# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 01:25:44 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: (3S)-4-hydroxy-3-{[(2S)-4-{[2-(2-methyl-1H-benzimidazol-1-yl)ethyl]amino}-4-oxo-2-(propan-2-yl)butanoyl]amino}butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](CC(=O)NCCn1c(C)nc2ccccc12)C(=O)N[C@H](CO)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
 3NS  3NS  '(3S)-4-hydroxy-3-{[(2S)-4-{[2-(2-methyl-1H-benzimidazol-1-yl)ethyl]amino}-4-oxo-2-(propan-2-yl)butanoyl]amino}butanoic acid'  peptide  60  30  .  2022-03-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_3NS
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
 3NS  C1    C  CH2   0  -0.337  -3.5476   0.7135   1.3261
 3NS  C2    C  CH2   0  -0.300  -2.6882   1.4600   0.3046
 3NS  N1    N  NH1   0  -0.629  -1.3120   1.5405   0.7241
 3NS  C14   C  CR56  0   0.130  -6.5810  -0.3692  -0.2992
 3NS  C15   C  CR16  0  -0.334  -7.2458  -1.2413  -1.1597
 3NS  C16   C  CR16  0  -0.274  -6.5094  -2.2498  -1.7584
 3NS  C17   C  CR16  0  -0.279  -5.1357  -2.3954  -1.5157
 3NS  C18   C  CR16  0  -0.311  -4.4565  -1.5385  -0.6648
 3NS  C19   C  CR56  0   0.337  -5.2076  -0.5343  -0.0658
 3NS  N3    N  N     0  -0.485  -7.0504   0.7059   0.4180
 3NS  N4    N  NR5   0  -0.536  -4.8748   0.4621   0.8175
 3NS  C20   C  CR5   0   0.433  -6.0143   1.1740   1.0608
 3NS  C21   C  CH3   0  -0.769  -6.0310   2.3448   1.9729
 3NS  C3    C  C     0   0.546  -0.4420   0.5297   0.5537
 3NS  O1    O  O     0  -0.494  -0.7529  -0.5210   0.0066
 3NS  C4    C  CH2   0  -0.562   0.9547   0.7737   1.0807
 3NS  C5    C  CH1   0  -0.382   2.0035   0.5868  -0.0178
 3NS  C6    C  CH1   0  -0.234   1.8506   1.6190  -1.1615
 3NS  C7    C  C     0   0.594   3.3937   0.6294   0.5963
 3NS  O2    O  O     0  -0.500   3.6619   1.3457   1.5518
 3NS  C8    C  CH3   0  -0.658   2.1322   3.0553  -0.7342
 3NS  C9    C  CH3   0  -0.674   2.6810   1.2511  -2.3880
 3NS  C13   C  CH2   0  -0.149   6.4949   0.8005  -0.4995
 3NS  N2    N  NH1   0  -0.628   4.2992  -0.1707   0.0078
 3NS  C10   C  CH1   0  -0.119   5.7060  -0.1851   0.3496
 3NS  C11   C  CH2   0  -0.597   6.2407  -1.6052   0.2285
 3NS  C12   C  C     0   0.559   5.6444  -2.5386   1.2487
 3NS  O3    O  OH1   0  -0.595   5.8232  -3.8123   0.9148
 3NS  O4    O  O     0  -0.437   5.0959  -2.1947   2.2648
 3NS  H1    H  HCH2  0   0.277  -3.0878  -0.2419   1.5805
 3NS  H1A   H  HCH2  0   0.284  -3.6228   1.2865   2.2493
 3NS  H2    H  HCH2  0   0.257  -2.7434   0.9641  -0.6652
 3NS  H2A   H  HCH2  0   0.269  -3.0644   2.4741   0.1701
 3NS  HN1   H  HNH1  0   0.406  -1.0091   2.3727   1.2022
 3NS  H15   H  HCR6  0   0.252  -8.3052  -1.1305  -1.3534
 3NS  H16   H  HCR6  0   0.251  -7.0015  -2.9412  -2.4301
 3NS  H17   H  HCR6  0   0.254  -4.5931  -3.1932  -2.0056
 3NS  H18   H  HCR6  0   0.265  -3.3928  -1.6440  -0.4885
 3NS  H21   H  HCH3  0   0.264  -5.3511   3.1278   1.6328
 3NS  H21A  H  HCH3  0   0.275  -7.0347   2.7594   2.0152
 3NS  H21B  H  HCH3  0   0.267  -5.7297   2.0677   2.9844
 3NS  H4    H  HCH2  0   0.257   1.0418   1.7620   1.5321
 3NS  H4A   H  HCH2  0   0.284   1.1257   0.0464   1.8788
 3NS  H5    H  HCH1  0   0.266   1.8464  -0.4031  -0.4581
 3NS  H6    H  HCH1  0   0.241   0.8013   1.5650  -1.4714
 3NS  H8    H  HCH3  0   0.222   3.1825   3.2040  -0.4785
 3NS  H8A   H  HCH3  0   0.233   1.8943   3.7389  -1.5501
 3NS  H8B   H  HCH3  0   0.227   1.5344   3.3603   0.1254
 3NS  H9    H  HCH3  0   0.228   2.4823   0.2275  -2.7136
 3NS  H9A   H  HCH3  0   0.236   2.4343   1.9121  -3.2202
 3NS  H9B   H  HCH3  0   0.226   3.7541   1.3412  -2.2102
 3NS  H13   H  HCH2  0   0.219   6.0877   1.8041  -0.3313
 3NS  H13A  H  HCH2  0   0.207   7.5352   0.8117  -0.1478
 3NS  HN2   H  HNH1  0   0.398   4.0205  -0.6718  -0.8213
 3NS  HO5   H  HOH1  0   0.461   6.6885   1.1591  -2.3967
 3NS  H10   H  HCH1  0   0.268   5.8007   0.1411   1.3858
 3NS  H11   H  HCH2  0   0.283   6.0873  -2.0059  -0.7759
 3NS  H11A  H  HCH2  0   0.300   7.3244  -1.6044   0.3868
 3NS  HO3   H  HOH1  0   0.480   5.4703  -4.3877   1.6101
 3NS  O5    O  OH1   0  -0.670   6.4046   0.4204  -1.8520

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
 3NS  C2   C1    single    1.530  0.020  1.530
 3NS  C1   N4    single    1.443  0.020  1.443
 3NS  C1   H1    single    0.970  0.020  1.090
 3NS  C1   H1A   single    0.970  0.020  1.090
 3NS  N1   C2    single    1.441  0.020  1.441
 3NS  C2   H2    single    0.970  0.020  1.090
 3NS  C2   H2A   single    0.970  0.020  1.090
 3NS  C3   N1    single    1.345  0.020  1.345
 3NS  N1   HN1   single    0.860  0.020  1.020
 3NS  O1   C3    double    1.225  0.020  1.225
 3NS  C4   C3    single    1.513  0.020  1.513
 3NS  C5   C4    single    1.530  0.020  1.530
 3NS  C4   H4    single    0.970  0.020  1.090
 3NS  C4   H4A   single    0.970  0.020  1.090
 3NS  C7   C5    single    1.520  0.020  1.520
 3NS  C5   C6    single    1.548  0.020  1.548
 3NS  C5   H5    single    0.970  0.020  1.090
 3NS  C6   C8    single    1.525  0.020  1.525
 3NS  C6   C9    single    1.526  0.020  1.526
 3NS  C6   H6    single    0.970  0.020  1.090
 3NS  O2   C7    double    1.224  0.020  1.224
 3NS  N2   C7    single    1.344  0.020  1.344
 3NS  C8   H8    single    0.970  0.020  1.090
 3NS  C8   H8A   single    0.970  0.020  1.090
 3NS  C8   H8B   single    0.970  0.020  1.090
 3NS  C9   H9    single    0.970  0.020  1.090
 3NS  C9   H9A   single    0.970  0.020  1.090
 3NS  C9   H9B   single    0.970  0.020  1.090
 3NS  C10  N2    single    1.448  0.020  1.448
 3NS  N2   HN2   single    0.860  0.020  1.020
 3NS  C11  C10   single    1.522  0.020  1.522
 3NS  C13  C10   single    1.521  0.020  1.521
 3NS  C10  H10   single    0.970  0.020  1.090
 3NS  C12  C11   single    1.506  0.020  1.506
 3NS  C11  H11   single    0.970  0.020  1.090
 3NS  C11  H11A  single    0.970  0.020  1.090
 3NS  O4   C12   double    1.205  0.020  1.205
 3NS  O3   C12   single    1.329  0.020  1.329
 3NS  O3   HO3   single    0.850  0.020  0.980
 3NS  O5   C13   single    1.408  0.020  1.408
 3NS  C13  H13   single    0.970  0.020  1.090
 3NS  C13  H13A  single    0.970  0.020  1.090
 3NS  O5   HO5   single    0.850  0.020  0.980
 3NS  C19  C14   aromatic  1.403  0.020  1.403
 3NS  C15  C14   aromatic  1.394  0.020  1.394
 3NS  C14  N3    aromatic  1.375  0.020  1.375
 3NS  C16  C15   aromatic  1.385  0.020  1.385
 3NS  C15  H15   single    0.930  0.020  1.080
 3NS  C17  C16   aromatic  1.403  0.020  1.403
 3NS  C16  H16   single    0.930  0.020  1.080
 3NS  C17  C18   aromatic  1.386  0.020  1.386
 3NS  C17  H17   single    0.930  0.020  1.080
 3NS  C18  C19   aromatic  1.390  0.020  1.390
 3NS  C18  H18   single    0.930  0.020  1.080
 3NS  C19  N4    aromatic  1.373  0.020  1.373
 3NS  C20  N3    aromatic  1.306  0.020  1.306
 3NS  N4   C20   aromatic  1.365  0.020  1.365
 3NS  C20  C21   single    1.484  0.020  1.484
 3NS  C21  H21   single    0.970  0.020  1.090
 3NS  C21  H21A  single    0.970  0.020  1.090
 3NS  C21  H21B  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
 3NS  H1A   C1   H1    107.00  3.000
 3NS  H1A   C1   N4    109.08  3.000
 3NS  H1    C1   N4    108.50  3.000
 3NS  H1A   C1   C2    110.37  3.000
 3NS  H1    C1   C2    110.28  3.000
 3NS  N4    C1   C2    111.49  3.000
 3NS  H2A   C2   H2    107.21  3.000
 3NS  H2A   C2   N1    108.28  3.000
 3NS  H2    C2   N1    109.42  3.000
 3NS  H2A   C2   C1    110.04  3.000
 3NS  H2    C2   C1    110.09  3.000
 3NS  N1    C2   C1    111.68  3.000
 3NS  HN1   N1   C3    119.15  3.000
 3NS  HN1   N1   C2    118.16  3.000
 3NS  C3    N1   C2    122.62  3.000
 3NS  N3    C14  C19   109.85  3.000
 3NS  N3    C14  C15   130.42  3.000
 3NS  C19   C14  C15   119.74  3.000
 3NS  H15   C15  C16   121.16  3.000
 3NS  H15   C15  C14   120.88  3.000
 3NS  C16   C15  C14   117.96  3.000
 3NS  H16   C16  C17   119.11  3.000
 3NS  H16   C16  C15   119.45  3.000
 3NS  C17   C16  C15   121.44  3.000
 3NS  H17   C17  C18   119.23  3.000
 3NS  H17   C17  C16   119.29  3.000
 3NS  C18   C17  C16   121.48  3.000
 3NS  H18   C18  C19   122.07  3.000
 3NS  H18   C18  C17   121.40  3.000
 3NS  C19   C18  C17   116.53  3.000
 3NS  N4    C19  C18   132.13  3.000
 3NS  N4    C19  C14   105.01  3.000
 3NS  C18   C19  C14   122.85  3.000
 3NS  C20   N3   C14   105.43  3.000
 3NS  C20   N4   C19   106.90  3.000
 3NS  C20   N4   C1    127.86  3.000
 3NS  C19   N4   C1    125.19  3.000
 3NS  C21   C20  N4    122.02  3.000
 3NS  C21   C20  N3    125.19  3.000
 3NS  N4    C20  N3    112.80  3.000
 3NS  H21B  C21  H21A  108.41  3.000
 3NS  H21B  C21  H21   107.40  3.000
 3NS  H21A  C21  H21   108.29  3.000
 3NS  H21B  C21  C20   111.48  3.000
 3NS  H21A  C21  C20   109.59  3.000
 3NS  H21   C21  C20   111.56  3.000
 3NS  C4    C3   O1    121.90  3.000
 3NS  C4    C3   N1    115.60  3.000
 3NS  O1    C3   N1    122.50  3.000
 3NS  H4A   C4   H4    106.76  3.000
 3NS  H4A   C4   C5    109.61  3.000
 3NS  H4    C4   C5    110.69  3.000
 3NS  H4A   C4   C3    106.94  3.000
 3NS  H4    C4   C3    111.36  3.000
 3NS  C5    C4   C3    111.29  3.000
 3NS  H5    C5   C7    108.60  3.000
 3NS  H5    C5   C6    106.95  3.000
 3NS  C7    C5   C6    111.72  3.000
 3NS  H5    C5   C4    107.50  3.000
 3NS  C6    C5   C4    112.41  3.000
 3NS  C7    C5   C4    109.47  3.000
 3NS  H6    C6   C9    106.38  3.000
 3NS  H6    C6   C8    107.61  3.000
 3NS  C9    C6   C8    110.60  3.000
 3NS  H6    C6   C5    105.71  3.000
 3NS  C9    C6   C5    112.29  3.000
 3NS  C8    C6   C5    113.75  3.000
 3NS  N2    C7   O2    122.86  3.000
 3NS  N2    C7   C5    114.99  3.000
 3NS  O2    C7   C5    122.15  3.000
 3NS  H8B   C8   H8A   107.15  3.000
 3NS  H8B   C8   H8    107.75  3.000
 3NS  H8A   C8   H8    107.45  3.000
 3NS  H8B   C8   C6    112.52  3.000
 3NS  H8A   C8   C6    109.91  3.000
 3NS  H8    C8   C6    111.83  3.000
 3NS  H9B   C9   H9A   107.26  3.000
 3NS  H9B   C9   H9    107.74  3.000
 3NS  H9A   C9   H9    107.41  3.000
 3NS  H9B   C9   C6    112.59  3.000
 3NS  H9A   C9   C6    110.12  3.000
 3NS  H9    C9   C6    111.49  3.000
 3NS  H13A  C13  H13   107.07  3.000
 3NS  H13A  C13  C10   108.61  3.000
 3NS  H13   C13  C10   108.36  3.000
 3NS  H13A  C13  O5    111.78  3.000
 3NS  H13   C13  O5    111.77  3.000
 3NS  C10   C13  O5    109.15  3.000
 3NS  HN2   N2   C10   117.25  3.000
 3NS  HN2   N2   C7    118.02  3.000
 3NS  C10   N2   C7    123.86  3.000
 3NS  H10   C10  C11   108.91  3.000
 3NS  H10   C10  N2    107.81  3.000
 3NS  C11   C10  N2    109.38  3.000
 3NS  H10   C10  C13   106.95  3.000
 3NS  C11   C10  C13   112.20  3.000
 3NS  N2    C10  C13   111.45  3.000
 3NS  H11A  C11  H11   105.79  3.000
 3NS  H11A  C11  C12   107.11  3.000
 3NS  H11   C11  C12   109.87  3.000
 3NS  H11A  C11  C10   109.60  3.000
 3NS  H11   C11  C10   111.48  3.000
 3NS  C12   C11  C10   112.66  3.000
 3NS  O4    C12  O3    123.15  3.000
 3NS  O3    C12  C11   111.76  3.000
 3NS  O4    C12  C11   125.08  3.000
 3NS  HO3   O3   C12   109.87  3.000
 3NS  HO5   O5   C13   108.55  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
 3NS  CONST_01  C17  C18  C19  C14     0.00   0.0  0
 3NS  CONST_02  C20  N4   C19  C14     0.00   0.0  0
 3NS  CONST_03  C17  C16  C15  C14     0.00   0.0  0
 3NS  CONST_04  N4   C20  N3   C14     0.00   0.0  0
 3NS  CONST_05  C18  C19  C14  C15     0.00   0.0  0
 3NS  CONST_06  N4   C19  C14  C15   180.00   0.0  0
 3NS  CONST_07  C20  N3   C14  C15   180.00   0.0  0
 3NS  CONST_08  C18  C17  C16  C15     0.00   0.0  0
 3NS  CONST_09  C19  C14  C15  C16     0.00   0.0  0
 3NS  CONST_10  N3   C14  C15  C16   180.00   0.0  0
 3NS  CONST_11  C19  C18  C17  C16     0.00   0.0  0
 3NS  CONST_12  N4   C19  C18  C17   180.00   0.0  0
 3NS  CONST_13  N3   C14  C19  C18   180.00   0.0  0
 3NS  CONST_14  C20  N4   C19  C18   180.00   0.0  0
 3NS  CONST_15  C20  N3   C14  C19     0.00   0.0  0
 3NS  CONST_16  N3   C20  N4   C19     0.00   0.0  0
 3NS  CONST_17  N4   C19  C14  N3      0.00   0.0  0
 3NS  CONST_18  C14  C19  N4   C1    180.00   0.0  0
 3NS  CONST_19  C18  C19  N4   C1      0.00   0.0  0
 3NS  CONST_20  N3   C20  N4   C1    180.00   0.0  0
 3NS  CONST_21  C21  C20  N3   C14   180.00   0.0  0
 3NS  CONST_22  C21  C20  N4   C19   180.00   0.0  0
 3NS  CONST_23  H18  C18  C19  C14   180.00   0.0  0
 3NS  CONST_24  H16  C16  C15  C14   180.00   0.0  0
 3NS  CONST_25  H17  C17  C16  C15   180.00   0.0  0
 3NS  CONST_26  H15  C15  C16  C17   180.00   0.0  0
 3NS  CONST_27  O1   C3   N1   C2      0.00   0.0  0
 3NS  CONST_28  C4   C3   N1   C2    180.00   0.0  0
 3NS  CONST_29  C10  N2   C7   C5    180.00   0.0  0
 3NS  CONST_30  C10  N2   C7   O2      0.00   0.0  0
 3NS  CONST_31  HN1  N1   C3   O1    180.00   0.0  0
 3NS  CONST_32  HN2  N2   C7   C5      0.00   0.0  0
 3NS  CONST_33  HO3  O3   C12  C11   180.00   0.0  0
 3NS  Var_01    C19  N4   C1   C2     78.60  30.0  2
 3NS  Var_02    H21  C21  C20  N3   -120.54  30.0  2
 3NS  Var_03    N4   C1   C2   N1   -171.50  30.0  3
 3NS  Var_04    C3   N1   C2   C1     81.34  30.0  2
 3NS  Var_05    C5   C4   C3   N1   -123.96  30.0  2
 3NS  Var_06    O4   C12  C11  C10   -18.84  30.0  1
 3NS  Var_07    H8   C8   C6   C5     67.36  30.0  3
 3NS  Var_08    H9   C9   C6   C5     52.38  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
 3NS  chir_01  C5   C4  C7   C6   positiv
 3NS  chir_02  C10  N2  C11  C13  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
 3NS  plan-1  C1   0.020
 3NS  plan-1  C14  0.020
 3NS  plan-1  C15  0.020
 3NS  plan-1  C16  0.020
 3NS  plan-1  C17  0.020
 3NS  plan-1  C18  0.020
 3NS  plan-1  C19  0.020
 3NS  plan-1  N3   0.020
 3NS  plan-1  N4   0.020
 3NS  plan-1  C20  0.020
 3NS  plan-1  C21  0.020
 3NS  plan-1  H15  0.020
 3NS  plan-1  H16  0.020
 3NS  plan-1  H17  0.020
 3NS  plan-1  H18  0.020
 3NS  plan-2  C2   0.020
 3NS  plan-2  N1   0.020
 3NS  plan-2  C3   0.020
 3NS  plan-2  O1   0.020
 3NS  plan-2  C4   0.020
 3NS  plan-2  HN1  0.020
 3NS  plan-3  C5   0.020
 3NS  plan-3  C7   0.020
 3NS  plan-3  O2   0.020
 3NS  plan-3  N2   0.020
 3NS  plan-3  C10  0.020
 3NS  plan-3  HN2  0.020
 3NS  plan-4  C11  0.020
 3NS  plan-4  C12  0.020
 3NS  plan-4  O3   0.020
 3NS  plan-4  O4   0.020
 3NS  plan-4  HO3  0.020

