FMODB

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

Last updated: 2024-04-25

All entries: 37426

Number of unique PDB entries: 7782

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FMODB ID: 2JVZR

Calculation Name: 3SIR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3SIR

Chain ID: A

ChEMBL ID:

UniProt ID: O01382

Base Structure: X-ray

Registration Date: 2023-09-20

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 214
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2655832.682406
FMO2-HF: Nuclear repulsion 2567952.767831
FMO2-HF: Total energy -87879.914575
FMO2-MP2: Total energy -88131.554727


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:1:ALA)


Summations of interaction energy for fragment #1(A:1:ALA)
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.
-3.2521.5140.088-2.381-2.4720.005
Interaction energy analysis for fragmet #1(A:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : 0.001
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].
3A3GLY00.0330.0143.547-2.3420.696-0.025-1.601-1.4130.000
4A4SER0-0.032-0.0583.351-0.3560.2130.015-0.183-0.4000.001
5A5VAL0-0.0710.0343.4540.1791.3660.099-0.596-0.6900.004
6A6THR0-0.0250.0135.760-0.824-0.852-0.001-0.0010.0310.000
7A7ASP-1-0.865-1.0169.4241.1291.1290.0000.0000.0000.000
8A8ARG11.0141.02612.372-0.597-0.5970.0000.0000.0000.000
9A9HIS0-0.137-0.01514.938-0.059-0.0590.0000.0000.0000.000
10A10ALA00.060-0.01712.862-0.034-0.0340.0000.0000.0000.000
11A11ALA00.0920.0578.7720.0090.0090.0000.0000.0000.000
12A12GLU-1-0.947-0.9649.721-0.301-0.3010.0000.0000.0000.000
13A13TYR0-0.152-0.15512.6940.0140.0140.0000.0000.0000.000
14A14ASN00.013-0.00616.341-0.045-0.0450.0000.0000.0000.000
15A15MET0-0.099-0.03317.7770.0110.0110.0000.0000.0000.000
16A16ARG10.9710.97018.2850.0520.0520.0000.0000.0000.000
17A17HIS0-0.056-0.00222.0000.0070.0070.0000.0000.0000.000
18A18LYS10.9140.98025.112-0.011-0.0110.0000.0000.0000.000
19A19ASN00.032-0.00128.561-0.009-0.0090.0000.0000.0000.000
20A20ARG10.8610.93722.1480.0450.0450.0000.0000.0000.000
21A21GLY00.0640.02126.0230.0090.0090.0000.0000.0000.000
22A22MET0-0.0140.01628.617-0.004-0.0040.0000.0000.0000.000
23A23ALA0-0.0020.00329.7190.0020.0020.0000.0000.0000.000
24A24LEU0-0.022-0.01131.261-0.001-0.0010.0000.0000.0000.000
25A25ILE00.0350.01532.6070.0030.0030.0000.0000.0000.000
26A26PHE0-0.010-0.01334.9450.0000.0000.0000.0000.0000.000
27A27ASN0-0.042-0.11337.387-0.001-0.0010.0000.0000.0000.000
28A28HIS10.8390.94239.404-0.009-0.0090.0000.0000.0000.000
29A29GLU-1-0.816-0.89841.2490.0000.0000.0000.0000.0000.000
30A30HIS0-0.053-0.04344.4180.0010.0010.0000.0000.0000.000
31A31PHE0-0.0050.00547.512-0.001-0.0010.0000.0000.0000.000
32A43ASN00.014-0.01138.8820.0010.0010.0000.0000.0000.000
33A44VAL00.0760.03238.252-0.001-0.0010.0000.0000.0000.000
34A45ASP-1-0.860-0.93734.676-0.019-0.0190.0000.0000.0000.000
35A46CYM-1-0.826-0.82934.409-0.009-0.0090.0000.0000.0000.000
36A47GLU-1-0.916-0.94036.115-0.019-0.0190.0000.0000.0000.000
37A48ASN0-0.042-0.04132.232-0.004-0.0040.0000.0000.0000.000
38A49LEU00.0300.02028.878-0.003-0.0030.0000.0000.0000.000
39A50THR00.0310.00230.824-0.002-0.0020.0000.0000.0000.000
40A51ARG10.9290.97432.1830.0310.0310.0000.0000.0000.000
41A52VAL0-0.009-0.00126.080-0.004-0.0040.0000.0000.0000.000
42A53LEU00.007-0.00926.661-0.004-0.0040.0000.0000.0000.000
43A54LYS10.9610.98728.6920.0230.0230.0000.0000.0000.000
44A55GLN0-0.021-0.01526.8600.0030.0030.0000.0000.0000.000
45A56LEU0-0.092-0.03722.574-0.008-0.0080.0000.0000.0000.000
46A57ASP-1-0.915-0.95125.112-0.049-0.0490.0000.0000.0000.000
47A58PHE0-0.063-0.03824.4280.0060.0060.0000.0000.0000.000
48A59GLU-1-0.923-0.96229.324-0.011-0.0110.0000.0000.0000.000
49A60VAL0-0.069-0.03231.7320.0040.0040.0000.0000.0000.000
50A61THR0-0.034-0.00434.126-0.001-0.0010.0000.0000.0000.000
51A62VAL00.0390.00536.5480.0010.0010.0000.0000.0000.000
52A63TYR0-0.022-0.00837.6210.0000.0000.0000.0000.0000.000
53A64LYS10.9710.97140.5370.0040.0040.0000.0000.0000.000
54A65ASP-1-0.737-0.85042.7840.0090.0090.0000.0000.0000.000
55A66CYS0-0.089-0.05443.4910.0000.0000.0000.0000.0000.000
56A67ARG10.8790.94645.937-0.009-0.0090.0000.0000.0000.000
57A68TYR00.1100.04736.9120.0000.0000.0000.0000.0000.000
58A69LYS10.8790.91942.011-0.018-0.0180.0000.0000.0000.000
59A70ASP-1-0.796-0.89343.3520.0150.0150.0000.0000.0000.000
60A71ILE0-0.0060.01037.8780.0010.0010.0000.0000.0000.000
61A72LEU0-0.067-0.03837.9940.0020.0020.0000.0000.0000.000
62A73ARG10.9991.00438.957-0.019-0.0190.0000.0000.0000.000
63A74THR00.0130.01438.5150.0010.0010.0000.0000.0000.000
64A75ILE0-0.0170.00434.2240.0010.0010.0000.0000.0000.000
65A76GLU-1-0.985-0.98536.3340.0340.0340.0000.0000.0000.000
66A77TYR0-0.010-0.03037.9260.0020.0020.0000.0000.0000.000
67A78SER00.022-0.00734.7410.0010.0010.0000.0000.0000.000
68A79ALA0-0.023-0.00433.5910.0010.0010.0000.0000.0000.000
69A80SER0-0.029-0.00834.6630.0030.0030.0000.0000.0000.000
70A81GLN0-0.0410.00935.135-0.002-0.0020.0000.0000.0000.000
71A82ASN00.0450.04633.5710.0060.0060.0000.0000.0000.000
72A83HIS0-0.017-0.05329.854-0.006-0.0060.0000.0000.0000.000
73A84SER0-0.029-0.04429.2330.0050.0050.0000.0000.0000.000
74A85ASP-1-0.908-0.94428.8420.0220.0220.0000.0000.0000.000
75A86SER0-0.060-0.04327.657-0.009-0.0090.0000.0000.0000.000
76A87ASP-1-0.750-0.85922.5570.0010.0010.0000.0000.0000.000
77A88CYS0-0.115-0.06322.7700.0110.0110.0000.0000.0000.000
78A89ILE00.0120.00524.752-0.003-0.0030.0000.0000.0000.000
79A90LEU0-0.0140.01025.2080.0040.0040.0000.0000.0000.000
80A91VAL00.0130.01327.905-0.003-0.0030.0000.0000.0000.000
81A92ALA00.007-0.00929.6290.0010.0010.0000.0000.0000.000
82A93ILE0-0.036-0.00831.703-0.001-0.0010.0000.0000.0000.000
83A94LEU00.0510.01932.5680.0000.0000.0000.0000.0000.000
84A95SER00.001-0.00535.8950.0000.0000.0000.0000.0000.000
85A96HIS0-0.066-0.05338.123-0.003-0.0030.0000.0000.0000.000
86A97GLY00.041-0.00440.5890.0010.0010.0000.0000.0000.000
87A98GLU-1-0.929-0.93541.378-0.003-0.0030.0000.0000.0000.000
88A99MET0-0.026-0.02444.4490.0000.0000.0000.0000.0000.000
89A100GLY00.0330.03344.5960.0000.0000.0000.0000.0000.000
90A101TYR00.0120.00241.6680.0000.0000.0000.0000.0000.000
91A102ILE00.0110.00846.3360.0010.0010.0000.0000.0000.000
92A103TYR00.0090.00041.6960.0000.0000.0000.0000.0000.000
93A104ALA0-0.009-0.00847.0010.0000.0000.0000.0000.0000.000
94A105LYS11.0561.04547.343-0.017-0.0170.0000.0000.0000.000
95A106ASP-1-0.877-0.92646.7910.0250.0250.0000.0000.0000.000
96A107THR0-0.073-0.09743.3420.0010.0010.0000.0000.0000.000
97A108GLN00.0440.03540.3780.0040.0040.0000.0000.0000.000
98A109TYR0-0.082-0.32240.5640.0020.0020.0000.0000.0000.000
99A110LYS11.3230.94540.452-0.023-0.0230.0000.0000.0000.000
100A111LEU00.043-0.10937.3150.0020.0020.0000.0000.0000.000
101A112ASH0-0.1330.35536.5330.0020.0020.0000.0000.0000.000
102A113ASN0-0.0530.01436.0260.0050.0050.0000.0000.0000.000
103A114ILE0-0.1220.11735.0160.0050.0050.0000.0000.0000.000
104A115TRP00.0720.02929.3540.0030.0030.0000.0000.0000.000
105A116SER0-0.086-0.05331.9020.0030.0030.0000.0000.0000.000
106A117PHE00.007-0.00533.6530.0030.0030.0000.0000.0000.000
107A118PHE00.0770.02429.4170.0000.0000.0000.0000.0000.000
108A119THR0-0.112-0.03628.8500.0070.0070.0000.0000.0000.000
109A120ALA00.1170.04226.653-0.003-0.0030.0000.0000.0000.000
110A121ASN0-0.005-0.01128.719-0.001-0.0010.0000.0000.0000.000
111A122HIS10.8340.91232.167-0.069-0.0690.0000.0000.0000.000
112A123CYS00.0100.02730.782-0.006-0.0060.0000.0000.0000.000
113A124PRO00.0590.03430.0350.0030.0030.0000.0000.0000.000
114A125SER00.0250.02129.6400.0020.0020.0000.0000.0000.000
115A126LEU0-0.027-0.01626.273-0.001-0.0010.0000.0000.0000.000
116A127ALA00.0320.02226.0990.0040.0040.0000.0000.0000.000
117A128GLY0-0.0120.00621.7320.0020.0020.0000.0000.0000.000
118A129LYS10.8400.93320.910-0.054-0.0540.0000.0000.0000.000
119A130PRO00.0280.02119.2600.0050.0050.0000.0000.0000.000
120A131LYS10.8380.92321.739-0.106-0.1060.0000.0000.0000.000
121A132LEU0-0.008-0.00721.0800.0060.0060.0000.0000.0000.000
122A133PHE0-0.033-0.01824.759-0.003-0.0030.0000.0000.0000.000
123A134PHE00.0110.00123.4180.0000.0000.0000.0000.0000.000
124A135ILE0-0.016-0.00628.4400.0000.0000.0000.0000.0000.000
125A136GLN00.0280.01531.010-0.004-0.0040.0000.0000.0000.000
126A137ALA0-0.023-0.01433.4680.0010.0010.0000.0000.0000.000
127A138CYS00.0560.03435.865-0.003-0.0030.0000.0000.0000.000
128A139GLN0-0.008-0.00935.9940.0020.0020.0000.0000.0000.000
129A140GLY0-0.055-0.02038.6150.0000.0000.0000.0000.0000.000
130A141ASP-1-0.953-0.97437.2510.0210.0210.0000.0000.0000.000
131A142ARG10.9810.97436.248-0.034-0.0340.0000.0000.0000.000
132A143LEU00.0110.00928.3550.0000.0000.0000.0000.0000.000
133A144ASP-1-0.855-0.92531.7670.0440.0440.0000.0000.0000.000
134A145GLY0-0.0080.03329.1180.0040.0040.0000.0000.0000.000
135A163SER0-0.068-0.03837.1510.0010.0010.0000.0000.0000.000
136A164TYR0-0.058-0.04232.3810.0010.0010.0000.0000.0000.000
137A165LYS10.9730.97432.488-0.043-0.0430.0000.0000.0000.000
138A166ILE00.028-0.01226.2000.0000.0000.0000.0000.0000.000
139A167PRO0-0.098-0.00327.0860.0040.0040.0000.0000.0000.000
140A168VAL00.084-0.05526.0540.0040.0040.0000.0000.0000.000
141A169HIS10.8460.91525.499-0.100-0.1000.0000.0000.0000.000
142A170ALA00.0860.04121.6020.0020.0020.0000.0000.0000.000
143A171ASP-1-0.764-0.82119.7240.1580.1580.0000.0000.0000.000
144A172PHE0-0.055-0.02121.248-0.019-0.0190.0000.0000.0000.000
145A173LEU00.0500.02219.0880.0130.0130.0000.0000.0000.000
146A174ILE0-0.022-0.00522.578-0.010-0.0100.0000.0000.0000.000
147A175ALA00.0170.01923.7540.0020.0020.0000.0000.0000.000
148A176TYR00.0400.01125.264-0.003-0.0030.0000.0000.0000.000
149A177SER00.0200.01328.323-0.001-0.0010.0000.0000.0000.000
150A178THR00.0160.00330.7100.0000.0000.0000.0000.0000.000
151A179VAL0-0.0200.01134.372-0.003-0.0030.0000.0000.0000.000
152A180PRO00.0090.01537.1020.0030.0030.0000.0000.0000.000
153A181GLY00.0660.01040.118-0.001-0.0010.0000.0000.0000.000
154A182PHE0-0.077-0.03942.1050.0010.0010.0000.0000.0000.000
155A183TYR00.0930.05845.159-0.001-0.0010.0000.0000.0000.000
156A184SER00.018-0.01446.2330.0000.0000.0000.0000.0000.000
157A185TRP0-0.0130.00042.4940.0000.0000.0000.0000.0000.000
158A186ARG10.9940.99346.7310.0140.0140.0000.0000.0000.000
159A187ASN0-0.053-0.03743.7250.0010.0010.0000.0000.0000.000
160A188THR00.0000.00343.593-0.001-0.0010.0000.0000.0000.000
161A189THR0-0.0320.00641.171-0.002-0.0020.0000.0000.0000.000
162A190ARG10.9660.98037.7300.0240.0240.0000.0000.0000.000
163A191GLY00.0640.04036.9790.0020.0020.0000.0000.0000.000
164A192SER00.0210.02233.169-0.003-0.0030.0000.0000.0000.000
165A193TRP00.1480.06031.235-0.001-0.0010.0000.0000.0000.000
166A194PHE00.0300.06525.642-0.004-0.0040.0000.0000.0000.000
167A195MET00.0240.01428.284-0.002-0.0020.0000.0000.0000.000
168A196GLN0-0.052-0.02929.995-0.007-0.0070.0000.0000.0000.000
169A197SER0-0.048-0.09326.441-0.005-0.0050.0000.0000.0000.000
170A198LEU0-0.0060.01623.951-0.009-0.0090.0000.0000.0000.000
171A199CYS0-0.055-0.04525.188-0.004-0.0040.0000.0000.0000.000
172A200ALA00.0080.01326.561-0.007-0.0070.0000.0000.0000.000
173A201GLU-1-0.837-0.93820.142-0.121-0.1210.0000.0000.0000.000
174A202LEU00.0650.02221.735-0.012-0.0120.0000.0000.0000.000
175A203ALA0-0.043-0.01122.853-0.008-0.0080.0000.0000.0000.000
176A204ALA0-0.080-0.02122.645-0.002-0.0020.0000.0000.0000.000
177A205ASN0-0.041-0.05817.418-0.036-0.0360.0000.0000.0000.000
178A206GLY00.0220.01717.959-0.013-0.0130.0000.0000.0000.000
179A207LYS10.9110.94618.6000.0950.0950.0000.0000.0000.000
180A208ARG10.8420.93615.6670.1670.1670.0000.0000.0000.000
181A209LEU00.0170.01412.502-0.064-0.0640.0000.0000.0000.000
182A210ASP-1-0.889-0.93311.333-0.105-0.1050.0000.0000.0000.000
183A211ILE00.0390.00713.5310.0120.0120.0000.0000.0000.000
184A212LEU00.0300.01113.1940.0010.0010.0000.0000.0000.000
185A213THR00.0100.03411.2170.0050.0050.0000.0000.0000.000
186A214LEU00.0350.03914.553-0.003-0.0030.0000.0000.0000.000
187A215LEU0-0.070-0.05317.7280.0060.0060.0000.0000.0000.000
188A216THR00.028-0.00916.0940.0180.0180.0000.0000.0000.000
189A217PHE0-0.014-0.01214.9500.0030.0030.0000.0000.0000.000
190A218VAL0-0.050-0.02420.0030.0040.0040.0000.0000.0000.000
191A219CYS0-0.043-0.00821.4450.0090.0090.0000.0000.0000.000
192A220GLN00.0550.02220.3610.0000.0000.0000.0000.0000.000
193A221ARG10.9370.97023.1470.0800.0800.0000.0000.0000.000
194A222VAL00.0080.01725.7800.0030.0030.0000.0000.0000.000
195A223ALA00.0080.01325.9780.0050.0050.0000.0000.0000.000
196A224VAL0-0.138-0.09326.1610.0010.0010.0000.0000.0000.000
197A225ASP-1-0.898-0.93528.209-0.047-0.0470.0000.0000.0000.000
198A226PHE0-0.099-0.03331.2500.0030.0030.0000.0000.0000.000
199A241GLN0-0.061-0.05132.1630.0030.0030.0000.0000.0000.000
200A242ILE00.0830.04424.798-0.004-0.0040.0000.0000.0000.000
201A243PRO0-0.090-0.03224.7080.0060.0060.0000.0000.0000.000
202A244CYS00.0340.01424.9660.0040.0040.0000.0000.0000.000
203A245ILE0-0.026-0.00819.8980.0030.0030.0000.0000.0000.000
204A246THR0-0.014-0.01821.9170.0130.0130.0000.0000.0000.000
205A247THR0-0.0020.01416.871-0.007-0.0070.0000.0000.0000.000
206A248MET0-0.0200.05919.4050.0060.0060.0000.0000.0000.000
207A249LEU0-0.051-0.01816.1360.0100.0100.0000.0000.0000.000
208A250THR0-0.014-0.01415.9450.0290.0290.0000.0000.0000.000
209A251ARG10.9380.97412.711-0.182-0.1820.0000.0000.0000.000
210A252ILE00.0280.0287.686-0.078-0.0780.0000.0000.0000.000
211A253LEU00.0130.00612.023-0.028-0.0280.0000.0000.0000.000
212A254ARG11.0030.9869.9100.2780.2780.0000.0000.0000.000
213A255PHE00.0030.00915.7420.0110.0110.0000.0000.0000.000
214A256SER00.0050.00616.502-0.005-0.0050.0000.0000.0000.000