# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 08:08:54 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: (2S)-2,4-dihydroxy-3,3-dimethyl-N-[3-(nonylamino)-3-oxopropyl]butanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCNC(=O)CCNC(=O)[C@@H](O)C(C)(C)CO
#
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
 MV1  MV1  (2S)-2,4-dihydroxy-3,3-dimethyl-N-[3-(nonylamino)-3-oxopropyl]butanamide  ligand  60  24  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MV1
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
 MV1  C     C  C     0   0.565   0.0105  -1.2819   0.3516
 MV1  N     N  NH1   0  -0.634  -3.6954  -0.6363   0.7431
 MV1  C1    C  CT    0  -0.197  -6.7326   0.5804  -0.4484
 MV1  C2    C  CH2   0  -0.108  -7.8140   1.5251   0.1046
 MV1  O2    O  OH1   0  -0.669  -8.5067   2.1302  -0.9620
 MV1  C3    C  CH3   0  -0.646  -7.4048  -0.4654  -1.3417
 MV1  C4    C  CH3   0  -0.662  -5.7067   1.3702  -1.2661
 MV1  C5    C  CH1   0  -0.029  -6.0649  -0.0986   0.7781
 MV1  C6    C  C     0   0.517  -4.9204  -1.0420   0.3872
 MV1  C8    C  CH2   0  -0.240  -2.5024  -1.4253   0.5264
 MV1  C9    C  CH2   0  -0.621  -1.2856  -0.5149   0.5210
 MV1  N15   N  NH1   0  -0.647   1.1037  -0.5214   0.1997
 MV1  C16   C  CH2   0  -0.232   2.4353  -1.0812   0.0892
 MV1  C17   C  CH2   0  -0.474   3.4919   0.0104   0.0770
 MV1  C18   C  CH2   0  -0.416   4.8946  -0.5743  -0.0273
 MV1  C19   C  CH2   0  -0.413   5.9921   0.4815  -0.0348
 MV1  C20   C  CH2   0  -0.412   7.3882  -0.1230  -0.1195
 MV1  C21   C  CH2   0  -0.412   8.5031   0.9149  -0.1282
 MV1  C22   C  CH2   0  -0.406   9.8925   0.2943  -0.2057
 MV1  C23   C  CH2   0  -0.419  11.0182   1.3209  -0.2117
 MV1  C24   C  CH3   0  -0.661  12.3979   0.6820  -0.2937
 MV1  O25   O  O     0  -0.505   0.0581  -2.5052   0.3651
 MV1  O5'   O  OH1   0  -0.665  -5.6499   0.8242   1.7620
 MV1  O6'   O  O     0  -0.497  -5.1344  -2.0890  -0.2107
 MV1  HN    H  HNH1  0   0.395  -3.6323   0.1399   1.3823
 MV1  H2    H  HCH2  0   0.197  -8.4955   0.9433   0.7434
 MV1  H2A   H  HCH2  0   0.201  -7.3582   2.2901   0.7424
 MV1  HO2   H  HOH1  0   0.457  -9.0430   2.8403  -0.5998
 MV1  H3    H  HCH3  0   0.233  -8.0142   0.0257  -2.0993
 MV1  H3A   H  HCH3  0   0.239  -6.6797  -1.0880  -1.8595
 MV1  H3B   H  HCH3  0   0.222  -8.0591  -1.1225  -0.7642
 MV1  H4    H  HCH3  0   0.218  -5.1801   2.1250  -0.6756
 MV1  H4A   H  HCH3  0   0.238  -4.9571   0.7144  -1.7107
 MV1  H4B   H  HCH3  0   0.248  -6.1983   1.9002  -2.0810
 MV1  H5    H  HCH1  0   0.261  -6.8221  -0.7300   1.2566
 MV1  H8    H  HCH2  0   0.241  -2.4005  -2.1874   1.3033
 MV1  H8A   H  HCH2  0   0.247  -2.5917  -1.9465  -0.4258
 MV1  H9    H  HCH2  0   0.278  -1.2325   0.0460   1.4604
 MV1  H9A   H  HCH2  0   0.276  -1.3766   0.2306  -0.2734
 MV1  HN15  H  HNH1  0   0.401   1.0049   0.4813   0.1950
 MV1  H16   H  HCH2  0   0.228   2.6175  -1.7577   0.9288
 MV1  H16A  H  HCH2  0   0.228   2.5148  -1.6836  -0.8208
 MV1  H17   H  HCH2  0   0.228   3.3139   0.6914  -0.7617
 MV1  H17A  H  HCH2  0   0.228   3.4110   0.6092   0.9902
 MV1  H18   H  HCH2  0   0.214   5.0604  -1.2609   0.8099
 MV1  H18A  H  HCH2  0   0.215   4.9686  -1.1819  -0.9357
 MV1  H19   H  HCH2  0   0.210   5.8388   1.1649  -0.8771
 MV1  H19A  H  HCH2  0   0.209   5.9150   1.0940   0.8703
 MV1  H20   H  HCH2  0   0.207   7.5360  -0.8049   0.7254
 MV1  H20A  H  HCH2  0   0.207   7.4613  -0.7418  -1.0209
 MV1  H21   H  HCH2  0   0.206   8.3617   1.5962  -0.9746
 MV1  H21A  H  HCH2  0   0.206   8.4306   1.5345   0.7729
 MV1  H22   H  HCH2  0   0.206  10.0310  -0.3890   0.6397
 MV1  H22A  H  HCH2  0   0.206   9.9632  -0.3255  -1.1069
 MV1  H23   H  HCH2  0   0.210  10.8808   2.0042  -1.0555
 MV1  H23A  H  HCH2  0   0.210  10.9510   1.9375   0.6901
 MV1  H24   H  HCH3  0   0.225  13.1904   1.4311  -0.2897
 MV1  H24A  H  HCH3  0   0.215  12.5722   0.0113   0.5501
 MV1  H24B  H  HCH3  0   0.215  12.5039   0.0926  -1.2068
 MV1  HO5'  H  HOH1  0   0.454  -5.3562   1.6433   1.3484

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
 MV1  C    C9    single  1.516  0.020  1.516
 MV1  C    N15   single  1.340  0.020  1.340
 MV1  C    O25   double  1.224  0.020  1.224
 MV1  N    C6    single  1.339  0.020  1.339
 MV1  N    C8    single  1.447  0.020  1.447
 MV1  C1   C2    single  1.539  0.020  1.539
 MV1  C1   C3    single  1.531  0.020  1.531
 MV1  C1   C4    single  1.531  0.020  1.531
 MV1  C1   C5    single  1.553  0.020  1.553
 MV1  C2   O2    single  1.408  0.020  1.408
 MV1  C5   C6    single  1.534  0.020  1.534
 MV1  C5   O5'   single  1.411  0.020  1.411
 MV1  C6   O6'   double  1.224  0.020  1.224
 MV1  C8   C9    single  1.520  0.020  1.520
 MV1  N15  C16   single  1.449  0.020  1.449
 MV1  C16  C17   single  1.519  0.020  1.519
 MV1  C17  C18   single  1.523  0.020  1.523
 MV1  C18  C19   single  1.523  0.020  1.523
 MV1  C19  C20   single  1.524  0.020  1.524
 MV1  C20  C21   single  1.523  0.020  1.523
 MV1  C21  C22   single  1.524  0.020  1.524
 MV1  C22  C23   single  1.524  0.020  1.524
 MV1  C23  C24   single  1.523  0.020  1.523
 MV1  N    HN    single  0.860  0.020  1.020
 MV1  C2   H2    single  0.970  0.020  1.090
 MV1  C2   H2A   single  0.970  0.020  1.090
 MV1  O2   HO2   single  0.850  0.020  0.980
 MV1  C3   H3    single  0.970  0.020  1.090
 MV1  C3   H3A   single  0.970  0.020  1.090
 MV1  C3   H3B   single  0.970  0.020  1.090
 MV1  C4   H4    single  0.970  0.020  1.090
 MV1  C4   H4A   single  0.970  0.020  1.090
 MV1  C4   H4B   single  0.970  0.020  1.090
 MV1  C5   H5    single  0.970  0.020  1.090
 MV1  C8   H8    single  0.970  0.020  1.090
 MV1  C8   H8A   single  0.970  0.020  1.090
 MV1  C9   H9    single  0.970  0.020  1.090
 MV1  C9   H9A   single  0.970  0.020  1.090
 MV1  N15  HN15  single  0.860  0.020  1.020
 MV1  C16  H16   single  0.970  0.020  1.090
 MV1  C16  H16A  single  0.970  0.020  1.090
 MV1  C17  H17   single  0.970  0.020  1.090
 MV1  C17  H17A  single  0.970  0.020  1.090
 MV1  C18  H18   single  0.970  0.020  1.090
 MV1  C18  H18A  single  0.970  0.020  1.090
 MV1  C19  H19   single  0.970  0.020  1.090
 MV1  C19  H19A  single  0.970  0.020  1.090
 MV1  C20  H20   single  0.970  0.020  1.090
 MV1  C20  H20A  single  0.970  0.020  1.090
 MV1  C21  H21   single  0.970  0.020  1.090
 MV1  C21  H21A  single  0.970  0.020  1.090
 MV1  C22  H22   single  0.970  0.020  1.090
 MV1  C22  H22A  single  0.970  0.020  1.090
 MV1  C23  H23   single  0.970  0.020  1.090
 MV1  C23  H23A  single  0.970  0.020  1.090
 MV1  C24  H24   single  0.970  0.020  1.090
 MV1  C24  H24A  single  0.970  0.020  1.090
 MV1  C24  H24B  single  0.970  0.020  1.090
 MV1  O5'  HO5'  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
 MV1  O25   C    N15   122.44  3.000
 MV1  O25   C    C9    122.53  3.000
 MV1  N15   C    C9    115.02  3.000
 MV1  HN    N    C8    117.62  3.000
 MV1  HN    N    C6    117.35  3.000
 MV1  C8    N    C6    123.34  3.000
 MV1  C5    C1   C4    111.05  3.000
 MV1  C5    C1   C3    110.55  3.000
 MV1  C4    C1   C3    109.57  3.000
 MV1  C5    C1   C2    106.67  3.000
 MV1  C4    C1   C2    110.25  3.000
 MV1  C3    C1   C2    108.70  3.000
 MV1  H2A   C2   H2    106.79  3.000
 MV1  H2A   C2   O2    110.22  3.000
 MV1  H2    C2   O2    111.23  3.000
 MV1  H2A   C2   C1    110.22  3.000
 MV1  H2    C2   C1    108.61  3.000
 MV1  O2    C2   C1    109.71  3.000
 MV1  HO2   O2   C2    107.85  3.000
 MV1  H3B   C3   H3A   107.87  3.000
 MV1  H3B   C3   H3    107.69  3.000
 MV1  H3A   C3   H3    107.47  3.000
 MV1  H3B   C3   C1    111.43  3.000
 MV1  H3A   C3   C1    112.11  3.000
 MV1  H3    C3   C1    110.09  3.000
 MV1  H4B   C4   H4A   107.32  3.000
 MV1  H4B   C4   H4    106.59  3.000
 MV1  H4A   C4   H4    107.71  3.000
 MV1  H4B   C4   C1    110.36  3.000
 MV1  H4A   C4   C1    111.59  3.000
 MV1  H4    C4   C1    112.98  3.000
 MV1  H5    C5   O5'   106.00  3.000
 MV1  H5    C5   C6    105.81  3.000
 MV1  O5'   C5   C6    111.13  3.000
 MV1  H5    C5   C1    107.44  3.000
 MV1  O5'   C5   C1    113.03  3.000
 MV1  C6    C5   C1    112.86  3.000
 MV1  O6'   C6   C5    121.33  3.000
 MV1  O6'   C6   N     123.29  3.000
 MV1  C5    C6   N     115.38  3.000
 MV1  H8A   C8   H8    107.18  3.000
 MV1  H8A   C8   C9    110.44  3.000
 MV1  H8    C8   C9    110.22  3.000
 MV1  H8A   C8   N     108.92  3.000
 MV1  H8    C8   N     110.53  3.000
 MV1  C9    C8   N     109.52  3.000
 MV1  H9A   C9   H9    106.14  3.000
 MV1  H9A   C9   C8    110.15  3.000
 MV1  H9    C9   C8    110.03  3.000
 MV1  H9A   C9   C     109.58  3.000
 MV1  H9    C9   C     108.27  3.000
 MV1  C8    C9   C     112.45  3.000
 MV1  HN15  N15  C16   118.31  3.000
 MV1  HN15  N15  C     119.03  3.000
 MV1  C16   N15  C     122.62  3.000
 MV1  H16A  C16  H16   106.61  3.000
 MV1  H16A  C16  C17   109.78  3.000
 MV1  H16   C16  C17   109.56  3.000
 MV1  H16A  C16  N15   110.06  3.000
 MV1  H16   C16  N15   109.49  3.000
 MV1  C17   C16  N15   111.24  3.000
 MV1  H17A  C17  H17   106.66  3.000
 MV1  H17A  C17  C18   109.58  3.000
 MV1  H17   C17  C18   109.63  3.000
 MV1  H17A  C17  C16   109.56  3.000
 MV1  H17   C17  C16   109.87  3.000
 MV1  C18   C17  C16   111.42  3.000
 MV1  H18A  C18  H18   106.02  3.000
 MV1  H18A  C18  C19   109.37  3.000
 MV1  H18   C18  C19   109.22  3.000
 MV1  H18A  C18  C17   109.39  3.000
 MV1  H18   C18  C17   109.13  3.000
 MV1  C19   C18  C17   113.44  3.000
 MV1  H19A  C19  H19   106.05  3.000
 MV1  H19A  C19  C20   109.40  3.000
 MV1  H19   C19  C20   109.45  3.000
 MV1  H19A  C19  C18   109.43  3.000
 MV1  H19   C19  C18   109.60  3.000
 MV1  C20   C19  C18   112.68  3.000
 MV1  H20A  C20  H20   105.90  3.000
 MV1  H20A  C20  C21   109.34  3.000
 MV1  H20   C20  C21   109.25  3.000
 MV1  H20A  C20  C19   109.32  3.000
 MV1  H20   C20  C19   109.13  3.000
 MV1  C21   C20  C19   113.61  3.000
 MV1  H21A  C21  H21   105.97  3.000
 MV1  H21A  C21  C22   109.42  3.000
 MV1  H21   C21  C22   109.36  3.000
 MV1  H21A  C21  C20   109.40  3.000
 MV1  H21   C21  C20   109.49  3.000
 MV1  C22   C21  C20   112.96  3.000
 MV1  H22A  C22  H22   105.87  3.000
 MV1  H22A  C22  C23   109.28  3.000
 MV1  H22   C22  C23   109.26  3.000
 MV1  H22A  C22  C21   109.33  3.000
 MV1  H22   C22  C21   109.26  3.000
 MV1  C23   C22  C21   113.55  3.000
 MV1  H23A  C23  H23   106.01  3.000
 MV1  H23A  C23  C24   109.66  3.000
 MV1  H23   C23  C24   109.52  3.000
 MV1  H23A  C23  C22   109.33  3.000
 MV1  H23   C23  C22   109.32  3.000
 MV1  C24   C23  C22   112.76  3.000
 MV1  H24B  C24  H24A  107.41  3.000
 MV1  H24B  C24  H24   107.66  3.000
 MV1  H24A  C24  H24   107.64  3.000
 MV1  H24B  C24  C23   111.07  3.000
 MV1  H24A  C24  C23   111.14  3.000
 MV1  H24   C24  C23   111.71  3.000
 MV1  HO5'  O5'  C5    110.26  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
 MV1  CONST_01  C8    N    C6   C5    180.00   0.0  0
 MV1  CONST_02  O6'   C6   N    C8      0.00   0.0  0
 MV1  CONST_03  C16   N15  C    C9    180.00   0.0  0
 MV1  CONST_04  O25   C    N15  C16     0.00   0.0  0
 MV1  CONST_05  HN    N    C6   C5      0.00   0.0  0
 MV1  CONST_06  HN15  N15  C    C9      0.00   0.0  0
 MV1  Var_01    N     C8   C9   C     177.79  30.0  1
 MV1  Var_02    C17   C16  N15  C    -173.86  30.0  3
 MV1  Var_03    C3    C1   C2   O2    -58.00  30.0  3
 MV1  Var_04    C9    C8   N    C6    157.93  30.0  3
 MV1  Var_05    N15   C    C9   C8    173.35  30.0  1
 MV1  Var_06    C18   C17  C16  N15   179.52  30.0  3
 MV1  Var_07    C19   C18  C17  C16  -179.66  30.0  3
 MV1  Var_08    C20   C19  C18  C17   179.18  30.0  3
 MV1  Var_09    C21   C20  C19  C18  -179.99  30.0  3
 MV1  Var_10    C22   C21  C20  C19   179.70  30.0  3
 MV1  Var_11    C23   C22  C21  C20  -179.85  30.0  3
 MV1  Var_12    C24   C23  C22  C21  -179.83  30.0  3
 MV1  Var_13    H3    C3   C1   C2     53.42  30.0  3
 MV1  Var_14    H4    C4   C1   C2     61.32  30.0  3
 MV1  Var_15    H24   C24  C23  C22  -179.59  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
 MV1  chir_01  C5  C1  C6  O5'  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
 MV1  plan-1  C     0.020
 MV1  plan-1  C9    0.020
 MV1  plan-1  N15   0.020
 MV1  plan-1  C16   0.020
 MV1  plan-1  O25   0.020
 MV1  plan-1  HN15  0.020
 MV1  plan-2  N     0.020
 MV1  plan-2  C5    0.020
 MV1  plan-2  C6    0.020
 MV1  plan-2  C8    0.020
 MV1  plan-2  O6'   0.020
 MV1  plan-2  HN    0.020

