# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 20:15:11 2022
#   Inital geometry file: a 105 line input string
#   Ligand name: (2~{S},6~{S})-2-azanyl-6-[[(4~{R})-4-azanyl-5-oxidanyl-5-oxidanylidene-pentanoyl]amino]heptanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCC[C@H](NC(=O)CC[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
 S2K  S2K  "(2~{S},6~{S})-2-azanyl-6-[[(4~{R})-4-azanyl-5-oxidanyl-5-oxidanylidene-pentanoyl]amino]heptanedioic acid"  ligand  40  22  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_S2K
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
 S2K  C10  C  CH2    0  -0.432  -11.5567  11.6213  -0.0020
 S2K  C01  C  C      0   0.410  -14.3064  11.5094   2.0485
 S2K  N01  N  NH2    0  -0.787   -9.5490  10.5613   0.9189
 S2K  C02  C  CH1    0  -0.156  -13.6841  12.9325   1.8825
 S2K  N02  N  NH1    0  -0.651  -14.4552  13.8810   2.6885
 S2K  N14  N  NH2    0  -0.800  -14.7575  18.1648   6.8383
 S2K  C03  C  CH2    0  -0.442  -14.5967  16.2044   5.3059
 S2K  C04  C  CH2    0  -0.435  -12.1713  13.0421   2.0857
 S2K  O04  O  O      0  -0.620  -12.5484   8.8262  -0.2216
 S2K  O05  O  OC    -1  -0.605  -10.4058   8.5371  -0.7707
 S2K  C06  C  C      0   0.537  -14.3951  14.0490   4.0178
 S2K  C07  C  CH1    0  -0.171  -15.5061  17.1882   6.0565
 S2K  C08  C  C      0   0.399  -16.4314  17.9215   5.0584
 S2K  C09  C  CH2    0  -0.431  -11.3896  12.9237   0.7755
 S2K  O09  O  O      0  -0.607  -15.9232  18.8879   4.4520
 S2K  C11  C  CH1    0  -0.217  -10.9718  10.3732   0.6669
 S2K  C12  C  C      0   0.379  -11.3355   9.1269  -0.1827
 S2K  O03  O  OC    -1  -0.608  -17.5850  17.4713   4.9135
 S2K  H1   H  HCH2   0   0.217  -12.6138  11.4452  -0.2135
 S2K  H2   H  HCH2   0   0.204  -11.0780  11.7448  -0.9820
 S2K  H3   H  HNH2   0   0.328   -9.2107   9.7768   1.4631
 S2K  H4   H  HNH2   0   0.317   -9.0608  10.4786   0.0339
 S2K  H6   H  HCH1   0   0.224  -13.8978  13.2455   0.8567
 S2K  H7   H  HNH1   0   0.390  -15.1596  14.4041   2.1965
 S2K  H11  H  HCH2   0   0.221  -13.9121  15.7490   6.0275
 S2K  H12  H  HCH2   0   0.213  -13.9768  16.7625   4.5957
 S2K  H13  H  HCH2   0   0.218  -11.8351  12.2980   2.8074
 S2K  H14  H  HCH2   0   0.214  -11.9328  14.0180   2.5157
 S2K  H18  H  HCH1   0   0.192  -16.1298  16.6064   6.7444
 S2K  H19  H  HCH2   0   0.211  -10.3290  13.0801   0.9836
 S2K  H20  H  HCH2   0   0.205  -11.6916  13.7511   0.1237
 S2K  H21  H  HCH1   0   0.216  -11.4636  10.2579   1.6370
 S2K  O02  O  O      0  -0.586  -13.7510  10.7037   2.8173
 S2K  H8   H  HNH2   0   0.327  -14.0070  17.7025   7.3388
 S2K  O1   O  OC    -1  -0.612  -15.3572  11.3224   1.4029
 S2K  O01  O  O      0  -0.507  -13.6282  13.4366   4.7518
 S2K  C05  C  CH2    0  -0.565  -15.3462  15.0930   4.5727
 S2K  H9   H  HNH2   0   0.324  -14.3143  18.8085   6.1937
 S2K  H15  H  HCH2   0   0.241  -15.9752  15.5130   3.7870
 S2K  H16  H  HCH2   0   0.245  -16.0186  14.5892   5.2742

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
 S2K  C10  C09  single  1.526  0.020  1.526
 S2K  C10  C11  single  1.532  0.020  1.532
 S2K  O04  C12  deloc   1.250  0.020  1.250
 S2K  C09  C04  single  1.530  0.020  1.530
 S2K  N01  C11  single  1.457  0.020  1.457
 S2K  C12  C11  single  1.551  0.020  1.551
 S2K  C12  O05  deloc   1.248  0.020  1.248
 S2K  C01  C02  single  1.562  0.020  1.562
 S2K  C01  O02  deloc   1.245  0.020  1.245
 S2K  C02  C04  single  1.530  0.020  1.530
 S2K  C02  N02  single  1.464  0.020  1.464
 S2K  N02  C06  single  1.341  0.020  1.341
 S2K  O09  C08  deloc   1.249  0.020  1.249
 S2K  C06  O01  double  1.226  0.020  1.226
 S2K  C06  C05  single  1.517  0.020  1.517
 S2K  C05  C03  single  1.528  0.020  1.528
 S2K  C08  O03  deloc   1.247  0.020  1.247
 S2K  C08  C07  single  1.546  0.020  1.546
 S2K  C03  C07  single  1.536  0.020  1.536
 S2K  C07  N14  single  1.458  0.020  1.458
 S2K  C01  O1   deloc   1.247  0.020  1.247
 S2K  C10  H1   single  0.970  0.020  1.090
 S2K  C10  H2   single  0.970  0.020  1.090
 S2K  N01  H3   single  0.890  0.020  1.040
 S2K  N01  H4   single  0.890  0.020  1.040
 S2K  C02  H6   single  0.970  0.020  1.090
 S2K  N02  H7   single  0.860  0.020  1.020
 S2K  N14  H8   single  0.890  0.020  1.040
 S2K  N14  H9   single  0.890  0.020  1.040
 S2K  C03  H11  single  0.970  0.020  1.090
 S2K  C03  H12  single  0.970  0.020  1.090
 S2K  C04  H13  single  0.970  0.020  1.090
 S2K  C04  H14  single  0.970  0.020  1.090
 S2K  C05  H15  single  0.970  0.020  1.090
 S2K  C05  H16  single  0.970  0.020  1.090
 S2K  C07  H18  single  0.970  0.020  1.090
 S2K  C09  H19  single  0.970  0.020  1.090
 S2K  C09  H20  single  0.970  0.020  1.090
 S2K  C11  H21  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
 S2K  H2   C10  H1   105.51  3.000
 S2K  H2   C10  C11  108.36  3.000
 S2K  H1   C10  C11  108.82  3.000
 S2K  H2   C10  C09  108.13  3.000
 S2K  H1   C10  C09  110.01  3.000
 S2K  C11  C10  C09  115.53  3.000
 S2K  O1   C01  O02  126.77  3.000
 S2K  O1   C01  C02  114.66  3.000
 S2K  O02  C01  C02  118.53  3.000
 S2K  H4   N01  H3   104.18  3.000
 S2K  H4   N01  C11  107.98  3.000
 S2K  H3   N01  C11  108.61  3.000
 S2K  H6   C02  C04  107.29  3.000
 S2K  H6   C02  N02  103.17  3.000
 S2K  C04  C02  N02  113.65  3.000
 S2K  H6   C02  C01  106.42  3.000
 S2K  N02  C02  C01  108.77  3.000
 S2K  C04  C02  C01  116.42  3.000
 S2K  H7   N02  C06  116.81  3.000
 S2K  H7   N02  C02  115.88  3.000
 S2K  C06  N02  C02  127.09  3.000
 S2K  H9   N14  H8   106.27  3.000
 S2K  H9   N14  C07  108.01  3.000
 S2K  H8   N14  C07  109.85  3.000
 S2K  H12  C03  H11  106.59  3.000
 S2K  H12  C03  C07  109.00  3.000
 S2K  H11  C03  C07  108.35  3.000
 S2K  H12  C03  C05  109.70  3.000
 S2K  H11  C03  C05  108.71  3.000
 S2K  C07  C03  C05  114.21  3.000
 S2K  H14  C04  H13  106.37  3.000
 S2K  H14  C04  C09  107.13  3.000
 S2K  H13  C04  C09  110.89  3.000
 S2K  H14  C04  C02  109.39  3.000
 S2K  H13  C04  C02  110.12  3.000
 S2K  C09  C04  C02  112.69  3.000
 S2K  C05  C06  N02  114.87  3.000
 S2K  C05  C06  O01  121.13  3.000
 S2K  N02  C06  O01  123.99  3.000
 S2K  H18  C07  C08  108.45  3.000
 S2K  H18  C07  C03  107.68  3.000
 S2K  C08  C07  C03  110.04  3.000
 S2K  H18  C07  N14  108.14  3.000
 S2K  C03  C07  N14  112.78  3.000
 S2K  C08  C07  N14  109.62  3.000
 S2K  O03  C08  O09  126.83  3.000
 S2K  O03  C08  C07  117.23  3.000
 S2K  O09  C08  C07  115.91  3.000
 S2K  H20  C09  H19  105.84  3.000
 S2K  H20  C09  C04  108.06  3.000
 S2K  H19  C09  C04  108.78  3.000
 S2K  H20  C09  C10  108.13  3.000
 S2K  H19  C09  C10  109.01  3.000
 S2K  C04  C09  C10  116.51  3.000
 S2K  H21  C11  C12  107.20  3.000
 S2K  H21  C11  N01  107.41  3.000
 S2K  C12  C11  N01  115.29  3.000
 S2K  H21  C11  C10  107.55  3.000
 S2K  C12  C11  C10  109.02  3.000
 S2K  N01  C11  C10  110.06  3.000
 S2K  C11  C12  O05  117.58  3.000
 S2K  O05  C12  O04  126.46  3.000
 S2K  C11  C12  O04  115.95  3.000
 S2K  H16  C05  H15  106.54  3.000
 S2K  H16  C05  C06  107.62  3.000
 S2K  H15  C05  C06  111.28  3.000
 S2K  H16  C05  C03  109.19  3.000
 S2K  H15  C05  C03  110.40  3.000
 S2K  C06  C05  C03  111.62  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
 S2K  CONST_01  C02  N02  C06  O01     0.00   0.0  0
 S2K  CONST_02  C05  C06  N02  C02   180.00   0.0  0
 S2K  CONST_03  H7   N02  C06  O01   180.00   0.0  0
 S2K  CONST_04  H7   N02  C06  C05     0.00   0.0  0
 S2K  Var_01    C02  C04  C09  C10   -60.29  30.0  3
 S2K  Var_02    C03  C05  C06  O01    58.03  30.0  3
 S2K  Var_03    C03  C05  C06  N02  -120.95  30.0  3
 S2K  Var_04    C11  C10  C09  C04   -67.56  30.0  2
 S2K  Var_05    C07  C03  C05  C06  -171.99  30.0  3
 S2K  Var_06    H13  C04  C09  C10    63.68  30.0  3
 S2K  Var_07    H14  C04  C09  C10   179.35  30.0  3
 S2K  Var_08    H15  C05  C06  O01  -178.14  30.0  3
 S2K  Var_09    H16  C05  C06  O01   -61.77  30.0  3
 S2K  Var_10    H19  C09  C04  C02   176.08  30.0  1
 S2K  Var_11    H20  C09  C04  C02    61.62  30.0  1
 S2K  Var_12    H15  C05  C06  N02     2.88  30.0  3
 S2K  Var_13    H16  C05  C06  N02   119.26  30.0  3
 S2K  Var_14    H1   C10  C09  C04    56.11  30.0  2
 S2K  Var_15    H2   C10  C09  C04   170.85  30.0  2
 S2K  Var_16    H11  C03  C05  C06   -50.88  30.0  3
 S2K  Var_17    H12  C03  C05  C06    65.32  30.0  3
 S2K  Var_18    H15  C05  C03  C07    63.69  30.0  1
 S2K  Var_19    H16  C05  C03  C07   -53.12  30.0  1
 S2K  Var_20    H19  C09  C10  C11    55.95  30.0  3
 S2K  Var_21    H20  C09  C10  C11   170.57  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
 S2K  chir_01  C02  C01  C04  N02  positiv
 S2K  chir_02  C07  N14  C08  C03  negativ
 S2K  chir_03  C11  C10  N01  C12  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
 S2K  plan-1  C02  0.020
 S2K  plan-1  N02  0.020
 S2K  plan-1  C06  0.020
 S2K  plan-1  H7   0.020
 S2K  plan-1  O01  0.020
 S2K  plan-1  C05  0.020
 S2K  plan-2  C01  0.020
 S2K  plan-2  C02  0.020
 S2K  plan-2  O02  0.020
 S2K  plan-2  O1   0.020
 S2K  plan-3  C07  0.020
 S2K  plan-3  C08  0.020
 S2K  plan-3  O09  0.020
 S2K  plan-3  O03  0.020
 S2K  plan-4  O04  0.020
 S2K  plan-4  O05  0.020
 S2K  plan-4  C11  0.020
 S2K  plan-4  C12  0.020

