# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 23:11:29 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: N-acetyl-L-alanyl-N-[(1S,5R)-5-amino-1,5-dicarboxypentyl]-D-glutamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NC(C)=O)C(=O)N[C@H](CCC(=O)N[C@@H](CCC[C@@H](N)C(O)=O)C(O)=O)C(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
 3KS  3KS  N-acetyl-L-alanyl-N-[(1S,5R)-5-amino-1,5-dicarboxypentyl]-D-glutamine  ligand  55  30  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3KS
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
 3KS  C15   C  C      0   0.526  -6.8599   2.7414  -0.3428
 3KS  O8    O  O      0  -0.512  -6.9006   2.7801  -1.5667
 3KS  C16   C  CH3    0  -0.776  -7.9288   3.3805   0.5086
 3KS  N3    N  NH1    0  -0.630  -5.8708   2.1400   0.3347
 3KS  C1    C  CH1    0  -0.199  -4.7473   1.4964  -0.2986
 3KS  C2    C  C      0   0.554  -4.1607   0.4900   0.6902
 3KS  O7    O  O      0  -0.503  -4.3622   0.5919   1.8940
 3KS  C     C  CH3    0  -0.651  -3.6681   2.4982  -0.7193
 3KS  N     N  NH1    0  -0.616  -3.3666  -0.4321   0.1431
 3KS  C3    C  CH1    0  -0.201  -2.7820  -1.5174   0.8968
 3KS  C4    C  C      0   0.416  -3.7886  -2.6698   1.1633
 3KS  O1    O  O      0  -0.592  -4.8970  -2.6086   0.6079
 3KS  C5    C  CH2    0  -0.457  -1.5393  -2.0324   0.1730
 3KS  C6    C  CH2    0  -0.564  -0.4369  -0.9842   0.0651
 3KS  C7    C  C      0   0.560   0.7401  -1.4768  -0.7494
 3KS  O6    O  O      0  -0.523   0.5841  -1.9818  -1.8567
 3KS  O     O  OC    -1  -0.615  -3.3669  -3.5648   1.9223
 3KS  C9    C  C      0   0.406   3.2741  -3.3215  -0.7529
 3KS  C8    C  CH1    0  -0.177   3.1597  -1.7762  -0.8167
 3KS  C10   C  CH2    0  -0.462   4.3760  -1.1300  -0.1547
 3KS  C11   C  CH2    0  -0.399   4.4220   0.3895  -0.2691
 3KS  C12   C  CH2    0  -0.419   5.7159   0.9657   0.2904
 3KS  C13   C  CH1    0  -0.210   5.8216   2.4893   0.1923
 3KS  C14   C  C      0   0.381   7.2485   2.9306   0.6040
 3KS  O3    O  O      0  -0.596   2.5396  -3.9265   0.0452
 3KS  O2    O  OC    -1  -0.621   4.1386  -3.8130  -1.5073
 3KS  O5    O  O      0  -0.609   7.3754   3.5784   1.6621
 3KS  O4    O  OC    -1  -0.626   8.1702   2.5804  -0.1641
 3KS  N1    N  NH1    0  -0.627   1.9483  -1.2771  -0.2093
 3KS  N2    N  NH2    0  -0.785   4.7342   3.1139   0.9308
 3KS  H161  H  HCH3   0   0.263  -8.9075   3.0195   0.1948
 3KS  H162  H  HCH3   0   0.248  -7.8127   3.1874   1.5734
 3KS  H163  H  HCH3   0   0.265  -7.9155   4.4595   0.3518
 3KS  H31   H  HNH1   0   0.396  -5.8794   2.1425   1.3431
 3KS  H11   H  HCH1   0   0.271  -5.1004   0.9651  -1.1858
 3KS  HC1   H  HCH3   0   0.248  -4.0974   3.2591  -1.3690
 3KS  HC2   H  HCH3   0   0.234  -3.2355   2.9910   0.1518
 3KS  HC3   H  HCH3   0   0.236  -2.8668   2.0044  -1.2684
 3KS  HN1   H  HNH1   0   0.392  -3.3852  -0.5300  -0.8608
 3KS  H32   H  HCH1   0   0.241  -2.4733  -1.1190   1.8672
 3KS  H51   H  HCH2   0   0.248  -1.1684  -2.8995   0.7204
 3KS  H52   H  HCH2   0   0.232  -1.8161  -2.3853  -0.8247
 3KS  H61   H  HCH2   0   0.258  -0.8194  -0.0874  -0.4322
 3KS  H62   H  HCH2   0   0.243  -0.1249  -0.6721   1.0646
 3KS  H81   H  HCH1   0   0.224   3.1559  -1.4842  -1.8715
 3KS  H101  H  HCH2   0   0.216   4.4133  -1.4217   0.9025
 3KS  H102  H  HCH2   0   0.230   5.2684  -1.5560  -0.6184
 3KS  H111  H  HCH2   0   0.202   4.3279   0.6743  -1.3238
 3KS  H112  H  HCH2   0   0.215   3.5706   0.8405   0.2440
 3KS  H121  H  HCH2   0   0.202   5.8231   0.6686   1.3422
 3KS  H122  H  HCH2   0   0.216   6.5647   0.5237  -0.2368
 3KS  H131  H  HCH1   0   0.204   5.6945   2.7586  -0.8642
 3KS  H12   H  HNH1   0   0.386   1.9933  -0.9685   0.7483
 3KS  H21   H  HNH2   0   0.321   4.8947   2.9555   1.9196
 3KS  H22   H  HNH2   0   0.332   4.8080   4.1189   0.8259

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
 3KS  O7   C2    double  1.225  0.020  1.225
 3KS  N2   C13   single  1.455  0.020  1.455
 3KS  O8   C15   double  1.225  0.020  1.225
 3KS  C13  C12   single  1.530  0.020  1.530
 3KS  C13  C14   single  1.549  0.020  1.549
 3KS  C12  C11   single  1.523  0.020  1.523
 3KS  C2   N     single  1.334  0.020  1.334
 3KS  C2   C1    single  1.528  0.020  1.528
 3KS  O3   C9    deloc   1.242  0.020  1.242
 3KS  C    C1    single  1.531  0.020  1.531
 3KS  C10  C11   single  1.525  0.020  1.525
 3KS  C10  C8    single  1.528  0.020  1.528
 3KS  C15  C16   single  1.509  0.020  1.509
 3KS  C15  N3    single  1.341  0.020  1.341
 3KS  N    C3    single  1.445  0.020  1.445
 3KS  N1   C8    single  1.444  0.020  1.444
 3KS  N1   C7    single  1.338  0.020  1.338
 3KS  C1   N3    single  1.441  0.020  1.441
 3KS  C9   C8    single  1.551  0.020  1.551
 3KS  C9   O2    deloc   1.248  0.020  1.248
 3KS  C14  O5    deloc   1.247  0.020  1.247
 3KS  C14  O4    deloc   1.250  0.020  1.250
 3KS  C6   C7    single  1.514  0.020  1.514
 3KS  C6   C5    single  1.525  0.020  1.525
 3KS  C7   O6    double  1.227  0.020  1.227
 3KS  O1   C4    deloc   1.241  0.020  1.241
 3KS  C3   C5    single  1.528  0.020  1.528
 3KS  C3   C4    single  1.553  0.020  1.553
 3KS  C4   O     deloc   1.247  0.020  1.247
 3KS  C16  H163  single  0.970  0.020  1.090
 3KS  C16  H162  single  0.970  0.020  1.090
 3KS  C16  H161  single  0.970  0.020  1.090
 3KS  N3   H31   single  0.860  0.020  1.020
 3KS  C1   H11   single  0.970  0.020  1.090
 3KS  C    HC1   single  0.970  0.020  1.090
 3KS  C    HC2   single  0.970  0.020  1.090
 3KS  C    HC3   single  0.970  0.020  1.090
 3KS  N    HN1   single  0.860  0.020  1.020
 3KS  C3   H32   single  0.970  0.020  1.090
 3KS  C5   H51   single  0.970  0.020  1.090
 3KS  C5   H52   single  0.970  0.020  1.090
 3KS  C6   H62   single  0.970  0.020  1.090
 3KS  C6   H61   single  0.970  0.020  1.090
 3KS  N1   H12   single  0.860  0.020  1.020
 3KS  C8   H81   single  0.970  0.020  1.090
 3KS  C10  H101  single  0.970  0.020  1.090
 3KS  C10  H102  single  0.970  0.020  1.090
 3KS  C11  H111  single  0.970  0.020  1.090
 3KS  C11  H112  single  0.970  0.020  1.090
 3KS  C12  H121  single  0.970  0.020  1.090
 3KS  C12  H122  single  0.970  0.020  1.090
 3KS  C13  H131  single  0.970  0.020  1.090
 3KS  N2   H22   single  0.890  0.020  1.040
 3KS  N2   H21   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
 3KS  N3    C15  C16   115.30  3.000
 3KS  N3    C15  O8    122.90  3.000
 3KS  C16   C15  O8    121.79  3.000
 3KS  H163  C16  H162  108.35  3.000
 3KS  H162  C16  H161  108.59  3.000
 3KS  H163  C16  H161  107.30  3.000
 3KS  H161  C16  C15   109.49  3.000
 3KS  H162  C16  C15   113.67  3.000
 3KS  H163  C16  C15   109.24  3.000
 3KS  H31   N3   C1    116.56  3.000
 3KS  H31   N3   C15   119.85  3.000
 3KS  C1    N3   C15   123.58  3.000
 3KS  H11   C1   C     108.83  3.000
 3KS  H11   C1   C2    109.22  3.000
 3KS  C     C1   C2    109.76  3.000
 3KS  H11   C1   N3    108.78  3.000
 3KS  C     C1   N3    112.20  3.000
 3KS  C2    C1   N3    108.00  3.000
 3KS  N     C2   O7    123.95  3.000
 3KS  N     C2   C1    114.73  3.000
 3KS  O7    C2   C1    121.20  3.000
 3KS  HC3   C    HC2   108.40  3.000
 3KS  HC3   C    HC1   107.81  3.000
 3KS  HC2   C    HC1   108.50  3.000
 3KS  HC3   C    C1    111.12  3.000
 3KS  HC2   C    C1    110.84  3.000
 3KS  HC1   C    C1    110.07  3.000
 3KS  HN1   N    C3    116.98  3.000
 3KS  HN1   N    C2    117.66  3.000
 3KS  C3    N    C2    123.09  3.000
 3KS  H32   C3   C5    108.28  3.000
 3KS  H32   C3   C4    107.52  3.000
 3KS  C5    C3   C4    111.00  3.000
 3KS  H32   C3   N     107.67  3.000
 3KS  C4    C3   N     112.62  3.000
 3KS  C5    C3   N     109.58  3.000
 3KS  O     C4   O1    127.57  3.000
 3KS  O     C4   C3    114.69  3.000
 3KS  O1    C4   C3    117.73  3.000
 3KS  H52   C5   H51   106.70  3.000
 3KS  H52   C5   C6    109.88  3.000
 3KS  H51   C5   C6    109.64  3.000
 3KS  H52   C5   C3    109.58  3.000
 3KS  H51   C5   C3    107.88  3.000
 3KS  C6    C5   C3    112.95  3.000
 3KS  H62   C6   H61   106.34  3.000
 3KS  H61   C6   C7    107.09  3.000
 3KS  H62   C6   C7    111.29  3.000
 3KS  H61   C6   C5    110.04  3.000
 3KS  H62   C6   C5    109.76  3.000
 3KS  C7    C6   C5    112.12  3.000
 3KS  N1    C7   O6    122.71  3.000
 3KS  O6    C7   C6    121.37  3.000
 3KS  N1    C7   C6    115.87  3.000
 3KS  O2    C9   O3    127.31  3.000
 3KS  O2    C9   C8    114.74  3.000
 3KS  O3    C9   C8    117.92  3.000
 3KS  H81   C8   N1    108.07  3.000
 3KS  H81   C8   C10   107.91  3.000
 3KS  N1    C8   C10   109.84  3.000
 3KS  H81   C8   C9    107.80  3.000
 3KS  N1    C8   C9    112.88  3.000
 3KS  C10   C8   C9    110.17  3.000
 3KS  H102  C10  H101  106.12  3.000
 3KS  H102  C10  C11   109.40  3.000
 3KS  H101  C10  C11   109.65  3.000
 3KS  H102  C10  C8    107.55  3.000
 3KS  H101  C10  C8    109.39  3.000
 3KS  C11   C10  C8    114.39  3.000
 3KS  H112  C11  H111  106.13  3.000
 3KS  H112  C11  C12   109.49  3.000
 3KS  H111  C11  C12   109.15  3.000
 3KS  H112  C11  C10   110.67  3.000
 3KS  H111  C11  C10   109.18  3.000
 3KS  C12   C11  C10   112.03  3.000
 3KS  H122  C12  H121  106.07  3.000
 3KS  H122  C12  C13   108.55  3.000
 3KS  H121  C12  C13   108.90  3.000
 3KS  H122  C12  C11   109.25  3.000
 3KS  H121  C12  C11   109.42  3.000
 3KS  C13   C12  C11   114.32  3.000
 3KS  H131  C13  N2    107.26  3.000
 3KS  H131  C13  C14   107.01  3.000
 3KS  N2    C13  C14   115.53  3.000
 3KS  H131  C13  C12   107.34  3.000
 3KS  C14   C13  C12   109.28  3.000
 3KS  N2    C13  C12   110.06  3.000
 3KS  O4    C14  O5    126.29  3.000
 3KS  O4    C14  C13   115.85  3.000
 3KS  O5    C14  C13   117.85  3.000
 3KS  H12   N1   C8    117.93  3.000
 3KS  H12   N1   C7    118.01  3.000
 3KS  C8    N1   C7    122.41  3.000
 3KS  H22   N2   H21   104.15  3.000
 3KS  H21   N2   C13   108.03  3.000
 3KS  H22   N2   C13   108.59  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
 3KS  CONST_01  C1    N3   C15  O8      0.00   0.0  0
 3KS  CONST_02  C1    N3   C15  C16   180.00   0.0  0
 3KS  CONST_03  C3    N    C2   C1    180.00   0.0  0
 3KS  CONST_04  C3    N    C2   O7      0.00   0.0  0
 3KS  CONST_05  C8    N1   C7   C6    180.00   0.0  0
 3KS  CONST_06  C8    N1   C7   O6      0.00   0.0  0
 3KS  CONST_07  H31   N3   C15  O8    180.00   0.0  0
 3KS  CONST_08  HN1   N    C2   C1      0.00   0.0  0
 3KS  CONST_09  H12   N1   C7   C6      0.00   0.0  0
 3KS  Var_01    C7    C6   C5   C3   -175.46  30.0  2
 3KS  Var_02    N1    C7   C6   C5   -132.42  30.0  3
 3KS  Var_03    C12   C11  C10  C8   -174.60  30.0  3
 3KS  Var_04    C13   C12  C11  C10   179.57  30.0  1
 3KS  Var_05    H163  C16  C15  O8    -64.30  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
 3KS  chir_01  C1   C2  C    N3   positiv
 3KS  chir_02  C3   N   C5   C4   positiv
 3KS  chir_03  C8   N1  C10  C9   negativ
 3KS  chir_04  C13  N2  C12  C14  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
 3KS  plan-1  C15  0.020
 3KS  plan-1  O8   0.020
 3KS  plan-1  C16  0.020
 3KS  plan-1  N3   0.020
 3KS  plan-1  C1   0.020
 3KS  plan-1  H31  0.020
 3KS  plan-2  C1   0.020
 3KS  plan-2  C2   0.020
 3KS  plan-2  O7   0.020
 3KS  plan-2  N    0.020
 3KS  plan-2  C3   0.020
 3KS  plan-2  HN1  0.020
 3KS  plan-3  C6   0.020
 3KS  plan-3  C7   0.020
 3KS  plan-3  O6   0.020
 3KS  plan-3  C8   0.020
 3KS  plan-3  N1   0.020
 3KS  plan-3  H12  0.020
 3KS  plan-4  C3   0.020
 3KS  plan-4  C4   0.020
 3KS  plan-4  O1   0.020
 3KS  plan-4  O    0.020
 3KS  plan-5  C9   0.020
 3KS  plan-5  C8   0.020
 3KS  plan-5  O3   0.020
 3KS  plan-5  O2   0.020
 3KS  plan-6  C13  0.020
 3KS  plan-6  C14  0.020
 3KS  plan-6  O5   0.020
 3KS  plan-6  O4   0.020

