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: JQ9Q9

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 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 212
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2431873.263549
FMO2-HF: Nuclear repulsion 2352462.754991
FMO2-HF: Total energy -79410.508558
FMO2-MP2: Total energy -79645.811026


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.
-5.484-1.1396.621-3.844-7.12-0.015
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 : -0.036 / q_NPA : -0.025
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].
3A6LYS10.8180.9002.779-0.8531.7570.399-1.289-1.720-0.008
4A7ARG10.9250.9625.4921.7061.7060.0000.0000.0000.000
5A8VAL00.0420.0236.4400.0210.0210.0000.0000.0000.000
6A9LEU00.0270.0259.3930.1280.1280.0000.0000.0000.000
7A10LEU0-0.015-0.01512.6460.0100.0100.0000.0000.0000.000
8A11ALA00.0390.02514.3660.0250.0250.0000.0000.0000.000
9A12GLY00.023-0.01317.7090.0180.0180.0000.0000.0000.000
10A13ALA00.0170.01216.9040.0180.0180.0000.0000.0000.000
11A14THR0-0.0160.00218.1210.0140.0140.0000.0000.0000.000
12A15GLY00.0230.00120.2950.0090.0090.0000.0000.0000.000
13A16LEU0-0.042-0.00719.622-0.004-0.0040.0000.0000.0000.000
14A17THR00.038-0.01415.8560.0150.0150.0000.0000.0000.000
15A18GLY0-0.007-0.00115.6210.0050.0050.0000.0000.0000.000
16A19GLU-1-0.896-0.95515.315-0.080-0.0800.0000.0000.0000.000
17A20HIS0-0.008-0.04315.399-0.023-0.0230.0000.0000.0000.000
18A21LEU0-0.037-0.0129.5960.0330.0330.0000.0000.0000.000
19A22LEU0-0.006-0.00610.783-0.051-0.0510.0000.0000.0000.000
20A23ASP-1-0.914-0.94811.7870.0190.0190.0000.0000.0000.000
21A24ARG10.8560.9176.720-0.980-0.9800.0000.0000.0000.000
22A25ILE00.0020.0007.1920.0530.0530.0000.0000.0000.000
23A26LEU00.000-0.0097.595-0.127-0.1270.0000.0000.0000.000
24A27SER0-0.065-0.0319.3940.0530.0530.0000.0000.0000.000
25A28GLU-1-0.772-0.8584.3302.0032.111-0.001-0.011-0.0960.000
26A29PRO00.005-0.0016.014-0.385-0.3850.0000.0000.0000.000
27A30THR0-0.026-0.0081.910-1.866-2.0913.240-1.080-1.935-0.001
28A31LEU00.0350.0404.653-1.303-1.202-0.001-0.009-0.0910.000
29A32ALA0-0.063-0.0325.4600.4590.4590.0000.0000.0000.000
30A33LYS10.8030.8968.7000.6930.6930.0000.0000.0000.000
31A34VAL00.0030.0069.413-0.220-0.2200.0000.0000.0000.000
32A35ILE00.0110.01311.1720.0970.0970.0000.0000.0000.000
33A36ALA00.0200.00114.561-0.003-0.0030.0000.0000.0000.000
34A37PRO0-0.0090.01816.5800.0320.0320.0000.0000.0000.000
35A38ALA00.0110.00120.1410.0140.0140.0000.0000.0000.000
36A39ARG10.9530.97922.4260.0570.0570.0000.0000.0000.000
37A40LYS10.9100.94024.4530.0680.0680.0000.0000.0000.000
38A41ALA00.0650.04123.397-0.011-0.0110.0000.0000.0000.000
39A42LEU0-0.023-0.01218.0950.0150.0150.0000.0000.0000.000
40A43ALA0-0.003-0.00419.343-0.001-0.0010.0000.0000.0000.000
41A44GLU-1-0.922-0.95718.710-0.134-0.1340.0000.0000.0000.000
42A45HIS00.0430.00712.416-0.023-0.0230.0000.0000.0000.000
43A46PRO0-0.011-0.01015.255-0.030-0.0300.0000.0000.0000.000
44A47ARG10.7670.8817.7000.3890.3890.0000.0000.0000.000
45A48LEU0-0.029-0.00712.359-0.092-0.0920.0000.0000.0000.000
46A49ASP-1-0.813-0.89114.643-0.317-0.3170.0000.0000.0000.000
47A50ASN0-0.007-0.02816.8520.0080.0080.0000.0000.0000.000
48A51PRO00.0290.03319.4280.0270.0270.0000.0000.0000.000
49A52VAL0-0.003-0.01222.5400.0040.0040.0000.0000.0000.000
50A53GLY0-0.010-0.01525.1020.0060.0060.0000.0000.0000.000
51A54PRO0-0.040-0.02526.038-0.003-0.0030.0000.0000.0000.000
52A55LEU00.0470.02521.102-0.007-0.0070.0000.0000.0000.000
53A56ALA00.0180.00624.602-0.014-0.0140.0000.0000.0000.000
54A57GLU-1-0.883-0.95326.873-0.101-0.1010.0000.0000.0000.000
55A58LEU00.0100.00023.305-0.007-0.0070.0000.0000.0000.000
56A59LEU0-0.027-0.00420.265-0.018-0.0180.0000.0000.0000.000
57A60PRO0-0.022-0.02422.420-0.022-0.0220.0000.0000.0000.000
58A61GLN0-0.049-0.01624.361-0.007-0.0070.0000.0000.0000.000
59A62LEU0-0.054-0.00418.224-0.010-0.0100.0000.0000.0000.000
60A63ASP-1-0.831-0.91018.893-0.344-0.3440.0000.0000.0000.000
61A64GLY00.0190.00116.609-0.042-0.0420.0000.0000.0000.000
62A65SER0-0.052-0.03314.1730.0320.0320.0000.0000.0000.000
63A66ILE0-0.039-0.03511.333-0.097-0.0970.0000.0000.0000.000
64A67ASP-1-0.815-0.8766.774-2.471-2.4710.0000.0000.0000.000
65A68THR00.011-0.0206.7060.3820.3820.0000.0000.0000.000
66A69ALA0-0.0050.0009.046-0.087-0.0870.0000.0000.0000.000
67A70PHE00.0310.0057.1520.0830.0830.0000.0000.0000.000
68A71CYS0-0.0320.00013.191-0.008-0.0080.0000.0000.0000.000
69A72CYS0-0.0120.00015.4720.0400.0400.0000.0000.0000.000
70A73LEU00.003-0.00218.2870.0090.0090.0000.0000.0000.000
71A74GLY00.0420.00921.8770.0090.0090.0000.0000.0000.000
72A75THR0-0.041-0.01624.6560.0050.0050.0000.0000.0000.000
73A76THR0-0.036-0.07628.2720.0070.0070.0000.0000.0000.000
74A77ILE00.0670.03331.800-0.003-0.0030.0000.0000.0000.000
75A78LYS10.8180.89835.173-0.009-0.0090.0000.0000.0000.000
76A79GLU-1-0.821-0.87631.9800.0030.0030.0000.0000.0000.000
77A80ALA0-0.019-0.00132.219-0.003-0.0030.0000.0000.0000.000
78A81GLY0-0.0140.00334.021-0.003-0.0030.0000.0000.0000.000
79A82SER0-0.030-0.05136.6220.0010.0010.0000.0000.0000.000
80A83GLU-1-0.891-0.95935.776-0.006-0.0060.0000.0000.0000.000
81A84GLU-1-0.830-0.89834.591-0.021-0.0210.0000.0000.0000.000
82A85ALA0-0.0020.00633.887-0.004-0.0040.0000.0000.0000.000
83A86PHE0-0.023-0.01529.212-0.003-0.0030.0000.0000.0000.000
84A87ARG10.7990.90329.9620.0270.0270.0000.0000.0000.000
85A88ALA00.0280.02529.195-0.005-0.0050.0000.0000.0000.000
86A89VAL0-0.050-0.03225.898-0.010-0.0100.0000.0000.0000.000
87A90ASP-1-0.762-0.89425.259-0.017-0.0170.0000.0000.0000.000
88A91PHE0-0.0050.00025.6170.0040.0040.0000.0000.0000.000
89A92ASP-1-0.844-0.93325.472-0.056-0.0560.0000.0000.0000.000
90A93LEU00.0080.00124.318-0.011-0.0110.0000.0000.0000.000
91A94PRO00.013-0.00721.290-0.018-0.0180.0000.0000.0000.000
92A95LEU00.0460.04820.903-0.015-0.0150.0000.0000.0000.000
93A96ALA0-0.0060.00222.561-0.012-0.0120.0000.0000.0000.000
94A97VAL0-0.011-0.01617.734-0.018-0.0180.0000.0000.0000.000
95A98GLY00.0220.01517.933-0.031-0.0310.0000.0000.0000.000
96A99LYS10.8910.92518.7650.1190.1190.0000.0000.0000.000
97A100ARG10.8440.91419.6690.2240.2240.0000.0000.0000.000
98A101ALA00.0510.01014.919-0.032-0.0320.0000.0000.0000.000
99A102LEU0-0.009-0.00116.176-0.047-0.0470.0000.0000.0000.000
100A103GLU-1-0.879-0.91117.904-0.196-0.1960.0000.0000.0000.000
101A104MET0-0.054-0.00816.335-0.003-0.0030.0000.0000.0000.000
102A105GLY00.000-0.00115.291-0.078-0.0780.0000.0000.0000.000
103A106ALA0-0.058-0.01012.180-0.037-0.0370.0000.0000.0000.000
104A107ARG10.8390.9006.630-0.295-0.2950.0000.0000.0000.000
105A108HIS0-0.037-0.0037.1800.0360.0360.0000.0000.0000.000
106A109TYR0-0.037-0.01310.740-0.128-0.1280.0000.0000.0000.000
107A110LEU0-0.0070.0058.7630.0710.0710.0000.0000.0000.000
108A111VAL0-0.003-0.00613.001-0.041-0.0410.0000.0000.0000.000
109A112VAL0-0.0110.00016.6160.0330.0330.0000.0000.0000.000
110A113SER0-0.029-0.03818.877-0.017-0.0170.0000.0000.0000.000
111A114ALA0-0.014-0.03521.7510.0040.0040.0000.0000.0000.000
112A115LEU00.0080.00724.070-0.001-0.0010.0000.0000.0000.000
113A116GLY00.005-0.00225.531-0.007-0.0070.0000.0000.0000.000
114A117ALA0-0.0330.00825.218-0.007-0.0070.0000.0000.0000.000
115A118ASP-1-0.773-0.88427.3290.0310.0310.0000.0000.0000.000
116A119ALA00.0160.02229.564-0.003-0.0030.0000.0000.0000.000
117A120LYS10.8300.88831.206-0.029-0.0290.0000.0000.0000.000
118A121SER0-0.0180.01132.8730.0000.0000.0000.0000.0000.000
119A122SER00.0490.01234.760-0.004-0.0040.0000.0000.0000.000
120A123ILE0-0.029-0.00633.889-0.003-0.0030.0000.0000.0000.000
121A124PHE00.0500.02533.8480.0010.0010.0000.0000.0000.000
122A125TYR00.0180.01626.5770.0010.0010.0000.0000.0000.000
123A126ASN00.000-0.02829.191-0.005-0.0050.0000.0000.0000.000
124A127ARG10.8830.96129.368-0.002-0.0020.0000.0000.0000.000
125A128VAL00.0290.01828.576-0.001-0.0010.0000.0000.0000.000
126A129LYS10.8560.93323.159-0.001-0.0010.0000.0000.0000.000
127A130GLY00.0430.01925.409-0.001-0.0010.0000.0000.0000.000
128A131GLU-1-0.874-0.94927.051-0.016-0.0160.0000.0000.0000.000
129A132LEU0-0.027-0.00421.888-0.005-0.0050.0000.0000.0000.000
130A133GLU-1-0.736-0.82121.9700.0360.0360.0000.0000.0000.000
131A134GLN0-0.030-0.00222.9940.0050.0050.0000.0000.0000.000
132A135ALA00.0190.00625.020-0.004-0.0040.0000.0000.0000.000
133A136LEU0-0.001-0.00919.098-0.011-0.0110.0000.0000.0000.000
134A137GLN0-0.056-0.04920.9640.0000.0000.0000.0000.0000.000
135A138GLU-1-0.930-0.96122.036-0.027-0.0270.0000.0000.0000.000
136A139GLN0-0.101-0.04720.498-0.015-0.0150.0000.0000.0000.000
137A140GLY00.0060.01421.050-0.014-0.0140.0000.0000.0000.000
138A141TRP0-0.045-0.02213.493-0.017-0.0170.0000.0000.0000.000
139A142PRO0-0.040-0.01113.4040.0300.0300.0000.0000.0000.000
140A143GLN00.014-0.0059.3190.0940.0940.0000.0000.0000.000
141A144LEU00.0040.00613.292-0.054-0.0540.0000.0000.0000.000
142A145THR0-0.019-0.02711.3620.0410.0410.0000.0000.0000.000
143A146ILE0-0.010-0.00514.067-0.033-0.0330.0000.0000.0000.000
144A147ALA00.0170.01315.4970.0220.0220.0000.0000.0000.000
145A148ARG10.7600.84017.333-0.088-0.0880.0000.0000.0000.000
146A149PRO00.0400.01419.4290.0110.0110.0000.0000.0000.000
147A150SER00.0330.01321.781-0.010-0.0100.0000.0000.0000.000
148A151LEU0-0.0090.00725.465-0.004-0.0040.0000.0000.0000.000
149A152LEU0-0.054-0.00927.861-0.008-0.0080.0000.0000.0000.000
150A153PHE00.0210.00126.2210.0110.0110.0000.0000.0000.000
151A154GLY00.0380.02628.341-0.007-0.0070.0000.0000.0000.000
152A155PRO0-0.063-0.03230.3600.0030.0030.0000.0000.0000.000
153A156ARG10.8190.88433.181-0.057-0.0570.0000.0000.0000.000
154A157GLU-1-0.926-0.94631.1640.0630.0630.0000.0000.0000.000
155A158GLU-1-0.808-0.91332.7470.0530.0530.0000.0000.0000.000
156A159PHE0-0.019-0.00429.407-0.004-0.0040.0000.0000.0000.000
157A160ARG10.9390.96129.430-0.018-0.0180.0000.0000.0000.000
158A161LEU00.0130.01121.890-0.003-0.0030.0000.0000.0000.000
159A162ALA00.0300.00424.448-0.001-0.0010.0000.0000.0000.000
160A163GLU-1-0.836-0.89725.9130.0260.0260.0000.0000.0000.000
161A164ILE0-0.021-0.00420.575-0.002-0.0020.0000.0000.0000.000
162A165LEU0-0.0580.00019.987-0.001-0.0010.0000.0000.0000.000
163A166ALA0-0.009-0.00722.583-0.009-0.0090.0000.0000.0000.000
164A167ALA0-0.027-0.01125.363-0.004-0.0040.0000.0000.0000.000
165A168PRO00.0140.01826.4550.0070.0070.0000.0000.0000.000
166A169ILE00.0260.02028.548-0.004-0.0040.0000.0000.0000.000
167A170ALA00.010-0.00531.0600.0050.0050.0000.0000.0000.000
168A171ARG10.8540.91232.467-0.023-0.0230.0000.0000.0000.000
169A172ILE00.0260.02535.0610.0010.0010.0000.0000.0000.000
170A173LEU00.0390.02730.9750.0040.0040.0000.0000.0000.000
171A174PRO0-0.0470.00132.197-0.004-0.0040.0000.0000.0000.000
172A175GLY00.0490.02128.2280.0040.0040.0000.0000.0000.000
173A176LYS10.8930.93826.907-0.073-0.0730.0000.0000.0000.000
174A177TYR00.0600.01226.3380.0050.0050.0000.0000.0000.000
175A178HIS00.001-0.00824.7560.0150.0150.0000.0000.0000.000
176A179GLY00.0540.02022.3400.0010.0010.0000.0000.0000.000
177A180ILE0-0.037-0.00820.8480.0090.0090.0000.0000.0000.000
178A181GLU-1-0.810-0.90420.1470.1530.1530.0000.0000.0000.000
179A182ALA0-0.0040.01019.1260.0080.0080.0000.0000.0000.000
180A183CYM-1-0.787-0.80116.3250.2100.2100.0000.0000.0000.000
181A184ASP-1-0.798-0.87915.1370.2550.2550.0000.0000.0000.000
182A185LEU0-0.0030.00215.2870.0410.0410.0000.0000.0000.000
183A186ALA00.0100.01212.9100.0080.0080.0000.0000.0000.000
184A187ARG10.7570.80110.922-0.278-0.2780.0000.0000.0000.000
185A188ALA0-0.034-0.01310.5800.1040.1040.0000.0000.0000.000
186A189LEU00.005-0.01011.1410.0540.0540.0000.0000.0000.000
187A190TRP00.009-0.0152.818-1.152-0.3360.305-0.304-0.816-0.003
188A191ARG10.8460.8946.248-0.562-0.5620.0000.0000.0000.000
189A192LEU00.0060.0067.2910.1600.1600.0000.0000.0000.000
190A193ALA0-0.009-0.0015.8020.0060.0060.0000.0000.0000.000
191A194LEU0-0.054-0.0252.460-1.275-0.4472.680-1.139-2.368-0.003
192A195GLU-1-0.922-0.9374.1010.5540.661-0.001-0.012-0.0940.000
193A196GLU-1-0.888-0.9205.7700.4720.4720.0000.0000.0000.000
194A197GLY00.018-0.0027.502-0.175-0.1750.0000.0000.0000.000
195A198LYS10.8290.91211.194-0.088-0.0880.0000.0000.0000.000
196A199GLY00.0180.02214.2980.0080.0080.0000.0000.0000.000
197A200VAL00.0130.00615.5300.0110.0110.0000.0000.0000.000
198A201ARG10.8230.89612.407-0.334-0.3340.0000.0000.0000.000
199A202PHE00.0250.01616.499-0.003-0.0030.0000.0000.0000.000
200A203VAL0-0.015-0.00514.4310.0210.0210.0000.0000.0000.000
201A204GLU-1-0.780-0.89117.8960.0810.0810.0000.0000.0000.000
202A205SER00.021-0.01620.0600.0260.0260.0000.0000.0000.000
203A206ASP-1-0.824-0.91121.1590.1640.1640.0000.0000.0000.000
204A207GLU-1-0.870-0.92517.0350.2500.2500.0000.0000.0000.000
205A208LEU00.0140.00815.5960.0430.0430.0000.0000.0000.000
206A209ARG10.8750.93517.155-0.141-0.1410.0000.0000.0000.000
207A210LYS10.9260.96317.684-0.286-0.2860.0000.0000.0000.000
208A211LEU0-0.019-0.00812.2200.0290.0290.0000.0000.0000.000
209A212GLY00.0410.03113.6460.0640.0640.0000.0000.0000.000
210A213LYS10.7120.82615.633-0.147-0.1470.0000.0000.0000.000
211A214GLY00.0210.03317.366-0.017-0.0170.0000.0000.0000.000
212A215SER0-0.0280.00014.4400.1250.1250.0000.0000.0000.000