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

tag_button

FMODB ID: ZV5GN

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 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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2170027.057969
FMO2-HF: Nuclear repulsion 2091215.329796
FMO2-HF: Total energy -78811.728173
FMO2-MP2: Total energy -79040.172932


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.
-4.083-0.6672.514-1.668-4.260.008
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 : 0.056 / q_NPA : 0.023
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].
3A3LEU00.0100.0022.468-3.100-0.4982.508-1.384-3.7250.007
4A4TYR00.0880.0345.110-0.0260.060-0.001-0.006-0.0780.000
5A5MET00.0070.0018.431-0.079-0.0790.0000.0000.0000.000
6A6ARG10.9180.9545.856-0.523-0.5230.0000.0000.0000.000
7A7PHE0-0.0120.0016.943-0.198-0.1980.0000.0000.0000.000
8A8THR00.0290.0349.0100.0060.0060.0000.0000.0000.000
9A9GLU-1-0.838-0.9155.5750.2710.2710.0000.0000.0000.000
10A10ASN0-0.021-0.0188.6370.0140.0140.0000.0000.0000.000
11A11PHE00.0670.03411.171-0.004-0.0040.0000.0000.0000.000
12A12GLU-1-0.932-0.96013.3750.1080.1080.0000.0000.0000.000
13A13ARG10.9550.97514.908-0.079-0.0790.0000.0000.0000.000
14A14ALA00.0750.03714.127-0.007-0.0070.0000.0000.0000.000
15A15LYS10.8710.94416.199-0.129-0.1290.0000.0000.0000.000
16A16LYS10.9310.96119.018-0.091-0.0910.0000.0000.0000.000
17A17GLU-1-0.920-0.96017.5190.1040.1040.0000.0000.0000.000
18A18ALA0-0.016-0.00519.898-0.005-0.0050.0000.0000.0000.000
19A19LEU0-0.014-0.01621.632-0.005-0.0050.0000.0000.0000.000
20A20MET0-0.010-0.00224.164-0.006-0.0060.0000.0000.0000.000
21A21SER0-0.026-0.01223.345-0.005-0.0050.0000.0000.0000.000
22A22LEU0-0.020-0.01025.803-0.003-0.0030.0000.0000.0000.000
23A23GLU-1-0.904-0.95327.5800.0580.0580.0000.0000.0000.000
24A24ILE0-0.074-0.02728.116-0.006-0.0060.0000.0000.0000.000
25A25ALA00.0200.01329.284-0.003-0.0030.0000.0000.0000.000
26A26LEU0-0.037-0.03731.280-0.003-0.0030.0000.0000.0000.000
27A27ARG10.9731.00033.276-0.053-0.0530.0000.0000.0000.000
28A28LYS10.8660.93934.219-0.055-0.0550.0000.0000.0000.000
29A29GLY00.0220.02336.066-0.001-0.0010.0000.0000.0000.000
30A30GLU-1-0.962-0.98732.5530.0650.0650.0000.0000.0000.000
31A31VAL0-0.070-0.03830.5460.0050.0050.0000.0000.0000.000
32A32ASP-1-0.762-0.86931.9750.0750.0750.0000.0000.0000.000
33A33GLU-1-0.822-0.94433.9690.0600.0600.0000.0000.0000.000
34A34ASP-1-0.940-0.97835.4860.0640.0640.0000.0000.0000.000
35A35ILE00.009-0.00529.1050.0020.0020.0000.0000.0000.000
36A36ILE0-0.0120.02231.2250.0040.0040.0000.0000.0000.000
37A37PRO0-0.007-0.00931.8770.0030.0030.0000.0000.0000.000
38A38LEU00.0460.02228.3510.0020.0020.0000.0000.0000.000
39A39LEU00.0270.00926.2050.0050.0050.0000.0000.0000.000
40A40LYS10.9590.98727.170-0.060-0.0600.0000.0000.0000.000
41A41LYS10.8980.97528.590-0.079-0.0790.0000.0000.0000.000
42A42ILE00.0180.02122.9260.0030.0030.0000.0000.0000.000
43A43ASN0-0.016-0.03323.3640.0120.0120.0000.0000.0000.000
44A44SER0-0.070-0.04024.5270.0000.0000.0000.0000.0000.000
45A45ILE0-0.0150.00022.4070.0000.0000.0000.0000.0000.000
46A46GLU-1-0.917-0.96619.7790.1390.1390.0000.0000.0000.000
47A47ASN0-0.083-0.06117.5410.0090.0090.0000.0000.0000.000
48A48TYR0-0.031-0.03917.2720.0100.0100.0000.0000.0000.000
49A49PHE00.0280.00915.227-0.007-0.0070.0000.0000.0000.000
50A50THR00.0350.03919.9400.0070.0070.0000.0000.0000.000
51A51THR0-0.005-0.01517.942-0.007-0.0070.0000.0000.0000.000
52A52SER00.0250.00421.277-0.011-0.0110.0000.0000.0000.000
53A53SER0-0.028-0.00523.1570.0090.0090.0000.0000.0000.000
54A54CYS0-0.034-0.00725.745-0.003-0.0030.0000.0000.0000.000
55A55SER0-0.022-0.02429.3260.0020.0020.0000.0000.0000.000
56A56GLY00.0080.00132.4010.0020.0020.0000.0000.0000.000
57A57ARG10.9180.93831.821-0.081-0.0810.0000.0000.0000.000
58A58ILE00.0240.01335.9350.0020.0020.0000.0000.0000.000
59A59SER0-0.093-0.05037.2330.0010.0010.0000.0000.0000.000
60A60VAL00.0760.04839.2780.0000.0000.0000.0000.0000.000
61A61MET0-0.045-0.01935.0750.0000.0000.0000.0000.0000.000
62A62GLU-1-0.716-0.85239.8050.0420.0420.0000.0000.0000.000
63A63MET0-0.017-0.01435.5500.0030.0030.0000.0000.0000.000
64A64PRO00.0340.02737.104-0.002-0.0020.0000.0000.0000.000
65A72ALA00.0120.00834.0980.0010.0010.0000.0000.0000.000
66A73LYS10.8920.95436.078-0.043-0.0430.0000.0000.0000.000
67A74TRP00.001-0.01232.4780.0000.0000.0000.0000.0000.000
68A75LEU0-0.058-0.02238.901-0.002-0.0020.0000.0000.0000.000
69A76GLY00.0110.00541.134-0.003-0.0030.0000.0000.0000.000
70A77LYN0-0.026-0.00234.8980.0050.0050.0000.0000.0000.000
71A78TRP00.0430.02639.153-0.001-0.0010.0000.0000.0000.000
72A79HIS00.0250.01736.3590.0020.0020.0000.0000.0000.000
73A80ARG10.8140.89037.971-0.045-0.0450.0000.0000.0000.000
74A81GLU-1-0.877-0.94141.0180.0460.0460.0000.0000.0000.000
75A82VAL0-0.037-0.01642.927-0.001-0.0010.0000.0000.0000.000
76A83SER0-0.014-0.01545.591-0.001-0.0010.0000.0000.0000.000
77A84LEU00.0610.01048.6540.0010.0010.0000.0000.0000.000
78A85TYR00.0720.01550.6650.0010.0010.0000.0000.0000.000
79A86GLU-1-0.746-0.83546.5260.0420.0420.0000.0000.0000.000
80A87VAL0-0.001-0.00445.3160.0010.0010.0000.0000.0000.000
81A88LEU00.0280.00647.4660.0000.0000.0000.0000.0000.000
82A89GLU-1-0.877-0.94549.7610.0310.0310.0000.0000.0000.000
83A90ALA0-0.039-0.01844.8570.0000.0000.0000.0000.0000.000
84A91ILE00.0470.01446.8550.0000.0000.0000.0000.0000.000
85A92LYS10.8870.96248.043-0.030-0.0300.0000.0000.0000.000
86A93LYS10.8390.92046.619-0.038-0.0380.0000.0000.0000.000
87A94HIS0-0.076-0.02945.1560.0000.0000.0000.0000.0000.000
88A95ARG10.8820.94746.424-0.033-0.0330.0000.0000.0000.000
89A96SER00.0070.00244.478-0.001-0.0010.0000.0000.0000.000
90A97GLY00.0320.02642.4490.0020.0020.0000.0000.0000.000
91A98GLN00.0770.04239.6180.0010.0010.0000.0000.0000.000
92A99LEU00.0100.01041.5440.0030.0030.0000.0000.0000.000
93A100TRP0-0.007-0.01939.3160.0000.0000.0000.0000.0000.000
94A101PHE00.0210.01541.3540.0000.0000.0000.0000.0000.000
95A102LEU0-0.087-0.04734.9590.0020.0020.0000.0000.0000.000
96A103VAL00.0510.03636.937-0.001-0.0010.0000.0000.0000.000
97A104ARG10.7850.87831.033-0.079-0.0790.0000.0000.0000.000
98A105SER00.0470.01330.384-0.003-0.0030.0000.0000.0000.000
99A106PRO0-0.0440.00930.4040.0030.0030.0000.0000.0000.000
100A107ILE0-0.047-0.02224.2110.0030.0030.0000.0000.0000.000
101A108LEU00.0700.02124.411-0.002-0.0020.0000.0000.0000.000
102A109HIS0-0.034-0.00719.1700.0170.0170.0000.0000.0000.000
103A110VAL0-0.008-0.01919.210-0.010-0.0100.0000.0000.0000.000
104A111GLY00.0050.02315.5120.0180.0180.0000.0000.0000.000
105A112ALA00.015-0.02214.274-0.017-0.0170.0000.0000.0000.000
106A113LYS10.9450.98512.824-0.173-0.1730.0000.0000.0000.000
107A114THR0-0.043-0.02411.2610.0200.0200.0000.0000.0000.000
108A115LEU00.0440.00911.373-0.014-0.0140.0000.0000.0000.000
109A116GLU-1-0.917-0.94713.0430.1520.1520.0000.0000.0000.000
110A117ASP-1-0.785-0.89115.7850.1710.1710.0000.0000.0000.000
111A118ALA00.0200.01714.931-0.011-0.0110.0000.0000.0000.000
112A119VAL00.011-0.00316.345-0.007-0.0070.0000.0000.0000.000
113A120LYS10.9390.97418.783-0.139-0.1390.0000.0000.0000.000
114A121LEU00.0100.01920.255-0.010-0.0100.0000.0000.0000.000
115A122VAL00.0040.00319.148-0.007-0.0070.0000.0000.0000.000
116A123ASN00.0310.00522.116-0.007-0.0070.0000.0000.0000.000
117A124LEU0-0.0020.01824.572-0.008-0.0080.0000.0000.0000.000
118A125ALA00.0600.03525.084-0.007-0.0070.0000.0000.0000.000
119A126VAL00.0270.01725.181-0.007-0.0070.0000.0000.0000.000
120A127SER0-0.087-0.05527.801-0.008-0.0080.0000.0000.0000.000
121A128CYS0-0.0100.00230.027-0.007-0.0070.0000.0000.0000.000
122A129GLY0-0.020-0.00631.378-0.004-0.0040.0000.0000.0000.000
123A130PHE0-0.0100.00727.784-0.001-0.0010.0000.0000.0000.000
124A131LYS10.9200.94227.348-0.074-0.0740.0000.0000.0000.000
125A132TYR0-0.0130.02425.6010.0020.0020.0000.0000.0000.000
126A133SER00.008-0.00523.3350.0100.0100.0000.0000.0000.000
127A134ASN0-0.110-0.05719.2970.0140.0140.0000.0000.0000.000
128A135ILE00.0380.02013.3760.0000.0000.0000.0000.0000.000
129A136LYS10.9320.98215.829-0.214-0.2140.0000.0000.0000.000
130A137SER00.002-0.01011.5740.0760.0760.0000.0000.0000.000
131A138ILE0-0.024-0.01111.391-0.070-0.0700.0000.0000.0000.000
132A139SER00.0650.01611.0420.1370.1370.0000.0000.0000.000
133A140ASN0-0.050-0.00911.1730.0940.0940.0000.0000.0000.000
134A141LYS10.8470.8955.617-0.551-0.5510.0000.0000.0000.000
135A142LYS10.8230.9273.4600.5511.2790.007-0.278-0.4570.001
136A143LEU00.0630.0268.041-0.152-0.1520.0000.0000.0000.000
137A144ILE00.0070.01911.183-0.045-0.0450.0000.0000.0000.000
138A145VAL00.0040.01214.6180.0040.0040.0000.0000.0000.000
139A146GLU-1-0.864-0.93417.8620.1700.1700.0000.0000.0000.000
140A147ILE00.0030.00120.879-0.006-0.0060.0000.0000.0000.000
141A148ARG10.9800.96524.332-0.133-0.1330.0000.0000.0000.000
142A149SER0-0.066-0.06027.0350.0000.0000.0000.0000.0000.000
143A150THR0-0.028-0.03830.0270.0040.0040.0000.0000.0000.000
144A151GLU-1-0.804-0.84832.2690.0740.0740.0000.0000.0000.000
145A152ARG10.7800.88330.259-0.088-0.0880.0000.0000.0000.000
146A153MET0-0.008-0.00334.818-0.003-0.0030.0000.0000.0000.000
147A154ASP-1-0.717-0.85935.1650.0780.0780.0000.0000.0000.000
148A155VAL00.0300.00338.315-0.001-0.0010.0000.0000.0000.000
149A156LEU00.0190.02142.0760.0000.0000.0000.0000.0000.000
150A157LEU0-0.034-0.03743.627-0.002-0.0020.0000.0000.0000.000
151A158GLY00.0700.02545.848-0.002-0.0020.0000.0000.0000.000
152A159GLU-1-0.955-0.97945.5640.0420.0420.0000.0000.0000.000
153A160ASN0-0.086-0.04546.338-0.001-0.0010.0000.0000.0000.000
154A161GLY0-0.0040.00048.107-0.002-0.0020.0000.0000.0000.000
155A162GLU-1-0.957-0.95850.1730.0280.0280.0000.0000.0000.000
156A163ILE0-0.065-0.03649.2900.0020.0020.0000.0000.0000.000
157A164PHE00.0500.02047.640-0.001-0.0010.0000.0000.0000.000
158A165VAL0-0.051-0.01049.381-0.001-0.0010.0000.0000.0000.000
159A166GLY00.0590.02452.377-0.001-0.0010.0000.0000.0000.000
160A167GLU-1-0.918-0.97753.5130.0310.0310.0000.0000.0000.000
161A168GLU-1-0.858-0.92454.1450.0300.0300.0000.0000.0000.000
162A169TYR0-0.017-0.01947.3700.0010.0010.0000.0000.0000.000
163A170LEU00.0370.00647.7660.0020.0020.0000.0000.0000.000
164A171ASN00.0240.01049.4990.0020.0020.0000.0000.0000.000
165A172LYS10.9010.95950.615-0.031-0.0310.0000.0000.0000.000
166A173ILE0-0.0130.00444.8440.0020.0020.0000.0000.0000.000
167A174VAL0-0.015-0.01745.7050.0020.0020.0000.0000.0000.000
168A175GLU-1-0.940-0.95746.2360.0380.0380.0000.0000.0000.000
169A176ILE00.0370.02443.3730.0020.0020.0000.0000.0000.000
170A177ALA0-0.021-0.02842.0240.0030.0030.0000.0000.0000.000
171A178ASN00.013-0.01041.8270.0050.0050.0000.0000.0000.000
172A179ASP-1-0.812-0.88643.4410.0450.0450.0000.0000.0000.000
173A180GLN0-0.088-0.05038.7670.0040.0040.0000.0000.0000.000
174A181MET0-0.026-0.00437.7550.0040.0040.0000.0000.0000.000
175A182ARG10.8700.93339.379-0.043-0.0430.0000.0000.0000.000
176A183ARG10.9510.98338.864-0.056-0.0560.0000.0000.0000.000
177A184PHE0-0.050-0.02834.4380.0030.0030.0000.0000.0000.000
178A185LYS10.9580.98735.669-0.052-0.0520.0000.0000.0000.000
179A186GLU-1-0.947-0.96537.4940.0560.0560.0000.0000.0000.000
180A187LYS10.7890.88833.479-0.074-0.0740.0000.0000.0000.000
181A188LEU00.0000.00631.2650.0040.0040.0000.0000.0000.000
182A189LYS10.9590.98633.518-0.056-0.0560.0000.0000.0000.000
183A190ARG10.9160.96034.414-0.068-0.0680.0000.0000.0000.000
184A191LEU00.003-0.00527.5740.0010.0010.0000.0000.0000.000
185A192GLU-1-0.936-0.97130.8350.0700.0700.0000.0000.0000.000
186A193SER0-0.014-0.01032.148-0.001-0.0010.0000.0000.0000.000
187A194LYS10.9230.94931.256-0.067-0.0670.0000.0000.0000.000
188A195ILE00.0460.02125.9060.0020.0020.0000.0000.0000.000
189A196ASN00.007-0.02227.5050.0070.0070.0000.0000.0000.000
190A197ALA0-0.0210.01828.7540.0000.0000.0000.0000.0000.000
191A198LEU0-0.034-0.01122.8420.0020.0020.0000.0000.0000.000
192A199ASN0-0.030-0.01224.0120.0120.0120.0000.0000.0000.000
193A200ARG10.9470.99517.799-0.160-0.1600.0000.0000.0000.000