# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 12:04:47 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: [(7~{S})-6,6-bis(oxidanyl)-4-phenyl-5,7,8,9-tetrahydrobenzo[7]annulen-7-yl]azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [NH3+][C@H]1CCc2cccc(c3ccccc3)c2CC1(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
 7ML  7ML  '[(7~{S})-6,6-bis(oxidanyl)-4-phenyl-5,7,8,9-tetrahydrobenzo[7]annulen-7-yl]azanium'  ligand  40  20  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7ML
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
 7ML  C1   C  CR16  0  -0.297  -2.7329   0.0542   1.1476
 7ML  C10  C  CR6   0   0.089   0.2812  -0.8054  -0.4681
 7ML  C11  C  CR6   0   0.144   1.3641  -1.6928  -0.4433
 7ML  C12  C  CR16  0  -0.334   1.1756  -3.0005  -0.0139
 7ML  C13  C  CH2   0  -0.679   0.5053   0.6158  -0.9081
 7ML  C14  C  CH2   0  -0.555   2.7393  -1.2356  -0.8403
 7ML  C15  C  CT    0   0.520   1.3504   1.4604   0.0617
 7ML  C16  C  CH2   0  -0.435   3.3413  -0.2036   0.1170
 7ML  C17  C  CH1   0  -0.152   2.8530   1.2129  -0.1255
 7ML  C2   C  CR16  0  -0.239  -3.8654   0.8588   1.1599
 7ML  C3   C  CR16  0  -0.262  -4.4550   1.2497  -0.0341
 7ML  C4   C  CR16  0  -0.242  -3.9074   0.8312  -1.2406
 7ML  C5   C  CR16  0  -0.281  -2.7748   0.0299  -1.2521
 7ML  C6   C  CR6   0   0.009  -2.1742  -0.3661  -0.0575
 7ML  C7   C  CR6   0   0.023  -0.9811  -1.2506  -0.0563
 7ML  C8   C  CR16  0  -0.237  -0.0727  -3.4398   0.4006
 7ML  C9   C  CR16  0  -0.299  -1.1439  -2.5648   0.3813
 7ML  N1   N  NT3   1  -0.793   3.5940   2.1361   0.7868
 7ML  O2   O  OH1   0  -0.659   1.0637   1.1800   1.3949
 7ML  H1   H  HCR6  0   0.256  -2.2817  -0.2523   2.0839
 7ML  H8   H  HCR6  0   0.252   2.0182  -3.6813   0.0008
 7ML  H10  H  HCH2  0   0.284   0.9699   0.6462  -1.8975
 7ML  H9   H  HCH2  0   0.284  -0.4537   1.1243  -1.0280
 7ML  H12  H  HCH2  0   0.277   3.4042  -2.0991  -0.8594
 7ML  H11  H  HCH2  0   0.258   2.7352  -0.8357  -1.8601
 7ML  H13  H  HCH2  0   0.261   3.1567  -0.5038   1.1512
 7ML  H14  H  HCH2  0   0.273   4.4248  -0.2047  -0.0235
 7ML  H15  H  HCH1  0   0.321   3.1272   1.5220  -1.1357
 7ML  H2   H  HCR6  0   0.259  -4.2866   1.1771   2.1046
 7ML  H3   H  HCR6  0   0.259  -5.3381   1.8751  -0.0260
 7ML  H4   H  HCR6  0   0.259  -4.3658   1.1244  -2.1762
 7ML  H5   H  HCR6  0   0.258  -2.3564  -0.2979  -2.1961
 7ML  H6   H  HCR6  0   0.257  -0.2090  -4.4602   0.7344
 7ML  H7   H  HCR6  0   0.252  -2.1235  -2.8994   0.6987
 7ML  H19  H  HNT3  0   0.477   4.6000   2.0758   0.6318
 7ML  H20  H  HNT3  0   0.472   3.3271   3.1103   0.6369
 7ML  H16  H  HOH1  0   0.462   0.2656   3.0741  -0.1898
 7ML  H17  H  HOH1  0   0.461   0.1138   1.0775   1.5291
 7ML  H18  H  HNT3  0   0.467   3.4271   1.9225   1.7714
 7ML  O1   O  OH1   0  -0.671   1.1958   2.8219  -0.2324

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
 7ML  C16  C14  single    1.531  0.020  1.531
 7ML  C16  C17  single    1.518  0.020  1.518
 7ML  N1   C17  single    1.495  0.020  1.495
 7ML  C14  C11  single    1.503  0.020  1.503
 7ML  C17  C15  single    1.534  0.020  1.534
 7ML  C12  C11  aromatic  1.389  0.020  1.389
 7ML  C12  C8   aromatic  1.387  0.020  1.387
 7ML  C11  C10  aromatic  1.400  0.020  1.400
 7ML  C8   C9   aromatic  1.383  0.020  1.383
 7ML  O2   C15  single    1.392  0.020  1.392
 7ML  C15  O1   single    1.401  0.020  1.401
 7ML  C15  C13  single    1.539  0.020  1.539
 7ML  C10  C13  single    1.505  0.020  1.505
 7ML  C10  C7   aromatic  1.400  0.020  1.400
 7ML  C9   C7   aromatic  1.395  0.020  1.395
 7ML  C7   C6   single    1.485  0.020  1.485
 7ML  C6   C5   aromatic  1.395  0.020  1.395
 7ML  C6   C1   aromatic  1.393  0.020  1.393
 7ML  C5   C4   aromatic  1.387  0.020  1.387
 7ML  C1   C2   aromatic  1.389  0.020  1.389
 7ML  C4   C3   aromatic  1.389  0.020  1.389
 7ML  C2   C3   aromatic  1.388  0.020  1.388
 7ML  C1   H1   single    0.930  0.020  1.080
 7ML  C12  H8   single    0.930  0.020  1.080
 7ML  C13  H10  single    0.970  0.020  1.090
 7ML  C13  H9   single    0.970  0.020  1.090
 7ML  C14  H12  single    0.970  0.020  1.090
 7ML  C14  H11  single    0.970  0.020  1.090
 7ML  C16  H13  single    0.970  0.020  1.090
 7ML  C16  H14  single    0.970  0.020  1.090
 7ML  C17  H15  single    0.970  0.020  1.090
 7ML  C2   H2   single    0.930  0.020  1.080
 7ML  C3   H3   single    0.930  0.020  1.080
 7ML  C4   H4   single    0.930  0.020  1.080
 7ML  C5   H5   single    0.930  0.020  1.080
 7ML  C8   H6   single    0.930  0.020  1.080
 7ML  C9   H7   single    0.930  0.020  1.080
 7ML  N1   H19  single    0.890  0.020  1.040
 7ML  N1   H20  single    0.890  0.020  1.040
 7ML  O1   H16  single    0.850  0.020  0.980
 7ML  O2   H17  single    0.850  0.020  0.980
 7ML  H18  N1   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
 7ML  H1   C1   C6   119.68  3.000
 7ML  H1   C1   C2   119.71  3.000
 7ML  C6   C1   C2   120.62  3.000
 7ML  C7   C10  C13  121.36  3.000
 7ML  C7   C10  C11  119.37  3.000
 7ML  C13  C10  C11  119.25  3.000
 7ML  C14  C11  C12  119.49  3.000
 7ML  C12  C11  C10  119.81  3.000
 7ML  C14  C11  C10  120.68  3.000
 7ML  H8   C12  C8   119.80  3.000
 7ML  H8   C12  C11  119.36  3.000
 7ML  C8   C12  C11  120.84  3.000
 7ML  H9   C13  H10  105.12  3.000
 7ML  H9   C13  C15  107.21  3.000
 7ML  H10  C13  C15  108.76  3.000
 7ML  H9   C13  C10  109.95  3.000
 7ML  H10  C13  C10  110.74  3.000
 7ML  C15  C13  C10  114.58  3.000
 7ML  H11  C14  H12  105.97  3.000
 7ML  H11  C14  C16  109.73  3.000
 7ML  H12  C14  C16  107.77  3.000
 7ML  H11  C14  C11  110.70  3.000
 7ML  H12  C14  C11  108.78  3.000
 7ML  C16  C14  C11  113.56  3.000
 7ML  O2   C15  O1   111.95  3.000
 7ML  O1   C15  C17  103.84  3.000
 7ML  O2   C15  C17  106.62  3.000
 7ML  O1   C15  C13  109.90  3.000
 7ML  O2   C15  C13  112.32  3.000
 7ML  C17  C15  C13  111.87  3.000
 7ML  H14  C16  H13  106.80  3.000
 7ML  H14  C16  C17  107.42  3.000
 7ML  H13  C16  C17  110.69  3.000
 7ML  H14  C16  C14  107.99  3.000
 7ML  H13  C16  C14  109.90  3.000
 7ML  C17  C16  C14  113.75  3.000
 7ML  H15  C17  N1   105.40  3.000
 7ML  H15  C17  C16  109.35  3.000
 7ML  N1   C17  C16  108.63  3.000
 7ML  H15  C17  C15  108.25  3.000
 7ML  N1   C17  C15  108.15  3.000
 7ML  C16  C17  C15  116.49  3.000
 7ML  H2   C2   C3   120.19  3.000
 7ML  H2   C2   C1   119.69  3.000
 7ML  C3   C2   C1   120.12  3.000
 7ML  H3   C3   C4   120.14  3.000
 7ML  H3   C3   C2   120.20  3.000
 7ML  C4   C3   C2   119.66  3.000
 7ML  H4   C4   C5   119.67  3.000
 7ML  H4   C4   C3   120.14  3.000
 7ML  C5   C4   C3   120.19  3.000
 7ML  H5   C5   C6   119.62  3.000
 7ML  H5   C5   C4   119.82  3.000
 7ML  C6   C5   C4   120.56  3.000
 7ML  C7   C6   C5   121.05  3.000
 7ML  C5   C6   C1   118.85  3.000
 7ML  C7   C6   C1   120.07  3.000
 7ML  C9   C7   C6   117.88  3.000
 7ML  C6   C7   C10  122.32  3.000
 7ML  C9   C7   C10  119.80  3.000
 7ML  H6   C8   C9   120.21  3.000
 7ML  H6   C8   C12  120.28  3.000
 7ML  C9   C8   C12  119.51  3.000
 7ML  H7   C9   C8   120.07  3.000
 7ML  H7   C9   C7   119.26  3.000
 7ML  C8   C9   C7   120.67  3.000
 7ML  H18  N1   H20  107.36  3.000
 7ML  H18  N1   H19  107.18  3.000
 7ML  H20  N1   H19  106.97  3.000
 7ML  H18  N1   C17  112.24  3.000
 7ML  H20  N1   C17  111.72  3.000
 7ML  H19  N1   C17  111.09  3.000
 7ML  H17  O2   C15  110.94  3.000
 7ML  H16  O1   C15  110.56  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
 7ML  CONST_03  C4  C5   C6   C1     0.00  0.0  0
 7ML  CONST_04  C4  C3   C2   C1     0.00  0.0  0
 7ML  CONST_05  C8  C9   C7   C10    0.00  0.0  0
 7ML  CONST_07  C9  C8   C12  C11    0.00  0.0  0
 7ML  CONST_08  C7  C9   C8   C12    0.00  0.0  0
 7ML  CONST_09  C7  C6   C1   C2   180.00  0.0  0
 7ML  CONST_10  C5  C6   C1   C2     0.00  0.0  0
 7ML  CONST_11  C5  C4   C3   C2     0.00  0.0  0
 7ML  CONST_12  C6  C5   C4   C3     0.00  0.0  0
 7ML  CONST_13  C6  C1   C2   C3     0.00  0.0  0
 7ML  CONST_14  C7  C6   C5   C4   180.00  0.0  0
 7ML  CONST_16  C8  C9   C7   C6   180.00  0.0  0
 7ML  CONST_17  H5  C5   C6   C1   180.00  0.0  0
 7ML  CONST_18  H3  C3   C2   C1   180.00  0.0  0
 7ML  CONST_19  H7  C9   C7   C10  180.00  0.0  0
 7ML  CONST_20  H6  C8   C12  C11  180.00  0.0  0
 7ML  CONST_21  H4  C4   C3   C2   180.00  0.0  0
 7ML  CONST_22  H1  C1   C2   C3   180.00  0.0  0
 7ML  CONST_23  H2  C2   C3   C4   180.00  0.0  0
 7ML  CONST_24  H8  C12  C8   C9   180.00  0.0  0

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
 7ML  chir_01  C17  C16  N1  C15  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
 7ML  plan-1  C1   0.020
 7ML  plan-1  C2   0.020
 7ML  plan-1  C3   0.020
 7ML  plan-1  C4   0.020
 7ML  plan-1  C5   0.020
 7ML  plan-1  C6   0.020
 7ML  plan-1  C7   0.020
 7ML  plan-1  H1   0.020
 7ML  plan-1  H2   0.020
 7ML  plan-1  H3   0.020
 7ML  plan-1  H4   0.020
 7ML  plan-1  H5   0.020
 7ML  plan-2  C10  0.020
 7ML  plan-2  C11  0.020
 7ML  plan-2  C12  0.020
 7ML  plan-2  C13  0.020
 7ML  plan-2  C14  0.020
 7ML  plan-2  C6   0.020
 7ML  plan-2  C7   0.020
 7ML  plan-2  C8   0.020
 7ML  plan-2  C9   0.020
 7ML  plan-2  H8   0.020
 7ML  plan-2  H6   0.020
 7ML  plan-2  H7   0.020

