# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 09:56:26 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: (2S,5R,6R)-6-{[(2-ethoxynaphthalen-1-yl)carbonyl]amino}-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOc1ccc2ccccc2c1C(=O)N[C@H]3[C@H]4SC(C)(C)[C@@H](N4C3=O)C([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
 NFN  NFN  (2S,5R,6R)-6-{[(2-ethoxynaphthalen-1-yl)carbonyl]amino}-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylate  ligand  50  29  .  2021-08-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NFN
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
 NFN  O1    O  O2     0  -0.462   3.3164   2.3242   0.3367
 NFN  C4    C  CR16   0  -0.297   5.0414  -0.5442  -1.1230
 NFN  C3    C  CR16   0  -0.387   4.7950   0.7542  -0.7745
 NFN  C10   C  CR66   0   0.077   4.1603  -1.5858  -0.7649
 NFN  C2    C  CR6    0   0.406   3.6352   1.0757  -0.0332
 NFN  C9    C  CR66   0   0.188   2.9906  -1.2687  -0.0236
 NFN  C1    C  CR6    0  -0.249   2.7508   0.0814   0.3319
 NFN  C5    C  CR16   0  -0.303   4.4191  -2.9292  -1.1239
 NFN  C6    C  CR16   0  -0.268   3.5560  -3.9271  -0.7673
 NFN  C7    C  CR16   0  -0.249   2.3945  -3.6169  -0.0296
 NFN  C8    C  CR16   0  -0.350   2.1166  -2.3278   0.3344
 NFN  C14   C  C      0   0.527  -1.7610  -0.6417   1.2522
 NFN  N2    N  N      0  -0.408  -2.8288   0.0105   0.7116
 NFN  C16   C  CH1    0  -0.148  -3.7810  -0.5364  -0.2331
 NFN  C21   C  C      0   0.418  -5.2319  -0.6187   0.2976
 NFN  O4    O  OC    -1  -0.599  -5.9959  -1.3210  -0.3920
 NFN  O5    O  O      0  -0.585  -5.4968   0.0133   1.3300
 NFN  C15   C  CT     0  -0.240  -3.6739   0.3435  -1.5162
 NFN  C19   C  CH3    0  -0.635  -4.6532   1.5146  -1.5122
 NFN  C20   C  CH3    0  -0.638  -3.8436  -0.4884  -2.7774
 NFN  S1    S  S2     0   0.027  -1.9485   1.0284  -1.4843
 NFN  C13   C  C      0  -0.199  -2.0460   1.1734   0.3189
 NFN  C12   C  C      0  -0.242  -0.8676   0.6039   1.1429
 NFN  N1    N  NH1    0  -0.615   0.3908   0.4250   0.5027
 NFN  C11   C  C      0   0.474   1.5655   0.4531   1.1689
 NFN  O2    O  O      0  -0.454   1.6648   0.7456   2.3464
 NFN  C17   C  CH2    0  -0.192   4.1784   3.4066  -0.0015
 NFN  C18   C  CH3    0  -0.680   3.5775   4.6712   0.5619
 NFN  H4    H  HCR6   0   0.267   5.9329  -0.7831  -1.6899
 NFN  H3    H  HCR6   0   0.289   5.4938   1.5233  -1.0723
 NFN  H5    H  HCR6   0   0.258   5.3169  -3.1545  -1.6870
 NFN  H6    H  HCR6   0   0.259   3.7599  -4.9526  -1.0451
 NFN  H7    H  HCR6   0   0.261   1.7145  -4.4100   0.2534
 NFN  H8    H  HCR6   0   0.251   1.2163  -2.1230   0.9002
 NFN  H16   H  HCH1   0   0.258  -3.4497  -1.5489  -0.4861
 NFN  H191  H  HCH3   0   0.244  -4.4699   2.1619  -2.3694
 NFN  H192  H  HCH3   0   0.242  -5.6781   1.1487  -1.5880
 NFN  H193  H  HCH3   0   0.244  -4.5792   2.1213  -0.6093
 NFN  H201  H  HCH3   0   0.240  -3.0976  -1.2811  -2.8382
 NFN  H202  H  HCH3   0   0.249  -4.8307  -0.9503  -2.7706
 NFN  H203  H  HCH3   0   0.239  -3.7657   0.1293  -3.6730
 NFN  H13   H  H      0   0.298  -2.4373   2.1396   0.6335
 NFN  H12   H  H      0   0.325  -0.7335   1.1229   2.0916
 NFN  HN1   H  HNH1   0   0.412   0.3908   0.1117  -0.4576
 NFN  H171  H  HCH2   0   0.230   4.2802   3.4821  -1.0887
 NFN  H172  H  HCH2   0   0.230   5.1756   3.2391   0.4170
 NFN  H181  H  HCH3   0   0.239   4.2228   5.5144   0.3169
 NFN  H182  H  HCH3   0   0.236   2.5926   4.8689   0.1392
 NFN  H183  H  HCH3   0   0.236   3.4888   4.6210   1.6471
 NFN  O3    O  O      0  -0.425  -1.5963  -1.7857   1.5875

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
 NFN  O1   C2    single    1.341  0.020  1.341
 NFN  O1   C17   single    1.424  0.020  1.424
 NFN  C4   C3    aromatic  1.367  0.020  1.367
 NFN  C4   C10   aromatic  1.411  0.020  1.411
 NFN  C4   H4    single    0.930  0.020  1.080
 NFN  C3   C2    aromatic  1.413  0.020  1.413
 NFN  C3   H3    single    0.930  0.020  1.080
 NFN  C10  C9    aromatic  1.421  0.020  1.421
 NFN  C10  C5    aromatic  1.414  0.020  1.414
 NFN  C2   C1    aromatic  1.380  0.020  1.380
 NFN  C9   C1    aromatic  1.417  0.020  1.417
 NFN  C9   C8    aromatic  1.419  0.020  1.419
 NFN  C1   C11   single    1.498  0.020  1.498
 NFN  C5   C6    aromatic  1.367  0.020  1.367
 NFN  C5   H5    single    0.930  0.020  1.080
 NFN  C6   C7    aromatic  1.411  0.020  1.411
 NFN  C6   H6    single    0.930  0.020  1.080
 NFN  C7   C8    aromatic  1.368  0.020  1.368
 NFN  C7   H7    single    0.930  0.020  1.080
 NFN  C8   H8    single    0.930  0.020  1.080
 NFN  O3   C14   double    1.203  0.020  1.203
 NFN  C14  N2    single    1.363  0.020  1.363
 NFN  C14  C12   single    1.537  0.020  1.537
 NFN  N2   C16   single    1.449  0.020  1.449
 NFN  N2   C13   single    1.456  0.020  1.456
 NFN  C16  C21   single    1.547  0.020  1.547
 NFN  C16  C15   single    1.560  0.020  1.560
 NFN  C16  H16   single    0.970  0.020  1.090
 NFN  C21  O4    deloc     1.246  0.020  1.246
 NFN  C21  O5    deloc     1.239  0.020  1.239
 NFN  C15  C19   single    1.527  0.020  1.527
 NFN  C15  C20   single    1.520  0.020  1.520
 NFN  C15  S1    single    1.857  0.020  1.857
 NFN  C19  H191  single    0.970  0.020  1.090
 NFN  C19  H192  single    0.970  0.020  1.090
 NFN  C19  H193  single    0.970  0.020  1.090
 NFN  C20  H201  single    0.970  0.020  1.090
 NFN  C20  H202  single    0.970  0.020  1.090
 NFN  C20  H203  single    0.970  0.020  1.090
 NFN  S1   C13   single    1.812  0.020  1.812
 NFN  C13  C12   single    1.547  0.020  1.547
 NFN  C13  H13   single    0.970  0.020  1.090
 NFN  C12  N1    single    1.423  0.020  1.423
 NFN  C12  H12   single    0.970  0.020  1.090
 NFN  N1   C11   single    1.351  0.020  1.351
 NFN  N1   HN1   single    0.860  0.020  1.020
 NFN  C11  O2    double    1.217  0.020  1.217
 NFN  C17  C18   single    1.509  0.020  1.509
 NFN  C17  H171  single    0.970  0.020  1.090
 NFN  C17  H172  single    0.970  0.020  1.090
 NFN  C18  H181  single    0.970  0.020  1.090
 NFN  C18  H182  single    0.970  0.020  1.090
 NFN  C18  H183  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
 NFN  C17   O1   C2    119.88  3.000
 NFN  H4    C4   C10   118.96  3.000
 NFN  H4    C4   C3    119.43  3.000
 NFN  C10   C4   C3    121.61  3.000
 NFN  H3    C3   C2    120.87  3.000
 NFN  H3    C3   C4    119.28  3.000
 NFN  C2    C3   C4    119.86  3.000
 NFN  C5    C10  C9    119.68  3.000
 NFN  C5    C10  C4    121.51  3.000
 NFN  C9    C10  C4    118.81  3.000
 NFN  C1    C2   C3    120.05  3.000
 NFN  C1    C2   O1    116.46  3.000
 NFN  C3    C2   O1    123.49  3.000
 NFN  C8    C9   C1    122.94  3.000
 NFN  C8    C9   C10   118.17  3.000
 NFN  C1    C9   C10   118.89  3.000
 NFN  C11   C1   C9    120.72  3.000
 NFN  C11   C1   C2    118.44  3.000
 NFN  C9    C1   C2    120.78  3.000
 NFN  H5    C5   C6    120.47  3.000
 NFN  H5    C5   C10   118.75  3.000
 NFN  C6    C5   C10   120.78  3.000
 NFN  H6    C6   C7    119.86  3.000
 NFN  H6    C6   C5    120.41  3.000
 NFN  C7    C6   C5    119.73  3.000
 NFN  H7    C7   C8    119.56  3.000
 NFN  H7    C7   C6    119.53  3.000
 NFN  C8    C7   C6    120.91  3.000
 NFN  H8    C8   C7    119.09  3.000
 NFN  H8    C8   C9    120.18  3.000
 NFN  C7    C8   C9    120.73  3.000
 NFN  C12   C14  N2     92.26  3.000
 NFN  C12   C14  O3    135.29  3.000
 NFN  N2    C14  O3    132.27  3.000
 NFN  C13   N2   C16   118.63  3.000
 NFN  C13   N2   C14    93.90  3.000
 NFN  C16   N2   C14   126.37  3.000
 NFN  H16   C16  C15   108.11  3.000
 NFN  H16   C16  C21   108.29  3.000
 NFN  C15   C16  C21   112.13  3.000
 NFN  H16   C16  N2    107.51  3.000
 NFN  C15   C16  N2    106.17  3.000
 NFN  C21   C16  N2    114.38  3.000
 NFN  O5    C21  O4    128.14  3.000
 NFN  O5    C21  C16   117.33  3.000
 NFN  O4    C21  C16   114.53  3.000
 NFN  S1    C15  C20   108.66  3.000
 NFN  S1    C15  C19   108.25  3.000
 NFN  C20   C15  C19   110.50  3.000
 NFN  S1    C15  C16   104.94  3.000
 NFN  C20   C15  C16   111.48  3.000
 NFN  C19   C15  C16   112.74  3.000
 NFN  H193  C19  H192  107.94  3.000
 NFN  H193  C19  H191  108.03  3.000
 NFN  H192  C19  H191  107.62  3.000
 NFN  H193  C19  C15   112.67  3.000
 NFN  H192  C19  C15   110.19  3.000
 NFN  H191  C19  C15   110.23  3.000
 NFN  H203  C20  H202  108.05  3.000
 NFN  H203  C20  H201  108.49  3.000
 NFN  H202  C20  H201  108.17  3.000
 NFN  H203  C20  C15   111.30  3.000
 NFN  H202  C20  C15   109.14  3.000
 NFN  H201  C20  C15   111.57  3.000
 NFN  C13   S1   C15    89.81  3.000
 NFN  H13   C13  C12   116.53  3.000
 NFN  H13   C13  S1    112.20  3.000
 NFN  C12   C13  S1    117.38  3.000
 NFN  H13   C13  N2    115.95  3.000
 NFN  C12   C13  N2     88.39  3.000
 NFN  S1    C13  N2    103.50  3.000
 NFN  H12   C12  N1    110.04  3.000
 NFN  H12   C12  C13   112.47  3.000
 NFN  N1    C12  C13   118.71  3.000
 NFN  H12   C12  C14   113.30  3.000
 NFN  N1    C12  C14   116.37  3.000
 NFN  C13   C12  C14    83.88  3.000
 NFN  HN1   N1   C11   118.38  3.000
 NFN  HN1   N1   C12   117.82  3.000
 NFN  C11   N1   C12   122.99  3.000
 NFN  O2    C11  N1    123.57  3.000
 NFN  O2    C11  C1    122.38  3.000
 NFN  N1    C11  C1    114.05  3.000
 NFN  H172  C17  H171  107.80  3.000
 NFN  H172  C17  C18   110.38  3.000
 NFN  H171  C17  C18   110.49  3.000
 NFN  H172  C17  O1    110.15  3.000
 NFN  H171  C17  O1    110.15  3.000
 NFN  C18   C17  O1    107.88  3.000
 NFN  H183  C18  H182  108.73  3.000
 NFN  H183  C18  H181  107.92  3.000
 NFN  H182  C18  H181  107.91  3.000
 NFN  H183  C18  C17   111.44  3.000
 NFN  H182  C18  C17   111.53  3.000
 NFN  H181  C18  C17   109.19  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
 NFN  CONST_01  C1    C2   C3   C4      0.00   0.0  0
 NFN  CONST_02  C1    C9   C10  C4      0.00   0.0  0
 NFN  CONST_03  C8    C9   C10  C4    180.00   0.0  0
 NFN  CONST_04  C6    C5   C10  C4    180.00   0.0  0
 NFN  CONST_05  C9    C10  C4   C3      0.00   0.0  0
 NFN  CONST_06  C5    C10  C4   C3    180.00   0.0  0
 NFN  CONST_07  C9    C1   C2   C3      0.00   0.0  0
 NFN  CONST_08  C2    C3   C4   C10     0.00   0.0  0
 NFN  CONST_09  C2    C1   C9   C10     0.00   0.0  0
 NFN  CONST_10  C7    C8   C9   C10     0.00   0.0  0
 NFN  CONST_11  C7    C6   C5   C10     0.00   0.0  0
 NFN  CONST_12  C8    C9   C1   C2    180.00   0.0  0
 NFN  CONST_13  C6    C5   C10  C9      0.00   0.0  0
 NFN  CONST_14  C6    C7   C8   C9      0.00   0.0  0
 NFN  CONST_15  C5    C10  C9   C1    180.00   0.0  0
 NFN  CONST_16  C7    C8   C9   C1    180.00   0.0  0
 NFN  CONST_17  C8    C9   C10  C5      0.00   0.0  0
 NFN  CONST_18  C8    C7   C6   C5      0.00   0.0  0
 NFN  CONST_20  C12   C14  N2   C13     0.00   0.0  0
 NFN  CONST_21  C4    C3   C2   O1    180.00   0.0  0
 NFN  CONST_22  C9    C1   C2   O1    180.00   0.0  0
 NFN  CONST_23  C11   C1   C2   C3    180.00   0.0  0
 NFN  CONST_24  C11   C1   C9   C10   180.00   0.0  0
 NFN  CONST_25  C11   C1   C9   C8      0.00   0.0  0
 NFN  CONST_27  C13   N2   C14  O3    180.00   0.0  0
 NFN  CONST_28  H5    C5   C10  C4      0.00   0.0  0
 NFN  CONST_29  H3    C3   C4   C10   180.00   0.0  0
 NFN  CONST_30  H8    C8   C9   C10   180.00   0.0  0
 NFN  CONST_31  H6    C6   C5   C10   180.00   0.0  0
 NFN  CONST_32  H4    C4   C3   C2    180.00   0.0  0
 NFN  CONST_33  H7    C7   C8   C9    180.00   0.0  0
 NFN  CONST_34  C12   N1   C11  C1    180.00   0.0  0
 NFN  CONST_35  O2    C11  N1   C12     0.00   0.0  0
 NFN  CONST_36  HN1   N1   C11  C1      0.00   0.0  0
 NFN  Var_01    N1    C11  C1   C2    107.98  30.0  2
 NFN  Var_02    H191  C19  C15  C16   173.78  30.0  3
 NFN  Var_03    H201  C20  C15  C16   -58.52  30.0  3
 NFN  Var_04    C18   C17  O1   C2   -179.05  30.0  3
 NFN  Var_05    H181  C18  C17  O1    179.87  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
 NFN  chir_01  C16  N2  C21  C15  negativ
 NFN  chir_02  C13  S1  N2   C12  negativ
 NFN  chir_03  C12  N1  C13  C14  negativ

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
 NFN  plan-1  O1   0.020
 NFN  plan-1  C4   0.020
 NFN  plan-1  C3   0.020
 NFN  plan-1  C10  0.020
 NFN  plan-1  C2   0.020
 NFN  plan-1  C9   0.020
 NFN  plan-1  C1   0.020
 NFN  plan-1  C5   0.020
 NFN  plan-1  C6   0.020
 NFN  plan-1  C7   0.020
 NFN  plan-1  C8   0.020
 NFN  plan-1  C11  0.020
 NFN  plan-1  H4   0.020
 NFN  plan-1  H3   0.020
 NFN  plan-1  H5   0.020
 NFN  plan-1  H6   0.020
 NFN  plan-1  H7   0.020
 NFN  plan-1  H8   0.020
 NFN  plan-2  C1   0.020
 NFN  plan-2  C12  0.020
 NFN  plan-2  N1   0.020
 NFN  plan-2  C11  0.020
 NFN  plan-2  O2   0.020
 NFN  plan-2  HN1  0.020
 NFN  plan-3  C14  0.020
 NFN  plan-3  N2   0.020
 NFN  plan-3  C16  0.020
 NFN  plan-3  C13  0.020
 NFN  plan-3  C12  0.020
 NFN  plan-3  O3   0.020
 NFN  plan-4  C16  0.020
 NFN  plan-4  C21  0.020
 NFN  plan-4  O4   0.020
 NFN  plan-4  O5   0.020

