# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 10:03:28 2022
#   Inital geometry file: a 129 line input string
#   Ligand name: ~{N}2-methyl-~{N}4-(4-oxidanylcyclohexyl)-5-[(1~{S})-1-phenylethyl]furan-2,4-dicarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1oc([C@@H](C)c2ccccc2)c(c1)C(=O)N[C@H]3CC[C@H](O)CC3
#
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
 V9K  V9K  ~{N}2-methyl-~{N}4-(4-oxidanylcyclohexyl)-5-[(1~{S})-1-phenylethyl]furan-2,4-dicarboxamide  ligand  53  27  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_V9K
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
 V9K  N1   N  NH1   0  -0.657  45.6615  16.2178  10.3923
 V9K  C4   C  CR5   0  -0.157  43.4131  16.6415   9.7132
 V9K  C5   C  C     0   0.494  44.5005  16.8198  10.7014
 V9K  C6   C  CH1   0  -0.052  46.8534  16.3074  11.2146
 V9K  C7   C  CH2   0  -0.453  47.6840  15.0372  11.0627
 V9K  C8   C  CH2   0  -0.479  48.9575  15.1158  11.8979
 V9K  C10  C  CH2   0  -0.463  48.9588  17.6065  11.7071
 V9K  C13  C  CH1   0  -0.465  41.7806  18.6081  10.3508
 V9K  C15  C  CR6   0   0.150  40.6187  18.1988  11.2394
 V9K  C17  C  CR16  0  -0.239  39.8108  17.5379  13.4212
 V9K  C20  C  CR16  0  -0.311  39.3259  18.0574  10.7402
 V9K  O1   O  O     0  -0.484  44.3365  17.4616  11.7332
 V9K  C11  C  CH2   0  -0.439  47.6853  17.5428  10.8708
 V9K  C9   C  CH1   0   0.089  49.7862  16.3433  11.5339
 V9K  O2   O  OH1   0  -0.672  50.9438  16.4653  12.3335
 V9K  C3   C  CR15  0  -0.351  43.2977  15.6396   8.7017
 V9K  C12  C  CR5   0   0.466  42.2882  17.4165   9.6108
 V9K  O3   O  O     0  -0.432  41.5192  16.9520   8.6180
 V9K  C2   C  CR5   0   0.243  42.1260  15.8730   8.0684
 V9K  C1   C  C     0   0.478  41.4874  15.1552   6.9539
 V9K  O    O  O     0  -0.481  42.0538  14.1964   6.4450
 V9K  N    N  NH1   0  -0.639  40.2925  15.6083   6.5534
 V9K  C    C  CH3   0  -0.512  39.5735  14.9905   5.4639
 V9K  C14  C  CH3   0  -0.651  41.4520  19.7712   9.4119
 V9K  C19  C  CR16  0  -0.238  38.2869  17.6630  11.5724
 V9K  C18  C  CR16  0  -0.266  38.5248  17.4031  12.9158
 V9K  C16  C  CR16  0  -0.301  40.8489  17.9291  12.5861
 V9K  H1   H  HNH1  0   0.404  45.7753  15.8219   9.4718
 V9K  H2   H  HCH1  0   0.241  46.5277  16.3841  12.2553
 V9K  H3   H  HCH2  0   0.246  47.0929  14.1684  11.3597
 V9K  H4   H  HCH2  0   0.224  47.9442  14.8978  10.0067
 V9K  H5   H  HCH2  0   0.221  48.6999  15.1636  12.9615
 V9K  H6   H  HCH2  0   0.237  49.5493  14.2070  11.7540
 V9K  H7   H  HCH2  0   0.238  49.5459  18.4830  11.4223
 V9K  H8   H  HCH2  0   0.220  48.7010  17.7248  12.7657
 V9K  H9   H  HCH1  0   0.292  42.5935  18.9252  11.0013
 V9K  H10  H  HCR6  0   0.253  40.0078  17.3389  14.4669
 V9K  H11  H  HCR6  0   0.252  39.1165  18.2587   9.6971
 V9K  H12  H  HCH2  0   0.219  47.9429  17.5095   9.8068
 V9K  H13  H  HCH2  0   0.243  47.0890  18.4445  11.0237
 V9K  H14  H  HCH1  0   0.184  50.0619  16.2615  10.4699
 V9K  H15  H  HOH1  0   0.443  51.4769  15.6723  12.2179
 V9K  H16  H  HCR5  0   0.278  43.9822  14.8350   8.4843
 V9K  H17  H  HNH1  0   0.409  39.8691  16.3950   7.0166
 V9K  H18  H  HCH3  0   0.253  38.6541  15.5457   5.3032
 V9K  H19  H  HCH3  0   0.241  40.1518  15.0091   4.5399
 V9K  H20  H  HCH3  0   0.240  39.3159  13.9545   5.6861
 V9K  H21  H  HCH3  0   0.247  41.1276  20.6313   9.9970
 V9K  H22  H  HCH3  0   0.245  42.3359  20.0654   8.8459
 V9K  H23  H  HCH3  0   0.235  40.6623  19.5357   8.6996
 V9K  H24  H  HCR6  0   0.253  37.2875  17.5603  11.1691
 V9K  H25  H  HCR6  0   0.253  37.7127  17.0995  13.5637
 V9K  H26  H  HCR6  0   0.253  41.8524  18.0247  12.9822

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
 V9K  C    N    single    1.444  0.020  1.444
 V9K  O    C1   double    1.224  0.020  1.224
 V9K  N    C1   single    1.339  0.020  1.339
 V9K  C1   C2   single    1.471  0.020  1.471
 V9K  C2   C3   aromatic  1.352  0.020  1.352
 V9K  C2   O3   aromatic  1.354  0.020  1.354
 V9K  C3   C4   aromatic  1.428  0.020  1.428
 V9K  O3   C12  aromatic  1.339  0.020  1.339
 V9K  C4   C12  aromatic  1.370  0.020  1.370
 V9K  C4   C5   single    1.480  0.020  1.480
 V9K  C12  C13  single    1.492  0.020  1.492
 V9K  C14  C13  single    1.530  0.020  1.530
 V9K  C5   N1   single    1.344  0.020  1.344
 V9K  C5   O1   double    1.226  0.020  1.226
 V9K  N1   C6   single    1.451  0.020  1.451
 V9K  C13  C15  single    1.519  0.020  1.519
 V9K  C11  C6   single    1.529  0.020  1.529
 V9K  C11  C10  single    1.525  0.020  1.525
 V9K  C6   C7   single    1.525  0.020  1.525
 V9K  C20  C15  aromatic  1.393  0.020  1.393
 V9K  C20  C19  aromatic  1.388  0.020  1.388
 V9K  C15  C16  aromatic  1.393  0.020  1.393
 V9K  C7   C8   single    1.525  0.020  1.525
 V9K  C10  C9   single    1.520  0.020  1.520
 V9K  C9   C8   single    1.525  0.020  1.525
 V9K  C9   O2   single    1.412  0.020  1.412
 V9K  C19  C18  aromatic  1.389  0.020  1.389
 V9K  C16  C17  aromatic  1.388  0.020  1.388
 V9K  C18  C17  aromatic  1.388  0.020  1.388
 V9K  N1   H1   single    0.860  0.020  1.020
 V9K  C6   H2   single    0.970  0.020  1.090
 V9K  C7   H3   single    0.970  0.020  1.090
 V9K  C7   H4   single    0.970  0.020  1.090
 V9K  C8   H5   single    0.970  0.020  1.090
 V9K  C8   H6   single    0.970  0.020  1.090
 V9K  C10  H7   single    0.970  0.020  1.090
 V9K  C10  H8   single    0.970  0.020  1.090
 V9K  C13  H9   single    0.970  0.020  1.090
 V9K  C17  H10  single    0.930  0.020  1.080
 V9K  C20  H11  single    0.930  0.020  1.080
 V9K  C11  H12  single    0.970  0.020  1.090
 V9K  C11  H13  single    0.970  0.020  1.090
 V9K  C9   H14  single    0.970  0.020  1.090
 V9K  O2   H15  single    0.850  0.020  0.980
 V9K  C3   H16  single    0.930  0.020  1.080
 V9K  N    H17  single    0.860  0.020  1.020
 V9K  C    H18  single    0.970  0.020  1.090
 V9K  C    H19  single    0.970  0.020  1.090
 V9K  C    H20  single    0.970  0.020  1.090
 V9K  C14  H21  single    0.970  0.020  1.090
 V9K  C14  H22  single    0.970  0.020  1.090
 V9K  C14  H23  single    0.970  0.020  1.090
 V9K  C19  H24  single    0.930  0.020  1.080
 V9K  C18  H25  single    0.930  0.020  1.080
 V9K  C16  H26  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
 V9K  H1   N1   C6   116.67  3.000
 V9K  H1   N1   C5   118.91  3.000
 V9K  C6   N1   C5   123.48  3.000
 V9K  C12  C4   C3   106.12  3.000
 V9K  C12  C4   C5   125.81  3.000
 V9K  C3   C4   C5   128.07  3.000
 V9K  O1   C5   C4   121.78  3.000
 V9K  O1   C5   N1   122.93  3.000
 V9K  C4   C5   N1   115.29  3.000
 V9K  H2   C6   C11  108.64  3.000
 V9K  H2   C6   C7   108.39  3.000
 V9K  C11  C6   C7   110.75  3.000
 V9K  H2   C6   N1   107.40  3.000
 V9K  C7   C6   N1   109.84  3.000
 V9K  C11  C6   N1   111.69  3.000
 V9K  H4   C7   H3   106.82  3.000
 V9K  H4   C7   C8   109.62  3.000
 V9K  H3   C7   C8   110.13  3.000
 V9K  H4   C7   C6   109.33  3.000
 V9K  H3   C7   C6   109.92  3.000
 V9K  C8   C7   C6   110.93  3.000
 V9K  H6   C8   H5   106.93  3.000
 V9K  H6   C8   C9   110.08  3.000
 V9K  H5   C8   C9   108.93  3.000
 V9K  H6   C8   C7   109.68  3.000
 V9K  H5   C8   C7   109.73  3.000
 V9K  C9   C8   C7   111.38  3.000
 V9K  H8   C10  H7   106.95  3.000
 V9K  H8   C10  C9   109.14  3.000
 V9K  H7   C10  C9   110.15  3.000
 V9K  H8   C10  C11  109.74  3.000
 V9K  H7   C10  C11  109.83  3.000
 V9K  C9   C10  C11  110.95  3.000
 V9K  H9   C13  C14  107.80  3.000
 V9K  H9   C13  C12  105.96  3.000
 V9K  C14  C13  C12  112.08  3.000
 V9K  H9   C13  C15  107.47  3.000
 V9K  C14  C13  C15  113.54  3.000
 V9K  C12  C13  C15  109.59  3.000
 V9K  C16  C15  C20  118.70  3.000
 V9K  C16  C15  C13  119.44  3.000
 V9K  C20  C15  C13  121.84  3.000
 V9K  H10  C17  C16  119.78  3.000
 V9K  H10  C17  C18  120.16  3.000
 V9K  C16  C17  C18  120.07  3.000
 V9K  H11  C20  C19  119.05  3.000
 V9K  H11  C20  C15  120.39  3.000
 V9K  C19  C20  C15  120.56  3.000
 V9K  H13  C11  H12  106.84  3.000
 V9K  H13  C11  C10  110.17  3.000
 V9K  H12  C11  C10  109.74  3.000
 V9K  H13  C11  C6   109.80  3.000
 V9K  H12  C11  C6   108.77  3.000
 V9K  C10  C11  C6   111.40  3.000
 V9K  H14  C9   O2   110.37  3.000
 V9K  H14  C9   C10  107.93  3.000
 V9K  O2   C9   C10  108.06  3.000
 V9K  H14  C9   C8   107.85  3.000
 V9K  O2   C9   C8   112.32  3.000
 V9K  C10  C9   C8   110.24  3.000
 V9K  H15  O2   C9   108.34  3.000
 V9K  H16  C3   C2   125.76  3.000
 V9K  H16  C3   C4   127.93  3.000
 V9K  C2   C3   C4   106.29  3.000
 V9K  O3   C12  C13  116.71  3.000
 V9K  C13  C12  C4   133.97  3.000
 V9K  O3   C12  C4   109.31  3.000
 V9K  C2   O3   C12  108.66  3.000
 V9K  C1   C2   O3   120.10  3.000
 V9K  O3   C2   C3   109.61  3.000
 V9K  C1   C2   C3   130.29  3.000
 V9K  N    C1   O    123.60  3.000
 V9K  N    C1   C2   116.66  3.000
 V9K  O    C1   C2   119.74  3.000
 V9K  H17  N    C    118.18  3.000
 V9K  H17  N    C1   120.15  3.000
 V9K  C    N    C1   121.67  3.000
 V9K  H20  C    H19  108.31  3.000
 V9K  H20  C    H18  108.40  3.000
 V9K  H19  C    H18  108.36  3.000
 V9K  H20  C    N    111.74  3.000
 V9K  H19  C    N    111.60  3.000
 V9K  H18  C    N    108.33  3.000
 V9K  H23  C14  H22  107.86  3.000
 V9K  H23  C14  H21  107.82  3.000
 V9K  H22  C14  H21  107.89  3.000
 V9K  H23  C14  C13  113.11  3.000
 V9K  H22  C14  C13  110.45  3.000
 V9K  H21  C14  C13  109.54  3.000
 V9K  H24  C19  C18  120.05  3.000
 V9K  H24  C19  C20  119.63  3.000
 V9K  C18  C19  C20  120.32  3.000
 V9K  H25  C18  C19  120.19  3.000
 V9K  H25  C18  C17  120.29  3.000
 V9K  C19  C18  C17  119.51  3.000
 V9K  H26  C16  C17  119.85  3.000
 V9K  H26  C16  C15  119.31  3.000
 V9K  C17  C16  C15  120.84  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
 V9K  CONST_01  O3   C2   C3   C4      0.00   0.0  0
 V9K  CONST_02  C2   O3   C12  C4      0.00   0.0  0
 V9K  CONST_03  C18  C19  C20  C15     0.00   0.0  0
 V9K  CONST_04  C18  C17  C16  C15     0.00   0.0  0
 V9K  CONST_05  C20  C15  C16  C17     0.00   0.0  0
 V9K  CONST_06  C20  C19  C18  C17     0.00   0.0  0
 V9K  CONST_07  C12  O3   C2   C3      0.00   0.0  0
 V9K  CONST_08  O3   C12  C4   C3      0.00   0.0  0
 V9K  CONST_09  C2   C3   C4   C12     0.00   0.0  0
 V9K  CONST_10  C16  C15  C20  C19     0.00   0.0  0
 V9K  CONST_11  C16  C17  C18  C19     0.00   0.0  0
 V9K  CONST_12  C1   C2   C3   C4    180.00   0.0  0
 V9K  CONST_13  C2   C3   C4   C5    180.00   0.0  0
 V9K  CONST_14  O3   C12  C4   C5    180.00   0.0  0
 V9K  CONST_15  C2   O3   C12  C13   180.00   0.0  0
 V9K  CONST_16  C3   C4   C12  C13   180.00   0.0  0
 V9K  CONST_17  C19  C20  C15  C13   180.00   0.0  0
 V9K  CONST_18  C17  C16  C15  C13   180.00   0.0  0
 V9K  CONST_19  C1   C2   O3   C12   180.00   0.0  0
 V9K  CONST_20  H24  C19  C20  C15   180.00   0.0  0
 V9K  CONST_21  H10  C17  C16  C15   180.00   0.0  0
 V9K  CONST_22  H26  C16  C15  C20   180.00   0.0  0
 V9K  CONST_23  H25  C18  C19  C20   180.00   0.0  0
 V9K  CONST_24  H16  C3   C4   C12   180.00   0.0  0
 V9K  CONST_25  H11  C20  C19  C18   180.00   0.0  0
 V9K  CONST_26  C6   N1   C5   C4    180.00   0.0  0
 V9K  CONST_27  O1   C5   N1   C6      0.00   0.0  0
 V9K  CONST_28  C    N    C1   C2    180.00   0.0  0
 V9K  CONST_29  H1   N1   C5   C4      0.00   0.0  0
 V9K  CONST_30  H17  N    C1   C2      0.00   0.0  0
 V9K  CONST_31  C    N    C1   O       0.00   0.0  0
 V9K  Var_01    C9   C10  C11  C6     56.48  30.0  1
 V9K  Var_02    C9   C8   C7   C6    -56.43  30.0  1
 V9K  Var_03    C3   C4   C5   N1     19.57  30.0  1
 V9K  Var_04    O    C1   C2   C3     -1.58  30.0  2
 V9K  Var_05    H18  C    N    C1   -178.23  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
 V9K  chir_01  C6   N1   C11  C7   positiv
 V9K  chir_02  C13  C15  C14  C12  positiv
 V9K  chir_03  C9   C10  C8   O2   positiv

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
 V9K  plan-1  C4   0.020
 V9K  plan-1  C5   0.020
 V9K  plan-1  C13  0.020
 V9K  plan-1  C3   0.020
 V9K  plan-1  C12  0.020
 V9K  plan-1  O3   0.020
 V9K  plan-1  C2   0.020
 V9K  plan-1  C1   0.020
 V9K  plan-1  H16  0.020
 V9K  plan-2  C13  0.020
 V9K  plan-2  C15  0.020
 V9K  plan-2  C17  0.020
 V9K  plan-2  C20  0.020
 V9K  plan-2  C19  0.020
 V9K  plan-2  C18  0.020
 V9K  plan-2  C16  0.020
 V9K  plan-2  H10  0.020
 V9K  plan-2  H11  0.020
 V9K  plan-2  H24  0.020
 V9K  plan-2  H25  0.020
 V9K  plan-2  H26  0.020
 V9K  plan-3  N1   0.020
 V9K  plan-3  C4   0.020
 V9K  plan-3  C5   0.020
 V9K  plan-3  C6   0.020
 V9K  plan-3  O1   0.020
 V9K  plan-3  H1   0.020
 V9K  plan-4  C2   0.020
 V9K  plan-4  C1   0.020
 V9K  plan-4  O    0.020
 V9K  plan-4  N    0.020
 V9K  plan-4  C    0.020
 V9K  plan-4  H17  0.020

