# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 18:26:46 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 6-[(2S,3S)-3-phenyloxiran-2-yl]naphthalene-2-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc2cc(ccc2c1)[C@@H]3O[C@H]3c4ccccc4
#
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
 4UP  4UP  6-[(2S,3S)-3-phenyloxiran-2-yl]naphthalene-2-carboximidamide  ligand  38  22  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_4UP
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
 4UP  N2   N  NH2   0  -0.805   6.5564  -1.5232   0.1718
 4UP  C1   C  C     0   0.333   5.9670  -0.2944   0.1380
 4UP  N1   N  N     0  -0.640   6.6669   0.7653   0.2808
 4UP  C2   C  CR6   0   0.006   4.4994  -0.3122  -0.1225
 4UP  C11  C  CR16  0  -0.361   3.6930   0.6453   0.4411
 4UP  C10  C  CR66  0   0.126   2.3034   0.6635   0.1993
 4UP  C5   C  CR66  0   0.136   1.7350  -0.3204  -0.6482
 4UP  C4   C  CR16  0  -0.299   2.5823  -1.2974  -1.2197
 4UP  C3   C  CR16  0  -0.282   3.9239  -1.2988  -0.9602
 4UP  C9   C  CR16  0  -0.293   1.4558   1.6402   0.7741
 4UP  C8   C  CR16  0  -0.314   0.1142   1.6418   0.5186
 4UP  C7   C  CR6   0   0.152  -0.4573   0.6619  -0.3283
 4UP  C6   C  CR16  0  -0.381   0.3458  -0.2910  -0.8999
 4UP  C12  C  CH1   0  -0.088  -1.9144   0.6365  -0.5962
 4UP  C13  C  CH1   0  -0.083  -2.9105   0.6757   0.4912
 4UP  O    O  O2    0  -0.471  -2.6559   1.8068  -0.3164
 4UP  C14  C  CR6   0   0.136  -4.2309   0.0136   0.3541
 4UP  C19  C  CR16  0  -0.304  -4.6368  -0.8944   1.3284
 4UP  C18  C  CR16  0  -0.244  -5.8519  -1.5548   1.2134
 4UP  C17  C  CR16  0  -0.263  -6.6778  -1.3063   0.1250
 4UP  C16  C  CR16  0  -0.239  -6.2811  -0.3940  -0.8447
 4UP  C15  C  CR16  0  -0.317  -5.0645   0.2640  -0.7330
 4UP  H1   H  HNH2  0   0.393   6.0098  -2.3073   0.4874
 4UP  H2   H  HNH2  0   0.385   7.5192  -1.5443   0.4686
 4UP  H3   H  H     0   0.333   6.1021   1.5916   0.1239
 4UP  H4   H  HCR6  0   0.263   4.1140   1.3956   1.1004
 4UP  H5   H  HCR6  0   0.260   2.1553  -2.0493  -1.8721
 4UP  H6   H  HCR6  0   0.265   4.5550  -2.0490  -1.4182
 4UP  H7   H  HCR6  0   0.259   1.8872   2.3986   1.4161
 4UP  H8   H  HCR6  0   0.261  -0.5131   2.4056   0.9594
 4UP  H9   H  HCR6  0   0.255  -0.0824  -1.0390  -1.5581
 4UP  H10  H  HCH1  0   0.268  -2.2076   0.1176  -1.5083
 4UP  H11  H  HCH1  0   0.269  -2.5304   0.7457   1.5101
 4UP  H12  H  HCR6  0   0.254  -3.9983  -1.0854   2.1832
 4UP  H13  H  HCR6  0   0.259  -6.1557  -2.2581   1.9779
 4UP  H14  H  HCR6  0   0.258  -7.6276  -1.8170   0.0346
 4UP  H15  H  HCR6  0   0.258  -6.9257  -0.1886  -1.6897
 4UP  H16  H  HCR6  0   0.256  -4.7729   0.9780  -1.4932

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
 4UP  N1   C1   double    1.278  0.020  1.278
 4UP  C9   C8   aromatic  1.366  0.020  1.366
 4UP  C9   C10  aromatic  1.415  0.020  1.415
 4UP  C11  C10  aromatic  1.411  0.020  1.411
 4UP  C11  C2   aromatic  1.373  0.020  1.373
 4UP  C8   C7   aromatic  1.416  0.020  1.416
 4UP  C1   N2   single    1.363  0.020  1.363
 4UP  C1   C2   single    1.491  0.020  1.491
 4UP  C10  C5   aromatic  1.418  0.020  1.418
 4UP  C2   C3   aromatic  1.416  0.020  1.416
 4UP  O    C12  single    1.413  0.020  1.413
 4UP  O    C13  single    1.413  0.020  1.413
 4UP  C7   C12  single    1.482  0.020  1.482
 4UP  C7   C6   aromatic  1.371  0.020  1.371
 4UP  C5   C6   aromatic  1.412  0.020  1.412
 4UP  C5   C4   aromatic  1.414  0.020  1.414
 4UP  C12  C13  single    1.475  0.020  1.475
 4UP  C3   C4   aromatic  1.367  0.020  1.367
 4UP  C13  C14  single    1.483  0.020  1.483
 4UP  C15  C14  aromatic  1.393  0.020  1.393
 4UP  C15  C16  aromatic  1.388  0.020  1.388
 4UP  C14  C19  aromatic  1.392  0.020  1.392
 4UP  C16  C17  aromatic  1.389  0.020  1.389
 4UP  C19  C18  aromatic  1.388  0.020  1.388
 4UP  C17  C18  aromatic  1.389  0.020  1.389
 4UP  N2   H1   single    0.890  0.020  1.040
 4UP  N2   H2   single    0.890  0.020  1.040
 4UP  N1   H3   single    0.890  0.020  1.040
 4UP  C11  H4   single    0.930  0.020  1.080
 4UP  C4   H5   single    0.930  0.020  1.080
 4UP  C3   H6   single    0.930  0.020  1.080
 4UP  C9   H7   single    0.930  0.020  1.080
 4UP  C8   H8   single    0.930  0.020  1.080
 4UP  C6   H9   single    0.930  0.020  1.080
 4UP  C12  H10  single    0.970  0.020  1.090
 4UP  C13  H11  single    0.970  0.020  1.090
 4UP  C19  H12  single    0.930  0.020  1.080
 4UP  C18  H13  single    0.930  0.020  1.080
 4UP  C17  H14  single    0.930  0.020  1.080
 4UP  C16  H15  single    0.930  0.020  1.080
 4UP  C15  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
 4UP  H2   N2   H1   114.22  3.000
 4UP  H2   N2   C1   116.06  3.000
 4UP  H1   N2   C1   118.37  3.000
 4UP  C2   C1   N1   124.65  3.000
 4UP  C2   C1   N2   114.79  3.000
 4UP  N1   C1   N2   120.52  3.000
 4UP  H3   N1   C1   110.71  3.000
 4UP  C3   C2   C11  119.34  3.000
 4UP  C3   C2   C1   120.77  3.000
 4UP  C11  C2   C1   119.89  3.000
 4UP  H4   C11  C10  118.55  3.000
 4UP  H4   C11  C2   120.29  3.000
 4UP  C10  C11  C2   121.15  3.000
 4UP  C9   C10  C5   118.80  3.000
 4UP  C5   C10  C11  119.24  3.000
 4UP  C9   C10  C11  121.96  3.000
 4UP  C6   C5   C4   122.13  3.000
 4UP  C4   C5   C10  118.75  3.000
 4UP  C6   C5   C10  119.12  3.000
 4UP  H5   C4   C3   120.05  3.000
 4UP  H5   C4   C5   119.13  3.000
 4UP  C3   C4   C5   120.82  3.000
 4UP  H6   C3   C4   119.54  3.000
 4UP  H6   C3   C2   119.76  3.000
 4UP  C4   C3   C2   120.69  3.000
 4UP  H7   C9   C8   120.08  3.000
 4UP  H7   C9   C10  119.04  3.000
 4UP  C8   C9   C10  120.88  3.000
 4UP  H8   C8   C7   119.88  3.000
 4UP  H8   C8   C9   119.61  3.000
 4UP  C7   C8   C9   120.51  3.000
 4UP  C12  C7   C6   119.26  3.000
 4UP  C6   C7   C8   119.61  3.000
 4UP  C12  C7   C8   121.13  3.000
 4UP  H9   C6   C7   120.08  3.000
 4UP  H9   C6   C5   118.83  3.000
 4UP  C7   C6   C5   121.09  3.000
 4UP  H10  C12  O    114.76  3.000
 4UP  H10  C12  C13  116.61  3.000
 4UP  O    C12  C13   58.52  3.000
 4UP  H10  C12  C7   115.10  3.000
 4UP  C13  C12  C7   122.03  3.000
 4UP  O    C12  C7   117.77  3.000
 4UP  H11  C13  C14  115.18  3.000
 4UP  H11  C13  O    114.85  3.000
 4UP  C14  C13  O    117.70  3.000
 4UP  H11  C13  C12  117.09  3.000
 4UP  C14  C13  C12  121.41  3.000
 4UP  O    C13  C12   58.55  3.000
 4UP  C13  O    C12   62.93  3.000
 4UP  C15  C14  C19  119.28  3.000
 4UP  C19  C14  C13  119.07  3.000
 4UP  C15  C14  C13  121.64  3.000
 4UP  H12  C19  C18  119.82  3.000
 4UP  H12  C19  C14  119.68  3.000
 4UP  C18  C19  C14  120.50  3.000
 4UP  H13  C18  C17  120.20  3.000
 4UP  H13  C18  C19  119.77  3.000
 4UP  C17  C18  C19  120.04  3.000
 4UP  H14  C17  C16  120.15  3.000
 4UP  H14  C17  C18  120.20  3.000
 4UP  C16  C17  C18  119.66  3.000
 4UP  H15  C16  C15  119.66  3.000
 4UP  H15  C16  C17  119.97  3.000
 4UP  C15  C16  C17  120.37  3.000
 4UP  H16  C15  C16  119.49  3.000
 4UP  H16  C15  C14  120.35  3.000
 4UP  C16  C15  C14  120.16  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
 4UP  CONST_01  C9   C10  C11  C2   180.00   0.0  0
 4UP  CONST_02  C5   C10  C11  C2     0.00   0.0  0
 4UP  CONST_03  C5   C4   C3   C2     0.00   0.0  0
 4UP  CONST_04  C8   C9   C10  C11  180.00   0.0  0
 4UP  CONST_05  C6   C5   C10  C11  180.00   0.0  0
 4UP  CONST_06  C4   C5   C10  C11    0.00   0.0  0
 4UP  CONST_07  C4   C3   C2   C11    0.00   0.0  0
 4UP  CONST_08  C7   C8   C9   C10    0.00   0.0  0
 4UP  CONST_09  C3   C2   C11  C10    0.00   0.0  0
 4UP  CONST_10  C7   C6   C5   C10    0.00   0.0  0
 4UP  CONST_11  C3   C4   C5   C10    0.00   0.0  0
 4UP  CONST_12  C8   C9   C10  C5     0.00   0.0  0
 4UP  CONST_13  C8   C7   C6   C5     0.00   0.0  0
 4UP  CONST_14  C9   C10  C5   C4   180.00   0.0  0
 4UP  CONST_15  C7   C6   C5   C4   180.00   0.0  0
 4UP  CONST_16  C6   C5   C4   C3   180.00   0.0  0
 4UP  CONST_17  C6   C7   C8   C9     0.00   0.0  0
 4UP  CONST_18  C6   C5   C10  C9     0.00   0.0  0
 4UP  CONST_19  C17  C16  C15  C14    0.00   0.0  0
 4UP  CONST_20  C17  C18  C19  C14    0.00   0.0  0
 4UP  CONST_21  C16  C15  C14  C19    0.00   0.0  0
 4UP  CONST_22  C16  C17  C18  C19    0.00   0.0  0
 4UP  CONST_23  C15  C14  C19  C18    0.00   0.0  0
 4UP  CONST_24  C15  C16  C17  C18    0.00   0.0  0
 4UP  CONST_25  C12  C7   C6   C5   180.00   0.0  0
 4UP  CONST_26  C12  C7   C8   C9   180.00   0.0  0
 4UP  CONST_27  C16  C15  C14  C13  180.00   0.0  0
 4UP  CONST_28  C18  C19  C14  C13  180.00   0.0  0
 4UP  CONST_29  C10  C11  C2   C1   180.00   0.0  0
 4UP  CONST_30  C4   C3   C2   C1   180.00   0.0  0
 4UP  CONST_31  H5   C4   C3   C2   180.00   0.0  0
 4UP  CONST_32  H7   C9   C10  C11    0.00   0.0  0
 4UP  CONST_33  H6   C3   C2   C11  180.00   0.0  0
 4UP  CONST_34  H8   C8   C9   C10  180.00   0.0  0
 4UP  CONST_35  H9   C6   C5   C10  180.00   0.0  0
 4UP  CONST_36  H4   C11  C10  C5   180.00   0.0  0
 4UP  CONST_37  H16  C15  C14  C13    0.00   0.0  0
 4UP  CONST_38  H12  C19  C14  C13    0.00   0.0  0
 4UP  CONST_39  H15  C16  C15  C14  180.00   0.0  0
 4UP  CONST_40  H13  C18  C19  C14  180.00   0.0  0
 4UP  CONST_41  H14  C17  C18  C19  180.00   0.0  0
 4UP  CONST_42  H3   N1   C1   C2     0.00   0.0  0
 4UP  CONST_44  H2   N2   C1   C2   180.00   0.0  0
 4UP  Var_01    O    C12  C7   C8    17.92  30.0  2
 4UP  Var_02    C15  C14  C13  C12  -52.75  30.0  2
 4UP  Var_03    C11  C2   C1   N2   147.45  30.0  2

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
 4UP  chir_01  C12  O  C7   C13  both
 4UP  chir_02  C13  O  C12  C14  both

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
 4UP  plan-1  C13  0.020
 4UP  plan-1  C14  0.020
 4UP  plan-1  C19  0.020
 4UP  plan-1  C18  0.020
 4UP  plan-1  C17  0.020
 4UP  plan-1  C16  0.020
 4UP  plan-1  C15  0.020
 4UP  plan-1  H12  0.020
 4UP  plan-1  H13  0.020
 4UP  plan-1  H14  0.020
 4UP  plan-1  H15  0.020
 4UP  plan-1  H16  0.020
 4UP  plan-2  C1   0.020
 4UP  plan-2  C2   0.020
 4UP  plan-2  C11  0.020
 4UP  plan-2  C10  0.020
 4UP  plan-2  C5   0.020
 4UP  plan-2  C4   0.020
 4UP  plan-2  C3   0.020
 4UP  plan-2  C9   0.020
 4UP  plan-2  C8   0.020
 4UP  plan-2  C7   0.020
 4UP  plan-2  C6   0.020
 4UP  plan-2  C12  0.020
 4UP  plan-2  H4   0.020
 4UP  plan-2  H5   0.020
 4UP  plan-2  H6   0.020
 4UP  plan-2  H7   0.020
 4UP  plan-2  H8   0.020
 4UP  plan-2  H9   0.020
 4UP  plan-3  N2   0.020
 4UP  plan-3  C1   0.020
 4UP  plan-3  N1   0.020
 4UP  plan-3  C2   0.020
 4UP  plan-3  H1   0.020
 4UP  plan-3  H2   0.020
 4UP  plan-3  H3   0.020

