# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 20:40:53 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: azanylidene-[4-[[(1~{S},2~{R},3~{R},4~{R},5~{S},6~{S},7~{S})-2-(hydroxymethyl)-3,4,5-tris(oxidanyl)-7-bicyclo[4.1.0]heptanyl]carbonylamino]butylimino]azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1[C@@H](O)[C@H](O)[C@@H](O)[C@H]2[C@@H]1[C@@H]2C(=O)NCCCCN=[N+]=N
#
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
 8P5  8P5  azanylidene-[4-[[(1~{S},2~{R},3~{R},4~{R},5~{S},6~{S},7~{S})-2-(hydroxymethyl)-3,4,5-tris(oxidanyl)-7-bicyclo[4.1.0]heptanyl]carbonylamino]butylimino]azanium  ligand  45  22  .  2022-09-16  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_8P5
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
 8P5  O3   O  OH1   0  -0.684  -5.2846   1.7994  -1.1530
 8P5  C4   C  CH1   0   0.048  -4.0530  -0.2595  -0.8790
 8P5  C5   C  CH1   0  -0.308  -3.4064  -1.1529   0.1792
 8P5  O4   O  OH1   0  -0.666  -5.1554  -0.9262  -1.4392
 8P5  C6   C  CH2   0  -0.120  -2.7253  -2.3981  -0.3752
 8P5  N1   N  N     0  -0.337   9.1282  -1.1830  -0.8864
 8P5  C7   C  CH1   0  -0.228  -2.4025  -0.3911   1.0189
 8P5  C8   C  CH1   0  -0.434  -1.2249   0.3122   0.3889
 8P5  C9   C  C     0   0.623   0.0792   0.2474   1.1013
 8P5  O6   O  OH1   0  -0.665  -3.6724  -3.3212  -0.8574
 8P5  C12  C  CH2   0  -0.230   2.5070   0.1216   0.8448
 8P5  C13  C  CH2   0  -0.495   3.5300   0.1761  -0.2774
 8P5  C14  C  CH2   0  -0.451   4.9459   0.0796   0.2782
 8P5  C15  C  CH2   0  -0.323   5.9465   0.1467  -0.8589
 8P5  O10  O  O     0  -0.510   0.1560   0.2360   2.3251
 8P5  N11  N  NH1   0  -0.664   1.1635   0.2025   0.3130
 8P5  N16  N  N     0  -0.117   7.3176   0.1336  -0.2996
 8P5  N17  N  N     1   0.530   8.1654  -0.5957  -0.5749
 8P5  C1   C  CH1   0  -0.278  -2.3427   1.0957   1.0266
 8P5  C2   C  CH1   0   0.056  -3.2782   1.8975   0.1418
 8P5  O2   O  OH1   0  -0.679  -3.6462   3.0558   0.8537
 8P5  C3   C  CH1   0  -0.015  -4.4914   1.0617  -0.2384
 8P5  H1   H  HOH1  0   0.465  -6.1734   1.8862  -0.7995
 8P5  H2   H  HCH1  0   0.192  -3.3070  -0.0397  -1.6634
 8P5  H3   H  HCH1  0   0.247  -4.2036  -1.4730   0.8619
 8P5  H4   H  HOH1  0   0.440  -5.6211  -0.2828  -1.9862
 8P5  H5   H  HCH2  0   0.187  -2.0184  -2.0958  -1.1611
 8P5  H6   H  HCH2  0   0.202  -2.1236  -2.8410   0.4306
 8P5  H8   H  HCH1  0   0.274  -2.1741  -0.8699   1.9651
 8P5  H9   H  HCH1  0   0.276  -1.1747   0.3410  -0.6954
 8P5  H10  H  HOH1  0   0.450  -3.1958  -4.1077  -1.1371
 8P5  H11  H  HCH2  0   0.236   2.6309  -0.8040   1.4146
 8P5  H12  H  HCH2  0   0.238   2.6778   0.9466   1.5410
 8P5  H13  H  HCH2  0   0.251   3.3524  -0.6434  -0.9799
 8P5  H14  H  HCH2  0   0.252   3.4153   1.1090  -0.8369
 8P5  H15  H  HCH2  0   0.268   5.1319   0.8962   0.9785
 8P5  H16  H  HCH2  0   0.267   5.0702  -0.8584   0.8229
 8P5  H17  H  HCH2  0   0.312   5.8444  -0.6738  -1.5671
 8P5  H18  H  HCH2  0   0.328   5.8892   1.0985  -1.3865
 8P5  H19  H  HNH1  0   0.403   1.0423   0.1933  -0.6869
 8P5  H20  H  HCH1  0   0.274  -2.1027   1.5621   1.9759
 8P5  H21  H  HCH1  0   0.215  -2.7589   2.1743  -0.7896
 8P5  H22  H  HOH1  0   0.447  -4.2628   3.5548   0.3070
 8P5  H23  H  HCH1  0   0.231  -5.0641   0.8346   0.6717
 8P5  H24  H  H     0   0.494   9.2980  -2.0551  -0.3735

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
 8P5  N1   N17  double  1.170  0.020  1.170
 8P5  N17  N16  double  1.152  0.020  1.152
 8P5  N16  C15  single  1.481  0.020  1.481
 8P5  C15  C14  single  1.516  0.020  1.516
 8P5  C14  C13  single  1.524  0.020  1.524
 8P5  C13  C12  single  1.519  0.020  1.519
 8P5  O10  C9   double  1.226  0.020  1.226
 8P5  C12  N11  single  1.447  0.020  1.447
 8P5  C9   N11  single  1.341  0.020  1.341
 8P5  C9   C8   single  1.487  0.020  1.487
 8P5  C8   C7   single  1.509  0.020  1.509
 8P5  C8   C1   single  1.507  0.020  1.507
 8P5  C6   O6   single  1.408  0.020  1.408
 8P5  C6   C5   single  1.524  0.020  1.524
 8P5  C7   C1   single  1.488  0.020  1.488
 8P5  C7   C5   single  1.514  0.020  1.514
 8P5  C1   C2   single  1.517  0.020  1.517
 8P5  C5   C4   single  1.528  0.020  1.528
 8P5  C4   O4   single  1.405  0.020  1.405
 8P5  C4   C3   single  1.532  0.020  1.532
 8P5  C2   C3   single  1.522  0.020  1.522
 8P5  C2   O2   single  1.408  0.020  1.408
 8P5  C3   O3   single  1.418  0.020  1.418
 8P5  O3   H1   single  0.850  0.020  0.980
 8P5  C4   H2   single  0.970  0.020  1.090
 8P5  C5   H3   single  0.970  0.020  1.090
 8P5  O4   H4   single  0.850  0.020  0.980
 8P5  C6   H5   single  0.970  0.020  1.090
 8P5  C6   H6   single  0.970  0.020  1.090
 8P5  C7   H8   single  0.970  0.020  1.090
 8P5  C8   H9   single  0.970  0.020  1.090
 8P5  O6   H10  single  0.850  0.020  0.980
 8P5  C12  H11  single  0.970  0.020  1.090
 8P5  C12  H12  single  0.970  0.020  1.090
 8P5  C13  H13  single  0.970  0.020  1.090
 8P5  C13  H14  single  0.970  0.020  1.090
 8P5  C14  H15  single  0.970  0.020  1.090
 8P5  C14  H16  single  0.970  0.020  1.090
 8P5  C15  H17  single  0.970  0.020  1.090
 8P5  C15  H18  single  0.970  0.020  1.090
 8P5  N11  H19  single  0.860  0.020  1.020
 8P5  C1   H20  single  0.970  0.020  1.090
 8P5  C2   H21  single  0.970  0.020  1.090
 8P5  O2   H22  single  0.850  0.020  0.980
 8P5  C3   H23  single  0.970  0.020  1.090
 8P5  N1   H24  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
 8P5  H1   O3   C3   109.11  3.000
 8P5  H2   C4   C3   108.57  3.000
 8P5  H2   C4   O4   109.95  3.000
 8P5  C3   C4   O4   110.57  3.000
 8P5  H2   C4   C5   108.80  3.000
 8P5  C3   C4   C5   109.61  3.000
 8P5  O4   C4   C5   109.31  3.000
 8P5  H3   C5   C7   106.46  3.000
 8P5  H3   C5   C6   108.23  3.000
 8P5  C7   C5   C6   108.45  3.000
 8P5  H3   C5   C4   107.09  3.000
 8P5  C7   C5   C4   111.73  3.000
 8P5  C6   C5   C4   114.52  3.000
 8P5  H4   O4   C4   106.77  3.000
 8P5  H6   C6   H5   106.44  3.000
 8P5  H6   C6   O6   110.81  3.000
 8P5  H5   C6   O6   111.59  3.000
 8P5  H6   C6   C5   107.90  3.000
 8P5  H5   C6   C5   108.83  3.000
 8P5  O6   C6   C5   111.08  3.000
 8P5  H24  N1   N17  115.46  3.000
 8P5  H8   C7   C1   115.34  3.000
 8P5  H8   C7   C8   113.92  3.000
 8P5  C1   C7   C8    60.35  3.000
 8P5  H8   C7   C5   113.65  3.000
 8P5  C1   C7   C5   122.15  3.000
 8P5  C8   C7   C5   121.34  3.000
 8P5  H9   C8   C1   116.31  3.000
 8P5  H9   C8   C9   116.03  3.000
 8P5  C1   C8   C9   118.06  3.000
 8P5  H9   C8   C7   117.73  3.000
 8P5  C1   C8   C7    59.12  3.000
 8P5  C9   C8   C7   117.64  3.000
 8P5  N11  C9   O10  122.38  3.000
 8P5  N11  C9   C8   115.39  3.000
 8P5  O10  C9   C8   122.23  3.000
 8P5  H10  O6   C6   107.62  3.000
 8P5  H12  C12  H11  106.81  3.000
 8P5  H12  C12  N11  109.69  3.000
 8P5  H11  C12  N11  110.11  3.000
 8P5  H12  C12  C13  109.76  3.000
 8P5  H11  C12  C13  109.80  3.000
 8P5  N11  C12  C13  110.59  3.000
 8P5  H14  C13  H13  107.06  3.000
 8P5  H14  C13  C14  109.75  3.000
 8P5  H13  C13  C14  109.72  3.000
 8P5  H14  C13  C12  109.74  3.000
 8P5  H13  C13  C12  109.76  3.000
 8P5  C14  C13  C12  110.73  3.000
 8P5  H16  C14  H15  107.65  3.000
 8P5  H16  C14  C15  109.70  3.000
 8P5  H15  C14  C15  109.61  3.000
 8P5  H16  C14  C13  110.00  3.000
 8P5  H15  C14  C13  110.16  3.000
 8P5  C15  C14  C13  109.69  3.000
 8P5  H18  C15  H17  109.78  3.000
 8P5  H18  C15  N16  103.84  3.000
 8P5  H17  C15  N16  109.02  3.000
 8P5  H18  C15  C14  111.53  3.000
 8P5  H17  C15  C14  113.12  3.000
 8P5  N16  C15  C14  109.11  3.000
 8P5  H19  N11  C12  118.42  3.000
 8P5  H19  N11  C9   119.11  3.000
 8P5  C12  N11  C9   122.44  3.000
 8P5  N17  N16  C15  126.64  3.000
 8P5  N16  N17  N1   170.84  3.000
 8P5  H20  C1   C2   114.81  3.000
 8P5  H20  C1   C8   115.47  3.000
 8P5  C2   C1   C8   119.05  3.000
 8P5  H20  C1   C7   116.30  3.000
 8P5  C2   C1   C7   120.02  3.000
 8P5  C8   C1   C7    60.53  3.000
 8P5  H21  C2   C3   107.61  3.000
 8P5  H21  C2   O2   110.11  3.000
 8P5  C3   C2   O2   111.70  3.000
 8P5  H21  C2   C1   109.58  3.000
 8P5  O2   C2   C1   107.52  3.000
 8P5  C3   C2   C1   110.31  3.000
 8P5  H22  O2   C2   107.84  3.000
 8P5  H23  C3   C2   108.78  3.000
 8P5  H23  C3   C4   108.48  3.000
 8P5  C2   C3   C4   110.48  3.000
 8P5  H23  C3   O3   110.51  3.000
 8P5  C2   C3   O3   108.75  3.000
 8P5  C4   C3   O3   109.82  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
 8P5  CONST_01  C12  N11  C9   C8    180.00   0.0  0
 8P5  CONST_02  H19  N11  C9   C8      0.00   0.0  0
 8P5  CONST_03  O10  C9   N11  C12     0.00   0.0  0
 8P5  Var_01    C1   C8   C7   C5    111.74  30.0  1
 8P5  Var_02    O10  C9   C8   C7    -34.26  30.0  3
 8P5  Var_03    C13  C12  N11  C9   -176.36  30.0  1
 8P5  Var_04    C15  C14  C13  C12  -179.58  30.0  2
 8P5  Var_05    N16  C15  C14  C13   176.64  30.0  1
 8P5  Var_06    N11  C12  C13  C14  -179.53  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
 8P5  chir_01  C4  C5  O4  C3  negativ
 8P5  chir_02  C5  C4  C7  C6  positiv
 8P5  chir_06  C2  C1  C3  O2  negativ
 8P5  chir_07  C3  O3  C4  C2  negativ
 8P5  chir_08  C7  C8  C1  C5  both
 8P5  chir_09  C8  C1  C7  C9  both
 8P5  chir_10  C1  C2  C7  C8  both

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
 8P5  plan-1  C8   0.020
 8P5  plan-1  C9   0.020
 8P5  plan-1  C12  0.020
 8P5  plan-1  O10  0.020
 8P5  plan-1  N11  0.020
 8P5  plan-1  H19  0.020
 8P5  plan-2  N1   0.020
 8P5  plan-2  C15  0.020
 8P5  plan-2  N16  0.020
 8P5  plan-2  N17  0.020
 8P5  plan-2  H24  0.020

