# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 07:10:30 2022
#   Inital geometry file: a 122 line input string
#   Ligand name: 1,2,3,9-tetramethoxy-6-methylidene-5~{H}-cyclohepta[a]naphthalen-8-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC1=CC=C2C(=CC1=O)C(=C)Cc3cc(OC)c(OC)c(OC)c23
#
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
 N9B  N9B  "1,2,3,9-tetramethoxy-6-methylidene-5~{H}-cyclohepta[a]naphthalen-8-one"
  ligand  45  25  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_N9B
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
 N9B  C11  C  CR6   0   0.013  6.5115  57.2605  87.4572
 N9B  C12  C  C     0   0.035  6.0270  56.0338  88.1303
 N9B  C13  C  C1    0  -0.264  5.6976  56.0768  89.4572
 N9B  C14  C  C1    0  -0.387  5.2601  55.0740  90.3525
 N9B  C15  C  C     0   0.292  5.1552  53.7216  90.2075
 N9B  C16  C  CH3   0  -0.446  4.3796  53.4484  92.4419
 N9B  C17  C  C     0   0.337  5.4606  52.9381  88.9967
 N9B  O3   O  O2    0  -0.429  4.7594  52.9139  91.1868
 N9B  C18  C  C1    0  -0.450  5.5968  53.5861  87.7125
 N9B  C19  C  C     0   0.128  5.8555  54.8623  87.3088
 N9B  C1   C  C     0   0.064  5.9244  55.1036  85.8469
 N9B  C    C  C2    0  -0.570  6.4910  54.2629  84.9846
 N9B  C3   C  CR6   0   0.052  6.1423  57.4922  86.1308
 N9B  C2   C  CH2   0  -0.563  5.3448  56.4252  85.4377
 N9B  C9   C  CR6   0   0.241  7.3477  58.2070  88.0737
 N9B  O2   O  O2    0  -0.483  7.7950  58.0420  89.3455
 N9B  C10  C  CH3   0  -0.411  8.9802  57.2648  89.4534
 N9B  C7   C  CR6   0   0.208  7.7599  59.3497  87.3971
 N9B  O1   O  O2    0  -0.478  8.6105  60.2235  87.9940
 N9B  C8   C  CH3   0  -0.409  7.9672  61.2652  88.7155
 N9B  C5   C  CR6   0   0.327  7.3298  59.5868  86.0842
 N9B  C4   C  CR16  0  -0.474  6.5341  58.6377  85.4536
 N9B  O    O  O2    0  -0.457  7.7587  60.7257  85.5228
 N9B  C6   C  CH3   0  -0.438  7.3689  61.0112  84.1936
 N9B  H1   H  H     0   0.275  5.7580  57.0454  89.9310
 N9B  H3   H  H     0   0.298  5.0101  55.4742  91.3269
 N9B  H4   H  HCH3  0   0.269  4.0749  52.6022  93.0517
 N9B  H5   H  HCH3  0   0.239  5.2115  53.9588  92.9328
 N9B  H6   H  HCH3  0   0.239  3.5401  54.1414  92.3495
 N9B  H7   H  H     0   0.266  5.4957  52.8631  86.9103
 N9B  H9   H  H     0   0.251  6.9674  53.3439  85.3010
 N9B  H10  H  H     0   0.252  6.5082  54.4821  83.9249
 N9B  H12  H  HCH2  0   0.273  5.3823  56.5515  84.3560
 N9B  H13  H  HCH3  0   0.241  9.2342  57.2141  90.5102
 N9B  H14  H  HCH3  0   0.224  8.8328  56.2486  89.0783
 N9B  H15  H  HCH3  0   0.227  9.8103  57.7238  88.9114
 N9B  H16  H  HCH3  0   0.237  8.7496  61.8900  89.1426
 N9B  H17  H  HCH3  0   0.222  7.3423  61.8827  88.0659
 N9B  H18  H  HCH3  0   0.221  7.3498  60.8728  89.5271
 N9B  H19  H  HCR6  0   0.281  6.2152  58.7688  84.4278
 N9B  H20  H  HCH3  0   0.262  7.8128  61.9711  83.9425
 N9B  H21  H  HCH3  0   0.231  7.7355  60.2584  83.4912
 N9B  H22  H  HCH3  0   0.231  6.2832  61.0875  84.0947
 N9B  H2   H  HCH2  0   0.273  4.2919  56.4818  85.7379
 N9B  O4   O  O     0  -0.448  5.4929  51.7138  89.0694

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
 N9B  C6   O    single    1.414  0.020  1.414
 N9B  C    C1   double    1.331  0.020  1.331
 N9B  C2   C1   single    1.500  0.020  1.500
 N9B  C2   C3   single    1.502  0.020  1.502
 N9B  C4   C3   aromatic  1.387  0.020  1.387
 N9B  C4   C5   aromatic  1.390  0.020  1.390
 N9B  O    C5   single    1.340  0.020  1.340
 N9B  C1   C19  single    1.483  0.020  1.483
 N9B  C3   C11  aromatic  1.396  0.020  1.396
 N9B  C5   C7   aromatic  1.402  0.020  1.402
 N9B  C19  C18  double    1.363  0.020  1.363
 N9B  C19  C12  single    1.441  0.020  1.441
 N9B  C11  C9   aromatic  1.405  0.020  1.405
 N9B  C11  C12  single    1.481  0.020  1.481
 N9B  C7   C9   aromatic  1.391  0.020  1.391
 N9B  C7   O1   single    1.358  0.020  1.358
 N9B  C18  C17  single    1.445  0.020  1.445
 N9B  C9   O2   single    1.358  0.020  1.358
 N9B  C12  C13  double    1.368  0.020  1.368
 N9B  O1   C8   single    1.421  0.020  1.421
 N9B  C17  O4   double    1.227  0.020  1.227
 N9B  C17  C15  single    1.474  0.020  1.474
 N9B  C10  O2   single    1.421  0.020  1.421
 N9B  C13  C14  single    1.414  0.020  1.414
 N9B  C15  C14  double    1.364  0.020  1.364
 N9B  C15  O3   single    1.330  0.020  1.330
 N9B  O3   C16  single    1.416  0.020  1.416
 N9B  C13  H1   single    0.930  0.020  1.080
 N9B  C14  H3   single    0.930  0.020  1.080
 N9B  C16  H4   single    0.970  0.020  1.090
 N9B  C16  H5   single    0.970  0.020  1.090
 N9B  C16  H6   single    0.970  0.020  1.090
 N9B  C18  H7   single    0.930  0.020  1.080
 N9B  C    H9   single    0.930  0.020  1.080
 N9B  C    H10  single    0.930  0.020  1.080
 N9B  C2   H12  single    0.970  0.020  1.090
 N9B  C10  H13  single    0.970  0.020  1.090
 N9B  C10  H14  single    0.970  0.020  1.090
 N9B  C10  H15  single    0.970  0.020  1.090
 N9B  C8   H16  single    0.970  0.020  1.090
 N9B  C8   H17  single    0.970  0.020  1.090
 N9B  C8   H18  single    0.970  0.020  1.090
 N9B  C4   H19  single    0.930  0.020  1.080
 N9B  C6   H20  single    0.970  0.020  1.090
 N9B  C6   H21  single    0.970  0.020  1.090
 N9B  C6   H22  single    0.970  0.020  1.090
 N9B  C2   H2   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
 N9B  C9   C11  C3   117.54  3.000
 N9B  C9   C11  C12  123.59  3.000
 N9B  C3   C11  C12  118.87  3.000
 N9B  C19  C12  C13  123.36  3.000
 N9B  C13  C12  C11  119.58  3.000
 N9B  C19  C12  C11  116.96  3.000
 N9B  H1   C13  C14  112.07  3.000
 N9B  H1   C13  C12  116.13  3.000
 N9B  C14  C13  C12  131.80  3.000
 N9B  H3   C14  C15  116.38  3.000
 N9B  H3   C14  C13  112.28  3.000
 N9B  C15  C14  C13  131.28  3.000
 N9B  O3   C15  C17  110.10  3.000
 N9B  O3   C15  C14  123.15  3.000
 N9B  C17  C15  C14  126.74  3.000
 N9B  H6   C16  H5   109.07  3.000
 N9B  H6   C16  H4   109.02  3.000
 N9B  H5   C16  H4   108.98  3.000
 N9B  H6   C16  O3   111.75  3.000
 N9B  H5   C16  O3   111.74  3.000
 N9B  H4   C16  O3   106.18  3.000
 N9B  C18  C17  O4   119.85  3.000
 N9B  O4   C17  C15  119.15  3.000
 N9B  C18  C17  C15  120.75  3.000
 N9B  C16  O3   C15  120.22  3.000
 N9B  H7   C18  C19  115.01  3.000
 N9B  H7   C18  C17  110.46  3.000
 N9B  C19  C18  C17  134.50  3.000
 N9B  C1   C19  C18  116.93  3.000
 N9B  C18  C19  C12  127.94  3.000
 N9B  C1   C19  C12  115.09  3.000
 N9B  C2   C1   C    122.98  3.000
 N9B  C2   C1   C19  113.22  3.000
 N9B  C    C1   C19  123.75  3.000
 N9B  H10  C    H9   116.82  3.000
 N9B  H10  C    C1   120.87  3.000
 N9B  H9   C    C1   122.30  3.000
 N9B  C4   C3   C2   120.76  3.000
 N9B  C4   C3   C11  121.74  3.000
 N9B  C2   C3   C11  117.45  3.000
 N9B  H2   C2   H12  107.39  3.000
 N9B  H2   C2   C3   110.30  3.000
 N9B  H12  C2   C3   110.95  3.000
 N9B  H2   C2   C1   109.99  3.000
 N9B  H12  C2   C1   111.08  3.000
 N9B  C3   C2   C1   107.15  3.000
 N9B  C7   C9   O2   117.25  3.000
 N9B  O2   C9   C11  121.66  3.000
 N9B  C7   C9   C11  121.09  3.000
 N9B  C10  O2   C9   114.34  3.000
 N9B  H15  C10  H14  108.83  3.000
 N9B  H15  C10  H13  108.91  3.000
 N9B  H14  C10  H13  108.74  3.000
 N9B  H15  C10  O2   111.48  3.000
 N9B  H14  C10  O2   111.71  3.000
 N9B  H13  C10  O2   107.09  3.000
 N9B  C5   C7   O1   119.68  3.000
 N9B  O1   C7   C9   120.04  3.000
 N9B  C5   C7   C9   120.25  3.000
 N9B  C8   O1   C7   114.29  3.000
 N9B  H18  C8   H17  108.75  3.000
 N9B  H18  C8   H16  108.71  3.000
 N9B  H17  C8   H16  108.66  3.000
 N9B  H18  C8   O1   111.69  3.000
 N9B  H17  C8   O1   111.80  3.000
 N9B  H16  C8   O1   107.13  3.000
 N9B  O    C5   C4   124.99  3.000
 N9B  O    C5   C7   115.97  3.000
 N9B  C4   C5   C7   119.03  3.000
 N9B  H19  C4   C5   121.07  3.000
 N9B  H19  C4   C3   118.66  3.000
 N9B  C5   C4   C3   120.27  3.000
 N9B  C6   O    C5   118.49  3.000
 N9B  H22  C6   H21  108.85  3.000
 N9B  H22  C6   H20  108.86  3.000
 N9B  H21  C6   H20  108.84  3.000
 N9B  H22  C6   O    111.90  3.000
 N9B  H21  C6   O    111.87  3.000
 N9B  H20  C6   O    106.43  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
 N9B  CONST_01  C5   C4   C3   C11     0.00   0.0  0
 N9B  CONST_02  C5   C7   C9   C11     0.00   0.0  0
 N9B  CONST_03  C7   C5   C4   C3      0.00   0.0  0
 N9B  CONST_04  C7   C9   C11  C3      0.00   0.0  0
 N9B  CONST_05  C4   C3   C11  C9      0.00   0.0  0
 N9B  CONST_06  C4   C5   C7   C9      0.00   0.0  0
 N9B  CONST_07  O1   C7   C9   C11   180.00   0.0  0
 N9B  CONST_08  O2   C9   C11  C12     0.00   0.0  0
 N9B  CONST_09  O    C5   C4   C3    180.00   0.0  0
 N9B  CONST_10  O2   C9   C11  C3    180.00   0.0  0
 N9B  CONST_11  O    C5   C7   C9    180.00   0.0  0
 N9B  CONST_12  C5   C7   C9   O2    180.00   0.0  0
 N9B  CONST_13  C4   C5   C7   O1    180.00   0.0  0
 N9B  CONST_14  H19  C4   C3   C11   180.00   0.0  0
 N9B  CONST_15  H19  C4   C3   C2      0.00   0.0  0
 N9B  CONST_16  H19  C4   C5   C7    180.00   0.0  0
 N9B  Var_01    C1   C2   C3   C11   -40.63  30.0  1
 N9B  Var_02    C3   C2   C1   C19    60.61  30.0  1
 N9B  Var_03    C4   C3   C2   C1    137.03  30.0  1
 N9B  Var_04    C3   C2   C1   C    -116.79  30.0  1
 N9B  Var_05    H12  C2   C3   C11  -162.04  30.0  1
 N9B  Var_06    H2   C2   C3   C11    79.08  30.0  1
 N9B  Var_07    H12  C2   C1   C19  -178.06  30.0  1
 N9B  Var_08    H2   C2   C1   C19   -59.30  30.0  1
 N9B  Var_09    H12  C2   C3   C4     15.62  30.0  1
 N9B  Var_10    H2   C2   C3   C4   -103.26  30.0  1
 N9B  Var_11    C10  O2   C9   C11    85.92  30.0  2
 N9B  Var_12    C8   O1   C7   C9    -91.11  30.0  2
 N9B  Var_13    C7   C9   O2   C10   -93.57  30.0  2
 N9B  Var_14    C6   O    C5   C7    179.30  30.0  1
 N9B  Var_15    C5   C7   O1   C8     90.64  30.0  2
 N9B  Var_16    C6   O    C5   C4      0.88  30.0  1
 N9B  Var_17    H9   C    C1   C19    -1.51   0.0  2
 N9B  Var_18    H10  C    C1   C19   179.52   0.0  2
 N9B  Var_19    H9   C    C1   C2    175.61   0.0  2
 N9B  Var_20    H10  C    C1   C2     -3.36   0.0  2
 N9B  Var_21    H12  C2   C1   C       4.54  30.0  1
 N9B  Var_22    H2   C2   C1   C     123.30  30.0  1
 N9B  Var_23    H4   C16  O3   C15   178.43  30.0  3
 N9B  Var_24    H5   C16  O3   C15   -62.87  30.0  3
 N9B  Var_25    H6   C16  O3   C15    59.67  30.0  3
 N9B  Var_26    H13  C10  O2   C9    179.63  30.0  3
 N9B  Var_27    H14  C10  O2   C9    -61.41  30.0  3
 N9B  Var_28    H15  C10  O2   C9     60.59  30.0  3
 N9B  Var_29    H16  C8   O1   C7    179.94  30.0  3
 N9B  Var_30    H17  C8   O1   C7    -61.12  30.0  3
 N9B  Var_31    H18  C8   O1   C7     61.00  30.0  3
 N9B  Var_32    H20  C6   O    C5    179.52  30.0  3
 N9B  Var_33    H21  C6   O    C5    -61.72  30.0  3
 N9B  Var_34    H22  C6   O    C5     60.73  30.0  3

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
 N9B  plan-1  C15  0.020
 N9B  plan-1  C17  0.020
 N9B  plan-1  C18  0.020
 N9B  plan-1  O4   0.020
 N9B  plan-2  C11  0.020
 N9B  plan-2  C12  0.020
 N9B  plan-2  C3   0.020
 N9B  plan-2  C2   0.020
 N9B  plan-2  C9   0.020
 N9B  plan-2  O2   0.020
 N9B  plan-2  C7   0.020
 N9B  plan-2  O1   0.020
 N9B  plan-2  C5   0.020
 N9B  plan-2  C4   0.020
 N9B  plan-2  O    0.020
 N9B  plan-2  H19  0.020
 N9B  plan-3  C19  0.020
 N9B  plan-3  C1   0.020
 N9B  plan-3  C    0.020
 N9B  plan-3  C2   0.020
 N9B  plan-3  H9   0.020
 N9B  plan-3  H10  0.020
 N9B  plan-4  C12  0.020
 N9B  plan-4  C17  0.020
 N9B  plan-4  C18  0.020
 N9B  plan-4  C19  0.020
 N9B  plan-4  C1   0.020
 N9B  plan-4  H7   0.020
 N9B  plan-5  C11  0.020
 N9B  plan-5  C12  0.020
 N9B  plan-5  C13  0.020
 N9B  plan-5  C14  0.020
 N9B  plan-5  C19  0.020
 N9B  plan-5  H1   0.020

