# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 06:15:38 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 5'-[(S)-[(3S)-3-amino-4-methoxy-4-oxobutyl](methyl)-lambda~4~-sulfanyl]-5'-deoxyadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@@H](N)CC[SH](C)C[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
 SMM  SMM  5'-[(S)-[(3S)-3-amino-4-methoxy-4-oxobutyl](methyl)-lambda~4~-sulfanyl]-5'-deoxyadenosine  ligand  54  28  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SMM
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
 SMM  N     N  NH2   0  -0.778  -3.1786   3.6706  -1.6849
 SMM  CA    C  CH1   0  -0.225  -4.2559   3.3777  -0.7706
 SMM  CB    C  CH2   0  -0.426  -3.7180   2.7915   0.5439
 SMM  CG    C  CH2   0  -0.549  -2.8228   3.7540   1.3053
 SMM  SD    S  SH1   0   0.261  -2.3305   2.9478   2.8669
 SMM  CE    C  CH3   0  -0.724  -1.4442   4.1026   3.9331
 SMM  C5'   C  CH2   0  -0.730  -0.4931   2.4100   1.9475
 SMM  C4'   C  CH1   0   0.005   0.2092   1.3788   2.7932
 SMM  O4'   O  O2    0  -0.496  -0.6841   0.3083   3.1771
 SMM  C1'   C  CH1   0   0.230  -0.5000  -0.7930   2.3592
 SMM  N9    N  NR5   0  -0.550  -1.7563  -1.1076   1.6795
 SMM  C4    C  CR56  0   0.522  -1.8980  -2.0202   0.6813
 SMM  N3    N  N     0  -0.517  -0.9482  -2.7515   0.0908
 SMM  C2    C  CR16  0   0.066  -1.4444  -3.5385  -0.8502
 SMM  N1    N  N     0  -0.476  -2.7095  -3.6573  -1.2354
 SMM  C6    C  CR6   0   0.461  -3.6515  -2.9139  -0.6404
 SMM  N6    N  NH2   0  -0.814  -4.9202  -3.0377  -1.0280
 SMM  C5    C  CR56  0  -0.002  -3.2511  -2.0359   0.3843
 SMM  N7    N  N     0  -0.453  -3.9300  -1.1555   1.1836
 SMM  C8    C  CR15  0   0.111  -3.0091  -0.6299   1.9419
 SMM  C2'   C  CH1   0  -0.055   0.6130  -0.4397   1.3501
 SMM  O2'   O  OH1   0  -0.685   1.4421  -1.5061   1.0088
 SMM  C3'   C  CH1   0   0.005   1.3632   0.6490   2.1103
 SMM  O3'   O  OH1   0  -0.673   2.2026   0.0979   3.0957
 SMM  C     C  C     0   0.564  -5.1597   4.5733  -0.4841
 SMM  O     O  O     0  -0.444  -4.9164   5.7079  -0.8102
 SMM  OXT   O  O2    0  -0.449  -6.2457   4.2179   0.1854
 SMM  CXT   C  CH3   0  -0.424  -7.1625   5.2467   0.5623
 SMM  HN1   H  HNH2  0   0.349  -2.6864   4.5096  -1.4049
 SMM  HN2   H  HNH2  0   0.359  -3.5488   3.8636  -2.6064
 SMM  HA1   H  HCH1  0   0.291  -4.8812   2.6034  -1.2252
 SMM  HB1   H  HCH2  0   0.262  -3.1597   1.8883   0.2911
 SMM  HB2   H  HCH2  0   0.254  -4.5544   2.4841   1.1752
 SMM  HG1   H  HCH2  0   0.287  -3.3382   4.6741   1.5803
 SMM  HG2   H  HCH2  0   0.292  -1.9187   4.0089   0.7567
 SMM  HD1   H  HSH1  0  -0.114  -3.5970   3.5316   3.4261
 SMM  HE1   H  HCH3  0   0.279  -0.4725   3.6901   4.1869
 SMM  HE2   H  HCH3  0   0.288  -1.3070   5.0448   3.4072
 SMM  HE3   H  HCH3  0   0.276  -2.0447   4.2677   4.8250
 SMM  H5'1  H  HCH2  0   0.213  -0.7559   2.0101   0.9623
 SMM  H5'2  H  HCH2  0   0.221   0.1603   3.2735   1.7933
 SMM  H4'   H  HCH1  0   0.242   0.5620   1.8336   3.7248
 SMM  H1'   H  HCH1  0   0.259  -0.2189  -1.6720   2.9508
 SMM  H2    H  HCR6  0   0.259  -0.7314  -4.1646  -1.3746
 SMM  HN61  H  HNH2  0   0.405  -5.1585  -3.6355  -1.8008
 SMM  HN62  H  HNH2  0   0.413  -5.6358  -2.4404  -0.6522
 SMM  H8    H  HCR5  0   0.292  -3.1804   0.1170   2.7012
 SMM  H2'   H  HCH1  0   0.235   0.1540   0.0147   0.4616
 SMM  HO2'  H  HOH1  0   0.461   0.8743  -2.1637   0.5652
 SMM  H3'   H  HCH1  0   0.239   1.9117   1.3151   1.4334
 SMM  HO3'  H  HOH1  0   0.450   2.7450  -0.5845   2.6852
 SMM  HXT1  H  HCH3  0   0.241  -7.5921   5.7351  -0.3119
 SMM  HXT2  H  HCH3  0   0.240  -6.6837   5.9949   1.1935
 SMM  HXT3  H  HCH3  0   0.253  -7.9501   4.7538   1.1240

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
 SMM  N    CA    single    1.443  0.020  1.443
 SMM  N    HN1   single    0.890  0.020  1.040
 SMM  N    HN2   single    0.890  0.020  1.040
 SMM  CA   CB    single    1.536  0.020  1.536
 SMM  CA   C     single    1.526  0.020  1.526
 SMM  CA   HA1   single    0.970  0.020  1.090
 SMM  CB   CG    single    1.519  0.020  1.519
 SMM  CB   HB1   single    0.970  0.020  1.090
 SMM  CB   HB2   single    0.970  0.020  1.090
 SMM  CG   SD    single    1.825  0.020  1.825
 SMM  CG   HG1   single    0.970  0.020  1.090
 SMM  CG   HG2   single    0.970  0.020  1.090
 SMM  SD   CE    single    1.804  0.020  1.804
 SMM  SD   C5'   single    2.124  0.020  2.124
 SMM  SD   HD1   single    1.200  0.020  1.300
 SMM  CE   HE1   single    0.970  0.020  1.090
 SMM  CE   HE2   single    0.970  0.020  1.090
 SMM  CE   HE3   single    0.970  0.020  1.090
 SMM  C5'  C4'   single    1.507  0.020  1.507
 SMM  C5'  H5'1  single    0.970  0.020  1.090
 SMM  C5'  H5'2  single    0.970  0.020  1.090
 SMM  C4'  O4'   single    1.446  0.020  1.446
 SMM  C4'  C3'   single    1.527  0.020  1.527
 SMM  C4'  H4'   single    0.970  0.020  1.090
 SMM  O4'  C1'   single    1.384  0.020  1.384
 SMM  C1'  N9    single    1.463  0.020  1.463
 SMM  C1'  C2'   single    1.543  0.020  1.543
 SMM  C1'  H1'   single    0.970  0.020  1.090
 SMM  N9   C4    aromatic  1.360  0.020  1.360
 SMM  N9   C8    aromatic  1.366  0.020  1.366
 SMM  C4   N3    aromatic  1.336  0.020  1.336
 SMM  C4   C5    aromatic  1.385  0.020  1.385
 SMM  N3   C2    aromatic  1.323  0.020  1.323
 SMM  C2   N1    aromatic  1.328  0.020  1.328
 SMM  C2   H2    single    0.930  0.020  1.080
 SMM  N1   C6    aromatic  1.339  0.020  1.339
 SMM  C6   N6    single    1.332  0.020  1.332
 SMM  C6   C5    aromatic  1.408  0.020  1.408
 SMM  N6   HN61  single    0.860  0.020  1.020
 SMM  N6   HN62  single    0.860  0.020  1.020
 SMM  C5   N7    aromatic  1.369  0.020  1.369
 SMM  N7   C8    aromatic  1.304  0.020  1.304
 SMM  C8   H8    single    0.930  0.020  1.080
 SMM  C2'  O2'   single    1.393  0.020  1.393
 SMM  C2'  C3'   single    1.525  0.020  1.525
 SMM  C2'  H2'   single    0.970  0.020  1.090
 SMM  O2'  HO2'  single    0.850  0.020  0.980
 SMM  C3'  O3'   single    1.407  0.020  1.407
 SMM  C3'  H3'   single    0.970  0.020  1.090
 SMM  O3'  HO3'  single    0.850  0.020  0.980
 SMM  C    O     double    1.205  0.020  1.205
 SMM  C    OXT   single    1.324  0.020  1.324
 SMM  OXT  CXT   single    1.429  0.020  1.429
 SMM  CXT  HXT1  single    0.970  0.020  1.090
 SMM  CXT  HXT2  single    0.970  0.020  1.090
 SMM  CXT  HXT3  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
 SMM  HN2   N    HN1   105.77  3.000
 SMM  HN2   N    CA    110.04  3.000
 SMM  HN1   N    CA    110.85  3.000
 SMM  HA1   CA   C     107.09  3.000
 SMM  HA1   CA   CB    106.59  3.000
 SMM  C     CA   CB    110.22  3.000
 SMM  HA1   CA   N     107.88  3.000
 SMM  C     CA   N     113.71  3.000
 SMM  CB    CA   N     110.99  3.000
 SMM  HB2   CB   HB1   107.02  3.000
 SMM  HB2   CB   CG    109.87  3.000
 SMM  HB1   CB   CG    109.81  3.000
 SMM  HB2   CB   CA    109.50  3.000
 SMM  HB1   CB   CA    107.25  3.000
 SMM  CG    CB   CA    113.17  3.000
 SMM  HG2   CG   HG1   108.81  3.000
 SMM  HG2   CG   SD    108.11  3.000
 SMM  HG1   CG   SD    106.54  3.000
 SMM  HG2   CG   CB    112.67  3.000
 SMM  HG1   CG   CB    112.50  3.000
 SMM  SD    CG   CB    107.94  3.000
 SMM  HD1   SD   C5'   171.40  3.000
 SMM  HD1   SD   CE     86.88  3.000
 SMM  C5'   SD   CE     89.59  3.000
 SMM  HD1   SD   CG     85.38  3.000
 SMM  C5'   SD   CG     88.56  3.000
 SMM  CE    SD   CG    110.82  3.000
 SMM  HE3   CE   HE2   109.54  3.000
 SMM  HE3   CE   HE1   111.10  3.000
 SMM  HE2   CE   HE1   109.22  3.000
 SMM  HE3   CE   SD    108.09  3.000
 SMM  HE2   CE   SD    109.31  3.000
 SMM  HE1   CE   SD    109.55  3.000
 SMM  H5'2  C5'  H5'1  107.75  3.000
 SMM  H5'2  C5'  C4'   109.93  3.000
 SMM  H5'1  C5'  C4'   111.51  3.000
 SMM  H5'2  C5'  SD    112.21  3.000
 SMM  H5'1  C5'  SD    105.92  3.000
 SMM  C4'   C5'  SD    109.48  3.000
 SMM  H4'   C4'  C3'   109.61  3.000
 SMM  H4'   C4'  O4'   106.30  3.000
 SMM  C3'   C4'  O4'   103.40  3.000
 SMM  H4'   C4'  C5'   110.08  3.000
 SMM  C3'   C4'  C5'   115.36  3.000
 SMM  O4'   C4'  C5'   111.57  3.000
 SMM  C1'   O4'  C4'   110.49  3.000
 SMM  H1'   C1'  C2'   110.58  3.000
 SMM  H1'   C1'  N9    107.37  3.000
 SMM  C2'   C1'  N9    111.40  3.000
 SMM  H1'   C1'  O4'   110.68  3.000
 SMM  C2'   C1'  O4'   107.47  3.000
 SMM  N9    C1'  O4'   109.36  3.000
 SMM  C8    N9   C4    106.26  3.000
 SMM  C8    N9   C1'   128.55  3.000
 SMM  C4    N9   C1'   125.10  3.000
 SMM  C5    C4   N3    126.39  3.000
 SMM  C5    C4   N9    105.47  3.000
 SMM  N3    C4   N9    128.14  3.000
 SMM  C2    N3   C4    111.91  3.000
 SMM  H2    C2   N1    115.77  3.000
 SMM  H2    C2   N3    116.15  3.000
 SMM  N1    C2   N3    128.08  3.000
 SMM  C6    N1   C2    119.45  3.000
 SMM  C5    C6   N6    122.73  3.000
 SMM  C5    C6   N1    118.00  3.000
 SMM  N6    C6   N1    119.27  3.000
 SMM  HN62  N6   HN61  118.16  3.000
 SMM  HN62  N6   C6    120.93  3.000
 SMM  HN61  N6   C6    120.29  3.000
 SMM  N7    C5   C6    133.23  3.000
 SMM  N7    C5   C4    110.60  3.000
 SMM  C6    C5   C4    116.17  3.000
 SMM  C8    N7   C5    104.39  3.000
 SMM  H8    C8   N7    125.20  3.000
 SMM  H8    C8   N9    121.52  3.000
 SMM  N7    C8   N9    113.27  3.000
 SMM  H2'   C2'  C3'   108.27  3.000
 SMM  H2'   C2'  O2'   111.54  3.000
 SMM  C3'   C2'  O2'   112.08  3.000
 SMM  H2'   C2'  C1'   108.79  3.000
 SMM  C3'   C2'  C1'   101.08  3.000
 SMM  O2'   C2'  C1'   114.46  3.000
 SMM  HO2'  O2'  C2'   106.32  3.000
 SMM  H3'   C3'  O3'   111.82  3.000
 SMM  H3'   C3'  C2'   111.83  3.000
 SMM  O3'   C3'  C2'   111.28  3.000
 SMM  H3'   C3'  C4'   111.33  3.000
 SMM  O3'   C3'  C4'   108.97  3.000
 SMM  C2'   C3'  C4'   101.10  3.000
 SMM  HO3'  O3'  C3'   108.36  3.000
 SMM  OXT   C    O     123.70  3.000
 SMM  OXT   C    CA    111.74  3.000
 SMM  O     C    CA    124.55  3.000
 SMM  CXT   OXT  C     117.80  3.000
 SMM  HXT3  CXT  HXT2  109.31  3.000
 SMM  HXT3  CXT  HXT1  109.43  3.000
 SMM  HXT2  CXT  HXT1  109.28  3.000
 SMM  HXT3  CXT  OXT   105.97  3.000
 SMM  HXT2  CXT  OXT   111.42  3.000
 SMM  HXT1  CXT  OXT   111.36  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
 SMM  CONST_01  C2    N3   C4   N9   180.00   0.0  0
 SMM  CONST_02  C6    C5   C4   N9   180.00   0.0  0
 SMM  CONST_03  N7    C5   C4   N9     0.00   0.0  0
 SMM  CONST_04  C5    N7   C8   N9     0.00   0.0  0
 SMM  CONST_05  N7    C8   N9   C4     0.00   0.0  0
 SMM  CONST_06  N1    C2   N3   C4     0.00   0.0  0
 SMM  CONST_07  N1    C6   C5   C4     0.00   0.0  0
 SMM  CONST_08  C8    N7   C5   C4     0.00   0.0  0
 SMM  CONST_09  C8    N9   C4   N3   180.00   0.0  0
 SMM  CONST_10  C6    C5   C4   N3     0.00   0.0  0
 SMM  CONST_11  N7    C5   C4   N3   180.00   0.0  0
 SMM  CONST_12  C6    N1   C2   N3     0.00   0.0  0
 SMM  CONST_13  C5    C4   N3   C2     0.00   0.0  0
 SMM  CONST_14  C5    C6   N1   C2     0.00   0.0  0
 SMM  CONST_15  N7    C5   C6   N1   180.00   0.0  0
 SMM  CONST_16  C8    N7   C5   C6   180.00   0.0  0
 SMM  CONST_17  C8    N9   C4   C5     0.00   0.0  0
 SMM  CONST_18  N3    C4   N9   C1'    0.00   0.0  0
 SMM  CONST_19  C5    C4   N9   C1'  180.00   0.0  0
 SMM  CONST_20  N7    C8   N9   C1'  180.00   0.0  0
 SMM  CONST_21  N6    C6   C5   C4   180.00   0.0  0
 SMM  CONST_22  N6    C6   N1   C2   180.00   0.0  0
 SMM  CONST_23  N7    C5   C6   N6     0.00   0.0  0
 SMM  CONST_24  H8    C8   N9   C1'    0.00   0.0  0
 SMM  CONST_25  H2    C2   N3   C4   180.00   0.0  0
 SMM  CONST_26  HN61  N6   C6   N1     0.00   0.0  0
 SMM  CONST_27  HN62  N6   C6   N1   180.00   0.0  0
 SMM  Var_01    SD    CG   CB   CA   177.43  30.0  3
 SMM  Var_02    HXT1  CXT  OXT  C     63.12  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
 SMM  chir_01  CA   N    CB   C    negativ
 SMM  chir_02  SD   C5'  CE   CG   negativ
 SMM  chir_03  C4'  O4'  C3'  C5'  negativ
 SMM  chir_04  C1'  O4'  N9   C2'  negativ
 SMM  chir_05  C2'  O2'  C1'  C3'  negativ
 SMM  chir_06  C3'  O3'  C4'  C2'  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
 SMM  plan-1  C1'   0.020
 SMM  plan-1  N9    0.020
 SMM  plan-1  C4    0.020
 SMM  plan-1  N3    0.020
 SMM  plan-1  C2    0.020
 SMM  plan-1  N1    0.020
 SMM  plan-1  C6    0.020
 SMM  plan-1  N6    0.020
 SMM  plan-1  C5    0.020
 SMM  plan-1  N7    0.020
 SMM  plan-1  C8    0.020
 SMM  plan-1  H2    0.020
 SMM  plan-1  H8    0.020
 SMM  plan-2  C6    0.020
 SMM  plan-2  N6    0.020
 SMM  plan-2  HN61  0.020
 SMM  plan-2  HN62  0.020
 SMM  plan-3  CA    0.020
 SMM  plan-3  C     0.020
 SMM  plan-3  O     0.020
 SMM  plan-3  OXT   0.020

