# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 20:52:37 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: (5S,10R)-5-methyl-10,11-dihydro-5H-5,10-epiminodibenzo[a,d][7]annulene
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]12N[C@H](Cc3ccccc13)c4ccccc24
#
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
 BMK  BMK  (5S,10R)-5-methyl-10,11-dihydro-5H-5,10-epiminodibenzo[a,d][7]annulene  ligand  32  17  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_BMK
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
 BMK  C7   C  CH3   0  -0.682   0.0936   2.2141   1.6291
 BMK  C    C  CT    0  -0.112   0.0010   0.8298   1.0182
 BMK  C5   C  CR6   0   0.174   1.2194   0.4162   0.1920
 BMK  C10  C  CR16  0  -0.326   2.1025   1.3361  -0.3641
 BMK  C14  C  CR16  0  -0.256   3.1827   0.9187  -1.1303
 BMK  C15  C  CR16  0  -0.261   3.3867  -0.4352  -1.3523
 BMK  C11  C  CR16  0  -0.291   2.5095  -1.3590  -0.8019
 BMK  C6   C  CR6   0   0.049   1.4250  -0.9538  -0.0311
 BMK  C4   C  CH2   0  -0.479   0.5098  -1.9962   0.5714
 BMK  C1   C  CH1   0  -0.211  -0.6898  -1.3590   1.2819
 BMK  N    N  NH1   0  -0.559  -0.2659  -0.1849   2.0472
 BMK  C3   C  CR6   0   0.155  -1.6078  -0.7115   0.2800
 BMK  C9   C  CR16  0  -0.340  -2.6586  -1.2244  -0.4543
 BMK  C13  C  CR16  0  -0.260  -3.3146  -0.3805  -1.3505
 BMK  C12  C  CR16  0  -0.258  -2.9080   0.9392  -1.5074
 BMK  C8   C  CR16  0  -0.348  -1.8361   1.4465  -0.7731
 BMK  C2   C  CR6   0   0.172  -1.2023   0.6084   0.1224
 BMK  H1   H  HCH3  0   0.232   0.1550   2.9961   0.8725
 BMK  H2   H  HCH3  0   0.246  -0.7916   2.4039   2.2351
 BMK  H3   H  HCH3  0   0.242   0.9731   2.3009   2.2694
 BMK  H4   H  HCR6  0   0.244   1.9574   2.3962  -0.2012
 BMK  H5   H  HCR6  0   0.251   3.8621   1.6502  -1.5487
 BMK  H6   H  HCR6  0   0.251   4.2263  -0.7724  -1.9467
 BMK  H7   H  HCR6  0   0.246   2.6714  -2.4176  -0.9714
 BMK  H8   H  HCH2  0   0.255   0.1760  -2.6961  -0.1993
 BMK  H9   H  HCH2  0   0.261   1.0786  -2.5917   1.2934
 BMK  H10  H  HCH1  0   0.254  -1.1927  -2.0910   1.9177
 BMK  H11  H  HNH1  0   0.348   0.5731  -0.3784   2.5854
 BMK  H13  H  HCR6  0   0.250  -2.9758  -2.2537  -0.3371
 BMK  H14  H  HCR6  0   0.254  -4.1511  -0.7557  -1.9263
 BMK  H15  H  HCR6  0   0.254  -3.4287   1.5803  -2.2069
 BMK  H16  H  HCR6  0   0.247  -1.5195   2.4739  -0.9072

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
 BMK  C12  C8   aromatic  1.395  0.020  1.395
 BMK  C12  C13  aromatic  1.390  0.020  1.390
 BMK  C8   C2   aromatic  1.381  0.020  1.381
 BMK  C13  C9   aromatic  1.395  0.020  1.395
 BMK  C2   C3   aromatic  1.390  0.020  1.390
 BMK  C2   C    single    1.516  0.020  1.516
 BMK  C9   C3   aromatic  1.381  0.020  1.381
 BMK  C7   C    single    1.516  0.020  1.516
 BMK  C3   C1   single    1.505  0.020  1.505
 BMK  C    C5   single    1.529  0.020  1.529
 BMK  C    N    single    1.470  0.020  1.470
 BMK  C10  C5   aromatic  1.391  0.020  1.391
 BMK  C10  C14  aromatic  1.389  0.020  1.389
 BMK  C5   C6   aromatic  1.403  0.020  1.403
 BMK  C14  C15  aromatic  1.387  0.020  1.387
 BMK  N    C1   single    1.464  0.020  1.464
 BMK  C1   C4   single    1.533  0.020  1.533
 BMK  C6   C4   single    1.512  0.020  1.512
 BMK  C6   C11  aromatic  1.391  0.020  1.391
 BMK  C15  C11  aromatic  1.388  0.020  1.388
 BMK  C7   H1   single    0.970  0.020  1.090
 BMK  C7   H2   single    0.970  0.020  1.090
 BMK  C7   H3   single    0.970  0.020  1.090
 BMK  C10  H4   single    0.930  0.020  1.080
 BMK  C14  H5   single    0.930  0.020  1.080
 BMK  C15  H6   single    0.930  0.020  1.080
 BMK  C11  H7   single    0.930  0.020  1.080
 BMK  C4   H8   single    0.970  0.020  1.090
 BMK  C4   H9   single    0.970  0.020  1.090
 BMK  C1   H10  single    0.970  0.020  1.090
 BMK  N    H11  single    0.890  0.020  1.040
 BMK  C9   H13  single    0.930  0.020  1.080
 BMK  C13  H14  single    0.930  0.020  1.080
 BMK  C12  H15  single    0.930  0.020  1.080
 BMK  C8   H16  single    0.930  0.020  1.080

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
 BMK  H3   C7   H2   108.34  3.000
 BMK  H3   C7   H1   107.75  3.000
 BMK  H2   C7   H1   107.87  3.000
 BMK  H3   C7   C    111.00  3.000
 BMK  H2   C7   C    109.48  3.000
 BMK  H1   C7   C    112.26  3.000
 BMK  C2   C    N     99.72  3.000
 BMK  N    C    C5   109.65  3.000
 BMK  C2   C    C5   105.88  3.000
 BMK  N    C    C7   111.06  3.000
 BMK  C5   C    C7   114.59  3.000
 BMK  C2   C    C7   114.83  3.000
 BMK  C6   C5   C10  119.28  3.000
 BMK  C6   C5   C    117.82  3.000
 BMK  C10  C5   C    122.88  3.000
 BMK  H4   C10  C14  118.80  3.000
 BMK  H4   C10  C5   120.16  3.000
 BMK  C14  C10  C5   121.04  3.000
 BMK  H5   C14  C15  120.36  3.000
 BMK  H5   C14  C10  119.89  3.000
 BMK  C15  C14  C10  119.74  3.000
 BMK  H6   C15  C11  120.05  3.000
 BMK  H6   C15  C14  120.40  3.000
 BMK  C11  C15  C14  119.56  3.000
 BMK  H7   C11  C6   119.18  3.000
 BMK  H7   C11  C15  119.58  3.000
 BMK  C6   C11  C15  121.25  3.000
 BMK  C4   C6   C11  119.46  3.000
 BMK  C11  C6   C5   119.13  3.000
 BMK  C4   C6   C5   121.40  3.000
 BMK  H9   C4   H8   105.98  3.000
 BMK  H9   C4   C1   109.08  3.000
 BMK  H8   C4   C1   110.72  3.000
 BMK  H9   C4   C6   108.85  3.000
 BMK  H8   C4   C6   110.20  3.000
 BMK  C1   C4   C6   111.82  3.000
 BMK  H10  C1   C3   113.26  3.000
 BMK  H10  C1   N    111.50  3.000
 BMK  C3   C1   N    100.34  3.000
 BMK  H10  C1   C4   110.58  3.000
 BMK  N    C1   C4   110.42  3.000
 BMK  C3   C1   C4   110.34  3.000
 BMK  H11  N    C1   111.31  3.000
 BMK  H11  N    C    110.65  3.000
 BMK  C1   N    C    103.91  3.000
 BMK  C2   C3   C9   120.97  3.000
 BMK  C9   C3   C1   131.17  3.000
 BMK  C2   C3   C1   107.83  3.000
 BMK  H13  C9   C13  120.44  3.000
 BMK  H13  C9   C3   121.21  3.000
 BMK  C13  C9   C3   118.35  3.000
 BMK  H14  C13  C12  119.68  3.000
 BMK  H14  C13  C9   119.70  3.000
 BMK  C12  C13  C9   120.62  3.000
 BMK  H15  C12  C8   119.64  3.000
 BMK  H15  C12  C13  119.64  3.000
 BMK  C8   C12  C13  120.72  3.000
 BMK  H16  C8   C2   121.45  3.000
 BMK  H16  C8   C12  120.28  3.000
 BMK  C2   C8   C12  118.26  3.000
 BMK  C8   C2   C3   121.07  3.000
 BMK  C3   C2   C    107.65  3.000
 BMK  C8   C2   C    131.21  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
 BMK  CONST_01  C15  C14  C10  C5     0.00  0.0  0
 BMK  CONST_02  C11  C15  C14  C10    0.00  0.0  0
 BMK  CONST_03  C6   C11  C15  C14    0.00  0.0  0
 BMK  CONST_04  C12  C13  C9   C3     0.00  0.0  0
 BMK  CONST_05  C8   C12  C13  C9     0.00  0.0  0
 BMK  CONST_06  C2   C8   C12  C13    0.00  0.0  0
 BMK  CONST_07  H5   C14  C10  C5   180.00  0.0  0
 BMK  CONST_08  H6   C15  C14  C10  180.00  0.0  0
 BMK  CONST_09  H7   C11  C15  C14  180.00  0.0  0
 BMK  CONST_10  H4   C10  C14  C15  180.00  0.0  0
 BMK  CONST_11  H14  C13  C9   C3   180.00  0.0  0
 BMK  CONST_12  H15  C12  C13  C9   180.00  0.0  0
 BMK  CONST_13  H16  C8   C12  C13  180.00  0.0  0
 BMK  CONST_14  H13  C9   C13  C12  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
 BMK  chir_01  C   C2  C5  N   positiv
 BMK  chir_02  C1  N   C4  C3  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
 BMK  plan-1  C    0.020
 BMK  plan-1  C5   0.020
 BMK  plan-1  C10  0.020
 BMK  plan-1  C14  0.020
 BMK  plan-1  C15  0.020
 BMK  plan-1  C11  0.020
 BMK  plan-1  C6   0.020
 BMK  plan-1  C4   0.020
 BMK  plan-1  H4   0.020
 BMK  plan-1  H5   0.020
 BMK  plan-1  H6   0.020
 BMK  plan-1  H7   0.020
 BMK  plan-2  C    0.020
 BMK  plan-2  C1   0.020
 BMK  plan-2  C3   0.020
 BMK  plan-2  C9   0.020
 BMK  plan-2  C13  0.020
 BMK  plan-2  C12  0.020
 BMK  plan-2  C8   0.020
 BMK  plan-2  C2   0.020
 BMK  plan-2  H13  0.020
 BMK  plan-2  H14  0.020
 BMK  plan-2  H15  0.020
 BMK  plan-2  H16  0.020

