# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jul  6 02:08:36 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: N-[(5alpha,6beta)-17-(cyclopropylmethyl)-3-hydroxy-7,8-didehydro-4,5-epoxymorphinan-6-yl]-3-iodobenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc2C[C@@H]3[C@@H]4C=C[C@@H](NC(=O)c5cccc(I)c5)[C@@H]6Oc1c2[C@]46CCN3CC7CC7
#
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
 CVV  CVV  N-[(5alpha,6beta)-17-(cyclopropylmethyl)-3-hydroxy-7,8-didehydro-4,5-epoxymorphinan-6-yl]-3-iodobenzamide  ligand  60  33  .  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_CVV
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
 CVV  N1   N  NH1   0  -0.660   0.3651   0.1111  -0.2456
 CVV  C4   C  CR16  0  -0.116  -4.3472   0.6038  -1.2846
 CVV  C5   C  CR16  0  -0.257  -2.8662   0.3123  -0.9797
 CVV  C6   C  C1    0  -0.174  -2.0869  -0.2226  -2.1435
 CVV  C7   C  C1    0  -0.257  -0.9636  -0.9073  -1.9521
 CVV  C8   C  CH1   0  -0.137  -0.3928  -1.0905  -0.5697
 CVV  C10  C  CR6   0  -0.020   2.0172   1.4386   0.9020
 CVV  C13  C  CR16  0  -0.222   3.3739   3.8298   1.3777
 CVV  C15  C  CR16  0  -0.290   1.3906   2.6593   0.6697
 CVV  C17  C  C     0  -0.218  -2.8404  -0.7098   0.1601
 CVV  C20  C  CR6   0   0.249  -3.3049  -4.3092  -0.3270
 CVV  C21  C  CR16  0  -0.353  -4.4640  -4.3637  -1.1077
 CVV  C22  C  CH2   0  -0.407  -3.5303  -0.1037   1.3845
 CVV  C26  C  CH2   0  -0.498  -7.9953   3.3907   0.7160
 CVV  C1   C  CR16  0  -0.335  -5.1014  -3.2129  -1.5590
 CVV  C11  C  CR16  0  -0.240   3.3218   1.4136   1.3907
 CVV  C12  C  CR6   0  -0.207   3.9876   2.6067   1.6127
 CVV  C14  C  CR16  0  -0.232   2.0678   3.8452   0.9099
 CVV  C16  C  CR15  0   0.049  -1.4699  -1.3263   0.5092
 CVV  C18  C  C     0   0.022  -3.5550  -1.9204  -0.3485
 CVV  C19  C  CR56  0   0.298  -2.8587  -3.0446   0.0229
 CVV  C2   C  CR66  0   0.082  -4.6355  -1.9462  -1.1975
 CVV  C23  C  CH2   0  -0.297  -4.9318   0.3844   1.0572
 CVV  C25  C  CH1   0  -0.255  -6.5783   2.9076   0.6549
 CVV  C27  C  CH2   0  -0.484  -7.4385   2.5650   1.8340
 CVV  O3   O  O     0  -0.506  -1.7008  -2.7451   0.6671
 CVV  C3   C  C     0  -0.533  -5.1158  -0.6477  -1.7854
 CVV  O4   O  OH1   0  -0.639  -2.6773  -5.4599   0.0082
 CVV  C9   C  C     0   0.547   1.3307   0.1259   0.6895
 CVV  H1   H  HNH1  0   0.411   0.2441   0.9101  -0.8471
 CVV  H2   H  HCR6  0   0.256  -4.3794   1.3434  -2.0902
 CVV  H3   H  HCR6  0   0.264  -2.4240   1.2608  -0.6481
 CVV  H4   H  H     0   0.254  -2.4510  -0.0443  -3.1500
 CVV  H5   H  H     0   0.260  -0.3961  -1.2983  -2.7874
 CVV  H6   H  HCH1  0   0.281   0.2926  -1.9408  -0.5575
 CVV  H7   H  HCR6  0   0.287   3.8922   4.7614   1.5582
 CVV  H8   H  HCR6  0   0.265   0.3644   2.7045   0.3283
 CVV  H9   H  HCR6  0   0.260  -4.8410  -5.3358  -1.4024
 CVV  H10  H  HCH2  0   0.243  -3.5791  -0.8327   2.1971
 CVV  H11  H  HCH2  0   0.236  -2.9252   0.7373   1.7383
 CVV  H14  H  HCH2  0   0.249  -8.1707   4.4447   0.8894
 CVV  H15  H  HCH2  0   0.241  -8.7163   2.9261   0.0531
 CVV  H16  H  HCR6  0   0.244  -5.9551  -3.3121  -2.2190
 CVV  H17  H  HCR6  0   0.282   3.8009   0.4633   1.5835
 CVV  H18  H  HCR6  0   0.279   1.5757   4.7926   0.7370
 CVV  H19  H  HCR5  0   0.269  -1.0979  -0.9675   1.4704
 CVV  H21  H  HCH2  0   0.202  -5.6139  -0.4738   0.9322
 CVV  H22  H  HCH2  0   0.261  -5.3127   0.9491   1.9084
 CVV  H23  H  HCH1  0   0.249  -5.8118   3.6586   0.8194
 CVV  H24  H  HCH2  0   0.248  -7.2308   3.0486   2.7801
 CVV  H25  H  HCH2  0   0.242  -7.7841   1.5420   1.9256
 CVV  H26  H  H     0   0.262  -6.1875  -0.5122  -1.6123
 CVV  H27  H  H     0   0.257  -5.0114  -0.7091  -2.8730
 CVV  H28  H  HOH1  0   0.474  -1.8854  -5.2773   0.5253
 CVV  N2   N  NT    0  -0.422  -4.9246   1.2468  -0.1105
 CVV  C24  C  CH2   0  -0.271  -6.2101   1.8672  -0.3709
 CVV  I1   I  I     0   0.067   5.9660   2.5652   2.3260
 CVV  O2   O  O     0  -0.482   1.6430  -0.8644   1.3349
 CVV  H12  H  HCH2  0   0.234  -6.1502   2.3518  -1.3504
 CVV  H13  H  HCH2  0   0.191  -7.0316   1.1321  -0.4434

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
 CVV  C15  C14  aromatic  1.387  0.020  1.387
 CVV  C15  C10  aromatic  1.392  0.020  1.392
 CVV  C14  C13  aromatic  1.387  0.020  1.387
 CVV  O2   C9   double    1.223  0.020  1.223
 CVV  C9   C10  single    1.497  0.020  1.497
 CVV  C9   N1   single    1.344  0.020  1.344
 CVV  C10  C11  aromatic  1.393  0.020  1.393
 CVV  C13  C12  aromatic  1.388  0.020  1.388
 CVV  N1   C8   single    1.457  0.020  1.457
 CVV  C8   C7   single    1.507  0.020  1.507
 CVV  C8   C16  single    1.543  0.020  1.543
 CVV  C11  C12  aromatic  1.384  0.020  1.384
 CVV  C12  I1   single    2.103  0.020  2.103
 CVV  C7   C6   double    1.329  0.020  1.329
 CVV  O4   C20  single    1.353  0.020  1.353
 CVV  O3   C16  single    1.446  0.020  1.446
 CVV  O3   C19  single    1.358  0.020  1.358
 CVV  C16  C17  single    1.543  0.020  1.543
 CVV  C20  C19  aromatic  1.386  0.020  1.386
 CVV  C20  C21  aromatic  1.399  0.020  1.399
 CVV  C19  C18  aromatic  1.374  0.020  1.374
 CVV  C6   C5   single    1.499  0.020  1.499
 CVV  C17  C18  single    1.495  0.020  1.495
 CVV  C17  C5   single    1.531  0.020  1.531
 CVV  C17  C22  single    1.530  0.020  1.530
 CVV  C21  C1   aromatic  1.391  0.020  1.391
 CVV  C18  C2   aromatic  1.374  0.020  1.374
 CVV  C5   C4   single    1.540  0.020  1.540
 CVV  C22  C23  single    1.520  0.020  1.520
 CVV  C1   C2   aromatic  1.397  0.020  1.397
 CVV  C2   C3   single    1.504  0.020  1.504
 CVV  C4   C3   single    1.552  0.020  1.552
 CVV  C4   N2   single    1.458  0.020  1.458
 CVV  C23  N2   single    1.452  0.020  1.452
 CVV  N2   C24  single    1.451  0.020  1.451
 CVV  C24  C25  single    1.507  0.020  1.507
 CVV  C25  C26  single    1.498  0.020  1.498
 CVV  C25  C27  single    1.499  0.020  1.499
 CVV  C26  C27  single    1.497  0.020  1.497
 CVV  N1   H1   single    0.860  0.020  1.020
 CVV  C4   H2   single    0.970  0.020  1.090
 CVV  C5   H3   single    0.970  0.020  1.090
 CVV  C6   H4   single    0.930  0.020  1.080
 CVV  C7   H5   single    0.930  0.020  1.080
 CVV  C8   H6   single    0.970  0.020  1.090
 CVV  C13  H7   single    0.930  0.020  1.080
 CVV  C15  H8   single    0.930  0.020  1.080
 CVV  C21  H9   single    0.930  0.020  1.080
 CVV  C22  H10  single    0.970  0.020  1.090
 CVV  C22  H11  single    0.970  0.020  1.090
 CVV  C24  H12  single    0.970  0.020  1.090
 CVV  C24  H13  single    0.970  0.020  1.090
 CVV  C26  H14  single    0.970  0.020  1.090
 CVV  C26  H15  single    0.970  0.020  1.090
 CVV  C1   H16  single    0.930  0.020  1.080
 CVV  C11  H17  single    0.930  0.020  1.080
 CVV  C14  H18  single    0.930  0.020  1.080
 CVV  C16  H19  single    0.970  0.020  1.090
 CVV  C23  H21  single    0.970  0.020  1.090
 CVV  C23  H22  single    0.970  0.020  1.090
 CVV  C25  H23  single    0.970  0.020  1.090
 CVV  C27  H24  single    0.970  0.020  1.090
 CVV  C27  H25  single    0.970  0.020  1.090
 CVV  C3   H26  single    0.970  0.020  1.090
 CVV  C3   H27  single    0.970  0.020  1.090
 CVV  O4   H28  single    0.850  0.020  0.980

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
 CVV  H1   N1   C9   119.53  3.000
 CVV  H1   N1   C8   117.30  3.000
 CVV  C9   N1   C8   122.51  3.000
 CVV  H2   C4   C3   107.04  3.000
 CVV  H2   C4   N2   106.45  3.000
 CVV  C3   C4   N2   114.80  3.000
 CVV  H2   C4   C5   107.58  3.000
 CVV  N2   C4   C5   107.76  3.000
 CVV  C3   C4   C5   112.81  3.000
 CVV  H3   C5   C17  110.19  3.000
 CVV  H3   C5   C6   109.47  3.000
 CVV  C17  C5   C6   109.33  3.000
 CVV  H3   C5   C4   106.48  3.000
 CVV  C17  C5   C4   106.85  3.000
 CVV  C6   C5   C4   114.44  3.000
 CVV  H4   C6   C7   120.11  3.000
 CVV  H4   C6   C5   119.14  3.000
 CVV  C7   C6   C5   120.75  3.000
 CVV  H5   C7   C8   117.73  3.000
 CVV  H5   C7   C6   121.18  3.000
 CVV  C8   C7   C6   120.98  3.000
 CVV  H6   C8   C16  108.14  3.000
 CVV  H6   C8   C7   110.04  3.000
 CVV  C16  C8   C7   113.31  3.000
 CVV  H6   C8   N1   108.25  3.000
 CVV  C16  C8   N1   109.49  3.000
 CVV  C7   C8   N1   107.51  3.000
 CVV  C9   C10  C11  117.62  3.000
 CVV  C11  C10  C15  119.73  3.000
 CVV  C9   C10  C15  122.62  3.000
 CVV  H7   C13  C14  119.86  3.000
 CVV  H7   C13  C12  121.26  3.000
 CVV  C14  C13  C12  118.88  3.000
 CVV  H8   C15  C14  118.82  3.000
 CVV  H8   C15  C10  121.07  3.000
 CVV  C14  C15  C10  120.09  3.000
 CVV  C18  C17  C16  100.25  3.000
 CVV  C18  C17  C22  112.17  3.000
 CVV  C16  C17  C22  112.19  3.000
 CVV  C22  C17  C5   108.88  3.000
 CVV  C18  C17  C5   106.22  3.000
 CVV  C16  C17  C5   116.75  3.000
 CVV  O4   C20  C19  124.34  3.000
 CVV  C19  C20  C21  116.32  3.000
 CVV  O4   C20  C21  119.32  3.000
 CVV  H9   C21  C1   119.65  3.000
 CVV  H9   C21  C20  118.37  3.000
 CVV  C1   C21  C20  121.92  3.000
 CVV  H11  C22  H10  107.27  3.000
 CVV  H11  C22  C23  109.43  3.000
 CVV  H10  C22  C23  109.46  3.000
 CVV  H11  C22  C17  108.27  3.000
 CVV  H10  C22  C17  110.54  3.000
 CVV  C23  C22  C17  111.75  3.000
 CVV  H15  C26  H14  114.04  3.000
 CVV  H15  C26  C27  117.88  3.000
 CVV  H14  C26  C27  118.53  3.000
 CVV  H15  C26  C25  117.77  3.000
 CVV  H14  C26  C25  118.28  3.000
 CVV  C27  C26  C25   60.06  3.000
 CVV  H16  C1   C2   120.22  3.000
 CVV  H16  C1   C21  118.87  3.000
 CVV  C2   C1   C21  120.89  3.000
 CVV  H17  C11  C12  121.04  3.000
 CVV  H17  C11  C10  119.54  3.000
 CVV  C12  C11  C10  119.41  3.000
 CVV  C11  C12  I1   119.32  3.000
 CVV  I1   C12  C13  119.37  3.000
 CVV  C11  C12  C13  121.30  3.000
 CVV  H18  C14  C15  119.95  3.000
 CVV  H18  C14  C13  119.47  3.000
 CVV  C15  C14  C13  120.57  3.000
 CVV  H19  C16  O3   106.31  3.000
 CVV  H19  C16  C17  111.76  3.000
 CVV  O3   C16  C17  105.96  3.000
 CVV  H19  C16  C8   109.13  3.000
 CVV  C17  C16  C8   113.63  3.000
 CVV  O3   C16  C8   109.75  3.000
 CVV  C2   C18  C19  123.38  3.000
 CVV  C2   C18  C17  126.95  3.000
 CVV  C19  C18  C17  109.18  3.000
 CVV  O3   C19  C18  112.33  3.000
 CVV  C18  C19  C20  121.02  3.000
 CVV  O3   C19  C20  126.54  3.000
 CVV  C3   C2   C18  118.45  3.000
 CVV  C3   C2   C1   125.10  3.000
 CVV  C18  C2   C1   116.04  3.000
 CVV  H22  C23  H21  105.98  3.000
 CVV  H22  C23  N2   108.79  3.000
 CVV  H21  C23  N2   111.97  3.000
 CVV  H22  C23  C22  108.69  3.000
 CVV  H21  C23  C22  110.17  3.000
 CVV  N2   C23  C22  111.07  3.000
 CVV  H23  C25  C27  116.36  3.000
 CVV  H23  C25  C26  116.01  3.000
 CVV  C27  C25  C26   59.93  3.000
 CVV  H23  C25  C24  114.10  3.000
 CVV  C27  C25  C24  121.19  3.000
 CVV  C26  C25  C24  118.78  3.000
 CVV  H25  C27  H24  114.14  3.000
 CVV  H25  C27  C25  117.72  3.000
 CVV  H24  C27  C25  118.36  3.000
 CVV  H25  C27  C26  117.72  3.000
 CVV  H24  C27  C26  118.52  3.000
 CVV  C25  C27  C26   60.00  3.000
 CVV  C19  O3   C16  107.49  3.000
 CVV  H27  C3   H26  104.93  3.000
 CVV  H27  C3   C2   108.03  3.000
 CVV  H26  C3   C2   110.97  3.000
 CVV  H27  C3   C4   108.59  3.000
 CVV  H26  C3   C4   109.53  3.000
 CVV  C2   C3   C4   114.32  3.000
 CVV  H28  O4   C20  110.68  3.000
 CVV  O2   C9   C10  121.22  3.000
 CVV  C10  C9   N1   115.98  3.000
 CVV  O2   C9   N1   122.80  3.000
 CVV  C23  N2   C24  113.20  3.000
 CVV  C24  N2   C4   113.26  3.000
 CVV  C23  N2   C4   112.81  3.000
 CVV  H13  C24  H12  106.06  3.000
 CVV  H13  C24  C25  108.81  3.000
 CVV  H12  C24  C25  108.48  3.000
 CVV  H13  C24  N2   112.71  3.000
 CVV  H12  C24  N2   107.54  3.000
 CVV  C25  C24  N2   112.93  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
 CVV  CONST_01  C13  C14  C15  C10     0.00   0.0  0
 CVV  CONST_02  C13  C12  C11  C10     0.00   0.0  0
 CVV  CONST_03  C12  C13  C14  C15     0.00   0.0  0
 CVV  CONST_04  C12  C11  C10  C15     0.00   0.0  0
 CVV  CONST_05  C2   C18  C19  C20     0.00   0.0  0
 CVV  CONST_06  C2   C1   C21  C20     0.00   0.0  0
 CVV  CONST_07  C18  C19  C20  C21     0.00   0.0  0
 CVV  CONST_08  C18  C2   C1   C21     0.00   0.0  0
 CVV  CONST_09  C19  C20  C21  C1      0.00   0.0  0
 CVV  CONST_10  C19  C18  C2   C1      0.00   0.0  0
 CVV  CONST_11  C14  C15  C10  C11     0.00   0.0  0
 CVV  CONST_12  C14  C13  C12  C11     0.00   0.0  0
 CVV  CONST_13  I1   C12  C11  C10   180.00   0.0  0
 CVV  CONST_14  C14  C13  C12  I1    180.00   0.0  0
 CVV  CONST_15  O4   C20  C21  C1    180.00   0.0  0
 CVV  CONST_16  C9   C10  C11  C12   180.00   0.0  0
 CVV  CONST_17  C9   C10  C15  C14   180.00   0.0  0
 CVV  CONST_18  O4   C20  C19  C18   180.00   0.0  0
 CVV  CONST_19  O4   C20  C19  O3      0.00   0.0  0
 CVV  CONST_20  H18  C14  C15  C10   180.00   0.0  0
 CVV  CONST_21  H8   C15  C14  C13   180.00   0.0  0
 CVV  CONST_22  H17  C11  C12  C13   180.00   0.0  0
 CVV  CONST_23  H7   C13  C14  C15   180.00   0.0  0
 CVV  CONST_24  H16  C1   C21  C20   180.00   0.0  0
 CVV  CONST_25  H9   C21  C20  C19   180.00   0.0  0
 CVV  CONST_26  C10  C9   N1   C8    180.00   0.0  0
 CVV  CONST_27  O2   C9   N1   C8      0.00   0.0  0
 CVV  CONST_28  H1   N1   C9   C10     0.00   0.0  0
 CVV  Var_01    C18  C2   C3   C4     -3.00  30.0  1
 CVV  Var_02    C22  C23  N2   C4     56.66  30.0  3
 CVV  Var_03    C8   C7   C6   C5     -3.98  30.0  1
 CVV  Var_04    N2   C23  C22  C17   -51.15  30.0  3
 CVV  Var_05    C18  C19  O3   C16   -11.09  30.0  1
 CVV  Var_06    C25  C24  N2   C4   -160.14  30.0  3
 CVV  Var_07    C27  C26  C25  C24   111.39  30.0  1
 CVV  Var_08    N2   C24  C25  C26  -165.32  30.0  3
 CVV  Var_09    C15  C10  C9   N1     28.41  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
 CVV  chir_01  C4   C5   C3   N2   negativ
 CVV  chir_02  C5   C4   C17  C6   negativ
 CVV  chir_03  C8   N1   C16  C7   negativ
 CVV  chir_04  C17  C5   C18  C16  negativ
 CVV  chir_05  C16  O3   C8   C17  negativ
 CVV  chir_06  C25  C24  C26  C27  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
 CVV  plan-1  C10  0.020
 CVV  plan-1  C13  0.020
 CVV  plan-1  C15  0.020
 CVV  plan-1  C11  0.020
 CVV  plan-1  C12  0.020
 CVV  plan-1  C14  0.020
 CVV  plan-1  C9   0.020
 CVV  plan-1  H7   0.020
 CVV  plan-1  H8   0.020
 CVV  plan-1  H17  0.020
 CVV  plan-1  H18  0.020
 CVV  plan-1  I1   0.020
 CVV  plan-2  C17  0.020
 CVV  plan-2  C20  0.020
 CVV  plan-2  C21  0.020
 CVV  plan-2  C1   0.020
 CVV  plan-2  C18  0.020
 CVV  plan-2  C19  0.020
 CVV  plan-2  C2   0.020
 CVV  plan-2  O3   0.020
 CVV  plan-2  C3   0.020
 CVV  plan-2  O4   0.020
 CVV  plan-2  H9   0.020
 CVV  plan-2  H16  0.020
 CVV  plan-3  N1   0.020
 CVV  plan-3  C8   0.020
 CVV  plan-3  C10  0.020
 CVV  plan-3  C9   0.020
 CVV  plan-3  H1   0.020
 CVV  plan-3  O2   0.020

