# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 17 16:32:05 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  38  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 PERFECT
;

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   0.534  -2.6336  -1.9066   0.8282
 N88  C1    C  CT    0   0.052  -2.0521  -0.8951  -0.1625
 N88  O1    O  OH1   0  -0.578  -3.6923  -2.5347   0.3530
 N88  C2    C  CH2   0  -0.499  -2.7772   0.4338   0.0723
 N88  O2    O  O     0  -0.425  -2.1851  -2.0703   1.9344
 N88  C3    C  CH1   0   0.052  -2.0138   1.5856  -0.5566
 N88  O3    O  OH1   0  -0.672  -2.7992   2.7451  -0.4292
 N88  C4    C  CH1   0  -0.030  -0.6705   1.7400   0.1423
 N88  O4    O  OH1   0  -0.670   0.0720   2.7052  -0.5690
 N88  C5    C  C     0  -0.075   0.0491   0.4129   0.1933
 N88  C6    C  C1    0  -0.217  -0.5735  -0.7587   0.0986
 N88  C13   C  C     0   0.534   1.5165   0.4931   0.4842
 N88  N14   N  NH1   0  -0.646   2.2899  -0.3585  -0.1981
 N88  C15   C  CT    0   0.096   3.7440  -0.5243  -0.0712
 N88  C16   C  CH3   0  -0.682   4.1242  -1.6499  -1.0315
 N88  C17   C  CH3   0  -0.639   4.4708   0.7591  -0.4766
 N88  C18   C  CH3   0  -0.645   4.1193  -0.9327   1.3534
 N88  O19   O  O     0  -0.499   1.9210   1.3063   1.3089
 N88  O30   O  OH1   0  -0.648  -2.2835  -1.2715  -1.4965
 N88  HO1   H  HOH1  0   0.486  -4.0502  -3.1356   1.0246
 N88  H2    H  HCH2  0   0.278  -3.7846   0.3697  -0.3445
 N88  H2A   H  HCH2  0   0.267  -2.8822   0.6161   1.1460
 N88  H3    H  HCH1  0   0.221  -1.8232   1.3576  -1.6155
 N88  HO3   H  HOH1  0   0.451  -2.3311   3.4712  -0.8545
 N88  H4    H  HCH1  0   0.238  -0.8596   2.0755   1.1720
 N88  HO4   H  HOH1  0   0.459   0.7459   3.0650   0.0163
 N88  H6    H  H     0   0.284  -0.0078  -1.6831   0.1738
 N88  HN14  H  HNH1  0   0.405   1.8395  -0.8996  -0.9196
 N88  H16   H  HCH3  0   0.239   3.8520  -1.4053  -2.0604
 N88  H16A  H  HCH3  0   0.243   5.2002  -1.8185  -1.0022
 N88  H16B  H  HCH3  0   0.239   3.6317  -2.5853  -0.7584
 N88  H17   H  HCH3  0   0.239   4.2352   1.5838   0.1938
 N88  H17A  H  HCH3  0   0.227   5.5498   0.6006  -0.4468
 N88  H17B  H  HCH3  0   0.228   4.2018   1.0530  -1.4924
 N88  H18   H  HCH3  0   0.229   3.5633  -1.8195   1.6612
 N88  H18A  H  HCH3  0   0.229   5.1829  -1.1711   1.3999
 N88  H18B  H  HCH3  0   0.240   3.9244  -0.1376   2.0703
 N88  HO30  H  HOH1  0   0.458  -1.7249  -2.0237  -1.7240

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    single  1.320  0.020  1.320
 N88  C1   C     single  1.531  0.020  1.531
 N88  C1   O30   single  1.405  0.020  1.405
 N88  O1   HO1   single  0.850  0.020  0.980
 N88  C2   C1    single  1.532  0.020  1.532
 N88  C2   H2    single  0.970  0.020  1.090
 N88  C2   H2A   single  0.970  0.020  1.090
 N88  O2   C     double  1.205  0.020  1.205
 N88  C3   C2    single  1.518  0.020  1.518
 N88  C3   H3    single  0.970  0.020  1.090
 N88  O3   C3    single  1.406  0.020  1.406
 N88  O3   HO3   single  0.850  0.020  0.980
 N88  C4   C3    single  1.522  0.020  1.522
 N88  C4   C5    single  1.510  0.020  1.510
 N88  C4   H4    single  0.970  0.020  1.090
 N88  O4   C4    single  1.410  0.020  1.410
 N88  O4   HO4   single  0.850  0.020  0.980
 N88  C5   C13   single  1.498  0.020  1.498
 N88  C5   C6    double  1.330  0.020  1.330
 N88  C6   C1    single  1.508  0.020  1.508
 N88  C6   H6    single  0.930  0.020  1.080
 N88  C13  N14   single  1.338  0.020  1.338
 N88  N14  C15   single  1.469  0.020  1.469
 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  1.227  0.020  1.227
 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    124.37  3.000
 N88  O2    C    C1    122.86  3.000
 N88  O1    C    C1    112.73  3.000
 N88  O30   C1   C6    110.49  3.000
 N88  C6    C1   C2    111.05  3.000
 N88  O30   C1   C2    107.45  3.000
 N88  C6    C1   C     108.68  3.000
 N88  C2    C1   C     107.11  3.000
 N88  O30   C1   C     112.02  3.000
 N88  HO1   O1   C     109.99  3.000
 N88  H2A   C2   H2    107.20  3.000
 N88  H2A   C2   C3    109.17  3.000
 N88  H2    C2   C3    110.51  3.000
 N88  C3    C2   C1    110.89  3.000
 N88  H2A   C2   C1    109.90  3.000
 N88  H2    C2   C1    109.10  3.000
 N88  H3    C3   C4    108.07  3.000
 N88  C4    C3   O3    111.57  3.000
 N88  H3    C3   O3    110.79  3.000
 N88  C4    C3   C2    109.30  3.000
 N88  O3    C3   C2    107.89  3.000
 N88  H3    C3   C2    109.19  3.000
 N88  HO3   O3   C3    108.07  3.000
 N88  H4    C4   C5    108.57  3.000
 N88  H4    C4   O4    110.74  3.000
 N88  C5    C4   O4    111.56  3.000
 N88  O4    C4   C3    107.61  3.000
 N88  H4    C4   C3    108.02  3.000
 N88  C5    C4   C3    110.29  3.000
 N88  HO4   O4   C4    108.53  3.000
 N88  C13   C5   C6    121.29  3.000
 N88  C6    C5   C4    123.26  3.000
 N88  C13   C5   C4    115.23  3.000
 N88  H6    C6   C5    120.06  3.000
 N88  H6    C6   C1    116.47  3.000
 N88  C5    C6   C1    123.44  3.000
 N88  O19   C13  N14   125.05  3.000
 N88  O19   C13  C5    119.27  3.000
 N88  N14   C13  C5    115.67  3.000
 N88  HN14  N14  C15   116.33  3.000
 N88  HN14  N14  C13   116.65  3.000
 N88  C15   N14  C13   126.88  3.000
 N88  C18   C15  C17   110.76  3.000
 N88  C17   C15  C16   109.48  3.000
 N88  C18   C15  C16   109.14  3.000
 N88  C17   C15  N14   110.66  3.000
 N88  C16   C15  N14   105.97  3.000
 N88  C18   C15  N14   110.71  3.000
 N88  H16B  C16  H16A  107.83  3.000
 N88  H16B  C16  H16   108.37  3.000
 N88  H16A  C16  H16   107.82  3.000
 N88  H16B  C16  C15   111.21  3.000
 N88  H16A  C16  C15   110.05  3.000
 N88  H16   C16  C15   111.42  3.000
 N88  H17B  C17  H17A  107.96  3.000
 N88  H17B  C17  H17   108.41  3.000
 N88  H17A  C17  H17   107.89  3.000
 N88  H17B  C17  C15   110.83  3.000
 N88  H17A  C17  C15   109.93  3.000
 N88  H17   C17  C15   111.69  3.000
 N88  H18B  C18  H18A  107.83  3.000
 N88  H18B  C18  H18   108.46  3.000
 N88  H18A  C18  H18   107.89  3.000
 N88  H18B  C18  C15   112.01  3.000
 N88  H18A  C18  C15   109.72  3.000
 N88  H18   C18  C15   110.80  3.000
 N88  HO30  O30  C1    109.72  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  HO1   O1   C    C1    180.00   0.0  0
 N88  CONST_04  O19   C13  N14  C15     0.00   0.0  0
 N88  Var_01    C4    C5   C6   C1      4.25  30.0  1
 N88  Var_02    N14   C13  C5   C4   -140.93  30.0  2
 N88  Var_03    C18   C15  N14  C13    59.87  30.0  3
 N88  Var_04    H18   C18  C15  N14    54.01  30.0  3
 N88  Var_05    H16   C16  C15  N14    59.53  30.0  3
 N88  Var_06    H17   C17  C15  N14    64.31  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
 N88  plan-2  HO1   0.020

