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: QVG4Y

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 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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2176383.918732
FMO2-HF: Nuclear repulsion 2097570.286382
FMO2-HF: Total energy -78813.63235
FMO2-MP2: Total energy -79042.023381


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.
-4.816-0.7472.019-1.866-4.2190.007
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 : 0.022
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].
3A3LEU00.0420.0112.585-3.310-0.4951.999-1.406-3.4080.005
4A4TYR00.0380.0115.3770.0510.123-0.001-0.003-0.0670.000
5A5MET00.0240.0138.161-0.038-0.0380.0000.0000.0000.000
6A6ARG10.9350.9615.357-0.343-0.3430.0000.0000.0000.000
7A7PHE00.0050.0136.365-0.289-0.2890.0000.0000.0000.000
8A8THR00.0190.0098.2530.0270.0270.0000.0000.0000.000
9A9GLU-1-0.848-0.9094.513-0.247-0.143-0.001-0.009-0.0930.000
10A10ASN0-0.003-0.0188.1530.0410.0410.0000.0000.0000.000
11A11PHE00.0380.01910.7980.0020.0020.0000.0000.0000.000
12A12GLU-1-0.826-0.88413.1440.0760.0760.0000.0000.0000.000
13A13ARG10.8930.93614.280-0.064-0.0640.0000.0000.0000.000
14A14ALA00.0270.00713.752-0.003-0.0030.0000.0000.0000.000
15A15LYS10.8430.92515.848-0.112-0.1120.0000.0000.0000.000
16A16LYS10.8440.90718.720-0.076-0.0760.0000.0000.0000.000
17A17GLU-1-0.791-0.89217.5330.0810.0810.0000.0000.0000.000
18A18ALA0-0.0270.01119.265-0.002-0.0020.0000.0000.0000.000
19A19LEU00.002-0.00221.082-0.005-0.0050.0000.0000.0000.000
20A20MET0-0.018-0.01023.822-0.005-0.0050.0000.0000.0000.000
21A21SER0-0.027-0.02622.669-0.004-0.0040.0000.0000.0000.000
22A22LEU0-0.018-0.00225.205-0.003-0.0030.0000.0000.0000.000
23A23GLU-1-0.809-0.90626.9800.0570.0570.0000.0000.0000.000
24A24ILE0-0.072-0.03527.280-0.006-0.0060.0000.0000.0000.000
25A25ALA00.0230.01728.805-0.003-0.0030.0000.0000.0000.000
26A26LEU0-0.018-0.02730.638-0.003-0.0030.0000.0000.0000.000
27A27ARG10.9160.96932.279-0.050-0.0500.0000.0000.0000.000
28A28LYS10.7730.87631.819-0.063-0.0630.0000.0000.0000.000
29A29GLY00.0400.03635.409-0.002-0.0020.0000.0000.0000.000
30A30GLU-1-0.868-0.91531.5070.0660.0660.0000.0000.0000.000
31A31VAL0-0.045-0.03729.8170.0060.0060.0000.0000.0000.000
32A32ASP-1-0.729-0.84231.4620.0770.0770.0000.0000.0000.000
33A33GLU-1-0.813-0.92333.5430.0590.0590.0000.0000.0000.000
34A34ASP-1-0.843-0.91034.8840.0610.0610.0000.0000.0000.000
35A35ILE0-0.058-0.03628.4770.0020.0020.0000.0000.0000.000
36A36ILE00.0140.03130.7530.0040.0040.0000.0000.0000.000
37A37PRO00.002-0.00431.4460.0020.0020.0000.0000.0000.000
38A38LEU00.0230.00728.1010.0010.0010.0000.0000.0000.000
39A39LEU00.0250.01425.7800.0050.0050.0000.0000.0000.000
40A40LYS10.8770.93726.683-0.060-0.0600.0000.0000.0000.000
41A41LYS10.8410.91628.003-0.067-0.0670.0000.0000.0000.000
42A42ILE00.0170.01022.6320.0020.0020.0000.0000.0000.000
43A43ASN0-0.027-0.04022.8950.0090.0090.0000.0000.0000.000
44A44SER0-0.065-0.03323.836-0.001-0.0010.0000.0000.0000.000
45A45ILE0-0.0080.01322.172-0.001-0.0010.0000.0000.0000.000
46A46GLU-1-0.804-0.89019.6520.1280.1280.0000.0000.0000.000
47A47ASN0-0.024-0.04317.3880.0010.0010.0000.0000.0000.000
48A48TYR0-0.023-0.04016.9330.0090.0090.0000.0000.0000.000
49A49PHE00.0320.02114.417-0.008-0.0080.0000.0000.0000.000
50A50THR00.0130.02319.2060.0100.0100.0000.0000.0000.000
51A51THR0-0.028-0.03217.3410.0030.0030.0000.0000.0000.000
52A52SER00.0140.01320.599-0.015-0.0150.0000.0000.0000.000
53A53SER0-0.031-0.03122.4730.0090.0090.0000.0000.0000.000
54A54CYS0-0.063-0.01925.390-0.003-0.0030.0000.0000.0000.000
55A55SER0-0.035-0.04129.1040.0020.0020.0000.0000.0000.000
56A56GLY00.0400.01031.9240.0040.0040.0000.0000.0000.000
57A57ARG10.8890.92429.954-0.090-0.0900.0000.0000.0000.000
58A58ILE00.0720.04035.4250.0020.0020.0000.0000.0000.000
59A59SER0-0.073-0.04336.7320.0020.0020.0000.0000.0000.000
60A60VAL00.0450.02738.888-0.001-0.0010.0000.0000.0000.000
61A61MET0-0.0200.00034.8560.0000.0000.0000.0000.0000.000
62A62GLU-1-0.669-0.79339.6030.0430.0430.0000.0000.0000.000
63A63MET00.004-0.00635.7170.0040.0040.0000.0000.0000.000
64A64PRO00.0300.03236.592-0.002-0.0020.0000.0000.0000.000
65A72ALA00.0130.00734.1180.0010.0010.0000.0000.0000.000
66A73LYS10.8220.90835.887-0.043-0.0430.0000.0000.0000.000
67A74TRP00.006-0.01432.1820.0000.0000.0000.0000.0000.000
68A75LEU0-0.075-0.02738.676-0.002-0.0020.0000.0000.0000.000
69A76GLY00.0150.00740.835-0.003-0.0030.0000.0000.0000.000
70A77LYN0-0.0170.00333.8760.0060.0060.0000.0000.0000.000
71A78TRP0-0.0040.00038.386-0.001-0.0010.0000.0000.0000.000
72A79HIS0-0.0240.00235.7440.0010.0010.0000.0000.0000.000
73A80ARG10.7940.85537.174-0.046-0.0460.0000.0000.0000.000
74A81GLU-1-0.834-0.91240.4290.0480.0480.0000.0000.0000.000
75A82VAL0-0.049-0.02642.566-0.001-0.0010.0000.0000.0000.000
76A83SER00.014-0.01345.324-0.001-0.0010.0000.0000.0000.000
77A84LEU00.0290.00748.2200.0010.0010.0000.0000.0000.000
78A85TYR00.027-0.01750.1550.0010.0010.0000.0000.0000.000
79A86GLU-1-0.722-0.79646.0360.0420.0420.0000.0000.0000.000
80A87VAL00.0110.00744.7850.0010.0010.0000.0000.0000.000
81A88LEU00.0250.01046.9550.0000.0000.0000.0000.0000.000
82A89GLU-1-0.845-0.90349.1160.0320.0320.0000.0000.0000.000
83A90ALA0-0.021-0.00144.2550.0000.0000.0000.0000.0000.000
84A91ILE00.0400.01046.3140.0000.0000.0000.0000.0000.000
85A92LYS10.8950.94447.558-0.032-0.0320.0000.0000.0000.000
86A93LYS10.7900.88346.271-0.038-0.0380.0000.0000.0000.000
87A94HIS0-0.058-0.02144.7820.0000.0000.0000.0000.0000.000
88A95ARG10.8170.88645.930-0.035-0.0350.0000.0000.0000.000
89A96SER00.0040.00843.327-0.002-0.0020.0000.0000.0000.000
90A97GLY00.0190.01341.7650.0020.0020.0000.0000.0000.000
91A98GLN00.011-0.00240.0720.0010.0010.0000.0000.0000.000
92A99LEU0-0.0110.00340.9780.0030.0030.0000.0000.0000.000
93A100TRP0-0.004-0.01738.8920.0000.0000.0000.0000.0000.000
94A101PHE00.0240.01040.4700.0010.0010.0000.0000.0000.000
95A102LEU0-0.059-0.02934.7130.0020.0020.0000.0000.0000.000
96A103VAL00.0280.01236.8910.0000.0000.0000.0000.0000.000
97A104ARG10.7720.84531.024-0.080-0.0800.0000.0000.0000.000
98A105SER00.037-0.00229.724-0.004-0.0040.0000.0000.0000.000
99A106PRO0-0.0360.01129.7470.0020.0020.0000.0000.0000.000
100A107ILE0-0.048-0.01223.6340.0050.0050.0000.0000.0000.000
101A108LEU00.0560.02223.848-0.005-0.0050.0000.0000.0000.000
102A109HIS0-0.024-0.01718.5150.0150.0150.0000.0000.0000.000
103A110VAL00.001-0.00218.646-0.011-0.0110.0000.0000.0000.000
104A111GLY00.0270.03414.8420.0220.0220.0000.0000.0000.000
105A112ALA00.004-0.01613.784-0.021-0.0210.0000.0000.0000.000
106A113LYS10.8350.90712.191-0.137-0.1370.0000.0000.0000.000
107A114THR0-0.038-0.04410.7790.0010.0010.0000.0000.0000.000
108A115LEU00.0330.00511.571-0.003-0.0030.0000.0000.0000.000
109A116GLU-1-0.775-0.86313.1770.1260.1260.0000.0000.0000.000
110A117ASP-1-0.755-0.82815.6060.1440.1440.0000.0000.0000.000
111A118ALA00.0160.02214.583-0.006-0.0060.0000.0000.0000.000
112A119VAL00.023-0.00116.317-0.002-0.0020.0000.0000.0000.000
113A120LYS10.8550.93218.717-0.123-0.1230.0000.0000.0000.000
114A121LEU00.0130.01719.659-0.007-0.0070.0000.0000.0000.000
115A122VAL0-0.0020.00419.050-0.005-0.0050.0000.0000.0000.000
116A123ASN00.0350.01121.963-0.004-0.0040.0000.0000.0000.000
117A124LEU0-0.0020.01824.535-0.007-0.0070.0000.0000.0000.000
118A125ALA00.0610.03524.878-0.007-0.0070.0000.0000.0000.000
119A126VAL00.0260.01024.982-0.006-0.0060.0000.0000.0000.000
120A127SER0-0.077-0.04427.638-0.008-0.0080.0000.0000.0000.000
121A128CYS0-0.0250.00429.978-0.006-0.0060.0000.0000.0000.000
122A129GLY00.0660.02330.821-0.005-0.0050.0000.0000.0000.000
123A130PHE0-0.042-0.00927.459-0.001-0.0010.0000.0000.0000.000
124A131LYS10.9110.94827.004-0.073-0.0730.0000.0000.0000.000
125A132TYR00.0150.02925.5900.0020.0020.0000.0000.0000.000
126A133SER0-0.006-0.02823.0780.0120.0120.0000.0000.0000.000
127A134ASN0-0.116-0.06518.7470.0160.0160.0000.0000.0000.000
128A135ILE00.0320.01313.170-0.001-0.0010.0000.0000.0000.000
129A136LYS10.8890.95015.089-0.238-0.2380.0000.0000.0000.000
130A137SER00.017-0.00210.7120.0810.0810.0000.0000.0000.000
131A138ILE00.005-0.00611.241-0.110-0.1100.0000.0000.0000.000
132A139SER00.0620.02010.6040.1700.1700.0000.0000.0000.000
133A140ASN0-0.043-0.00110.6660.1100.1100.0000.0000.0000.000
134A141LYS10.8320.8874.770-0.623-0.555-0.001-0.001-0.0660.000
135A142LYS10.8390.9233.2900.3561.3660.023-0.447-0.5850.002
136A143LEU00.0060.0107.861-0.140-0.1400.0000.0000.0000.000
137A144ILE00.0080.02310.640-0.070-0.0700.0000.0000.0000.000
138A145VAL00.0020.01014.1060.0060.0060.0000.0000.0000.000
139A146GLU-1-0.741-0.83517.4020.1980.1980.0000.0000.0000.000
140A147ILE00.0090.00120.318-0.007-0.0070.0000.0000.0000.000
141A148ARG10.8490.90822.536-0.155-0.1550.0000.0000.0000.000
142A149SER0-0.024-0.03326.804-0.001-0.0010.0000.0000.0000.000
143A150THR0-0.015-0.03530.1290.0050.0050.0000.0000.0000.000
144A151GLU-1-0.775-0.83832.1700.0760.0760.0000.0000.0000.000
145A152ARG10.7920.85830.405-0.092-0.0920.0000.0000.0000.000
146A153MET00.0040.00834.584-0.003-0.0030.0000.0000.0000.000
147A154ASP-1-0.732-0.80334.8950.0830.0830.0000.0000.0000.000
148A155VAL00.0260.00338.127-0.001-0.0010.0000.0000.0000.000
149A156LEU00.0190.02841.8330.0000.0000.0000.0000.0000.000
150A157LEU0-0.035-0.03743.201-0.002-0.0020.0000.0000.0000.000
151A158GLY00.0700.02945.654-0.002-0.0020.0000.0000.0000.000
152A159GLU-1-0.907-0.96244.3810.0460.0460.0000.0000.0000.000
153A160ASN0-0.060-0.02945.582-0.001-0.0010.0000.0000.0000.000
154A161GLY00.0080.00847.649-0.002-0.0020.0000.0000.0000.000
155A162GLU-1-0.900-0.92149.8080.0290.0290.0000.0000.0000.000
156A163ILE0-0.071-0.05149.2020.0030.0030.0000.0000.0000.000
157A164PHE0-0.015-0.00846.966-0.001-0.0010.0000.0000.0000.000
158A165VAL0-0.023-0.00748.9960.0000.0000.0000.0000.0000.000
159A166GLY00.0690.03052.143-0.001-0.0010.0000.0000.0000.000
160A167GLU-1-0.861-0.92953.2100.0310.0310.0000.0000.0000.000
161A168GLU-1-0.831-0.90653.4370.0310.0310.0000.0000.0000.000
162A169TYR0-0.008-0.00846.7830.0010.0010.0000.0000.0000.000
163A170LEU00.0210.00347.0770.0020.0020.0000.0000.0000.000
164A171ASN00.0130.00548.7770.0020.0020.0000.0000.0000.000
165A172LYS10.9030.94549.619-0.032-0.0320.0000.0000.0000.000
166A173ILE0-0.0150.00044.2420.0020.0020.0000.0000.0000.000
167A174VAL0-0.001-0.00844.9460.0030.0030.0000.0000.0000.000
168A175GLU-1-0.934-0.95845.4680.0390.0390.0000.0000.0000.000
169A176ILE00.0330.01143.1070.0020.0020.0000.0000.0000.000
170A177ALA0-0.009-0.00941.4230.0030.0030.0000.0000.0000.000
171A178ASN00.017-0.00341.1910.0050.0050.0000.0000.0000.000
172A179ASP-1-0.778-0.87742.5770.0460.0460.0000.0000.0000.000
173A180GLN0-0.073-0.04338.1520.0030.0030.0000.0000.0000.000
174A181MET0-0.0340.00437.5150.0050.0050.0000.0000.0000.000
175A182ARG10.8100.88738.665-0.044-0.0440.0000.0000.0000.000
176A183ARG10.9380.97338.509-0.058-0.0580.0000.0000.0000.000
177A184PHE0-0.031-0.01634.1440.0040.0040.0000.0000.0000.000
178A185LYS10.8960.93535.045-0.055-0.0550.0000.0000.0000.000
179A186GLU-1-0.854-0.89936.9940.0600.0600.0000.0000.0000.000
180A187LYS10.7770.89233.008-0.076-0.0760.0000.0000.0000.000
181A188LEU0-0.009-0.00430.6680.0030.0030.0000.0000.0000.000
182A189LYS10.8820.92733.178-0.060-0.0600.0000.0000.0000.000
183A190ARG10.7970.88534.224-0.065-0.0650.0000.0000.0000.000
184A191LEU00.0410.02427.3210.0000.0000.0000.0000.0000.000
185A192GLU-1-0.796-0.87430.6860.0650.0650.0000.0000.0000.000
186A193SER0-0.049-0.02731.980-0.002-0.0020.0000.0000.0000.000
187A194LYS10.8610.90931.098-0.065-0.0650.0000.0000.0000.000
188A195ILE00.0210.00924.7360.0010.0010.0000.0000.0000.000
189A196ASN00.0310.01426.8460.0050.0050.0000.0000.0000.000
190A197ALA0-0.017-0.00428.2880.0000.0000.0000.0000.0000.000
191A198LEU0-0.034-0.00822.3980.0020.0020.0000.0000.0000.000
192A199ASN0-0.028-0.01523.2870.0090.0090.0000.0000.0000.000
193A200ARG10.8350.90418.765-0.128-0.1280.0000.0000.0000.000