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: K29N3

Calculation Name: 5W7I-A-Xray372

Preferred Name: Synaptosomal nerve-associated protein 25 (SNAP-25)

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5W7I

Chain ID: A

ChEMBL ID: CHEMBL2364159

UniProt ID: P60880

Base Structure: X-ray

Registration Date: 2023-09-26

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 OptHSide
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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2666929.131397
FMO2-HF: Nuclear repulsion 2576518.128205
FMO2-HF: Total energy -90411.003191
FMO2-MP2: Total energy -90672.795876


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:53:ILE)


Summations of interaction energy for fragment #1(A:53:ILE)
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.
-2.867-0.5750.062-0.825-1.529-0.001
Interaction energy analysis for fragmet #1(A:53:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.047 / q_NPA : -0.046
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].
3A55ASP-1-0.799-0.8713.365-4.233-2.1080.062-0.807-1.380-0.001
4A56TYR0-0.021-0.0314.3220.5780.7450.000-0.018-0.1490.000
5A57SER0-0.037-0.0327.5380.4740.4740.0000.0000.0000.000
6A58THR0-0.009-0.0258.9070.2270.2270.0000.0000.0000.000
7A59TRP0-0.117-0.0668.4590.2030.2030.0000.0000.0000.000
8A60ASP-1-0.780-0.88112.540-0.121-0.1210.0000.0000.0000.000
9A61ILE00.0700.02015.725-0.015-0.0150.0000.0000.0000.000
10A62VAL00.0010.02417.904-0.001-0.0010.0000.0000.0000.000
11A63LYS10.9200.97611.091-0.095-0.0950.0000.0000.0000.000
12A64ALA00.019-0.00213.647-0.003-0.0030.0000.0000.0000.000
13A65THR0-0.009-0.01214.571-0.012-0.0120.0000.0000.0000.000
14A66GLN0-0.029-0.00817.3220.0100.0100.0000.0000.0000.000
15A67TYR0-0.013-0.01012.5100.0280.0280.0000.0000.0000.000
16A68GLY0-0.048-0.01814.323-0.014-0.0140.0000.0000.0000.000
17A69ILE0-0.0130.00010.106-0.015-0.0150.0000.0000.0000.000
18A70TYR0-0.018-0.01513.118-0.001-0.0010.0000.0000.0000.000
19A71GLU-1-0.842-0.95213.185-0.337-0.3370.0000.0000.0000.000
20A72ARG10.8140.91611.6060.5130.5130.0000.0000.0000.000
21A73CYS0-0.016-0.01313.6210.0350.0350.0000.0000.0000.000
22A74ARG10.9510.99017.0830.2750.2750.0000.0000.0000.000
23A75GLU-1-0.875-0.92613.379-0.562-0.5620.0000.0000.0000.000
24A76LEU0-0.027-0.01515.7610.0320.0320.0000.0000.0000.000
25A77VAL0-0.012-0.00418.8850.0300.0300.0000.0000.0000.000
26A78GLU-1-0.822-0.88421.541-0.167-0.1670.0000.0000.0000.000
27A79ALA0-0.075-0.02520.4550.0110.0110.0000.0000.0000.000
28A80GLY0-0.004-0.00622.4590.0100.0100.0000.0000.0000.000
29A81TYR0-0.061-0.01822.2150.0170.0170.0000.0000.0000.000
30A82ASP-1-0.815-0.91124.223-0.091-0.0910.0000.0000.0000.000
31A83VAL0-0.008-0.01724.4590.0040.0040.0000.0000.0000.000
32A84ARG10.8260.89826.5550.0750.0750.0000.0000.0000.000
33A85GLN0-0.056-0.00926.1520.0100.0100.0000.0000.0000.000
34A86PRO0-0.021-0.00927.323-0.005-0.0050.0000.0000.0000.000
35A87ASP-1-0.732-0.87824.880-0.021-0.0210.0000.0000.0000.000
36A88LYS10.7660.85723.177-0.001-0.0010.0000.0000.0000.000
37A89GLU-1-0.871-0.92225.5140.0310.0310.0000.0000.0000.000
38A90ASN0-0.032-0.01329.541-0.003-0.0030.0000.0000.0000.000
39A91VAL00.0140.02326.6470.0010.0010.0000.0000.0000.000
40A92THR00.015-0.01927.272-0.010-0.0100.0000.0000.0000.000
41A93LEU00.0520.01221.8260.0040.0040.0000.0000.0000.000
42A94LEU00.0240.01724.124-0.003-0.0030.0000.0000.0000.000
43A95HIS00.0180.04026.438-0.004-0.0040.0000.0000.0000.000
44A96TRP00.0470.02521.7370.0050.0050.0000.0000.0000.000
45A97ALA00.0240.00721.9430.0020.0020.0000.0000.0000.000
46A98ALA00.0030.00122.9830.0020.0020.0000.0000.0000.000
47A99ILE00.0040.00324.1650.0030.0030.0000.0000.0000.000
48A100ASN0-0.042-0.02620.1470.0220.0220.0000.0000.0000.000
49A101ASN00.003-0.00621.349-0.013-0.0130.0000.0000.0000.000
50A102ARG10.8970.94717.0770.0590.0590.0000.0000.0000.000
51A103ILE00.014-0.00721.630-0.005-0.0050.0000.0000.0000.000
52A104ASP-1-0.820-0.90220.803-0.133-0.1330.0000.0000.0000.000
53A105LEU00.0190.01317.584-0.002-0.0020.0000.0000.0000.000
54A106VAL0-0.017-0.00121.7510.0040.0040.0000.0000.0000.000
55A107LYS10.8560.92025.3320.1110.1110.0000.0000.0000.000
56A108TYR0-0.037-0.01921.8240.0020.0020.0000.0000.0000.000
57A109TYR00.0590.00320.151-0.004-0.0040.0000.0000.0000.000
58A110ILE00.0090.01025.8610.0060.0060.0000.0000.0000.000
59A111SER0-0.104-0.04827.1040.0010.0010.0000.0000.0000.000
60A112LYS10.7840.88225.2840.1600.1600.0000.0000.0000.000
61A113GLY00.0210.01428.7090.0020.0020.0000.0000.0000.000
62A114ALA0-0.024-0.01128.2770.0070.0070.0000.0000.0000.000
63A115ILE0-0.035-0.01730.4290.0020.0020.0000.0000.0000.000
64A116VAL00.0130.00132.4730.0010.0010.0000.0000.0000.000
65A117ASP-1-0.774-0.90233.141-0.030-0.0300.0000.0000.0000.000
66A118GLN0-0.079-0.03632.9160.0020.0020.0000.0000.0000.000
67A119LEU0-0.001-0.01233.7540.0000.0000.0000.0000.0000.000
68A120GLY00.0330.00732.250-0.004-0.0040.0000.0000.0000.000
69A121GLY00.005-0.00231.7960.0030.0030.0000.0000.0000.000
70A122ASP-1-0.892-0.93732.4630.0210.0210.0000.0000.0000.000
71A123LEU0-0.050-0.02634.1210.0000.0000.0000.0000.0000.000
72A124ASN0-0.029-0.01435.666-0.004-0.0040.0000.0000.0000.000
73A125SER00.018-0.00333.9670.0000.0000.0000.0000.0000.000
74A126THR00.0360.03633.944-0.003-0.0030.0000.0000.0000.000
75A127PRO00.008-0.00329.1990.0040.0040.0000.0000.0000.000
76A128LEU00.0310.01930.7250.0020.0020.0000.0000.0000.000
77A129HIS00.0430.02233.0200.0030.0030.0000.0000.0000.000
78A130TRP00.0160.01126.3370.0040.0040.0000.0000.0000.000
79A131ALA0-0.007-0.00528.8730.0050.0050.0000.0000.0000.000
80A132THR0-0.046-0.04029.8750.0030.0030.0000.0000.0000.000
81A133ARG10.7700.85231.804-0.011-0.0110.0000.0000.0000.000
82A134GLN0-0.047-0.00525.9140.0080.0080.0000.0000.0000.000
83A135GLY00.0290.02128.9030.0050.0050.0000.0000.0000.000
84A136HIS0-0.058-0.02524.498-0.003-0.0030.0000.0000.0000.000
85A137LEU00.0480.01728.904-0.006-0.0060.0000.0000.0000.000
86A138SER0-0.008-0.00827.140-0.001-0.0010.0000.0000.0000.000
87A139MET0-0.0280.01925.282-0.007-0.0070.0000.0000.0000.000
88A140VAL00.0360.01829.129-0.003-0.0030.0000.0000.0000.000
89A141VAL0-0.049-0.02932.642-0.002-0.0020.0000.0000.0000.000
90A142GLN0-0.056-0.04028.357-0.008-0.0080.0000.0000.0000.000
91A143LEU00.0390.00229.421-0.003-0.0030.0000.0000.0000.000
92A144MET00.0050.01432.5340.0010.0010.0000.0000.0000.000
93A145LYS10.8890.95633.9450.0480.0480.0000.0000.0000.000
94A146TYR0-0.055-0.02430.119-0.004-0.0040.0000.0000.0000.000
95A147GLY0-0.005-0.00435.159-0.001-0.0010.0000.0000.0000.000
96A148ALA0-0.033-0.00634.7440.0020.0020.0000.0000.0000.000
97A149ASP-1-0.825-0.92936.906-0.018-0.0180.0000.0000.0000.000
98A150PRO0-0.043-0.03739.0280.0020.0020.0000.0000.0000.000
99A151SER0-0.041-0.04439.9920.0040.0040.0000.0000.0000.000
100A152LEU0-0.0060.02239.1570.0020.0020.0000.0000.0000.000
101A153ILE0-0.018-0.01141.2030.0020.0020.0000.0000.0000.000
102A154ASP-1-0.780-0.88637.8570.0040.0040.0000.0000.0000.000
103A155GLY0-0.009-0.00339.0790.0010.0010.0000.0000.0000.000
104A156GLU-1-0.878-0.91538.1590.0230.0230.0000.0000.0000.000
105A157GLY00.0070.00241.8830.0010.0010.0000.0000.0000.000
106A158CYS0-0.069-0.02340.5720.0000.0000.0000.0000.0000.000
107A159SER00.0710.04641.049-0.001-0.0010.0000.0000.0000.000
108A160CYS0-0.007-0.00636.4280.0020.0020.0000.0000.0000.000
109A161ILE0-0.006-0.00139.0470.0020.0020.0000.0000.0000.000
110A162HIS00.017-0.01241.3610.0020.0020.0000.0000.0000.000
111A163LEU0-0.045-0.01036.0570.0030.0030.0000.0000.0000.000
112A164ALA0-0.003-0.01436.6700.0030.0030.0000.0000.0000.000
113A165ALA0-0.016-0.01037.7220.0030.0030.0000.0000.0000.000
114A166GLN0-0.0020.01038.2430.0060.0060.0000.0000.0000.000
115A167PHE0-0.026-0.02634.3510.0040.0040.0000.0000.0000.000
116A168GLY00.0120.01135.3440.0020.0020.0000.0000.0000.000
117A169HIS00.0030.01631.487-0.001-0.0010.0000.0000.0000.000
118A170THR00.039-0.00235.858-0.004-0.0040.0000.0000.0000.000
119A171SER00.0000.00034.156-0.002-0.0020.0000.0000.0000.000
120A172ILE00.0210.01232.389-0.004-0.0040.0000.0000.0000.000
121A173VAL00.0190.02036.850-0.002-0.0020.0000.0000.0000.000
122A174ALA00.0130.00840.206-0.002-0.0020.0000.0000.0000.000
123A175TYR0-0.031-0.02437.316-0.003-0.0030.0000.0000.0000.000
124A176LEU00.019-0.00338.398-0.002-0.0020.0000.0000.0000.000
125A177ILE00.0140.02541.359-0.001-0.0010.0000.0000.0000.000
126A178ALA0-0.033-0.01042.416-0.001-0.0010.0000.0000.0000.000
127A179LYS10.8040.90040.3310.0200.0200.0000.0000.0000.000
128A180GLY00.0250.02343.697-0.002-0.0020.0000.0000.0000.000
129A181GLN0-0.043-0.01642.8440.0010.0010.0000.0000.0000.000
130A182ASP-1-0.832-0.92846.138-0.002-0.0020.0000.0000.0000.000
131A183VAL0-0.014-0.00447.5230.0010.0010.0000.0000.0000.000
132A184ASP-1-0.826-0.93348.5030.0060.0060.0000.0000.0000.000
133A185MET0-0.053-0.01145.7880.0000.0000.0000.0000.0000.000
134A186MET0-0.016-0.00548.5250.0010.0010.0000.0000.0000.000
135A187ASP-1-0.739-0.85045.4990.0070.0070.0000.0000.0000.000
136A188GLN00.0360.02046.7320.0010.0010.0000.0000.0000.000
137A189ASN0-0.072-0.04345.2330.0010.0010.0000.0000.0000.000
138A190GLY0-0.069-0.05549.4360.0010.0010.0000.0000.0000.000
139A191MET0-0.026-0.00647.0040.0000.0000.0000.0000.0000.000
140A192THR00.0460.00948.290-0.001-0.0010.0000.0000.0000.000
141A193PRO00.0320.00244.4610.0020.0020.0000.0000.0000.000
142A194LEU00.0320.02145.5320.0020.0020.0000.0000.0000.000
143A195MET0-0.0420.01547.8890.0020.0020.0000.0000.0000.000
144A196TRP00.010-0.01342.5540.0040.0040.0000.0000.0000.000
145A197ALA00.0100.01243.3410.0020.0020.0000.0000.0000.000
146A198ALA00.0030.00044.4170.0020.0020.0000.0000.0000.000
147A199TYR0-0.067-0.02144.3730.0020.0020.0000.0000.0000.000
148A200ARG10.8790.93337.432-0.026-0.0260.0000.0000.0000.000
149A201THR0-0.0200.01039.3860.0020.0020.0000.0000.0000.000
150A202HIS0-0.044-0.00241.136-0.001-0.0010.0000.0000.0000.000
151A203SER0-0.016-0.03640.3100.0030.0030.0000.0000.0000.000
152A204VAL00.0210.01342.418-0.002-0.0020.0000.0000.0000.000
153A205ASP-1-0.846-0.89041.0400.0120.0120.0000.0000.0000.000
154A206PRO00.0420.01639.9320.0030.0030.0000.0000.0000.000
155A207THR00.0500.01842.343-0.002-0.0020.0000.0000.0000.000
156A208ARG10.9080.93043.166-0.017-0.0170.0000.0000.0000.000
157A209LEU0-0.0080.00341.915-0.002-0.0020.0000.0000.0000.000
158A210LEU0-0.018-0.00244.714-0.002-0.0020.0000.0000.0000.000
159A211LEU0-0.007-0.00647.381-0.001-0.0010.0000.0000.0000.000
160A212THR0-0.099-0.04048.128-0.001-0.0010.0000.0000.0000.000
161A213PHE0-0.012-0.00646.057-0.002-0.0020.0000.0000.0000.000
162A214ASN0-0.030-0.01151.5460.0010.0010.0000.0000.0000.000
163A215VAL00.0090.00550.6740.0000.0000.0000.0000.0000.000
164A216SER0-0.0010.00153.8640.0000.0000.0000.0000.0000.000
165A217VAL0-0.006-0.01154.2210.0010.0010.0000.0000.0000.000
166A218ASN0-0.040-0.01855.7900.0020.0020.0000.0000.0000.000
167A219LEU0-0.0020.01754.5420.0000.0000.0000.0000.0000.000
168A220GLY00.0300.00055.7460.0010.0010.0000.0000.0000.000
169A221ASP-1-0.742-0.87152.1680.0120.0120.0000.0000.0000.000
170A222LYS10.8850.93352.100-0.006-0.0060.0000.0000.0000.000
171A223TYR0-0.056-0.03353.735-0.001-0.0010.0000.0000.0000.000
172A224HIS0-0.014-0.02551.6120.0000.0000.0000.0000.0000.000
173A225LYS10.8490.94556.226-0.008-0.0080.0000.0000.0000.000
174A226ASN00.0080.01153.3110.0000.0000.0000.0000.0000.000
175A227THR00.0630.00654.4290.0000.0000.0000.0000.0000.000
176A228ALA00.0310.01051.0610.0010.0010.0000.0000.0000.000
177A229LEU00.0480.02551.8860.0020.0020.0000.0000.0000.000
178A230HIS00.0050.02553.9670.0020.0020.0000.0000.0000.000
179A231TRP00.0150.00349.1890.0020.0020.0000.0000.0000.000
180A232ALA00.0280.02049.3440.0020.0020.0000.0000.0000.000
181A233VAL0-0.003-0.00850.4220.0020.0020.0000.0000.0000.000
182A234LEU0-0.045-0.02850.9120.0020.0020.0000.0000.0000.000
183A235ALA0-0.031-0.01246.3510.0020.0020.0000.0000.0000.000
184A236GLY0-0.067-0.02647.1500.0020.0020.0000.0000.0000.000
185A237ASN0-0.012-0.01345.1370.0020.0020.0000.0000.0000.000
186A238THR00.016-0.01847.879-0.002-0.0020.0000.0000.0000.000
187A239THR0-0.009-0.00344.967-0.001-0.0010.0000.0000.0000.000
188A240VAL00.0170.01346.233-0.002-0.0020.0000.0000.0000.000
189A241ILE0-0.024-0.01048.922-0.002-0.0020.0000.0000.0000.000
190A242SER00.020-0.01452.205-0.001-0.0010.0000.0000.0000.000
191A243LEU0-0.0020.00747.563-0.001-0.0010.0000.0000.0000.000
192A244LEU0-0.003-0.00251.105-0.001-0.0010.0000.0000.0000.000
193A245LEU0-0.030-0.01353.946-0.001-0.0010.0000.0000.0000.000
194A246GLU-1-0.980-0.97554.3020.0130.0130.0000.0000.0000.000
195A247ALA0-0.024-0.00554.310-0.001-0.0010.0000.0000.0000.000
196A248GLY00.0090.00656.426-0.001-0.0010.0000.0000.0000.000
197A249ALA0-0.055-0.03356.3770.0000.0000.0000.0000.0000.000
198A250ASN00.002-0.00658.5030.0010.0010.0000.0000.0000.000
199A251VAL00.0300.00160.0570.0000.0000.0000.0000.0000.000
200A252ASP-1-0.801-0.88361.6150.0140.0140.0000.0000.0000.000
201A253ALA0-0.043-0.01361.5550.0000.0000.0000.0000.0000.000
202A254GLN0-0.031-0.01961.7760.0010.0010.0000.0000.0000.000
203A255ASN0-0.001-0.00157.677-0.001-0.0010.0000.0000.0000.000
204A256ILE0-0.027-0.01658.960-0.001-0.0010.0000.0000.0000.000
205A257LYS10.7990.88957.668-0.019-0.0190.0000.0000.0000.000
206A258GLY00.0320.01562.5260.0000.0000.0000.0000.0000.000
207A259GLU-1-0.814-0.88159.2940.0190.0190.0000.0000.0000.000
208A260SER0-0.011-0.01561.1960.0000.0000.0000.0000.0000.000
209A261ALA00.0400.01557.6590.0010.0010.0000.0000.0000.000
210A262LEU00.0460.01658.9730.0010.0010.0000.0000.0000.000
211A263ASP-1-0.814-0.87761.4530.0170.0170.0000.0000.0000.000
212A264LEU00.0170.01855.8390.0010.0010.0000.0000.0000.000
213A265ALA00.0080.00057.3210.0020.0020.0000.0000.0000.000
214A266LYS10.9040.93058.354-0.016-0.0160.0000.0000.0000.000
215A267GLN0-0.074-0.03658.7750.0020.0020.0000.0000.0000.000
216A268ARG10.8710.94450.089-0.028-0.0280.0000.0000.0000.000
217A269LYS10.8190.91156.426-0.023-0.0230.0000.0000.0000.000
218A270ASN00.0390.03453.0020.0000.0000.0000.0000.0000.000
219A271VAL00.0610.01756.954-0.001-0.0010.0000.0000.0000.000
220A272TRP00.0270.01753.258-0.001-0.0010.0000.0000.0000.000
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