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: 82RQY

Calculation Name: 3GGY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GGY

Chain ID: A

ChEMBL ID:

UniProt ID: P53843

Base Structure: X-ray

Registration Date: 2023-06-19

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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2023173.235242
FMO2-HF: Nuclear repulsion 1947389.578244
FMO2-HF: Total energy -75783.656998
FMO2-MP2: Total energy -76004.975671


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:6:ILE)


Summations of interaction energy for fragment #1(A:6:ILE)
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.
-5.452-1.6610.323-1.494-2.6210.006
Interaction energy analysis for fragmet #1(A:6:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.050 / q_NPA : 0.016
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].
3A8PHE00.0450.0183.8181.7993.214-0.007-0.605-0.8040.003
4A9THR00.1050.0426.4060.5400.5400.0000.0000.0000.000
5A10ILE0-0.031-0.0133.415-1.145-0.3770.035-0.269-0.5340.001
6A11LYS10.9070.9602.745-3.156-1.5970.296-0.619-1.2360.002
7A12LEU00.0680.0445.705-0.795-0.746-0.001-0.001-0.0470.000
8A13LYS10.9710.9938.051-1.634-1.6340.0000.0000.0000.000
9A14THR0-0.054-0.0476.735-0.423-0.4230.0000.0000.0000.000
10A15CYS0-0.0100.0109.353-0.341-0.3410.0000.0000.0000.000
11A16LEU00.0510.02711.351-0.176-0.1760.0000.0000.0000.000
12A17LYS10.9300.96812.328-0.792-0.7920.0000.0000.0000.000
13A18MET0-0.0090.01113.150-0.105-0.1050.0000.0000.0000.000
14A19CYS0-0.005-0.00515.012-0.097-0.0970.0000.0000.0000.000
15A20ILE00.0230.02017.157-0.056-0.0560.0000.0000.0000.000
16A21GLN0-0.011-0.01318.136-0.050-0.0500.0000.0000.0000.000
17A22ARG10.7790.86918.479-0.369-0.3690.0000.0000.0000.000
18A23LEU00.0260.01120.856-0.033-0.0330.0000.0000.0000.000
19A24ARG10.8200.89422.054-0.323-0.3230.0000.0000.0000.000
20A25TYR0-0.056-0.01823.771-0.024-0.0240.0000.0000.0000.000
21A26ALA0-0.032-0.01824.983-0.022-0.0220.0000.0000.0000.000
22A27GLN00.011-0.00726.312-0.028-0.0280.0000.0000.0000.000
23A28GLU-1-0.902-0.94128.2810.1550.1550.0000.0000.0000.000
24A29LYS10.9280.95629.053-0.158-0.1580.0000.0000.0000.000
25A30GLN0-0.012-0.04128.818-0.017-0.0170.0000.0000.0000.000
26A31GLN00.0390.03632.551-0.012-0.0120.0000.0000.0000.000
27A32ALA0-0.030-0.01034.283-0.010-0.0100.0000.0000.0000.000
28A33ILE0-0.046-0.03433.388-0.009-0.0090.0000.0000.0000.000
29A34ALA00.0910.05736.721-0.008-0.0080.0000.0000.0000.000
30A35LYS10.9450.97238.624-0.088-0.0880.0000.0000.0000.000
31A36GLN0-0.046-0.02939.816-0.008-0.0080.0000.0000.0000.000
32A37SER00.0500.01140.285-0.007-0.0070.0000.0000.0000.000
33A38ARG10.9130.96541.967-0.088-0.0880.0000.0000.0000.000
34A39ARG10.9260.97744.702-0.069-0.0690.0000.0000.0000.000
35A40GLN0-0.020-0.01243.118-0.003-0.0030.0000.0000.0000.000
36A41VAL00.0390.03546.264-0.003-0.0030.0000.0000.0000.000
37A42ALA00.0520.02748.695-0.003-0.0030.0000.0000.0000.000
38A43GLN0-0.033-0.01150.391-0.002-0.0020.0000.0000.0000.000
39A44LEU0-0.060-0.03248.902-0.003-0.0030.0000.0000.0000.000
40A45LEU00.0740.05452.669-0.002-0.0020.0000.0000.0000.000
41A46LEU00.0200.01754.415-0.003-0.0030.0000.0000.0000.000
42A47THR0-0.122-0.06855.092-0.002-0.0020.0000.0000.0000.000
43A48ASN00.0660.04457.6380.0000.0000.0000.0000.0000.000
44A49LYS10.8480.93553.877-0.043-0.0430.0000.0000.0000.000
45A50GLU-1-0.760-0.90654.0020.0450.0450.0000.0000.0000.000
46A51GLN00.0210.02753.0170.0020.0020.0000.0000.0000.000
47A52LYS10.9540.96850.350-0.045-0.0450.0000.0000.0000.000
48A53ALA00.0050.00649.3050.0030.0030.0000.0000.0000.000
49A54HIS0-0.020-0.01549.1050.0040.0040.0000.0000.0000.000
50A55TYR00.0400.00447.0040.0020.0020.0000.0000.0000.000
51A56ARG10.8150.89842.756-0.066-0.0660.0000.0000.0000.000
52A57VAL00.0120.00244.2090.0050.0050.0000.0000.0000.000
53A58GLU-1-0.868-0.93744.2070.0650.0650.0000.0000.0000.000
54A59THR0-0.081-0.04039.7010.0030.0030.0000.0000.0000.000
55A60LEU0-0.027-0.00939.7630.0050.0050.0000.0000.0000.000
56A61ILE00.0080.01039.9510.0050.0050.0000.0000.0000.000
57A62HIS0-0.039-0.00934.2470.0070.0070.0000.0000.0000.000
58A63ASP-1-0.892-0.96535.7200.1090.1090.0000.0000.0000.000
59A64ASP-1-0.801-0.88335.1720.1060.1060.0000.0000.0000.000
60A65ILE0-0.0100.00934.9840.0060.0060.0000.0000.0000.000
61A66HIS10.8300.89728.717-0.148-0.1480.0000.0000.0000.000
62A67ILE0-0.007-0.00830.9090.0140.0140.0000.0000.0000.000
63A68GLU-1-0.775-0.87230.9390.1280.1280.0000.0000.0000.000
64A69LEU0-0.036-0.01828.0600.0100.0100.0000.0000.0000.000
65A70LEU0-0.031-0.02125.9080.0200.0200.0000.0000.0000.000
66A71GLU-1-0.883-0.94226.2720.1740.1740.0000.0000.0000.000
67A72ILE0-0.030-0.01627.2700.0110.0110.0000.0000.0000.000
68A73LEU00.007-0.00623.3590.0190.0190.0000.0000.0000.000
69A74GLU-1-0.775-0.85522.5330.2950.2950.0000.0000.0000.000
70A75LEU00.0270.01122.4450.0280.0280.0000.0000.0000.000
71A76TYR0-0.061-0.06922.3690.0120.0120.0000.0000.0000.000
72A77CYS0-0.066-0.03418.3580.0410.0410.0000.0000.0000.000
73A78GLU-1-0.873-0.93118.3400.3610.3610.0000.0000.0000.000
74A79LEU0-0.047-0.00619.9710.0180.0180.0000.0000.0000.000
75A80LEU00.011-0.01016.7570.0150.0150.0000.0000.0000.000
76A81LEU0-0.070-0.03513.9050.0790.0790.0000.0000.0000.000
77A82ALA0-0.023-0.01415.7340.0410.0410.0000.0000.0000.000
78A83ARG10.9020.96417.937-0.274-0.2740.0000.0000.0000.000
79A84VAL00.0120.00711.0800.0180.0180.0000.0000.0000.000
80A85GLN0-0.056-0.04013.3560.0220.0220.0000.0000.0000.000
81A86VAL00.0620.03714.357-0.039-0.0390.0000.0000.0000.000
82A87ILE00.0350.01814.284-0.024-0.0240.0000.0000.0000.000
83A88ASN0-0.115-0.06310.9380.0350.0350.0000.0000.0000.000
84A89ASP-1-0.868-0.91513.4360.1470.1470.0000.0000.0000.000
85A90ILE0-0.057-0.01215.904-0.033-0.0330.0000.0000.0000.000
86A91SER0-0.023-0.01715.7350.0120.0120.0000.0000.0000.000
87A92THR00.020-0.00417.060-0.014-0.0140.0000.0000.0000.000
88A93GLU-1-0.762-0.88420.4710.1380.1380.0000.0000.0000.000
89A94GLU-1-0.813-0.88122.8970.0760.0760.0000.0000.0000.000
90A95GLN00.0260.01419.9950.0010.0010.0000.0000.0000.000
91A96LEU0-0.044-0.01420.0210.0100.0100.0000.0000.0000.000
92A97VAL00.0220.00123.0760.0060.0060.0000.0000.0000.000
93A98LYS10.8180.88826.703-0.074-0.0740.0000.0000.0000.000
94A99GLU-1-0.871-0.93223.1010.1200.1200.0000.0000.0000.000
95A100HIS10.7390.85522.114-0.177-0.1770.0000.0000.0000.000
96A101MET00.0180.02824.8180.0190.0190.0000.0000.0000.000
97A102ASP-1-0.950-0.95827.8080.1360.1360.0000.0000.0000.000
98A103ASP-1-0.795-0.90423.2650.2220.2220.0000.0000.0000.000
99A104GLY00.0550.00824.5530.0210.0210.0000.0000.0000.000
100A105ILE0-0.052-0.02419.3740.0210.0210.0000.0000.0000.000
101A106ASN0-0.0010.00222.1110.0210.0210.0000.0000.0000.000
102A107GLU-1-0.721-0.82723.7800.1740.1740.0000.0000.0000.000
103A108ALA0-0.0080.00821.7870.0030.0030.0000.0000.0000.000
104A109ILE0-0.023-0.02516.3980.0210.0210.0000.0000.0000.000
105A110ARG10.8040.88620.349-0.147-0.1470.0000.0000.0000.000
106A111SER0-0.006-0.02123.043-0.014-0.0140.0000.0000.0000.000
107A112LEU0-0.042-0.02518.9180.0000.0000.0000.0000.0000.000
108A113ILE0-0.039-0.02217.5970.0060.0060.0000.0000.0000.000
109A114TYR00.0260.00620.840-0.012-0.0120.0000.0000.0000.000
110A115ALA00.0300.00723.439-0.013-0.0130.0000.0000.0000.000
111A116ILE0-0.072-0.02018.585-0.003-0.0030.0000.0000.0000.000
112A117LEU0-0.038-0.01422.456-0.005-0.0050.0000.0000.0000.000
113A118PHE00.0140.00425.527-0.011-0.0110.0000.0000.0000.000
114A119VAL0-0.022-0.00224.116-0.007-0.0070.0000.0000.0000.000
115A120ASP-1-0.808-0.89823.5480.1820.1820.0000.0000.0000.000
116A121GLU-1-0.795-0.86323.6810.1930.1930.0000.0000.0000.000
117A122VAL0-0.047-0.02019.3320.0140.0140.0000.0000.0000.000
118A123LYS10.8910.92718.556-0.182-0.1820.0000.0000.0000.000
119A124GLU-1-0.786-0.88514.8270.4030.4030.0000.0000.0000.000
120A125LEU00.0420.02215.0490.0740.0740.0000.0000.0000.000
121A126SER0-0.012-0.01716.5090.0120.0120.0000.0000.0000.000
122A127GLN00.017-0.01010.234-0.087-0.0870.0000.0000.0000.000
123A128LEU00.001-0.00112.1830.0820.0820.0000.0000.0000.000
124A129LYS10.9450.98014.237-0.249-0.2490.0000.0000.0000.000
125A130ASP-1-0.887-0.94112.0960.2720.2720.0000.0000.0000.000
126A131LEU0-0.084-0.0517.4790.0350.0350.0000.0000.0000.000
127A132MET00.013-0.00211.247-0.057-0.0570.0000.0000.0000.000
128A133ALA0-0.0020.01614.550-0.049-0.0490.0000.0000.0000.000
129A134TRP0-0.074-0.0297.986-0.032-0.0320.0000.0000.0000.000
130A135LYS10.7610.88310.891-0.310-0.3100.0000.0000.0000.000
131A136ILE0-0.0290.00413.182-0.034-0.0340.0000.0000.0000.000
132A137ASN00.0400.01516.919-0.020-0.0200.0000.0000.0000.000
133A138VAL00.030-0.00118.3670.0240.0240.0000.0000.0000.000
134A139GLU-1-0.902-0.95420.0510.0630.0630.0000.0000.0000.000
135A140PHE00.0250.01918.6300.0140.0140.0000.0000.0000.000
136A141VAL0-0.043-0.02517.7700.0100.0100.0000.0000.0000.000
137A142ASN0-0.019-0.01721.1630.0100.0100.0000.0000.0000.000
138A143GLY00.0700.05124.240-0.004-0.0040.0000.0000.0000.000
139A144VAL0-0.057-0.02622.912-0.001-0.0010.0000.0000.0000.000
140A145ILE0-0.046-0.03821.440-0.001-0.0010.0000.0000.0000.000
141A146ALA0-0.062-0.02025.834-0.005-0.0050.0000.0000.0000.000
142A147ASP-1-0.909-0.95628.6630.0740.0740.0000.0000.0000.000
143A148HIS0-0.020-0.00528.3230.0000.0000.0000.0000.0000.000
144A149ILE00.004-0.00327.7660.0000.0000.0000.0000.0000.000
145A150ASP-1-0.837-0.93227.5240.1370.1370.0000.0000.0000.000
146A151VAL0-0.060-0.00926.5060.0150.0150.0000.0000.0000.000
147A152PRO0-0.024-0.01528.257-0.012-0.0120.0000.0000.0000.000
148A153GLU-1-0.826-0.92231.2510.0990.0990.0000.0000.0000.000
149A154LYS10.8370.90930.197-0.159-0.1590.0000.0000.0000.000
150A155ILE00.0230.00627.4550.0010.0010.0000.0000.0000.000
151A156ILE00.0550.03930.8380.0010.0010.0000.0000.0000.000
152A157LYS10.8690.92932.456-0.093-0.0930.0000.0000.0000.000
153A158LYS10.7890.88432.226-0.128-0.1280.0000.0000.0000.000
154A159CYS0-0.063-0.00629.3250.0070.0070.0000.0000.0000.000
155A160SER0-0.049-0.02531.803-0.004-0.0040.0000.0000.0000.000
156A161PRO0-0.0080.01935.100-0.005-0.0050.0000.0000.0000.000
157A162SER0-0.014-0.02137.993-0.002-0.0020.0000.0000.0000.000
158A163VAL00.0020.00141.4960.0020.0020.0000.0000.0000.000
159A164PRO00.0090.01042.979-0.001-0.0010.0000.0000.0000.000
160A165LYS10.8480.92645.340-0.061-0.0610.0000.0000.0000.000
161A166GLU-1-0.725-0.86948.8550.0530.0530.0000.0000.0000.000
162A167GLU-1-0.842-0.91751.2590.0550.0550.0000.0000.0000.000
163A168LEU0-0.031-0.01243.9130.0000.0000.0000.0000.0000.000
164A169VAL00.0480.02647.5260.0020.0020.0000.0000.0000.000
165A170ASP-1-0.794-0.90749.1670.0490.0490.0000.0000.0000.000
166A171LEU0-0.048-0.01647.964-0.001-0.0010.0000.0000.0000.000
167A172TYR0-0.013-0.04941.4010.0000.0000.0000.0000.0000.000
168A173LEU0-0.0130.00148.2680.0010.0010.0000.0000.0000.000
169A174LYS10.8790.93251.176-0.050-0.0500.0000.0000.0000.000
170A175GLU-1-0.941-0.96446.6280.0720.0720.0000.0000.0000.000
171A176ILE0-0.064-0.03746.2830.0010.0010.0000.0000.0000.000
172A177ALA00.004-0.00949.502-0.001-0.0010.0000.0000.0000.000
173A178LYS10.9600.98651.848-0.059-0.0590.0000.0000.0000.000
174A179THR0-0.090-0.04946.8920.0010.0010.0000.0000.0000.000
175A180TYR0-0.067-0.05645.1660.0010.0010.0000.0000.0000.000
176A181ASP-1-0.909-0.92451.9460.0490.0490.0000.0000.0000.000
177A182VAL0-0.059-0.02553.547-0.002-0.0020.0000.0000.0000.000
178A183PRO0-0.016-0.01556.369-0.001-0.0010.0000.0000.0000.000
179A184TYR0-0.014-0.03259.6330.0000.0000.0000.0000.0000.000
180A185SER00.0160.00161.0880.0010.0010.0000.0000.0000.000
181A186LYS10.7960.88358.239-0.038-0.0380.0000.0000.0000.000
182A187LEU00.0320.03254.6920.0010.0010.0000.0000.0000.000
183A188GLU-1-0.818-0.89857.6970.0420.0420.0000.0000.0000.000
184A189ASN0-0.080-0.03260.367-0.001-0.0010.0000.0000.0000.000
185A190SER0-0.094-0.05555.0580.0010.0010.0000.0000.0000.000
186A191LEU0-0.0420.00455.6820.0010.0010.0000.0000.0000.000