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: G5271

Calculation Name: 2I3F-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2I3F

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-23

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2581016.987551
FMO2-HF: Nuclear repulsion 2498688.71535
FMO2-HF: Total energy -82328.272201
FMO2-MP2: Total energy -82571.462475


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:11:ASP)


Summations of interaction energy for fragment #1(A:11:ASP)
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.
-144.58-139.3527.603-5.664-7.1650.067
Interaction energy analysis for fragmet #1(A:11:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.852 / q_NPA : -0.932
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].
3A13GLY0-0.004-0.0133.258-8.309-6.4680.029-0.798-1.0710.003
4A14ILE00.0130.0103.127-6.585-5.5850.032-0.290-0.7420.000
5A15ILE0-0.0140.0034.919-4.537-4.400-0.001-0.007-0.1290.000
6A16VAL00.004-0.0028.003-3.105-3.1050.0000.0000.0000.000
7A17ILE00.0070.0116.312-2.105-2.1050.0000.0000.0000.000
8A18LEU0-0.011-0.0187.719-2.393-2.3930.0000.0000.0000.000
9A19TRP0-0.011-0.01310.686-2.635-2.6350.0000.0000.0000.000
10A20LYS10.9661.01212.747-18.136-18.1360.0000.0000.0000.000
11A21GLN0-0.068-0.04011.912-0.408-0.4080.0000.0000.0000.000
12A22VAL0-0.056-0.01015.347-0.996-0.9960.0000.0000.0000.000
13A23THR0-0.049-0.02617.684-0.534-0.5340.0000.0000.0000.000
14A24VAL00.0340.02120.514-0.303-0.3030.0000.0000.0000.000
15A25LYS10.9420.96323.710-12.538-12.5380.0000.0000.0000.000
16A26GLU-1-0.884-0.95226.4349.7249.7240.0000.0000.0000.000
17A27ASP-1-0.961-0.99029.7699.8999.8990.0000.0000.0000.000
18A28GLY00.0180.02328.206-0.083-0.0830.0000.0000.0000.000
19A29LYS10.9130.96627.403-10.116-10.1160.0000.0000.0000.000
20A30VAL0-0.020-0.02121.4350.3660.3660.0000.0000.0000.000
21A31PRO00.0220.02020.291-0.174-0.1740.0000.0000.0000.000
22A32LEU00.0260.00020.7790.8720.8720.0000.0000.0000.000
23A33GLU-1-0.865-0.94918.60616.57016.5700.0000.0000.0000.000
24A34PRO0-0.017-0.01416.1081.2621.2620.0000.0000.0000.000
25A35PHE00.0570.02815.6021.4091.4090.0000.0000.0000.000
26A36LEU00.0020.00116.5930.9590.9590.0000.0000.0000.000
27A37THR0-0.036-0.01711.5281.2671.2670.0000.0000.0000.000
28A38ALA00.0160.00511.7862.4322.4320.0000.0000.0000.000
29A39ALA00.009-0.00612.3821.3341.3340.0000.0000.0000.000
30A40LYS10.9440.9819.670-29.332-29.3320.0000.0000.0000.000
31A41GLU-1-0.836-0.9146.44448.30748.3070.0000.0000.0000.000
32A42VAL0-0.0090.0039.2121.7441.7440.0000.0000.0000.000
33A43LEU0-0.058-0.04011.110-1.127-1.1270.0000.0000.0000.000
34A44ARG10.8930.9441.981-101.719-99.5427.544-4.547-5.1730.064
35A45VAL0-0.022-0.0108.881-0.870-0.8700.0000.0000.0000.000
36A46VAL0-0.024-0.01611.676-1.722-1.7220.0000.0000.0000.000
37A47ASP-1-0.899-0.96210.41025.96025.9600.0000.0000.0000.000
38A48ALA0-0.048-0.01710.300-0.952-0.9520.0000.0000.0000.000
39A49PHE0-0.050-0.02612.090-1.591-1.5910.0000.0000.0000.000
40A50GLY00.0140.01715.408-1.009-1.0090.0000.0000.0000.000
41A51SER00.000-0.00916.821-0.278-0.2780.0000.0000.0000.000
42A52GLY00.0240.01319.832-0.584-0.5840.0000.0000.0000.000
43A53PHE00.0230.00716.982-0.617-0.6170.0000.0000.0000.000
44A54ARG10.9600.99019.610-12.567-12.5670.0000.0000.0000.000
45A55ILE00.000-0.00720.9360.2010.2010.0000.0000.0000.000
46A56VAL00.0730.04118.480-0.047-0.0470.0000.0000.0000.000
47A57LYS10.9510.98214.240-20.041-20.0410.0000.0000.0000.000
48A58ASN0-0.034-0.03317.9320.9530.9530.0000.0000.0000.000
49A59ASP-1-0.875-0.91520.54313.23313.2330.0000.0000.0000.000
50A60ILE0-0.014-0.01415.627-0.182-0.1820.0000.0000.0000.000
51A61ALA0-0.006-0.00516.4920.0800.0800.0000.0000.0000.000
52A62GLY0-0.039-0.02417.863-0.208-0.2080.0000.0000.0000.000
53A63ASN00.002-0.01521.354-0.902-0.9020.0000.0000.0000.000
54A64ILE00.0620.03915.492-0.366-0.3660.0000.0000.0000.000
55A65LYS10.9360.97919.643-14.709-14.7090.0000.0000.0000.000
56A66LYS10.8980.93321.122-12.631-12.6310.0000.0000.0000.000
57A67LEU00.0540.04921.942-0.486-0.4860.0000.0000.0000.000
58A68TYR00.0210.00616.568-0.066-0.0660.0000.0000.0000.000
59A69ARG10.8800.94222.699-11.710-11.7100.0000.0000.0000.000
60A70ALA0-0.013-0.01425.815-0.392-0.3920.0000.0000.0000.000
61A71ASN00.0500.03224.529-0.827-0.8270.0000.0000.0000.000
62A72GLN0-0.063-0.02325.307-0.434-0.4340.0000.0000.0000.000
63A73THR0-0.047-0.03127.542-0.113-0.1130.0000.0000.0000.000
64A74VAL0-0.0010.00829.983-0.222-0.2220.0000.0000.0000.000
65A75HIS0-0.038-0.01527.5040.0920.0920.0000.0000.0000.000
66A76ALA00.0020.01927.718-0.062-0.0620.0000.0000.0000.000
67A77GLU-1-0.892-0.94825.85911.96011.9600.0000.0000.0000.000
68A78THR0-0.049-0.03624.8040.5090.5090.0000.0000.0000.000
69A79LEU00.002-0.01022.340-0.231-0.2310.0000.0000.0000.000
70A80GLN00.0490.01426.230-0.074-0.0740.0000.0000.0000.000
71A81GLU-1-0.874-0.92129.35210.23610.2360.0000.0000.0000.000
72A82LEU00.0350.02226.543-0.267-0.2670.0000.0000.0000.000
73A83ILE0-0.034-0.01528.261-0.264-0.2640.0000.0000.0000.000
74A84ILE0-0.054-0.04131.599-0.362-0.3620.0000.0000.0000.000
75A85ALA0-0.0160.00233.200-0.322-0.3220.0000.0000.0000.000
76A86GLU-1-0.798-0.88831.35710.23010.2300.0000.0000.0000.000
77A87ASN0-0.063-0.02535.153-0.180-0.1800.0000.0000.0000.000
78A88SER00.0550.02036.158-0.264-0.2640.0000.0000.0000.000
79A89PRO00.0250.01435.3230.3340.3340.0000.0000.0000.000
80A90ASP-1-0.925-0.95934.5958.8618.8610.0000.0000.0000.000
81A91GLY0-0.042-0.00833.7830.0810.0810.0000.0000.0000.000
82A92LEU0-0.040-0.04129.9280.3280.3280.0000.0000.0000.000
83A93ALA00.008-0.01427.5390.5020.5020.0000.0000.0000.000
84A94THR0-0.004-0.00427.7940.4110.4110.0000.0000.0000.000
85A95VAL00.0140.01329.3520.3000.3000.0000.0000.0000.000
86A96ALA0-0.050-0.02824.7530.3350.3350.0000.0000.0000.000
87A97LEU00.016-0.00223.5990.6410.6410.0000.0000.0000.000
88A98LEU00.0280.03325.3810.3590.3590.0000.0000.0000.000
89A99TRP0-0.010-0.02425.2160.2680.2680.0000.0000.0000.000
90A100LEU0-0.053-0.01318.4070.4780.4780.0000.0000.0000.000
91A101LYS10.8420.91521.494-10.866-10.8660.0000.0000.0000.000
92A102ARG10.8700.91523.400-10.440-10.4400.0000.0000.0000.000
93A103ALA0-0.034-0.02120.2320.1480.1480.0000.0000.0000.000
94A104PHE00.018-0.00816.2700.7390.7390.0000.0000.0000.000
95A105GLN00.0490.02720.0190.1420.1420.0000.0000.0000.000
96A106PHE0-0.059-0.02120.355-0.055-0.0550.0000.0000.0000.000
97A107ILE0-0.017-0.02015.6480.1270.1270.0000.0000.0000.000
98A108ALA00.0540.02618.7350.3930.3930.0000.0000.0000.000
99A109SER0-0.029-0.02819.785-0.316-0.3160.0000.0000.0000.000
100A110PHE0-0.020-0.02716.645-0.258-0.2580.0000.0000.0000.000
101A111LEU00.014-0.00514.4800.0350.0350.0000.0000.0000.000
102A112ARG10.9350.96918.217-12.424-12.4240.0000.0000.0000.000
103A113ARG10.8190.89520.729-12.352-12.3520.0000.0000.0000.000
104A114LEU0-0.033-0.01316.382-0.289-0.2890.0000.0000.0000.000
105A115VAL0-0.026-0.01716.014-0.061-0.0610.0000.0000.0000.000
106A116VAL0-0.0010.01119.286-0.278-0.2780.0000.0000.0000.000
107A117THR0-0.094-0.04322.808-0.802-0.8020.0000.0000.0000.000
108A118ASP-1-0.848-0.91723.50012.44312.4430.0000.0000.0000.000
109A119LYS10.8310.91225.511-11.304-11.3040.0000.0000.0000.000
110A120SER00.0510.02524.0920.7060.7060.0000.0000.0000.000
111A121LEU00.0490.02517.757-0.060-0.0600.0000.0000.0000.000
112A122GLU-1-0.885-0.95122.02811.71911.7190.0000.0000.0000.000
113A123GLN0-0.019-0.01824.608-0.198-0.1980.0000.0000.0000.000
114A124CYS0-0.054-0.01322.384-0.174-0.1740.0000.0000.0000.000
115A125VAL00.0240.00021.677-0.031-0.0310.0000.0000.0000.000
116A126THR0-0.017-0.00623.561-0.307-0.3070.0000.0000.0000.000
117A127GLU-1-0.827-0.90027.08110.78710.7870.0000.0000.0000.000
118A128ALA0-0.0220.00723.566-0.205-0.2050.0000.0000.0000.000
119A129TYR00.008-0.02425.560-0.322-0.3220.0000.0000.0000.000
120A130ASN00.000-0.00926.864-0.336-0.3360.0000.0000.0000.000
121A131CYS0-0.0660.00727.655-0.218-0.2180.0000.0000.0000.000
122A132THR00.041-0.01125.2290.1450.1450.0000.0000.0000.000
123A133LEU00.0440.00323.497-0.327-0.3270.0000.0000.0000.000
124A134ARG10.8720.94727.969-9.862-9.8620.0000.0000.0000.000
125A135PRO0-0.001-0.00230.777-0.217-0.2170.0000.0000.0000.000
126A136CYS0-0.0200.02229.939-0.180-0.1800.0000.0000.0000.000
127A137HIS00.0190.04326.499-0.142-0.1420.0000.0000.0000.000
128A138SER00.0940.04532.064-0.204-0.2040.0000.0000.0000.000
129A139ALA00.0610.00834.1340.2000.2000.0000.0000.0000.000
130A140VAL0-0.020-0.01134.5680.1040.1040.0000.0000.0000.000
131A141ILE00.0500.01329.2370.1830.1830.0000.0000.0000.000
132A142GLN0-0.0130.00430.2120.2470.2470.0000.0000.0000.000
133A143LYS10.9250.96530.976-8.434-8.4340.0000.0000.0000.000
134A144VAL0-0.0170.00127.4730.1420.1420.0000.0000.0000.000
135A145PHE00.0120.01023.3110.3800.3800.0000.0000.0000.000
136A146TRP00.004-0.00226.7810.3970.3970.0000.0000.0000.000
137A147GLY00.008-0.00128.5880.0340.0340.0000.0000.0000.000
138A148GLY00.0120.00324.6720.1890.1890.0000.0000.0000.000
139A149VAL0-0.019-0.01723.7540.4790.4790.0000.0000.0000.000
140A150LYS10.9230.96424.985-10.848-10.8480.0000.0000.0000.000
141A151LEU0-0.069-0.02422.640-0.053-0.0530.0000.0000.0000.000
142A152ALA0-0.018-0.00320.9920.8070.8070.0000.0000.0000.000
143A153PRO0-0.046-0.00416.813-0.310-0.3100.0000.0000.0000.000
144A154SER00.0510.01919.432-0.106-0.1060.0000.0000.0000.000
145A155ARG10.9190.94717.785-13.562-13.5620.0000.0000.0000.000
146A156GLU-1-0.873-0.94116.17916.28616.2860.0000.0000.0000.000
147A157ARG10.8860.94214.839-15.314-15.3140.0000.0000.0000.000
148A158PHE0-0.012-0.01213.6171.5651.5650.0000.0000.0000.000
149A159TYR00.0920.01811.9391.6421.6420.0000.0000.0000.000
150A160ARG10.9580.97210.182-16.791-16.7910.0000.0000.0000.000
151A161LYS10.8450.9489.531-20.157-20.1570.0000.0000.0000.000
152A162LEU0-0.0470.0067.1583.2043.2040.0000.0000.0000.000
153A163HIS00.0520.0064.4156.9617.034-0.001-0.022-0.0500.000
154A164PRO00.0110.0116.303-4.228-4.2280.0000.0000.0000.000
155A165ASP-1-0.850-0.9158.97718.66118.6610.0000.0000.0000.000
156A166LEU00.001-0.03010.5641.0701.0700.0000.0000.0000.000
157A167ASN00.0210.01613.166-0.671-0.6710.0000.0000.0000.000
158A168ILE0-0.0190.0026.802-0.109-0.1090.0000.0000.0000.000
159A169ALA0-0.029-0.0019.1490.8230.8230.0000.0000.0000.000
160A170LYS10.8710.92010.093-16.079-16.0790.0000.0000.0000.000
161A171ALA00.0630.03811.634-0.375-0.3750.0000.0000.0000.000
162A172LYS10.8390.8996.948-27.153-27.1530.0000.0000.0000.000
163A173ILE0-0.017-0.00210.0520.1010.1010.0000.0000.0000.000
164A174GLU-1-0.838-0.91112.40516.10316.1030.0000.0000.0000.000
165A175GLU-1-0.806-0.90611.31521.83621.8360.0000.0000.0000.000
166A176PHE0-0.027-0.01711.068-0.315-0.3150.0000.0000.0000.000
167A177LEU0-0.026-0.00912.968-1.041-1.0410.0000.0000.0000.000
168A178ILE00.0230.03516.250-0.940-0.9400.0000.0000.0000.000
169A179GLU-1-0.905-0.97513.68917.20017.2000.0000.0000.0000.000
170A180LEU0-0.068-0.01916.064-0.409-0.4090.0000.0000.0000.000
171A181HIS10.7890.90317.372-13.836-13.8360.0000.0000.0000.000
172A182ASP-1-0.800-0.89620.87212.62312.6230.0000.0000.0000.000
173A183PRO00.0210.00518.648-0.616-0.6160.0000.0000.0000.000
174A184LEU0-0.0150.00320.720-0.469-0.4690.0000.0000.0000.000
175A185CYS0-0.020-0.01222.476-0.683-0.6830.0000.0000.0000.000
176A186CYS0-0.0410.00925.035-0.654-0.6540.0000.0000.0000.000
177A187ILE00.006-0.00422.460-0.454-0.4540.0000.0000.0000.000
178A188VAL0-0.029-0.02126.025-0.420-0.4200.0000.0000.0000.000
179A189GLN0-0.0120.00628.415-0.370-0.3700.0000.0000.0000.000
180A190PHE00.010-0.00829.473-0.396-0.3960.0000.0000.0000.000
181A191PHE00.015-0.01128.297-0.240-0.2400.0000.0000.0000.000
182A192PHE0-0.012-0.00131.960-0.203-0.2030.0000.0000.0000.000
183A193GLN0-0.028-0.00434.071-0.175-0.1750.0000.0000.0000.000
184A194ARG10.8760.94233.688-9.250-9.2500.0000.0000.0000.000
185A195GLU-1-0.953-0.96336.5347.7677.7670.0000.0000.0000.000
186A196LEU0-0.029-0.02032.505-0.016-0.0160.0000.0000.0000.000
187A197GLU-1-0.758-0.83630.33510.83410.8340.0000.0000.0000.000
188A198ASP-1-0.845-0.92533.6978.8868.8860.0000.0000.0000.000
189A199GLN0-0.068-0.04333.2820.0890.0890.0000.0000.0000.000
190A200CYS0-0.083-0.01828.4630.2280.2280.0000.0000.0000.000
191A201TRP00.0070.00331.0540.1650.1650.0000.0000.0000.000
192A202GLY00.0090.00127.8880.2060.2060.0000.0000.0000.000
193A203ASP-1-0.816-0.87925.56911.90211.9020.0000.0000.0000.000
194A204GLU-1-0.788-0.88127.55510.09910.0990.0000.0000.0000.000
195A205VAL00.0070.00726.5710.0220.0220.0000.0000.0000.000
196A206TYR0-0.061-0.05319.169-0.023-0.0230.0000.0000.0000.000
197A207GLN0-0.023-0.03125.0930.6550.6550.0000.0000.0000.000
198A208ARG10.8060.90827.048-10.305-10.3050.0000.0000.0000.000
199A209LYS10.9940.98427.365-9.745-9.7450.0000.0000.0000.000
200A210ASP-1-0.852-0.92425.71112.10312.1030.0000.0000.0000.000
201A211SER00.0340.01621.267-0.023-0.0230.0000.0000.0000.000
202A212SER00.0280.00521.5330.8740.8740.0000.0000.0000.000
203A213GLU-1-0.946-0.97422.96710.09810.0980.0000.0000.0000.000
204A214TRP0-0.040-0.04718.041-0.269-0.2690.0000.0000.0000.000
205A215LEU0-0.0160.00119.199-0.038-0.0380.0000.0000.0000.000
206A216LYS10.9020.97423.243-11.631-11.6310.0000.0000.0000.000