# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 21:21:03 2022
#   Inital geometry file: a 117 line input string
#   Ligand name: N~5~-[N-(2-{2-[2-(triaza-1,2-dien-2-ium-1-yl)ethoxy]ethoxy}ethyl)carbamimidoyl]-L-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCNC(=N)NCCOCCOCCN=[N+]=N)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
 562  562  N~5~-[N-(2-{2-[2-(triaza-1,2-dien-2-ium-1-yl)ethoxy]ethoxy}ethyl)carbamimidoyl]-L-ornithine  L-peptide  48  23  .  2019-03-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_562
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
 562  N    N  NH2    0  -0.788  -21.6654  19.6985  -23.3829
 562  CA   C  CH1    0  -0.221  -20.8409  20.1492  -22.2684
 562  C    C  C      0   0.390  -20.7044  21.6920  -22.1252
 562  O    O  O      0  -0.612  -19.9005  22.0961  -21.2589
 562  CB   C  CH2    0  -0.423  -19.4724  19.4727  -22.3188
 562  CG   C  CH2    0  -0.441  -19.5264  17.9514  -22.2730
 562  CD   C  CH2    0  -0.228  -18.1354  17.3459  -22.1642
 562  NE   N  NH1    0  -0.665  -18.2052  15.9009  -22.1531
 562  CZ   C  C      0   0.606  -17.0939  15.1542  -21.8691
 562  NH1  N  N      0  -0.733  -15.9980  15.7272  -21.5181
 562  C01  C  CH2    0  -0.177  -18.4374  11.6737  -21.9575
 562  NH2  N  NH1    0  -0.672  -17.2706  13.7888  -21.9144
 562  N08  N  N      0  -0.330  -22.2580   4.4514  -26.9245
 562  O01  O  O2     0  -0.484  -19.4991  10.9272  -22.4924
 562  C02  C  CH2    0  -0.321  -18.4339  13.1189  -22.4490
 562  N02  N  N      0  -0.127  -21.7014   5.3482  -24.8637
 562  O02  O  O2     0  -0.477  -20.4788   8.4178  -23.3003
 562  C03  C  CH2    0  -0.178  -19.2481  10.4020  -23.7740
 562  N03  N  N      1   0.538  -21.8935   4.8846  -25.9008
 562  C04  C  CH2    0  -0.190  -20.3921   9.5151  -24.1896
 562  C05  C  CH2    0  -0.169  -21.4144   7.4491  -23.6658
 562  C06  C  CH2    0  -0.361  -20.7161   6.3958  -24.5295
 562  H1   H  HNH2   0   0.330  -22.5152  20.2498  -23.3863
 562  H2   H  HNH2   0   0.320  -21.2000  19.9593  -24.2462
 562  H4   H  HCH1   0   0.207  -21.3328  19.8048  -21.3468
 562  OXT  O  OC    -1  -0.603  -21.4246  22.3997  -22.8569
 562  H6   H  HCH2   0   0.218  -18.8807  19.8393  -21.4789
 562  H7   H  HCH2   0   0.204  -18.9445  19.7913  -23.2266
 562  H8   H  HCH2   0   0.216  -20.0303  17.5673  -23.1642
 562  H9   H  HCH2   0   0.212  -20.1250  17.6288  -21.4148
 562  H10  H  HCH2   0   0.223  -17.6629  17.6764  -21.2382
 562  H11  H  HCH2   0   0.203  -17.5031  17.7150  -22.9824
 562  H12  H  HNH1   0   0.389  -18.8475  15.5144  -22.8269
 562  H13  H  H      0   0.310  -15.3079  15.0375  -21.2430
 562  H14  H  HCH2   0   0.241  -18.5490  11.6684  -20.8710
 562  H15  H  HCH2   0   0.206  -17.4724  11.1994  -22.1867
 562  H16  H  HNH1   0   0.382  -16.4086  13.2744  -22.0114
 562  H17  H  H      0   0.495  -21.7852   3.5914  -27.2328
 562  H18  H  HCH2   0   0.232  -18.4672  13.1523  -23.5460
 562  H19  H  HCH2   0   0.242  -19.3383  13.6066  -22.0816
 562  H20  H  HCH2   0   0.212  -18.3112   9.8278  -23.7824
 562  H21  H  HCH2   0   0.216  -19.1469  11.1891  -24.5316
 562  H22  H  HCH2   0   0.225  -21.3334  10.0791  -24.1927
 562  H23  H  HCH2   0   0.222  -20.2041   9.1911  -25.2204
 562  H24  H  HCH2   0   0.244  -22.2675   7.8740  -24.2058
 562  H25  H  HCH2   0   0.268  -21.7950   6.9738  -22.7598
 562  H26  H  HCH2   0   0.336  -19.9465   5.8793  -23.9562
 562  H27  H  HCH2   0   0.316  -20.2907   6.7984  -25.4483

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
 562  N08  N03  double  1.170  0.020  1.170
 562  N03  N02  double  1.152  0.020  1.152
 562  N02  C06  single  1.476  0.020  1.476
 562  C04  C03  single  1.506  0.020  1.506
 562  C04  O02  single  1.415  0.020  1.415
 562  C03  O01  single  1.408  0.020  1.408
 562  C06  C05  single  1.531  0.020  1.531
 562  O02  C05  single  1.395  0.020  1.395
 562  N    CA   single  1.458  0.019  1.458
 562  O01  C01  single  1.404  0.020  1.404
 562  C02  C01  single  1.526  0.020  1.526
 562  C02  NH2  single  1.445  0.020  1.445
 562  NE   CD   single  1.447  0.020  1.447
 562  NE   CZ   single  1.369  0.020  1.369
 562  CG   CD   single  1.521  0.020  1.521
 562  CG   CB   single  1.523  0.020  1.523
 562  CA   CB   single  1.521  0.033  1.521
 562  CA   C    single  1.525  0.021  1.525
 562  NH2  CZ   single  1.378  0.020  1.378
 562  CZ   NH1  double  1.286  0.020  1.286
 562  C    O    deloc   1.231  0.020  1.231
 562  N    H1   single  0.890  0.020  1.040
 562  N    H2   single  0.890  0.020  1.040
 562  CA   H4   single  0.970  0.020  1.090
 562  C    OXT  deloc   1.247  0.020  1.247
 562  CB   H6   single  0.970  0.020  1.090
 562  CB   H7   single  0.970  0.020  1.090
 562  CG   H8   single  0.970  0.020  1.090
 562  CG   H9   single  0.970  0.020  1.090
 562  CD   H10  single  0.970  0.020  1.090
 562  CD   H11  single  0.970  0.020  1.090
 562  NE   H12  single  0.890  0.020  1.040
 562  NH1  H13  single  0.890  0.020  1.040
 562  C01  H14  single  0.970  0.020  1.090
 562  C01  H15  single  0.970  0.020  1.090
 562  NH2  H16  single  0.890  0.020  1.040
 562  N08  H17  single  0.890  0.020  1.040
 562  C02  H18  single  0.970  0.020  1.090
 562  C02  H19  single  0.970  0.020  1.090
 562  C03  H20  single  0.970  0.020  1.090
 562  C03  H21  single  0.970  0.020  1.090
 562  C04  H22  single  0.970  0.020  1.090
 562  C04  H23  single  0.970  0.020  1.090
 562  C05  H24  single  0.970  0.020  1.090
 562  C05  H25  single  0.970  0.020  1.090
 562  C06  H26  single  0.970  0.020  1.090
 562  C06  H27  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
 562  H2   N    H1   104.01  3.000
 562  H2   N    CA   108.15  3.000
 562  H1   N    CA   107.99  3.000
 562  H4   CA   CB   106.84  3.000
 562  H4   CA   C    105.82  3.000
 562  CB   CA   C    110.50  1.500
 562  H4   CA   N    106.91  3.000
 562  C    CA   N    111.00  2.800
 562  CB   CA   N    110.40  1.500
 562  OXT  C    O    126.53  3.000
 562  OXT  C    CA   120.80  1.700
 562  O    C    CA   120.80  1.700
 562  H7   CB   H6   106.17  3.000
 562  H7   CB   CG   109.39  3.000
 562  H6   CB   CG   109.37  3.000
 562  H7   CB   CA   109.25  3.000
 562  H6   CB   CA   108.16  3.000
 562  CG   CB   CA   114.18  3.000
 562  H9   CG   H8   106.46  3.000
 562  H9   CG   CD   109.07  3.000
 562  H8   CG   CD   109.87  3.000
 562  H9   CG   CB   109.71  3.000
 562  H8   CG   CB   110.04  3.000
 562  CD   CG   CB   111.55  3.000
 562  H11  CD   H10  106.34  3.000
 562  H11  CD   NE   111.67  3.000
 562  H10  CD   NE   108.49  3.000
 562  H11  CD   CG   109.85  3.000
 562  H10  CD   CG   109.64  3.000
 562  NE   CD   CG   110.73  3.000
 562  H12  NE   CZ   116.55  3.000
 562  H12  NE   CD   114.12  3.000
 562  CZ   NE   CD   120.49  3.000
 562  NH2  CZ   NH1  124.07  3.000
 562  NH1  CZ   NE   120.38  3.000
 562  NH2  CZ   NE   115.46  3.000
 562  H13  NH1  CZ   110.56  3.000
 562  H15  C01  H14  107.16  3.000
 562  H15  C01  C02  109.84  3.000
 562  H14  C01  C02  108.97  3.000
 562  H15  C01  O01  110.79  3.000
 562  H14  C01  O01  107.41  3.000
 562  C02  C01  O01  112.49  3.000
 562  H16  NH2  C02  114.59  3.000
 562  H16  NH2  CZ   113.52  3.000
 562  C02  NH2  CZ   125.10  3.000
 562  H17  N08  N03  115.38  3.000
 562  C03  O01  C01  114.23  3.000
 562  H19  C02  H18  107.32  3.000
 562  H19  C02  NH2  109.60  3.000
 562  H18  C02  NH2  112.33  3.000
 562  H19  C02  C01  108.23  3.000
 562  H18  C02  C01  110.51  3.000
 562  NH2  C02  C01  108.76  3.000
 562  C06  N02  N03  126.91  3.000
 562  C05  O02  C04  114.51  3.000
 562  H21  C03  H20  106.91  3.000
 562  H21  C03  C04  107.57  3.000
 562  H20  C03  C04  109.75  3.000
 562  H21  C03  O01  112.18  3.000
 562  H20  C03  O01  110.73  3.000
 562  C04  C03  O01  109.61  3.000
 562  N02  N03  N08  171.37  3.000
 562  H23  C04  H22  107.23  3.000
 562  H23  C04  C03  107.65  3.000
 562  H22  C04  C03  110.47  3.000
 562  H23  C04  O02  111.84  3.000
 562  H22  C04  O02  110.35  3.000
 562  C03  C04  O02  109.25  3.000
 562  H25  C05  H24  107.85  3.000
 562  H25  C05  C06  109.13  3.000
 562  H24  C05  C06  110.12  3.000
 562  H25  C05  O02  108.58  3.000
 562  H24  C05  O02  112.45  3.000
 562  C06  C05  O02  108.64  3.000
 562  H27  C06  H26  110.05  3.000
 562  H27  C06  C05  113.56  3.000
 562  H26  C06  C05  110.57  3.000
 562  H27  C06  N02  109.38  3.000
 562  H26  C06  N02  104.72  3.000
 562  C05  C06  N02  108.15  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
 562  CONST_01  NH2  CZ   NE   CD    180.00   0.0  0
 562  CONST_02  NH1  CZ   NE   CD      0.00   0.0  0
 562  CONST_03  C02  NH2  CZ   NE      0.00   0.0  0
 562  CONST_04  C02  NH2  CZ   NH1   180.00   0.0  0
 562  CONST_06  H13  NH1  CZ   NE    180.00   0.0  0
 562  Var_01    CD   CG   CB   CA   -173.42  30.0  1
 562  Var_02    NE   CD   CG   CB   -178.68  30.0  3
 562  Var_03    CZ   NE   CD   CG   -170.55  30.0  1
 562  Var_04    C01  C02  NH2  CZ   -163.60  30.0  1
 562  Var_05    C04  C03  O01  C01   174.55  30.0  1
 562  Var_06    O01  C01  C02  NH2  -176.69  30.0  3
 562  Var_07    O02  C04  C03  O01   -62.95  30.0  2
 562  Var_08    O02  C05  C06  N02   177.71  30.0  3
 562  Var_09    C05  C06  N02  N03   133.36  30.0  3
 562  Var_10    C06  C05  O02  C04    91.22  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
 562  chir_01  CA  N  CB  C  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
 562  plan-1  CD   0.020
 562  plan-1  NE   0.020
 562  plan-1  CZ   0.020
 562  plan-1  NH1  0.020
 562  plan-1  NH2  0.020
 562  plan-1  C02  0.020
 562  plan-1  H12  0.020
 562  plan-1  H13  0.020
 562  plan-1  H16  0.020
 562  plan-2  CA   0.020
 562  plan-2  C    0.020
 562  plan-2  O    0.020
 562  plan-2  OXT  0.020
 562  plan-3  N08  0.020
 562  plan-3  N02  0.020
 562  plan-3  N03  0.020
 562  plan-3  C06  0.020
 562  plan-3  H17  0.020

