# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jun 10 19:33:34 2020
#   Inital geometry file: a 156 line input string
#   Ligand name: (3~{S})-3-[[(3~{S},6~{S},10~{a}~{S})-6-(isoquinolin-1-ylcarbonylamino)-5-oxidanylidene-2,3,6,7,8,9,10,10~{a}-octahydro-1~{H}-pyrrolo[1,2-a]azocin-3-yl]carbonylamino]-4-oxidanyl-butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H](CC(O)=O)NC(=O)[C@@H]1CC[C@@H]2CCCC[C@H](NC(=O)c3nccc4ccccc34)C(=O)N12
#
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
 N7N  N7N  '(3~{S})-3-[[(3~{S},6~{S},10~{a}~{S})-6-(isoquinolin-1-ylcarbonylamino)-5-oxidanylidene-2,3,6,7,8,9,10,10~{a}-octahydro-1~{H}-pyrrolo[1,2-a]azocin-3-yl]carbonylamino]-4-oxidanyl-butanoic acid'  ligand  64  35  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_N7N
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
 N7N  C4   C  CH1    0  -0.176   0.8719   2.4791   1.5856
 N7N  C5   C  C      0   0.564  -0.4854   2.1328   0.9491
 N7N  C6   C  CH2    0  -0.469   1.4628   2.8283  -1.5838
 N7N  C7   C  CH1    0  -0.040  -0.0505   2.7116  -1.5588
 N7N  C9   C  CH1    0  -0.196  -1.9719   1.4829  -0.7814
 N7N  C10  C  CH2    0  -0.495  -2.0379   1.6543  -2.3074
 N7N  C11  C  CH2    0  -0.438  -0.5872   1.8589  -2.6984
 N7N  C12  C  C      0   0.572  -1.9722  -0.0094  -0.4586
 N7N  C1   C  CH2    0  -0.465   1.2520   3.9582   1.5645
 N7N  C2   C  CH2    0  -0.453   1.2275   4.6939   0.2336
 N7N  C3   C  CH2    0  -0.466   2.0343   4.0902  -0.9141
 N7N  N8   N  NT     0  -0.480  -0.7091   2.0983  -0.3856
 N7N  N13  N  NH1    0  -0.650   1.9507   1.6537   1.1020
 N7N  O14  O  O      0  -0.493  -1.3874   1.8230   1.7186
 N7N  O16  O  O      0  -0.466   1.1443  -0.2754   1.9515
 N7N  C17  C  CR6    0   0.072   3.2103  -0.3451   0.7425
 N7N  N18  N  N      0  -0.439   4.2750   0.4116   0.6635
 N7N  C19  C  CR16   0  -0.076   5.4385  -0.1146   0.2401
 N7N  C20  C  CR16   0  -0.382   5.5676  -1.4267  -0.1127
 N7N  C21  C  CR66   0   0.042   3.1947  -1.7120   0.3435
 N7N  C22  C  CR66   0   0.208   4.4326  -2.2628  -0.0829
 N7N  C23  C  CR16   0  -0.300   4.4973  -3.6167  -0.4855
 N7N  C24  C  CR16   0  -0.243   3.3682  -4.3852  -0.4945
 N7N  C25  C  CR16   0  -0.248   2.1287  -3.8286  -0.1165
 N7N  C26  C  CR16   0  -0.320   2.0357  -2.5273   0.2949
 N7N  O27  O  O      0  -0.469  -0.9519  -0.6769  -0.4772
 N7N  N28  N  NH1    0  -0.631  -3.1978  -0.5176  -0.2665
 N7N  C29  C  CH2    0  -0.159  -3.3326  -2.5441  -1.6489
 N7N  O30  O  OC    -1  -0.619  -5.9976  -1.0292   2.1025
 N7N  C32  C  CH2    0  -0.590  -4.8843  -2.1490   0.3193
 N7N  O33  O  O      0  -0.610  -4.1018  -2.1058   2.5612
 N7N  C34  C  CH1    0  -0.085  -3.4927  -1.9391  -0.2600
 N7N  O35  O  OH1    0  -0.672  -4.1966  -1.8879  -2.5494
 N7N  H1   H  HCH1   0   0.277   0.7061   2.2256   2.6348
 N7N  H2   H  HCH2   0   0.236   1.9036   1.9050  -1.2160
 N7N  H3   H  HCH2   0   0.253   1.7405   2.8721  -2.6396
 N7N  H4   H  HCH1   0   0.241  -0.4717   3.7178  -1.6863
 N7N  H5   H  HCH1   0   0.273  -2.8228   1.9720  -0.3012
 N7N  H6   H  HCH2   0   0.260  -2.5159   0.8048  -2.7966
 N7N  H7   H  HCH2   0   0.251  -2.6234   2.5417  -2.5544
 N7N  H8   H  HCH2   0   0.248  -0.4683   2.3623  -3.6576
 N7N  H9   H  HCH2   0   0.239  -0.0462   0.9108  -2.7392
 N7N  H10  H  HCH2   0   0.258   0.5796   4.4725   2.2538
 N7N  H11  H  HCH2   0   0.248   2.2500   4.0352   2.0071
 N7N  H12  H  HCH2   0   0.231   0.1932   4.8492  -0.0848
 N7N  H13  H  HCH2   0   0.247   1.6153   5.6977   0.4222
 N7N  H14  H  HCH2   0   0.229   3.0651   3.9099  -0.5912
 N7N  H15  H  HCH2   0   0.244   2.1094   4.8631  -1.6823
 N7N  H16  H  HNH1   0   0.405   2.7804   2.0857   0.7261
 N7N  H17  H  HCR6   0   0.271   6.2829   0.5619   0.2022
 N7N  H18  H  HCR6   0   0.274   6.5248  -1.8197  -0.4296
 N7N  H19  H  HCR6   0   0.264   5.4501  -4.0266  -0.7961
 N7N  H20  H  HCR6   0   0.268   3.4172  -5.4202  -0.8065
 N7N  H21  H  HCR6   0   0.266   1.2379  -4.4414  -0.1598
 N7N  H22  H  HCR6   0   0.288   1.0732  -2.1190   0.5583
 N7N  H23  H  HNH1   0   0.388  -3.9814   0.1147  -0.3048
 N7N  H24  H  HCH2   0   0.210  -2.2866  -2.4520  -1.9627
 N7N  H25  H  HCH2   0   0.195  -3.5527  -3.6185  -1.5789
 N7N  H27  H  HCH2   0   0.237  -5.1138  -3.2186   0.2595
 N7N  H28  H  HCH2   0   0.215  -5.6328  -1.6392  -0.2924
 N7N  H29  H  HCH1   0   0.240  -2.7743  -2.4389   0.3933
 N7N  H30  H  HOH1   0   0.454  -3.9926  -2.1951  -3.4364
 N7N  C31  C  C      0   0.410  -5.0016  -1.7137   1.7927
 N7N  C15  C  C      0   0.554   1.9947   0.3317   1.3241

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
 N7N  C25  C24  aromatic  1.410  0.020  1.410
 N7N  C25  C26  aromatic  1.368  0.020  1.368
 N7N  C24  C23  aromatic  1.366  0.020  1.366
 N7N  C26  C21  aromatic  1.418  0.020  1.418
 N7N  C23  C22  aromatic  1.414  0.020  1.414
 N7N  O16  C15  double    1.219  0.020  1.219
 N7N  C21  C22  aromatic  1.420  0.020  1.420
 N7N  C21  C17  aromatic  1.424  0.020  1.424
 N7N  C22  C20  aromatic  1.410  0.020  1.410
 N7N  C15  C17  single    1.508  0.020  1.508
 N7N  C15  N13  single    1.341  0.020  1.341
 N7N  C17  N18  aromatic  1.309  0.020  1.309
 N7N  C20  C19  aromatic  1.365  0.020  1.365
 N7N  C11  C7   single    1.521  0.020  1.521
 N7N  C11  C10  single    1.516  0.020  1.516
 N7N  C7   C6   single    1.518  0.020  1.518
 N7N  C7   N8   single    1.479  0.020  1.479
 N7N  N18  C19  aromatic  1.345  0.020  1.345
 N7N  N13  C4   single    1.442  0.020  1.442
 N7N  C10  C9   single    1.537  0.020  1.537
 N7N  C4   C5   single    1.539  0.020  1.539
 N7N  C4   C1   single    1.527  0.020  1.527
 N7N  C6   C3   single    1.539  0.020  1.539
 N7N  C3   C2   single    1.527  0.020  1.527
 N7N  N8   C5   single    1.354  0.020  1.354
 N7N  N8   C9   single    1.459  0.020  1.459
 N7N  C5   O14  double    1.225  0.020  1.225
 N7N  C9   C12  single    1.527  0.020  1.527
 N7N  C1   C2   single    1.521  0.020  1.521
 N7N  C12  O27  double    1.219  0.020  1.219
 N7N  C12  N28  single    1.341  0.020  1.341
 N7N  N28  C34  single    1.452  0.020  1.452
 N7N  C34  C29  single    1.523  0.020  1.523
 N7N  C34  C32  single    1.522  0.020  1.522
 N7N  O35  C29  single    1.410  0.020  1.410
 N7N  C32  C31  single    1.541  0.020  1.541
 N7N  C31  O33  deloc     1.247  0.020  1.247
 N7N  C31  O30  deloc     1.248  0.020  1.248
 N7N  C4   H1   single    0.970  0.020  1.090
 N7N  C6   H2   single    0.970  0.020  1.090
 N7N  C6   H3   single    0.970  0.020  1.090
 N7N  C7   H4   single    0.970  0.020  1.090
 N7N  C9   H5   single    0.970  0.020  1.090
 N7N  C10  H6   single    0.970  0.020  1.090
 N7N  C10  H7   single    0.970  0.020  1.090
 N7N  C11  H8   single    0.970  0.020  1.090
 N7N  C11  H9   single    0.970  0.020  1.090
 N7N  C1   H10  single    0.970  0.020  1.090
 N7N  C1   H11  single    0.970  0.020  1.090
 N7N  C2   H12  single    0.970  0.020  1.090
 N7N  C2   H13  single    0.970  0.020  1.090
 N7N  C3   H14  single    0.970  0.020  1.090
 N7N  C3   H15  single    0.970  0.020  1.090
 N7N  N13  H16  single    0.860  0.020  1.020
 N7N  C19  H17  single    0.930  0.020  1.080
 N7N  C20  H18  single    0.930  0.020  1.080
 N7N  C23  H19  single    0.930  0.020  1.080
 N7N  C24  H20  single    0.930  0.020  1.080
 N7N  C25  H21  single    0.930  0.020  1.080
 N7N  C26  H22  single    0.930  0.020  1.080
 N7N  N28  H23  single    0.860  0.020  1.020
 N7N  C29  H24  single    0.970  0.020  1.090
 N7N  C29  H25  single    0.970  0.020  1.090
 N7N  C32  H27  single    0.970  0.020  1.090
 N7N  C32  H28  single    0.970  0.020  1.090
 N7N  C34  H29  single    0.970  0.020  1.090
 N7N  O35  H30  single    0.850  0.020  0.980

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
 N7N  H1   C4   N13  107.63  3.000
 N7N  H1   C4   C1   106.01  3.000
 N7N  N13  C4   C1   111.32  3.000
 N7N  H1   C4   C5   102.20  3.000
 N7N  C1   C4   C5   115.58  3.000
 N7N  N13  C4   C5   113.11  3.000
 N7N  O14  C5   N8   119.41  3.000
 N7N  O14  C5   C4   116.52  3.000
 N7N  N8   C5   C4   124.01  3.000
 N7N  H3   C6   H2   104.95  3.000
 N7N  H3   C6   C3   107.05  3.000
 N7N  H2   C6   C3   113.49  3.000
 N7N  H3   C6   C7   105.81  3.000
 N7N  H2   C6   C7   109.47  3.000
 N7N  C3   C6   C7   115.22  3.000
 N7N  H4   C7   N8   107.53  3.000
 N7N  H4   C7   C11  106.94  3.000
 N7N  N8   C7   C11  101.81  3.000
 N7N  H4   C7   C6   108.06  3.000
 N7N  N8   C7   C6   119.27  3.000
 N7N  C11  C7   C6   112.49  3.000
 N7N  H5   C9   N8   111.46  3.000
 N7N  H5   C9   C12  110.15  3.000
 N7N  N8   C9   C12  110.79  3.000
 N7N  H5   C9   C10  110.67  3.000
 N7N  C12  C9   C10  108.60  3.000
 N7N  N8   C9   C10  105.03  3.000
 N7N  H7   C10  H6   107.26  3.000
 N7N  H7   C10  C11  110.19  3.000
 N7N  H6   C10  C11  114.12  3.000
 N7N  H7   C10  C9   109.78  3.000
 N7N  H6   C10  C9   112.17  3.000
 N7N  C11  C10  C9   103.30  3.000
 N7N  H9   C11  H8   108.30  3.000
 N7N  H9   C11  C10  111.50  3.000
 N7N  H8   C11  C10  113.18  3.000
 N7N  H9   C11  C7   109.86  3.000
 N7N  H8   C11  C7   111.22  3.000
 N7N  C10  C11  C7   102.71  3.000
 N7N  N28  C12  O27  124.03  3.000
 N7N  N28  C12  C9   113.64  3.000
 N7N  O27  C12  C9   122.12  3.000
 N7N  H11  C1   H10  105.85  3.000
 N7N  H11  C1   C2   109.54  3.000
 N7N  H10  C1   C2   108.35  3.000
 N7N  H11  C1   C4   106.83  3.000
 N7N  H10  C1   C4   107.11  3.000
 N7N  C2   C1   C4   118.46  3.000
 N7N  H13  C2   H12  104.80  3.000
 N7N  H13  C2   C3   107.79  3.000
 N7N  H12  C2   C3   109.70  3.000
 N7N  H13  C2   C1   106.72  3.000
 N7N  H12  C2   C1   109.80  3.000
 N7N  C3   C2   C1   117.25  3.000
 N7N  H15  C3   H14  105.02  3.000
 N7N  H15  C3   C2   106.56  3.000
 N7N  H14  C3   C2   109.92  3.000
 N7N  H15  C3   C6   107.44  3.000
 N7N  H14  C3   C6   110.06  3.000
 N7N  C2   C3   C6   117.07  3.000
 N7N  C9   N8   C7   110.19  3.000
 N7N  C9   N8   C5   114.90  3.000
 N7N  C7   N8   C5   134.28  3.000
 N7N  H16  N13  C15  117.20  3.000
 N7N  H16  N13  C4   119.70  3.000
 N7N  C15  N13  C4   122.22  3.000
 N7N  C21  C17  N18  123.17  3.000
 N7N  N18  C17  C15  114.81  3.000
 N7N  C21  C17  C15  122.01  3.000
 N7N  C19  N18  C17  119.77  3.000
 N7N  H17  C19  C20  121.19  3.000
 N7N  H17  C19  N18  116.17  3.000
 N7N  C20  C19  N18  122.63  3.000
 N7N  H18  C20  C22  120.19  3.000
 N7N  H18  C20  C19  120.57  3.000
 N7N  C22  C20  C19  119.24  3.000
 N7N  C26  C21  C22  118.63  3.000
 N7N  C22  C21  C17  116.53  3.000
 N7N  C26  C21  C17  124.79  3.000
 N7N  C23  C22  C21  119.78  3.000
 N7N  C21  C22  C20  118.55  3.000
 N7N  C23  C22  C20  121.66  3.000
 N7N  H19  C23  C24  120.83  3.000
 N7N  H19  C23  C22  118.98  3.000
 N7N  C24  C23  C22  120.19  3.000
 N7N  H20  C24  C25  119.64  3.000
 N7N  H20  C24  C23  120.18  3.000
 N7N  C25  C24  C23  120.18  3.000
 N7N  H21  C25  C26  119.66  3.000
 N7N  H21  C25  C24  119.29  3.000
 N7N  C26  C25  C24  121.05  3.000
 N7N  H22  C26  C25  119.63  3.000
 N7N  H22  C26  C21  120.24  3.000
 N7N  C25  C26  C21  120.12  3.000
 N7N  H23  N28  C34  117.17  3.000
 N7N  H23  N28  C12  117.88  3.000
 N7N  C34  N28  C12  123.88  3.000
 N7N  H25  C29  H24  106.95  3.000
 N7N  H25  C29  O35  111.90  3.000
 N7N  H24  C29  O35  111.28  3.000
 N7N  H25  C29  C34  108.01  3.000
 N7N  H24  C29  C34  109.15  3.000
 N7N  O35  C29  C34  109.46  3.000
 N7N  H28  C32  H27  106.34  3.000
 N7N  H28  C32  C34  110.42  3.000
 N7N  H27  C32  C34  107.78  3.000
 N7N  H28  C32  C31  110.57  3.000
 N7N  H27  C32  C31  108.18  3.000
 N7N  C34  C32  C31  113.24  3.000
 N7N  H29  C34  C32  108.10  3.000
 N7N  H29  C34  C29  107.13  3.000
 N7N  C32  C34  C29  112.85  3.000
 N7N  H29  C34  N28  108.49  3.000
 N7N  C32  C34  N28  108.81  3.000
 N7N  C29  C34  N28  111.31  3.000
 N7N  H30  O35  C29  108.11  3.000
 N7N  O33  C31  C32  116.47  3.000
 N7N  O33  C31  O30  126.56  3.000
 N7N  C32  C31  O30  116.95  3.000
 N7N  C17  C15  O16  122.51  3.000
 N7N  C17  C15  N13  113.89  3.000
 N7N  O16  C15  N13  123.59  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
 N7N  CONST_01  C25  C26  C21  C17   180.00   0.0  0
 N7N  CONST_02  C23  C22  C21  C17   180.00   0.0  0
 N7N  CONST_03  C20  C22  C21  C17     0.00   0.0  0
 N7N  CONST_04  C20  C19  N18  C17     0.00   0.0  0
 N7N  CONST_05  C26  C21  C17  N18   180.00   0.0  0
 N7N  CONST_06  C22  C21  C17  N18     0.00   0.0  0
 N7N  CONST_07  C22  C20  C19  N18     0.00   0.0  0
 N7N  CONST_08  C23  C22  C20  C19   180.00   0.0  0
 N7N  CONST_09  C21  C22  C20  C19     0.00   0.0  0
 N7N  CONST_10  C21  C17  N18  C19     0.00   0.0  0
 N7N  CONST_11  C24  C23  C22  C20   180.00   0.0  0
 N7N  CONST_12  C26  C21  C22  C20   180.00   0.0  0
 N7N  CONST_13  C24  C25  C26  C21     0.00   0.0  0
 N7N  CONST_14  C24  C23  C22  C21     0.00   0.0  0
 N7N  CONST_15  C25  C24  C23  C22     0.00   0.0  0
 N7N  CONST_16  C25  C26  C21  C22     0.00   0.0  0
 N7N  CONST_17  C26  C25  C24  C23     0.00   0.0  0
 N7N  CONST_18  C26  C21  C22  C23     0.00   0.0  0
 N7N  CONST_19  C26  C21  C17  C15     0.00   0.0  0
 N7N  CONST_20  C22  C21  C17  C15   180.00   0.0  0
 N7N  CONST_21  C19  N18  C17  C15   180.00   0.0  0
 N7N  CONST_22  H22  C26  C21  C17     0.00   0.0  0
 N7N  CONST_23  H17  C19  N18  C17   180.00   0.0  0
 N7N  CONST_24  H18  C20  C19  N18   180.00   0.0  0
 N7N  CONST_25  H19  C23  C22  C20     0.00   0.0  0
 N7N  CONST_26  H21  C25  C26  C21   180.00   0.0  0
 N7N  CONST_27  H20  C24  C23  C22   180.00   0.0  0
 N7N  CONST_28  C17  C15  N13  C4    180.00   0.0  0
 N7N  CONST_29  O16  C15  N13  C4      0.00   0.0  0
 N7N  CONST_31  H23  N28  C12  C9      0.00   0.0  0
 N7N  CONST_32  H16  N13  C15  C17     0.00   0.0  0
 N7N  CONST_33  C34  N28  C12  O27     0.00   0.0  0
 N7N  Var_01    C9   C10  C11  C7    -38.11  30.0  1
 N7N  Var_02    C21  C17  C15  N13  -152.02  30.0  2
 N7N  Var_03    C34  C32  C31  O30   134.10  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
 N7N  chir_01  C4   N13  C5   C1   positiv
 N7N  chir_02  C7   N8   C11  C6   positiv
 N7N  chir_03  C9   N8   C10  C12  negativ
 N7N  chir_04  C34  N28  C29  C32  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
 N7N  plan-1  C17  0.020
 N7N  plan-1  N18  0.020
 N7N  plan-1  C19  0.020
 N7N  plan-1  C20  0.020
 N7N  plan-1  C21  0.020
 N7N  plan-1  C22  0.020
 N7N  plan-1  C23  0.020
 N7N  plan-1  C24  0.020
 N7N  plan-1  C25  0.020
 N7N  plan-1  C26  0.020
 N7N  plan-1  H17  0.020
 N7N  plan-1  H18  0.020
 N7N  plan-1  H19  0.020
 N7N  plan-1  H20  0.020
 N7N  plan-1  H21  0.020
 N7N  plan-1  H22  0.020
 N7N  plan-1  C15  0.020
 N7N  plan-2  C4   0.020
 N7N  plan-2  N13  0.020
 N7N  plan-2  O16  0.020
 N7N  plan-2  C17  0.020
 N7N  plan-2  H16  0.020
 N7N  plan-2  C15  0.020
 N7N  plan-3  C9   0.020
 N7N  plan-3  C12  0.020
 N7N  plan-3  O27  0.020
 N7N  plan-3  N28  0.020
 N7N  plan-3  C34  0.020
 N7N  plan-3  H23  0.020
 N7N  plan-4  C4   0.020
 N7N  plan-4  C5   0.020
 N7N  plan-4  C7   0.020
 N7N  plan-4  C9   0.020
 N7N  plan-4  N8   0.020
 N7N  plan-4  O14  0.020
 N7N  plan-5  O30  0.020
 N7N  plan-5  C32  0.020
 N7N  plan-5  O33  0.020
 N7N  plan-5  C31  0.020

