Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: KG2Z3

Calculation Name: 4AXG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4AXG

Chain ID: A

ChEMBL ID:

UniProt ID: Q9VMA3

Base Structure: X-ray

Registration Date: 2023-09-22

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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2085921.117043
FMO2-HF: Nuclear repulsion 2011511.71817
FMO2-HF: Total energy -74409.398873
FMO2-MP2: Total energy -74626.809794


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:66:HIS)


Summations of interaction energy for fragment #1(A:66:HIS)
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.
-5.892-3.9-0.012-0.769-1.2120.001
Interaction energy analysis for fragmet #1(A:66:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.014
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].
3A68TYR0-0.019-0.0073.807-4.427-2.637-0.011-0.746-1.0340.001
4A69LYS10.8480.9204.4140.9221.124-0.001-0.023-0.1780.000
5A70HIS10.8050.8647.039-0.695-0.6950.0000.0000.0000.000
6A71PRO00.0280.02010.286-0.195-0.1950.0000.0000.0000.000
7A72LEU0-0.0060.00613.1880.0210.0210.0000.0000.0000.000
8A73MET0-0.029-0.00316.1920.0140.0140.0000.0000.0000.000
9A74ASN0-0.059-0.05119.703-0.014-0.0140.0000.0000.0000.000
10A75VAL00.0010.00918.218-0.021-0.0210.0000.0000.0000.000
11A76TRP00.0180.00218.4620.0040.0040.0000.0000.0000.000
12A77THR0-0.017-0.01819.203-0.045-0.0450.0000.0000.0000.000
13A78LEU0-0.022-0.00219.2050.0400.0400.0000.0000.0000.000
14A79TRP00.0240.00121.637-0.025-0.0250.0000.0000.0000.000
15A80TYR0-0.033-0.02824.5050.0020.0020.0000.0000.0000.000
16A81LEU00.0040.02326.2410.0060.0060.0000.0000.0000.000
17A82GLU-1-0.871-0.93729.505-0.329-0.3290.0000.0000.0000.000
18A83ASN0-0.007-0.02031.2520.0130.0130.0000.0000.0000.000
19A84ASP-1-0.831-0.89634.796-0.175-0.1750.0000.0000.0000.000
20A85ARG10.8760.95036.6180.1790.1790.0000.0000.0000.000
21A86SER00.0080.00338.054-0.007-0.0070.0000.0000.0000.000
22A87LYS10.8310.90340.1940.1890.1890.0000.0000.0000.000
23A88SER0-0.006-0.01041.192-0.008-0.0080.0000.0000.0000.000
24A89TRP00.0220.00840.8480.0060.0060.0000.0000.0000.000
25A90GLU-1-0.864-0.92337.881-0.198-0.1980.0000.0000.0000.000
26A91ASP-1-0.865-0.93533.079-0.234-0.2340.0000.0000.0000.000
27A92MET0-0.054-0.01832.964-0.011-0.0110.0000.0000.0000.000
28A93GLN0-0.003-0.00328.915-0.031-0.0310.0000.0000.0000.000
29A94ASN00.0120.00526.0020.0150.0150.0000.0000.0000.000
30A95GLU-1-0.859-0.94222.310-0.396-0.3960.0000.0000.0000.000
31A96ILE0-0.051-0.02018.553-0.029-0.0290.0000.0000.0000.000
32A97THR00.033-0.00415.409-0.064-0.0640.0000.0000.0000.000
33A98SER0-0.0050.00517.4000.1060.1060.0000.0000.0000.000
34A99PHE0-0.012-0.00513.571-0.102-0.1020.0000.0000.0000.000
35A100ASP-1-0.843-0.93113.015-0.209-0.2090.0000.0000.0000.000
36A101THR0-0.006-0.0219.6670.1050.1050.0000.0000.0000.000
37A102VAL00.0290.00810.761-0.143-0.1430.0000.0000.0000.000
38A103GLU-1-0.752-0.8525.5750.2440.2440.0000.0000.0000.000
39A104ASP-1-0.767-0.8458.303-1.784-1.7840.0000.0000.0000.000
40A105PHE00.0000.0149.994-0.072-0.0720.0000.0000.0000.000
41A106TRP00.0290.00010.112-0.043-0.0430.0000.0000.0000.000
42A107SER0-0.056-0.0348.026-0.261-0.2610.0000.0000.0000.000
43A108LEU0-0.0210.00110.267-0.009-0.0090.0000.0000.0000.000
44A109TYR00.008-0.00813.5550.0700.0700.0000.0000.0000.000
45A110ASN0-0.022-0.01711.1690.1910.1910.0000.0000.0000.000
46A111HIS0-0.080-0.0409.781-0.075-0.0750.0000.0000.0000.000
47A112ILE0-0.0440.00015.1180.0500.0500.0000.0000.0000.000
48A113LYS10.8720.93418.5590.4720.4720.0000.0000.0000.000
49A114PRO00.0900.06721.5410.0140.0140.0000.0000.0000.000
50A115PRO00.0520.01623.2350.0070.0070.0000.0000.0000.000
51A116SER0-0.087-0.07226.5170.0150.0150.0000.0000.0000.000
52A117GLU-1-0.939-0.97824.716-0.402-0.4020.0000.0000.0000.000
53A118ILE0-0.0420.01025.442-0.014-0.0140.0000.0000.0000.000
54A119LYS10.8810.92928.0400.3200.3200.0000.0000.0000.000
55A120LEU0-0.023-0.00231.4190.0060.0060.0000.0000.0000.000
56A121GLY0-0.025-0.01934.4330.0010.0010.0000.0000.0000.000
57A122SER00.001-0.00129.464-0.009-0.0090.0000.0000.0000.000
58A123ASP-1-0.796-0.88229.908-0.190-0.1900.0000.0000.0000.000
59A124TYR0-0.024-0.02322.584-0.026-0.0260.0000.0000.0000.000
60A125SER0-0.014-0.02525.4820.0430.0430.0000.0000.0000.000
61A126LEU00.0060.02219.920-0.035-0.0350.0000.0000.0000.000
62A127PHE00.017-0.00323.8020.0380.0380.0000.0000.0000.000
63A128LYS10.9040.97223.4600.0140.0140.0000.0000.0000.000
64A129LYS10.8660.92721.9150.3320.3320.0000.0000.0000.000
65A130ASN0-0.055-0.04124.1980.0050.0050.0000.0000.0000.000
66A131ILE00.0100.03227.2860.0190.0190.0000.0000.0000.000
67A132ARG10.8830.93728.0580.1390.1390.0000.0000.0000.000
68A133PRO00.0120.02728.7020.0190.0190.0000.0000.0000.000
69A134MET0-0.029-0.03130.8840.0050.0050.0000.0000.0000.000
70A135TRP00.043-0.00234.6100.0100.0100.0000.0000.0000.000
71A136GLU-1-0.839-0.91337.198-0.090-0.0900.0000.0000.0000.000
72A137ASP-1-0.832-0.91233.578-0.128-0.1280.0000.0000.0000.000
73A138ALA00.0510.02135.9080.0070.0070.0000.0000.0000.000
74A139ALA00.0120.01832.5070.0090.0090.0000.0000.0000.000
75A140ASN00.012-0.01231.9210.0130.0130.0000.0000.0000.000
76A141LYS10.8200.93735.8570.0910.0910.0000.0000.0000.000
77A142GLN0-0.007-0.01339.396-0.001-0.0010.0000.0000.0000.000
78A143GLY00.0790.06237.3600.0070.0070.0000.0000.0000.000
79A144GLY0-0.009-0.03136.9390.0000.0000.0000.0000.0000.000
80A145ARG10.8590.94735.0760.0970.0970.0000.0000.0000.000
81A146TRP00.0330.02133.9840.0010.0010.0000.0000.0000.000
82A147VAL0-0.064-0.02634.338-0.012-0.0120.0000.0000.0000.000
83A148ILE00.0760.04032.0310.0100.0100.0000.0000.0000.000
84A149THR0-0.034-0.02735.365-0.014-0.0140.0000.0000.0000.000
85A150LEU00.0190.01032.1380.0080.0080.0000.0000.0000.000
86A151ASN00.0110.00236.578-0.013-0.0130.0000.0000.0000.000
87A152LYS10.9380.96139.2190.1160.1160.0000.0000.0000.000
88A153SER00.0440.04633.1600.0090.0090.0000.0000.0000.000
89A154SER0-0.065-0.07032.511-0.016-0.0160.0000.0000.0000.000
90A155LYS10.9090.93028.6040.2700.2700.0000.0000.0000.000
91A156THR00.0640.03027.058-0.013-0.0130.0000.0000.0000.000
92A157ASP-1-0.840-0.87827.367-0.122-0.1220.0000.0000.0000.000
93A158LEU0-0.047-0.01529.0080.0050.0050.0000.0000.0000.000
94A159ASP-1-0.760-0.87424.171-0.288-0.2880.0000.0000.0000.000
95A160ASN00.0140.00424.178-0.027-0.0270.0000.0000.0000.000
96A161LEU00.0320.02824.9630.0100.0100.0000.0000.0000.000
97A162TRP0-0.003-0.01623.2140.0210.0210.0000.0000.0000.000
98A163LEU0-0.013-0.00118.150-0.003-0.0030.0000.0000.0000.000
99A164ASP-1-0.830-0.92421.525-0.091-0.0910.0000.0000.0000.000
100A165VAL0-0.031-0.01423.6190.0250.0250.0000.0000.0000.000
101A166LEU0-0.042-0.02219.9720.0100.0100.0000.0000.0000.000
102A167LEU0-0.002-0.00317.1310.0090.0090.0000.0000.0000.000
103A168CYS0-0.066-0.03120.4710.0440.0440.0000.0000.0000.000
104A169LEU0-0.070-0.03222.3650.0230.0230.0000.0000.0000.000
105A170ILE0-0.019-0.01115.8500.0210.0210.0000.0000.0000.000
106A171GLY0-0.025-0.00618.8390.0340.0340.0000.0000.0000.000
107A172GLU-1-0.890-0.94019.7950.0520.0520.0000.0000.0000.000
108A173ALA0-0.015-0.00423.0050.0240.0240.0000.0000.0000.000
109A174PHE0-0.037-0.03425.133-0.001-0.0010.0000.0000.0000.000
110A175ASP-1-0.813-0.90227.7840.0910.0910.0000.0000.0000.000
111A176HIS0-0.033-0.02430.1420.0050.0050.0000.0000.0000.000
112A177SER00.0610.02526.206-0.019-0.0190.0000.0000.0000.000
113A178ASP-1-0.921-0.95528.2690.0060.0060.0000.0000.0000.000
114A179GLN0-0.036-0.02529.957-0.017-0.0170.0000.0000.0000.000
115A180ILE0-0.034-0.00526.671-0.016-0.0160.0000.0000.0000.000
116A181CYS0-0.036-0.00928.6380.0030.0030.0000.0000.0000.000
117A182GLY00.0590.00926.470-0.017-0.0170.0000.0000.0000.000
118A183ALA0-0.0190.00826.2470.0210.0210.0000.0000.0000.000
119A184VAL0-0.023-0.00627.217-0.024-0.0240.0000.0000.0000.000
120A185ILE0-0.0100.00026.9510.0200.0200.0000.0000.0000.000
121A186ASN0-0.062-0.02829.833-0.002-0.0020.0000.0000.0000.000
122A187ILE00.0290.01328.8790.0170.0170.0000.0000.0000.000
123A188ARG10.7670.83532.9420.1930.1930.0000.0000.0000.000
124A189GLY00.0110.02635.3600.0070.0070.0000.0000.0000.000
125A190LYS10.8610.93336.7560.1160.1160.0000.0000.0000.000
126A191SER0-0.043-0.05238.6830.0060.0060.0000.0000.0000.000
127A192ASN00.0490.03733.342-0.008-0.0080.0000.0000.0000.000
128A193LYS10.9260.95534.0310.1470.1470.0000.0000.0000.000
129A194ILE00.0660.03728.653-0.017-0.0170.0000.0000.0000.000
130A195SER0-0.038-0.02031.2740.0190.0190.0000.0000.0000.000
131A196ILE00.0400.02128.267-0.016-0.0160.0000.0000.0000.000
132A197TRP0-0.047-0.02730.6810.0110.0110.0000.0000.0000.000
133A198THR00.0430.02831.362-0.001-0.0010.0000.0000.0000.000
134A199ALA00.0880.03033.569-0.006-0.0060.0000.0000.0000.000
135A200ASP-1-0.842-0.92235.249-0.023-0.0230.0000.0000.0000.000
136A201GLY0-0.045-0.02338.7420.0030.0030.0000.0000.0000.000
137A202ASN0-0.121-0.08340.9380.0030.0030.0000.0000.0000.000
138A203ASN00.0030.01237.5100.0090.0090.0000.0000.0000.000
139A204GLU-1-0.922-0.96439.6870.0030.0030.0000.0000.0000.000
140A205GLU-1-0.934-0.96738.5140.0430.0430.0000.0000.0000.000
141A206ALA00.0490.02835.2570.0010.0010.0000.0000.0000.000
142A207ALA0-0.0090.00335.537-0.003-0.0030.0000.0000.0000.000
143A208LEU00.014-0.00236.812-0.005-0.0050.0000.0000.0000.000
144A209GLU-1-0.752-0.83731.7390.0380.0380.0000.0000.0000.000
145A210ILE00.007-0.00131.291-0.002-0.0020.0000.0000.0000.000
146A211GLY0-0.005-0.00732.825-0.006-0.0060.0000.0000.0000.000
147A212HIS00.001-0.02735.000-0.007-0.0070.0000.0000.0000.000
148A213LYS10.8240.90429.358-0.063-0.0630.0000.0000.0000.000
149A214LEU0-0.019-0.00629.268-0.006-0.0060.0000.0000.0000.000
150A215ARG10.8840.93931.514-0.006-0.0060.0000.0000.0000.000
151A216ASP-1-0.920-0.96031.9450.0230.0230.0000.0000.0000.000
152A217ALA0-0.045-0.02027.2770.0010.0010.0000.0000.0000.000
153A218LEU0-0.018-0.00727.544-0.012-0.0120.0000.0000.0000.000
154A219ARG10.9030.95930.2890.0030.0030.0000.0000.0000.000
155A220LEU0-0.0150.01533.161-0.007-0.0070.0000.0000.0000.000
156A221GLY00.0420.01535.7690.0100.0100.0000.0000.0000.000
157A222ARG10.8700.91739.4180.0140.0140.0000.0000.0000.000
158A223ASN0-0.020-0.00638.1490.0040.0040.0000.0000.0000.000
159A224ASN00.0150.01435.571-0.004-0.0040.0000.0000.0000.000
160A225SER00.0260.00838.7860.0060.0060.0000.0000.0000.000
161A226LEU0-0.0180.01134.517-0.008-0.0080.0000.0000.0000.000
162A227GLN00.0180.00638.6390.0090.0090.0000.0000.0000.000
163A228TYR00.0430.02536.591-0.007-0.0070.0000.0000.0000.000
164A229GLN00.0150.00939.575-0.004-0.0040.0000.0000.0000.000
165A230LEU00.0570.03639.942-0.004-0.0040.0000.0000.0000.000
166A231HIS00.0070.00335.734-0.005-0.0050.0000.0000.0000.000
167A232LYS10.8020.89140.9300.0590.0590.0000.0000.0000.000
168A233ASP-1-0.810-0.90044.472-0.053-0.0530.0000.0000.0000.000
169A234THR0-0.065-0.04140.388-0.002-0.0020.0000.0000.0000.000
170A235MET0-0.045-0.00541.721-0.008-0.0080.0000.0000.0000.000
171A236VAL00.0120.00745.7560.0050.0050.0000.0000.0000.000
172A237LYS10.8990.96146.3520.0910.0910.0000.0000.0000.000
173A238GLN00.019-0.01747.322-0.006-0.0060.0000.0000.0000.000
174A239GLY00.0040.00849.1240.0030.0030.0000.0000.0000.000
175A240SER00.0060.00550.7270.0030.0030.0000.0000.0000.000
176A241ASN0-0.041-0.01947.150-0.003-0.0030.0000.0000.0000.000
177A242VAL00.0190.01743.7990.0010.0010.0000.0000.0000.000
178A243LYS10.9070.95646.4280.0440.0440.0000.0000.0000.000
179A244SER0-0.031-0.03944.103-0.006-0.0060.0000.0000.0000.000
180A245ILE0-0.053-0.01343.4890.0030.0030.0000.0000.0000.000
181A246TYR00.0720.04040.9180.0060.0060.0000.0000.0000.000
182A247THR0-0.018-0.02342.512-0.006-0.0060.0000.0000.0000.000
183A248LEU0-0.059-0.00138.2980.0050.0050.0000.0000.0000.000