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: 3JNQL

Calculation Name: 3DTO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DTO

Chain ID: A

ChEMBL ID:

UniProt ID: Q9K916

Base Structure: X-ray

Registration Date: 2023-09-20

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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2155642.95607
FMO2-HF: Nuclear repulsion 2076242.600477
FMO2-HF: Total energy -79400.355594
FMO2-MP2: Total energy -79630.678615


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:2:ASN)


Summations of interaction energy for fragment #1(A:2:ASN)
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.
-20.815-17.4127.237-4.615-6.0250.03
Interaction energy analysis for fragmet #1(A:2:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.007
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].
3A4GLN00.002-0.0023.189-2.1581.1440.215-1.704-1.8130.005
4A5ALA00.0230.0042.095-9.229-10.0346.998-2.671-3.5220.023
5A6ILE00.0100.0333.530-4.384-3.5470.025-0.238-0.6240.002
6A7LEU00.0500.0205.591-1.211-1.142-0.001-0.002-0.0660.000
7A8GLN0-0.031-0.0186.188-0.056-0.0560.0000.0000.0000.000
8A9SER0-0.032-0.0236.775-0.791-0.7910.0000.0000.0000.000
9A10ALA00.0340.0269.378-0.286-0.2860.0000.0000.0000.000
10A11GLU-1-0.846-0.91011.1380.8460.8460.0000.0000.0000.000
11A12ALA0-0.047-0.03012.397-0.142-0.1420.0000.0000.0000.000
12A13TRP0-0.046-0.01613.616-0.097-0.0970.0000.0000.0000.000
13A14VAL00.0590.02015.340-0.056-0.0560.0000.0000.0000.000
14A15LYS10.9240.97516.797-0.357-0.3570.0000.0000.0000.000
15A16LYS10.8170.89617.867-0.076-0.0760.0000.0000.0000.000
16A17GLN0-0.093-0.05719.910-0.042-0.0420.0000.0000.0000.000
17A18LEU00.0470.04621.104-0.005-0.0050.0000.0000.0000.000
18A19MET0-0.119-0.06622.6100.0240.0240.0000.0000.0000.000
19A20ASP-1-0.872-0.92024.2620.0290.0290.0000.0000.0000.000
20A21GLU-1-0.805-0.89126.9460.0460.0460.0000.0000.0000.000
21A22TYR0-0.064-0.03729.3050.0000.0000.0000.0000.0000.000
22A23SER0-0.055-0.01829.0210.0080.0080.0000.0000.0000.000
23A24GLY00.0320.00728.969-0.007-0.0070.0000.0000.0000.000
24A25HIS0-0.057-0.04327.9100.0180.0180.0000.0000.0000.000
25A26ASP-1-0.823-0.91125.3300.1700.1700.0000.0000.0000.000
26A27TRP00.1160.04816.5590.0250.0250.0000.0000.0000.000
27A28TYR0-0.070-0.04221.4650.0550.0550.0000.0000.0000.000
28A29HIS10.7760.89623.213-0.194-0.1940.0000.0000.0000.000
29A30ILE00.0700.06018.0890.0370.0370.0000.0000.0000.000
30A31ARG10.8080.90915.570-0.617-0.6170.0000.0000.0000.000
31A32ARG10.7590.84018.517-0.196-0.1960.0000.0000.0000.000
32A33VAL00.0430.03720.0150.0200.0200.0000.0000.0000.000
33A34THR00.014-0.00614.3310.0320.0320.0000.0000.0000.000
34A35LEU0-0.046-0.03515.8020.0760.0760.0000.0000.0000.000
35A36MET0-0.0470.00217.875-0.001-0.0010.0000.0000.0000.000
36A37ALA00.0610.02717.610-0.006-0.0060.0000.0000.0000.000
37A38LYS10.8390.90612.583-1.279-1.2790.0000.0000.0000.000
38A39ALA0-0.0190.00016.097-0.012-0.0120.0000.0000.0000.000
39A40ILE0-0.004-0.00818.896-0.032-0.0320.0000.0000.0000.000
40A41GLY00.0380.02217.384-0.038-0.0380.0000.0000.0000.000
41A42GLU-1-0.824-0.90414.5021.0061.0060.0000.0000.0000.000
42A43GLN0-0.023-0.01516.982-0.031-0.0310.0000.0000.0000.000
43A44GLU-1-0.766-0.86520.4300.2120.2120.0000.0000.0000.000
44A45LYS10.7180.86417.132-0.462-0.4620.0000.0000.0000.000
45A46VAL00.0080.03316.826-0.044-0.0440.0000.0000.0000.000
46A47ASP-1-0.797-0.91310.7740.1760.1760.0000.0000.0000.000
47A48VAL0-0.005-0.01911.636-0.009-0.0090.0000.0000.0000.000
48A49PHE00.0100.0156.8770.1430.1430.0000.0000.0000.000
49A50VAL00.0380.02810.2620.0400.0400.0000.0000.0000.000
50A51VAL0-0.018-0.00912.9020.0160.0160.0000.0000.0000.000
51A52GLN0-0.021-0.01811.4920.1030.1030.0000.0000.0000.000
52A53ILE00.0050.0028.7430.0220.0220.0000.0000.0000.000
53A54ALA00.0210.01712.700-0.086-0.0860.0000.0000.0000.000
54A55ALA0-0.021-0.01916.271-0.032-0.0320.0000.0000.0000.000
55A56LEU0-0.056-0.03212.089-0.007-0.0070.0000.0000.0000.000
56A57PHE00.012-0.02713.400-0.033-0.0330.0000.0000.0000.000
57A58HIS0-0.056-0.01717.935-0.049-0.0490.0000.0000.0000.000
58A59ASP-1-0.782-0.89820.9660.1840.1840.0000.0000.0000.000
59A60LEU0-0.075-0.01918.811-0.017-0.0170.0000.0000.0000.000
60A61ILE0-0.037-0.01922.062-0.027-0.0270.0000.0000.0000.000
61A62ASP-1-0.965-0.97525.0810.0160.0160.0000.0000.0000.000
62A70GLU-1-0.791-0.90126.233-0.084-0.0840.0000.0000.0000.000
63A71THR0-0.028-0.02624.690-0.025-0.0250.0000.0000.0000.000
64A72ALA00.0080.00323.433-0.020-0.0200.0000.0000.0000.000
65A73LYS10.9390.96221.1610.1940.1940.0000.0000.0000.000
66A74GLN0-0.076-0.05220.1000.0090.0090.0000.0000.0000.000
67A75GLN00.0170.00919.125-0.023-0.0230.0000.0000.0000.000
68A76LEU00.0130.00816.507-0.035-0.0350.0000.0000.0000.000
69A77ILE0-0.013-0.00115.036-0.042-0.0420.0000.0000.0000.000
70A78ASP-1-0.805-0.89514.912-0.449-0.4490.0000.0000.0000.000
71A79TRP0-0.032-0.0209.431-0.126-0.1260.0000.0000.0000.000
72A80MET0-0.013-0.00610.514-0.093-0.0930.0000.0000.0000.000
73A81GLU-1-0.919-0.96510.109-0.949-0.9490.0000.0000.0000.000
74A82ALA0-0.064-0.02610.537-0.269-0.2690.0000.0000.0000.000
75A83ALA0-0.072-0.0266.978-0.206-0.2060.0000.0000.0000.000
76A84GLY0-0.021-0.0155.679-1.068-1.0680.0000.0000.0000.000
77A85VAL0-0.035-0.0136.781-0.394-0.3940.0000.0000.0000.000
78A86PRO00.0030.0066.7380.3370.3370.0000.0000.0000.000
79A87SER00.0430.0009.7160.1420.1420.0000.0000.0000.000
80A88GLN00.0120.00213.2670.0550.0550.0000.0000.0000.000
81A89LYS10.8070.8937.4400.5320.5320.0000.0000.0000.000
82A90ILE00.0040.02911.7770.1530.1530.0000.0000.0000.000
83A91ASP-1-0.891-0.95713.171-0.297-0.2970.0000.0000.0000.000
84A92HIS0-0.056-0.04515.2310.0460.0460.0000.0000.0000.000
85A93THR0-0.020-0.05213.4950.0990.0990.0000.0000.0000.000
86A94MET0-0.046-0.01615.9190.0550.0550.0000.0000.0000.000
87A95ASP-1-0.918-0.95018.967-0.040-0.0400.0000.0000.0000.000
88A96ILE0-0.0100.01118.4460.0250.0250.0000.0000.0000.000
89A97ILE0-0.041-0.00818.4170.0100.0100.0000.0000.0000.000
90A98ASN0-0.047-0.02621.8500.0100.0100.0000.0000.0000.000
91A99THR0-0.057-0.02924.3070.0110.0110.0000.0000.0000.000
92A100ILE0-0.072-0.01923.5340.0180.0180.0000.0000.0000.000
93A111ALA00.0380.01424.0960.0060.0060.0000.0000.0000.000
94A112THR00.0400.01619.982-0.006-0.0060.0000.0000.0000.000
95A113ARG10.8310.90020.827-0.191-0.1910.0000.0000.0000.000
96A114GLU-1-0.793-0.90915.9500.1660.1660.0000.0000.0000.000
97A115ALA00.0420.01818.9300.0340.0340.0000.0000.0000.000
98A116MET0-0.010-0.00721.5550.0140.0140.0000.0000.0000.000
99A117VAL00.0160.01319.4410.0120.0120.0000.0000.0000.000
100A118VAL00.0040.00218.3760.0280.0280.0000.0000.0000.000
101A119GLN00.0340.02021.104-0.005-0.0050.0000.0000.0000.000
102A120ASP-1-0.740-0.85024.8210.1800.1800.0000.0000.0000.000
103A121ALA0-0.015-0.01421.7300.0000.0000.0000.0000.0000.000
104A122ASP-1-0.810-0.89623.6360.2040.2040.0000.0000.0000.000
105A123ARG10.8460.92825.287-0.137-0.1370.0000.0000.0000.000
106A124LEU00.014-0.00625.523-0.008-0.0080.0000.0000.0000.000
107A125ASP-1-0.749-0.84326.1600.2490.2490.0000.0000.0000.000
108A126ALA0-0.041-0.00728.066-0.011-0.0110.0000.0000.0000.000
109A127LEU00.0220.00531.080-0.012-0.0120.0000.0000.0000.000
110A128GLY00.033-0.01031.6510.0160.0160.0000.0000.0000.000
111A129ALA0-0.003-0.01033.062-0.007-0.0070.0000.0000.0000.000
112A130ILE0-0.0080.00028.065-0.010-0.0100.0000.0000.0000.000
113A131GLY00.0530.04132.234-0.008-0.0080.0000.0000.0000.000
114A132ILE0-0.0170.00033.953-0.011-0.0110.0000.0000.0000.000
115A133ALA00.001-0.00334.930-0.009-0.0090.0000.0000.0000.000
116A134ARG10.8590.91329.403-0.181-0.1810.0000.0000.0000.000
117A135THR00.0190.01135.487-0.010-0.0100.0000.0000.0000.000
118A136PHE00.005-0.00338.469-0.008-0.0080.0000.0000.0000.000
119A137ALA0-0.016-0.00437.251-0.007-0.0070.0000.0000.0000.000
120A138TYR0-0.004-0.00933.664-0.003-0.0030.0000.0000.0000.000
121A139SER0-0.001-0.02639.464-0.005-0.0050.0000.0000.0000.000
122A140GLY00.0030.00442.714-0.005-0.0050.0000.0000.0000.000
123A141ASN0-0.052-0.02640.394-0.005-0.0050.0000.0000.0000.000
124A142LYN0-0.0350.01041.089-0.006-0.0060.0000.0000.0000.000
125A143GLY0-0.0290.00644.307-0.004-0.0040.0000.0000.0000.000
126A144GLN0-0.0160.00444.9520.0000.0000.0000.0000.0000.000
127A145PRO00.0080.00647.6800.0030.0030.0000.0000.0000.000
128A146ILE00.022-0.00345.5410.0020.0020.0000.0000.0000.000
129A147TYR0-0.003-0.02147.0990.0040.0040.0000.0000.0000.000
130A148ASP-1-0.836-0.92349.8820.0490.0490.0000.0000.0000.000
131A149PRO0-0.041-0.01353.2060.0010.0010.0000.0000.0000.000
132A150GLU-1-0.954-0.97255.4120.0420.0420.0000.0000.0000.000
133A151LEU0-0.069-0.02551.334-0.002-0.0020.0000.0000.0000.000
134A152PRO0-0.011-0.00153.2640.0030.0030.0000.0000.0000.000
135A153ILE0-0.011-0.01748.2640.0020.0020.0000.0000.0000.000
136A154ARG10.7350.82946.379-0.056-0.0560.0000.0000.0000.000
137A155GLU-1-0.846-0.88448.4810.0500.0500.0000.0000.0000.000
138A156THR0-0.123-0.08749.671-0.003-0.0030.0000.0000.0000.000
139A157MET0-0.031-0.00543.2120.0000.0000.0000.0000.0000.000
140A158THR0-0.021-0.02145.320-0.001-0.0010.0000.0000.0000.000
141A159VAL0-0.0040.00745.9580.0010.0010.0000.0000.0000.000
142A160GLU-1-0.776-0.89848.1280.0400.0400.0000.0000.0000.000
143A161GLU-1-0.797-0.87441.4050.0620.0620.0000.0000.0000.000
144A162TYR00.0780.00240.4480.0020.0020.0000.0000.0000.000
145A163ARG10.8540.94645.343-0.029-0.0290.0000.0000.0000.000
146A164HIS0-0.064-0.06047.770-0.003-0.0030.0000.0000.0000.000
147A165GLY0-0.0040.01749.1130.0000.0000.0000.0000.0000.000
148A166LYS10.9010.95048.377-0.035-0.0350.0000.0000.0000.000
149A167SER00.034-0.00146.651-0.001-0.0010.0000.0000.0000.000
150A168THR0-0.023-0.02347.4450.0010.0010.0000.0000.0000.000
151A169ALA00.0280.02042.9760.0020.0020.0000.0000.0000.000
152A170ILE0-0.007-0.00843.3310.0050.0050.0000.0000.0000.000
153A171ASN0-0.0040.01445.2220.0040.0040.0000.0000.0000.000
154A172HIS00.0310.01437.636-0.001-0.0010.0000.0000.0000.000
155A173PHE00.0100.01038.4830.0040.0040.0000.0000.0000.000
156A174TYR00.0560.02841.4780.0020.0020.0000.0000.0000.000
157A175GLU-1-0.779-0.84443.9490.0600.0600.0000.0000.0000.000
158A176LYS10.8030.88238.224-0.073-0.0730.0000.0000.0000.000
159A177LEU00.0110.01835.2230.0040.0040.0000.0000.0000.000
160A178PHE0-0.037-0.03637.2060.0090.0090.0000.0000.0000.000
161A179LYS10.8240.91438.266-0.084-0.0840.0000.0000.0000.000
162A180LEU00.0410.00233.242-0.002-0.0020.0000.0000.0000.000
163A181LYN00.0110.02633.5350.0070.0070.0000.0000.0000.000
164A182ASP-1-0.899-0.94934.1870.1120.1120.0000.0000.0000.000
165A183LEU0-0.022-0.01933.922-0.001-0.0010.0000.0000.0000.000
166A184MET0-0.0490.03328.9810.0070.0070.0000.0000.0000.000
167A185ASN0-0.089-0.06827.594-0.020-0.0200.0000.0000.0000.000
168A186THR0-0.047-0.03423.9800.0000.0000.0000.0000.0000.000
169A187GLU-1-0.880-0.94227.0360.1590.1590.0000.0000.0000.000
170A188THR0-0.044-0.04623.8060.0070.0070.0000.0000.0000.000
171A189GLY00.0220.00826.6990.0100.0100.0000.0000.0000.000
172A190LYS10.8620.91927.385-0.142-0.1420.0000.0000.0000.000
173A191GLN0-0.0140.00229.397-0.019-0.0190.0000.0000.0000.000
174A192LEU00.006-0.00224.821-0.004-0.0040.0000.0000.0000.000
175A193ALA00.0120.00129.469-0.008-0.0080.0000.0000.0000.000
176A194LYS10.9790.98631.807-0.150-0.1500.0000.0000.0000.000
177A195GLU-1-0.978-0.98530.2830.2430.2430.0000.0000.0000.000
178A196ARG10.8740.91126.000-0.276-0.2760.0000.0000.0000.000
179A197HIS0-0.033-0.02233.493-0.002-0.0020.0000.0000.0000.000
180A198VAL00.0160.00636.735-0.008-0.0080.0000.0000.0000.000
181A199PHE0-0.0030.00936.126-0.005-0.0050.0000.0000.0000.000
182A200MET0-0.0360.02036.072-0.003-0.0030.0000.0000.0000.000
183A201GLU-1-0.873-0.92639.2530.1020.1020.0000.0000.0000.000
184A202GLN0-0.041-0.03341.530-0.002-0.0020.0000.0000.0000.000
185A203PHE0-0.009-0.00540.616-0.004-0.0040.0000.0000.0000.000
186A204ILE0-0.003-0.01042.705-0.006-0.0060.0000.0000.0000.000
187A205GLU-1-0.794-0.85345.0700.0930.0930.0000.0000.0000.000
188A206ARG10.8060.90445.726-0.102-0.1020.0000.0000.0000.000
189A207PHE00.0220.00946.007-0.004-0.0040.0000.0000.0000.000
190A208LEU00.0110.00347.979-0.005-0.0050.0000.0000.0000.000
191A209SER0-0.039-0.03650.363-0.004-0.0040.0000.0000.0000.000
192A210GLU-1-0.951-0.98848.9160.0880.0880.0000.0000.0000.000
193A211TRP0-0.038-0.01551.204-0.002-0.0020.0000.0000.0000.000
194A212ASN0-0.095-0.04653.645-0.006-0.0060.0000.0000.0000.000
195A213GLY0-0.044-0.01556.138-0.003-0.0030.0000.0000.0000.000