# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  8 20:57:04 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: ~{N}-(5-oxidanylidene-7,8-dihydro-6~{H}-naphthalen-2-yl)ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Nc1ccc2C(=O)CCCc2c1
#
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
 ZHA  ZHA  ~{N}-(5-oxidanylidene-7,8-dihydro-6~{H}-naphthalen-2-yl)ethanamide  ligand  28  15  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_ZHA
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
 ZHA  C13  C  CH2   0  -0.552  -3.8611  -0.2302  -0.2613
 ZHA  C01  C  CR16  0  -0.247  -0.4476   1.4953  -0.0210
 ZHA  C02  C  CR6   0  -0.083  -1.4244   0.5027  -0.0974
 ZHA  C03  C  CR6   0   0.137  -1.0259  -0.8392  -0.1280
 ZHA  C04  C  CR16  0  -0.391   0.3249  -1.1405  -0.0794
 ZHA  C05  C  CR6   0   0.421   1.2991  -0.1440  -0.0041
 ZHA  C06  C  CR16  0  -0.314   0.8991   1.1966   0.0232
 ZHA  N07  N  NH1   0  -0.731   2.6230  -0.5688   0.0467
 ZHA  C08  C  C     0   0.525   3.7725   0.1617   0.1352
 ZHA  C09  C  CH3   0  -0.756   5.0281  -0.6703   0.1272
 ZHA  O10  O  O     0  -0.447   3.8031   1.3738   0.1855
 ZHA  C11  C  CH2   0  -0.496  -2.0427  -1.9419  -0.2211
 ZHA  C12  C  CH2   0  -0.453  -3.3763  -1.5231   0.3777
 ZHA  C14  C  C     0   0.358  -2.8550   0.8906  -0.1468
 ZHA  O15  O  O     0  -0.358  -3.1975   2.0513  -0.1176
 ZHA  H1   H  HCH2  0   0.251  -4.0389  -0.3967  -1.3308
 ZHA  H2   H  HCH2  0   0.265  -4.8095   0.1015   0.1624
 ZHA  H3   H  HCR6  0   0.263  -0.7548   2.5328   0.0030
 ZHA  H4   H  HCR6  0   0.223   0.6292  -2.1819  -0.0965
 ZHA  H5   H  HCR6  0   0.283   1.6231   1.9912   0.0784
 ZHA  H6   H  HNH1  0   0.385   2.7425  -1.5678   0.0148
 ZHA  H7   H  HCH3  0   0.263   5.4223  -0.7125  -0.8895
 ZHA  H8   H  HCH3  0   0.269   5.7826  -0.2033   0.7551
 ZHA  H9   H  HCH3  0   0.233   4.8820  -1.6937   0.4680
 ZHA  H10  H  HCH2  0   0.241  -2.1836  -2.2066  -1.2750
 ZHA  H11  H  HCH2  0   0.240  -1.6632  -2.8400   0.2700
 ZHA  H12  H  HCH2  0   0.231  -3.2652  -1.3835   1.4564
 ZHA  H13  H  HCH2  0   0.239  -4.1184  -2.3102   0.2383

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
 ZHA  O10  C08  double    1.214  0.020  1.214
 ZHA  C08  C09  single    1.506  0.020  1.506
 ZHA  C08  N07  single    1.365  0.020  1.365
 ZHA  C06  C01  aromatic  1.380  0.020  1.380
 ZHA  C06  C05  aromatic  1.399  0.020  1.399
 ZHA  C01  C02  aromatic  1.395  0.020  1.395
 ZHA  O15  C14  double    1.211  0.020  1.211
 ZHA  N07  C05  single    1.391  0.020  1.391
 ZHA  C05  C04  aromatic  1.396  0.020  1.396
 ZHA  C02  C14  single    1.483  0.020  1.483
 ZHA  C02  C03  aromatic  1.400  0.020  1.400
 ZHA  C14  C13  single    1.510  0.020  1.510
 ZHA  C04  C03  aromatic  1.385  0.020  1.385
 ZHA  C03  C11  single    1.503  0.020  1.503
 ZHA  C13  C12  single    1.522  0.020  1.522
 ZHA  C11  C12  single    1.521  0.020  1.521
 ZHA  C13  H1   single    0.970  0.020  1.090
 ZHA  C13  H2   single    0.970  0.020  1.090
 ZHA  C01  H3   single    0.930  0.020  1.080
 ZHA  C04  H4   single    0.930  0.020  1.080
 ZHA  C06  H5   single    0.930  0.020  1.080
 ZHA  N07  H6   single    0.860  0.020  1.020
 ZHA  C09  H7   single    0.970  0.020  1.090
 ZHA  C09  H8   single    0.970  0.020  1.090
 ZHA  C09  H9   single    0.970  0.020  1.090
 ZHA  C11  H10  single    0.970  0.020  1.090
 ZHA  C11  H11  single    0.970  0.020  1.090
 ZHA  C12  H12  single    0.970  0.020  1.090
 ZHA  C12  H13  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
 ZHA  H2   C13  H1   106.50  3.000
 ZHA  H2   C13  C14  108.92  3.000
 ZHA  H1   C13  C14  107.13  3.000
 ZHA  H2   C13  C12  111.86  3.000
 ZHA  H1   C13  C12  109.40  3.000
 ZHA  C14  C13  C12  112.73  3.000
 ZHA  H3   C01  C06  118.93  3.000
 ZHA  H3   C01  C02  118.98  3.000
 ZHA  C06  C01  C02  122.08  3.000
 ZHA  C14  C02  C03  121.63  3.000
 ZHA  C03  C02  C01  118.94  3.000
 ZHA  C14  C02  C01  119.43  3.000
 ZHA  C11  C03  C04  120.16  3.000
 ZHA  C11  C03  C02  120.80  3.000
 ZHA  C04  C03  C02  119.04  3.000
 ZHA  H4   C04  C05  119.37  3.000
 ZHA  H4   C04  C03  118.80  3.000
 ZHA  C05  C04  C03  121.83  3.000
 ZHA  N07  C05  C06  124.32  3.000
 ZHA  N07  C05  C04  116.63  3.000
 ZHA  C06  C05  C04  119.06  3.000
 ZHA  H5   C06  C05  121.07  3.000
 ZHA  H5   C06  C01  119.88  3.000
 ZHA  C05  C06  C01  119.05  3.000
 ZHA  H6   N07  C08  115.67  3.000
 ZHA  H6   N07  C05  114.51  3.000
 ZHA  C08  N07  C05  129.82  3.000
 ZHA  O10  C08  C09  122.07  3.000
 ZHA  C09  C08  N07  113.96  3.000
 ZHA  O10  C08  N07  123.95  3.000
 ZHA  H9   C09  H8   108.43  3.000
 ZHA  H9   C09  H7   107.69  3.000
 ZHA  H8   C09  H7   107.71  3.000
 ZHA  H9   C09  C08  113.94  3.000
 ZHA  H8   C09  C08  109.76  3.000
 ZHA  H7   C09  C08  109.11  3.000
 ZHA  H11  C11  H10  106.18  3.000
 ZHA  H11  C11  C12  110.75  3.000
 ZHA  H10  C11  C12  109.42  3.000
 ZHA  H11  C11  C03  109.92  3.000
 ZHA  H10  C11  C03  108.89  3.000
 ZHA  C12  C11  C03  111.52  3.000
 ZHA  H13  C12  H12  106.70  3.000
 ZHA  H13  C12  C11  110.34  3.000
 ZHA  H12  C12  C11  109.54  3.000
 ZHA  H13  C12  C13  110.04  3.000
 ZHA  H12  C12  C13  109.77  3.000
 ZHA  C11  C12  C13  110.37  3.000
 ZHA  O15  C14  C02  121.52  3.000
 ZHA  C02  C14  C13  116.81  3.000
 ZHA  O15  C14  C13  121.66  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
 ZHA  CONST_01  C04  C05  C06  C01    0.00   0.0  0
 ZHA  CONST_02  C04  C03  C02  C01    0.00   0.0  0
 ZHA  CONST_03  C05  C06  C01  C02    0.00   0.0  0
 ZHA  CONST_04  C05  C04  C03  C02    0.00   0.0  0
 ZHA  CONST_05  C06  C01  C02  C03    0.00   0.0  0
 ZHA  CONST_06  C06  C05  C04  C03    0.00   0.0  0
 ZHA  CONST_07  N07  C05  C06  C01  180.00   0.0  0
 ZHA  CONST_08  N07  C05  C04  C03  180.00   0.0  0
 ZHA  CONST_09  H5   C06  C01  C02  180.00   0.0  0
 ZHA  CONST_10  H4   C04  C03  C02  180.00   0.0  0
 ZHA  CONST_11  H3   C01  C02  C03  180.00   0.0  0
 ZHA  CONST_12  C08  N07  C05  C04  180.00   0.0  0
 ZHA  CONST_13  C08  N07  C05  C06    0.00   0.0  0
 ZHA  CONST_14  H6   N07  C05  C04    0.00   0.0  0
 ZHA  CONST_15  O10  C08  N07  C05    0.00   0.0  0
 ZHA  CONST_16  C09  C08  N07  C05  180.00   0.0  0
 ZHA  Var_01    C01  C02  C14  C13  178.62  30.0  1
 ZHA  Var_02    C03  C11  C12  C13   54.24  30.0  1
 ZHA  Var_03    C12  C13  C14  C02   29.30  30.0  1
 ZHA  Var_04    C12  C11  C03  C02  -27.31  30.0  1
 ZHA  Var_05    C14  C13  C12  C11  -55.93  30.0  1
 ZHA  Var_06    H7   C09  C08  N07   95.99  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
 ZHA  plan-1  C05  0.020
 ZHA  plan-1  N07  0.020
 ZHA  plan-1  C08  0.020
 ZHA  plan-1  C09  0.020
 ZHA  plan-1  O10  0.020
 ZHA  plan-1  H6   0.020
 ZHA  plan-2  C01  0.020
 ZHA  plan-2  C02  0.020
 ZHA  plan-2  C03  0.020
 ZHA  plan-2  C04  0.020
 ZHA  plan-2  C05  0.020
 ZHA  plan-2  C06  0.020
 ZHA  plan-2  N07  0.020
 ZHA  plan-2  C11  0.020
 ZHA  plan-2  C14  0.020
 ZHA  plan-2  H3   0.020
 ZHA  plan-2  H4   0.020
 ZHA  plan-2  H5   0.020
 ZHA  plan-3  C13  0.020
 ZHA  plan-3  C02  0.020
 ZHA  plan-3  C14  0.020
 ZHA  plan-3  O15  0.020

