# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 20:53:43 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  37  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  OC    -1  -0.616   5.1715   0.3418   1.3004
 DDD  C3    C  C      0   0.415   4.3373   0.8635   0.5331
 DDD  O32   O  O      0  -0.588   4.4168   1.9767  -0.0126
 DDD  CA4   C  CH1    0  -0.208   3.0908  -0.0135   0.2308
 DDD  CB2   C  CH2    0  -0.476   3.5375  -1.1848  -0.6508
 DDD  CG2   C  CH2    0  -0.586   2.5511  -2.3679  -0.8115
 DDD  CD1   C  C      0   0.529   1.2147  -2.2615  -0.1028
 DDD  OE1   O  O      0  -0.498   0.8154  -3.1630   0.6233
 DDD  N2    N  NT     0  -0.428   0.4886  -1.1425  -0.3461
 DDD  CA3   C  CH2    0  -0.229   1.0778  -0.0482  -1.1202
 DDD  N3    N  NT     0  -0.386   2.0202   0.7455  -0.3950
 DDD  CD2   C  CH2    0  -0.394   1.5020   1.8063   0.4498
 DDD  SD    S  S2     0  -0.041  -0.2966   1.8402   0.7412
 DDD  CB1   C  CH2    0  -0.581  -0.5719   0.1897   1.4362
 DDD  CA2   C  CH1    0  -0.231  -0.7331  -0.9111   0.3855
 DDD  C2    C  C      0   0.569  -1.9024  -0.6844  -0.5813
 DDD  O2    O  O      0  -0.498  -1.7901  -0.8870  -1.7831
 DDD  N1    N  NH1    0  -0.636  -3.0457  -0.3040  -0.0122
 DDD  CA1   C  CH2    0  -0.408  -4.2747  -0.1041  -0.7365
 DDD  C1    C  C      0   0.399  -5.4139   0.2910   0.2256
 DDD  O11   O  OC    -1  -0.608  -6.5102   0.5151  -0.3139
 DDD  O12   O  O      0  -0.598  -5.1363   0.3430   1.4396
 DDD  HA4   H  HCH1   0   0.203   2.7608  -0.4276   1.2010
 DDD  HB21  H  HCH2   0   0.241   3.8078  -0.7943  -1.6348
 DDD  HB22  H  HCH2   0   0.259   4.4543  -1.5740  -0.2115
 DDD  HG21  H  HCH2   0   0.275   2.3491  -2.5432  -1.8721
 DDD  HG22  H  HCH2   0   0.268   3.0121  -3.2815  -0.4402
 DDD  HA31  H  HCH2   0   0.277   1.5509  -0.4714  -2.0053
 DDD  HA32  H  HCH2   0   0.284   0.2755   0.5811  -1.4927
 DDD  HD21  H  HCH2   0   0.259   1.9850   1.7683   1.4281
 DDD  HD22  H  HCH2   0   0.269   1.7070   2.7953   0.0329
 DDD  HB11  H  HCH2   0   0.296   0.2548  -0.0575   2.1050
 DDD  HB12  H  HCH2   0   0.289  -1.4565   0.2555   2.0703
 DDD  HA2   H  HCH1   0   0.309  -0.9586  -1.8331   0.9284
 DDD  HN1   H  HNH1   0   0.387  -3.1401  -0.1942   0.9876
 DDD  HA11  H  HCH2   0   0.242  -4.1572   0.6775  -1.4927
 DDD  HA12  H  HCH2   0   0.241  -4.5642  -1.0142  -1.2712

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    deloc   1.248  0.020  1.248
 DDD  C3   O32   deloc   1.242  0.020  1.242
 DDD  C3   CA4   single  1.554  0.020  1.554
 DDD  CA4  CB2   single  1.533  0.020  1.533
 DDD  CA4  N3    single  1.454  0.020  1.454
 DDD  CA4  HA4   single  0.970  0.020  1.090
 DDD  CB2  CG2   single  1.549  0.020  1.549
 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  1.224  0.020  1.224
 DDD  CD1  N2    single  1.356  0.020  1.356
 DDD  N2   CA2   single  1.443  0.020  1.443
 DDD  N2   CA3   single  1.464  0.020  1.464
 DDD  CA3  N3    single  1.430  0.020  1.430
 DDD  CA3  HA31  single  0.970  0.020  1.090
 DDD  CA3  HA32  single  0.970  0.020  1.090
 DDD  N3   CD2   single  1.452  0.020  1.452
 DDD  CD2  SD    single  1.822  0.020  1.822
 DDD  CD2  HD21  single  0.970  0.020  1.090
 DDD  CD2  HD22  single  0.970  0.020  1.090
 DDD  SD   CB1   single  1.812  0.020  1.812
 DDD  CB1  CA2   single  1.530  0.020  1.530
 DDD  CB1  HB11  single  0.970  0.020  1.090
 DDD  CB1  HB12  single  0.970  0.020  1.090
 DDD  CA2  C2    single  1.534  0.020  1.534
 DDD  CA2  HA2   single  0.970  0.020  1.090
 DDD  C2   O2    double  1.224  0.020  1.224
 DDD  C2   N1    single  1.332  0.020  1.332
 DDD  N1   CA1   single  1.441  0.020  1.441
 DDD  N1   HN1   single  0.860  0.020  1.020
 DDD  CA1  C1    single  1.542  0.020  1.542
 DDD  CA1  HA11  single  0.970  0.020  1.090
 DDD  CA1  HA12  single  0.970  0.020  1.090
 DDD  C1   O12   deloc   1.246  0.020  1.246
 DDD  C1   O11   deloc   1.242  0.020  1.242

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  CA4   C3   O32   118.14  3.000
 DDD  CA4   C3   O31   114.83  3.000
 DDD  O32   C3   O31   127.01  3.000
 DDD  HA4   CA4  N3    110.71  3.000
 DDD  HA4   CA4  CB2   107.79  3.000
 DDD  N3    CA4  CB2   111.47  3.000
 DDD  HA4   CA4  C3    106.27  3.000
 DDD  N3    CA4  C3    112.32  3.000
 DDD  CB2   CA4  C3    108.03  3.000
 DDD  HB22  CB2  HB21  106.43  3.000
 DDD  HB22  CB2  CG2   107.77  3.000
 DDD  HB21  CB2  CG2   109.71  3.000
 DDD  HB22  CB2  CA4   106.65  3.000
 DDD  HB21  CB2  CA4   108.48  3.000
 DDD  CG2   CB2  CA4   117.25  3.000
 DDD  HG22  CG2  HG21  105.93  3.000
 DDD  HG22  CG2  CD1   105.82  3.000
 DDD  HG21  CG2  CD1   107.56  3.000
 DDD  HG22  CG2  CB2   109.63  3.000
 DDD  HG21  CG2  CB2   109.92  3.000
 DDD  CD1   CG2  CB2   117.34  3.000
 DDD  N2    CD1  OE1   122.64  3.000
 DDD  N2    CD1  CG2   116.48  3.000
 DDD  OE1   CD1  CG2   120.85  3.000
 DDD  CA2   N2   CA3   119.28  3.000
 DDD  CA3   N2   CD1   119.75  3.000
 DDD  CA2   N2   CD1   119.66  3.000
 DDD  HA32  CA3  HA31  105.51  3.000
 DDD  HA32  CA3  N3    109.84  3.000
 DDD  HA31  CA3  N3    109.98  3.000
 DDD  HA32  CA3  N2    108.49  3.000
 DDD  HA31  CA3  N2    108.30  3.000
 DDD  N3    CA3  N2    114.34  3.000
 DDD  CD2   N3   CA3   117.75  3.000
 DDD  CD2   N3   CA4   113.19  3.000
 DDD  CA3   N3   CA4   114.44  3.000
 DDD  HD22  CD2  HD21  106.88  3.000
 DDD  HD22  CD2  SD    103.26  3.000
 DDD  HD21  CD2  SD    107.10  3.000
 DDD  HD22  CD2  N3    111.86  3.000
 DDD  HD21  CD2  N3    109.76  3.000
 DDD  SD    CD2  N3    117.32  3.000
 DDD  CB1   SD   CD2   101.21  3.000
 DDD  HB12  CB1  HB11  105.77  3.000
 DDD  HB12  CB1  CA2   110.94  3.000
 DDD  HB11  CB1  CA2   109.73  3.000
 DDD  HB12  CB1  SD    106.94  3.000
 DDD  HB11  CB1  SD    109.03  3.000
 DDD  CA2   CB1  SD    114.07  3.000
 DDD  HA2   CA2  C2    106.28  3.000
 DDD  HA2   CA2  CB1   106.70  3.000
 DDD  C2    CA2  CB1   114.00  3.000
 DDD  HA2   CA2  N2    106.93  3.000
 DDD  C2    CA2  N2    110.46  3.000
 DDD  CB1   CA2  N2    111.99  3.000
 DDD  N1    C2   O2    123.05  3.000
 DDD  N1    C2   CA2   115.28  3.000
 DDD  O2    C2   CA2   121.63  3.000
 DDD  HN1   N1   CA1   113.75  3.000
 DDD  HN1   N1   C2    122.27  3.000
 DDD  CA1   N1   C2    123.84  3.000
 DDD  HA12  CA1  HA11  106.55  3.000
 DDD  HA12  CA1  C1    108.80  3.000
 DDD  HA11  CA1  C1    109.12  3.000
 DDD  HA12  CA1  N1    110.85  3.000
 DDD  HA11  CA1  N1    110.80  3.000
 DDD  C1    CA1  N1    110.61  3.000
 DDD  O12   C1   O11   127.73  3.000
 DDD  O11   C1   CA1   115.29  3.000
 DDD  O12   C1   CA1   116.98  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  CA1  N1   C2   O2      0.00   0.0  0
 DDD  Var_01    CD1  CG2  CB2  CA4     0.99  30.0  3
 DDD  Var_02    N2   CA3  N3   CA4    53.63  30.0  3
 DDD  Var_03    SD   CD2  N3   CA4  -126.60  30.0  3
 DDD  Var_04    N2   CD1  CG2  CB2    53.27  30.0  3
 DDD  Var_05    N3   CA3  N2   CD1   -76.09  30.0  3
 DDD  Var_06    CA2  CB1  SD   CD2   -83.69  30.0  3
 DDD  Var_07    C1   CA1  N1   C2    178.26  30.0  3
 DDD  Var_08    O12  C1   CA1  N1     -1.88  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-4  CA1  0.020
 DDD  plan-4  C1   0.020
 DDD  plan-4  O11  0.020
 DDD  plan-4  O12  0.020

