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【求助】10金币求加氢键
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本人是解单晶初学者，想对我的数据加氢键，自己用汞软件加氢，测量后发现如下A类错误，望有高人出现。不知传个cif文件够不够。附件中有cif文件和A类错误。急。。。同时希望虫友能“授我于鱼，更能授我于渔”谢谢各位虫友！ 附件如下： cif文件： http://www.namipan.com/d/100924g ... 598ee4be019d6660000 错误： http://www.namipan.com/d/checkCI ... 3e68de6d992ed310000 10金币求加氢键 |
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lipan504(金币+1): 2010-12-14 11:25:13
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checkCIF/PLATON report (publication check) No syntax errors found. CIF dictionaryPlease wait while processing .... Interpreting this reportDatablock: 100924g -------------------------------------------------------------------------------- Bond precision: C-C = 0.0070 A Wavelength=0.71073 Cell: a=5.3521(5) b=15.5146(16) c=15.5615(14) alpha=114.351(2) beta=95.145(1) gamma=97.072(1) Temperature: 298 K Calculated Reported Volume 1154.07(19) 1154.07(19) Space group P -1 P-1 Hall group -P 1 -P1 Moiety formula C22 H16 F3 N O7 S C F3 O2 S,C15 H11 N O4,C6 H5 O Sum formula C22 H16 F3 N O7 S C22 H16 F3 N O7 S Mr 495.43 495.42 Dx,g cm-3 1.426 1.426 Z 2 2 Mu (mm-1) 0.207 0.207 F000 508.0 508.0 F000' 508.60 h,k,lmax 6,18,18 6,18,18 Nref 4085 4008 Tmin,Tmax 0.921,0.961 0.913,0.962 Tmin' 0.911 Correction method= MULTI-SCAN Data completeness= 0.981 Theta(max)= 25.020 R(reflections)= 0.0660( 2079) wR2(reflections)= 0.1627( 4008) S = 1.001 Npar= 312 -------------------------------------------------------------------------------- The following ALERTS were generated. Each ALERT has the format test-name_ALERT_alert-type_alert-level. Click on the hyperlinks for more details of the test. --------------------------------------------------------------------------------Alert level A PLAT726_ALERT_2_A H...A Calc 8.92000, Rep 2.48000 Dev... 6.44 Ang. H15A -O2 1.555 1.555 # 55 PLAT726_ALERT_2_A H...A Calc 4.21000, Rep 2.53700 Dev... 1.67 Ang. H13A -O7 1.555 1.555 # 55 PLAT707_ALERT_1_A D...A Calc 8.565(5), Rep 3.201(6), Dev.. 1072.80 Sigma C15 -O2 1.555 1.555 # 55 PLAT707_ALERT_1_A D...A Calc 3.72(3), Rep 3.404(3), Dev.. 10.53 Sigma C13 -O7 1.555 1.555 # 55 PLAT728_ALERT_1_A D-H..A Calc 66.00, Rep 131.03 Dev... 65.03 Deg. C15 -H15A -O2 1.555 1.555 1.555 # 99 PLAT728_ALERT_1_A D-H..A Calc 54.00, Rep 148.77 Dev... 94.77 Deg. C13 -H13A -O7 1.555 1.555 1.555 # 99 --------------------------------------------------------------------------------Alert level B PLAT242_ALERT_2_B Check Low Ueq as Compared to Neighbors for C14 PLAT242_ALERT_2_B Check Low Ueq as Compared to Neighbors for C17 PLAT601_ALERT_2_B Structure Contains Solvent Accessible VOIDS of . 108.00 A**3 --------------------------------------------------------------------------------Alert level C PLAT220_ALERT_2_C Large Non-Solvent C Ueq(max)/Ueq(min) ... 3.06 Ratio PLAT230_ALERT_2_C Hirshfeld Test Diff for N1 -- C1 .. 5.11 su PLAT241_ALERT_2_C Check High Ueq as Compared to Neighbors for O5 PLAT241_ALERT_2_C Check High Ueq as Compared to Neighbors for C19 PLAT241_ALERT_2_C Check High Ueq as Compared to Neighbors for C21 PLAT241_ALERT_2_C Check High Ueq as Compared to Neighbors for C22 PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for C20 PLAT331_ALERT_2_C Small Average Phenyl C-C Dist. C17 -C22 1.36 Ang. PLAT340_ALERT_3_C Low Bond Precision on C-C Bonds (x 1000) Ang .. 7 PLAT042_ALERT_1_C Calc. and Reported MoietyFormula Strings Differ ? --------------------------------------------------------------------------------Alert level G PLAT301_ALERT_3_G Note: Main Residue Disorder ................... 3.00 Perc. PLAT779_ALERT_4_G Suspect or Irrelevant (Bond) Angle in CIF .... # 64 O7 -C16 -O7' 1.555 1.555 1.555 44.00 Deg. PLAT793_ALERT_4_G The Model has Chirality at C8 (Verify) .... S PLAT793_ALERT_4_G The Model has Chirality at C9 (Verify) .... S PLAT793_ALERT_4_G The Model has Chirality at C12 (Verify) .... S -------------------------------------------------------------------------------- 6 ALERT level A = In general: serious problem 3 ALERT level B = Potentially serious problem 10 ALERT level C = Check and explain 5 ALERT level G = General alerts; check 5 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 13 ALERT type 2 Indicator that the structure model may be wrong or deficient 2 ALERT type 3 Indicator that the structure quality may be low 4 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Publication of your CIF You should always attempt to resolve as many as possible of the alerts in all categories. Often the minor alerts point to easily fixed oversights, errors and omissions in your CIF or refinement strategy, so attention to these fine details can be worthwhile. In order to resolve some of the more serious problems it may be necessary to carry out additional measurements or structure refinements. However, the nature of your study may justify the reported deviations from the submission requirements of the journal and these should be commented upon in the discussion or experimental section of a paper - after all, they might represent an interesting feature. If level A alerts remain, which you believe to be justified deviations, and you intend to submit this CIF for publication in Acta Crystallographica Section C or Section E, you should additionally insert an explanation in your CIF using the Validation Reply Form (VRF) below. Your explanation will be considered as part of the review process. If you intend to submit to another section of Acta Crystallographica or Journal of Applied Crystallography or Journal of Synchrotron Radiation, you should make sure that at least a basic structural check is run on the final version of your CIF prior to submission. # start Validation Reply Form _vrf_PLAT726_100924g ; PROBLEM: H...A Calc 8.92000, Rep 2.48000 Dev... 6.44 Ang. RESPONSE: ... ; _vrf_PLAT707_100924g ; PROBLEM: D...A Calc 8.565(5), Rep 3.201(6), Dev.. 1072.80 Sigma RESPONSE: ... ; _vrf_PLAT728_100924g ; PROBLEM: D-H..A Calc 66.00, Rep 131.03 Dev... 65.03 Deg. RESPONSE: ... ; # end Validation Reply FormIf you wish to submit your CIF for publication in Acta Crystallographica Section C or E, you should upload your CIF via the web. If your CIF is to form part of a submission to another IUCr journal, you will be asked, either during electronic submission or by the Co-editor handling your paper, to upload your CIF via our web site. -------------------------------------------------------------------------------- PLATON version of 22/10/2010; check.def file version of 11/10/2010 Datablock 100924g - ellipsoid plot -------------------------------------------------------------------------------- Download CIF editor (publCIF) from the IUCr Download CIF editor (enCIFer) from the CCDC Test a new CIF entry 你氢键的对称操作码有问题 |
2楼2010-12-14 11:17:22
3楼2010-12-14 11:26:14
4楼2010-12-14 11:31:46
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(Analysis of Potential Hydrogen Bonds and Schemes with d\(D...A\) < R\(D\)+R\(A\)+0.50, d\(H...A\) < R\(H\)+R\(A\)-0.12 Ang., D-H...A > 100.0 Deg)s (====================================================================================================================================)s (Note: - ARU codes in [] are with reference to the Coordinates printed above \(Possibly transformed, when MOVE .NE. 1.555\))s (====================================================================================================================================)s ( )s (Nr Typ Res Donor --- H....Acceptor [ ARU ] D - H H...A D...A D - H...A A..H..A* A'..H..A" Sum\(XY,YZ\) Sum\(XZ\))s (------------------------------------------------------------------------------------------------------------------------------------)s ( )s ( 1 1 C\(3\) --H\(3\) ..O\(4\) [ 2867.01] 0.93 2.51 3.342\(5\) 149)s ( 2 Intra 1 C\(12\) --H\(12\) ..O\(7'\) [ ] 0.98 2.30 2.688\(8\) 103)s ( 3 1 C\(15\) --H\(15A\) ..O\(2\) [ 2767.01] 0.97 2.48 3.201\(6\) 131)s ( 4 Intra 1 C\(18\) --H\(18\) ..O\(6\) [ ] 0.93 2.42 2.740\(6\) 100)s ( )s (:: No Classic Hydrogen Bonds Found)s ( )s ( )s (Translation of ARU-code to Equivalent Position Code)s (===================================================)s ( [ 2767. ] = 2-x,1-y,2-z)s ( [ 2867. ] = 3-x,1-y,2-z)s |
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lipan504(金币+1): 2010-12-14 11:51:39
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loop_ _geom_hbond_atom_site_label_D _geom_hbond_atom_site_label_H _geom_hbond_atom_site_label_A _geom_hbond_distance_DH _geom_hbond_distance_HA _geom_hbond_distance_DA _geom_hbond_angle_DHA _geom_hbond_site_symmetry_A c3 H3 O4 0.93 2.51 3.342(5) 149 2_867 。。。。。 自己按照这样的格式编辑在cif文件的“_diffrn_measured_fraction_theta_max 0.981 _diffrn_reflns_theta_full 25.02 _diffrn_measured_fraction_theta_full 0.981 _refine_diff_density_max 0.409 _refine_diff_density_min -0.297 _refine_diff_density_rms 0.074 #===================== End of CIF submission ===========================”前面 |
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