# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 06:18:45 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: (3S)-3-hydroxy-4-({(1S)-3-methyl-1-[(3-methylbutyl)carbamoyl]butyl}amino)-4-oxobutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CCNC(=O)[C@H](CC(C)C)NC(=O)[C@@H](O)CC(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
 E6C  E6C  '(3S)-3-hydroxy-4-({(1S)-3-methyl-1-[(3-methylbutyl)carbamoyl]butyl}amino)-4-oxobutanoic acid'  ligand  49  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 PERFECT
;

data_comp_E6C
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
 E6C  O1    O  OH1    0  -0.662   0.6725   1.9103  -3.8212
 E6C  C2    C  CH2    0  -0.597   1.7392  -0.1287  -3.0259
 E6C  C3    C  CH1    0  -0.080   0.4668   0.7062  -3.1310
 E6C  C4    C  C      0   0.525  -0.0537   0.9785  -1.7269
 E6C  O5    O  O      0  -0.497   0.2997   1.9637  -1.0935
 E6C  N6    N  NH1    0  -0.629  -0.8824   0.0498  -1.2230
 E6C  C7    C  CH1    0  -0.210  -1.2300   0.0265   0.1734
 E6C  C8    C  C      0   0.560   0.0070  -0.2885   1.0191
 E6C  O9    O  O      0  -0.491   0.8867  -1.0324   0.6136
 E6C  N10   N  NH1    0  -0.640   0.0069   0.2630   2.2386
 E6C  C11   C  CH2    0  -0.240   1.0549   0.0376   3.2132
 E6C  C12   C  CH2    0  -0.452   0.5999   0.4742   4.5969
 E6C  C13   C  CH1    0  -0.239   1.6919   0.3675   5.6621
 E6C  C14   C  CH3    0  -0.650   1.1964   0.9595   6.9778
 E6C  C15   C  CH3    0  -0.660   2.1516  -1.0727   5.8721
 E6C  C16   C  C      0   0.416   2.2886  -0.5543  -4.4016
 E6C  O17   O  O      0  -0.612   1.4483  -0.9283  -5.2433
 E6C  O18   O  OC    -1  -0.614   3.5258  -0.5237  -4.5462
 E6C  C19   C  CH2    0  -0.441  -2.3029  -1.0311   0.4346
 E6C  C20   C  CH1    0  -0.234  -3.6195  -0.8195  -0.3171
 E6C  C21   C  CH3    0  -0.651  -4.5877  -1.9439   0.0377
 E6C  C22   C  CH3    0  -0.664  -4.2420   0.5412  -0.0226
 E6C  HO1   H  HOH1   0   0.439   1.2202   2.4794  -3.2681
 E6C  H21   H  HCH2   0   0.221   2.4957   0.4212  -2.4583
 E6C  H22   H  HCH2   0   0.242   1.5246  -1.0347  -2.4479
 E6C  H3    H  HCH1   0   0.247  -0.2747   0.1421  -3.7019
 E6C  HN6   H  HNH1   0   0.402  -1.0538  -0.7831  -1.7649
 E6C  H7    H  HCH1   0   0.270  -1.6161   1.0090   0.4579
 E6C  HN1   H  HNH1   0   0.398  -0.7007   0.9461   2.4595
 E6C  H111  H  HCH2   0   0.229   1.9612   0.5847   2.9308
 E6C  H112  H  HCH2   0   0.238   1.3111  -1.0224   3.2079
 E6C  H121  H  HCH2   0   0.225  -0.2666  -0.1225   4.9036
 E6C  H122  H  HCH2   0   0.231   0.2594   1.5140   4.5457
 E6C  H13   H  HCH1   0   0.218   2.5523   0.9574   5.3234
 E6C  H141  H  HCH3   0   0.227   1.9685   0.9176   7.7473
 E6C  H142  H  HCH3   0   0.225   0.8979   2.0028   6.8628
 E6C  H143  H  HCH3   0   0.214   0.3303   0.4046   7.3468
 E6C  H151  H  HCH3   0   0.214   1.3182  -1.6981   6.2031
 E6C  H152  H  HCH3   0   0.230   2.5589  -1.5181   4.9639
 E6C  H153  H  HCH3   0   0.229   2.9295  -1.1276   6.6352
 E6C  H191  H  HCH2   0   0.245  -1.8948  -2.0159   0.1811
 E6C  H192  H  HCH2   0   0.245  -2.5063  -1.0488   1.5093
 E6C  H20   H  HCH1   0   0.223  -3.4234  -0.8772  -1.3932
 E6C  H211  H  HCH3   0   0.228  -5.5199  -1.8510  -0.5217
 E6C  H212  H  HCH3   0   0.226  -4.1630  -2.9237  -0.1875
 E6C  H213  H  HCH3   0   0.215  -4.8355  -1.9257   1.1016
 E6C  H221  H  HCH3   0   0.217  -4.3892   0.6828   1.0512
 E6C  H222  H  HCH3   0   0.230  -3.6272   1.3658  -0.3871
 E6C  H223  H  HCH3   0   0.233  -5.2166   0.6329  -0.5043

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
 E6C  O1   C3    single  1.403  0.020  1.403
 E6C  O1   HO1   single  0.850  0.020  0.980
 E6C  C2   C3    single  1.526  0.020  1.526
 E6C  C2   C16   single  1.541  0.020  1.541
 E6C  C2   H21   single  0.970  0.020  1.090
 E6C  C2   H22   single  0.970  0.020  1.090
 E6C  C3   C4    single  1.522  0.020  1.522
 E6C  C3   H3    single  0.970  0.020  1.090
 E6C  C4   O5    double  1.223  0.020  1.223
 E6C  C4   N6    single  1.343  0.020  1.343
 E6C  N6   C7    single  1.439  0.020  1.439
 E6C  N6   HN6   single  0.860  0.020  1.020
 E6C  C7   C8    single  1.531  0.020  1.531
 E6C  C7   C19   single  1.529  0.020  1.529
 E6C  C7   H7    single  0.970  0.020  1.090
 E6C  C8   O9    double  1.221  0.020  1.221
 E6C  C8   N10   single  1.338  0.020  1.338
 E6C  N10  C11   single  1.449  0.020  1.449
 E6C  N10  HN1   single  0.860  0.020  1.020
 E6C  C11  C12   single  1.521  0.020  1.521
 E6C  C11  H111  single  0.970  0.020  1.090
 E6C  C11  H112  single  0.970  0.020  1.090
 E6C  C12  C13   single  1.529  0.020  1.529
 E6C  C12  H121  single  0.970  0.020  1.090
 E6C  C12  H122  single  0.970  0.020  1.090
 E6C  C13  C14   single  1.526  0.020  1.526
 E6C  C13  C15   single  1.526  0.020  1.526
 E6C  C13  H13   single  0.970  0.020  1.090
 E6C  C14  H141  single  0.970  0.020  1.090
 E6C  C14  H142  single  0.970  0.020  1.090
 E6C  C14  H143  single  0.970  0.020  1.090
 E6C  C15  H151  single  0.970  0.020  1.090
 E6C  C15  H152  single  0.970  0.020  1.090
 E6C  C15  H153  single  0.970  0.020  1.090
 E6C  C16  O17   deloc   1.247  0.020  1.247
 E6C  C16  O18   deloc   1.246  0.020  1.246
 E6C  C19  C20   single  1.531  0.020  1.531
 E6C  C19  H191  single  0.970  0.020  1.090
 E6C  C19  H192  single  0.970  0.020  1.090
 E6C  C20  C21   single  1.526  0.020  1.526
 E6C  C20  C22   single  1.525  0.020  1.525
 E6C  C20  H20   single  0.970  0.020  1.090
 E6C  C21  H211  single  0.970  0.020  1.090
 E6C  C21  H212  single  0.970  0.020  1.090
 E6C  C21  H213  single  0.970  0.020  1.090
 E6C  C22  H221  single  0.970  0.020  1.090
 E6C  C22  H222  single  0.970  0.020  1.090
 E6C  C22  H223  single  0.970  0.020  1.090

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
 E6C  HO1   O1   C3    107.92  3.000
 E6C  H22   C2   H21   106.11  3.000
 E6C  H22   C2   C16   108.20  3.000
 E6C  H21   C2   C16   110.82  3.000
 E6C  H22   C2   C3    108.99  3.000
 E6C  H21   C2   C3    109.72  3.000
 E6C  C16   C2   C3    112.76  3.000
 E6C  H3    C3   C4    110.01  3.000
 E6C  H3    C3   C2    108.63  3.000
 E6C  C4    C3   C2    108.64  3.000
 E6C  H3    C3   O1    106.59  3.000
 E6C  C4    C3   O1    110.51  3.000
 E6C  C2    C3   O1    112.41  3.000
 E6C  N6    C4   O5    122.75  3.000
 E6C  N6    C4   C3    115.69  3.000
 E6C  O5    C4   C3    121.52  3.000
 E6C  HN6   N6   C7    117.84  3.000
 E6C  HN6   N6   C4    118.33  3.000
 E6C  C7    N6   C4    121.62  3.000
 E6C  H7    C7   C19   109.23  3.000
 E6C  H7    C7   C8    109.06  3.000
 E6C  C19   C7   C8    109.28  3.000
 E6C  H7    C7   N6    108.86  3.000
 E6C  C19   C7   N6    110.27  3.000
 E6C  C8    C7   N6    110.13  3.000
 E6C  N10   C8   O9    123.61  3.000
 E6C  N10   C8   C7    114.73  3.000
 E6C  O9    C8   C7    121.59  3.000
 E6C  HN1   N10  C11   117.76  3.000
 E6C  HN1   N10  C8    118.62  3.000
 E6C  C11   N10  C8    123.28  3.000
 E6C  H112  C11  H111  106.84  3.000
 E6C  H112  C11  C12   110.72  3.000
 E6C  H111  C11  C12   109.80  3.000
 E6C  H112  C11  N10   108.54  3.000
 E6C  H111  C11  N10   110.32  3.000
 E6C  C12   C11  N10   110.55  3.000
 E6C  H122  C12  H121  106.51  3.000
 E6C  H122  C12  C13   108.71  3.000
 E6C  H121  C12  C13   109.37  3.000
 E6C  H122  C12  C11   108.84  3.000
 E6C  H121  C12  C11   109.57  3.000
 E6C  C13   C12  C11   113.59  3.000
 E6C  H13   C13  C15   108.28  3.000
 E6C  H13   C13  C14   108.21  3.000
 E6C  C15   C13  C14   110.20  3.000
 E6C  H13   C13  C12   107.91  3.000
 E6C  C15   C13  C12   112.13  3.000
 E6C  C14   C13  C12   109.98  3.000
 E6C  H143  C14  H142  107.71  3.000
 E6C  H143  C14  H141  107.66  3.000
 E6C  H142  C14  H141  107.74  3.000
 E6C  H143  C14  C13   110.59  3.000
 E6C  H142  C14  C13   111.65  3.000
 E6C  H141  C14  C13   111.32  3.000
 E6C  H153  C15  H152  107.20  3.000
 E6C  H153  C15  H151  107.63  3.000
 E6C  H152  C15  H151  107.65  3.000
 E6C  H153  C15  C13   111.01  3.000
 E6C  H152  C15  C13   112.54  3.000
 E6C  H151  C15  C13   110.60  3.000
 E6C  O18   C16  O17   126.74  3.000
 E6C  O18   C16  C2    116.79  3.000
 E6C  O17   C16  C2    116.44  3.000
 E6C  H192  C19  H191  106.38  3.000
 E6C  H192  C19  C20   108.95  3.000
 E6C  H191  C19  C20   109.33  3.000
 E6C  H192  C19  C7    108.03  3.000
 E6C  H191  C19  C7    108.71  3.000
 E6C  C20   C19  C7    115.08  3.000
 E6C  H20   C20  C22   108.05  3.000
 E6C  H20   C20  C21   107.65  3.000
 E6C  C22   C20  C21   110.71  3.000
 E6C  H20   C20  C19   108.73  3.000
 E6C  C22   C20  C19   112.31  3.000
 E6C  C21   C20  C19   109.25  3.000
 E6C  H213  C21  H212  107.71  3.000
 E6C  H213  C21  H211  107.70  3.000
 E6C  H212  C21  H211  107.64  3.000
 E6C  H213  C21  C20   110.98  3.000
 E6C  H212  C21  C20   111.52  3.000
 E6C  H211  C21  C20   111.12  3.000
 E6C  H223  C22  H222  107.00  3.000
 E6C  H223  C22  H221  107.61  3.000
 E6C  H222  C22  H221  107.83  3.000
 E6C  H223  C22  C20   110.76  3.000
 E6C  H222  C22  C20   112.32  3.000
 E6C  H221  C22  C20   111.11  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
 E6C  CONST_01  C7    N6   C4   C3    180.00   0.0  0
 E6C  CONST_02  C7    N6   C4   O5      0.00   0.0  0
 E6C  CONST_03  C11   N10  C8   C7    180.00   0.0  0
 E6C  CONST_04  C11   N10  C8   O9      0.00   0.0  0
 E6C  CONST_05  HN6   N6   C4   C3      0.00   0.0  0
 E6C  CONST_06  HN1   N10  C8   C7      0.00   0.0  0
 E6C  Var_01    O17   C16  C2   C3    -41.68  30.0  3
 E6C  Var_02    C21   C20  C19  C7    179.95  30.0  3
 E6C  Var_03    C12   C11  N10  C8   -164.64  30.0  3
 E6C  Var_04    C13   C12  C11  N10  -175.53  30.0  3
 E6C  Var_05    C14   C13  C12  C11   174.09  30.0  3
 E6C  Var_06    H141  C14  C13  C12  -178.55  30.0  3
 E6C  Var_07    H151  C15  C13  C12   -60.56  30.0  3
 E6C  Var_08    H211  C21  C20  C19  -177.09  30.0  3
 E6C  Var_09    H221  C22  C20  C19   -55.78  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
 E6C  chir_01  C3  O1  C2  C4   negativ
 E6C  chir_02  C7  N6  C8  C19  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
 E6C  plan-1  C3   0.020
 E6C  plan-1  C4   0.020
 E6C  plan-1  O5   0.020
 E6C  plan-1  N6   0.020
 E6C  plan-1  C7   0.020
 E6C  plan-1  HN6  0.020
 E6C  plan-2  C7   0.020
 E6C  plan-2  C8   0.020
 E6C  plan-2  O9   0.020
 E6C  plan-2  N10  0.020
 E6C  plan-2  C11  0.020
 E6C  plan-2  HN1  0.020
 E6C  plan-3  C2   0.020
 E6C  plan-3  C16  0.020
 E6C  plan-3  O17  0.020
 E6C  plan-3  O18  0.020

