# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 23:56:28 2022
#   Inital geometry file: a 160 line input string
#   Ligand name: N-[(1S,2R,3R,4S,5R)-5-amino-2-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-4-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl]oxy}-3-hydroxycyclohexyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@@H]1[C@@H](O)[C@H](OC[C@]1(C)O)O[C@H]2[C@H](N)C[C@H](NC(C)=O)[C@@H](O[C@H]3OC(=CC[C@H]3N)CN)[C@@H]2O
#
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
 DVM  DVM  N-[(1S,2R,3R,4S,5R)-5-amino-2-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-4-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl]oxy}-3-hydroxycyclohexyl]acetamide  ligand  73  34  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DVM
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
 DVM  C13  C  CH1   0   0.201  -3.2154  -0.2004  -1.0938
 DVM  N21  N  NH2   0  -0.787   4.4069  -1.6686   2.4298
 DVM  C22  C  CH2   0  -0.464   0.6672   2.3573  -0.8330
 DVM  C23  C  CH1   0   0.071  -4.5358   0.5224  -0.8046
 DVM  C42  C  CH1   0  -0.000   1.4532   0.1442   0.0086
 DVM  O    O  O     0  -0.507   3.0459   3.9846   0.8324
 DVM  CH3  C  CH3   0  -0.779   5.0987   3.2109  -0.1239
 DVM  C11  C  CH1   0   0.329   3.1150  -1.5087   0.3622
 DVM  C12  C  CH1   0  -0.106  -0.7803   2.0097  -0.4919
 DVM  C21  C  CH1   0  -0.210   3.6521  -2.4280   1.4492
 DVM  C31  C  CH2   0  -0.461   4.4424  -3.5344   0.7403
 DVM  C32  C  CH1   0  -0.062   1.6516   1.6560   0.1009
 DVM  C33  C  CH1   0  -0.080  -5.2050  -0.0364   0.4568
 DVM  C41  C  C1    0  -0.394   5.3479  -2.9431  -0.2988
 DVM  C43  C  CT    0   0.146  -5.3145  -1.5714   0.3732
 DVM  C51  C  C     0   0.386   5.1995  -1.6984  -0.7503
 DVM  C52  C  CH1   0   0.026   0.0192  -0.2241   0.3704
 DVM  C53  C  CH2   0  -0.189  -3.9448  -2.1498   0.0240
 DVM  C61  C  CH2   0  -0.381   6.0924  -1.0148  -1.7357
 DVM  C62  C  CH1   0   0.042  -0.9732   0.4965  -0.5405
 DVM  C83  C  CH3   0  -0.683  -5.7830  -2.1739   1.6929
 DVM  N12  N  NH2   0  -0.815  -1.7571   2.6583  -1.3583
 DVM  N32  N  NH1   0  -0.647   3.0271   1.9817  -0.2048
 DVM  N33  N  NH1   0  -0.604  -6.4793   0.6241   0.6808
 DVM  N61  N  NH2   0  -0.795   5.3776  -0.7058  -2.9692
 DVM  O11  O  O2    0  -0.497   2.3398  -0.5083   0.8966
 DVM  O23  O  OH1   0  -0.714  -4.3613   1.9054  -0.6745
 DVM  O43  O  OH1   0  -0.678  -6.2418  -1.8476  -0.6640
 DVM  O51  O  O2    0  -0.517   4.1943  -0.8805  -0.3307
 DVM  O53  O  O2    0  -0.487  -3.3917  -1.5834  -1.1462
 DVM  O62  O  O2    0  -0.523  -2.2747   0.1510  -0.1168
 DVM  H1   H  HCH1  0   0.241  -2.8487   0.0788  -2.0891
 DVM  H3   H  HNH2  0   0.345   5.3092  -1.4074   2.0497
 DVM  H5   H  HCH2  0   0.233   0.8809   2.0702  -1.8688
 DVM  H6   H  HCH2  0   0.263   0.8047   3.4376  -0.7649
 DVM  H7   H  HCH1  0   0.190  -5.1927   0.3060  -1.6601
 DVM  H8   H  HCH1  0   0.244   1.6421  -0.1742  -1.0278
 DVM  H9   H  HCH3  0   0.270   5.2336   3.9685  -0.8969
 DVM  H10  H  HCH3  0   0.266   5.6556   3.5368   0.7533
 DVM  H11  H  HCH3  0   0.239   5.5359   2.2802  -0.4827
 DVM  H12  H  HCH1  0   0.222   2.5537  -2.1087  -0.3692
 DVM  H13  H  HCH1  0   0.248  -0.9902   2.3463   0.5295
 DVM  H14  H  HCH1  0   0.260   2.7906  -2.8708   1.9543
 DVM  H15  H  HCH2  0   0.250   5.0235  -4.0928   1.4787
 DVM  H16  H  HCH2  0   0.244   3.7609  -4.2607   0.2845
 DVM  H17  H  HCH1  0   0.254   1.4451   1.9704   1.1303
 DVM  H18  H  HCH1  0   0.228  -4.5443   0.1889   1.3028
 DVM  H19  H  H     0   0.245   6.1627  -3.5363  -0.6931
 DVM  H22  H  HCH1  0   0.220  -0.1645   0.1007   1.4069
 DVM  H23  H  HCH2  0   0.203  -3.2721  -2.0331   0.8833
 DVM  H24  H  HCH2  0   0.243  -4.0303  -3.2226  -0.1667
 DVM  H25  H  HCH2  0   0.217   6.5351  -0.1310  -1.2515
 DVM  H26  H  HCH2  0   0.247   6.9203  -1.6842  -1.9711
 DVM  H27  H  HCH1  0   0.228  -0.8042   0.1491  -1.5723
 DVM  H28  H  HCH3  0   0.243  -6.7763  -1.8122   1.9578
 DVM  H29  H  HCH3  0   0.237  -5.8339  -3.2639   1.6272
 DVM  H30  H  HCH3  0   0.233  -5.1018  -1.9245   2.5070
 DVM  H34  H  HNH2  0   0.375  -1.7102   3.6628  -1.2324
 DVM  H35  H  HNH2  0   0.362  -1.5295   2.4889  -2.3327
 DVM  H37  H  HNH1  0   0.394   3.5942   1.2650  -0.6276
 DVM  H38  H  HNH1  0   0.342  -7.2430   0.0189   0.4123
 DVM  H40  H  HNH2  0   0.339   4.6634  -0.0118  -2.7882
 DVM  H41  H  HNH2  0   0.356   6.0214  -0.2640  -3.6133
 DVM  H43  H  HOH1  0   0.465  -3.4461   2.1653  -0.9393
 DVM  H44  H  HOH1  0   0.449  -6.4497  -2.7878  -0.6499
 DVM  C93  C  CH3   0  -0.526  -6.6856   1.1429   2.0155
 DVM  O52  O  OH1   0  -0.662  -0.0962  -1.6180   0.2521
 DVM  C    C  C     0   0.521   3.6339   3.1012   0.2219
 DVM  H2   H  HNH2  0   0.352   4.6080  -2.2669   3.2209
 DVM  H31  H  HCH3  0   0.226  -7.6780   1.5908   2.0808
 DVM  H32  H  HCH3  0   0.193  -6.6030   0.4022   2.8225
 DVM  H33  H  HCH3  0   0.222  -5.9600   1.9311   2.2220
 DVM  H45  H  HOH1  0   0.455  -0.9777  -1.8755   0.5393

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
 DVM  O    C    double  1.224  0.020  1.224
 DVM  CH3  C    single  1.509  0.020  1.509
 DVM  C    N32  single  1.343  0.020  1.343
 DVM  N32  C32  single  1.446  0.020  1.446
 DVM  C32  C22  single  1.527  0.020  1.527
 DVM  C32  C42  single  1.528  0.020  1.528
 DVM  C22  C12  single  1.527  0.020  1.527
 DVM  C12  N12  single  1.458  0.020  1.458
 DVM  C12  C62  single  1.526  0.020  1.526
 DVM  O11  C42  single  1.414  0.020  1.414
 DVM  O11  C11  single  1.374  0.020  1.374
 DVM  C93  N33  single  1.447  0.020  1.447
 DVM  C42  C52  single  1.524  0.020  1.524
 DVM  O23  C23  single  1.400  0.020  1.400
 DVM  C62  C52  single  1.528  0.020  1.528
 DVM  C62  O62  single  1.412  0.020  1.412
 DVM  C52  O52  single  1.404  0.020  1.404
 DVM  C31  C41  single  1.500  0.020  1.500
 DVM  C31  C21  single  1.533  0.020  1.533
 DVM  O51  C11  single  1.428  0.020  1.428
 DVM  O51  C51  single  1.362  0.020  1.362
 DVM  N21  C21  single  1.452  0.020  1.452
 DVM  O62  C13  single  1.401  0.020  1.401
 DVM  C11  C21  single  1.522  0.020  1.522
 DVM  C41  C51  double  1.332  0.020  1.332
 DVM  N33  C33  single  1.453  0.020  1.453
 DVM  C33  C23  single  1.533  0.020  1.533
 DVM  C33  C43  single  1.541  0.020  1.541
 DVM  C51  C61  single  1.495  0.020  1.495
 DVM  C23  C13  single  1.533  0.020  1.533
 DVM  C13  O53  single  1.395  0.020  1.395
 DVM  C83  C43  single  1.524  0.020  1.524
 DVM  C61  N61  single  1.459  0.020  1.459
 DVM  C43  C53  single  1.527  0.020  1.527
 DVM  C43  O43  single  1.418  0.020  1.418
 DVM  O53  C53  single  1.413  0.020  1.413
 DVM  C13  H1   single  0.970  0.020  1.090
 DVM  N21  H2   single  0.890  0.020  1.040
 DVM  N21  H3   single  0.890  0.020  1.040
 DVM  C22  H5   single  0.970  0.020  1.090
 DVM  C22  H6   single  0.970  0.020  1.090
 DVM  C23  H7   single  0.970  0.020  1.090
 DVM  C42  H8   single  0.970  0.020  1.090
 DVM  CH3  H9   single  0.970  0.020  1.090
 DVM  CH3  H10  single  0.970  0.020  1.090
 DVM  CH3  H11  single  0.970  0.020  1.090
 DVM  C11  H12  single  0.970  0.020  1.090
 DVM  C12  H13  single  0.970  0.020  1.090
 DVM  C21  H14  single  0.970  0.020  1.090
 DVM  C31  H15  single  0.970  0.020  1.090
 DVM  C31  H16  single  0.970  0.020  1.090
 DVM  C32  H17  single  0.970  0.020  1.090
 DVM  C33  H18  single  0.970  0.020  1.090
 DVM  C41  H19  single  0.930  0.020  1.080
 DVM  C52  H22  single  0.970  0.020  1.090
 DVM  C53  H23  single  0.970  0.020  1.090
 DVM  C53  H24  single  0.970  0.020  1.090
 DVM  C61  H25  single  0.970  0.020  1.090
 DVM  C61  H26  single  0.970  0.020  1.090
 DVM  C62  H27  single  0.970  0.020  1.090
 DVM  C83  H28  single  0.970  0.020  1.090
 DVM  C83  H29  single  0.970  0.020  1.090
 DVM  C83  H30  single  0.970  0.020  1.090
 DVM  C93  H31  single  0.970  0.020  1.090
 DVM  C93  H32  single  0.970  0.020  1.090
 DVM  C93  H33  single  0.970  0.020  1.090
 DVM  N12  H34  single  0.890  0.020  1.040
 DVM  N12  H35  single  0.890  0.020  1.040
 DVM  N32  H37  single  0.860  0.020  1.020
 DVM  N33  H38  single  0.890  0.020  1.040
 DVM  N61  H40  single  0.890  0.020  1.040
 DVM  N61  H41  single  0.890  0.020  1.040
 DVM  O23  H43  single  0.850  0.020  0.980
 DVM  O43  H44  single  0.850  0.020  0.980
 DVM  O52  H45  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
 DVM  H1   C13  O62  110.15  3.000
 DVM  H1   C13  O53  105.11  3.000
 DVM  O62  C13  O53  111.08  3.000
 DVM  H1   C13  C23  109.83  3.000
 DVM  O53  C13  C23  111.45  3.000
 DVM  O62  C13  C23  109.18  3.000
 DVM  H3   N21  H2   105.58  3.000
 DVM  H3   N21  C21  110.15  3.000
 DVM  H2   N21  C21  108.79  3.000
 DVM  H6   C22  H5   107.09  3.000
 DVM  H6   C22  C32  109.59  3.000
 DVM  H5   C22  C32  109.39  3.000
 DVM  H6   C22  C12  109.32  3.000
 DVM  H5   C22  C12  109.65  3.000
 DVM  C32  C22  C12  111.70  3.000
 DVM  H7   C23  O23  109.94  3.000
 DVM  H7   C23  C33  107.90  3.000
 DVM  O23  C23  C33  109.75  3.000
 DVM  H7   C23  C13  105.95  3.000
 DVM  C33  C23  C13  111.06  3.000
 DVM  O23  C23  C13  112.09  3.000
 DVM  H8   C42  O11  110.50  3.000
 DVM  H8   C42  C52  108.37  3.000
 DVM  O11  C42  C52  109.22  3.000
 DVM  H8   C42  C32  108.72  3.000
 DVM  C52  C42  C32  110.31  3.000
 DVM  O11  C42  C32  109.71  3.000
 DVM  H11  CH3  H10  108.41  3.000
 DVM  H11  CH3  H9   108.09  3.000
 DVM  H10  CH3  H9   107.44  3.000
 DVM  H11  CH3  C    113.76  3.000
 DVM  H10  CH3  C    109.49  3.000
 DVM  H9   CH3  C    109.45  3.000
 DVM  H12  C11  O51  107.64  3.000
 DVM  H12  C11  O11  111.58  3.000
 DVM  O51  C11  O11  107.15  3.000
 DVM  H12  C11  C21  109.00  3.000
 DVM  O51  C11  C21  110.22  3.000
 DVM  O11  C11  C21  111.17  3.000
 DVM  H13  C12  N12  106.80  3.000
 DVM  H13  C12  C62  108.06  3.000
 DVM  N12  C12  C62  109.73  3.000
 DVM  H13  C12  C22  108.65  3.000
 DVM  C62  C12  C22  109.78  3.000
 DVM  N12  C12  C22  113.64  3.000
 DVM  H14  C21  C31  109.13  3.000
 DVM  H14  C21  C11  107.27  3.000
 DVM  C31  C21  C11  106.71  3.000
 DVM  H14  C21  N21  108.05  3.000
 DVM  C11  C21  N21  110.49  3.000
 DVM  C31  C21  N21  114.94  3.000
 DVM  H16  C31  H15  105.86  3.000
 DVM  H16  C31  C41  110.41  3.000
 DVM  H15  C31  C41  110.39  3.000
 DVM  H16  C31  C21  110.49  3.000
 DVM  H15  C31  C21  109.29  3.000
 DVM  C41  C31  C21  110.30  3.000
 DVM  H17  C32  N32  108.25  3.000
 DVM  H17  C32  C42  108.44  3.000
 DVM  N32  C32  C42  109.49  3.000
 DVM  H17  C32  C22  108.73  3.000
 DVM  C42  C32  C22  109.50  3.000
 DVM  N32  C32  C22  112.35  3.000
 DVM  H18  C33  N33  108.42  3.000
 DVM  H18  C33  C43  106.81  3.000
 DVM  N33  C33  C43  113.51  3.000
 DVM  H18  C33  C23  107.26  3.000
 DVM  C43  C33  C23  110.45  3.000
 DVM  N33  C33  C23  110.12  3.000
 DVM  H19  C41  C51  118.19  3.000
 DVM  H19  C41  C31  119.40  3.000
 DVM  C51  C41  C31  122.41  3.000
 DVM  O43  C43  C83  110.80  3.000
 DVM  O43  C43  C53  110.21  3.000
 DVM  C83  C43  C53  108.90  3.000
 DVM  O43  C43  C33  106.26  3.000
 DVM  C53  C43  C33  109.02  3.000
 DVM  C83  C43  C33  111.63  3.000
 DVM  O51  C51  C61  111.67  3.000
 DVM  C61  C51  C41  125.73  3.000
 DVM  O51  C51  C41  122.59  3.000
 DVM  H22  C52  O52  111.00  3.000
 DVM  H22  C52  C62  108.28  3.000
 DVM  O52  C52  C62  111.39  3.000
 DVM  H22  C52  C42  108.00  3.000
 DVM  O52  C52  C42  107.30  3.000
 DVM  C62  C52  C42  110.83  3.000
 DVM  H24  C53  H23  106.79  3.000
 DVM  H24  C53  O53  106.24  3.000
 DVM  H23  C53  O53  111.46  3.000
 DVM  H24  C53  C43  109.96  3.000
 DVM  H23  C53  C43  109.29  3.000
 DVM  O53  C53  C43  112.87  3.000
 DVM  H26  C61  H25  106.41  3.000
 DVM  H26  C61  N61  108.64  3.000
 DVM  H25  C61  N61  113.51  3.000
 DVM  H26  C61  C51  108.36  3.000
 DVM  H25  C61  C51  108.50  3.000
 DVM  N61  C61  C51  111.19  3.000
 DVM  H27  C62  O62  110.21  3.000
 DVM  H27  C62  C52  108.06  3.000
 DVM  O62  C62  C52  107.73  3.000
 DVM  H27  C62  C12  108.85  3.000
 DVM  O62  C62  C12  110.46  3.000
 DVM  C52  C62  C12  111.50  3.000
 DVM  H30  C83  H29  107.58  3.000
 DVM  H30  C83  H28  108.18  3.000
 DVM  H29  C83  H28  107.65  3.000
 DVM  H30  C83  C43  111.34  3.000
 DVM  H29  C83  C43  110.87  3.000
 DVM  H28  C83  C43  111.06  3.000
 DVM  H35  N12  H34  105.92  3.000
 DVM  H35  N12  C12  110.24  3.000
 DVM  H34  N12  C12  109.64  3.000
 DVM  H37  N32  C32  117.66  3.000
 DVM  H37  N32  C    118.17  3.000
 DVM  C32  N32  C    123.39  3.000
 DVM  H38  N33  C93  110.61  3.000
 DVM  H38  N33  C33  110.46  3.000
 DVM  C93  N33  C33  115.50  3.000
 DVM  H41  N61  H40  105.27  3.000
 DVM  H41  N61  C61  108.60  3.000
 DVM  H40  N61  C61  109.87  3.000
 DVM  C11  O11  C42  116.45  3.000
 DVM  H43  O23  C23  110.52  3.000
 DVM  H44  O43  C43  108.69  3.000
 DVM  C51  O51  C11  116.30  3.000
 DVM  C53  O53  C13  114.57  3.000
 DVM  C62  O62  C13  118.10  3.000
 DVM  H33  C93  H32  107.34  3.000
 DVM  H33  C93  H31  107.28  3.000
 DVM  H32  C93  H31  107.54  3.000
 DVM  H33  C93  N33  109.80  3.000
 DVM  H32  C93  N33  115.17  3.000
 DVM  H31  C93  N33  109.40  3.000
 DVM  H45  O52  C52  108.42  3.000
 DVM  N32  C    CH3  115.24  3.000
 DVM  N32  C    O    122.88  3.000
 DVM  CH3  C    O    121.87  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
 DVM  CONST_01  C32  N32  C    O       0.00   0.0  0
 DVM  CONST_02  C32  N32  C    CH3   180.00   0.0  0
 DVM  CONST_03  H37  N32  C    O     180.00   0.0  0
 DVM  Var_01    C43  C53  O53  C13    58.95  30.0  1
 DVM  Var_02    C41  C51  O51  C11   -14.91  30.0  1
 DVM  Var_03    C51  C41  C31  C21   -16.10  30.0  1
 DVM  Var_04    O51  C51  C41  C31    -1.82  30.0  1
 DVM  Var_05    N61  C61  C51  C41   115.68  30.0  3
 DVM  Var_06    H31  C93  N33  C33  -178.45  30.0  3
 DVM  Var_07    H40  N61  C61  C51    66.57  30.0  3
 DVM  Var_08    H9   CH3  C    O     -70.74  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
 DVM  chir_01  C13  O62  C23  O53  positiv
 DVM  chir_02  C23  O23  C33  C13  positiv
 DVM  chir_03  C42  O11  C32  C52  positiv
 DVM  chir_04  C11  O51  O11  C21  positiv
 DVM  chir_05  C12  N12  C22  C62  positiv
 DVM  chir_06  C21  N21  C31  C11  positiv
 DVM  chir_07  C32  N32  C22  C42  negativ
 DVM  chir_08  C33  N33  C23  C43  positiv
 DVM  chir_09  C43  C53  C83  C33  negativ
 DVM  chir_10  C52  C42  C62  O52  negativ
 DVM  chir_11  C62  O62  C12  C52  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
 DVM  plan-1  O    0.020
 DVM  plan-1  CH3  0.020
 DVM  plan-1  C32  0.020
 DVM  plan-1  N32  0.020
 DVM  plan-1  H37  0.020
 DVM  plan-1  C    0.020

