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: 3J89L

Calculation Name: 3ASG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ASG

Chain ID: A

ChEMBL ID:

UniProt ID: Q2W8Q0

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 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1758567.99641
FMO2-HF: Nuclear repulsion 1689020.816424
FMO2-HF: Total energy -69547.179986
FMO2-MP2: Total energy -69754.698849


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:43:ASP)


Summations of interaction energy for fragment #1(A:43:ASP)
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.
-59.128-53.0380.876-3.03-3.9350.022
Interaction energy analysis for fragmet #1(A:43:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.853 / q_NPA : -0.939
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].
3A45ARG10.8810.9493.578-36.563-34.773-0.008-0.859-0.9230.003
4A46GLN00.0650.0233.247-11.991-9.9400.111-1.001-1.1600.007
5A47VAL00.0570.0342.834-10.777-8.5900.774-1.165-1.7960.012
6A48TYR0-0.015-0.0105.634-8.974-8.912-0.001-0.005-0.0560.000
7A49TYR0-0.029-0.0297.921-4.882-4.8820.0000.0000.0000.000
8A50ARG10.8510.9087.324-35.816-35.8160.0000.0000.0000.000
9A51ASP-1-0.805-0.9019.17729.99429.9940.0000.0000.0000.000
10A52LYS10.8990.95311.465-22.067-22.0670.0000.0000.0000.000
11A53GLY00.0400.00912.754-2.096-2.0960.0000.0000.0000.000
12A54ILE00.0090.00312.105-2.203-2.2030.0000.0000.0000.000
13A55SER0-0.078-0.03115.330-1.729-1.7290.0000.0000.0000.000
14A56HIS00.0170.00617.096-1.695-1.6950.0000.0000.0000.000
15A57ALA00.0180.01418.303-1.042-1.0420.0000.0000.0000.000
16A58LYS10.7850.87916.564-19.758-19.7580.0000.0000.0000.000
17A59ALA0-0.027-0.00721.289-0.584-0.5840.0000.0000.0000.000
18A60GLY00.0140.01523.460-0.435-0.4350.0000.0000.0000.000
19A61ARG10.8730.94120.332-15.207-15.2070.0000.0000.0000.000
20A62TYR00.0340.00321.4830.4710.4710.0000.0000.0000.000
21A63SER00.0810.03621.0860.4620.4620.0000.0000.0000.000
22A64GLN0-0.009-0.01119.0680.4390.4390.0000.0000.0000.000
23A65ALA0-0.009-0.00316.9921.0391.0390.0000.0000.0000.000
24A66VAL00.0270.02016.2621.1921.1920.0000.0000.0000.000
25A67MET0-0.0040.00316.3960.7770.7770.0000.0000.0000.000
26A68LEU0-0.082-0.02112.6570.7790.7790.0000.0000.0000.000
27A69LEU00.0340.01111.8531.9671.9670.0000.0000.0000.000
28A70GLU-1-0.770-0.86312.40917.58917.5890.0000.0000.0000.000
29A71GLN0-0.083-0.0399.8860.5530.5530.0000.0000.0000.000
30A72VAL0-0.069-0.0427.0162.8772.8770.0000.0000.0000.000
31A73TYR0-0.011-0.0048.8981.6651.6650.0000.0000.0000.000
32A74ASP-1-0.791-0.89110.56423.77423.7740.0000.0000.0000.000
33A75ALA0-0.031-0.00312.359-0.381-0.3810.0000.0000.0000.000
34A76ASP-1-0.904-0.94114.28317.19117.1910.0000.0000.0000.000
35A77ALA0-0.074-0.04410.284-0.580-0.5800.0000.0000.0000.000
36A78PHE0-0.030-0.01111.0681.9901.9900.0000.0000.0000.000
37A79ASP-1-0.740-0.85110.33828.99528.9950.0000.0000.0000.000
38A80VAL00.0730.02512.722-0.826-0.8260.0000.0000.0000.000
39A81ASP-1-0.845-0.91814.06718.69818.6980.0000.0000.0000.000
40A82VAL00.0150.00410.247-0.996-0.9960.0000.0000.0000.000
41A83ALA00.0430.03413.690-1.130-1.1300.0000.0000.0000.000
42A84LEU00.0020.00816.442-1.238-1.2380.0000.0000.0000.000
43A85HIS0-0.055-0.05216.602-2.059-2.0590.0000.0000.0000.000
44A86LEU00.0100.01715.033-0.640-0.6400.0000.0000.0000.000
45A87GLY00.0580.03817.902-0.800-0.8000.0000.0000.0000.000
46A88ILE0-0.050-0.03320.920-0.893-0.8930.0000.0000.0000.000
47A89ALA0-0.025-0.01519.830-0.683-0.6830.0000.0000.0000.000
48A90TYR0-0.014-0.01918.426-0.455-0.4550.0000.0000.0000.000
49A91VAL0-0.0100.00123.242-0.625-0.6250.0000.0000.0000.000
50A92LYS10.8530.92125.107-11.837-11.8370.0000.0000.0000.000
51A93THR0-0.056-0.04623.892-0.153-0.1530.0000.0000.0000.000
52A94GLY00.0220.02526.695-0.170-0.1700.0000.0000.0000.000
53A95ALA00.0050.01824.728-0.294-0.2940.0000.0000.0000.000
54A96VAL0-0.012-0.02425.9100.3720.3720.0000.0000.0000.000
55A97ASP-1-0.833-0.91327.19510.46810.4680.0000.0000.0000.000
56A98ARG10.9220.95318.925-15.223-15.2230.0000.0000.0000.000
57A99GLY00.011-0.00222.8250.6710.6710.0000.0000.0000.000
58A100THR0-0.047-0.04223.5450.1730.1730.0000.0000.0000.000
59A101GLU-1-0.951-0.95821.64314.05814.0580.0000.0000.0000.000
60A102LEU00.0100.01317.4280.2550.2550.0000.0000.0000.000
61A103LEU0-0.057-0.01220.7770.4100.4100.0000.0000.0000.000
62A104GLU-1-0.792-0.88323.14711.06511.0650.0000.0000.0000.000
63A105ARG10.7990.89417.588-16.724-16.7240.0000.0000.0000.000
64A106SER0-0.043-0.05619.6250.5110.5110.0000.0000.0000.000
65A107LEU0-0.069-0.03020.8720.0000.0000.0000.0000.0000.000
66A108ALA0-0.018-0.00823.646-0.384-0.3840.0000.0000.0000.000
67A109ASP-1-0.844-0.91619.44215.44015.4400.0000.0000.0000.000
68A110ALA0-0.020-0.00520.6590.3900.3900.0000.0000.0000.000
69A111PRO0-0.0050.00422.670-0.315-0.3150.0000.0000.0000.000
70A112ASP-1-0.917-0.95223.92513.12713.1270.0000.0000.0000.000
71A113ASN00.0340.01620.878-0.585-0.5850.0000.0000.0000.000
72A114VAL00.0500.00524.794-0.138-0.1380.0000.0000.0000.000
73A115LYS10.8500.94621.261-14.992-14.9920.0000.0000.0000.000
74A116VAL00.0290.01521.788-0.101-0.1010.0000.0000.0000.000
75A117ALA00.0480.03024.595-0.364-0.3640.0000.0000.0000.000
76A118THR0-0.063-0.05228.242-0.551-0.5510.0000.0000.0000.000
77A119VAL0-0.042-0.02224.532-0.378-0.3780.0000.0000.0000.000
78A120LEU00.0320.05026.806-0.206-0.2060.0000.0000.0000.000
79A121GLY00.0670.02928.441-0.334-0.3340.0000.0000.0000.000
80A122LEU0-0.051-0.04331.250-0.363-0.3630.0000.0000.0000.000
81A123THR0-0.038-0.03028.770-0.192-0.1920.0000.0000.0000.000
82A124TYR0-0.054-0.07229.989-0.245-0.2450.0000.0000.0000.000
83A125VAL0-0.028-0.01733.658-0.302-0.3020.0000.0000.0000.000
84A126GLN0-0.086-0.03033.188-0.393-0.3930.0000.0000.0000.000
85A127VAL0-0.031-0.02132.875-0.143-0.1430.0000.0000.0000.000
86A128GLN00.0160.01835.719-0.251-0.2510.0000.0000.0000.000
87A129LYS10.9310.99832.174-9.897-9.8970.0000.0000.0000.000
88A130TYR00.019-0.03636.8360.2400.2400.0000.0000.0000.000
89A131ASP-1-0.874-0.93739.0118.1908.1900.0000.0000.0000.000
90A132LEU00.0050.00833.3570.0520.0520.0000.0000.0000.000
91A133ALA0-0.024-0.00934.6780.2110.2110.0000.0000.0000.000
92A134VAL00.0020.00335.7530.1270.1270.0000.0000.0000.000
93A135PRO0-0.002-0.00435.8310.0180.0180.0000.0000.0000.000
94A136LEU0-0.0070.01630.5430.1060.1060.0000.0000.0000.000
95A137LEU0-0.010-0.02733.4540.0740.0740.0000.0000.0000.000
96A138ILE00.0140.00735.669-0.052-0.0520.0000.0000.0000.000
97A139LYS10.9670.98933.778-9.460-9.4600.0000.0000.0000.000
98A140VAL00.0030.00031.1240.0330.0330.0000.0000.0000.000
99A141ALA0-0.034-0.02633.8000.0120.0120.0000.0000.0000.000
100A142GLU-1-0.875-0.91637.0857.6937.6930.0000.0000.0000.000
101A143ALA0-0.013-0.00332.775-0.020-0.0200.0000.0000.0000.000
102A144ASN0-0.038-0.03132.124-0.067-0.0670.0000.0000.0000.000
103A145PRO00.0530.03935.236-0.048-0.0480.0000.0000.0000.000
104A146ILE00.0260.00935.918-0.241-0.2410.0000.0000.0000.000
105A147ASN0-0.0250.00132.837-0.152-0.1520.0000.0000.0000.000
106A148PHE00.0190.00036.571-0.038-0.0380.0000.0000.0000.000
107A149ASN00.0170.01434.496-0.345-0.3450.0000.0000.0000.000
108A150VAL00.0120.00733.450-0.086-0.0860.0000.0000.0000.000
109A151ARG10.8960.94636.623-7.987-7.9870.0000.0000.0000.000
110A152PHE00.014-0.00240.164-0.176-0.1760.0000.0000.0000.000
111A153ARG10.8950.93336.876-8.714-8.7140.0000.0000.0000.000
112A154LEU00.0270.02739.060-0.037-0.0370.0000.0000.0000.000
113A155GLY00.0640.03040.316-0.131-0.1310.0000.0000.0000.000
114A156VAL0-0.039-0.02541.661-0.160-0.1600.0000.0000.0000.000
115A157ALA0-0.0010.01139.851-0.111-0.1110.0000.0000.0000.000
116A158LEU0-0.021-0.01241.984-0.106-0.1060.0000.0000.0000.000
117A159LYS10.8430.92044.826-6.459-6.4590.0000.0000.0000.000
118A160ASN0-0.065-0.04343.993-0.218-0.2180.0000.0000.0000.000
119A161LEU0-0.043-0.01642.015-0.082-0.0820.0000.0000.0000.000
120A162GLY00.0340.02146.363-0.082-0.0820.0000.0000.0000.000
121A163ARG10.8580.93144.840-7.262-7.2620.0000.0000.0000.000
122A164PHE00.021-0.01849.0560.1000.1000.0000.0000.0000.000
123A165ASP-1-0.782-0.89251.3036.0556.0550.0000.0000.0000.000
124A166GLU-1-0.803-0.88446.0817.0427.0420.0000.0000.0000.000
125A167ALA0-0.024-0.00546.6530.1550.1550.0000.0000.0000.000
126A168ILE00.0160.00347.7180.0680.0680.0000.0000.0000.000
127A169ASP-1-0.842-0.91948.0826.4606.4600.0000.0000.0000.000
128A170SER0-0.055-0.02943.8390.1490.1490.0000.0000.0000.000
129A171PHE0-0.018-0.02944.7770.1560.1560.0000.0000.0000.000
130A172LYS10.8790.94947.290-6.237-6.2370.0000.0000.0000.000
131A173ILE00.0170.01743.7350.0120.0120.0000.0000.0000.000
132A174ALA0-0.037-0.02043.7800.0840.0840.0000.0000.0000.000
133A175LEU0-0.021-0.03044.7950.0380.0380.0000.0000.0000.000
134A176GLY00.0000.00847.948-0.065-0.0650.0000.0000.0000.000
135A177LEU0-0.047-0.01040.9050.0360.0360.0000.0000.0000.000
136A178ARG10.8760.93839.003-7.883-7.8830.0000.0000.0000.000
137A179PRO00.0760.04546.131-0.055-0.0550.0000.0000.0000.000
138A180ASN00.0280.02349.016-0.196-0.1960.0000.0000.0000.000
139A181GLU-1-0.772-0.86843.3957.4837.4830.0000.0000.0000.000
140A182GLY00.0480.03147.780-0.055-0.0550.0000.0000.0000.000
141A183LYS10.8340.88942.203-7.630-7.6300.0000.0000.0000.000
142A184VAL0-0.018-0.00145.1810.0000.0000.0000.0000.0000.000
143A185HIS10.8240.89647.887-6.337-6.3370.0000.0000.0000.000
144A186ARG10.8280.87350.718-6.212-6.2120.0000.0000.0000.000
145A187ALA0-0.0180.00047.851-0.068-0.0680.0000.0000.0000.000
146A188ILE0-0.0010.01149.818-0.035-0.0350.0000.0000.0000.000
147A189ALA00.0110.02251.647-0.093-0.0930.0000.0000.0000.000
148A190PHE00.0500.01151.805-0.067-0.0670.0000.0000.0000.000
149A191SER0-0.082-0.04050.8310.0450.0450.0000.0000.0000.000
150A192TYR0-0.021-0.03853.1700.0070.0070.0000.0000.0000.000
151A193GLU-1-0.855-0.91956.5425.5985.5980.0000.0000.0000.000
152A194GLN0-0.093-0.05854.667-0.083-0.0830.0000.0000.0000.000
153A195MET0-0.0390.00255.6430.0320.0320.0000.0000.0000.000
154A196GLY00.0160.01258.610-0.077-0.0770.0000.0000.0000.000
155A197ARG10.7800.87355.851-5.791-5.7910.0000.0000.0000.000
156A198HIS00.048-0.00460.6180.1110.1110.0000.0000.0000.000
157A199GLU-1-0.937-0.96662.3944.9044.9040.0000.0000.0000.000
158A200GLU-1-0.806-0.87558.3325.6275.6270.0000.0000.0000.000
159A201ALA0-0.015-0.01357.6890.0960.0960.0000.0000.0000.000
160A202LEU00.0010.00858.4490.0620.0620.0000.0000.0000.000
161A203PRO00.009-0.00259.3090.0160.0160.0000.0000.0000.000
162A204HIS00.0410.04254.1650.1080.1080.0000.0000.0000.000
163A205PHE00.0300.00555.8680.0810.0810.0000.0000.0000.000
164A206LYS10.9290.97057.654-5.032-5.0320.0000.0000.0000.000
165A207LYS10.8310.88755.593-5.589-5.5890.0000.0000.0000.000
166A208ALA0-0.033-0.02553.4370.0910.0910.0000.0000.0000.000
167A209ASN00.0140.00654.4240.1500.1500.0000.0000.0000.000
168A210GLU-1-0.766-0.83856.9725.5915.5910.0000.0000.0000.000
169A211LEU0-0.055-0.03151.6670.0530.0530.0000.0000.0000.000
170A212ASP-1-0.841-0.87652.6526.2696.2690.0000.0000.0000.000
171A213GLU-1-0.987-0.99053.9615.4405.4400.0000.0000.0000.000
172A214GLY0-0.0160.00354.077-0.013-0.0130.0000.0000.0000.000
173A215ALA0-0.068-0.04455.1410.0330.0330.0000.0000.0000.000
174A216SER0-0.002-0.02056.292-0.120-0.1200.0000.0000.0000.000
175A217VAL00.0590.01058.2690.0030.0030.0000.0000.0000.000
176A218GLU-1-0.863-0.90859.5905.4315.4310.0000.0000.0000.000
177A219LEU0-0.007-0.01655.321-0.020-0.0200.0000.0000.0000.000
178A220ALA0-0.037-0.00959.4410.0280.0280.0000.0000.0000.000
179A221LEU0-0.025-0.02161.850-0.046-0.0460.0000.0000.0000.000
180A222VAL0-0.0020.02058.386-0.036-0.0360.0000.0000.0000.000
181A223PRO00.0100.01759.8660.0620.0620.0000.0000.0000.000
182A224ARG10.8780.93555.081-5.518-5.5180.0000.0000.0000.000