# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 19:03:19 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: (1R,4R,5R)-3-(tert-butylcarbamoyl)-1,4,5-trihydroxycyclohex-2-ene-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)NC(=O)C1=C[C@](O)(C[C@@H](O)[C@@H]1O)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
 N88  N88  '(1R,4R,5R)-3-(tert-butylcarbamoyl)-1,4,5-trihydroxycyclohex-2-ene-1-carboxylic acid'  ligand  37  19  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_N88
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
 N88  C     C  C      0   0.417  -2.6497  -1.8990   0.7030
 N88  C1    C  CT     0   0.030  -2.0777  -0.7765  -0.2087
 N88  O1    O  OC    -1  -0.598  -3.2974  -2.7796   0.0948
 N88  C2    C  CH2    0  -0.485  -2.7666   0.5503   0.1168
 N88  O2    O  O      0  -0.574  -2.4201  -1.8221   1.9167
 N88  C3    C  CH1    0   0.056  -2.0232   1.7141  -0.5067
 N88  O3    O  OH1    0  -0.677  -2.7781   2.8896  -0.3193
 N88  C4    C  CH1    0  -0.028  -0.6492   1.8297   0.1387
 N88  O4    O  OH1    0  -0.676   0.0753   2.8099  -0.5759
 N88  C5    C  C      0  -0.095   0.0566   0.4933   0.1322
 N88  C6    C  C1     0  -0.185  -0.5930  -0.6634   0.0064
 N88  C13   C  C      0   0.537   1.5252   0.5500   0.4096
 N88  N14   N  NH1    0  -0.652   2.2796  -0.3668  -0.2107
 N88  C15   C  CT     0   0.099   3.7270  -0.5637  -0.0615
 N88  C16   C  CH3    0  -0.682   4.0712  -1.7985  -0.8926
 N88  C17   C  CH3    0  -0.638   4.4909   0.6455  -0.6047
 N88  C18   C  CH3    0  -0.648   4.0940  -0.8313   1.3983
 N88  O19   O  O      0  -0.508   1.9638   1.4052   1.1754
 N88  O30   O  OH1    0  -0.696  -2.2935  -1.1443  -1.5523
 N88  H2    H  HCH2   0   0.247  -3.7978   0.5172  -0.2444
 N88  H2A   H  HCH2   0   0.236  -2.8068   0.6868   1.2014
 N88  H3    H  HCH1   0   0.204  -1.8803   1.5153  -1.5801
 N88  HO3   H  HOH1   0   0.445  -2.2938   3.6199  -0.7187
 N88  H4    H  HCH1   0   0.225  -0.7969   2.1456   1.1819
 N88  HO4   H  HOH1   0   0.455   0.8061   3.1040  -0.0226
 N88  H6    H  H      0   0.255  -0.0415  -1.5990   0.0378
 N88  HN14  H  HNH1   0   0.402   1.8215  -0.9369  -0.9038
 N88  H16   H  HCH3   0   0.238   3.8049  -1.6593  -1.9426
 N88  H16A  H  HCH3   0   0.242   5.1418  -1.9955  -0.8449
 N88  H16B  H  HCH3   0   0.239   3.5507  -2.6833  -0.5208
 N88  H17   H  HCH3   0   0.238   4.2388   1.5553  -0.0624
 N88  H17A  H  HCH3   0   0.225   5.5662   0.4852  -0.5121
 N88  H17B  H  HCH3   0   0.226   4.2643   0.8003  -1.6610
 N88  H18   H  HCH3   0   0.228   3.5140  -1.6666   1.7936
 N88  H18A  H  HCH3   0   0.227   5.1504  -1.0951   1.4682
 N88  H18B  H  HCH3   0   0.241   3.9240   0.0372   2.0306
 N88  HO30  H  HOH1   0   0.429  -2.8328  -1.9552  -1.4552

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
 N88  C    O1    deloc   1.251  0.020  1.251
 N88  C1   C     single  1.555  0.020  1.555
 N88  C1   O30   single  1.410  0.020  1.410
 N88  C2   C1    single  1.530  0.020  1.530
 N88  C2   H2    single  0.970  0.020  1.090
 N88  C2   H2A   single  0.970  0.020  1.090
 N88  O2   C     deloc   1.238  0.020  1.238
 N88  C3   C2    single  1.515  0.020  1.515
 N88  C3   H3    single  0.970  0.020  1.090
 N88  O3   C3    single  1.410  0.020  1.410
 N88  O3   HO3   single  0.850  0.020  0.980
 N88  C4   C3    single  1.522  0.020  1.522
 N88  C4   C5    single  1.511  0.020  1.511
 N88  C4   H4    single  0.970  0.020  1.090
 N88  O4   C4    single  1.413  0.020  1.413
 N88  O4   HO4   single  0.850  0.020  0.980
 N88  C5   C13   single  1.496  0.020  1.496
 N88  C5   C6    double  1.333  0.020  1.333
 N88  C6   C1    single  1.504  0.020  1.504
 N88  C6   H6    single  0.930  0.020  1.080
 N88  C13  N14   single  1.340  0.020  1.340
 N88  N14  C15   single  1.468  0.020  1.468
 N88  N14  HN14  single  0.860  0.020  1.020
 N88  C15  C18   single  1.529  0.020  1.529
 N88  C16  C15   single  1.528  0.020  1.528
 N88  C16  H16   single  0.970  0.020  1.090
 N88  C16  H16A  single  0.970  0.020  1.090
 N88  C16  H16B  single  0.970  0.020  1.090
 N88  C17  C15   single  1.530  0.020  1.530
 N88  C17  H17   single  0.970  0.020  1.090
 N88  C17  H17A  single  0.970  0.020  1.090
 N88  C17  H17B  single  0.970  0.020  1.090
 N88  C18  H18   single  0.970  0.020  1.090
 N88  C18  H18A  single  0.970  0.020  1.090
 N88  C18  H18B  single  0.970  0.020  1.090
 N88  O19  C13   double  1.229  0.020  1.229
 N88  O30  HO30  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
 N88  O2    C    O1    128.07  3.000
 N88  O2    C    C1    117.50  3.000
 N88  O1    C    C1    114.43  3.000
 N88  O30   C1   C6    107.88  3.000
 N88  C6    C1   C2    110.41  3.000
 N88  O30   C1   C2    111.11  3.000
 N88  C6    C1   C     109.48  3.000
 N88  C2    C1   C     109.61  3.000
 N88  O30   C1   C     108.31  3.000
 N88  H2A   C2   H2    107.27  3.000
 N88  H2A   C2   C3    109.28  3.000
 N88  H2    C2   C3    110.49  3.000
 N88  C3    C2   C1    110.95  3.000
 N88  H2A   C2   C1    109.62  3.000
 N88  H2    C2   C1    109.16  3.000
 N88  H3    C3   C4    108.05  3.000
 N88  C4    C3   O3    111.33  3.000
 N88  H3    C3   O3    110.47  3.000
 N88  C4    C3   C2    109.07  3.000
 N88  O3    C3   C2    108.85  3.000
 N88  H3    C3   C2    109.04  3.000
 N88  HO3   O3   C3    107.94  3.000
 N88  H4    C4   C5    108.71  3.000
 N88  H4    C4   O4    110.44  3.000
 N88  C5    C4   O4    111.83  3.000
 N88  O4    C4   C3    107.52  3.000
 N88  H4    C4   C3    107.62  3.000
 N88  C5    C4   C3    110.64  3.000
 N88  HO4   O4   C4    108.09  3.000
 N88  C13   C5   C6    121.94  3.000
 N88  C6    C5   C4    122.70  3.000
 N88  C13   C5   C4    115.10  3.000
 N88  H6    C6   C5    119.82  3.000
 N88  H6    C6   C1    116.13  3.000
 N88  C5    C6   C1    124.04  3.000
 N88  O19   C13  N14   124.32  3.000
 N88  O19   C13  C5    119.50  3.000
 N88  N14   C13  C5    116.18  3.000
 N88  HN14  N14  C15   116.24  3.000
 N88  HN14  N14  C13   116.73  3.000
 N88  C15   N14  C13   126.86  3.000
 N88  C18   C15  C17   110.95  3.000
 N88  C17   C15  C16   109.46  3.000
 N88  C18   C15  C16   108.90  3.000
 N88  C17   C15  N14   110.49  3.000
 N88  C16   C15  N14   105.97  3.000
 N88  C18   C15  N14   110.93  3.000
 N88  H16B  C16  H16A  107.87  3.000
 N88  H16B  C16  H16   108.33  3.000
 N88  H16A  C16  H16   107.74  3.000
 N88  H16B  C16  C15   111.24  3.000
 N88  H16A  C16  C15   110.10  3.000
 N88  H16   C16  C15   111.42  3.000
 N88  H17B  C17  H17A  107.91  3.000
 N88  H17B  C17  H17   108.39  3.000
 N88  H17A  C17  H17   107.98  3.000
 N88  H17B  C17  C15   110.62  3.000
 N88  H17A  C17  C15   110.23  3.000
 N88  H17   C17  C15   111.59  3.000
 N88  H18B  C18  H18A  107.89  3.000
 N88  H18B  C18  H18   108.51  3.000
 N88  H18A  C18  H18   107.84  3.000
 N88  H18B  C18  C15   112.20  3.000
 N88  H18A  C18  C15   109.63  3.000
 N88  H18   C18  C15   110.63  3.000
 N88  HO30  O30  C1    101.88  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
 N88  CONST_01  C15   N14  C13  C5    180.00   0.0  0
 N88  CONST_02  HN14  N14  C13  C5      0.00   0.0  0
 N88  CONST_03  O19   C13  N14  C15     0.00   0.0  0
 N88  Var_01    C4    C5   C6   C1      3.08  30.0  1
 N88  Var_02    N14   C13  C5   C4   -147.19  30.0  2
 N88  Var_03    C18   C15  N14  C13    57.51  30.0  3
 N88  Var_04    H18   C18  C15  N14    54.28  30.0  3
 N88  Var_05    H16   C16  C15  N14    59.40  30.0  3
 N88  Var_06    H17   C17  C15  N14    61.28  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
 N88  chir_01  C1  O30  C2  C6  positiv
 N88  chir_02  C3  O3   C2  C4  positiv
 N88  chir_03  C4  O4   C3  C5  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
 N88  plan-1  C5    0.020
 N88  plan-1  C13   0.020
 N88  plan-1  N14   0.020
 N88  plan-1  C15   0.020
 N88  plan-1  O19   0.020
 N88  plan-1  HN14  0.020
 N88  plan-2  C     0.020
 N88  plan-2  C1    0.020
 N88  plan-2  O1    0.020
 N88  plan-2  O2    0.020

