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: 4L97N

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 OptAll
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 -2674000.066552
FMO2-HF: Nuclear repulsion 2583588.91711
FMO2-HF: Total energy -90411.149442
FMO2-MP2: Total energy -90672.869279


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.
-3.678-1.0340.506-1.189-1.962-0.006
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 : -0.044
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-1-0.812-0.8782.866-5.341-2.8730.505-1.162-1.811-0.006
4A56TYR0-0.010-0.0244.1140.6510.8270.001-0.027-0.1510.000
5A57SER0-0.028-0.0287.3030.5110.5110.0000.0000.0000.000
6A58THR0-0.011-0.0238.6090.2460.2460.0000.0000.0000.000
7A59TRP0-0.120-0.0698.1490.2600.2600.0000.0000.0000.000
8A60ASP-1-0.782-0.88212.282-0.164-0.1640.0000.0000.0000.000
9A61ILE00.0690.01815.348-0.021-0.0210.0000.0000.0000.000
10A62VAL0-0.0070.03117.6810.0030.0030.0000.0000.0000.000
11A63LYS10.9450.98310.4050.0340.0340.0000.0000.0000.000
12A64ALA00.009-0.00113.488-0.002-0.0020.0000.0000.0000.000
13A65THR0-0.011-0.02014.440-0.001-0.0010.0000.0000.0000.000
14A66GLN0-0.039-0.01517.1950.0130.0130.0000.0000.0000.000
15A67TYR00.000-0.00712.2430.0240.0240.0000.0000.0000.000
16A68GLY0-0.028-0.00914.570-0.003-0.0030.0000.0000.0000.000
17A69ILE0-0.026-0.00410.347-0.004-0.0040.0000.0000.0000.000
18A70TYR0-0.018-0.01913.313-0.018-0.0180.0000.0000.0000.000
19A71GLU-1-0.834-0.94413.380-0.344-0.3440.0000.0000.0000.000
20A72ARG10.7930.91011.5070.6090.6090.0000.0000.0000.000
21A73CYS0-0.024-0.02013.5720.0330.0330.0000.0000.0000.000
22A74ARG10.9400.98917.0610.2810.2810.0000.0000.0000.000
23A75GLU-1-0.865-0.92312.954-0.624-0.6240.0000.0000.0000.000
24A76LEU0-0.019-0.00715.4290.0320.0320.0000.0000.0000.000
25A77VAL0-0.019-0.00918.7060.0320.0320.0000.0000.0000.000
26A78GLU-1-0.858-0.90321.259-0.177-0.1770.0000.0000.0000.000
27A79ALA0-0.047-0.01120.2880.0100.0100.0000.0000.0000.000
28A80GLY0-0.023-0.01222.2640.0120.0120.0000.0000.0000.000
29A81TYR0-0.062-0.02322.1370.0170.0170.0000.0000.0000.000
30A82ASP-1-0.800-0.90924.098-0.105-0.1050.0000.0000.0000.000
31A83VAL0-0.018-0.02324.0640.0040.0040.0000.0000.0000.000
32A84ARG10.8170.90426.2080.0860.0860.0000.0000.0000.000
33A85GLN0-0.048-0.00926.0220.0120.0120.0000.0000.0000.000
34A86PRO0-0.019-0.00227.056-0.007-0.0070.0000.0000.0000.000
35A87ASP-1-0.724-0.86624.505-0.041-0.0410.0000.0000.0000.000
36A88LYS10.7560.84322.9130.0200.0200.0000.0000.0000.000
37A89GLU-1-0.853-0.90825.3370.0180.0180.0000.0000.0000.000
38A90ASN0-0.022-0.01229.321-0.002-0.0020.0000.0000.0000.000
39A91VAL00.0130.02526.3280.0010.0010.0000.0000.0000.000
40A92THR00.025-0.01426.942-0.011-0.0110.0000.0000.0000.000
41A93LEU00.0420.01021.5590.0040.0040.0000.0000.0000.000
42A94LEU00.0310.02323.771-0.004-0.0040.0000.0000.0000.000
43A95HIS00.0090.03226.397-0.004-0.0040.0000.0000.0000.000
44A96TRP00.0280.00621.5860.0080.0080.0000.0000.0000.000
45A97ALA00.0200.00721.7710.0020.0020.0000.0000.0000.000
46A98ALA0-0.013-0.00522.8040.0040.0040.0000.0000.0000.000
47A99ILE00.0140.00423.9340.0050.0050.0000.0000.0000.000
48A100ASN0-0.032-0.01919.9600.0260.0260.0000.0000.0000.000
49A101ASN00.0150.00321.131-0.014-0.0140.0000.0000.0000.000
50A102ARG10.8790.95417.1240.0610.0610.0000.0000.0000.000
51A103ILE0-0.009-0.02321.590-0.010-0.0100.0000.0000.0000.000
52A104ASP-1-0.807-0.90121.243-0.129-0.1290.0000.0000.0000.000
53A105LEU00.0160.02217.619-0.006-0.0060.0000.0000.0000.000
54A106VAL0-0.008-0.00321.8760.0030.0030.0000.0000.0000.000
55A107LYS10.8310.90825.1710.1130.1130.0000.0000.0000.000
56A108TYR0-0.043-0.03321.4220.0010.0010.0000.0000.0000.000
57A109TYR00.0610.00020.088-0.004-0.0040.0000.0000.0000.000
58A110ILE00.0180.01525.8980.0060.0060.0000.0000.0000.000
59A111SER0-0.105-0.05727.1740.0010.0010.0000.0000.0000.000
60A112LYS10.8160.90125.0830.1700.1700.0000.0000.0000.000
61A113GLY00.0300.02028.5190.0010.0010.0000.0000.0000.000
62A114ALA0-0.028-0.01628.2090.0070.0070.0000.0000.0000.000
63A115ILE0-0.025-0.01630.3650.0030.0030.0000.0000.0000.000
64A116VAL00.019-0.00332.2330.0020.0020.0000.0000.0000.000
65A117ASP-1-0.769-0.89132.849-0.033-0.0330.0000.0000.0000.000
66A118GLN0-0.069-0.03532.4720.0020.0020.0000.0000.0000.000
67A119LEU0-0.004-0.00933.5390.0010.0010.0000.0000.0000.000
68A120GLY00.012-0.00532.195-0.004-0.0040.0000.0000.0000.000
69A121GLY00.0220.01531.7940.0040.0040.0000.0000.0000.000
70A122ASP-1-0.899-0.94232.3470.0140.0140.0000.0000.0000.000
71A123LEU0-0.039-0.01933.5260.0000.0000.0000.0000.0000.000
72A124ASN0-0.0020.00335.958-0.004-0.0040.0000.0000.0000.000
73A125SER00.028-0.00334.1000.0000.0000.0000.0000.0000.000
74A126THR0-0.022-0.00133.754-0.003-0.0030.0000.0000.0000.000
75A127PRO00.012-0.00629.1170.0050.0050.0000.0000.0000.000
76A128LEU00.0310.02730.6460.0020.0020.0000.0000.0000.000
77A129HIS00.0330.02033.1960.0030.0030.0000.0000.0000.000
78A130TRP00.0190.00726.4680.0040.0040.0000.0000.0000.000
79A131ALA0-0.024-0.01128.6880.0050.0050.0000.0000.0000.000
80A132THR0-0.041-0.04029.7060.0050.0050.0000.0000.0000.000
81A133ARG10.7610.84631.783-0.007-0.0070.0000.0000.0000.000
82A134GLN0-0.041-0.00325.7980.0090.0090.0000.0000.0000.000
83A135GLY00.0490.03228.8180.0060.0060.0000.0000.0000.000
84A136HIS0-0.061-0.03024.438-0.003-0.0030.0000.0000.0000.000
85A137LEU00.0430.01128.730-0.007-0.0070.0000.0000.0000.000
86A138SER0-0.027-0.02326.868-0.001-0.0010.0000.0000.0000.000
87A139MET0-0.0190.02125.173-0.008-0.0080.0000.0000.0000.000
88A140VAL00.0160.01428.991-0.004-0.0040.0000.0000.0000.000
89A141VAL0-0.037-0.02532.284-0.002-0.0020.0000.0000.0000.000
90A142GLN0-0.041-0.03028.141-0.008-0.0080.0000.0000.0000.000
91A143LEU00.0380.01129.583-0.003-0.0030.0000.0000.0000.000
92A144MET00.0100.01932.5980.0010.0010.0000.0000.0000.000
93A145LYS10.8810.95333.9770.0470.0470.0000.0000.0000.000
94A146TYR0-0.035-0.01629.776-0.004-0.0040.0000.0000.0000.000
95A147GLY0-0.007-0.00134.854-0.001-0.0010.0000.0000.0000.000
96A148ALA0-0.034-0.01134.9260.0020.0020.0000.0000.0000.000
97A149ASP-1-0.827-0.92437.086-0.020-0.0200.0000.0000.0000.000
98A150PRO0-0.038-0.04038.9890.0020.0020.0000.0000.0000.000
99A151SER0-0.032-0.04739.9980.0040.0040.0000.0000.0000.000
100A152LEU0-0.0110.02039.0380.0020.0020.0000.0000.0000.000
101A153ILE0-0.028-0.01241.1430.0020.0020.0000.0000.0000.000
102A154ASP-1-0.759-0.87637.3940.0010.0010.0000.0000.0000.000
103A155GLY0-0.026-0.01038.7150.0010.0010.0000.0000.0000.000
104A156GLU-1-0.860-0.90637.5000.0220.0220.0000.0000.0000.000
105A157GLY00.0220.01841.3560.0010.0010.0000.0000.0000.000
106A158CYS0-0.090-0.04240.2640.0000.0000.0000.0000.0000.000
107A159SER00.0680.03640.712-0.001-0.0010.0000.0000.0000.000
108A160CYS0-0.023-0.01136.1010.0020.0020.0000.0000.0000.000
109A161ILE0-0.006-0.00338.7750.0020.0020.0000.0000.0000.000
110A162HIS00.028-0.00241.3210.0020.0020.0000.0000.0000.000
111A163LEU0-0.060-0.01735.9970.0040.0040.0000.0000.0000.000
112A164ALA00.009-0.00636.4290.0030.0030.0000.0000.0000.000
113A165ALA0-0.012-0.00437.4900.0030.0030.0000.0000.0000.000
114A166GLN0-0.0010.00737.9620.0060.0060.0000.0000.0000.000
115A167PHE00.000-0.01434.0540.0040.0040.0000.0000.0000.000
116A168GLY00.0310.02435.0620.0030.0030.0000.0000.0000.000
117A169HIS0-0.0070.02031.502-0.001-0.0010.0000.0000.0000.000
118A170THR00.027-0.01435.746-0.005-0.0050.0000.0000.0000.000
119A171SER00.0080.00633.864-0.002-0.0020.0000.0000.0000.000
120A172ILE00.0100.00932.300-0.004-0.0040.0000.0000.0000.000
121A173VAL00.0140.01236.707-0.003-0.0030.0000.0000.0000.000
122A174ALA00.0150.01340.049-0.002-0.0020.0000.0000.0000.000
123A175TYR0-0.026-0.02437.113-0.003-0.0030.0000.0000.0000.000
124A176LEU00.0290.00038.148-0.003-0.0030.0000.0000.0000.000
125A177ILE00.0260.03341.118-0.001-0.0010.0000.0000.0000.000
126A178ALA0-0.026-0.00442.415-0.001-0.0010.0000.0000.0000.000
127A179LYS10.7760.88340.2250.0170.0170.0000.0000.0000.000
128A180GLY00.0130.02043.538-0.002-0.0020.0000.0000.0000.000
129A181GLN0-0.034-0.00542.6320.0000.0000.0000.0000.0000.000
130A182ASP-1-0.816-0.92845.963-0.001-0.0010.0000.0000.0000.000
131A183VAL0-0.019-0.00847.4510.0010.0010.0000.0000.0000.000
132A184ASP-1-0.806-0.91948.4190.0070.0070.0000.0000.0000.000
133A185MET0-0.0220.00345.7110.0000.0000.0000.0000.0000.000
134A186MET0-0.026-0.00848.1380.0010.0010.0000.0000.0000.000
135A187ASP-1-0.723-0.82745.2490.0060.0060.0000.0000.0000.000
136A188GLN00.0220.00946.3860.0010.0010.0000.0000.0000.000
137A189ASN0-0.054-0.03544.8060.0010.0010.0000.0000.0000.000
138A190GLY0-0.062-0.05549.0600.0000.0000.0000.0000.0000.000
139A191MET0-0.0120.00246.9960.0000.0000.0000.0000.0000.000
140A192THR00.007-0.01147.909-0.001-0.0010.0000.0000.0000.000
141A193PRO00.014-0.00444.4030.0020.0020.0000.0000.0000.000
142A194LEU00.0430.02645.3200.0020.0020.0000.0000.0000.000
143A195MET0-0.0500.01047.8820.0020.0020.0000.0000.0000.000
144A196TRP00.007-0.02242.3030.0040.0040.0000.0000.0000.000
145A197ALA00.0130.01243.0790.0030.0030.0000.0000.0000.000
146A198ALA00.0040.00344.1490.0030.0030.0000.0000.0000.000
147A199TYR0-0.068-0.02344.2360.0020.0020.0000.0000.0000.000
148A200ARG10.8510.92137.271-0.026-0.0260.0000.0000.0000.000
149A201THR0-0.0130.00639.1360.0020.0020.0000.0000.0000.000
150A202HIS0-0.0070.01341.174-0.001-0.0010.0000.0000.0000.000
151A203SER0-0.025-0.04040.4480.0030.0030.0000.0000.0000.000
152A204VAL00.0250.00142.552-0.002-0.0020.0000.0000.0000.000
153A205ASP-1-0.813-0.87641.1500.0150.0150.0000.0000.0000.000
154A206PRO00.0440.02239.7150.0030.0030.0000.0000.0000.000
155A207THR00.0190.00942.204-0.003-0.0030.0000.0000.0000.000
156A208ARG10.9020.93143.232-0.021-0.0210.0000.0000.0000.000
157A209LEU0-0.0040.00041.807-0.002-0.0020.0000.0000.0000.000
158A210LEU0-0.030-0.00244.325-0.002-0.0020.0000.0000.0000.000
159A211LEU00.005-0.00647.326-0.001-0.0010.0000.0000.0000.000
160A212THR0-0.095-0.04447.966-0.001-0.0010.0000.0000.0000.000
161A213PHE0-0.010-0.00145.985-0.002-0.0020.0000.0000.0000.000
162A214ASN0-0.029-0.01951.5120.0010.0010.0000.0000.0000.000
163A215VAL00.0100.01350.505-0.001-0.0010.0000.0000.0000.000
164A216SER0-0.0050.00253.6160.0000.0000.0000.0000.0000.000
165A217VAL0-0.001-0.01853.9230.0000.0000.0000.0000.0000.000
166A218ASN0-0.036-0.00855.5270.0020.0020.0000.0000.0000.000
167A219LEU0-0.0080.01354.7010.0000.0000.0000.0000.0000.000
168A220GLY00.030-0.00155.6000.0010.0010.0000.0000.0000.000
169A221ASP-1-0.784-0.89252.0170.0110.0110.0000.0000.0000.000
170A222LYS10.8570.91351.700-0.004-0.0040.0000.0000.0000.000
171A223TYR0-0.0250.00953.435-0.001-0.0010.0000.0000.0000.000
172A224HIS0-0.008-0.02251.2770.0000.0000.0000.0000.0000.000
173A225LYS10.8110.91056.050-0.008-0.0080.0000.0000.0000.000
174A226ASN00.0000.01052.9390.0000.0000.0000.0000.0000.000
175A227THR00.0690.00754.2810.0000.0000.0000.0000.0000.000
176A228ALA00.0260.00951.0690.0010.0010.0000.0000.0000.000
177A229LEU00.0530.02951.6720.0020.0020.0000.0000.0000.000
178A230HIS0-0.0020.02053.9510.0020.0020.0000.0000.0000.000
179A231TRP00.0250.00449.1240.0020.0020.0000.0000.0000.000
180A232ALA00.0270.02649.1960.0020.0020.0000.0000.0000.000
181A233VAL00.010-0.00550.1280.0020.0020.0000.0000.0000.000
182A234LEU0-0.058-0.03250.5570.0020.0020.0000.0000.0000.000
183A235ALA0-0.019-0.00446.0290.0020.0020.0000.0000.0000.000
184A236GLY0-0.050-0.02447.0010.0030.0030.0000.0000.0000.000
185A237ASN0-0.006-0.00545.1010.0020.0020.0000.0000.0000.000
186A238THR00.018-0.01547.691-0.002-0.0020.0000.0000.0000.000
187A239THR0-0.051-0.02144.731-0.001-0.0010.0000.0000.0000.000
188A240VAL00.0100.01446.164-0.002-0.0020.0000.0000.0000.000
189A241ILE0-0.020-0.00748.902-0.002-0.0020.0000.0000.0000.000
190A242SER00.027-0.01252.225-0.001-0.0010.0000.0000.0000.000
191A243LEU00.0000.01047.673-0.001-0.0010.0000.0000.0000.000
192A244LEU0-0.007-0.00551.076-0.002-0.0020.0000.0000.0000.000
193A245LEU0-0.044-0.01853.861-0.001-0.0010.0000.0000.0000.000
194A246GLU-1-0.981-0.97954.0900.0150.0150.0000.0000.0000.000
195A247ALA0-0.027-0.01154.179-0.001-0.0010.0000.0000.0000.000
196A248GLY00.0140.01456.312-0.001-0.0010.0000.0000.0000.000
197A249ALA0-0.050-0.03056.228-0.001-0.0010.0000.0000.0000.000
198A250ASN00.007-0.01258.3840.0010.0010.0000.0000.0000.000
199A251VAL00.0400.00659.8430.0000.0000.0000.0000.0000.000
200A252ASP-1-0.796-0.86861.3230.0150.0150.0000.0000.0000.000
201A253ALA0-0.033-0.00661.212-0.001-0.0010.0000.0000.0000.000
202A254GLN0-0.033-0.02761.6530.0010.0010.0000.0000.0000.000
203A255ASN0-0.008-0.01557.317-0.001-0.0010.0000.0000.0000.000
204A256ILE0-0.022-0.02358.5630.0000.0000.0000.0000.0000.000
205A257LYS10.7970.88957.220-0.019-0.0190.0000.0000.0000.000
206A258GLY00.0250.01962.2890.0000.0000.0000.0000.0000.000
207A259GLU-1-0.792-0.86258.6930.0200.0200.0000.0000.0000.000
208A260SER00.005-0.00761.0330.0000.0000.0000.0000.0000.000
209A261ALA00.0200.00657.2630.0010.0010.0000.0000.0000.000
210A262LEU00.0440.01958.4640.0020.0020.0000.0000.0000.000
211A263ASP-1-0.806-0.87561.1220.0180.0180.0000.0000.0000.000
212A264LEU00.0020.01155.4580.0010.0010.0000.0000.0000.000
213A265ALA00.0100.00357.0970.0020.0020.0000.0000.0000.000
214A266LYS10.8800.92958.109-0.017-0.0170.0000.0000.0000.000
215A267GLN0-0.077-0.04658.3380.0020.0020.0000.0000.0000.000
216A268ARG10.8660.93349.928-0.030-0.0300.0000.0000.0000.000
217A269LYS10.8200.91255.856-0.024-0.0240.0000.0000.0000.000
218A270ASN00.0470.03352.6370.0000.0000.0000.0000.0000.000
219A271VAL00.0680.02156.422-0.001-0.0010.0000.0000.0000.000
220A272TRP00.0240.02553.130-0.001-0.0010.0000.0000.0000.000
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