# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 14:13:16 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: (8S)-1,3-dimethyl-8-{[2-(morpholin-4-yl)ethyl]sulfanyl}-6-sulfanylidene-1,3,6,7,8,9-hexahydro-2H-purin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N(C)C2=C(N[C@@H](N2)SCCN3CCOCC3)C1=S
#
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
 M0M  M0M  (8S)-1,3-dimethyl-8-{[2-(morpholin-4-yl)ethyl]sulfanyl}-6-sulfanylidene-1,3,6,7,8,9-hexahydro-2H-purin-2-one  ligand  43  22  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M0M
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
 M0M  C11   C  CH2   0  -0.311   3.3276  -1.0696   0.7558
 M0M  C12   C  CH2   0  -0.186   3.8447  -2.4148   0.2823
 M0M  C14   C  CH2   0  -0.189   5.3058  -1.3837  -1.1942
 M0M  C02   C  CR6   0   0.164  -2.2856  -0.3385  -1.1763
 M0M  C03   C  CR56  0   0.134  -1.8875   0.7562  -0.4382
 M0M  C04   C  CR56  0   0.686  -1.9242   0.7474   0.9359
 M0M  C06   C  CR15  0  -0.062  -0.9444   2.7082   0.3202
 M0M  C08   C  CH2   0  -0.573   1.4265   1.2353   0.1769
 M0M  C15   C  CH2   0  -0.306   4.8271  -0.0151  -0.7506
 M0M  C19   C  CR6   0   0.748  -2.8119  -1.4357   0.9692
 M0M  N05   N  NR15  0  -0.654  -1.4713   1.9073   1.4153
 M0M  N10   N  NT    0  -0.424   3.4448  -0.0871  -0.3086
 M0M  N16   N  NR15  0  -0.665  -1.3370   1.9803  -0.8630
 M0M  N17   N  NR6   0  -0.585  -2.3473  -0.3117   1.6437
 M0M  N20   N  NR6   0  -0.566  -2.7591  -1.4099  -0.4065
 M0M  O13   O  O2    0  -0.484   5.1807  -2.3365  -0.1616
 M0M  O22   O  O     0  -0.482  -3.2402  -2.3947   1.5786
 M0M  S01   S  S1    0  -0.409  -2.2214  -0.3555  -2.8569
 M0M  S07   S  S2    0  -0.003   0.8747   2.9397   0.4678
 M0M  H112  H  HCH2  0   0.243   2.2818  -1.1930   1.0436
 M0M  H111  H  HCH2  0   0.200   3.8783  -0.7532   1.6587
 M0M  H122  H  HCH2  0   0.238   3.8117  -3.1354   1.1004
 M0M  H121  H  HCH2  0   0.201   3.1950  -2.7865  -0.5228
 M0M  H141  H  HCH2  0   0.201   4.7336  -1.6987  -2.0784
 M0M  H142  H  HCH2  0   0.237   6.3593  -1.3396  -1.4744
 M0M  H061  H  HCR5  0   0.320  -1.3448   3.7218   0.3403
 M0M  H081  H  HCH2  0   0.276   0.9893   0.8805  -0.7577
 M0M  H082  H  HCH2  0   0.263   1.0770   0.6023   0.9938
 M0M  H091  H  HCH2  0   0.243   3.2466   1.9298  -0.7029
 M0M  H092  H  HCH2  0   0.207   3.3948   1.5709   1.0160
 M0M  H151  H  HCH2  0   0.199   5.4906   0.3678   0.0439
 M0M  H152  H  HCH2  0   0.244   4.9024   0.6751  -1.5943
 M0M  H181  H  HCH3  0   0.276  -3.0650   0.4905   3.4455
 M0M  H183  H  HCH3  0   0.291  -2.6523  -1.2271   3.4895
 M0M  H182  H  HCH3  0   0.270  -1.3621  -0.0264   3.4706
 M0M  H213  H  HCH3  0   0.254  -2.6793  -3.4881  -0.7223
 M0M  H212  H  HCH3  0   0.253  -4.3041  -2.7830  -0.8009
 M0M  H211  H  HCH3  0   0.262  -3.1529  -2.5080  -2.1178
 M0M  H051  H  HNR5  0   0.431  -1.2786   2.1211   2.3813
 M0M  H161  H  HNR5  0   0.391  -1.9202   2.5133  -1.4937
 M0M  C09   C  CH2   0  -0.253   2.9462   1.2197   0.0720
 M0M  C18   C  CH3   0  -0.565  -2.3580  -0.2613   3.0987
 M0M  C21   C  CH3   0  -0.519  -3.2557  -2.6238  -1.0453

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
 M0M  C14  O13   single  1.411  0.020  1.411
 M0M  C14  C15   single  1.516  0.020  1.516
 M0M  O13  C12   single  1.410  0.020  1.410
 M0M  C15  N10   single  1.453  0.020  1.453
 M0M  N10  C11   single  1.453  0.020  1.453
 M0M  N10  C09   single  1.450  0.020  1.450
 M0M  C08  S07   single  1.815  0.020  1.815
 M0M  C08  C09   single  1.523  0.020  1.523
 M0M  S01  C02   double  1.682  0.020  1.682
 M0M  C12  C11   single  1.517  0.020  1.517
 M0M  C21  N20   single  1.459  0.020  1.459
 M0M  S07  C06   single  1.840  0.020  1.840
 M0M  C02  N20   single  1.402  0.020  1.402
 M0M  C02  C03   single  1.379  0.020  1.379
 M0M  N20  C19   single  1.377  0.020  1.377
 M0M  N16  C03   single  1.408  0.020  1.408
 M0M  N16  C06   single  1.444  0.020  1.444
 M0M  C03  C04   double  1.375  0.020  1.375
 M0M  C19  O22   double  1.214  0.020  1.214
 M0M  C19  N17   single  1.391  0.020  1.391
 M0M  C06  N05   single  1.455  0.020  1.455
 M0M  C04  N17   single  1.342  0.020  1.342
 M0M  C04  N05   single  1.334  0.020  1.334
 M0M  N17  C18   single  1.456  0.020  1.456
 M0M  C11  H112  single  0.970  0.020  1.090
 M0M  C11  H111  single  0.970  0.020  1.090
 M0M  C12  H122  single  0.970  0.020  1.090
 M0M  C12  H121  single  0.970  0.020  1.090
 M0M  C14  H141  single  0.970  0.020  1.090
 M0M  C14  H142  single  0.970  0.020  1.090
 M0M  C06  H061  single  0.970  0.020  1.090
 M0M  C08  H081  single  0.970  0.020  1.090
 M0M  C08  H082  single  0.970  0.020  1.090
 M0M  C09  H091  single  0.970  0.020  1.090
 M0M  C09  H092  single  0.970  0.020  1.090
 M0M  C15  H151  single  0.970  0.020  1.090
 M0M  C15  H152  single  0.970  0.020  1.090
 M0M  C18  H181  single  0.970  0.020  1.090
 M0M  C18  H183  single  0.970  0.020  1.090
 M0M  C18  H182  single  0.970  0.020  1.090
 M0M  C21  H213  single  0.970  0.020  1.090
 M0M  C21  H212  single  0.970  0.020  1.090
 M0M  C21  H211  single  0.970  0.020  1.090
 M0M  N05  H051  single  0.860  0.020  1.020
 M0M  N16  H161  single  0.890  0.020  1.040

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
 M0M  H111  C11  H112  107.14  3.000
 M0M  H111  C11  N10   111.41  3.000
 M0M  H112  C11  N10   110.28  3.000
 M0M  H111  C11  C12   109.85  3.000
 M0M  H112  C11  C12   107.98  3.000
 M0M  N10   C11  C12   110.09  3.000
 M0M  H121  C12  H122  107.95  3.000
 M0M  H121  C12  O13   110.38  3.000
 M0M  H122  C12  O13   107.55  3.000
 M0M  H121  C12  C11   109.08  3.000
 M0M  H122  C12  C11   109.96  3.000
 M0M  O13   C12  C11   111.84  3.000
 M0M  H142  C14  H141  107.92  3.000
 M0M  H142  C14  O13   107.52  3.000
 M0M  H141  C14  O13   110.43  3.000
 M0M  H142  C14  C15   110.08  3.000
 M0M  H141  C14  C15   109.24  3.000
 M0M  O13   C14  C15   111.57  3.000
 M0M  S01   C02  N20   123.64  3.000
 M0M  N20   C02  C03   114.23  3.000
 M0M  S01   C02  C03   122.13  3.000
 M0M  N16   C03  C04   108.52  3.000
 M0M  C04   C03  C02   121.49  3.000
 M0M  N16   C03  C02   129.91  3.000
 M0M  N17   C04  N05   127.12  3.000
 M0M  N05   C04  C03   110.16  3.000
 M0M  N17   C04  C03   122.72  3.000
 M0M  H061  C06  S07   104.17  3.000
 M0M  H061  C06  N16   112.59  3.000
 M0M  S07   C06  N16   113.46  3.000
 M0M  H061  C06  N05   111.40  3.000
 M0M  N16   C06  N05   103.93  3.000
 M0M  S07   C06  N05   111.52  3.000
 M0M  H082  C08  H081  108.93  3.000
 M0M  H082  C08  S07   109.11  3.000
 M0M  H081  C08  S07   108.71  3.000
 M0M  H082  C08  C09   111.43  3.000
 M0M  H081  C08  C09   109.72  3.000
 M0M  S07   C08  C09   108.90  3.000
 M0M  H152  C15  H151  107.17  3.000
 M0M  H152  C15  N10   109.37  3.000
 M0M  H151  C15  N10   111.72  3.000
 M0M  H152  C15  C14   108.82  3.000
 M0M  H151  C15  C14   109.51  3.000
 M0M  N10   C15  C14   110.15  3.000
 M0M  O22   C19  N20   121.98  3.000
 M0M  O22   C19  N17   120.85  3.000
 M0M  N20   C19  N17   117.17  3.000
 M0M  H051  N05  C06   122.35  3.000
 M0M  H051  N05  C04   126.42  3.000
 M0M  C06   N05  C04   109.32  3.000
 M0M  C15   N10  C09   111.25  3.000
 M0M  C09   N10  C11   112.92  3.000
 M0M  C15   N10  C11   109.45  3.000
 M0M  H161  N16  C06   113.72  3.000
 M0M  H161  N16  C03   114.91  3.000
 M0M  C06   N16  C03   107.30  3.000
 M0M  C19   N17  C18   120.68  3.000
 M0M  C18   N17  C04   120.13  3.000
 M0M  C19   N17  C04   119.16  3.000
 M0M  C21   N20  C19   114.13  3.000
 M0M  C19   N20  C02   125.17  3.000
 M0M  C21   N20  C02   120.70  3.000
 M0M  C14   O13  C12   110.61  3.000
 M0M  C08   S07  C06    99.77  3.000
 M0M  H092  C09  H091  106.75  3.000
 M0M  H092  C09  N10   111.85  3.000
 M0M  H091  C09  N10   107.75  3.000
 M0M  H092  C09  C08   110.10  3.000
 M0M  H091  C09  C08   108.44  3.000
 M0M  N10   C09  C08   111.74  3.000
 M0M  H182  C18  H183  108.53  3.000
 M0M  H182  C18  H181  109.65  3.000
 M0M  H183  C18  H181  108.94  3.000
 M0M  H182  C18  N17   110.00  3.000
 M0M  H183  C18  N17   109.38  3.000
 M0M  H181  C18  N17   110.30  3.000
 M0M  H211  C21  H212  109.23  3.000
 M0M  H211  C21  H213  109.18  3.000
 M0M  H212  C21  H213  109.11  3.000
 M0M  H211  C21  N20   108.19  3.000
 M0M  H212  C21  N20   110.57  3.000
 M0M  H213  C21  N20   110.53  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
 M0M  CONST_01  N17   C19  N20  C02     0.00   0.0  0
 M0M  CONST_02  C19   N17  C04  C03     0.00   0.0  0
 M0M  CONST_03  C06   N05  C04  C03     0.00   0.0  0
 M0M  CONST_04  N20   C19  N17  C04     0.00   0.0  0
 M0M  CONST_05  N17   C04  N05  C06   180.00   0.0  0
 M0M  CONST_06  N05   C04  N17  C19   180.00   0.0  0
 M0M  CONST_07  O22   C19  N20  C02   180.00   0.0  0
 M0M  CONST_08  C18   N17  C04  C03   180.00   0.0  0
 M0M  CONST_09  O22   C19  N17  C04   180.00   0.0  0
 M0M  CONST_10  N20   C19  N17  C18   180.00   0.0  0
 M0M  CONST_11  N05   C04  N17  C18     0.00   0.0  0
 M0M  CONST_12  N17   C19  N20  C21   180.00   0.0  0
 M0M  CONST_13  H051  N05  C04  C03   180.00   0.0  0
 M0M  CONST_14  O22   C19  N17  C18     0.00   0.0  0
 M0M  CONST_15  O22   C19  N20  C21     0.00   0.0  0
 M0M  Var_01    C14   C15  N10  C11    56.75  30.0  1
 M0M  Var_02    C15   C14  O13  C12    57.29  30.0  1
 M0M  Var_03    C15   N10  C11  C12   -56.44  30.0  1
 M0M  Var_04    O13   C14  C15  N10   -57.65  30.0  1
 M0M  Var_05    O13   C12  C11  N10    57.20  30.0  1
 M0M  Var_06    H122  C12  O13  C14  -177.99  30.0  1
 M0M  Var_07    C08   C09  N10  C11   -71.73  30.0  3
 M0M  Var_08    H213  C21  N20  C02   120.80  30.0  3
 M0M  Var_09    H181  C18  N17  C04    64.72  30.0  3
 M0M  Var_10    C09   C08  S07  C06   172.62  30.0  1
 M0M  Var_11    S07   C08  C09  N10  -173.58  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
 M0M  chir_01  C06  S07  N16  N05  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
 M0M  plan-1  C02   0.020
 M0M  plan-1  C03   0.020
 M0M  plan-1  C04   0.020
 M0M  plan-1  C06   0.020
 M0M  plan-1  C19   0.020
 M0M  plan-1  N05   0.020
 M0M  plan-1  N16   0.020
 M0M  plan-1  N17   0.020
 M0M  plan-1  N20   0.020
 M0M  plan-1  O22   0.020
 M0M  plan-1  S01   0.020
 M0M  plan-1  H051  0.020
 M0M  plan-1  H161  0.020
 M0M  plan-1  C18   0.020
 M0M  plan-1  C21   0.020

