  0.020  1.090
 S7H  C04  H042  single  0.970  0.020  1.090
 S7H  C05  H051  single  0.970  0.020  1.090
 S7H  C06  H061  single  0.970  0.020  1.090
 S7H  C06  H062  single  0.970  0.020  1.090
 S7H  C06  H2    single  0.970  0.020  1.090
 S7H  O07  H1    single  0.850  0.020  0.980

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
 S7H  C15   N10  C08   124.13  3.000
 S7H  C15   N10  C11   117.26  3.000
 S7H  C08   N10  C11   118.55  3.000
 S7H  H111  C11  H112  107.36  3.000
 S7H  H111  C11  C12   109.75  3.000
 S7H  H112  C11  C12   109.55  3.000
 S7H  H111  C11  N10   108.21  3.000
 S7H  H112  C11  N10   109.02  3.000
 S7H  C12   C11  N10   112.79  3.000
 S7H  H121  C12  O14   115.60  3.000
 S7H  H121  C12  C13   117.86  3.000
 S7H  O14   C12  C13    59.27  3.000
 S7H  H121  C12  C11   112.12  3.000
 S7H  O14   C12  C11   117.80  3.000
 S7H  C13   C12  C11   124.06  3.000
 S7H  H132  C13  H131  113.84  3.000
 S7H  H132  C13  O14   116.32  3.000
 S7H  H131  C13  O14   116.27  3.000
 S7H  H132  C13  C12   119.21  3.000
 S7H  H131  C13  C12   121.19  3.000
 S7H  O14   C13  C12    58.60  3.000
 S7H  H182  C18  H181  107.26  3.000
 S7H  H182  C18  N17   109.16  3.000
 S7H  H181  C18  N17   108.13  3.000
 S7H  H182  C18  C19   109.42  3.000
 S7H  H181  C18  C19   109.64  3.000
 S7H  N17   C18  C19   113.06  3.000
 S7H  H191  C19  O21   115.53  3.000
 S7H  H191  C19  C20   117.75  3.000
 S7H  O21   C19  C20    59.24  3.000
 S7H  H191  C19  C18   111.96  3.000
 S7H  O21   C19  C18   117.90  3.000
 S7H  C20   C19  C18   124.37  3.000
 S7H  H201  C20  H202  113.78  3.000
 S7H  H201  C20  O21   116.26  3.000
 S7H  H202  C20  O21   116.38  3.000
 S7H  H201  C20  C19   121.33  3.000
 S7H  H202  C20  C19   119.13  3.000
 S7H  O21   C20  C19    58.56  3.000
 S7H  O01   C02  N17   122.01  3.000
 S7H  N17   C02  N03   115.95  3.000
 S7H  O01   C02  N03   122.04  3.000
 S7H  H042  C04  H041  106.56  3.000
 S7H  H042  C04  N03   108.74  3.000
 S7H  H041  C04  N03   106.38  3.000
 S7H  H042  C04  C05   110.36  3.000
 S7H  H041  C04  C05   108.49  3.000
 S7H  N03   C04  C05   115.85  3.000
 S7H  H051  C05  O07   105.88  3.000
 S7H  H051  C05  C06   108.28  3.000
 S7H  O07   C05  C06   110.78  3.000
 S7H  H051  C05  C04   104.70  3.000
 S7H  O07   C05  C04   113.75  3.000
 S7H  C06   C05  C04   112.88  3.000
 S7H  H2    C06  H062  107.33  3.000
 S7H  H2    C06  H061  107.48  3.000
 S7H  H062  C06  H061  107.90  3.000
 S7H  H2    C06  C05   109.94  3.000
 S7H  H062  C06  C05   112.23  3.000
 S7H  H061  C06  C05   111.75  3.000
 S7H  O09   C08  N03   121.30  3.000
 S7H  O09   C08  N10   121.95  3.000
 S7H  N03   C08  N10   116.75  3.000
 S7H  O16   C15  N17   122.61  3.000
 S7H  O16   C15  N10   122.44  3.000
 S7H  N17   C15  N10   114.90  3.000
 S7H  C08   N03  C04   117.85  3.000
 S7H  C08   N03  C02   123.49  3.000
 S7H  C04   N03  C02   118.64  3.000
 S7H  C15   N17  C02   124.64  3.000
 S7H  C15   N17  C18   117.09  3.000
 S7H  C02   N17  C18   118.27  3.000
 S7H  H1    O07  C05   107.16  3.000
 S7H  C13   O14  C12    62.14  3.000
 S7H  C20   O21  C19    62.19  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
 S7H  CONST_01  C02   N03  C08  N10     0.00   0.0  0
 S7H  CONST_02  C02   N17  C15  N10     0.00   0.0  0
 S7H  CONST_03  N17   C02  N03  C08     0.00   0.0  0
 S7H  CONST_04  N17   C15  N10  C08     0.00   0.0  0
 S7H  CONST_05  N03   C02  N17  C15     0.00   0.0  0
 S7H  CONST_06  N03   C08  N10  C15     0.00   0.0  0
 S7H  CONST_07  C04   N03  C08  N10   180.00   0.0  0
 S7H  CONST_08  C18   N17  C15  N10   180.00   0.0  0
 S7H  CONST_09  N03   C08  N10  C11   180.00   0.0  0
 S7H  CONST_10  N17   C15  N10  C11   180.00   0.0  0
 S7H  CONST_11  N03   C02  N17  C18   180.00   0.0  0
 S7H  CONST_12  O09   C08  N03  C02   180.00   0.0  0
 S7H  CONST_13  O16   C15  N17  C02   180.00   0.0  0
 S7H  CONST_14  N17   C02  N03  C04   180.00   0.0  0
 S7H  CONST_15  O01   C02  N03  C08   180.00   0.0  0
 S7H  CONST_16  O16   C15  N10  C08   180.00   0.0  0
 S7H  CONST_17  O01   C02  N17  C15   180.00   0.0  0
 S7H  CONST_18  O09   C08  N10  C15   180.00   0.0  0
 S7H  CONST_19  O09   C08  N10  C11     0.00   0.0  0
 S7H  CONST_20  O16   C15  N10  C11     0.00   0.0  0
 S7H  CONST_21  O01   C02  N17  C18     0.00   0.0  0
 S7H  CONST_22  O16   C15  N17  C18     0.00   0.0  0
 S7H  CONST_23  O01   C02  N03  C04     0.00   0.0  0
 S7H  CONST_24  O09   C08  N03  C04     0.00   0.0  0
 S7H  Var_01    C13   C12  C11  N10    34.05  30.0  3
 S7H  Var_02    O14   C13  C12  C11  -104.65  30.0  1
 S7H  Var_03    C08   N10  C11  C12   -94.24  30.0  2
 S7H  Var_04    O21   C20  C19  C18   104.63  30.0  1
 S7H  Var_05    C02   N17  C18  C19    91.86  30.0  2
 S7H  Var_06    N17   C18  C19  C20   -30.84  30.0  1
 S7H  Var_07    H131  C13  O14  C12  -112.04  30.0  1
 S7H  Var_08    H121  C12  O14  C13  -108.54  30.0  1
 S7H  Var_09    H202  C20  O21  C19  -109.50  30.0  1
 S7H  Var_10    H191  C19  O21  C20   108.44  30.0  1
 S7H  Var_11    C05   C04  N03  C02   107.02  30.0  2

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
 S7H  chir_03  C05  C06  O07  C04  negativ
 S7H  chir_04  C12  C11  C13  O14  both
 S7H  chir_05  C19  O21  C18  C20  both

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
 S7H  plan-1  N10  0.020
 S7H  plan-1  C11  0.020
 S7H  plan-1  C18  0.020
 S7H  plan-1  C02  0.020
 S7H  plan-1  C04  0.020
 S7H  plan-1  C08  0.020
 S7H  plan-1  C15  0.020
 S7H  plan-1  N03  0.020
 S7H  plan-1  N17  0.020
 S7H  plan-1  O01  0.020
 S7H  plan-1  O09  0.020
 S7H  plan-1  O16  0.020

