CheckCIF-PLAT410-420

PLAT410 Type_2 Test for short non-bonding intra H..H contacts

Short intramolecular contacts may arise when H-atoms are in (false) calculated positions. Short intramolecular contacts may also be a sign for a false structure with the molecule sitting on a site with improper site symmetry (e.g. '2' instead of '-1') which may happen when a lattice translation is missed. Short contacts are defined using a van der Waals radius of 1.2 Angstrom. For intramolecular contacts alerts are generated for contacts less than 2.0 Angstrom.

(http://journals.iucr.org/services/cif/checking/PLAT410.html)

警告原因：分子内两个氢距离较近。

解决策略：检查加氢是否正确并重新加氢，或采用DFIX命令将两个氢距离限制在2.1以上，否则需要给出合理解释。

PLAT411 Type_2 Test for short non-bonding inter H..H contacts

Short intermolecular H..H contacts may indicate incorrectly determined structures (i.e. wrong symmetry, missed translation symmetry, wrong position with reference to the symmetry elements, hydrogen atoms on atoms where there should not be any etc..) Short intermolecular contacts may be indicative for inconsistent symmetry data (e.g. coordinates for space-group P43 and symmetry specified as P41 or P21/n & P21/c confusions). Short contacts are defined using a van der Waals radius of 1.2 Angstrom. For intermolecular contacts, an alert is generated for contacts less than 2.4 Angstrom.

(http://journals.iucr.org/services/cif/checking/PLAT411.html)

警告原因：分子间两个氢距离较近。

解决策略：检查加氢是否正确并重新加氢，或采用DFIX命令将两个氢距离限制在2.1以上，否则需要给出合理解释。

PLAT412 Type_2 Test for short non-bonding intra H..H contacts (involving XH3)

Short intramolecular contacts may arise when H-atoms are in (false) calculated positions. Short intramolecular contacts may also be a sign for a false structure with the molecule sitting on a site with improper site symmetry (e.g. '2' instead of '-1') which may happen when a lattice translation is missed. Short contacts are defined using a van der Waals radius of 1.2 Angstrom. Short H .. H contact involving CH3 H-atoms are often hampered by the fact that they involve H atoms at not optimal calculated positions.

(http://journals.iucr.org/services/cif/checking/PLAT412.html)

例：PLAT412_ALERT_2_C Short Intra XH3 .. XHn H9 .. H13C .. 1.87 Ang

警告原因：H9和H13C之间的距离太近。

解决策略：在ins文件中添加“DFIX 2.45 0.01 H9 H13C”(尝试比1.87大的数值)。

PLAT413 Type_2 Test for short non-bonding inter H..H contacts (involving XH3)

Short intermolecular H..H contacts may indicate incorrectly determined structures (i.e. wrong symmetry, missed translation symmetry, wrong position with reference to the symmetry elements, hydrogen atoms on atoms where there should not be any etc..). Short intermolecular contacts may be indicative for inconsistent symmetry data (e.g. coordinates for space-group P43 and symmetry specified as P41 or P21/n & P21/c confusions). Short contacts are defined using a van der Waals radius of 1.2 Angstrom. Short H .. H contact involving CH3 H-atoms are often hampered by the fact that they involve H atoms at not optimal calculated positions.

(http://journals.iucr.org/services/cif/checking/PLAT413.html)

例：PLAT413_ALERT_2_A Short Inter XH3 .. XHn H18’ .. H19C .. 1.72 Ang.

警告原因：分子间/内两个氢距离较近。

解决策略：检查加氢是否正确并重新加氢，或采用DFIX命令将两个氢距离限制在2.1以上，否则需要给出合理解释。若在结构中这两个H原子实际上离得很远(即其中一个氢原子为等效原子)，但是有这个警告，可尝试“BUMP 0.02”命令。其作用为：

If two atoms that are not connected according to the connectivity table approach each other to a distance shorter than the expected shortest non-bonding distance, BUMP generates a restraint that pushes those atoms apart. Those 'anti-bumping' restraints are generated for the element types C, N, O and S and also for hydrogen atoms that are not bonded to the same atom. This restraint is used almost exclusively for the refinement of macromolecular structures and can help to avoid energetically unfavourable side-chain conformations. It also helps to generate a solvent model with acceptable hydrogen bonding distances that is consistent with the diffraction data.

PLAT414 Type_2 Test for short non-bonding intra D-H..H-X contacts

Short non-bonding intra D-H..H-X contact.

(http://journals.iucr.org/services/cif/checking/PLAT414.html)

例：PLAT414_ALERT_2_B Short Intra D-H..H-X H1BA .. H0BA .. 1.84 Ang.

警告原因：分子间/内两个氢距离较近。

解决策略：检查加氢是否正确并重新加氢，或采用DFIX命令将两个氢距离限制在2.1以上，否则需要给出合理解释。

PLAT415 Type_2 Test for short non-bonding inter D-H..H-X contacts

Short non-bonding inter D-H..H-X contact.

(http://journals.iucr.org/services/cif/checking/PLAT415.html)

例：PLAT415_ALERT_2_B Short Inter D-H..H-X H1 .. H19A .. 1.97 Ang.

警告原因：分子间/内两个氢距离较近。

解决策略：检查加氢是否正确并重新加氢，或采用DFIX命令将两个氢距离限制在2.1以上，否则需要给出合理解释。

PLAT416 Type_2 Test for short non-bonding intra D-H..H-D contacts

Short non-bonding intra D-H..H-D contacts may be related to disordered or misplaced H-atoms.

(http://journals.iucr.org/services/cif/checking/PLAT416.html)

例：PLAT416_ALERT_2_B Short Intra D-H..H-D H9B .. H10B .. 1.13 Ang.

警告原因：分子间/内两个氢距离较近。

解决策略：检查加氢是否正确并重新加氢，或采用DFIX命令将两个氢距离限制在2.1以上，否则需要给出合理解释。

PLAT417 Type_2 Test for short non-bonding inter D-H..H-D contacts

Short non-bonding inter D-H..H-D contacts may be related to disordered or misplaced H-atoms. Experience has shown that any intermolecular H...H separation of less than 1.8 Angstroms between unit-occupancy H atoms is a clear indicator that one or both of these H atoms may be wrongly placed.

(http://journals.iucr.org/services/cif/checking/PLAT417.html)

例：PLAT417_ALERT_2_B Short Inter D-H..H-D H1BB .. H30B .. 1.90 Ang.

警告原因：分子间/内两个氢距离较近。

解决策略：检查加氢是否正确并重新加氢，或采用DFIX命令将两个氢距离限制在2.1以上，否则需要给出合理解释。

PLAT420 Type_2 Test for D-H without acceptor

Potential hydrogen bond donors are checked for the presence of suitable acceptors using commonly used (Jeffrey) H-bond criteria. As a general rule there should be an acceptor for each donor. Exceptions are very rare for O-H and more common for -NH and -NH2. A common error is an -OH on a calculated position pointing in the wrong direction.

(http://journals.iucr.org/services/cif/checking/PLAT420.html)

例：PLAT420_ALERT_2_B D-H Without Acceptor O3 - H3

警告原因：O3上的氢未和氢键受体形成氢键。

解决策略：找到一个合适的氢键受体原子，并把H3限制在O3和氢键受体之间，否则需要给出合理解释。