# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 23:42:28 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: amino{[4-({N-[(2S)-3-carboxy-2-hydroxypropanoyl]-L-leucyl}amino)butyl]amino}methaniminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](NC(=O)[C@@H](O)CC(O)=O)C(=O)NCCCCNC(N)=[NH2+]
#
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
 E64  E64  amino{[4-({N-[(2S)-3-carboxy-2-hydroxypropanoyl]-L-leucyl}amino)butyl]amino}methaniminium  ligand  54  25  .  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_E64
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
 E64  C1    C  C      0   0.423  14.5402  16.8365  15.9408
 E64  O1    O  O      0  -0.747  13.7211  16.5168  16.8060
 E64  O2    O  OC    -1  -0.547  14.8074  18.0266  15.5920
 E64  C2    C  CH2    0  -0.609  15.3383  15.7430  15.2250
 E64  C3    C  CH1    0  -0.089  15.0788  15.7370  13.7256
 E64  O3    O  OH1    0  -0.613  13.7834  15.2461  13.4684
 E64  C4    C  C      0   0.463  16.1726  14.9762  12.9737
 E64  O4    O  O      0  -0.475  17.3535  15.2116  13.1867
 E64  N1    N  NH1    0  -0.588  15.7535  14.1026  12.0461
 E64  C6    C  CH1    0  -0.146  16.6512  13.5235  11.0690
 E64  C7    C  CH2    0  -0.431  16.0193  12.2986  10.4206
 E64  C8    C  CH1    0  -0.193  15.8103  11.1132  11.3647
 E64  C9    C  CH3    0  -0.673  15.0093  10.0288  10.6501
 E64  C10   C  CH3    0  -0.654  17.1330  10.5508  11.8763
 E64  C11   C  C      0   0.562  16.9673  14.5916  10.0180
 E64  O5    O  O      0  -0.592  16.1000  14.9970   9.2563
 E64  N2    N  NH1    0  -0.578  18.2334  15.0280  10.0189
 E64  C12   C  CH2    0  -0.275  18.7303  16.1058   9.1915
 E64  C13   C  CH2    0  -0.515  18.8785  17.4228   9.9475
 E64  C14   C  CH2    0  -0.480  17.5661  17.9600  10.5021
 E64  C15   C  CH2    0  -0.286  17.7337  19.3423  11.1237
 E64  N3    N  NH1    0  -0.648  16.4953  19.8734  11.6651
 E64  C16   C  C      0   0.778  15.9441  19.4663  12.8084
 E64  N4    N  NH2    0  -0.792  16.6263  18.8083  13.7264
 E64  N5    N  NC2    1  -0.750  14.6671  19.7617  13.0603
 E64  H21   H  HCH2   0   0.285  16.4009  15.9308  15.3906
 E64  H22   H  HCH2   0   0.250  15.1126  14.7561  15.6357
 E64  H3    H  HCH1   0   0.239  15.1740  16.7641  13.3535
 E64  HO3   H  HOH1   0   0.466  13.3707  15.7812  12.7850
 E64  HN1   H  HNH1   0   0.388  14.7602  14.0041  11.9031
 E64  H6    H  HCH1   0   0.226  17.5687  13.2295  11.5822
 E64  H71   H  HCH2   0   0.220  15.0656  12.5900   9.9702
 E64  H72   H  HCH2   0   0.257  16.6611  11.9802   9.5923
 E64  H8    H  HCH1   0   0.170  15.2273  11.4497  12.2297
 E64  H91   H  HCH3   0   0.239  14.8572   9.1603  11.2926
 E64  H92   H  HCH3   0   0.237  14.0280  10.3949  10.3436
 E64  H93   H  HCH3   0   0.223  15.5321   9.6891   9.7529
 E64  H101  H  HCH3   0   0.209  16.9628   9.7055  12.5446
 E64  H102  H  HCH3   0   0.231  17.7520  10.1977  11.0477
 E64  H103  H  HCH3   0   0.230  17.7140  11.2870  12.4339
 E64  HN2   H  HNH1   0   0.388  18.8541  14.6692  10.7260
 E64  H121  H  HCH2   0   0.270  19.7001  15.8094   8.7882
 E64  H122  H  HCH2   0   0.253  18.0537  16.2270   8.3469
 E64  H131  H  HCH2   0   0.276  19.6024  17.2958  10.7588
 E64  H132  H  HCH2   0   0.270  19.3182  18.1488   9.2569
 E64  H141  H  HCH2   0   0.229  16.8197  18.0174   9.7043
 E64  H142  H  HCH2   0   0.203  17.1768  17.2710  11.2557
 E64  H151  H  HCH2   0   0.198  18.5015  19.3355  11.8994
 E64  H152  H  HCH2   0   0.312  18.0781  20.0560  10.3755
 E64  HN3   H  HNH1   0   0.426  15.8874  20.3446  11.0137
 E64  HN41  H  HNH2   0   0.420  16.0897  18.4360  14.5396
 E64  HN42  H  HNH2   0   0.432  17.6071  18.6121  13.6245
 E64  HN51  H  HNC2   0   0.460  14.0533  20.0541  12.3194
 E64  HN52  H  HNC2   0   0.448  14.2436  19.4068  13.9059

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
 E64  C1   O1    deloc   1.234  0.020  1.234
 E64  C1   O2    deloc   1.269  0.020  1.269
 E64  C1   C2    single  1.531  0.020  1.531
 E64  C2   C3    single  1.522  0.020  1.522
 E64  C2   H21   single  0.970  0.020  1.090
 E64  C2   H22   single  0.970  0.020  1.090
 E64  C3   O3    single  1.409  0.020  1.409
 E64  C3   C4    single  1.530  0.020  1.530
 E64  C3   H3    single  0.970  0.020  1.090
 E64  O3   HO3   single  0.850  0.020  0.980
 E64  C4   O4    double  1.223  0.020  1.223
 E64  C4   N1    single  1.341  0.020  1.341
 E64  N1   C6    single  1.448  0.020  1.448
 E64  N1   HN1   single  0.860  0.020  1.020
 E64  C6   C7    single  1.523  0.020  1.523
 E64  C6   C11   single  1.531  0.020  1.531
 E64  C6   H6    single  0.970  0.020  1.090
 E64  C7   C8    single  1.530  0.020  1.530
 E64  C7   H71   single  0.970  0.020  1.090
 E64  C7   H72   single  0.970  0.020  1.090
 E64  C8   C9    single  1.526  0.020  1.526
 E64  C8   C10   single  1.526  0.020  1.526
 E64  C8   H8    single  0.970  0.020  1.090
 E64  C9   H91   single  0.970  0.020  1.090
 E64  C9   H92   single  0.970  0.020  1.090
 E64  C9   H93   single  0.970  0.020  1.090
 E64  C10  H101  single  0.970  0.020  1.090
 E64  C10  H102  single  0.970  0.020  1.090
 E64  C10  H103  single  0.970  0.020  1.090
 E64  C11  O5    double  1.223  0.020  1.223
 E64  C11  N2    single  1.339  0.020  1.339
 E64  N2   C12   single  1.447  0.020  1.447
 E64  N2   HN2   single  0.860  0.020  1.020
 E64  C12  C13   single  1.526  0.020  1.526
 E64  C12  H121  single  0.970  0.020  1.090
 E64  C12  H122  single  0.970  0.020  1.090
 E64  C13  C14   single  1.523  0.020  1.523
 E64  C13  H131  single  0.970  0.020  1.090
 E64  C13  H132  single  0.970  0.020  1.090
 E64  C14  C15   single  1.525  0.020  1.525
 E64  C14  H141  single  0.970  0.020  1.090
 E64  C14  H142  single  0.970  0.020  1.090
 E64  C15  N3    single  1.452  0.020  1.452
 E64  C15  H151  single  0.970  0.020  1.090
 E64  C15  H152  single  0.970  0.020  1.090
 E64  N3   C16   single  1.333  0.020  1.333
 E64  N3   HN3   single  0.890  0.020  1.040
 E64  C16  N4    single  1.320  0.020  1.320
 E64  C16  N5    double  1.335  0.020  1.335
 E64  N4   HN41  single  0.860  0.020  1.020
 E64  N4   HN42  single  0.860  0.020  1.020
 E64  N5   HN51  single  0.890  0.020  1.040
 E64  N5   HN52  single  0.890  0.020  1.040

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
 E64  C2    C1   O2    115.57  3.000
 E64  C2    C1   O1    119.26  3.000
 E64  O2    C1   O1    125.16  3.000
 E64  H22   C2   H21   107.43  3.000
 E64  H22   C2   C3    109.37  3.000
 E64  H21   C2   C3    108.43  3.000
 E64  H22   C2   C1    111.20  3.000
 E64  H21   C2   C1    108.27  3.000
 E64  C3    C2   C1    111.99  3.000
 E64  H3    C3   C4    103.71  3.000
 E64  H3    C3   O3    110.14  3.000
 E64  C4    C3   O3    113.23  3.000
 E64  H3    C3   C2    108.41  3.000
 E64  C4    C3   C2    111.36  3.000
 E64  O3    C3   C2    109.75  3.000
 E64  HO3   O3   C3    109.30  3.000
 E64  N1    C4   O4    123.20  3.000
 E64  N1    C4   C3    116.12  3.000
 E64  O4    C4   C3    120.61  3.000
 E64  HN1   N1   C6    118.42  3.000
 E64  HN1   N1   C4    118.00  3.000
 E64  C6    N1   C4    122.24  3.000
 E64  H6    C6   C11   109.69  3.000
 E64  H6    C6   C7    109.40  3.000
 E64  C11   C6   C7    110.76  3.000
 E64  H6    C6   N1    108.16  3.000
 E64  C11   C6   N1    108.19  3.000
 E64  C7    C6   N1    110.59  3.000
 E64  H72   C7   H71   106.07  3.000
 E64  H72   C7   C8    108.76  3.000
 E64  H71   C7   C8    109.96  3.000
 E64  H72   C7   C6    108.22  3.000
 E64  H71   C7   C6    108.82  3.000
 E64  C8    C7   C6    114.65  3.000
 E64  H8    C8   C10   108.04  3.000
 E64  H8    C8   C9    107.98  3.000
 E64  C10   C8   C9    110.50  3.000
 E64  H8    C8   C7    108.77  3.000
 E64  C10   C8   C7    111.97  3.000
 E64  C9    C8   C7    109.47  3.000
 E64  H93   C9   H92   107.70  3.000
 E64  H93   C9   H91   107.63  3.000
 E64  H92   C9   H91   107.88  3.000
 E64  H93   C9   C8    110.76  3.000
 E64  H92   C9   C8    111.41  3.000
 E64  H91   C9   C8    111.29  3.000
 E64  H103  C10  H102  107.69  3.000
 E64  H103  C10  H101  107.03  3.000
 E64  H102  C10  H101  107.61  3.000
 E64  H103  C10  C8    112.60  3.000
 E64  H102  C10  C8    110.85  3.000
 E64  H101  C10  C8    110.85  3.000
 E64  N2    C11  O5    124.23  3.000
 E64  N2    C11  C6    114.96  3.000
 E64  O5    C11  C6    120.80  3.000
 E64  HN2   N2   C12   117.08  3.000
 E64  HN2   N2   C11   117.84  3.000
 E64  C12   N2   C11   124.55  3.000
 E64  H122  C12  H121  107.20  3.000
 E64  H122  C12  C13   110.40  3.000
 E64  H121  C12  C13   109.35  3.000
 E64  H122  C12  N2    108.24  3.000
 E64  H121  C12  N2    108.31  3.000
 E64  C13   C12  N2    113.15  3.000
 E64  H132  C13  H131  106.20  3.000
 E64  H132  C13  C14   110.01  3.000
 E64  H131  C13  C14   109.93  3.000
 E64  H132  C13  C12   107.40  3.000
 E64  H131  C13  C12   109.35  3.000
 E64  C14   C13  C12   113.66  3.000
 E64  H142  C14  H141  107.03  3.000
 E64  H142  C14  C15   109.24  3.000
 E64  H141  C14  C15   108.95  3.000
 E64  H142  C14  C13   109.62  3.000
 E64  H141  C14  C13   109.93  3.000
 E64  C15   C14  C13   111.94  3.000
 E64  H152  C15  H151  105.64  3.000
 E64  H152  C15  N3    106.61  3.000
 E64  H151  C15  N3    109.71  3.000
 E64  H152  C15  C14   110.39  3.000
 E64  H151  C15  C14   111.19  3.000
 E64  N3    C15  C14   112.94  3.000
 E64  HN3   N3   C16   116.59  3.000
 E64  HN3   N3   C15   116.39  3.000
 E64  C16   N3   C15   124.10  3.000
 E64  N5    C16  N4    118.28  3.000
 E64  N5    C16  N3    119.34  3.000
 E64  N4    C16  N3    122.36  3.000
 E64  HN42  N4   HN41  120.75  3.000
 E64  HN42  N4   C16   122.08  3.000
 E64  HN41  N4   C16   117.03  3.000
 E64  HN52  N5   HN51  117.59  3.000
 E64  HN52  N5   C16   118.77  3.000
 E64  HN51  N5   C16   120.62  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
 E64  CONST_01  C6    N1   C4   C3    180.00   0.0  0
 E64  CONST_02  C6    N1   C4   O4      0.00   0.0  0
 E64  CONST_03  C12   N2   C11  C6    180.00   0.0  0
 E64  CONST_04  C12   N2   C11  O5      0.00   0.0  0
 E64  CONST_07  HN1   N1   C4   C3      0.00   0.0  0
 E64  CONST_08  HN2   N2   C11  C6      0.00   0.0  0
 E64  CONST_09  HN41  N4   C16  N3    180.00   0.0  0
 E64  CONST_10  HN42  N4   C16  N3      0.00   0.0  0
 E64  CONST_12  HN52  N5   C16  N3    180.00   0.0  0
 E64  CONST_13  HN3   N3   C16  N4    180.00   0.0  0
 E64  Var_01    C3    C2   C1   O1    119.13  30.0  3
 E64  Var_02    C9    C8   C7   C6    172.54  30.0  3
 E64  Var_03    C13   C12  N2   C11   101.46  30.0  3
 E64  Var_04    C14   C13  C12  N2    -61.70  30.0  3
 E64  Var_05    C15   C14  C13  C12  -174.15  30.0  3
 E64  Var_06    N3    C15  C14  C13  -179.76  30.0  3
 E64  Var_07    C16   N3   C15  C14    75.48  30.0  3
 E64  Var_08    H91   C9   C8   C7    179.04  30.0  3
 E64  Var_09    H101  C10  C8   C7   -179.82  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
 E64  chir_01  C3  C2  O3  C4   positiv
 E64  chir_02  C6  N1  C7  C11  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
 E64  plan-1  C3    0.020
 E64  plan-1  C4    0.020
 E64  plan-1  O4    0.020
 E64  plan-1  N1    0.020
 E64  plan-1  C6    0.020
 E64  plan-1  HN1   0.020
 E64  plan-2  C6    0.020
 E64  plan-2  C11   0.020
 E64  plan-2  O5    0.020
 E64  plan-2  N2    0.020
 E64  plan-2  C12   0.020
 E64  plan-2  HN2   0.020
 E64  plan-3  C15   0.020
 E64  plan-3  N3    0.020
 E64  plan-3  C16   0.020
 E64  plan-3  N4    0.020
 E64  plan-3  N5    0.020
 E64  plan-3  HN3   0.020
 E64  plan-3  HN41  0.020
 E64  plan-3  HN42  0.020
 E64  plan-3  HN51  0.020
 E64  plan-3  HN52  0.020
 E64  plan-4  C1    0.020
 E64  plan-4  O1    0.020
 E64  plan-4  O2    0.020
 E64  plan-4  C2    0.020

