FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: Z64MN

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:

Apendix: None


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 214
LigandResidueName
LigandFragmentNumber 0
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2659565.704665
FMO2-HF: Nuclear repulsion 2571678.735488
FMO2-HF: Total energy -87886.969177
FMO2-MP2: Total energy -88137.911626


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.
-2.2041.0440.203-1.568-1.8820.004
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 : 0.031 / q_NPA : -0.002
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].
3A3GLY00.0220.0053.887-1.1260.833-0.011-1.042-0.9060.000
4A4SER0-0.023-0.0153.688-0.3280.0370.002-0.069-0.2970.000
5A5VAL0-0.053-0.0123.1840.1691.0930.212-0.457-0.6790.004
6A6THR0-0.008-0.0105.646-0.681-0.6810.0000.0000.0000.000
7A7ASP-1-0.781-0.8799.4530.6490.6490.0000.0000.0000.000
8A8ARG10.9070.93212.574-0.470-0.4700.0000.0000.0000.000
9A9HIS0-0.076-0.04014.949-0.095-0.0950.0000.0000.0000.000
10A10ALA00.001-0.00712.795-0.045-0.0450.0000.0000.0000.000
11A11ALA00.0550.0349.112-0.013-0.0130.0000.0000.0000.000
12A12GLU-1-0.812-0.86710.304-0.058-0.0580.0000.0000.0000.000
13A13TYR0-0.037-0.04813.102-0.010-0.0100.0000.0000.0000.000
14A14ASN0-0.018-0.01516.798-0.045-0.0450.0000.0000.0000.000
15A15MET0-0.063-0.01317.8470.0140.0140.0000.0000.0000.000
16A16ARG10.9600.97018.7510.0570.0570.0000.0000.0000.000
17A17HIS0-0.050-0.01722.3700.0030.0030.0000.0000.0000.000
18A18LYS10.8310.90325.506-0.014-0.0140.0000.0000.0000.000
19A19ASN00.0160.00828.502-0.008-0.0080.0000.0000.0000.000
20A20ARG10.8350.90121.9540.0170.0170.0000.0000.0000.000
21A21GLY00.0550.00626.0370.0110.0110.0000.0000.0000.000
22A22MET0-0.050-0.00628.756-0.005-0.0050.0000.0000.0000.000
23A23ALA00.0000.00329.7770.0060.0060.0000.0000.0000.000
24A24LEU0-0.040-0.02231.341-0.005-0.0050.0000.0000.0000.000
25A25ILE00.0490.02532.6820.0060.0060.0000.0000.0000.000
26A26PHE0-0.001-0.00935.058-0.003-0.0030.0000.0000.0000.000
27A27ASN0-0.039-0.07637.7060.0020.0020.0000.0000.0000.000
28A28HIS10.8410.93439.711-0.037-0.0370.0000.0000.0000.000
29A29GLU-1-0.759-0.88241.3770.0210.0210.0000.0000.0000.000
30A30HIS0-0.045-0.03344.5970.0000.0000.0000.0000.0000.000
31A31PHE00.0380.03148.034-0.001-0.0010.0000.0000.0000.000
32A43ASN00.0580.01339.0950.0010.0010.0000.0000.0000.000
33A44VAL00.0230.00337.709-0.001-0.0010.0000.0000.0000.000
34A45ASP-1-0.824-0.91434.4570.0210.0210.0000.0000.0000.000
35A46CYM-1-0.797-0.84134.1340.0210.0210.0000.0000.0000.000
36A47GLU-1-0.804-0.86935.3030.0010.0010.0000.0000.0000.000
37A48ASN0-0.026-0.00832.732-0.006-0.0060.0000.0000.0000.000
38A49LEU00.0290.01428.614-0.002-0.0020.0000.0000.0000.000
39A50THR00.008-0.02530.9510.0000.0000.0000.0000.0000.000
40A51ARG10.7430.85232.7720.0000.0000.0000.0000.0000.000
41A52VAL00.0180.00626.693-0.003-0.0030.0000.0000.0000.000
42A53LEU00.000-0.00926.741-0.002-0.0020.0000.0000.0000.000
43A54LYS10.8820.94428.632-0.006-0.0060.0000.0000.0000.000
44A55GLN0-0.023-0.00627.893-0.001-0.0010.0000.0000.0000.000
45A56LEU0-0.046-0.01122.666-0.009-0.0090.0000.0000.0000.000
46A57ASP-1-0.803-0.87025.065-0.029-0.0290.0000.0000.0000.000
47A58PHE0-0.014-0.01224.3960.0050.0050.0000.0000.0000.000
48A59GLU-1-0.812-0.90229.1950.0030.0030.0000.0000.0000.000
49A60VAL0-0.102-0.04831.4140.0060.0060.0000.0000.0000.000
50A61THR0-0.018-0.00334.106-0.004-0.0040.0000.0000.0000.000
51A62VAL00.0390.01336.4660.0030.0030.0000.0000.0000.000
52A63TYR00.0020.00037.521-0.002-0.0020.0000.0000.0000.000
53A64LYS10.8590.90940.636-0.018-0.0180.0000.0000.0000.000
54A65ASP-1-0.818-0.89843.2230.0260.0260.0000.0000.0000.000
55A66CYS0-0.043-0.01443.9470.0010.0010.0000.0000.0000.000
56A67ARG10.8780.93445.967-0.024-0.0240.0000.0000.0000.000
57A68TYR00.1200.04337.4450.0020.0020.0000.0000.0000.000
58A69LYS10.8190.89442.305-0.034-0.0340.0000.0000.0000.000
59A70ASP-1-0.771-0.86143.9130.0330.0330.0000.0000.0000.000
60A71ILE00.0120.03838.4820.0000.0000.0000.0000.0000.000
61A72LEU0-0.046-0.02538.0060.0020.0020.0000.0000.0000.000
62A73ARG10.8750.91039.739-0.033-0.0330.0000.0000.0000.000
63A74THR00.0060.00439.012-0.001-0.0010.0000.0000.0000.000
64A75ILE0-0.0310.00534.6990.0010.0010.0000.0000.0000.000
65A76GLU-1-0.910-0.93836.6690.0480.0480.0000.0000.0000.000
66A77TYR0-0.047-0.04138.6640.0000.0000.0000.0000.0000.000
67A78SER00.004-0.01235.5990.0000.0000.0000.0000.0000.000
68A79ALA0-0.001-0.00233.9540.0010.0010.0000.0000.0000.000
69A80SER0-0.063-0.02634.9440.0020.0020.0000.0000.0000.000
70A81GLN00.0230.01935.676-0.003-0.0030.0000.0000.0000.000
71A82ASN00.0520.03234.2830.0090.0090.0000.0000.0000.000
72A83HIS00.010-0.01829.865-0.006-0.0060.0000.0000.0000.000
73A84SER0-0.004-0.02129.4270.0050.0050.0000.0000.0000.000
74A85ASP-1-0.836-0.90828.7920.0150.0150.0000.0000.0000.000
75A86SER0-0.045-0.01228.062-0.009-0.0090.0000.0000.0000.000
76A87ASP-1-0.720-0.84122.4060.0220.0220.0000.0000.0000.000
77A88CYS0-0.109-0.04823.0490.0160.0160.0000.0000.0000.000
78A89ILE00.0130.00725.130-0.010-0.0100.0000.0000.0000.000
79A90LEU0-0.0050.01025.5440.0100.0100.0000.0000.0000.000
80A91VAL00.0040.00728.243-0.007-0.0070.0000.0000.0000.000
81A92ALA00.0190.00229.8990.0060.0060.0000.0000.0000.000
82A93ILE0-0.047-0.02331.948-0.004-0.0040.0000.0000.0000.000
83A94LEU00.0220.00732.7040.0030.0030.0000.0000.0000.000
84A95SER0-0.027-0.02436.230-0.003-0.0030.0000.0000.0000.000
85A96HIS00.0070.00038.309-0.002-0.0020.0000.0000.0000.000
86A97GLY00.0440.01240.9160.0020.0020.0000.0000.0000.000
87A98GLU-1-0.834-0.88141.7020.0240.0240.0000.0000.0000.000
88A99MET0-0.063-0.03844.898-0.001-0.0010.0000.0000.0000.000
89A100GLY00.0460.03544.7450.0010.0010.0000.0000.0000.000
90A101TYR0-0.020-0.02942.071-0.001-0.0010.0000.0000.0000.000
91A102ILE0-0.0010.00246.5480.0010.0010.0000.0000.0000.000
92A103TYR00.0220.01641.846-0.001-0.0010.0000.0000.0000.000
93A104ALA00.0070.01047.5790.0000.0000.0000.0000.0000.000
94A105LYS11.0130.99947.713-0.032-0.0320.0000.0000.0000.000
95A106ASP-1-0.765-0.86047.5140.0410.0410.0000.0000.0000.000
96A107THR0-0.018-0.03143.8570.0020.0020.0000.0000.0000.000
97A108GLN00.0580.04040.1070.0060.0060.0000.0000.0000.000
98A109TYR00.0660.02440.9320.0030.0030.0000.0000.0000.000
99A110LYS10.8690.92641.036-0.042-0.0420.0000.0000.0000.000
100A111LEU00.0130.00437.7440.0020.0020.0000.0000.0000.000
101A112ASH0-0.069-0.06136.5670.0040.0040.0000.0000.0000.000
102A113ASN00.0250.01736.5710.0070.0070.0000.0000.0000.000
103A114ILE00.0080.02333.9020.0030.0030.0000.0000.0000.000
104A115TRP00.0370.01729.8600.0030.0030.0000.0000.0000.000
105A116SER0-0.073-0.05032.1060.0050.0050.0000.0000.0000.000
106A117PHE00.0450.02434.1250.0030.0030.0000.0000.0000.000
107A118PHE00.0900.03829.6310.0000.0000.0000.0000.0000.000
108A119THR0-0.048-0.02829.4540.0080.0080.0000.0000.0000.000
109A120ALA00.0710.03127.460-0.007-0.0070.0000.0000.0000.000
110A121ASN0-0.031-0.02629.559-0.001-0.0010.0000.0000.0000.000
111A122HIS10.8240.91432.927-0.086-0.0860.0000.0000.0000.000
112A123CYS00.0180.02831.301-0.006-0.0060.0000.0000.0000.000
113A124PRO00.0530.02630.5650.0060.0060.0000.0000.0000.000
114A125SER0-0.025-0.01329.8050.0050.0050.0000.0000.0000.000
115A126LEU00.0220.00127.017-0.002-0.0020.0000.0000.0000.000
116A127ALA0-0.004-0.00726.4170.0150.0150.0000.0000.0000.000
117A128GLY00.0020.01622.441-0.003-0.0030.0000.0000.0000.000
118A129LYS10.8160.92621.423-0.053-0.0530.0000.0000.0000.000
119A130PRO0-0.014-0.00219.6250.0050.0050.0000.0000.0000.000
120A131LYS10.7920.89922.263-0.152-0.1520.0000.0000.0000.000
121A132LEU0-0.0020.00121.2890.0110.0110.0000.0000.0000.000
122A133PHE00.000-0.00425.240-0.012-0.0120.0000.0000.0000.000
123A134PHE00.0210.01123.5640.0080.0080.0000.0000.0000.000
124A135ILE0-0.028-0.01528.793-0.006-0.0060.0000.0000.0000.000
125A136GLN00.0410.03931.2980.0040.0040.0000.0000.0000.000
126A137ALA0-0.0080.00533.784-0.003-0.0030.0000.0000.0000.000
127A138CYS00.009-0.00536.367-0.003-0.0030.0000.0000.0000.000
128A139GLN0-0.041-0.02136.2700.0020.0020.0000.0000.0000.000
129A140GLY00.009-0.00738.889-0.003-0.0030.0000.0000.0000.000
130A141ASP-1-0.910-0.93337.4810.0530.0530.0000.0000.0000.000
131A142ARG10.8420.89136.256-0.071-0.0710.0000.0000.0000.000
132A143LEU00.0220.01628.401-0.001-0.0010.0000.0000.0000.000
133A144ASP-1-0.792-0.88732.8760.0820.0820.0000.0000.0000.000
134A145GLY00.0210.02130.0510.0060.0060.0000.0000.0000.000
135A163SER00.0080.02337.7310.0000.0000.0000.0000.0000.000
136A164TYR0-0.018-0.02132.9530.0000.0000.0000.0000.0000.000
137A165LYS10.8710.93433.157-0.072-0.0720.0000.0000.0000.000
138A166ILE00.0430.01626.8100.0000.0000.0000.0000.0000.000
139A167PRO0-0.039-0.01228.1120.0030.0030.0000.0000.0000.000
140A168VAL00.0240.01325.7570.0010.0010.0000.0000.0000.000
141A169HIS10.8400.91926.068-0.138-0.1380.0000.0000.0000.000
142A170ALA00.0830.03622.4810.0060.0060.0000.0000.0000.000
143A171ASP-1-0.779-0.87420.8500.1800.1800.0000.0000.0000.000
144A172PHE0-0.037-0.00921.923-0.020-0.0200.0000.0000.0000.000
145A173LEU0-0.0010.00419.2760.0220.0220.0000.0000.0000.000
146A174ILE0-0.026-0.02022.939-0.018-0.0180.0000.0000.0000.000
147A175ALA00.0220.02024.0680.0090.0090.0000.0000.0000.000
148A176TYR00.0210.00725.672-0.011-0.0110.0000.0000.0000.000
149A177SER00.010-0.00928.4340.0000.0000.0000.0000.0000.000
150A178THR0-0.026-0.00830.977-0.003-0.0030.0000.0000.0000.000
151A179VAL00.0120.02134.660-0.002-0.0020.0000.0000.0000.000
152A180PRO00.0210.00837.4580.0020.0020.0000.0000.0000.000
153A181GLY00.0270.01340.638-0.002-0.0020.0000.0000.0000.000
154A182PHE0-0.042-0.02942.557-0.001-0.0010.0000.0000.0000.000
155A183TYR00.021-0.00444.9790.0000.0000.0000.0000.0000.000
156A184SER0-0.011-0.00146.286-0.001-0.0010.0000.0000.0000.000
157A185TRP00.0310.02042.0670.0000.0000.0000.0000.0000.000
158A186ARG10.9760.99047.016-0.007-0.0070.0000.0000.0000.000
159A187ASN0-0.0100.00144.397-0.001-0.0010.0000.0000.0000.000
160A188THR00.028-0.00343.7790.0000.0000.0000.0000.0000.000
161A189THR0-0.023-0.01940.760-0.001-0.0010.0000.0000.0000.000
162A190ARG10.8680.93537.374-0.011-0.0110.0000.0000.0000.000
163A191GLY00.0690.04936.8630.0020.0020.0000.0000.0000.000
164A192SER0-0.008-0.01933.3840.0000.0000.0000.0000.0000.000
165A193TRP00.0650.02431.3860.0000.0000.0000.0000.0000.000
166A194PHE00.0150.01925.917-0.001-0.0010.0000.0000.0000.000
167A195MET00.0290.02028.3960.0020.0020.0000.0000.0000.000
168A196GLN0-0.014-0.01729.834-0.007-0.0070.0000.0000.0000.000
169A197SER00.007-0.00425.851-0.006-0.0060.0000.0000.0000.000
170A198LEU0-0.033-0.01424.254-0.003-0.0030.0000.0000.0000.000
171A199CYS0-0.035-0.02425.338-0.004-0.0040.0000.0000.0000.000
172A200ALA00.0140.01026.602-0.007-0.0070.0000.0000.0000.000
173A201GLU-1-0.753-0.85820.544-0.028-0.0280.0000.0000.0000.000
174A202LEU0-0.023-0.01922.087-0.011-0.0110.0000.0000.0000.000
175A203ALA00.0060.00023.454-0.008-0.0080.0000.0000.0000.000
176A204ALA0-0.045-0.00423.164-0.009-0.0090.0000.0000.0000.000
177A205ASN0-0.048-0.05318.207-0.036-0.0360.0000.0000.0000.000
178A206GLY00.0410.03418.347-0.007-0.0070.0000.0000.0000.000
179A207LYS10.7830.86719.0580.0510.0510.0000.0000.0000.000
180A208ARG10.8530.92916.0230.0880.0880.0000.0000.0000.000
181A209LEU0-0.0080.00313.196-0.049-0.0490.0000.0000.0000.000
182A210ASP-1-0.832-0.88711.4910.1580.1580.0000.0000.0000.000
183A211ILE00.021-0.01213.9360.0050.0050.0000.0000.0000.000
184A212LEU00.0030.00613.185-0.006-0.0060.0000.0000.0000.000
185A213THR00.003-0.01810.958-0.022-0.0220.0000.0000.0000.000
186A214LEU0-0.0100.01214.206-0.016-0.0160.0000.0000.0000.000
187A215LEU00.003-0.02117.441-0.007-0.0070.0000.0000.0000.000
188A216THR00.0030.00316.1630.0070.0070.0000.0000.0000.000
189A217PHE00.003-0.00215.148-0.008-0.0080.0000.0000.0000.000
190A218VAL0-0.067-0.02419.880-0.007-0.0070.0000.0000.0000.000
191A219CYS0-0.059-0.03421.563-0.001-0.0010.0000.0000.0000.000
192A220GLN00.004-0.00319.7600.0010.0010.0000.0000.0000.000
193A221ARG10.8360.90823.0470.0010.0010.0000.0000.0000.000
194A222VAL00.0510.01825.741-0.001-0.0010.0000.0000.0000.000
195A223ALA0-0.033-0.01125.7020.0000.0000.0000.0000.0000.000
196A224VAL0-0.058-0.02726.027-0.001-0.0010.0000.0000.0000.000
197A225ASP-1-0.952-0.96428.3930.0090.0090.0000.0000.0000.000
198A226PHE0-0.067-0.02931.0560.0000.0000.0000.0000.0000.000
199A241GLN0-0.069-0.03532.7210.0040.0040.0000.0000.0000.000
200A242ILE00.0750.03625.524-0.004-0.0040.0000.0000.0000.000
201A243PRO0-0.049-0.01924.7980.0030.0030.0000.0000.0000.000
202A244CYS00.0150.00625.2900.0090.0090.0000.0000.0000.000
203A245ILE0-0.005-0.00420.118-0.003-0.0030.0000.0000.0000.000
204A246THR00.0100.01222.4510.0190.0190.0000.0000.0000.000
205A247THR0-0.005-0.02017.607-0.019-0.0190.0000.0000.0000.000
206A248MET0-0.0060.00320.2360.0150.0150.0000.0000.0000.000
207A249LEU0-0.050-0.01416.976-0.008-0.0080.0000.0000.0000.000
208A250THR0-0.032-0.02416.7090.0450.0450.0000.0000.0000.000
209A251ARG10.8630.95913.518-0.185-0.1850.0000.0000.0000.000
210A252ILE00.0340.0128.149-0.035-0.0350.0000.0000.0000.000
211A253LEU0-0.0060.00212.707-0.054-0.0540.0000.0000.0000.000
212A254ARG10.8690.88710.2060.1220.1220.0000.0000.0000.000
213A255PHE00.0100.01916.0300.0000.0000.0000.0000.0000.000
214A256SER00.0050.00716.999-0.008-0.0080.0000.0000.0000.000