Table 9.
Crystalline intramolecular geometries for α-GlcNAc, α-GalNAc, β-ManNAc crystals. Bond lengths are in Å, while valance angles and dihedral angles are in degree.
| CRYS | MDadd | MDdrude | MDadd – CRYS (%err) | MDdrude – CRYS (%err) | |
|---|---|---|---|---|---|
| ACGLUA11 (N-acetyl-α-D-glucosamine) | |||||
| C1-C2 | 1.534 | 1.523 | 1.557 | −0.01 (0.00) | 0.02 (0.00) |
| C2-C3 | 1.53 | 1.512 | 1.548 | −0.02 (0.00) | 0.02 (0.00) |
| C2-N | 1.457 | 1.463 | 1.469 | 0.01 (0.00) | 0.01 (0.00) |
| C-CT | 1.508 | 1.502 | 1.523 | −0.01 (0.00) | 0.02 (0.00) |
| C-O | 1.235 | 1.225 | 1.259 | −0.01 (0.00) | 0.02 (0.00) |
| C1-C2-N | 111.055 | 113.41 | 114.732 | 2.36 (−0.03) | 3.68 (−0.01) |
| C3-C2-N | 110.338 | 111.7 | 114.007 | 1.36 (−0.01) | 3.67 (−0.01) |
| C1-C2-C3 | 110.075 | 110.686 | 109.231 | 0.61 (−0.04) | −0.84 (−0.02) |
| C2-N-C3 | 35.802 | 34.781 | 33.976 | −1.02 (−0.01) | −1.83 (−0.01) |
| N-C-CT | 116.011 | 116.455 | 121.857 | 0.44 (−0.02) | 5.85 (−0.01) |
| N-C-O | 123.056 | 123.093 | 124.496 | 0.04 (−0.02) | 1.44 (−0.01) |
| O-C-CT | 120.931 | 120.247 | 113.452 | −0.68 (−0.02) | −7.48 (−0.01) |
| C1-C2-N-C | 140.89 | 124.569 | 140.417 | −16.32 (−0.52) | −0.47 (−0.04) |
| C3-C2-N-C | −96.769 | −109.356 | −92.367 | −12.59 (−0.56) | 4.4 (−0.06) |
| AGALAM10 (N-acetyl-α-D-galactosamine) | |||||
| C1-C2 | 1.52 | 1.525 | 1.552 | 0.01 (0.00) | 0.03 (0.00) |
| C2-C3 | 1.529 | 1.519 | 1.549 | −0.01 (0.00) | 0.02 (0.00) |
| C2-N | 1.454 | 1.46 | 1.463 | 0.01 (0.00) | 0.01 (0.00) |
| C-CT | 1.503 | 1.505 | 1.525 | 0 (0.00) | 0.02 (0.00) |
| C-O | 1.239 | 1.227 | 1.259 | −0.01 (0.00) | 0.02 (0.00) |
| C1-C2-N | 111.776 | 113.371 | 115.99 | 1.59 (−0.06) | 4.21 (−0.01) |
| C3-C2-N | 110.094 | 111.953 | 114.331 | 1.86 (−0.05) | 4.24 (−0.02) |
| C1-C2-C3 | 110.222 | 110.377 | 108.63 | 0.16 (−0.04) | −1.59 (−0.02) |
| C2-N-C3 | 35.962 | 34.794 | 33.897 | −1.17 (−0.02) | −2.07 (−0.01) |
| N-C-CT | 116.003 | 116.012 | 121.261 | 0.01 (−0.02) | 5.26 (−0.01) |
| N-C-O | 123.923 | 122.74 | 124.385 | −1.18 (−0.02) | 0.46 (−0.02) |
| O-C-CT | 120.063 | 121.036 | 114.165 | 0.97 (−0.03) | −5.9 (−0.01) |
| C1-C2-N-C | 81.588 | 76.039 | 74.151 | −5.55 (−0.23) | −7.44 (−0.08) |
| C3-C2-N-C | −155.558 | −158.119 | −157.993 | −2.56 (−0.26) | −2.43 (−0.07) |
| NACMAN10 (N-acetyl-β-D-mannosamine monohydrate) | |||||
| C1-C2 | 1.537 | 1.514 | 1.547 | −0.02 (0.00) | 0.01 (0.00) |
| C2-C3 | 1.537 | 1.519 | 1.548 | −0.02 (0.00) | 0.01 (0.00) |
| C2-N | 1.459 | 1.465 | 1.468 | 0.01 (0.00) | 0.01 (0.00) |
| C-CT | 1.503 | 1.505 | 1.524 | 0 (0.00) | 0.02 (0.00) |
| C-O | 1.248 | 1.228 | 1.26 | −0.02 (0.00) | 0.01 (0.00) |
| C1-C2-N | 110.03 | 112.903 | 114.727 | 2.87 (−0.02) | 4.7 (−0.01) |
| C3-C2-N | 114.082 | 114.222 | 115.817 | 0.14 (−0.02) | 1.74 (−0.01) |
| C1-C2-C3 | 107.223 | 107.351 | 104.809 | 0.13 (−0.05) | −2.41 (−0.01) |
| C2-N-C3 | 33.921 | 33.565 | 33.049 | −0.36 (−0.01) | −0.87 (−0.01) |
| N-C-CT | 116.757 | 116.153 | 121.437 | −0.6 (−0.01) | 4.68 (−0.01) |
| N-C-O | 122.048 | 123.043 | 124.24 | 0.99 (−0.01) | 2.19 (−0.02) |
| O-C-CT | 121.194 | 120.591 | 114.121 | −0.6 (−0.01) | −7.07 (−0.01) |
| C1-C2-N-C | −126.826 | −130.526 | −141.428 | −3.7 (−0.11) | −14.6 (−0.03) |
| C3-C2-N-C | 112.635 | 106.304 | 96.048 | −6.33 (−0.18) | −16.59 (−0.03) |
add
additive force field,
drude: Drude polarizable force field parameters.