# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 01:31:43 2022
#   Inital geometry file: a 142 line input string
#   Ligand name: 3'-deoxy-3'-(4-{[(4-sulfamoylphenyl)amino]methyl}-1H-1,2,3-triazol-1-yl)thymidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN([C@H]2C[C@@H]([C@@H](CO)O2)n3cc(CNc4ccc(cc4)[S](N)(=O)=O)nn3)C(=O)NC1=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
 U4V  U4V  3'-deoxy-3'-(4-{[(4-sulfamoylphenyl)amino]methyl}-1H-1,2,3-triazol-1-yl)thymidine  ligand  56  33  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_U4V
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
 U4V  C19  C  CR6   0  -0.257  -1.8679   3.3256  84.9750
 U4V  C18  C  CR16  0  -0.203  -0.5529   3.3500  84.5055
 U4V  C17  C  CR16  0  -0.339   0.0625   4.5495  84.2438
 U4V  C16  C  CR6   0   0.414  -0.6100   5.7729  84.4536
 U4V  C13  C  CR5   0   0.156  -1.5260   8.7262  83.5233
 U4V  C14  C  CH2   0  -0.404  -0.4916   8.2457  84.4922
 U4V  C02  C  CR6   0   0.555  -5.7062  13.2308  76.8995
 U4V  C03  C  CR6   0  -0.187  -6.0851  11.9273  77.4029
 U4V  C04  C  CH3   0  -0.706  -7.5306  11.5500  77.4064
 U4V  C05  C  CR16  0   0.041  -5.1149  11.1034  77.8413
 U4V  N06  N  NR6   0  -0.566  -3.7861  11.4305  77.8393
 U4V  C07  C  CH1   0   0.200  -2.7422  10.5017  78.3186
 U4V  C08  C  CH2   0  -0.507  -2.3352  10.7623  79.7698
 U4V  C09  C  CH1   0  -0.138  -3.1699   9.7355  80.5236
 U4V  N10  N  NR5   0  -0.273  -2.6595   9.3717  81.8236
 U4V  N11  N  N     0  -0.096  -3.4382   9.4858  82.8879
 U4V  N12  N  N     0  -0.308  -2.7636   9.1003  83.9131
 U4V  N15  N  NH1   0  -0.683   0.0333   6.9365  84.2019
 U4V  S20  S  S     0   1.351  -2.6335   1.7876  85.3257
 U4V  O21  O  OS    0  -0.657  -3.9776   2.0501  85.8288
 U4V  N22  N  NC2   0  -0.888  -2.6370   1.0793  83.8256
 U4V  O23  O  OS    0  -0.671  -1.7585   0.9543  86.1411
 U4V  C24  C  CR16  0  -0.225  -2.5476   4.5174  85.1843
 U4V  C25  C  CR16  0  -0.335  -1.9317   5.7288  84.9295
 U4V  C26  C  CR15  0  -0.076  -1.4477   8.8974  82.1651
 U4V  C27  C  CH1   0   0.041  -3.2029   8.5668  79.5355
 U4V  C28  C  CH2   0  -0.175  -4.3599   7.6083  79.6850
 U4V  O29  O  OH1   0  -0.656  -5.5729   8.3176  79.6800
 U4V  O30  O  O2    0  -0.489  -3.2329   9.1969  78.2611
 U4V  C31  C  CR6   0   0.729  -3.3536  12.6599  77.4046
 U4V  N32  N  NR16  0  -0.733  -4.3450  13.4842  76.9436
 U4V  O33  O  O     0  -0.481  -2.1849  12.9930  77.4274
 U4V  H1   H  HCR6  0   0.277  -0.0077   2.4297  84.3392
 U4V  H2   H  HCR6  0   0.269   1.0826   4.5598  83.8794
 U4V  H3   H  HCH2  0   0.290   0.3555   8.9316  84.4942
 U4V  H4   H  HCH2  0   0.267  -0.9174   8.2817  85.4992
 U4V  H5   H  HCH3  0   0.245  -7.6701  10.5497  77.8135
 U4V  H6   H  HCH3  0   0.244  -8.1230  12.2411  78.0076
 U4V  H7   H  HCH3  0   0.244  -7.9480  11.5613  76.3985
 U4V  H9   H  HCH1  0   0.283  -1.8970  10.6107  77.6389
 U4V  H10  H  HCH2  0   0.282  -1.2690  10.5594  79.8857
 U4V  H11  H  HCH2  0   0.297  -2.5200  11.7850  80.0918
 U4V  H12  H  HCH1  0   0.310  -4.1771  10.1141  80.7028
 U4V  H13  H  HNH1  0   0.400   0.9831   6.8857  83.8755
 U4V  H14  H  HNC2  0   0.411  -2.8195   0.0818  83.8892
 U4V  H15  H  HNC2  0   0.409  -3.3006   1.5148  83.1925
 U4V  H16  H  HCR6  0   0.275  -3.5666   4.5140  85.5464
 U4V  H17  H  HCR6  0   0.271  -2.4918   6.6383  85.0952
 U4V  H18  H  HCR5  0   0.320  -0.6540   8.7284  81.4562
 U4V  H19  H  HCH1  0   0.262  -2.2803   7.9779  79.6286
 U4V  H20  H  HCH2  0   0.219  -4.2083   7.0564  80.6216
 U4V  H21  H  HCH2  0   0.232  -4.3091   6.8719  78.8738
 U4V  H22  H  HOH1  0   0.467  -6.3003   7.6895  79.7204
 U4V  H23  H  HNR6  0   0.422  -4.0374  14.3913  76.6142
 U4V  H8   H  HCR6  0   0.322  -5.3564  10.1229  78.2254
 U4V  O01  O  O     0  -0.449  -6.4777  14.0681  76.4686

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
 U4V  O01  C02  double    1.217  0.020  1.217
 U4V  C02  N32  single    1.385  0.020  1.385
 U4V  C02  C03  single    1.448  0.020  1.448
 U4V  N32  C31  single    1.369  0.020  1.369
 U4V  C04  C03  single    1.494  0.020  1.494
 U4V  C03  C05  double    1.346  0.020  1.346
 U4V  O33  C31  double    1.215  0.020  1.215
 U4V  C31  N06  single    1.374  0.020  1.374
 U4V  O30  C07  single    1.395  0.020  1.395
 U4V  O30  C27  single    1.422  0.020  1.422
 U4V  O29  C28  single    1.405  0.020  1.405
 U4V  N06  C05  single    1.368  0.020  1.368
 U4V  N06  C07  single    1.477  0.020  1.477
 U4V  C07  C08  single    1.530  0.020  1.530
 U4V  C28  C27  single    1.510  0.020  1.510
 U4V  C27  C09  single    1.531  0.020  1.531
 U4V  C08  C09  single    1.523  0.020  1.523
 U4V  C09  N10  single    1.443  0.020  1.443
 U4V  N10  C26  aromatic  1.345  0.020  1.345
 U4V  N10  N11  aromatic  1.324  0.020  1.324
 U4V  C26  C13  aromatic  1.371  0.020  1.371
 U4V  N11  N12  aromatic  1.286  0.020  1.286
 U4V  C13  N12  aromatic  1.350  0.020  1.350
 U4V  C13  C14  single    1.497  0.020  1.497
 U4V  N15  C14  single    1.440  0.020  1.440
 U4V  N15  C16  single    1.353  0.020  1.353
 U4V  C16  C25  aromatic  1.405  0.020  1.405
 U4V  C16  C17  aromatic  1.412  0.020  1.412
 U4V  C25  C24  aromatic  1.383  0.020  1.383
 U4V  C17  C18  aromatic  1.373  0.020  1.373
 U4V  C24  C19  aromatic  1.388  0.020  1.388
 U4V  C18  C19  aromatic  1.397  0.020  1.397
 U4V  C19  S20  single    1.753  0.020  1.753
 U4V  N22  S20  single    1.659  0.020  1.659
 U4V  O21  S20  double    1.459  0.020  1.459
 U4V  S20  O23  double    1.458  0.020  1.458
 U4V  C18  H1   single    0.930  0.020  1.080
 U4V  C17  H2   single    0.930  0.020  1.080
 U4V  C14  H3   single    0.970  0.020  1.090
 U4V  C14  H4   single    0.970  0.020  1.090
 U4V  C04  H5   single    0.970  0.020  1.090
 U4V  C04  H6   single    0.970  0.020  1.090
 U4V  C04  H7   single    0.970  0.020  1.090
 U4V  C05  H8   single    0.930  0.020  1.080
 U4V  C07  H9   single    0.970  0.020  1.090
 U4V  C08  H10  single    0.970  0.020  1.090
 U4V  C08  H11  single    0.970  0.020  1.090
 U4V  C09  H12  single    0.970  0.020  1.090
 U4V  N15  H13  single    0.860  0.020  1.020
 U4V  N22  H14  single    0.890  0.020  1.040
 U4V  N22  H15  single    0.890  0.020  1.040
 U4V  C24  H16  single    0.930  0.020  1.080
 U4V  C25  H17  single    0.930  0.020  1.080
 U4V  C26  H18  single    0.930  0.020  1.080
 U4V  C27  H19  single    0.970  0.020  1.090
 U4V  C28  H20  single    0.970  0.020  1.090
 U4V  C28  H21  single    0.970  0.020  1.090
 U4V  O29  H22  single    0.850  0.020  0.980
 U4V  N32  H23  single    0.860  0.020  1.020

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
 U4V  C24  C19  S20  120.61  3.000
 U4V  S20  C19  C18  119.59  3.000
 U4V  C24  C19  C18  119.79  3.000
 U4V  H1   C18  C17  119.18  3.000
 U4V  H1   C18  C19  120.73  3.000
 U4V  C17  C18  C19  120.08  3.000
 U4V  H2   C17  C16  119.36  3.000
 U4V  H2   C17  C18  119.63  3.000
 U4V  C16  C17  C18  121.01  3.000
 U4V  C25  C16  N15  122.48  3.000
 U4V  C25  C16  C17  118.11  3.000
 U4V  N15  C16  C17  119.41  3.000
 U4V  C26  C13  N12  107.68  3.000
 U4V  N12  C13  C14  122.38  3.000
 U4V  C26  C13  C14  129.93  3.000
 U4V  H4   C14  H3   106.27  3.000
 U4V  H4   C14  N15  110.94  3.000
 U4V  H3   C14  N15  106.80  3.000
 U4V  H4   C14  C13  108.45  3.000
 U4V  H3   C14  C13  109.65  3.000
 U4V  N15  C14  C13  114.41  3.000
 U4V  N32  C02  C03  114.26  3.000
 U4V  C03  C02  O01  125.20  3.000
 U4V  N32  C02  O01  120.55  3.000
 U4V  C05  C03  C04  122.81  3.000
 U4V  C05  C03  C02  118.40  3.000
 U4V  C04  C03  C02  118.78  3.000
 U4V  H7   C04  H6   107.14  3.000
 U4V  H7   C04  H5   107.81  3.000
 U4V  H6   C04  H5   107.84  3.000
 U4V  H7   C04  C03  111.43  3.000
 U4V  H6   C04  C03  111.51  3.000
 U4V  H5   C04  C03  110.91  3.000
 U4V  H8   C05  N06  115.75  3.000
 U4V  H8   C05  C03  120.67  3.000
 U4V  N06  C05  C03  123.57  3.000
 U4V  C31  N06  C07  116.28  3.000
 U4V  C07  N06  C05  122.37  3.000
 U4V  C31  N06  C05  121.34  3.000
 U4V  H9   C07  O30  109.91  3.000
 U4V  H9   C07  C08  111.61  3.000
 U4V  O30  C07  C08  106.98  3.000
 U4V  H9   C07  N06  106.42  3.000
 U4V  C08  C07  N06  112.88  3.000
 U4V  O30  C07  N06  109.03  3.000
 U4V  H11  C08  H10  108.01  3.000
 U4V  H11  C08  C09  113.21  3.000
 U4V  H10  C08  C09  110.94  3.000
 U4V  H11  C08  C07  113.32  3.000
 U4V  H10  C08  C07  109.21  3.000
 U4V  C09  C08  C07  102.06  3.000
 U4V  H12  C09  C27  110.56  3.000
 U4V  H12  C09  N10  105.43  3.000
 U4V  C27  C09  N10  113.36  3.000
 U4V  H12  C09  C08  110.69  3.000
 U4V  N10  C09  C08  114.96  3.000
 U4V  C27  C09  C08  101.95  3.000
 U4V  C26  N10  N11  110.87  3.000
 U4V  N11  N10  C09  119.63  3.000
 U4V  C26  N10  C09  129.50  3.000
 U4V  N12  N11  N10  107.85  3.000
 U4V  N11  N12  C13  109.48  3.000
 U4V  H13  N15  C14  117.11  3.000
 U4V  H13  N15  C16  117.77  3.000
 U4V  C14  N15  C16  124.82  3.000
 U4V  O23  S20  N22  105.25  3.000
 U4V  O23  S20  O21  117.58  3.000
 U4V  N22  S20  O21  112.75  3.000
 U4V  O23  S20  C19  110.56  3.000
 U4V  O21  S20  C19  108.27  3.000
 U4V  N22  S20  C19  101.22  3.000
 U4V  H15  N22  H14  110.05  3.000
 U4V  H15  N22  S20  112.47  3.000
 U4V  H14  N22  S20  111.28  3.000
 U4V  H16  C24  C25  118.96  3.000
 U4V  H16  C24  C19  120.62  3.000
 U4V  C25  C24  C19  120.43  3.000
 U4V  H17  C25  C24  118.57  3.000
 U4V  H17  C25  C16  120.85  3.000
 U4V  C24  C25  C16  120.58  3.000
 U4V  H18  C26  N10  123.49  3.000
 U4V  H18  C26  C13  132.39  3.000
 U4V  N10  C26  C13  104.12  3.000
 U4V  H19  C27  O30  109.35  3.000
 U4V  H19  C27  C28  107.15  3.000
 U4V  O30  C27  C28  110.72  3.000
 U4V  H19  C27  C09  109.66  3.000
 U4V  C28  C27  C09  115.93  3.000
 U4V  O30  C27  C09  103.92  3.000
 U4V  H21  C28  H20  106.69  3.000
 U4V  H21  C28  O29  112.10  3.000
 U4V  H20  C28  O29  112.09  3.000
 U4V  H21  C28  C27  108.51  3.000
 U4V  H20  C28  C27  107.33  3.000
 U4V  O29  C28  C27  109.92  3.000
 U4V  H22  O29  C28  108.85  3.000
 U4V  C27  O30  C07  111.72  3.000
 U4V  O33  C31  N32  122.52  3.000
 U4V  O33  C31  N06  122.82  3.000
 U4V  N32  C31  N06  114.66  3.000
 U4V  H23  N32  C31  115.38  3.000
 U4V  H23  N32  C02  116.87  3.000
 U4V  C31  N32  C02  127.74  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
 U4V  CONST_01  C16  C25  C24  C19     0.00   0.0  0
 U4V  CONST_02  C16  C17  C18  C19     0.00   0.0  0
 U4V  CONST_03  C25  C16  C17  C18     0.00   0.0  0
 U4V  CONST_04  C25  C24  C19  C18     0.00   0.0  0
 U4V  CONST_05  C24  C25  C16  C17     0.00   0.0  0
 U4V  CONST_06  C24  C19  C18  C17     0.00   0.0  0
 U4V  CONST_07  N11  N10  C26  C13     0.00   0.0  0
 U4V  CONST_08  N10  N11  N12  C13     0.00   0.0  0
 U4V  CONST_09  N12  C13  C26  N10     0.00   0.0  0
 U4V  CONST_10  C26  C13  N12  N11     0.00   0.0  0
 U4V  CONST_11  C26  N10  N11  N12     0.00   0.0  0
 U4V  CONST_12  C09  N10  C26  C13   180.00   0.0  0
 U4V  CONST_13  N12  N11  N10  C09   180.00   0.0  0
 U4V  CONST_14  N06  C31  N32  C02     0.00   0.0  0
 U4V  CONST_15  C31  N32  C02  C03     0.00   0.0  0
 U4V  CONST_16  N32  C31  N06  C05     0.00   0.0  0
 U4V  CONST_17  N32  C31  N06  C07   180.00   0.0  0
 U4V  CONST_18  N15  C16  C17  C18   180.00   0.0  0
 U4V  CONST_19  S20  C19  C18  C17   180.00   0.0  0
 U4V  CONST_20  N10  C26  C13  C14   180.00   0.0  0
 U4V  CONST_21  N11  N12  C13  C14   180.00   0.0  0
 U4V  CONST_22  C24  C25  C16  N15   180.00   0.0  0
 U4V  CONST_23  C25  C24  C19  S20   180.00   0.0  0
 U4V  CONST_24  C31  N32  C02  O01   180.00   0.0  0
 U4V  CONST_25  O33  C31  N32  C02   180.00   0.0  0
 U4V  CONST_26  O33  C31  N06  C05   180.00   0.0  0
 U4V  CONST_27  O33  C31  N06  C07     0.00   0.0  0
 U4V  CONST_28  H17  C25  C24  C19   180.00   0.0  0
 U4V  CONST_29  H2   C17  C18  C19   180.00   0.0  0
 U4V  CONST_30  H16  C24  C19  C18   180.00   0.0  0
 U4V  CONST_31  H1   C18  C17  C16   180.00   0.0  0
 U4V  CONST_32  H18  C26  N10  C09     0.00   0.0  0
 U4V  CONST_33  H23  N32  C02  C03   180.00   0.0  0
 U4V  CONST_34  C14  N15  C16  C17   180.00   0.0  0
 U4V  CONST_35  C25  C16  N15  C14     0.00   0.0  0
 U4V  CONST_36  H13  N15  C16  C17     0.00   0.0  0
 U4V  Var_01    N22  S20  C19  C18   -62.75  30.0  2
 U4V  Var_02    C13  C14  N15  C16   -77.01  30.0  3
 U4V  Var_03    N15  C14  C13  N12   123.35  30.0  2
 U4V  Var_04    H5   C04  C03  C02  -179.76  30.0  3
 U4V  Var_05    H14  N22  S20  C19   164.66  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
 U4V  chir_01  C07  O30  N06  C08  negativ
 U4V  chir_02  C09  N10  C27  C08  positiv
 U4V  chir_03  C27  O30  C09  C28  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
 U4V  plan-1  C13  0.020
 U4V  plan-1  C14  0.020
 U4V  plan-1  C09  0.020
 U4V  plan-1  N10  0.020
 U4V  plan-1  N11  0.020
 U4V  plan-1  N12  0.020
 U4V  plan-1  C26  0.020
 U4V  plan-1  H18  0.020
 U4V  plan-2  C19  0.020
 U4V  plan-2  C18  0.020
 U4V  plan-2  C17  0.020
 U4V  plan-2  C16  0.020
 U4V  plan-2  N15  0.020
 U4V  plan-2  S20  0.020
 U4V  plan-2  C24  0.020
 U4V  plan-2  C25  0.020
 U4V  plan-2  H1   0.020
 U4V  plan-2  H2   0.020
 U4V  plan-2  H16  0.020
 U4V  plan-2  H17  0.020
 U4V  plan-3  C02  0.020
 U4V  plan-3  C03  0.020
 U4V  plan-3  C04  0.020
 U4V  plan-3  C05  0.020
 U4V  plan-3  N06  0.020
 U4V  plan-3  C07  0.020
 U4V  plan-3  C31  0.020
 U4V  plan-3  N32  0.020
 U4V  plan-3  O33  0.020
 U4V  plan-3  H23  0.020
 U4V  plan-3  H8   0.020
 U4V  plan-3  O01  0.020
 U4V  plan-4  C16  0.020
 U4V  plan-4  C14  0.020
 U4V  plan-4  N15  0.020
 U4V  plan-4  H13  0.020

