Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: R8GK8

Calculation Name: 2IT2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2IT2

Chain ID: A

ChEMBL ID:

UniProt ID: O58796

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 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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2170301.312449
FMO2-HF: Nuclear repulsion 2091488.073466
FMO2-HF: Total energy -78813.238983
FMO2-MP2: Total energy -79041.584624


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-3.847-0.7592.656-1.575-4.1660.007
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.050 / q_NPA : 0.020
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].
3A3LEU00.0210.0062.450-2.883-0.4072.656-1.412-3.7200.007
4A4TYR00.0800.0285.162-0.0420.039-0.001-0.005-0.0740.000
5A5MET00.0100.0038.482-0.082-0.0820.0000.0000.0000.000
6A6ARG10.9290.9575.753-0.486-0.4860.0000.0000.0000.000
7A7PHE0-0.0010.0096.799-0.244-0.2440.0000.0000.0000.000
8A8THR00.0210.0238.821-0.005-0.0050.0000.0000.0000.000
9A9GLU-1-0.839-0.9134.882-0.415-0.339-0.001-0.003-0.0710.000
10A10ASN00.006-0.0048.4790.0530.0530.0000.0000.0000.000
11A11PHE00.0630.03010.9440.0020.0020.0000.0000.0000.000
12A12GLU-1-0.834-0.90013.1730.0730.0730.0000.0000.0000.000
13A13ARG10.9020.94414.674-0.048-0.0480.0000.0000.0000.000
14A14ALA00.0470.02313.926-0.004-0.0040.0000.0000.0000.000
15A15LYS10.8530.92616.018-0.108-0.1080.0000.0000.0000.000
16A16LYS10.8320.90418.793-0.074-0.0740.0000.0000.0000.000
17A17GLU-1-0.814-0.90617.6290.0550.0550.0000.0000.0000.000
18A18ALA0-0.025-0.00219.602-0.003-0.0030.0000.0000.0000.000
19A19LEU0-0.003-0.01221.419-0.003-0.0030.0000.0000.0000.000
20A20MET0-0.0050.00023.982-0.005-0.0050.0000.0000.0000.000
21A21SER0-0.041-0.02523.051-0.003-0.0030.0000.0000.0000.000
22A22LEU0-0.024-0.01225.585-0.002-0.0020.0000.0000.0000.000
23A23GLU-1-0.898-0.94827.3530.0480.0480.0000.0000.0000.000
24A24ILE0-0.079-0.03427.866-0.005-0.0050.0000.0000.0000.000
25A25ALA00.0300.01729.042-0.003-0.0030.0000.0000.0000.000
26A26LEU0-0.035-0.03631.031-0.002-0.0020.0000.0000.0000.000
27A27ARG10.9550.99532.717-0.042-0.0420.0000.0000.0000.000
28A28LYS10.8000.89232.484-0.050-0.0500.0000.0000.0000.000
29A29GLY00.0230.02335.825-0.001-0.0010.0000.0000.0000.000
30A30GLU-1-0.881-0.93432.2130.0530.0530.0000.0000.0000.000
31A31VAL0-0.059-0.02930.2640.0050.0050.0000.0000.0000.000
32A32ASP-1-0.741-0.86131.5950.0690.0690.0000.0000.0000.000
33A33GLU-1-0.840-0.93933.7180.0530.0530.0000.0000.0000.000
34A34ASP-1-0.896-0.93435.1840.0580.0580.0000.0000.0000.000
35A35ILE0-0.001-0.01428.6590.0020.0020.0000.0000.0000.000
36A36ILE0-0.0080.01831.0000.0040.0040.0000.0000.0000.000
37A37PRO0-0.005-0.01031.6690.0020.0020.0000.0000.0000.000
38A38LEU00.0280.00828.1790.0020.0020.0000.0000.0000.000
39A39LEU00.0280.01726.0120.0050.0050.0000.0000.0000.000
40A40LYS10.9700.99126.970-0.053-0.0530.0000.0000.0000.000
41A41LYS10.8650.94528.409-0.067-0.0670.0000.0000.0000.000
42A42ILE00.0290.02222.7700.0030.0030.0000.0000.0000.000
43A43ASN0-0.028-0.04523.1810.0090.0090.0000.0000.0000.000
44A44SER0-0.051-0.02024.356-0.001-0.0010.0000.0000.0000.000
45A45ILE0-0.0150.00622.2760.0010.0010.0000.0000.0000.000
46A46GLU-1-0.825-0.91120.1000.1350.1350.0000.0000.0000.000
47A47ASN0-0.067-0.06017.5050.0030.0030.0000.0000.0000.000
48A48TYR0-0.017-0.03317.1380.0090.0090.0000.0000.0000.000
49A49PHE00.0360.02214.865-0.007-0.0070.0000.0000.0000.000
50A50THR00.0310.03719.7390.0070.0070.0000.0000.0000.000
51A51THR0-0.022-0.02217.720-0.001-0.0010.0000.0000.0000.000
52A52SER00.0260.01221.015-0.010-0.0100.0000.0000.0000.000
53A53SER0-0.039-0.01622.8780.0090.0090.0000.0000.0000.000
54A54CYS0-0.043-0.02225.474-0.003-0.0030.0000.0000.0000.000
55A55SER0-0.041-0.02829.0500.0020.0020.0000.0000.0000.000
56A56GLY00.0270.00932.1310.0020.0020.0000.0000.0000.000
57A57ARG10.9060.92630.534-0.077-0.0770.0000.0000.0000.000
58A58ILE00.0410.02035.6440.0020.0020.0000.0000.0000.000
59A59SER0-0.077-0.04436.8000.0000.0000.0000.0000.0000.000
60A60VAL00.0630.04338.9720.0000.0000.0000.0000.0000.000
61A61MET0-0.044-0.01634.8720.0000.0000.0000.0000.0000.000
62A62GLU-1-0.669-0.81639.5510.0380.0380.0000.0000.0000.000
63A63MET0-0.010-0.01035.5160.0030.0030.0000.0000.0000.000
64A64PRO00.0350.02936.747-0.002-0.0020.0000.0000.0000.000
65A72ALA00.0040.00233.8580.0010.0010.0000.0000.0000.000
66A73LYS10.8260.90935.829-0.039-0.0390.0000.0000.0000.000
67A74TRP00.000-0.01332.1920.0000.0000.0000.0000.0000.000
68A75LEU0-0.048-0.01238.584-0.002-0.0020.0000.0000.0000.000
69A76GLY00.0200.00840.815-0.002-0.0020.0000.0000.0000.000
70A77LYN0-0.0200.00634.2100.0050.0050.0000.0000.0000.000
71A78TRP00.0110.00938.832-0.001-0.0010.0000.0000.0000.000
72A79HIS00.0070.01036.1030.0020.0020.0000.0000.0000.000
73A80ARG10.8010.85737.687-0.040-0.0400.0000.0000.0000.000
74A81GLU-1-0.854-0.92140.7400.0440.0440.0000.0000.0000.000
75A82VAL0-0.028-0.01142.591-0.001-0.0010.0000.0000.0000.000
76A83SER00.003-0.01245.302-0.001-0.0010.0000.0000.0000.000
77A84LEU00.0470.00748.3570.0010.0010.0000.0000.0000.000
78A85TYR00.0650.01550.3630.0000.0000.0000.0000.0000.000
79A86GLU-1-0.732-0.79846.1220.0380.0380.0000.0000.0000.000
80A87VAL00.005-0.00244.9470.0010.0010.0000.0000.0000.000
81A88LEU00.0230.01047.1600.0000.0000.0000.0000.0000.000
82A89GLU-1-0.834-0.90449.5690.0280.0280.0000.0000.0000.000
83A90ALA0-0.021-0.00444.5430.0000.0000.0000.0000.0000.000
84A91ILE00.0460.01246.5410.0000.0000.0000.0000.0000.000
85A92LYS10.8860.95147.729-0.028-0.0280.0000.0000.0000.000
86A93LYS10.7820.88046.419-0.033-0.0330.0000.0000.0000.000
87A94HIS0-0.086-0.03644.8380.0000.0000.0000.0000.0000.000
88A95ARG10.8780.93846.164-0.030-0.0300.0000.0000.0000.000
89A96SER0-0.003-0.00144.355-0.001-0.0010.0000.0000.0000.000
90A97GLY00.0350.02442.2070.0020.0020.0000.0000.0000.000
91A98GLN00.0510.03139.6460.0010.0010.0000.0000.0000.000
92A99LEU00.0010.00541.3050.0020.0020.0000.0000.0000.000
93A100TRP0-0.006-0.01939.0980.0000.0000.0000.0000.0000.000
94A101PHE00.0220.01741.1110.0000.0000.0000.0000.0000.000
95A102LEU0-0.067-0.03734.7370.0020.0020.0000.0000.0000.000
96A103VAL00.0500.03136.860-0.001-0.0010.0000.0000.0000.000
97A104ARG10.7700.84331.052-0.073-0.0730.0000.0000.0000.000
98A105SER00.0510.01629.964-0.003-0.0030.0000.0000.0000.000
99A106PRO0-0.0470.00530.1300.0020.0020.0000.0000.0000.000
100A107ILE0-0.053-0.03223.9250.0050.0050.0000.0000.0000.000
101A108LEU00.0540.01724.208-0.003-0.0030.0000.0000.0000.000
102A109HIS0-0.038-0.01618.9310.0130.0130.0000.0000.0000.000
103A110VAL0-0.018-0.02619.100-0.011-0.0110.0000.0000.0000.000
104A111GLY00.0140.02815.3050.0170.0170.0000.0000.0000.000
105A112ALA00.009-0.02014.093-0.012-0.0120.0000.0000.0000.000
106A113LYS10.8390.91512.702-0.158-0.1580.0000.0000.0000.000
107A114THR0-0.050-0.04811.1710.0190.0190.0000.0000.0000.000
108A115LEU00.0470.01111.326-0.015-0.0150.0000.0000.0000.000
109A116GLU-1-0.808-0.88913.0090.1420.1420.0000.0000.0000.000
110A117ASP-1-0.752-0.82815.7340.1610.1610.0000.0000.0000.000
111A118ALA00.0270.02614.785-0.010-0.0100.0000.0000.0000.000
112A119VAL00.011-0.00416.302-0.006-0.0060.0000.0000.0000.000
113A120LYS10.8620.93618.739-0.140-0.1400.0000.0000.0000.000
114A121LEU00.0060.01719.889-0.009-0.0090.0000.0000.0000.000
115A122VAL0-0.0010.00019.128-0.007-0.0070.0000.0000.0000.000
116A123ASN00.0260.00322.064-0.005-0.0050.0000.0000.0000.000
117A124LEU0-0.0030.01424.539-0.007-0.0070.0000.0000.0000.000
118A125ALA00.0600.03124.984-0.007-0.0070.0000.0000.0000.000
119A126VAL00.0250.01425.164-0.007-0.0070.0000.0000.0000.000
120A127SER0-0.090-0.05127.764-0.008-0.0080.0000.0000.0000.000
121A128CYS0-0.024-0.00529.972-0.006-0.0060.0000.0000.0000.000
122A129GLY00.0140.00531.342-0.004-0.0040.0000.0000.0000.000
123A130PHE0-0.023-0.00227.742-0.001-0.0010.0000.0000.0000.000
124A131LYS10.9270.94827.308-0.073-0.0730.0000.0000.0000.000
125A132TYR0-0.0130.02225.8020.0030.0030.0000.0000.0000.000
126A133SER00.016-0.00923.2250.0090.0090.0000.0000.0000.000
127A134ASN0-0.108-0.05819.1110.0150.0150.0000.0000.0000.000
128A135ILE00.0320.01813.354-0.002-0.0020.0000.0000.0000.000
129A136LYS10.8870.94115.768-0.195-0.1950.0000.0000.0000.000
130A137SER00.014-0.00411.2190.0650.0650.0000.0000.0000.000
131A138ILE0-0.015-0.01011.497-0.066-0.0660.0000.0000.0000.000
132A139SER00.0620.01710.7390.1390.1390.0000.0000.0000.000
133A140ASN0-0.042-0.00410.8410.0820.0820.0000.0000.0000.000
134A141LYS10.8280.8865.182-0.163-0.1630.0000.0000.0000.000
135A142LYS10.8460.9383.7200.8171.2720.002-0.155-0.3010.000
136A143LEU00.0290.0098.267-0.103-0.1030.0000.0000.0000.000
137A144ILE0-0.0040.01410.929-0.056-0.0560.0000.0000.0000.000
138A145VAL00.0020.01314.3750.0090.0090.0000.0000.0000.000
139A146GLU-1-0.754-0.84517.7050.1670.1670.0000.0000.0000.000
140A147ILE00.0140.00620.647-0.003-0.0030.0000.0000.0000.000
141A148ARG10.8770.91922.976-0.141-0.1410.0000.0000.0000.000
142A149SER0-0.036-0.04826.9080.0000.0000.0000.0000.0000.000
143A150THR0-0.017-0.02529.9760.0050.0050.0000.0000.0000.000
144A151GLU-1-0.768-0.84232.2220.0710.0710.0000.0000.0000.000
145A152ARG10.7910.86930.376-0.085-0.0850.0000.0000.0000.000
146A153MET0-0.003-0.00134.755-0.003-0.0030.0000.0000.0000.000
147A154ASP-1-0.719-0.80834.8990.0760.0760.0000.0000.0000.000
148A155VAL00.0310.00538.164-0.001-0.0010.0000.0000.0000.000
149A156LEU00.0180.02441.9100.0000.0000.0000.0000.0000.000
150A157LEU0-0.029-0.03543.417-0.002-0.0020.0000.0000.0000.000
151A158GLY00.0640.03045.615-0.002-0.0020.0000.0000.0000.000
152A159GLU-1-0.938-0.97744.5820.0410.0410.0000.0000.0000.000
153A160ASN0-0.066-0.03245.839-0.001-0.0010.0000.0000.0000.000
154A161GLY0-0.0050.00247.867-0.002-0.0020.0000.0000.0000.000
155A162GLU-1-0.937-0.94849.9310.0260.0260.0000.0000.0000.000
156A163ILE0-0.059-0.03249.1070.0020.0020.0000.0000.0000.000
157A164PHE00.025-0.00247.412-0.001-0.0010.0000.0000.0000.000
158A165VAL0-0.043-0.00649.171-0.001-0.0010.0000.0000.0000.000
159A166GLY00.0610.02652.148-0.001-0.0010.0000.0000.0000.000
160A167GLU-1-0.896-0.97253.2860.0290.0290.0000.0000.0000.000
161A168GLU-1-0.845-0.91153.8740.0280.0280.0000.0000.0000.000
162A169TYR0-0.004-0.00947.1360.0010.0010.0000.0000.0000.000
163A170LEU00.0280.00647.2990.0020.0020.0000.0000.0000.000
164A171ASN00.0260.01149.2250.0020.0020.0000.0000.0000.000
165A172LYS10.9010.94650.328-0.030-0.0300.0000.0000.0000.000
166A173ILE0-0.020-0.00444.6260.0020.0020.0000.0000.0000.000
167A174VAL0-0.009-0.01445.4450.0020.0020.0000.0000.0000.000
168A175GLU-1-0.930-0.95245.9530.0360.0360.0000.0000.0000.000
169A176ILE00.0270.01443.3960.0020.0020.0000.0000.0000.000
170A177ALA0-0.014-0.01441.7820.0030.0030.0000.0000.0000.000
171A178ASN00.007-0.01941.5520.0040.0040.0000.0000.0000.000
172A179ASP-1-0.786-0.86843.1760.0430.0430.0000.0000.0000.000
173A180GLN0-0.115-0.06438.5240.0030.0030.0000.0000.0000.000
174A181MET0-0.027-0.00237.4700.0040.0040.0000.0000.0000.000
175A182ARG10.8150.89539.074-0.041-0.0410.0000.0000.0000.000
176A183ARG10.9590.98338.820-0.054-0.0540.0000.0000.0000.000
177A184PHE0-0.044-0.02434.2800.0030.0030.0000.0000.0000.000
178A185LYS10.9250.95435.433-0.049-0.0490.0000.0000.0000.000
179A186GLU-1-0.851-0.90137.2700.0560.0560.0000.0000.0000.000
180A187LYS10.7810.88633.327-0.072-0.0720.0000.0000.0000.000
181A188LEU0-0.0040.00030.9200.0040.0040.0000.0000.0000.000
182A189LYS10.8930.94733.350-0.056-0.0560.0000.0000.0000.000
183A190ARG10.8140.89634.039-0.063-0.0630.0000.0000.0000.000
184A191LEU00.0190.00827.4260.0010.0010.0000.0000.0000.000
185A192GLU-1-0.823-0.90930.6980.0640.0640.0000.0000.0000.000
186A193SER0-0.063-0.03231.995-0.001-0.0010.0000.0000.0000.000
187A194LYS10.9500.96431.295-0.063-0.0630.0000.0000.0000.000
188A195ILE00.0060.00725.2660.0030.0030.0000.0000.0000.000
189A196ASN00.0160.00727.3970.0050.0050.0000.0000.0000.000
190A197ALA0-0.019-0.00228.7370.0000.0000.0000.0000.0000.000
191A198LEU0-0.036-0.01322.7840.0030.0030.0000.0000.0000.000
192A199ASN0-0.038-0.01923.9480.0100.0100.0000.0000.0000.000
193A200ARG10.8690.93518.839-0.145-0.1450.0000.0000.0000.000