# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 01:44:16 2021
#   Inital geometry file: a 80 line input string
#   Ligand name: (2~{S})-2-azanyl-6-(1,3-oxazol-5-ylcarbonylamino)hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCNC(=O)c1ocnc1)C(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
 EE3  EE3  '(2~{S})-2-azanyl-6-(1,3-oxazol-5-ylcarbonylamino)hexanoic acid'  ligand  32  17  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EE3
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
 EE3  C35  C  CH1   0  -0.197  57.3990  22.6878  -7.9382
 EE3  C36  C  CH2   0  -0.446  57.5655  21.1687  -7.7928
 EE3  C37  C  CH2   0  -0.431  56.4497  20.4732  -7.0223
 EE3  C38  C  CH2   0  -0.429  56.7814  19.0148  -6.7309
 EE3  C39  C  CH2   0  -0.282  55.6225  18.2980  -6.0485
 EE3  C41  C  C     0   0.489  56.5439  16.4924  -4.6780
 EE3  C43  C  CR5   0   0.185  56.7880  15.0451  -4.5601
 EE3  C44  C  CR15  0  -0.168  57.4112  14.3243  -3.6012
 EE3  C46  C  CR15  0   0.182  56.7527  12.9714  -5.0750
 EE3  C48  C  C     0   0.534  56.1082  22.9693  -8.6799
 EE3  N34  N  NH2   0  -0.793  57.4423  23.3219  -6.6365
 EE3  N40  N  NH1   0  -0.644  55.8947  16.9020  -5.7747
 EE3  N45  N  N     0  -0.411  57.3778  12.9961  -3.9498
 EE3  O42  O  O     0  -0.484  56.9268  17.2326  -3.7818
 EE3  O47  O  O     0  -0.395  56.3645  14.1709  -5.5081
 EE3  O50  O  O     0  -0.455  55.9573  22.7036  -9.8483
 EE3  H1   H  HCH1  0   0.261  58.1967  23.0298  -8.6139
 EE3  H2   H  HCH2  0   0.239  57.6595  20.7296  -8.7884
 EE3  H3   H  HCH2  0   0.241  58.5247  20.9938  -7.2949
 EE3  H4   H  HCH2  0   0.228  56.2607  21.0011  -6.0846
 EE3  H5   H  HCH2  0   0.221  55.5179  20.5161  -7.5965
 EE3  H6   H  HCH2  0   0.224  57.0294  18.4942  -7.6608
 EE3  H7   H  HCH2  0   0.229  57.6674  18.9613  -6.0921
 EE3  H8   H  HCH2  0   0.243  55.3667  18.7983  -5.1137
 EE3  H9   H  HCH2  0   0.253  54.7352  18.3327  -6.6817
 EE3  H10  H  HCR5  0   0.288  57.8768  14.6729  -2.6940
 EE3  H11  H  HCR5  0   0.305  56.5118  12.1167  -5.6881
 EE3  H13  H  HNH2  0   0.352  58.3210  23.0796  -6.1960
 EE3  H14  H  HNH2  0   0.352  57.4551  24.3294  -6.7349
 EE3  H16  H  HNH1  0   0.409  55.6625  16.2364  -6.4944
 EE3  O1   O  OH1   0  -0.579  55.1603  23.5166  -7.9343
 EE3  H12  H  HOH1  0   0.478  54.3683  23.6576  -8.4748

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
 EE3  O50  C48  double    1.208  0.020  1.208
 EE3  C48  C35  single    1.515  0.020  1.515
 EE3  C35  C36  single    1.535  0.020  1.535
 EE3  C35  N34  single    1.449  0.020  1.449
 EE3  C36  C37  single    1.524  0.020  1.524
 EE3  C37  C38  single    1.524  0.020  1.524
 EE3  C38  C39  single    1.524  0.020  1.524
 EE3  C39  N40  single    1.448  0.020  1.448
 EE3  N40  C41  single    1.339  0.020  1.339
 EE3  O47  C46  aromatic  1.333  0.020  1.333
 EE3  O47  C43  aromatic  1.357  0.020  1.357
 EE3  C46  N45  aromatic  1.287  0.020  1.287
 EE3  C43  C41  single    1.473  0.020  1.473
 EE3  C43  C44  aromatic  1.352  0.020  1.352
 EE3  C41  O42  double    1.224  0.020  1.224
 EE3  N45  C44  aromatic  1.373  0.020  1.373
 EE3  C35  H1   single    0.970  0.020  1.090
 EE3  C36  H2   single    0.970  0.020  1.090
 EE3  C36  H3   single    0.970  0.020  1.090
 EE3  C37  H4   single    0.970  0.020  1.090
 EE3  C37  H5   single    0.970  0.020  1.090
 EE3  C38  H6   single    0.970  0.020  1.090
 EE3  C38  H7   single    0.970  0.020  1.090
 EE3  C39  H8   single    0.970  0.020  1.090
 EE3  C39  H9   single    0.970  0.020  1.090
 EE3  C44  H10  single    0.930  0.020  1.080
 EE3  C46  H11  single    0.930  0.020  1.080
 EE3  N34  H13  single    0.890  0.020  1.040
 EE3  N34  H14  single    0.890  0.020  1.040
 EE3  N40  H16  single    0.860  0.020  1.020
 EE3  C48  O1   single    1.324  0.020  1.324
 EE3  O1   H12  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
 EE3  H1   C35  N34  113.22  3.000
 EE3  H1   C35  C48  105.03  3.000
 EE3  N34  C35  C48  112.58  3.000
 EE3  H1   C35  C36  106.69  3.000
 EE3  N34  C35  C36  110.17  3.000
 EE3  C48  C35  C36  108.82  3.000
 EE3  H3   C36  H2   105.95  3.000
 EE3  H3   C36  C37  109.80  3.000
 EE3  H2   C36  C37  109.90  3.000
 EE3  H3   C36  C35  107.23  3.000
 EE3  H2   C36  C35  108.72  3.000
 EE3  C37  C36  C35  114.84  3.000
 EE3  H5   C37  H4   106.49  3.000
 EE3  H5   C37  C38  108.83  3.000
 EE3  H4   C37  C38  109.63  3.000
 EE3  H5   C37  C36  109.88  3.000
 EE3  H4   C37  C36  109.88  3.000
 EE3  C38  C37  C36  111.97  3.000
 EE3  H7   C38  H6   106.83  3.000
 EE3  H7   C38  C39  109.36  3.000
 EE3  H6   C38  C39  109.22  3.000
 EE3  H7   C38  C37  109.57  3.000
 EE3  H6   C38  C37  110.01  3.000
 EE3  C39  C38  C37  111.74  3.000
 EE3  H9   C39  H8   106.99  3.000
 EE3  H9   C39  N40  107.05  3.000
 EE3  H8   C39  N40  108.92  3.000
 EE3  H9   C39  C38  110.10  3.000
 EE3  H8   C39  C38  110.27  3.000
 EE3  N40  C39  C38  113.27  3.000
 EE3  O42  C41  N40  124.52  3.000
 EE3  O42  C41  C43  118.95  3.000
 EE3  N40  C41  C43  116.53  3.000
 EE3  O47  C43  C44  107.21  3.000
 EE3  C44  C43  C41  131.10  3.000
 EE3  O47  C43  C41  121.70  3.000
 EE3  H10  C44  N45  122.48  3.000
 EE3  H10  C44  C43  128.59  3.000
 EE3  N45  C44  C43  108.93  3.000
 EE3  H11  C46  O47  117.58  3.000
 EE3  H11  C46  N45  128.33  3.000
 EE3  O47  C46  N45  114.09  3.000
 EE3  O1   C48  O50  123.10  3.000
 EE3  O1   C48  C35  114.26  3.000
 EE3  O50  C48  C35  122.63  3.000
 EE3  H14  N34  H13  105.63  3.000
 EE3  H14  N34  C35  110.41  3.000
 EE3  H13  N34  C35  108.19  3.000
 EE3  H16  N40  C41  119.67  3.000
 EE3  H16  N40  C39  117.29  3.000
 EE3  C41  N40  C39  122.74  3.000
 EE3  C46  N45  C44  104.61  3.000
 EE3  C46  O47  C43  105.17  3.000
 EE3  H12  O1   C48  109.33  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
 EE3  CONST_01  N45  C46  O47  C43     0.00   0.0  0
 EE3  CONST_02  C46  N45  C44  C43     0.00   0.0  0
 EE3  CONST_03  C46  O47  C43  C44     0.00   0.0  0
 EE3  CONST_04  O47  C46  N45  C44     0.00   0.0  0
 EE3  CONST_05  O47  C43  C44  N45     0.00   0.0  0
 EE3  CONST_06  C46  O47  C43  C41   180.00   0.0  0
 EE3  CONST_07  N45  C44  C43  C41   180.00   0.0  0
 EE3  CONST_08  H11  C46  O47  C43   180.00   0.0  0
 EE3  CONST_09  H10  C44  N45  C46   180.00   0.0  0
 EE3  CONST_10  C43  C41  N40  C39   180.00   0.0  0
 EE3  CONST_11  H16  N40  C41  C43     0.00   0.0  0
 EE3  CONST_12  O42  C41  N40  C39     0.00   0.0  0
 EE3  CONST_13  H12  O1   C48  C35   180.00   0.0  0
 EE3  Var_01    N40  C41  C43  C44   179.48  30.0  2
 EE3  Var_02    C38  C37  C36  C35  -171.20  30.0  3
 EE3  Var_03    C39  C38  C37  C36  -175.94  30.0  3
 EE3  Var_04    N40  C39  C38  C37   179.09  30.0  3
 EE3  Var_05    C41  N40  C39  C38    84.68  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
 EE3  chir_01  C35  C48  C36  N34  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
 EE3  plan-1  C41  0.020
 EE3  plan-1  C43  0.020
 EE3  plan-1  C44  0.020
 EE3  plan-1  C46  0.020
 EE3  plan-1  N45  0.020
 EE3  plan-1  O47  0.020
 EE3  plan-1  H10  0.020
 EE3  plan-1  H11  0.020
 EE3  plan-2  C39  0.020
 EE3  plan-2  C41  0.020
 EE3  plan-2  C43  0.020
 EE3  plan-2  N40  0.020
 EE3  plan-2  O42  0.020
 EE3  plan-2  H16  0.020
 EE3  plan-3  C35  0.020
 EE3  plan-3  C48  0.020
 EE3  plan-3  O50  0.020
 EE3  plan-3  O1   0.020
 EE3  plan-3  H12  0.020

