# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 23:36:19 2022
#   Inital geometry file: a 79 line input string
#   Ligand name: 6-[(4R,5S)-5-methyl-2-oxoimidazolidin-4-yl]hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1NC(=O)N[C@@H]1CCCCCC(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
 DTB  DTB  '6-[(4R,5S)-5-methyl-2-oxoimidazolidin-4-yl]hexanoic acid'  ligand  32  15  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DTB
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
 DTB  CN    C  CR5    0   0.623  -3.6165  -1.1969   0.2969
 DTB  O     O  O      0  -0.524  -3.9637  -2.2593   0.7895
 DTB  N2    N  NR15   0  -0.653  -2.6779  -1.0257  -0.6786
 DTB  CR    C  CR15   0  -0.088  -2.3415   0.3798  -0.8449
 DTB  CS    C  CR15   0  -0.057  -3.6614   1.0217  -0.3657
 DTB  N1    N  NR15   0  -0.657  -4.0972   0.0423   0.6170
 DTB  CT    C  CH3    0  -0.686  -3.5642   2.4253   0.1927
 DTB  CE    C  CH2    0  -0.421  -1.0999   0.7910  -0.0590
 DTB  CD    C  CH2    0  -0.423   0.1667   0.0781  -0.5198
 DTB  CG    C  CH2    0  -0.407   1.4118   0.5753   0.2042
 DTB  CB    C  CH2    0  -0.404   2.6934  -0.1103  -0.2538
 DTB  CA    C  CH2    0  -0.579   3.9236   0.4071   0.4746
 DTB  C     C  C      0   0.409   5.2658  -0.2338   0.0805
 DTB  OI1   O  O      0  -0.611   5.2349  -1.2716  -0.6102
 DTB  OI2   O  OC    -1  -0.634   6.2925   0.3354   0.5091
 DTB  HN2   H  HNR5   0   0.392  -1.9948  -1.7505  -0.8339
 DTB  HCR   H  HCR5   0   0.251  -2.1826   0.6096  -1.9016
 DTB  HCS   H  HCR5   0   0.246  -4.3562   1.0312  -1.2157
 DTB  HN1   H  HNR5   0   0.390  -5.0214   0.1056   1.0153
 DTB  HCT1  H  HCH3   0   0.236  -3.1814   3.1086  -0.5659
 DTB  HCT2  H  HCH3   0   0.245  -4.5501   2.7847   0.4890
 DTB  HCT3  H  HCH3   0   0.234  -2.9110   2.4734   1.0630
 DTB  HCE1  H  HCH2   0   0.230  -0.9558   1.8684  -0.1808
 DTB  HCE2  H  HCH2   0   0.222  -1.2570   0.6148   1.0100
 DTB  HCD1  H  HCH2   0   0.208   0.0739  -1.0016  -0.3628
 DTB  HCD2  H  HCH2   0   0.214   0.2903   0.2215  -1.5991
 DTB  HCG1  H  HCH2   0   0.205   1.5036   1.6576   0.0577
 DTB  HCG2  H  HCH2   0   0.206   1.2863   0.4282   1.2829
 DTB  HCB1  H  HCH2   0   0.202   2.6011  -1.1895  -0.1035
 DTB  HCB2  H  HCH2   0   0.200   2.8115   0.0342  -1.3325
 DTB  HCA1  H  HCH2   0   0.211   4.0009   1.4924   0.3469
 DTB  HCA2  H  HCH2   0   0.219   3.7918   0.2597   1.5543

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
 DTB  CN  O     double  1.221  0.020  1.221
 DTB  CN  N2    single  1.365  0.020  1.365
 DTB  CN  N1    single  1.367  0.020  1.367
 DTB  N2  CR    single  1.455  0.020  1.455
 DTB  N2  HN2   single  0.890  0.020  1.040
 DTB  CR  CS    single  1.544  0.020  1.544
 DTB  CR  CE    single  1.526  0.020  1.526
 DTB  CR  HCR   single  0.970  0.020  1.090
 DTB  CS  N1    single  1.454  0.020  1.454
 DTB  CS  CT    single  1.514  0.020  1.514
 DTB  CS  HCS   single  0.970  0.020  1.090
 DTB  N1  HN1   single  0.890  0.020  1.040
 DTB  CT  HCT1  single  0.970  0.020  1.090
 DTB  CT  HCT2  single  0.970  0.020  1.090
 DTB  CT  HCT3  single  0.970  0.020  1.090
 DTB  CE  CD    single  1.525  0.020  1.525
 DTB  CE  HCE1  single  0.970  0.020  1.090
 DTB  CE  HCE2  single  0.970  0.020  1.090
 DTB  CD  CG    single  1.524  0.020  1.524
 DTB  CD  HCD1  single  0.970  0.020  1.090
 DTB  CD  HCD2  single  0.970  0.020  1.090
 DTB  CG  CB    single  1.524  0.020  1.524
 DTB  CG  HCG1  single  0.970  0.020  1.090
 DTB  CG  HCG2  single  0.970  0.020  1.090
 DTB  CB  CA    single  1.520  0.020  1.520
 DTB  CB  HCB1  single  0.970  0.020  1.090
 DTB  CB  HCB2  single  0.970  0.020  1.090
 DTB  CA  C     single  1.539  0.020  1.539
 DTB  CA  HCA1  single  0.970  0.020  1.090
 DTB  CA  HCA2  single  0.970  0.020  1.090
 DTB  C   OI1   deloc   1.247  0.020  1.247
 DTB  C   OI2   deloc   1.250  0.020  1.250

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
 DTB  N1    CN  N2    107.19  3.000
 DTB  N1    CN  O     126.44  3.000
 DTB  N2    CN  O     126.37  3.000
 DTB  HN2   N2  CR    121.36  3.000
 DTB  HN2   N2  CN    119.08  3.000
 DTB  CR    N2  CN    111.22  3.000
 DTB  HCR   CR  CE    108.84  3.000
 DTB  HCR   CR  CS    109.69  3.000
 DTB  CE    CR  CS    115.07  3.000
 DTB  HCR   CR  N2    110.32  3.000
 DTB  CE    CR  N2    112.93  3.000
 DTB  CS    CR  N2     99.70  3.000
 DTB  HCS   CS  CT    108.56  3.000
 DTB  HCS   CS  N1    109.84  3.000
 DTB  CT    CS  N1    113.24  3.000
 DTB  HCS   CS  CR    107.71  3.000
 DTB  CT    CS  CR    116.43  3.000
 DTB  N1    CS  CR    100.71  3.000
 DTB  HN1   N1  CS    119.95  3.000
 DTB  HN1   N1  CN    118.15  3.000
 DTB  CS    N1  CN    110.30  3.000
 DTB  HCT3  CT  HCT2  108.09  3.000
 DTB  HCT3  CT  HCT1  108.53  3.000
 DTB  HCT2  CT  HCT1  107.45  3.000
 DTB  HCT3  CT  CS    111.98  3.000
 DTB  HCT2  CT  CS    110.35  3.000
 DTB  HCT1  CT  CS    110.30  3.000
 DTB  HCE2  CE  HCE1  106.63  3.000
 DTB  HCE2  CE  CD    109.82  3.000
 DTB  HCE1  CE  CD    108.51  3.000
 DTB  HCE2  CE  CR    110.05  3.000
 DTB  HCE1  CE  CR    108.38  3.000
 DTB  CD    CE  CR    113.22  3.000
 DTB  HCD2  CD  HCD1  106.25  3.000
 DTB  HCD2  CD  CG    109.45  3.000
 DTB  HCD1  CD  CG    108.84  3.000
 DTB  HCD2  CD  CE    109.28  3.000
 DTB  HCD1  CD  CE    110.33  3.000
 DTB  CG    CD  CE    112.50  3.000
 DTB  HCG2  CG  HCG1  105.88  3.000
 DTB  HCG2  CG  CB    109.37  3.000
 DTB  HCG1  CG  CB    109.49  3.000
 DTB  HCG2  CG  CD    109.29  3.000
 DTB  HCG1  CG  CD    109.10  3.000
 DTB  CB    CG  CD    113.43  3.000
 DTB  HCB2  CB  HCB1  105.95  3.000
 DTB  HCB2  CB  CA    109.87  3.000
 DTB  HCB1  CB  CA    109.77  3.000
 DTB  HCB2  CB  CG    109.11  3.000
 DTB  HCB1  CB  CG    109.37  3.000
 DTB  CA    CB  CG    112.54  3.000
 DTB  HCA2  CA  HCA1  104.85  3.000
 DTB  HCA2  CA  C     107.50  3.000
 DTB  HCA1  CA  C     108.73  3.000
 DTB  HCA2  CA  CB    109.17  3.000
 DTB  HCA1  CA  CB    109.78  3.000
 DTB  C     CA  CB    116.19  3.000
 DTB  OI2   C   OI1   126.11  3.000
 DTB  OI2   C   CA    116.05  3.000
 DTB  OI1   C   CA    117.83  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
 DTB  CONST_01  CS   N1  CN  N2     0.00   0.0  0
 DTB  CONST_02  N1   CN  N2  CR     0.00   0.0  0
 DTB  CONST_03  CR   N2  CN  O    180.00   0.0  0
 DTB  CONST_04  CS   N1  CN  O    180.00   0.0  0
 DTB  Var_01    CG   CD  CE  CR   175.75  30.0  3
 DTB  Var_02    CB   CG  CD  CE  -179.22  30.0  3
 DTB  Var_03    CA   CB  CG  CD   179.63  30.0  3
 DTB  Var_04    C    CA  CB  CG   179.74  30.0  3
 DTB  Var_05    OI1  C   CA  CB   -12.52  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
 DTB  chir_01  CR  N2  CS  CE  negativ
 DTB  chir_02  CS  N1  CR  CT  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
 DTB  plan-1  CN   0.020
 DTB  plan-1  O    0.020
 DTB  plan-1  N2   0.020
 DTB  plan-1  CR   0.020
 DTB  plan-1  CS   0.020
 DTB  plan-1  N1   0.020
 DTB  plan-1  HN2  0.020
 DTB  plan-1  HN1  0.020
 DTB  plan-2  CA   0.020
 DTB  plan-2  C    0.020
 DTB  plan-2  OI1  0.020
 DTB  plan-2  OI2  0.020

