# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 07:33:09 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: (2R)-N-{3-[(5-fluoro-4-oxopentyl)amino]-3-oxopropyl}-2,4-dihydroxy-3,3-dimethylbutanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(CO)[C@@H](O)C(=O)NCCC(=O)NCCCC(=O)CF
#
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
 ENV  ENV  (2R)-N-{3-[(5-fluoro-4-oxopentyl)amino]-3-oxopropyl}-2,4-dihydroxy-3,3-dimethylbutanamide  ligand  47  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_ENV
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
 ENV  C2    C  C     0   0.338  -6.5180  -0.7355   0.3516
 ENV  C3    C  CH2   0  -0.094  -7.9683  -0.3842   0.5884
 ENV  C4    C  CH2   0  -0.587  -5.5585   0.4074   0.5322
 ENV  F4    F  F     0  -0.361  -8.7708  -1.4857   0.3956
 ENV  O5    O  O     0  -0.389  -6.1836  -1.8529   0.0456
 ENV  C6    C  CH2   0  -0.429  -4.0964   0.0282   0.3710
 ENV  C7    C  CH2   0  -0.280  -3.1944   1.2415   0.5729
 ENV  N8    N  NH1   0  -0.636  -1.7872   0.9233   0.4825
 ENV  C9    C  C     0   0.562  -1.1318   0.7917  -0.6815
 ENV  C10   C  CH2   0  -0.590   0.3106   0.3482  -0.5616
 ENV  O11   O  O     0  -0.506  -1.6563   1.0046  -1.7675
 ENV  H3    H  HCH2  0   0.248  -8.0941  -0.0176   1.6106
 ENV  H3A   H  HCH2  0   0.248  -8.2729   0.4140  -0.0941
 ENV  H4    H  HCH2  0   0.280  -5.8375   1.1936  -0.1793
 ENV  H6    H  HCH2  0   0.236  -3.8290  -0.7448   1.0948
 ENV  H6A   H  HCH2  0   0.240  -3.9225  -0.3884  -0.6226
 ENV  H7    H  HCH2  0   0.241  -3.4325   2.0146  -0.1597
 ENV  HN8   H  HNH1  0   0.401  -1.3043   0.6946   1.3358
 ENV  C8    C  CH2   0  -0.275   1.2002   1.0090  -1.6109
 ENV  H10   H  HCH2  0   0.259   0.6958   0.5535   0.4385
 ENV  N2    N  NH1   0  -0.623   2.5638   0.5371  -1.5437
 ENV  C91   C  C     0   0.517   3.4551   1.0098  -0.6638
 ENV  C101  C  CH1   0  -0.026   4.8539   0.3841  -0.7207
 ENV  C11   C  CT    0  -0.200   5.1627  -0.5159   0.5076
 ENV  O3    O  O     0  -0.496   3.1895   1.8987   0.1356
 ENV  O4    O  OH1   0  -0.666   5.0727  -0.2699  -1.9512
 ENV  C12   C  CH2   0  -0.106   6.5926  -1.0491   0.3179
 ENV  C13   C  CH3   0  -0.643   5.1092   0.2989   1.8021
 ENV  C14   C  CH3   0  -0.668   4.1677  -1.6781   0.5908
 ENV  O51   O  OH1   0  -0.670   6.9478  -1.8477   1.4220
 ENV  H4A   H  HCH2  0   0.275  -5.7396   0.8461   1.5201
 ENV  H7A   H  HCH2  0   0.250  -3.3669   1.6759   1.5584
 ENV  H10A  H  HCH2  0   0.275   0.3403  -0.7378  -0.6948
 ENV  H12   H  HCH2  0   0.258   0.8275   0.7905  -2.6092
 ENV  H13   H  HCH2  0   0.248   1.1838   2.0930  -1.4884
 ENV  H14   H  HNH1  0   0.398   2.8622  -0.1455  -2.2194
 ENV  H15   H  HCH1  0   0.260   5.5520   1.2290  -0.6958
 ENV  H16   H  HOH1  0   0.454   4.8639  -1.2068  -1.8723
 ENV  H17   H  HCH2  0   0.198   6.6592  -1.6306  -0.6090
 ENV  H18   H  HCH2  0   0.199   7.2742  -0.1925   0.2099
 ENV  H19   H  HCH3  0   0.238   4.1007   0.6292   2.0377
 ENV  H20   H  HCH3  0   0.232   5.4603  -0.3053   2.6374
 ENV  H21   H  HCH3  0   0.222   5.7476   1.1835   1.7424
 ENV  H22   H  HCH3  0   0.222   4.1947  -2.3230  -0.2919
 ENV  H23   H  HCH3  0   0.251   4.3861  -2.3158   1.4462
 ENV  H24   H  HCH3  0   0.237   3.1442  -1.3195   0.7085
 ENV  H25   H  HOH1  0   0.457   7.8221  -2.2100   1.2550

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
 ENV  C2    C3    single  1.511  0.020  1.511
 ENV  C3    F4    single  1.376  0.020  1.376
 ENV  C3    H3    single  0.970  0.020  1.090
 ENV  C3    H3A   single  0.970  0.020  1.090
 ENV  C4    C2    single  1.503  0.020  1.503
 ENV  C4    C6    single  1.519  0.020  1.519
 ENV  C4    H4    single  0.970  0.020  1.090
 ENV  O5    C2    double  1.206  0.020  1.206
 ENV  C6    H6    single  0.970  0.020  1.090
 ENV  C6    H6A   single  0.970  0.020  1.090
 ENV  C7    C6    single  1.525  0.020  1.525
 ENV  C7    H7    single  0.970  0.020  1.090
 ENV  N8    C7    single  1.446  0.020  1.446
 ENV  N8    HN8   single  0.860  0.020  1.020
 ENV  C9    N8    single  1.342  0.020  1.342
 ENV  C10   C9    single  1.514  0.020  1.514
 ENV  C10   C8    single  1.526  0.020  1.526
 ENV  C10   H10   single  0.970  0.020  1.090
 ENV  O11   C9    double  1.225  0.020  1.225
 ENV  C8    N2    single  1.444  0.020  1.444
 ENV  N2    C91   single  1.339  0.020  1.339
 ENV  C91   C101  single  1.533  0.020  1.533
 ENV  C101  C11   single  1.554  0.020  1.554
 ENV  C91   O3    double  1.225  0.020  1.225
 ENV  C101  O4    single  1.411  0.020  1.411
 ENV  C11   C12   single  1.538  0.020  1.538
 ENV  C11   C13   single  1.531  0.020  1.531
 ENV  C11   C14   single  1.532  0.020  1.532
 ENV  C12   O51   single  1.408  0.020  1.408
 ENV  C4    H4A   single  0.970  0.020  1.090
 ENV  C7    H7A   single  0.970  0.020  1.090
 ENV  C10   H10A  single  0.970  0.020  1.090
 ENV  C8    H12   single  0.970  0.020  1.090
 ENV  C8    H13   single  0.970  0.020  1.090
 ENV  N2    H14   single  0.860  0.020  1.020
 ENV  C101  H15   single  0.970  0.020  1.090
 ENV  O4    H16   single  0.850  0.020  0.980
 ENV  C12   H17   single  0.970  0.020  1.090
 ENV  C12   H18   single  0.970  0.020  1.090
 ENV  C13   H19   single  0.970  0.020  1.090
 ENV  C13   H20   single  0.970  0.020  1.090
 ENV  C13   H21   single  0.970  0.020  1.090
 ENV  C14   H22   single  0.970  0.020  1.090
 ENV  C14   H23   single  0.970  0.020  1.090
 ENV  C14   H24   single  0.970  0.020  1.090
 ENV  O51   H25   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
 ENV  O5    C2    C4    123.92  3.000
 ENV  O5    C2    C3    121.43  3.000
 ENV  C4    C2    C3    114.65  3.000
 ENV  H3A   C3    H3    107.87  3.000
 ENV  H3A   C3    F4    109.53  3.000
 ENV  H3    C3    F4    109.41  3.000
 ENV  H3A   C3    C2    109.83  3.000
 ENV  H3    C3    C2    109.57  3.000
 ENV  F4    C3    C2    110.59  3.000
 ENV  H4A   C4    H4    104.82  3.000
 ENV  H4A   C4    C6    110.77  3.000
 ENV  H4    C4    C6    110.80  3.000
 ENV  H4A   C4    C2    107.89  3.000
 ENV  H4    C4    C2    107.75  3.000
 ENV  C6    C4    C2    114.32  3.000
 ENV  H6A   C6    H6    107.11  3.000
 ENV  H6A   C6    C7    109.27  3.000
 ENV  H6    C6    C7    109.30  3.000
 ENV  C7    C6    C4    110.89  3.000
 ENV  H6A   C6    C4    110.20  3.000
 ENV  H6    C6    C4    110.00  3.000
 ENV  H7A   C7    H7    106.85  3.000
 ENV  H7A   C7    N8    107.34  3.000
 ENV  H7    C7    N8    109.05  3.000
 ENV  H7A   C7    C6    110.05  3.000
 ENV  N8    C7    C6    113.10  3.000
 ENV  H7    C7    C6    110.22  3.000
 ENV  HN8   N8    C9    118.59  3.000
 ENV  C9    N8    C7    123.44  3.000
 ENV  HN8   N8    C7    117.64  3.000
 ENV  O11   C9    C10   121.96  3.000
 ENV  O11   C9    N8    122.88  3.000
 ENV  C10   C9    N8    115.16  3.000
 ENV  H10A  C10   H10   106.77  3.000
 ENV  H10A  C10   C8    109.27  3.000
 ENV  H10   C10   C8    110.06  3.000
 ENV  H10A  C10   C9    107.88  3.000
 ENV  H10   C10   C9    110.72  3.000
 ENV  C8    C10   C9    111.97  3.000
 ENV  H13   C8    H12   107.31  3.000
 ENV  H13   C8    N2    109.48  3.000
 ENV  H12   C8    N2    107.49  3.000
 ENV  H13   C8    C10   110.13  3.000
 ENV  H12   C8    C10   110.14  3.000
 ENV  N2    C8    C10   112.14  3.000
 ENV  H14   N2    C91   118.93  3.000
 ENV  H14   N2    C8    118.07  3.000
 ENV  C91   N2    C8    122.94  3.000
 ENV  O3    C91   C101  121.21  3.000
 ENV  O3    C91   N2    122.75  3.000
 ENV  C101  C91   N2    116.03  3.000
 ENV  H15   C101  O4    106.16  3.000
 ENV  H15   C101  C11   107.57  3.000
 ENV  O4    C101  C11   112.97  3.000
 ENV  H15   C101  C91   105.40  3.000
 ENV  O4    C101  C91   111.29  3.000
 ENV  C11   C101  C91   112.85  3.000
 ENV  C14   C11   C13   109.59  3.000
 ENV  C14   C11   C12   110.34  3.000
 ENV  C13   C11   C12   108.75  3.000
 ENV  C14   C11   C101  110.68  3.000
 ENV  C13   C11   C101  110.69  3.000
 ENV  C12   C11   C101  106.74  3.000
 ENV  H16   O4    C101  110.24  3.000
 ENV  H18   C12   H17   107.00  3.000
 ENV  H18   C12   O51   111.24  3.000
 ENV  H17   C12   O51   110.29  3.000
 ENV  H18   C12   C11   108.56  3.000
 ENV  H17   C12   C11   110.17  3.000
 ENV  O51   C12   C11   109.54  3.000
 ENV  H21   C13   H20   107.62  3.000
 ENV  H21   C13   H19   107.94  3.000
 ENV  H20   C13   H19   107.55  3.000
 ENV  H21   C13   C11   111.38  3.000
 ENV  H20   C13   C11   110.00  3.000
 ENV  H19   C13   C11   112.18  3.000
 ENV  H24   C14   H23   107.21  3.000
 ENV  H24   C14   H22   107.70  3.000
 ENV  H23   C14   H22   106.48  3.000
 ENV  H24   C14   C11   111.46  3.000
 ENV  H23   C14   C11   110.89  3.000
 ENV  H22   C14   C11   112.80  3.000
 ENV  H25   O51   C12   107.88  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
 ENV  CONST_01  C10   C9   N8   C7     180.00   0.0  0
 ENV  CONST_02  O11   C9   N8   C7       0.00   0.0  0
 ENV  CONST_03  C101  C91  N2   C8     180.00   0.0  0
 ENV  CONST_04  O3    C91  N2   C8       0.00   0.0  0
 ENV  CONST_05  HN8   N8   C9   C10      0.00   0.0  0
 ENV  CONST_06  H14   N2   C91  C101     0.00   0.0  0
 ENV  Var_01    C7    C6   C4   C2    -179.86  30.0  3
 ENV  Var_02    C6    C4   C2   C3     176.65  30.0  1
 ENV  Var_03    F4    C3   C2   C4     179.74  30.0  3
 ENV  Var_04    N8    C7   C6   C4     177.68  30.0  1
 ENV  Var_05    C9    N8   C7   C6      80.99  30.0  1
 ENV  Var_06    C8    C10  C9   N8    -144.03  30.0  1
 ENV  Var_07    N2    C8   C10  C9    -177.05  30.0  3
 ENV  Var_08    C91   N2   C8   C10    -81.43  30.0  3
 ENV  Var_09    O51   C12  C11  C101   178.43  30.0  3
 ENV  Var_10    H19   C13  C11  C101    68.15  30.0  3
 ENV  Var_11    H22   C14  C11  C101    60.21  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
 ENV  chir_01  C101  C91  C11  O4  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
 ENV  plan-1  C7    0.020
 ENV  plan-1  N8    0.020
 ENV  plan-1  C9    0.020
 ENV  plan-1  C10   0.020
 ENV  plan-1  O11   0.020
 ENV  plan-1  HN8   0.020
 ENV  plan-2  C8    0.020
 ENV  plan-2  N2    0.020
 ENV  plan-2  C91   0.020
 ENV  plan-2  C101  0.020
 ENV  plan-2  O3    0.020
 ENV  plan-2  H14   0.020
 ENV  plan-3  C2    0.020
 ENV  plan-3  C3    0.020
 ENV  plan-3  C4    0.020
 ENV  plan-3  O5    0.020

