# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 13:53:40 2022
#   Inital geometry file: a 130 line input string
#   Ligand name: 5'-O-(L-leucylsulfamoyl)adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N)C(=O)N[S](=O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
#
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
 LSS  LSS  5'-O-(L-leucylsulfamoyl)adenosine  ligand  56  31  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LSS
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
 LSS  C1    C  C     0   0.563   2.2395  -0.6028  -0.5219
 LSS  N1    N  N     0  -0.473  -4.4931  -2.8733  -0.8812
 LSS  O1    O  O     0  -0.403   1.7200  -0.4476  -1.5978
 LSS  S1    S  S     0   1.631   3.0141   1.9792  -0.4280
 LSS  C2    C  CR16  0   0.049  -4.8937  -1.6230  -1.0939
 LSS  N2    N  NC1   0  -0.835   2.7429   0.4656   0.2062
 LSS  O2    O  OH1   0  -0.650  -3.4210   2.4145   2.0422
 LSS  N3    N  N     0  -0.456  -4.2673  -0.4970  -0.7966
 LSS  O3    O  OH1   0  -0.663  -2.5633   4.5080   0.4356
 LSS  C4    C  CR56  0   0.495  -3.0928  -0.7268  -0.2177
 LSS  N4    N  NH2   0  -0.790   1.5354  -2.9744  -0.3025
 LSS  O4    O  O2    0  -0.481  -1.1755   2.0766  -0.6548
 LSS  C5    C  CR56  0   0.011  -2.5424  -1.9660   0.0636
 LSS  O5    O  OC2   0  -0.566   1.5559   2.5450  -0.6777
 LSS  C6    C  CR6   0   0.469  -3.3086  -3.0889  -0.2982
 LSS  N6    N  NH2   0  -0.815  -2.8975  -4.3398  -0.0911
 LSS  C7    C  CH1   0  -0.225   4.3103  -3.6748   0.6081
 LSS  N7    N  N     0  -0.472  -1.3150  -1.8274   0.6605
 LSS  C8    C  CR15  0   0.136  -1.1351  -0.5438   0.7392
 LSS  C9    C  CH2   0  -0.411   3.9036  -2.3787  -0.0932
 LSS  N9    N  NR5   0  -0.540  -2.1749   0.1830   0.2298
 LSS  CA    C  CH1   0  -0.251   2.4449  -1.9585   0.1530
 LSS  C10   C  CH3   0  -0.652   5.7290  -4.0552   0.1948
 LSS  C11   C  CH3   0  -0.667   4.2065  -3.5597   2.1247
 LSS  O1A   O  OS    0  -0.630   3.6649   2.7137   0.6280
 LSS  C21   C  CH1   0   0.206  -2.2541   1.6151   0.1136
 LSS  C22   C  CH1   0  -0.050  -2.1604   2.3494   1.4512
 LSS  C23   C  CH1   0  -0.033  -1.5782   3.6965   1.0141
 LSS  C24   C  CH1   0  -0.048  -0.6186   3.2588  -0.0875
 LSS  C25   C  CH2   0  -0.191   0.7730   2.9883   0.4455
 LSS  O2A   O  OS    0  -0.607   3.5906   1.8784  -1.7387
 LSS  HN2   H  HNC1  0   0.453   3.1501   0.3064   1.1212
 LSS  HO2   H  HOH1  0   0.472  -3.3170   2.5816   2.9843
 LSS  HO3   H  HOH1  0   0.453  -3.3295   4.5150   1.0212
 LSS  HN4   H  HNH2  0   0.369   0.5847  -2.7540  -0.0268
 LSS  HN4A  H  HNH2  0   0.343   1.5504  -3.0347  -1.3131
 LSS  HN6   H  HNH2  0   0.406  -3.4982  -5.1142  -0.3161
 LSS  HN6A  H  HNH2  0   0.410  -2.0433  -4.5306   0.4020
 LSS  H7    H  HCH1  0   0.225   3.6323  -4.4656   0.2761
 LSS  H8    H  HCR5  0   0.282  -0.2602  -0.0735   1.1612
 LSS  H9    H  HCH2  0   0.230   4.5800  -1.5781   0.2249
 LSS  H9A   H  HCH2  0   0.241   4.0498  -2.4922  -1.1731
 LSS  HA    H  HCH1  0   0.271   2.2932  -1.8216   1.2287
 LSS  H10   H  HCH3  0   0.213   6.4464  -3.2893   0.5001
 LSS  H10A  H  HCH3  0   0.227   6.0334  -4.9948   0.6579
 LSS  H10B  H  HCH3  0   0.225   5.8127  -4.1751  -0.8868
 LSS  H11   H  HCH3  0   0.229   3.1839  -3.3774   2.4585
 LSS  H11A  H  HCH3  0   0.231   4.5421  -4.4782   2.6094
 LSS  H11B  H  HCH3  0   0.214   4.8291  -2.7421   2.4977
 LSS  H21   H  HCH1  0   0.270  -3.2124   1.8312  -0.3694
 LSS  H22   H  HCH1  0   0.253  -1.4365   1.8433   2.1028
 LSS  H23   H  HCH1  0   0.262  -1.0603   4.2049   1.8377
 LSS  H24   H  HCH1  0   0.286  -0.5522   4.0258  -0.8647
 LSS  H25   H  HCH2  0   0.248   0.7698   2.2297   1.2348
 LSS  H25A  H  HCH2  0   0.282   1.1961   3.9081   0.8510
 LSS  H2    H  HCR6  0   0.255  -5.8617  -1.5190  -1.5720

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
 LSS  C1   O1    double    1.205  0.020  1.205
 LSS  C1   N2    single    1.387  0.020  1.387
 LSS  C1   CA    single    1.528  0.020  1.528
 LSS  N1   C2    aromatic  1.330  0.020  1.330
 LSS  N1   C6    aromatic  1.338  0.020  1.338
 LSS  S1   N2    single    1.663  0.020  1.663
 LSS  S1   O5    single    1.584  0.020  1.584
 LSS  S1   O1A   deloc     1.442  0.020  1.442
 LSS  S1   O2A   deloc     1.435  0.020  1.435
 LSS  C2   N3    aromatic  1.322  0.020  1.322
 LSS  O2   C22   single    1.394  0.020  1.394
 LSS  N3   C4    aromatic  1.329  0.020  1.329
 LSS  O3   C23   single    1.401  0.020  1.401
 LSS  C4   C5    aromatic  1.385  0.020  1.385
 LSS  C4   N9    aromatic  1.368  0.020  1.368
 LSS  N4   CA    single    1.438  0.020  1.438
 LSS  O4   C21   single    1.402  0.020  1.402
 LSS  O4   C24   single    1.425  0.020  1.425
 LSS  C5   C6    aromatic  1.407  0.020  1.407
 LSS  C5   N7    aromatic  1.372  0.020  1.372
 LSS  O5   C25   single    1.439  0.020  1.439
 LSS  C6   N6    single    1.333  0.020  1.333
 LSS  C7   C9    single    1.529  0.020  1.529
 LSS  C7   C10   single    1.526  0.020  1.526
 LSS  C7   C11   single    1.524  0.020  1.524
 LSS  N7   C8    aromatic  1.299  0.020  1.299
 LSS  C8   N9    aromatic  1.367  0.020  1.367
 LSS  C9   CA    single    1.538  0.020  1.538
 LSS  N9   C21   single    1.439  0.020  1.439
 LSS  C21  C22   single    1.529  0.020  1.529
 LSS  C22  C23   single    1.531  0.020  1.531
 LSS  C23  C24   single    1.525  0.020  1.525
 LSS  C24  C25   single    1.515  0.020  1.515
 LSS  C2   H2    single    0.930  0.020  1.080
 LSS  N2   HN2   single    0.860  0.020  1.020
 LSS  O2   HO2   single    0.850  0.020  0.980
 LSS  O3   HO3   single    0.850  0.020  0.980
 LSS  N4   HN4   single    0.890  0.020  1.040
 LSS  N4   HN4A  single    0.890  0.020  1.040
 LSS  N6   HN6   single    0.860  0.020  1.020
 LSS  N6   HN6A  single    0.860  0.020  1.020
 LSS  C7   H7    single    0.970  0.020  1.090
 LSS  C8   H8    single    0.930  0.020  1.080
 LSS  C9   H9    single    0.970  0.020  1.090
 LSS  C9   H9A   single    0.970  0.020  1.090
 LSS  CA   HA    single    0.970  0.020  1.090
 LSS  C10  H10   single    0.970  0.020  1.090
 LSS  C10  H10A  single    0.970  0.020  1.090
 LSS  C10  H10B  single    0.970  0.020  1.090
 LSS  C11  H11   single    0.970  0.020  1.090
 LSS  C11  H11A  single    0.970  0.020  1.090
 LSS  C11  H11B  single    0.970  0.020  1.090
 LSS  C21  H21   single    0.970  0.020  1.090
 LSS  C22  H22   single    0.970  0.020  1.090
 LSS  C23  H23   single    0.970  0.020  1.090
 LSS  C24  H24   single    0.970  0.020  1.090
 LSS  C25  H25   single    0.970  0.020  1.090
 LSS  C25  H25A  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
 LSS  CA    C1   N2    113.74  3.000
 LSS  CA    C1   O1    124.51  3.000
 LSS  N2    C1   O1    121.73  3.000
 LSS  C6    N1   C2    119.20  3.000
 LSS  O2A   S1   O1A   121.55  3.000
 LSS  O2A   S1   O5    104.53  3.000
 LSS  O1A   S1   O5    110.43  3.000
 LSS  O2A   S1   N2    110.47  3.000
 LSS  O1A   S1   N2    104.95  3.000
 LSS  O5    S1   N2    103.60  3.000
 LSS  H2    C2   N3    116.12  3.000
 LSS  H2    C2   N1    115.43  3.000
 LSS  N3    C2   N1    128.45  3.000
 LSS  HN2   N2   S1    114.92  3.000
 LSS  HN2   N2   C1    119.89  3.000
 LSS  S1    N2   C1    124.04  3.000
 LSS  HO2   O2   C22   108.99  3.000
 LSS  C4    N3   C2    111.67  3.000
 LSS  HO3   O3   C23   108.18  3.000
 LSS  N9    C4   C5    105.19  3.000
 LSS  N9    C4   N3    128.35  3.000
 LSS  C5    C4   N3    126.46  3.000
 LSS  HN4A  N4   HN4   107.35  3.000
 LSS  HN4A  N4   CA    110.42  3.000
 LSS  HN4   N4   CA    110.70  3.000
 LSS  C24   O4   C21   110.82  3.000
 LSS  N7    C5   C6    132.83  3.000
 LSS  N7    C5   C4    110.71  3.000
 LSS  C6    C5   C4    116.46  3.000
 LSS  C25   O5   S1    119.20  3.000
 LSS  N6    C6   C5    122.76  3.000
 LSS  N6    C6   N1    119.47  3.000
 LSS  C5    C6   N1    117.76  3.000
 LSS  HN6A  N6   HN6   118.13  3.000
 LSS  HN6A  N6   C6    121.12  3.000
 LSS  HN6   N6   C6    120.25  3.000
 LSS  H7    C7   C11   108.33  3.000
 LSS  H7    C7   C10   108.30  3.000
 LSS  C11   C7   C10   110.58  3.000
 LSS  H7    C7   C9    108.00  3.000
 LSS  C11   C7   C9    111.97  3.000
 LSS  C10   C7   C9    109.54  3.000
 LSS  C8    N7   C5    104.49  3.000
 LSS  H8    C8   N9    122.05  3.000
 LSS  H8    C8   N7    124.52  3.000
 LSS  N9    C8   N7    113.43  3.000
 LSS  H9A   C9   H9    106.24  3.000
 LSS  H9A   C9   CA    108.22  3.000
 LSS  H9    C9   CA    109.85  3.000
 LSS  H9A   C9   C7    109.19  3.000
 LSS  H9    C9   C7    108.80  3.000
 LSS  CA    C9   C7    114.24  3.000
 LSS  C21   N9   C8    126.95  3.000
 LSS  C21   N9   C4    126.77  3.000
 LSS  C8    N9   C4    106.18  3.000
 LSS  HA    CA   C9    108.83  3.000
 LSS  HA    CA   N4    108.18  3.000
 LSS  C9    CA   N4    110.88  3.000
 LSS  HA    CA   C1    107.71  3.000
 LSS  C9    CA   C1    107.41  3.000
 LSS  N4    CA   C1    113.70  3.000
 LSS  H10B  C10  H10A  107.74  3.000
 LSS  H10B  C10  H10   107.66  3.000
 LSS  H10A  C10  H10   107.57  3.000
 LSS  H10B  C10  C7    111.54  3.000
 LSS  H10A  C10  C7    111.06  3.000
 LSS  H10   C10  C7    111.10  3.000
 LSS  H11B  C11  H11A  107.62  3.000
 LSS  H11B  C11  H11   107.73  3.000
 LSS  H11A  C11  H11   107.03  3.000
 LSS  H11B  C11  C7    110.93  3.000
 LSS  H11A  C11  C7    110.93  3.000
 LSS  H11   C11  C7    112.38  3.000
 LSS  H21   C21  C22   110.18  3.000
 LSS  H21   C21  N9    106.28  3.000
 LSS  C22   C21  N9    113.82  3.000
 LSS  H21   C21  O4    111.51  3.000
 LSS  C22   C21  O4    105.92  3.000
 LSS  N9    C21  O4    109.23  3.000
 LSS  H22   C22  C23   108.93  3.000
 LSS  H22   C22  C21   109.78  3.000
 LSS  C23   C22  C21   101.31  3.000
 LSS  H22   C22  O2    111.49  3.000
 LSS  C23   C22  O2    115.08  3.000
 LSS  C21   C22  O2    109.75  3.000
 LSS  H23   C23  C24   112.21  3.000
 LSS  H23   C23  C22   111.87  3.000
 LSS  C24   C23  C22   101.12  3.000
 LSS  H23   C23  O3    111.92  3.000
 LSS  C24   C23  O3    108.08  3.000
 LSS  C22   C23  O3    111.11  3.000
 LSS  H24   C24  C25   108.63  3.000
 LSS  H24   C24  C23   110.49  3.000
 LSS  C25   C24  C23   112.04  3.000
 LSS  H24   C24  O4    108.82  3.000
 LSS  C25   C24  O4    110.55  3.000
 LSS  C23   C24  O4    106.25  3.000
 LSS  H25A  C25  H25   108.51  3.000
 LSS  H25A  C25  C24   109.67  3.000
 LSS  H25   C25  C24   112.01  3.000
 LSS  H25A  C25  O5    109.81  3.000
 LSS  H25   C25  O5    110.54  3.000
 LSS  C24   C25  O5    106.27  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
 LSS  CONST_01  C4    N3   C2  N1     0.00   0.0  0
 LSS  CONST_02  C4    C5   C6  N1     0.00   0.0  0
 LSS  CONST_03  N7    C5   C6  N1   180.00   0.0  0
 LSS  CONST_04  C5    C6   N1  C2     0.00   0.0  0
 LSS  CONST_05  C5    C4   N3  C2     0.00   0.0  0
 LSS  CONST_06  N9    C4   N3  C2   180.00   0.0  0
 LSS  CONST_07  C6    N1   C2  N3     0.00   0.0  0
 LSS  CONST_08  C6    C5   C4  N3     0.00   0.0  0
 LSS  CONST_09  N7    C5   C4  N3   180.00   0.0  0
 LSS  CONST_10  C8    N9   C4  N3   180.00   0.0  0
 LSS  CONST_11  C8    N7   C5  C4     0.00   0.0  0
 LSS  CONST_12  N7    C8   N9  C4     0.00   0.0  0
 LSS  CONST_13  C8    N9   C4  C5     0.00   0.0  0
 LSS  CONST_14  N9    C8   N7  C5     0.00   0.0  0
 LSS  CONST_15  N9    C4   C5  C6   180.00   0.0  0
 LSS  CONST_16  C8    N7   C5  C6   180.00   0.0  0
 LSS  CONST_17  N9    C4   C5  N7     0.00   0.0  0
 LSS  CONST_18  C21   N9   C4  N3     0.00   0.0  0
 LSS  CONST_19  C21   N9   C4  C5   180.00   0.0  0
 LSS  CONST_20  C21   N9   C8  N7   180.00   0.0  0
 LSS  CONST_21  N6    C6   N1  C2   180.00   0.0  0
 LSS  CONST_22  N6    C6   C5  C4   180.00   0.0  0
 LSS  CONST_23  N7    C5   C6  N6     0.00   0.0  0
 LSS  CONST_24  H2    C2   N3  C4   180.00   0.0  0
 LSS  CONST_25  H8    C8   N9  C4   180.00   0.0  0
 LSS  CONST_26  HN6   N6   C6  N1     0.00   0.0  0
 LSS  CONST_27  HN6A  N6   C6  N1   180.00   0.0  0
 LSS  CONST_28  S1    N2   C1  O1     0.00   0.0  0
 LSS  CONST_30  HN2   N2   C1  O1   180.00   0.0  0
 LSS  Var_01    C24   C25  O5  S1  -171.37  30.0  3
 LSS  Var_02    O5    S1   N2  C1    70.17  30.0  2
 LSS  Var_03    C10   C7   C9  CA   175.02  30.0  2
 LSS  Var_04    H10   C10  C7  C9    62.07  30.0  3
 LSS  Var_05    H11   C11  C7  C9    62.72  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
 LSS  chir_01  CA   C1  N4   C9   negativ
 LSS  chir_02  C21  O4  N9   C22  negativ
 LSS  chir_03  C22  O2  C21  C23  negativ
 LSS  chir_04  C23  O3  C24  C22  positiv
 LSS  chir_05  C24  O4  C23  C25  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
 LSS  plan-1  N1    0.020
 LSS  plan-1  C2    0.020
 LSS  plan-1  N3    0.020
 LSS  plan-1  C4    0.020
 LSS  plan-1  C5    0.020
 LSS  plan-1  C6    0.020
 LSS  plan-1  N6    0.020
 LSS  plan-1  N7    0.020
 LSS  plan-1  C8    0.020
 LSS  plan-1  N9    0.020
 LSS  plan-1  C21   0.020
 LSS  plan-1  H8    0.020
 LSS  plan-1  H2    0.020
 LSS  plan-2  C6    0.020
 LSS  plan-2  N6    0.020
 LSS  plan-2  HN6   0.020
 LSS  plan-2  HN6A  0.020
 LSS  plan-3  C1    0.020
 LSS  plan-3  O1    0.020
 LSS  plan-3  S1    0.020
 LSS  plan-3  N2    0.020
 LSS  plan-3  CA    0.020
 LSS  plan-3  HN2   0.020

