# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 16:05:59 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: (5R,10S)-5-[(carboxymethyl)carbamoyl]-7-oxo-3-thia-1,6-diazabicyclo[4.4.1]undecane-10-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CNC(=O)[C@@H]1CSCN2CN1C(=O)CC[C@H]2C(O)=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
 DDD  DDD  '(5R,10S)-5-[(carboxymethyl)carbamoyl]-7-oxo-3-thia-1,6-diazabicyclo[4.4.1]undecane-10-carboxylic acid'  ligand  39  22  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DDD
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
 DDD  O31   O  OH1   0  -0.589   5.0973   0.4913   1.2344
 DDD  C3    C  C     0   0.546   4.2894   0.9390   0.2826
 DDD  O32   O  O     0  -0.425   4.5080   1.9228  -0.3746
 DDD  CA4   C  CH1   0  -0.208   3.0808   0.0304   0.1077
 DDD  CB2   C  CH2   0  -0.483   3.5361  -1.1579  -0.7571
 DDD  CG2   C  CH2   0  -0.588   2.5528  -2.3472  -0.8699
 DDD  CD1   C  C     0   0.534   1.2259  -2.2360  -0.1450
 DDD  OE1   O  O     0  -0.485   0.8417  -3.1246   0.6004
 DDD  N2    N  NT    0  -0.434   0.4903  -1.1217  -0.3965
 DDD  CA3   C  CH2   0  -0.233   1.0554  -0.0447  -1.2069
 DDD  N3    N  NT    0  -0.393   2.0026   0.7715  -0.5080
 DDD  CD2   C  CH2   0  -0.412   1.4922   1.8565   0.3167
 DDD  SD    S  S2    0  -0.018  -0.2927   1.8760   0.6592
 DDD  CB1   C  CH2   0  -0.584  -0.5316   0.2367   1.3918
 DDD  CA2   C  CH1   0  -0.239  -0.7129  -0.8818   0.3625
 DDD  C2    C  C     0   0.588  -1.9029  -0.6681  -0.5772
 DDD  O2    O  O     0  -0.476  -1.8218  -0.8384  -1.7818
 DDD  N1    N  NH1   0  -0.653  -3.0485  -0.3170   0.0243
 DDD  CA1   C  CH2   0  -0.369  -4.2626  -0.1372  -0.7227
 DDD  C1    C  C     0   0.522  -5.3679   0.3247   0.1917
 DDD  O11   O  OH1   0  -0.584  -6.4890   0.5182  -0.4793
 DDD  O12   O  O     0  -0.434  -5.2461   0.4898   1.3787
 DDD  HO31  H  HOH1  0   0.485   5.8883   1.0482   1.2903
 DDD  HA4   H  HCH1  0   0.262   2.8066  -0.3499   1.1057
 DDD  HB21  H  HCH2  0   0.268   3.7810  -0.7815  -1.7515
 DDD  HB22  H  HCH2  0   0.284   4.4655  -1.5373  -0.3339
 DDD  HG21  H  HCH2  0   0.288   2.3382  -2.5424  -1.9239
 DDD  HG22  H  HCH2  0   0.282   3.0288  -3.2472  -0.4869
 DDD  HA31  H  HCH2  0   0.290   1.5178  -0.4794  -2.0914
 DDD  HA32  H  HCH2  0   0.297   0.2477   0.5777  -1.5773
 DDD  HD21  H  HCH2  0   0.271   2.0101   1.8632   1.2790
 DDD  HD22  H  HCH2  0   0.287   1.6703   2.8291  -0.1481
 DDD  HB11  H  HCH2  0   0.302   0.3124   0.0057   2.0442
 DDD  HB12  H  HCH2  0   0.297  -1.3991   0.3089   2.0484
 DDD  HA2   H  HCH1  0   0.321  -0.9244  -1.7954   0.9251
 DDD  HN1   H  HNH1  0   0.405  -3.1132  -0.2657   1.0288
 DDD  HA11  H  HCH2  0   0.295  -4.1297   0.6037  -1.5155
 DDD  HA12  H  HCH2  0   0.292  -4.5804  -1.0644  -1.2103
 DDD  HO11  H  HOH1  0   0.490  -7.1952   0.8041   0.1199

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
 DDD  O31  C3    single  1.326  0.020  1.326
 DDD  O31  HO31  single  0.850  0.020  0.980
 DDD  C3   O32   double  1.203  0.020  1.203
 DDD  C3   CA4   single  1.522  0.020  1.522
 DDD  CA4  CB2   single  1.539  0.020  1.539
 DDD  CA4  N3    single  1.446  0.020  1.446
 DDD  CA4  HA4   single  0.970  0.020  1.090
 DDD  CB2  CG2   single  1.547  0.020  1.547
 DDD  CB2  HB21  single  0.970  0.020  1.090
 DDD  CB2  HB22  single  0.970  0.020  1.090
 DDD  CG2  CD1   single  1.516  0.020  1.516
 DDD  CG2  HG21  single  0.970  0.020  1.090
 DDD  CG2  HG22  single  0.970  0.020  1.090
 DDD  CD1  OE1   double  1.222  0.020  1.222
 DDD  CD1  N2    single  1.359  0.020  1.359
 DDD  N2   CA2   single  1.443  0.020  1.443
 DDD  N2   CA3   single  1.462  0.020  1.462
 DDD  CA3  N3    single  1.432  0.020  1.432
 DDD  CA3  HA31  single  0.970  0.020  1.090
 DDD  CA3  HA32  single  0.970  0.020  1.090
 DDD  N3   CD2   single  1.455  0.020  1.455
 DDD  CD2  SD    single  1.818  0.020  1.818
 DDD  CD2  HD21  single  0.970  0.020  1.090
 DDD  CD2  HD22  single  0.970  0.020  1.090
 DDD  SD   CB1   single  1.811  0.020  1.811
 DDD  CB1  CA2   single  1.531  0.020  1.531
 DDD  CB1  HB11  single  0.970  0.020  1.090
 DDD  CB1  HB12  single  0.970  0.020  1.090
 DDD  CA2  C2    single  1.531  0.020  1.531
 DDD  CA2  HA2   single  0.970  0.020  1.090
 DDD  C2   O2    double  1.219  0.020  1.219
 DDD  C2   N1    single  1.341  0.020  1.341
 DDD  N1   CA1   single  1.437  0.020  1.437
 DDD  N1   HN1   single  0.860  0.020  1.020
 DDD  CA1  C1    single  1.507  0.020  1.507
 DDD  CA1  HA11  single  0.970  0.020  1.090
 DDD  CA1  HA12  single  0.970  0.020  1.090
 DDD  C1   O12   double  1.205  0.020  1.205
 DDD  C1   O11   single  1.321  0.020  1.321
 DDD  O11  HO11  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
 DDD  HO31  O31  C3    110.15  3.000
 DDD  CA4   C3   O32   124.72  3.000
 DDD  CA4   C3   O31   111.38  3.000
 DDD  O32   C3   O31   123.87  3.000
 DDD  HA4   CA4  N3    112.13  3.000
 DDD  HA4   CA4  CB2   108.42  3.000
 DDD  N3    CA4  CB2   112.16  3.000
 DDD  HA4   CA4  C3    107.42  3.000
 DDD  N3    CA4  C3    109.58  3.000
 DDD  CB2   CA4  C3    106.90  3.000
 DDD  HB22  CB2  HB21  106.42  3.000
 DDD  HB22  CB2  CG2   107.63  3.000
 DDD  HB21  CB2  CG2   109.96  3.000
 DDD  HB22  CB2  CA4   107.64  3.000
 DDD  HB21  CB2  CA4   108.19  3.000
 DDD  CG2   CB2  CA4   116.53  3.000
 DDD  HG22  CG2  HG21  106.12  3.000
 DDD  HG22  CG2  CD1   105.97  3.000
 DDD  HG21  CG2  CD1   107.59  3.000
 DDD  HG22  CG2  CB2   109.40  3.000
 DDD  HG21  CG2  CB2   109.42  3.000
 DDD  CD1   CG2  CB2   117.71  3.000
 DDD  N2    CD1  OE1   122.62  3.000
 DDD  N2    CD1  CG2   116.46  3.000
 DDD  OE1   CD1  CG2   120.90  3.000
 DDD  CA2   N2   CA3   119.45  3.000
 DDD  CA3   N2   CD1   119.84  3.000
 DDD  CA2   N2   CD1   119.38  3.000
 DDD  HA32  CA3  HA31  105.54  3.000
 DDD  HA32  CA3  N3    109.40  3.000
 DDD  HA31  CA3  N3    110.06  3.000
 DDD  HA32  CA3  N2    108.92  3.000
 DDD  HA31  CA3  N2    108.69  3.000
 DDD  N3    CA3  N2    113.90  3.000
 DDD  CD2   N3   CA3   118.00  3.000
 DDD  CD2   N3   CA4   113.72  3.000
 DDD  CA3   N3   CA4   114.13  3.000
 DDD  HD22  CD2  HD21  106.97  3.000
 DDD  HD22  CD2  SD    103.34  3.000
 DDD  HD21  CD2  SD    107.43  3.000
 DDD  HD22  CD2  N3    111.43  3.000
 DDD  HD21  CD2  N3    109.71  3.000
 DDD  SD    CD2  N3    117.33  3.000
 DDD  CB1   SD   CD2   101.30  3.000
 DDD  HB12  CB1  HB11  105.62  3.000
 DDD  HB12  CB1  CA2   111.04  3.000
 DDD  HB11  CB1  CA2   109.81  3.000
 DDD  HB12  CB1  SD    106.77  3.000
 DDD  HB11  CB1  SD    109.35  3.000
 DDD  CA2   CB1  SD    113.89  3.000
 DDD  HA2   CA2  C2    106.38  3.000
 DDD  HA2   CA2  CB1   106.70  3.000
 DDD  C2    CA2  CB1   113.75  3.000
 DDD  HA2   CA2  N2    107.04  3.000
 DDD  C2    CA2  N2    110.39  3.000
 DDD  CB1   CA2  N2    112.12  3.000
 DDD  N1    C2   O2    122.46  3.000
 DDD  N1    C2   CA2   115.16  3.000
 DDD  O2    C2   CA2   122.35  3.000
 DDD  HN1   N1   CA1   117.23  3.000
 DDD  HN1   N1   C2    121.03  3.000
 DDD  CA1   N1   C2    121.43  3.000
 DDD  HA12  CA1  HA11  106.64  3.000
 DDD  HA12  CA1  C1    108.47  3.000
 DDD  HA11  CA1  C1    108.75  3.000
 DDD  HA12  CA1  N1    111.77  3.000
 DDD  HA11  CA1  N1    111.05  3.000
 DDD  C1    CA1  N1    110.03  3.000
 DDD  O12   C1   O11   124.49  3.000
 DDD  O11   C1   CA1   111.05  3.000
 DDD  O12   C1   CA1   124.46  3.000
 DDD  HO11  O11  C1    110.34  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
 DDD  CONST_01  CA2   N2   CD1  CG2   180.00   0.0  0
 DDD  CONST_02  CA3   N2   CD1  CG2     0.00   0.0  0
 DDD  CONST_03  CA2   N2   CD1  OE1     0.00   0.0  0
 DDD  CONST_04  CA3   N2   CD1  OE1   180.00   0.0  0
 DDD  CONST_05  CA1   N1   C2   CA2   180.00   0.0  0
 DDD  CONST_06  HN1   N1   C2   CA2     0.00   0.0  0
 DDD  CONST_07  HO31  O31  C3   CA4   180.00   0.0  0
 DDD  CONST_08  CA1   N1   C2   O2      0.00   0.0  0
 DDD  CONST_09  HO11  O11  C1   CA1   180.00   0.0  0
 DDD  Var_01    CD1   CG2  CB2  CA4     0.95  30.0  3
 DDD  Var_02    N2    CA3  N3   CA4    53.95  30.0  3
 DDD  Var_03    SD    CD2  N3   CA4  -125.55  30.0  3
 DDD  Var_04    N2    CD1  CG2  CB2    52.73  30.0  3
 DDD  Var_05    N3    CA3  N2   CD1   -76.69  30.0  3
 DDD  Var_06    CA2   CB1  SD   CD2   -83.75  30.0  3
 DDD  Var_07    C1    CA1  N1   C2   -177.00  30.0  3
 DDD  Var_08    O12   C1   CA1  N1     -1.36  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
 DDD  chir_01  CA4  C3  CB2  N3   positiv
 DDD  chir_02  CA2  N2  C2   CB1  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
 DDD  plan-1  CG2   0.020
 DDD  plan-1  CD1   0.020
 DDD  plan-1  OE1   0.020
 DDD  plan-1  N2    0.020
 DDD  plan-1  CA3   0.020
 DDD  plan-1  CA2   0.020
 DDD  plan-2  CA2   0.020
 DDD  plan-2  C2    0.020
 DDD  plan-2  O2    0.020
 DDD  plan-2  N1    0.020
 DDD  plan-2  CA1   0.020
 DDD  plan-2  HN1   0.020
 DDD  plan-3  O31   0.020
 DDD  plan-3  C3    0.020
 DDD  plan-3  O32   0.020
 DDD  plan-3  CA4   0.020
 DDD  plan-3  HO31  0.020
 DDD  plan-4  CA1   0.020
 DDD  plan-4  C1    0.020
 DDD  plan-4  O11   0.020
 DDD  plan-4  O12   0.020
 DDD  plan-4  HO11  0.020

