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: 89V9Y

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 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 212
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2422225.569914
FMO2-HF: Nuclear repulsion 2342816.122423
FMO2-HF: Total energy -79409.447491
FMO2-MP2: Total energy -79644.778999


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.
0.502-0.85514.699-4.45-8.892-0.015
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 : 0.023 / q_NPA : 0.003
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].
3A6LYS10.8040.8912.3692.6922.0975.857-1.943-3.319-0.010
4A7ARG10.9190.9574.6952.1182.222-0.001-0.008-0.0950.000
5A8VAL00.0400.0206.221-0.057-0.0570.0000.0000.0000.000
6A9LEU00.0280.0298.8770.1730.1730.0000.0000.0000.000
7A10LEU0-0.011-0.01012.167-0.002-0.0020.0000.0000.0000.000
8A11ALA00.0290.01813.7230.0370.0370.0000.0000.0000.000
9A12GLY00.033-0.00917.2310.0250.0250.0000.0000.0000.000
10A13ALA00.0120.00216.5110.0310.0310.0000.0000.0000.000
11A14THR00.0280.01117.8170.0130.0130.0000.0000.0000.000
12A15GLY0-0.0170.01420.5780.0210.0210.0000.0000.0000.000
13A16LEU00.001-0.00220.161-0.007-0.0070.0000.0000.0000.000
14A17THR00.034-0.01216.4090.0180.0180.0000.0000.0000.000
15A18GLY0-0.016-0.00715.9430.0050.0050.0000.0000.0000.000
16A19GLU-1-0.911-0.95215.555-0.178-0.1780.0000.0000.0000.000
17A20HIS0-0.021-0.01815.963-0.027-0.0270.0000.0000.0000.000
18A21LEU0-0.042-0.0189.8800.0270.0270.0000.0000.0000.000
19A22LEU0-0.009-0.01011.185-0.060-0.0600.0000.0000.0000.000
20A23ASP-1-0.895-0.94411.981-0.171-0.1710.0000.0000.0000.000
21A24ARG10.8300.9147.434-0.963-0.9630.0000.0000.0000.000
22A25ILE0-0.004-0.0037.137-0.022-0.0220.0000.0000.0000.000
23A26LEU0-0.006-0.0127.584-0.229-0.2290.0000.0000.0000.000
24A27SER0-0.073-0.0379.2900.0180.0180.0000.0000.0000.000
25A28GLU-1-0.837-0.9114.1140.7090.849-0.001-0.014-0.1250.000
26A29PRO00.0200.0066.091-0.384-0.3840.0000.0000.0000.000
27A30THR0-0.038-0.0122.2681.516-2.0697.259-1.118-2.557-0.005
28A31LEU00.0450.0433.815-1.215-0.9060.008-0.104-0.2130.000
29A32ALA0-0.080-0.0415.0550.4730.499-0.001-0.001-0.0240.000
30A33LYS10.9380.9597.4791.1651.1650.0000.0000.0000.000
31A34VAL00.0120.0198.957-0.266-0.2660.0000.0000.0000.000
32A35ILE00.0380.02511.0030.1010.1010.0000.0000.0000.000
33A36ALA00.010-0.00814.185-0.017-0.0170.0000.0000.0000.000
34A37PRO00.0010.02316.1660.0480.0480.0000.0000.0000.000
35A38ALA0-0.010-0.00319.7060.0160.0160.0000.0000.0000.000
36A39ARG10.9750.99121.9040.1350.1350.0000.0000.0000.000
37A40LYS10.9080.93624.0380.1500.1500.0000.0000.0000.000
38A41ALA00.0370.02523.149-0.016-0.0160.0000.0000.0000.000
39A42LEU0-0.016-0.00317.4860.0210.0210.0000.0000.0000.000
40A43ALA0-0.006-0.00419.818-0.002-0.0020.0000.0000.0000.000
41A44GLU-1-0.919-0.95819.028-0.265-0.2650.0000.0000.0000.000
42A45HIS00.0710.02112.655-0.034-0.0340.0000.0000.0000.000
43A46PRO00.0070.00115.165-0.028-0.0280.0000.0000.0000.000
44A47ARG10.7660.8877.7660.9530.9530.0000.0000.0000.000
45A48LEU0-0.035-0.01412.498-0.119-0.1190.0000.0000.0000.000
46A49ASP-1-0.886-0.92814.758-0.449-0.4490.0000.0000.0000.000
47A50ASN00.007-0.02116.7950.0050.0050.0000.0000.0000.000
48A51PRO00.0380.04219.0070.0440.0440.0000.0000.0000.000
49A52VAL00.003-0.01522.1210.0050.0050.0000.0000.0000.000
50A53GLY0-0.013-0.01324.7340.0130.0130.0000.0000.0000.000
51A54PRO0-0.031-0.02225.522-0.008-0.0080.0000.0000.0000.000
52A55LEU00.0430.01720.508-0.008-0.0080.0000.0000.0000.000
53A56ALA00.0170.00224.235-0.021-0.0210.0000.0000.0000.000
54A57GLU-1-0.884-0.95226.498-0.194-0.1940.0000.0000.0000.000
55A58LEU0-0.025-0.01022.737-0.011-0.0110.0000.0000.0000.000
56A59LEU0-0.028-0.00820.101-0.027-0.0270.0000.0000.0000.000
57A60PRO0-0.023-0.02522.235-0.033-0.0330.0000.0000.0000.000
58A61GLN0-0.043-0.01724.442-0.008-0.0080.0000.0000.0000.000
59A62LEU0-0.0450.00217.842-0.013-0.0130.0000.0000.0000.000
60A63ASP-1-0.844-0.90220.150-0.496-0.4960.0000.0000.0000.000
61A64GLY0-0.045-0.03716.260-0.052-0.0520.0000.0000.0000.000
62A65SER0-0.043-0.02113.1960.0310.0310.0000.0000.0000.000
63A66ILE0-0.030-0.02510.937-0.083-0.0830.0000.0000.0000.000
64A67ASP-1-0.792-0.8726.609-3.724-3.7240.0000.0000.0000.000
65A68THR00.009-0.0116.7200.0670.0670.0000.0000.0000.000
66A69ALA00.0050.0088.9790.0730.0730.0000.0000.0000.000
67A70PHE00.0330.0117.3850.0520.0520.0000.0000.0000.000
68A71CYS0-0.0280.00212.8790.0130.0130.0000.0000.0000.000
69A72CYS0-0.014-0.01115.2520.0620.0620.0000.0000.0000.000
70A73LEU00.003-0.00618.1230.0210.0210.0000.0000.0000.000
71A74GLY00.0350.00821.6540.0110.0110.0000.0000.0000.000
72A75THR0-0.005-0.00124.7880.0100.0100.0000.0000.0000.000
73A76THR00.002-0.01928.3730.0120.0120.0000.0000.0000.000
74A77ILE00.0560.01631.760-0.005-0.0050.0000.0000.0000.000
75A78LYS10.8990.95735.0770.0130.0130.0000.0000.0000.000
76A79GLU-1-0.899-0.96032.147-0.038-0.0380.0000.0000.0000.000
77A80ALA0-0.054-0.01132.310-0.006-0.0060.0000.0000.0000.000
78A81GLY00.0040.00434.045-0.004-0.0040.0000.0000.0000.000
79A82SER00.0080.00036.6250.0020.0020.0000.0000.0000.000
80A83GLU-1-0.915-0.96235.905-0.045-0.0450.0000.0000.0000.000
81A84GLU-1-0.884-0.95634.857-0.068-0.0680.0000.0000.0000.000
82A85ALA0-0.0060.00233.883-0.009-0.0090.0000.0000.0000.000
83A86PHE0-0.027-0.02329.493-0.007-0.0070.0000.0000.0000.000
84A87ARG10.8930.94930.0990.0870.0870.0000.0000.0000.000
85A88ALA00.0370.03629.560-0.011-0.0110.0000.0000.0000.000
86A89VAL0-0.041-0.02325.845-0.017-0.0170.0000.0000.0000.000
87A90ASP-1-0.798-0.92025.376-0.097-0.0970.0000.0000.0000.000
88A91PHE0-0.036-0.01525.424-0.002-0.0020.0000.0000.0000.000
89A92ASP-1-0.849-0.93425.719-0.155-0.1550.0000.0000.0000.000
90A93LEU0-0.037-0.01823.662-0.023-0.0230.0000.0000.0000.000
91A94PRO00.0250.01320.973-0.035-0.0350.0000.0000.0000.000
92A95LEU00.0550.04920.880-0.040-0.0400.0000.0000.0000.000
93A96ALA0-0.010-0.00722.496-0.030-0.0300.0000.0000.0000.000
94A97VAL0-0.006-0.01117.252-0.028-0.0280.0000.0000.0000.000
95A98GLY00.0180.00917.890-0.061-0.0610.0000.0000.0000.000
96A99LYS10.9560.97618.8170.2360.2360.0000.0000.0000.000
97A100ARG10.8600.91619.4700.4180.4180.0000.0000.0000.000
98A101ALA00.0350.00414.803-0.045-0.0450.0000.0000.0000.000
99A102LEU0-0.010-0.00616.132-0.084-0.0840.0000.0000.0000.000
100A103GLU-1-0.935-0.94817.747-0.390-0.3900.0000.0000.0000.000
101A104MET0-0.091-0.02916.0340.0050.0050.0000.0000.0000.000
102A105GLY0-0.003-0.00514.921-0.099-0.0990.0000.0000.0000.000
103A106ALA0-0.067-0.01012.179-0.148-0.1480.0000.0000.0000.000
104A107ARG10.9490.9537.3521.7411.7410.0000.0000.0000.000
105A108HIS00.0000.0207.0080.3770.3770.0000.0000.0000.000
106A109TYR0-0.034-0.01310.595-0.114-0.1140.0000.0000.0000.000
107A110LEU0-0.0020.0038.6310.1080.1080.0000.0000.0000.000
108A111VAL00.0000.00012.873-0.027-0.0270.0000.0000.0000.000
109A112VAL0-0.012-0.00316.4310.0580.0580.0000.0000.0000.000
110A113SER0-0.043-0.03318.529-0.022-0.0220.0000.0000.0000.000
111A114ALA0-0.023-0.03821.6120.0110.0110.0000.0000.0000.000
112A115LEU00.0390.01523.960-0.003-0.0030.0000.0000.0000.000
113A116GLY0-0.027-0.01825.602-0.010-0.0100.0000.0000.0000.000
114A117ALA0-0.056-0.00925.153-0.009-0.0090.0000.0000.0000.000
115A118ASP-1-0.830-0.93327.1830.0050.0050.0000.0000.0000.000
116A119ALA0-0.0100.00429.618-0.002-0.0020.0000.0000.0000.000
117A120LYS10.9220.95931.2680.0110.0110.0000.0000.0000.000
118A121SER00.0210.03532.9060.0050.0050.0000.0000.0000.000
119A122SER00.0420.00334.732-0.007-0.0070.0000.0000.0000.000
120A123ILE0-0.042-0.01233.987-0.003-0.0030.0000.0000.0000.000
121A124PHE00.0470.02134.065-0.001-0.0010.0000.0000.0000.000
122A125TYR00.0170.00427.018-0.003-0.0030.0000.0000.0000.000
123A126ASN00.029-0.00429.452-0.010-0.0100.0000.0000.0000.000
124A127ARG10.9170.97829.5550.0300.0300.0000.0000.0000.000
125A128VAL00.0020.00728.708-0.006-0.0060.0000.0000.0000.000
126A129LYS10.8930.95823.8570.0580.0580.0000.0000.0000.000
127A130GLY00.0530.02625.498-0.008-0.0080.0000.0000.0000.000
128A131GLU-1-0.910-0.97626.949-0.077-0.0770.0000.0000.0000.000
129A132LEU0-0.032-0.00821.944-0.012-0.0120.0000.0000.0000.000
130A133GLU-1-0.756-0.84622.018-0.041-0.0410.0000.0000.0000.000
131A134GLN0-0.034-0.01522.931-0.011-0.0110.0000.0000.0000.000
132A135ALA00.0270.01824.990-0.010-0.0100.0000.0000.0000.000
133A136LEU0-0.014-0.02119.194-0.022-0.0220.0000.0000.0000.000
134A137GLN0-0.076-0.05320.585-0.021-0.0210.0000.0000.0000.000
135A138GLU-1-0.923-0.94621.808-0.134-0.1340.0000.0000.0000.000
136A139GLN0-0.109-0.04920.446-0.034-0.0340.0000.0000.0000.000
137A140GLY00.0130.01720.163-0.019-0.0190.0000.0000.0000.000
138A141TRP0-0.053-0.02213.420-0.072-0.0720.0000.0000.0000.000
139A142PRO0-0.065-0.02012.5250.0460.0460.0000.0000.0000.000
140A143GLN0-0.006-0.0168.256-0.159-0.1590.0000.0000.0000.000
141A144LEU00.0020.00812.578-0.096-0.0960.0000.0000.0000.000
142A145THR0-0.025-0.03511.1110.1290.1290.0000.0000.0000.000
143A146ILE0-0.007-0.00414.013-0.041-0.0410.0000.0000.0000.000
144A147ALA00.0130.01715.6230.0540.0540.0000.0000.0000.000
145A148ARG10.7740.85017.433-0.071-0.0710.0000.0000.0000.000
146A149PRO00.0350.01519.5100.0250.0250.0000.0000.0000.000
147A150SER00.0470.02921.813-0.015-0.0150.0000.0000.0000.000
148A151LEU0-0.0010.01025.437-0.009-0.0090.0000.0000.0000.000
149A152LEU0-0.035-0.00427.900-0.013-0.0130.0000.0000.0000.000
150A153PHE00.0270.01626.8750.0150.0150.0000.0000.0000.000
151A154GLY00.0250.01529.011-0.011-0.0110.0000.0000.0000.000
152A155PRO0-0.075-0.04031.1970.0060.0060.0000.0000.0000.000
153A156ARG10.8640.91233.949-0.061-0.0610.0000.0000.0000.000
154A157GLU-1-0.947-0.95531.7260.0700.0700.0000.0000.0000.000
155A158GLU-1-0.824-0.92233.3360.0510.0510.0000.0000.0000.000
156A159PHE0-0.019-0.00430.146-0.008-0.0080.0000.0000.0000.000
157A160ARG10.9630.97429.9550.0110.0110.0000.0000.0000.000
158A161LEU00.0450.02322.231-0.005-0.0050.0000.0000.0000.000
159A162ALA0-0.002-0.01725.132-0.005-0.0050.0000.0000.0000.000
160A163GLU-1-0.841-0.90326.2420.0000.0000.0000.0000.0000.000
161A164ILE0-0.030-0.00621.318-0.006-0.0060.0000.0000.0000.000
162A165LEU0-0.063-0.01920.368-0.006-0.0060.0000.0000.0000.000
163A166ALA0-0.026-0.02122.849-0.007-0.0070.0000.0000.0000.000
164A167ALA0-0.036-0.01325.098-0.004-0.0040.0000.0000.0000.000
165A168PRO0-0.0070.01626.5950.0120.0120.0000.0000.0000.000
166A169ILE00.0450.02728.896-0.005-0.0050.0000.0000.0000.000
167A170ALA00.0200.00331.6860.0080.0080.0000.0000.0000.000
168A171ARG10.8340.89633.1670.0020.0020.0000.0000.0000.000
169A172ILE00.0380.02735.9270.0030.0030.0000.0000.0000.000
170A173LEU00.0500.02631.7420.0070.0070.0000.0000.0000.000
171A174PRO0-0.0550.00232.734-0.007-0.0070.0000.0000.0000.000
172A175GLY00.0530.02429.2700.0070.0070.0000.0000.0000.000
173A176LYS10.9380.96727.839-0.086-0.0860.0000.0000.0000.000
174A177TYR00.026-0.01627.1000.0070.0070.0000.0000.0000.000
175A178HIS00.0080.00825.9150.0190.0190.0000.0000.0000.000
176A179GLY00.0560.03123.1620.0000.0000.0000.0000.0000.000
177A180ILE0-0.041-0.01821.8530.0120.0120.0000.0000.0000.000
178A181GLU-1-0.905-0.96021.4360.1720.1720.0000.0000.0000.000
179A182ALA0-0.0030.00119.8620.0140.0140.0000.0000.0000.000
180A183CYM-1-0.842-0.88417.6200.2430.2430.0000.0000.0000.000
181A184ASP-1-0.820-0.90316.4610.3260.3260.0000.0000.0000.000
182A185LEU0-0.014-0.01316.1100.0690.0690.0000.0000.0000.000
183A186ALA00.0240.01213.7200.0170.0170.0000.0000.0000.000
184A187ARG10.8020.88412.149-0.395-0.3950.0000.0000.0000.000
185A188ALA0-0.025-0.02411.2150.2120.2120.0000.0000.0000.000
186A189LEU00.0080.00411.1970.0940.0940.0000.0000.0000.000
187A190TRP00.0570.0193.017-1.075-0.3770.099-0.180-0.6170.000
188A191ARG10.8300.8836.445-0.745-0.7450.0000.0000.0000.000
189A192LEU00.0160.0097.4400.3200.3200.0000.0000.0000.000
190A193ALA0-0.015-0.0045.706-0.173-0.1730.0000.0000.0000.000
191A194LEU0-0.073-0.0322.534-2.578-1.2531.479-1.020-1.7830.000
192A195GLU-1-0.963-0.9674.0421.0551.2760.000-0.062-0.1590.000
193A196GLU-1-0.966-0.9605.1630.1410.1410.0000.0000.0000.000
194A197GLY00.0230.0006.6200.2730.2730.0000.0000.0000.000
195A198LYS10.8530.92610.2500.2570.2570.0000.0000.0000.000
196A199GLY00.0070.00713.2570.0800.0800.0000.0000.0000.000
197A200VAL00.0190.00514.667-0.044-0.0440.0000.0000.0000.000
198A201ARG10.8720.94712.461-0.404-0.4040.0000.0000.0000.000
199A202PHE00.0050.00116.303-0.031-0.0310.0000.0000.0000.000
200A203VAL0-0.032-0.01014.4030.0400.0400.0000.0000.0000.000
201A204GLU-1-0.791-0.90917.8520.0760.0760.0000.0000.0000.000
202A205SER00.004-0.03220.0490.0460.0460.0000.0000.0000.000
203A206ASP-1-0.885-0.94421.3360.2290.2290.0000.0000.0000.000
204A207GLU-1-0.886-0.94117.5720.3460.3460.0000.0000.0000.000
205A208LEU00.0240.00515.6110.0800.0800.0000.0000.0000.000
206A209ARG10.9961.01517.431-0.214-0.2140.0000.0000.0000.000
207A210LYS10.9280.96417.541-0.542-0.5420.0000.0000.0000.000
208A211LEU0-0.019-0.01012.0080.0640.0640.0000.0000.0000.000
209A212GLY00.0290.02814.3710.1050.1050.0000.0000.0000.000
210A213LYS10.8150.89216.235-0.245-0.2450.0000.0000.0000.000
211A214GLY0-0.0200.00917.979-0.018-0.0180.0000.0000.0000.000
212A215SER00.0020.01114.4760.1030.1030.0000.0000.0000.000