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

tag_button

FMODB ID: NNGNQ

Calculation Name: 2A35-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2A35

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HX10

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 212
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2425374.666109
FMO2-HF: Nuclear repulsion 2345964.471406
FMO2-HF: Total energy -79410.194703
FMO2-MP2: Total energy -79645.58312


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:4:THR)


Summations of interaction energy for fragment #1(A:4:THR)
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.
-7.267-2.3366.738-4.026-7.641-0.02
Interaction energy analysis for fragmet #1(A:4:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.044 / q_NPA : -0.032
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].
3A6LYS10.8010.8942.518-2.0800.6191.161-1.600-2.260-0.013
4A7ARG10.9320.9675.2191.6681.756-0.001-0.002-0.0840.000
5A8VAL00.0370.0166.348-0.027-0.0270.0000.0000.0000.000
6A9LEU00.0200.0289.0890.1460.1460.0000.0000.0000.000
7A10LEU0-0.008-0.01012.262-0.001-0.0010.0000.0000.0000.000
8A11ALA00.0310.01913.9090.0290.0290.0000.0000.0000.000
9A12GLY00.035-0.01017.4380.0160.0160.0000.0000.0000.000
10A13ALA00.005-0.00116.5960.0200.0200.0000.0000.0000.000
11A14THR00.0250.01517.8750.0110.0110.0000.0000.0000.000
12A15GLY0-0.0290.00620.6700.0130.0130.0000.0000.0000.000
13A16LEU0-0.006-0.00520.070-0.002-0.0020.0000.0000.0000.000
14A17THR00.024-0.02315.9360.0150.0150.0000.0000.0000.000
15A18GLY0-0.022-0.00815.8970.0050.0050.0000.0000.0000.000
16A19GLU-1-0.883-0.94215.559-0.054-0.0540.0000.0000.0000.000
17A20HIS0-0.027-0.04715.448-0.010-0.0100.0000.0000.0000.000
18A21LEU0-0.043-0.0179.5710.0320.0320.0000.0000.0000.000
19A22LEU0-0.003-0.00611.051-0.032-0.0320.0000.0000.0000.000
20A23ASP-1-0.913-0.95111.8150.0920.0920.0000.0000.0000.000
21A24ARG10.8390.9126.820-0.963-0.9630.0000.0000.0000.000
22A25ILE00.0100.0057.1480.0960.0960.0000.0000.0000.000
23A26LEU0-0.006-0.0087.462-0.041-0.0410.0000.0000.0000.000
24A27SER0-0.058-0.0249.2930.0710.0710.0000.0000.0000.000
25A28GLU-1-0.793-0.8804.0922.2672.3980.000-0.016-0.1150.000
26A29PRO00.0210.0085.879-0.344-0.3440.0000.0000.0000.000
27A30THR0-0.034-0.0131.945-2.476-2.5442.930-1.041-1.821-0.001
28A31LEU00.0480.0434.514-1.323-1.188-0.001-0.011-0.1230.000
29A32ALA0-0.084-0.0475.2470.4060.425-0.001-0.001-0.0170.000
30A33LYS10.8330.9038.0710.6880.6880.0000.0000.0000.000
31A34VAL00.0000.0128.968-0.231-0.2310.0000.0000.0000.000
32A35ILE00.0220.01911.0010.0870.0870.0000.0000.0000.000
33A36ALA00.011-0.00414.306-0.017-0.0170.0000.0000.0000.000
34A37PRO0-0.0030.02616.2330.0360.0360.0000.0000.0000.000
35A38ALA0-0.0010.00119.8100.0090.0090.0000.0000.0000.000
36A39ARG10.9730.98721.9770.0590.0590.0000.0000.0000.000
37A40LYS10.9150.94224.0580.0520.0520.0000.0000.0000.000
38A41ALA00.0360.02323.120-0.010-0.0100.0000.0000.0000.000
39A42LEU0-0.018-0.00417.7530.0130.0130.0000.0000.0000.000
40A43ALA0-0.005-0.00419.601-0.003-0.0030.0000.0000.0000.000
41A44GLU-1-0.917-0.95718.823-0.093-0.0930.0000.0000.0000.000
42A45HIS00.0580.00912.668-0.026-0.0260.0000.0000.0000.000
43A46PRO00.0040.00015.525-0.029-0.0290.0000.0000.0000.000
44A47ARG10.7640.8847.9500.0780.0780.0000.0000.0000.000
45A48LEU0-0.031-0.01212.445-0.097-0.0970.0000.0000.0000.000
46A49ASP-1-0.806-0.88214.615-0.277-0.2770.0000.0000.0000.000
47A50ASN00.012-0.02316.795-0.001-0.0010.0000.0000.0000.000
48A51PRO00.0350.03819.1250.0280.0280.0000.0000.0000.000
49A52VAL00.008-0.01122.1670.0020.0020.0000.0000.0000.000
50A53GLY0-0.008-0.01024.7600.0060.0060.0000.0000.0000.000
51A54PRO0-0.044-0.02825.633-0.004-0.0040.0000.0000.0000.000
52A55LEU00.0430.01820.688-0.005-0.0050.0000.0000.0000.000
53A56ALA00.0140.00324.458-0.014-0.0140.0000.0000.0000.000
54A57GLU-1-0.873-0.94626.747-0.107-0.1070.0000.0000.0000.000
55A58LEU0-0.015-0.00922.818-0.007-0.0070.0000.0000.0000.000
56A59LEU0-0.029-0.00820.182-0.018-0.0180.0000.0000.0000.000
57A60PRO0-0.019-0.02222.483-0.022-0.0220.0000.0000.0000.000
58A61GLN0-0.043-0.01324.503-0.006-0.0060.0000.0000.0000.000
59A62LEU0-0.050-0.00218.063-0.008-0.0080.0000.0000.0000.000
60A63ASP-1-0.864-0.91919.589-0.313-0.3130.0000.0000.0000.000
61A64GLY00.007-0.00816.520-0.030-0.0300.0000.0000.0000.000
62A65SER0-0.061-0.03213.8140.0190.0190.0000.0000.0000.000
63A66ILE0-0.031-0.03111.245-0.066-0.0660.0000.0000.0000.000
64A67ASP-1-0.802-0.8696.873-2.715-2.7150.0000.0000.0000.000
65A68THR00.000-0.0216.7210.2630.2630.0000.0000.0000.000
66A69ALA00.0040.0089.148-0.019-0.0190.0000.0000.0000.000
67A70PHE00.0340.0107.1370.0720.0720.0000.0000.0000.000
68A71CYS0-0.039-0.00113.1540.0030.0030.0000.0000.0000.000
69A72CYS0-0.014-0.00715.3020.0380.0380.0000.0000.0000.000
70A73LEU00.0080.00218.1130.0150.0150.0000.0000.0000.000
71A74GLY00.0350.00921.7580.0060.0060.0000.0000.0000.000
72A75THR0-0.035-0.01924.7280.0070.0070.0000.0000.0000.000
73A76THR0-0.021-0.03528.3070.0050.0050.0000.0000.0000.000
74A77ILE00.0580.01731.602-0.003-0.0030.0000.0000.0000.000
75A78LYS10.8270.90734.994-0.002-0.0020.0000.0000.0000.000
76A79GLU-1-0.812-0.89832.052-0.004-0.0040.0000.0000.0000.000
77A80ALA0-0.042-0.00332.420-0.003-0.0030.0000.0000.0000.000
78A81GLY0-0.0010.00134.157-0.003-0.0030.0000.0000.0000.000
79A82SER0-0.037-0.05236.7430.0000.0000.0000.0000.0000.000
80A83GLU-1-0.892-0.95335.988-0.020-0.0200.0000.0000.0000.000
81A84GLU-1-0.842-0.90334.847-0.033-0.0330.0000.0000.0000.000
82A85ALA0-0.0050.00334.165-0.005-0.0050.0000.0000.0000.000
83A86PHE0-0.019-0.02129.295-0.003-0.0030.0000.0000.0000.000
84A87ARG10.8490.92130.1820.0460.0460.0000.0000.0000.000
85A88ALA00.0360.03729.582-0.006-0.0060.0000.0000.0000.000
86A89VAL0-0.051-0.03226.213-0.010-0.0100.0000.0000.0000.000
87A90ASP-1-0.778-0.90425.577-0.043-0.0430.0000.0000.0000.000
88A91PHE0-0.016-0.00925.4100.0000.0000.0000.0000.0000.000
89A92ASP-1-0.858-0.94225.702-0.082-0.0820.0000.0000.0000.000
90A93LEU0-0.013-0.00524.018-0.013-0.0130.0000.0000.0000.000
91A94PRO00.019-0.00320.951-0.021-0.0210.0000.0000.0000.000
92A95LEU00.0540.05920.864-0.022-0.0220.0000.0000.0000.000
93A96ALA0-0.004-0.00322.475-0.017-0.0170.0000.0000.0000.000
94A97VAL0-0.005-0.01317.627-0.019-0.0190.0000.0000.0000.000
95A98GLY00.0210.01017.869-0.038-0.0380.0000.0000.0000.000
96A99LYS10.8930.93218.7940.1480.1480.0000.0000.0000.000
97A100ARG10.8540.91819.7910.2470.2470.0000.0000.0000.000
98A101ALA00.0440.00415.122-0.031-0.0310.0000.0000.0000.000
99A102LEU0-0.005-0.00116.357-0.054-0.0540.0000.0000.0000.000
100A103GLU-1-0.884-0.91217.833-0.232-0.2320.0000.0000.0000.000
101A104MET0-0.077-0.02316.3810.0010.0010.0000.0000.0000.000
102A105GLY0-0.007-0.00515.246-0.074-0.0740.0000.0000.0000.000
103A106ALA0-0.066-0.01112.289-0.080-0.0800.0000.0000.0000.000
104A107ARG10.9510.9537.0550.5270.5270.0000.0000.0000.000
105A108HIS0-0.0140.0047.2560.0540.0540.0000.0000.0000.000
106A109TYR0-0.037-0.01610.830-0.119-0.1190.0000.0000.0000.000
107A110LEU0-0.0020.0048.6020.0710.0710.0000.0000.0000.000
108A111VAL0-0.001-0.00212.851-0.034-0.0340.0000.0000.0000.000
109A112VAL0-0.0050.00316.4140.0350.0350.0000.0000.0000.000
110A113SER0-0.047-0.04818.518-0.014-0.0140.0000.0000.0000.000
111A114ALA0-0.017-0.03221.5950.0060.0060.0000.0000.0000.000
112A115LEU00.0330.01323.944-0.002-0.0020.0000.0000.0000.000
113A116GLY0-0.011-0.01525.584-0.005-0.0050.0000.0000.0000.000
114A117ALA0-0.0460.00625.080-0.005-0.0050.0000.0000.0000.000
115A118ASP-1-0.765-0.89327.1580.0020.0020.0000.0000.0000.000
116A119ALA00.0030.02029.587-0.001-0.0010.0000.0000.0000.000
117A120LYS10.8390.90031.2360.0010.0010.0000.0000.0000.000
118A121SER0-0.0010.01932.8240.0020.0020.0000.0000.0000.000
119A122SER00.0460.00834.704-0.004-0.0040.0000.0000.0000.000
120A123ILE0-0.029-0.00634.057-0.001-0.0010.0000.0000.0000.000
121A124PHE00.0410.02133.9420.0000.0000.0000.0000.0000.000
122A125TYR00.0210.00826.776-0.001-0.0010.0000.0000.0000.000
123A126ASN0-0.012-0.02329.432-0.004-0.0040.0000.0000.0000.000
124A127ARG10.9030.96729.5300.0130.0130.0000.0000.0000.000
125A128VAL00.0160.01528.683-0.003-0.0030.0000.0000.0000.000
126A129LYS10.8720.94723.2510.0240.0240.0000.0000.0000.000
127A130GLY00.0430.02125.472-0.003-0.0030.0000.0000.0000.000
128A131GLU-1-0.874-0.94726.916-0.040-0.0400.0000.0000.0000.000
129A132LEU0-0.033-0.00921.845-0.007-0.0070.0000.0000.0000.000
130A133GLU-1-0.728-0.82621.843-0.009-0.0090.0000.0000.0000.000
131A134GLN0-0.043-0.01323.026-0.002-0.0020.0000.0000.0000.000
132A135ALA00.0280.01725.232-0.005-0.0050.0000.0000.0000.000
133A136LEU0-0.008-0.01819.184-0.013-0.0130.0000.0000.0000.000
134A137GLN0-0.076-0.05920.904-0.007-0.0070.0000.0000.0000.000
135A138GLU-1-0.930-0.95022.212-0.071-0.0710.0000.0000.0000.000
136A139GLN0-0.101-0.04620.427-0.018-0.0180.0000.0000.0000.000
137A140GLY00.0170.01720.807-0.014-0.0140.0000.0000.0000.000
138A141TRP0-0.057-0.02413.532-0.035-0.0350.0000.0000.0000.000
139A142PRO0-0.056-0.01613.1930.0280.0280.0000.0000.0000.000
140A143GLN0-0.008-0.0179.1950.0290.0290.0000.0000.0000.000
141A144LEU00.0060.01113.341-0.056-0.0560.0000.0000.0000.000
142A145THR0-0.020-0.02211.3230.0550.0550.0000.0000.0000.000
143A146ILE0-0.010-0.00314.019-0.033-0.0330.0000.0000.0000.000
144A147ALA00.0180.01715.5610.0260.0260.0000.0000.0000.000
145A148ARG10.7820.85017.413-0.046-0.0460.0000.0000.0000.000
146A149PRO00.0240.01219.4830.0120.0120.0000.0000.0000.000
147A150SER00.0480.02121.804-0.010-0.0100.0000.0000.0000.000
148A151LEU0-0.0070.00825.320-0.003-0.0030.0000.0000.0000.000
149A152LEU0-0.038-0.00427.801-0.006-0.0060.0000.0000.0000.000
150A153PHE00.0240.00726.2330.0100.0100.0000.0000.0000.000
151A154GLY00.0300.01828.457-0.006-0.0060.0000.0000.0000.000
152A155PRO0-0.066-0.03230.4370.0020.0020.0000.0000.0000.000
153A156ARG10.8350.89333.197-0.049-0.0490.0000.0000.0000.000
154A157GLU-1-0.939-0.95031.3680.0480.0480.0000.0000.0000.000
155A158GLU-1-0.806-0.91532.8480.0450.0450.0000.0000.0000.000
156A159PHE0-0.028-0.00629.414-0.003-0.0030.0000.0000.0000.000
157A160ARG10.9570.97029.471-0.006-0.0060.0000.0000.0000.000
158A161LEU00.0320.01421.993-0.001-0.0010.0000.0000.0000.000
159A162ALA00.008-0.01224.633-0.001-0.0010.0000.0000.0000.000
160A163GLU-1-0.834-0.88925.9550.0210.0210.0000.0000.0000.000
161A164ILE0-0.023-0.00620.718-0.001-0.0010.0000.0000.0000.000
162A165LEU0-0.054-0.00520.039-0.002-0.0020.0000.0000.0000.000
163A166ALA0-0.024-0.02122.628-0.003-0.0030.0000.0000.0000.000
164A167ALA0-0.033-0.00825.096-0.003-0.0030.0000.0000.0000.000
165A168PRO0-0.0040.01726.5100.0070.0070.0000.0000.0000.000
166A169ILE00.0290.01628.659-0.004-0.0040.0000.0000.0000.000
167A170ALA00.0170.00331.4500.0050.0050.0000.0000.0000.000
168A171ARG10.8480.90432.846-0.027-0.0270.0000.0000.0000.000
169A172ILE00.0400.02735.1960.0010.0010.0000.0000.0000.000
170A173LEU00.0410.02531.0180.0040.0040.0000.0000.0000.000
171A174PRO0-0.0460.00332.187-0.003-0.0030.0000.0000.0000.000
172A175GLY00.0450.01828.6380.0030.0030.0000.0000.0000.000
173A176LYS10.9310.95927.110-0.075-0.0750.0000.0000.0000.000
174A177TYR00.046-0.00226.2230.0060.0060.0000.0000.0000.000
175A178HIS00.0040.00224.9910.0130.0130.0000.0000.0000.000
176A179GLY00.0570.03122.4400.0000.0000.0000.0000.0000.000
177A180ILE0-0.042-0.01420.9840.0100.0100.0000.0000.0000.000
178A181GLU-1-0.835-0.91120.3860.1340.1340.0000.0000.0000.000
179A182ALA0-0.0010.00419.2100.0060.0060.0000.0000.0000.000
180A183CYM-1-0.840-0.84416.7530.2150.2150.0000.0000.0000.000
181A184ASP-1-0.832-0.91315.4390.2360.2360.0000.0000.0000.000
182A185LEU0-0.003-0.00515.3540.0310.0310.0000.0000.0000.000
183A186ALA00.0140.00913.1430.0010.0010.0000.0000.0000.000
184A187ARG10.8130.85811.072-0.297-0.2970.0000.0000.0000.000
185A188ALA0-0.017-0.01810.5010.0910.0910.0000.0000.0000.000
186A189LEU00.0080.00411.1230.0390.0390.0000.0000.0000.000
187A190TRP00.024-0.0032.694-1.266-0.4640.528-0.316-1.014-0.002
188A191ARG10.8350.8886.252-0.493-0.4930.0000.0000.0000.000
189A192LEU00.0010.0037.4230.1250.1250.0000.0000.0000.000
190A193ALA0-0.017-0.0075.7290.0080.0080.0000.0000.0000.000
191A194LEU0-0.065-0.0282.467-1.219-0.2442.123-1.024-2.074-0.004
192A195GLU-1-0.923-0.9404.1080.5070.657-0.001-0.015-0.1330.000
193A196GLU-1-0.969-0.9645.910-0.106-0.1060.0000.0000.0000.000
194A197GLY00.018-0.0027.502-0.147-0.1470.0000.0000.0000.000
195A198LYS10.8420.92511.2010.1060.1060.0000.0000.0000.000
196A199GLY00.0150.00914.1490.0220.0220.0000.0000.0000.000
197A200VAL00.0140.00215.5230.0010.0010.0000.0000.0000.000
198A201ARG10.8250.90512.553-0.240-0.2400.0000.0000.0000.000
199A202PHE00.0090.00616.628-0.010-0.0100.0000.0000.0000.000
200A203VAL0-0.027-0.00714.3480.0160.0160.0000.0000.0000.000
201A204GLU-1-0.795-0.90517.8240.0460.0460.0000.0000.0000.000
202A205SER00.029-0.01620.0300.0230.0230.0000.0000.0000.000
203A206ASP-1-0.842-0.92821.3250.1370.1370.0000.0000.0000.000
204A207GLU-1-0.870-0.92017.3720.1860.1860.0000.0000.0000.000
205A208LEU00.013-0.00115.5600.0390.0390.0000.0000.0000.000
206A209ARG10.9220.97017.188-0.117-0.1170.0000.0000.0000.000
207A210LYS10.9340.97017.685-0.237-0.2370.0000.0000.0000.000
208A211LEU0-0.016-0.00912.1930.0350.0350.0000.0000.0000.000
209A212GLY00.0230.02613.8490.0630.0630.0000.0000.0000.000
210A213LYS10.7550.85415.604-0.144-0.1440.0000.0000.0000.000
211A214GLY0-0.0010.02017.426-0.003-0.0030.0000.0000.0000.000
212A215SER0-0.0210.00214.5180.1140.1140.0000.0000.0000.000