Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: G6861

Calculation Name: 5CS0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5CS0

Chain ID: A

ChEMBL ID:

UniProt ID: Q00955

Base Structure: X-ray

Registration Date: 2023-06-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2339633.299884
FMO2-HF: Nuclear repulsion 2255616.499122
FMO2-HF: Total energy -84016.800763
FMO2-MP2: Total energy -84266.247952


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:797:LYS)


Summations of interaction energy for fragment #1(A:797:LYS)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
64.13268.970.989-2.095-3.7320.003
Interaction energy analysis for fragmet #1(A:797:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 1.052 / q_NPA : 1.019
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A799ALA00.0710.0323.3971.1803.5690.021-1.001-1.4100.004
4A800TYR00.0170.0082.3910.7232.0460.950-0.790-1.483-0.001
5A801LYS10.9890.9843.22940.93041.7900.020-0.293-0.5870.000
6A802PHE00.0050.0175.1222.9633.062-0.001-0.005-0.0920.000
7A803LYS10.9940.9877.78623.06123.0610.0000.0000.0000.000
8A804SER00.0160.0137.9211.7141.7140.0000.0000.0000.000
9A805LEU0-0.024-0.0178.5371.0561.0560.0000.0000.0000.000
10A806VAL00.0300.02111.0781.4311.4310.0000.0000.0000.000
11A807SER00.0220.01013.0851.3811.3810.0000.0000.0000.000
12A808THR0-0.0200.00013.2801.0801.0800.0000.0000.0000.000
13A809LEU0-0.018-0.01215.1850.9420.9420.0000.0000.0000.000
14A810GLU-1-0.895-0.96517.142-13.121-13.1210.0000.0000.0000.000
15A811ASN0-0.044-0.03018.1551.0581.0580.0000.0000.0000.000
16A812ILE0-0.037-0.00719.5690.5360.5360.0000.0000.0000.000
17A813LEU0-0.033-0.01421.2250.6390.6390.0000.0000.0000.000
18A814LYS10.8780.93321.23013.07213.0720.0000.0000.0000.000
19A815GLY00.0160.03024.8980.3450.3450.0000.0000.0000.000
20A816TYR0-0.046-0.01621.4240.1510.1510.0000.0000.0000.000
21A817ASP-1-0.848-0.91325.617-10.454-10.4540.0000.0000.0000.000
22A818ASN00.014-0.02723.831-0.733-0.7330.0000.0000.0000.000
23A819GLN00.0630.02824.795-0.693-0.6930.0000.0000.0000.000
24A820VAL00.0290.03024.485-0.130-0.1300.0000.0000.0000.000
25A821ILE00.0410.02219.779-0.292-0.2920.0000.0000.0000.000
26A822MET0-0.0320.01321.176-0.592-0.5920.0000.0000.0000.000
27A823ASN00.007-0.02522.640-0.187-0.1870.0000.0000.0000.000
28A824ALA0-0.0120.00921.425-0.052-0.0520.0000.0000.0000.000
29A825SER00.003-0.01518.428-0.658-0.6580.0000.0000.0000.000
30A826LEU0-0.044-0.01119.082-0.485-0.4850.0000.0000.0000.000
31A827GLN00.007-0.01221.396-0.202-0.2020.0000.0000.0000.000
32A828GLN00.006-0.00116.0610.5060.5060.0000.0000.0000.000
33A829LEU0-0.0120.00716.123-0.586-0.5860.0000.0000.0000.000
34A830ILE0-0.0030.00118.248-0.168-0.1680.0000.0000.0000.000
35A831GLU-1-0.962-0.97818.921-14.195-14.1950.0000.0000.0000.000
36A832VAL0-0.041-0.03113.692-0.151-0.1510.0000.0000.0000.000
37A833LEU0-0.029-0.01517.038-0.411-0.4110.0000.0000.0000.000
38A834ARG10.8960.95818.91212.55112.5510.0000.0000.0000.000
39A835ASN0-0.0010.02116.9230.5480.5480.0000.0000.0000.000
40A836PRO00.0730.00918.105-0.828-0.8280.0000.0000.0000.000
41A837LYS10.9210.95215.08014.93514.9350.0000.0000.0000.000
42A838LEU0-0.0180.01912.799-1.261-1.2610.0000.0000.0000.000
43A839PRO00.0590.03113.631-1.593-1.5930.0000.0000.0000.000
44A840TYR0-0.051-0.05014.258-1.199-1.1990.0000.0000.0000.000
45A841SER0-0.083-0.0439.849-1.638-1.6380.0000.0000.0000.000
46A842GLU-1-0.799-0.8889.481-26.986-26.9860.0000.0000.0000.000
47A843TRP00.0570.0199.639-2.636-2.6360.0000.0000.0000.000
48A844LYS10.9350.9638.25921.47321.4730.0000.0000.0000.000
49A845LEU0-0.053-0.0274.747-2.145-1.978-0.001-0.006-0.1600.000
50A846HIS00.0300.0116.649-6.406-6.4060.0000.0000.0000.000
51A847ILE00.0470.0238.1170.4800.4800.0000.0000.0000.000
52A848SER0-0.047-0.0406.8331.3031.3030.0000.0000.0000.000
53A849ALA0-0.068-0.0185.658-1.795-1.7950.0000.0000.0000.000
54A850LEU0-0.007-0.0047.7151.4931.4930.0000.0000.0000.000
55A851HIS00.0130.01710.2941.0491.0490.0000.0000.0000.000
56A852SER0-0.0090.01712.3751.2871.2870.0000.0000.0000.000
57A853ARG10.9190.94912.67023.03623.0360.0000.0000.0000.000
58A854LEU0-0.071-0.02314.0680.8630.8630.0000.0000.0000.000
59A855PRO00.012-0.00216.9610.4590.4590.0000.0000.0000.000
60A856ALA00.0920.05020.218-0.299-0.2990.0000.0000.0000.000
61A857LYS10.9981.01721.72911.38911.3890.0000.0000.0000.000
62A858LEU00.0060.00019.007-0.010-0.0100.0000.0000.0000.000
63A859ASP-1-0.861-0.95216.675-19.066-19.0660.0000.0000.0000.000
64A860GLU-1-0.831-0.90918.897-13.247-13.2470.0000.0000.0000.000
65A861GLN0-0.128-0.08021.7260.1830.1830.0000.0000.0000.000
66A862MET0-0.069-0.04416.2050.2970.2970.0000.0000.0000.000
67A863GLU-1-0.905-0.93316.901-16.469-16.4690.0000.0000.0000.000
68A864GLU-1-0.892-0.96218.887-11.715-11.7150.0000.0000.0000.000
69A865LEU0-0.045-0.01721.9720.5900.5900.0000.0000.0000.000
70A866VAL00.0190.00816.2350.3910.3910.0000.0000.0000.000
71A867ALA00.0080.01719.6010.1410.1410.0000.0000.0000.000
72A868ARG10.8680.93320.42511.90011.9000.0000.0000.0000.000
73A869SER0-0.038-0.03521.4140.5280.5280.0000.0000.0000.000
74A870LEU00.0150.01415.9980.2050.2050.0000.0000.0000.000
75A871ARG10.9060.96420.66712.64112.6410.0000.0000.0000.000
76A872ARG10.9370.97423.35110.77410.7740.0000.0000.0000.000
77A873GLY00.0030.01123.7330.3520.3520.0000.0000.0000.000
78A874ALA0-0.035-0.00824.1750.1960.1960.0000.0000.0000.000
79A875VAL00.0300.02222.537-0.647-0.6470.0000.0000.0000.000
80A876PHE00.0440.02216.3390.1420.1420.0000.0000.0000.000
81A877PRO00.0120.02419.9660.3710.3710.0000.0000.0000.000
82A878ALA00.0420.01220.342-0.097-0.0970.0000.0000.0000.000
83A879ARG11.0281.00521.33411.67811.6780.0000.0000.0000.000
84A880GLN0-0.067-0.03424.4050.0420.0420.0000.0000.0000.000
85A881LEU00.0410.02017.8470.3280.3280.0000.0000.0000.000
86A882SER00.0800.03821.121-0.400-0.4000.0000.0000.0000.000
87A883LYS10.8950.97122.01312.21612.2160.0000.0000.0000.000
88A884LEU0-0.065-0.03622.0550.3760.3760.0000.0000.0000.000
89A885ILE00.0570.02917.2480.1660.1660.0000.0000.0000.000
90A886ASP-1-0.872-0.94521.168-13.789-13.7890.0000.0000.0000.000
91A887MET0-0.111-0.06323.8200.5240.5240.0000.0000.0000.000
92A888ALA00.0040.00822.0070.3330.3330.0000.0000.0000.000
93A889VAL0-0.007-0.01820.762-0.017-0.0170.0000.0000.0000.000
94A890LYS10.8940.95623.50010.79410.7940.0000.0000.0000.000
95A891ASN00.004-0.00426.6000.5760.5760.0000.0000.0000.000
96A892PRO00.005-0.01727.187-0.363-0.3630.0000.0000.0000.000
97A893GLU-1-0.930-0.94527.794-10.867-10.8670.0000.0000.0000.000
98A894TYR00.006-0.00323.168-0.350-0.3500.0000.0000.0000.000
99A895ASN0-0.086-0.03222.541-1.087-1.0870.0000.0000.0000.000
100A896PRO00.0150.01524.0900.3500.3500.0000.0000.0000.000
101A897ASP-1-0.849-0.91923.953-11.912-11.9120.0000.0000.0000.000
102A898LYS10.8460.91523.87811.18311.1830.0000.0000.0000.000
103A899LEU00.0450.02419.146-0.403-0.4030.0000.0000.0000.000
104A900LEU00.0160.01317.647-1.075-1.0750.0000.0000.0000.000
105A901GLY00.001-0.00117.284-0.962-0.9620.0000.0000.0000.000
106A902ALA00.0290.00016.228-0.726-0.7260.0000.0000.0000.000
107A903VAL0-0.028-0.00412.961-1.577-1.5770.0000.0000.0000.000
108A904VAL0-0.012-0.02512.507-1.894-1.8940.0000.0000.0000.000
109A905GLU-1-0.869-0.91112.482-21.726-21.7260.0000.0000.0000.000
110A906PRO00.0130.0039.038-0.023-0.0230.0000.0000.0000.000
111A907LEU0-0.032-0.02111.1650.0820.0820.0000.0000.0000.000
112A908ALA0-0.004-0.01513.3461.2691.2690.0000.0000.0000.000
113A909ASP-1-0.883-0.92913.306-20.809-20.8090.0000.0000.0000.000
114A910ILE0-0.034-0.01610.2960.9810.9810.0000.0000.0000.000
115A911ALA0-0.035-0.01914.8221.0761.0760.0000.0000.0000.000
116A912HIS00.0300.00718.0731.2581.2580.0000.0000.0000.000
117A913LYS10.9250.99112.46924.19424.1940.0000.0000.0000.000
118A914TYR0-0.040-0.05514.7651.1691.1690.0000.0000.0000.000
119A915SER0-0.095-0.06320.0800.8980.8980.0000.0000.0000.000
120A916ASN0-0.068-0.03623.1760.7820.7820.0000.0000.0000.000
121A917GLY0-0.012-0.00823.6570.4510.4510.0000.0000.0000.000
122A918LEU0-0.008-0.01419.400-0.253-0.2530.0000.0000.0000.000
123A919GLU-1-0.864-0.92822.005-11.361-11.3610.0000.0000.0000.000
124A920ALA00.0000.00624.357-0.006-0.0060.0000.0000.0000.000
125A921HIS00.0540.02515.8020.4200.4200.0000.0000.0000.000
126A922GLU-1-0.829-0.91220.372-13.298-13.2980.0000.0000.0000.000
127A923HIS0-0.0010.04021.591-0.298-0.2980.0000.0000.0000.000
128A924SER0-0.065-0.03020.211-0.027-0.0270.0000.0000.0000.000
129A925ILE00.0310.02116.720-0.342-0.3420.0000.0000.0000.000
130A926PHE0-0.002-0.01820.0730.0480.0480.0000.0000.0000.000
131A927VAL00.0060.00523.2320.3330.3330.0000.0000.0000.000
132A928HIS00.0070.00818.1990.5190.5190.0000.0000.0000.000
133A929PHE0-0.009-0.00817.6520.0850.0850.0000.0000.0000.000
134A930LEU0-0.051-0.02922.3770.3490.3490.0000.0000.0000.000
135A931GLU-1-0.778-0.89924.271-10.838-10.8380.0000.0000.0000.000
136A932GLU-1-0.962-0.96619.627-15.816-15.8160.0000.0000.0000.000
137A933TYR0-0.093-0.07323.6750.3290.3290.0000.0000.0000.000
138A934TYR00.019-0.00726.2880.2590.2590.0000.0000.0000.000
139A935GLU-1-0.847-0.93725.652-10.789-10.7890.0000.0000.0000.000
140A936VAL0-0.055-0.01625.1940.1190.1190.0000.0000.0000.000
141A937GLU-1-0.766-0.90428.111-10.197-10.1970.0000.0000.0000.000
142A938LYS10.8710.95730.16310.79910.7990.0000.0000.0000.000
143A939LEU0-0.107-0.04529.9050.2520.2520.0000.0000.0000.000
144A940PHE0-0.044-0.01530.4140.2030.2030.0000.0000.0000.000
145A961ASP-1-0.868-0.96326.094-12.094-12.0940.0000.0000.0000.000
146A962LEU00.021-0.00928.403-0.181-0.1810.0000.0000.0000.000
147A963ASP-1-0.832-0.89523.878-12.734-12.7340.0000.0000.0000.000
148A964LYS10.9720.99724.27210.98110.9810.0000.0000.0000.000
149A965VAL0-0.052-0.03225.288-0.017-0.0170.0000.0000.0000.000
150A966ALA00.0280.02026.6550.1620.1620.0000.0000.0000.000
151A967LEU00.018-0.00320.9720.0340.0340.0000.0000.0000.000
152A968THR0-0.030-0.00724.757-0.101-0.1010.0000.0000.0000.000
153A969VAL0-0.014-0.00126.7230.1280.1280.0000.0000.0000.000
154A970LEU0-0.0020.00322.6370.2130.2130.0000.0000.0000.000
155A971SER00.0380.04224.0900.2900.2900.0000.0000.0000.000
156A972HIS10.9360.96325.50310.05910.0590.0000.0000.0000.000
157A973SER0-0.118-0.06327.6280.3030.3030.0000.0000.0000.000
158A974LYS10.9470.96225.07212.15112.1510.0000.0000.0000.000
159A975VAL00.0350.02627.980-0.151-0.1510.0000.0000.0000.000
160A976SER0-0.069-0.02030.002-0.109-0.1090.0000.0000.0000.000
161A977ALA00.0660.01926.0200.0410.0410.0000.0000.0000.000
162A978LYS10.8340.91425.07311.71611.7160.0000.0000.0000.000
163A979ASN00.0150.00126.923-0.234-0.2340.0000.0000.0000.000
164A980ASN0-0.050-0.01128.3060.3540.3540.0000.0000.0000.000
165A981LEU00.0310.02522.3770.0970.0970.0000.0000.0000.000
166A982ILE00.0650.01825.497-0.020-0.0200.0000.0000.0000.000
167A983LEU0-0.055-0.02628.2330.2860.2860.0000.0000.0000.000
168A984ALA0-0.013-0.00427.2020.2090.2090.0000.0000.0000.000
169A985ILE0-0.016-0.00623.6430.0570.0570.0000.0000.0000.000
170A986LEU00.0250.00627.6310.1520.1520.0000.0000.0000.000
171A987LYS10.9330.95531.0978.9998.9990.0000.0000.0000.000
172A988HIS0-0.0080.00126.2050.3230.3230.0000.0000.0000.000
173A989TYR00.028-0.06025.7850.0310.0310.0000.0000.0000.000
174A990GLN00.0290.03331.1130.2260.2260.0000.0000.0000.000
175A991PRO0-0.063-0.03433.4750.2420.2420.0000.0000.0000.000
176A992LEU00.0150.00129.3860.1900.1900.0000.0000.0000.000
177A993CYS0-0.034-0.00332.7100.0020.0020.0000.0000.0000.000
178A994LYS10.9490.99535.0027.7787.7780.0000.0000.0000.000
179A995LEU0-0.040-0.01935.9460.1950.1950.0000.0000.0000.000
180A996SER00.0040.00733.9390.1340.1340.0000.0000.0000.000
181A997SER00.0630.02336.113-0.132-0.1320.0000.0000.0000.000
182A998LYS10.9610.96731.7389.7669.7660.0000.0000.0000.000
183A999VAL00.0100.00730.272-0.200-0.2000.0000.0000.0000.000
184A1000SER00.0560.00932.019-0.192-0.1920.0000.0000.0000.000
185A1001ALA0-0.034-0.00134.070-0.030-0.0300.0000.0000.0000.000
186A1002ILE0-0.045-0.01527.471-0.100-0.1000.0000.0000.0000.000
187A1003PHE00.018-0.00626.487-0.254-0.2540.0000.0000.0000.000
188A1004SER0-0.0090.01131.0620.1080.1080.0000.0000.0000.000
189A1005THR00.021-0.00330.9990.2270.2270.0000.0000.0000.000
190A1006PRO00.0190.00828.3580.1470.1470.0000.0000.0000.000
191A1007LEU0-0.0150.00330.5040.0220.0220.0000.0000.0000.000
192A1008GLN00.0000.00733.3050.2690.2690.0000.0000.0000.000
193A1009HIS10.8760.93230.12010.28310.2830.0000.0000.0000.000
194A1010ILE0-0.025-0.01029.5470.1040.1040.0000.0000.0000.000
195A1011VAL0-0.052-0.03233.5070.1430.1430.0000.0000.0000.000
196A1012GLU-1-0.928-0.95936.285-8.652-8.6520.0000.0000.0000.000
197A1013LEU0-0.078-0.01132.127-0.013-0.0130.0000.0000.0000.000
198A1014GLU-1-0.919-0.95836.729-7.460-7.4600.0000.0000.0000.000
199A1015SER00.0290.01636.4870.0230.0230.0000.0000.0000.000
200A1016LYS10.9460.96239.2267.4647.4640.0000.0000.0000.000
201A1017ALA0-0.040-0.03534.835-0.004-0.0040.0000.0000.0000.000
202A1018THR00.0780.05133.240-0.139-0.1390.0000.0000.0000.000
203A1019ALA00.0250.03635.593-0.007-0.0070.0000.0000.0000.000
204A1020LYS10.9460.95336.7628.1038.1030.0000.0000.0000.000
205A1021VAL00.0490.02131.7590.0530.0530.0000.0000.0000.000
206A1022ALA00.0740.04434.959-0.057-0.0570.0000.0000.0000.000
207A1023LEU0-0.063-0.03336.9710.1160.1160.0000.0000.0000.000
208A1024GLN0-0.009-0.01435.4140.0470.0470.0000.0000.0000.000
209A1025ALA00.0260.02134.186-0.009-0.0090.0000.0000.0000.000
210A1026ARG10.9280.96335.8447.5017.5010.0000.0000.0000.000
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