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

tag_button

FMODB ID: GNJV1

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 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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2024127.187466
FMO2-HF: Nuclear repulsion 1948344.803386
FMO2-HF: Total energy -75782.38408
FMO2-MP2: Total energy -76003.769326


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.
-5.665-1.720.24-1.515-2.6720.006
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 : 0.057 / q_NPA : 0.025
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].
3A8PHE00.0390.0123.8181.7513.267-0.003-0.650-0.8640.003
4A9THR00.1010.0426.4060.5130.5130.0000.0000.0000.000
5A10ILE0-0.026-0.0093.066-1.502-0.5210.072-0.363-0.6900.001
6A11LYS10.8970.9532.908-2.798-1.3920.172-0.501-1.0780.002
7A12LEU00.0700.0455.705-0.810-0.768-0.001-0.001-0.0400.000
8A13LYS10.9740.9948.418-1.607-1.6070.0000.0000.0000.000
9A14THR0-0.046-0.0346.706-0.463-0.4630.0000.0000.0000.000
10A15CYS0-0.0050.0079.353-0.339-0.3390.0000.0000.0000.000
11A16LEU00.0390.02311.351-0.168-0.1680.0000.0000.0000.000
12A17LYS10.9210.96312.179-0.835-0.8350.0000.0000.0000.000
13A18MET0-0.0160.01213.214-0.110-0.1100.0000.0000.0000.000
14A19CYS00.0160.00315.004-0.100-0.1000.0000.0000.0000.000
15A20ILE00.0360.02717.320-0.055-0.0550.0000.0000.0000.000
16A21GLN0-0.022-0.01417.886-0.051-0.0510.0000.0000.0000.000
17A22ARG10.8330.92118.245-0.359-0.3590.0000.0000.0000.000
18A23LEU00.0470.02120.794-0.032-0.0320.0000.0000.0000.000
19A24ARG10.8600.93922.550-0.320-0.3200.0000.0000.0000.000
20A25TYR0-0.025-0.00423.685-0.025-0.0250.0000.0000.0000.000
21A26ALA0-0.034-0.01724.921-0.021-0.0210.0000.0000.0000.000
22A27GLN00.005-0.01525.903-0.029-0.0290.0000.0000.0000.000
23A28GLU-1-0.898-0.93528.4490.1490.1490.0000.0000.0000.000
24A29LYS10.9180.95329.181-0.150-0.1500.0000.0000.0000.000
25A30GLN0-0.002-0.02928.792-0.017-0.0170.0000.0000.0000.000
26A31GLN00.0670.04632.517-0.007-0.0070.0000.0000.0000.000
27A32ALA0-0.029-0.01034.225-0.010-0.0100.0000.0000.0000.000
28A33ILE0-0.036-0.03033.453-0.009-0.0090.0000.0000.0000.000
29A34ALA00.1060.06636.652-0.008-0.0080.0000.0000.0000.000
30A35LYS10.9550.97638.560-0.087-0.0870.0000.0000.0000.000
31A36GLN0-0.063-0.04340.005-0.008-0.0080.0000.0000.0000.000
32A37SER00.0200.00139.933-0.006-0.0060.0000.0000.0000.000
33A38ARG10.9430.98441.793-0.086-0.0860.0000.0000.0000.000
34A39ARG10.9180.97244.206-0.068-0.0680.0000.0000.0000.000
35A40GLN0-0.023-0.00843.216-0.002-0.0020.0000.0000.0000.000
36A41VAL00.0460.03846.246-0.003-0.0030.0000.0000.0000.000
37A42ALA00.0550.02948.629-0.003-0.0030.0000.0000.0000.000
38A43GLN0-0.009-0.00350.333-0.002-0.0020.0000.0000.0000.000
39A44LEU0-0.079-0.03648.746-0.003-0.0030.0000.0000.0000.000
40A45LEU00.0710.05152.581-0.002-0.0020.0000.0000.0000.000
41A46LEU0-0.018-0.00354.702-0.003-0.0030.0000.0000.0000.000
42A47THR0-0.143-0.08454.970-0.002-0.0020.0000.0000.0000.000
43A48ASN00.0540.02857.5720.0000.0000.0000.0000.0000.000
44A49LYS10.8760.95053.489-0.042-0.0420.0000.0000.0000.000
45A50GLU-1-0.701-0.88253.9330.0440.0440.0000.0000.0000.000
46A51GLN0-0.0110.00552.9880.0020.0020.0000.0000.0000.000
47A52LYS10.9340.95350.425-0.043-0.0430.0000.0000.0000.000
48A53ALA00.0130.00649.2570.0030.0030.0000.0000.0000.000
49A54HIS0-0.006-0.00449.0350.0040.0040.0000.0000.0000.000
50A55TYR00.0340.01547.0870.0020.0020.0000.0000.0000.000
51A56ARG10.8190.89443.339-0.062-0.0620.0000.0000.0000.000
52A57VAL00.0160.00544.1390.0040.0040.0000.0000.0000.000
53A58GLU-1-0.848-0.93144.1990.0610.0610.0000.0000.0000.000
54A59THR0-0.064-0.02839.6830.0030.0030.0000.0000.0000.000
55A60LEU0-0.027-0.00839.7750.0040.0040.0000.0000.0000.000
56A61ILE00.0030.00839.8860.0050.0050.0000.0000.0000.000
57A62HIS0-0.0110.00034.1000.0050.0050.0000.0000.0000.000
58A63ASP-1-0.912-0.97035.6850.1050.1050.0000.0000.0000.000
59A64ASP-1-0.815-0.90435.1190.1050.1050.0000.0000.0000.000
60A65ILE0-0.0180.00934.9810.0070.0070.0000.0000.0000.000
61A66HIS10.7970.87628.763-0.143-0.1430.0000.0000.0000.000
62A67ILE00.014-0.00130.9090.0140.0140.0000.0000.0000.000
63A68GLU-1-0.848-0.92030.9390.1250.1250.0000.0000.0000.000
64A69LEU0-0.058-0.02928.0590.0100.0100.0000.0000.0000.000
65A70LEU0-0.039-0.02925.9030.0200.0200.0000.0000.0000.000
66A71GLU-1-0.888-0.93726.2720.1710.1710.0000.0000.0000.000
67A72ILE0-0.051-0.02627.2700.0110.0110.0000.0000.0000.000
68A73LEU0-0.008-0.01623.3440.0180.0180.0000.0000.0000.000
69A74GLU-1-0.816-0.89322.5440.2880.2880.0000.0000.0000.000
70A75LEU00.0360.02022.4450.0280.0280.0000.0000.0000.000
71A76TYR0-0.075-0.06722.3480.0130.0130.0000.0000.0000.000
72A77CYS0-0.053-0.02518.4710.0450.0450.0000.0000.0000.000
73A78GLU-1-0.887-0.95218.3400.3530.3530.0000.0000.0000.000
74A79LEU0-0.0340.00119.9710.0210.0210.0000.0000.0000.000
75A80LEU00.009-0.01216.7550.0180.0180.0000.0000.0000.000
76A81LEU0-0.070-0.03714.0490.0840.0840.0000.0000.0000.000
77A82ALA0-0.034-0.02615.8050.0460.0460.0000.0000.0000.000
78A83ARG10.9590.99318.022-0.275-0.2750.0000.0000.0000.000
79A84VAL0-0.0080.00611.1470.0200.0200.0000.0000.0000.000
80A85GLN0-0.043-0.03813.433-0.001-0.0010.0000.0000.0000.000
81A86VAL00.0610.04014.434-0.039-0.0390.0000.0000.0000.000
82A87ILE00.0350.01614.226-0.026-0.0260.0000.0000.0000.000
83A88ASN0-0.067-0.04110.7500.0240.0240.0000.0000.0000.000
84A89ASP-1-0.920-0.93613.4170.1440.1440.0000.0000.0000.000
85A90ILE0-0.065-0.00715.779-0.034-0.0340.0000.0000.0000.000
86A91SER0-0.018-0.02015.6350.0100.0100.0000.0000.0000.000
87A92THR00.005-0.00416.971-0.016-0.0160.0000.0000.0000.000
88A93GLU-1-0.777-0.89220.4010.1280.1280.0000.0000.0000.000
89A94GLU-1-0.842-0.92922.8400.0780.0780.0000.0000.0000.000
90A95GLN00.0750.03219.9590.0100.0100.0000.0000.0000.000
91A96LEU0-0.043-0.01420.2580.0110.0110.0000.0000.0000.000
92A97VAL00.015-0.00723.0290.0070.0070.0000.0000.0000.000
93A98LYS10.8720.94626.738-0.070-0.0700.0000.0000.0000.000
94A99GLU-1-0.967-0.98224.0140.1030.1030.0000.0000.0000.000
95A100HIS10.7660.87521.128-0.186-0.1860.0000.0000.0000.000
96A101MET00.0250.02824.8180.0180.0180.0000.0000.0000.000
97A102ASP-1-0.940-0.95827.8080.1340.1340.0000.0000.0000.000
98A103ASP-1-0.820-0.90323.6940.2190.2190.0000.0000.0000.000
99A104GLY00.0490.00424.5530.0210.0210.0000.0000.0000.000
100A105ILE0-0.060-0.03019.4190.0210.0210.0000.0000.0000.000
101A106ASN00.0130.01722.1350.0210.0210.0000.0000.0000.000
102A107GLU-1-0.800-0.88123.8670.1720.1720.0000.0000.0000.000
103A108ALA00.0000.00021.7570.0030.0030.0000.0000.0000.000
104A109ILE0-0.032-0.02616.6430.0210.0210.0000.0000.0000.000
105A110ARG10.8140.87720.442-0.142-0.1420.0000.0000.0000.000
106A111SER00.009-0.00423.130-0.015-0.0150.0000.0000.0000.000
107A112LEU0-0.042-0.02118.7960.0010.0010.0000.0000.0000.000
108A113ILE0-0.043-0.02218.0020.0050.0050.0000.0000.0000.000
109A114TYR00.014-0.00120.926-0.011-0.0110.0000.0000.0000.000
110A115ALA00.0270.00623.540-0.013-0.0130.0000.0000.0000.000
111A116ILE0-0.066-0.01718.644-0.003-0.0030.0000.0000.0000.000
112A117LEU0-0.042-0.01822.541-0.005-0.0050.0000.0000.0000.000
113A118PHE00.0230.00625.605-0.011-0.0110.0000.0000.0000.000
114A119VAL0-0.030-0.00624.079-0.006-0.0060.0000.0000.0000.000
115A120ASP-1-0.884-0.92523.6380.1690.1690.0000.0000.0000.000
116A121GLU-1-0.820-0.89823.7630.1830.1830.0000.0000.0000.000
117A122VAL0-0.096-0.05419.3450.0170.0170.0000.0000.0000.000
118A123LYS11.0210.99418.425-0.189-0.1890.0000.0000.0000.000
119A124GLU-1-0.837-0.92414.3370.4040.4040.0000.0000.0000.000
120A125LEU00.0460.02215.1420.0720.0720.0000.0000.0000.000
121A126SER0-0.014-0.01516.5580.0110.0110.0000.0000.0000.000
122A127GLN00.029-0.00210.878-0.108-0.1080.0000.0000.0000.000
123A128LEU0-0.001-0.00512.2640.0820.0820.0000.0000.0000.000
124A129LYS11.0071.01914.327-0.207-0.2070.0000.0000.0000.000
125A130ASP-1-0.933-0.96512.0510.2640.2640.0000.0000.0000.000
126A131LEU0-0.102-0.0587.6950.0300.0300.0000.0000.0000.000
127A132MET00.014-0.00711.315-0.050-0.0500.0000.0000.0000.000
128A133ALA00.0020.01814.615-0.047-0.0470.0000.0000.0000.000
129A134TRP0-0.073-0.0258.180-0.037-0.0370.0000.0000.0000.000
130A135LYS10.7710.88110.983-0.290-0.2900.0000.0000.0000.000
131A136ILE0-0.0290.00213.148-0.032-0.0320.0000.0000.0000.000
132A137ASN00.0280.01316.888-0.027-0.0270.0000.0000.0000.000
133A138VAL00.0390.00118.3820.0240.0240.0000.0000.0000.000
134A139GLU-1-0.897-0.95520.0830.0520.0520.0000.0000.0000.000
135A140PHE00.0220.01618.7000.0140.0140.0000.0000.0000.000
136A141VAL0-0.049-0.02517.8570.0100.0100.0000.0000.0000.000
137A142ASN0-0.012-0.01621.2220.0100.0100.0000.0000.0000.000
138A143GLY00.0710.05024.291-0.004-0.0040.0000.0000.0000.000
139A144VAL0-0.055-0.02322.8510.0000.0000.0000.0000.0000.000
140A145ILE0-0.049-0.04321.553-0.001-0.0010.0000.0000.0000.000
141A146ALA0-0.068-0.02425.901-0.004-0.0040.0000.0000.0000.000
142A147ASP-1-0.902-0.94728.7290.0690.0690.0000.0000.0000.000
143A148HIS0-0.023-0.00828.4100.0010.0010.0000.0000.0000.000
144A149ILE00.005-0.00127.7880.0010.0010.0000.0000.0000.000
145A150ASP-1-0.856-0.94127.6000.1310.1310.0000.0000.0000.000
146A151VAL0-0.070-0.01426.6020.0150.0150.0000.0000.0000.000
147A152PRO0-0.006-0.00828.213-0.012-0.0120.0000.0000.0000.000
148A153GLU-1-0.838-0.92631.3450.0950.0950.0000.0000.0000.000
149A154LYS10.9230.95830.043-0.161-0.1610.0000.0000.0000.000
150A155ILE00.0140.00527.6110.0010.0010.0000.0000.0000.000
151A156ILE00.0550.03630.9360.0010.0010.0000.0000.0000.000
152A157LYS10.8920.94032.548-0.090-0.0900.0000.0000.0000.000
153A158LYS10.8620.93632.187-0.126-0.1260.0000.0000.0000.000
154A159CYS0-0.055-0.00329.3090.0060.0060.0000.0000.0000.000
155A160SER0-0.032-0.01031.896-0.005-0.0050.0000.0000.0000.000
156A161PRO0-0.0260.00935.189-0.005-0.0050.0000.0000.0000.000
157A162SER0-0.043-0.03038.087-0.003-0.0030.0000.0000.0000.000
158A163VAL0-0.001-0.01041.5880.0020.0020.0000.0000.0000.000
159A164PRO0-0.0020.00443.028-0.001-0.0010.0000.0000.0000.000
160A165LYS10.9410.98945.436-0.062-0.0620.0000.0000.0000.000
161A166GLU-1-0.722-0.87248.9520.0520.0520.0000.0000.0000.000
162A167GLU-1-0.897-0.95751.3210.0530.0530.0000.0000.0000.000
163A168LEU0-0.048-0.02143.9450.0010.0010.0000.0000.0000.000
164A169VAL00.0390.02147.6650.0020.0020.0000.0000.0000.000
165A170ASP-1-0.846-0.93449.2150.0490.0490.0000.0000.0000.000
166A171LEU0-0.084-0.03647.930-0.001-0.0010.0000.0000.0000.000
167A172TYR0-0.008-0.04841.3700.0000.0000.0000.0000.0000.000
168A173LEU0-0.0130.00348.2540.0010.0010.0000.0000.0000.000
169A174LYS10.9480.97151.112-0.049-0.0490.0000.0000.0000.000
170A175GLU-1-0.969-0.97746.9490.0690.0690.0000.0000.0000.000
171A176ILE0-0.072-0.04146.4240.0010.0010.0000.0000.0000.000
172A177ALA00.008-0.00949.439-0.001-0.0010.0000.0000.0000.000
173A178LYS10.9590.98551.758-0.058-0.0580.0000.0000.0000.000
174A179THR0-0.077-0.03546.9350.0010.0010.0000.0000.0000.000
175A180TYR0-0.090-0.06145.2380.0010.0010.0000.0000.0000.000
176A181ASP-1-0.909-0.92551.8870.0480.0480.0000.0000.0000.000
177A182VAL0-0.058-0.02153.591-0.002-0.0020.0000.0000.0000.000
178A183PRO0-0.023-0.01956.307-0.001-0.0010.0000.0000.0000.000
179A184TYR00.0590.02259.5690.0000.0000.0000.0000.0000.000
180A185SER0-0.003-0.01061.0230.0010.0010.0000.0000.0000.000
181A186LYS10.8520.92358.195-0.037-0.0370.0000.0000.0000.000
182A187LEU00.0480.03754.2040.0010.0010.0000.0000.0000.000
183A188GLU-1-0.907-0.95057.6310.0410.0410.0000.0000.0000.000
184A189ASN0-0.097-0.03460.358-0.001-0.0010.0000.0000.0000.000
185A190SER0-0.079-0.04354.9480.0000.0000.0000.0000.0000.000
186A191LEU0-0.031-0.00355.3770.0010.0010.0000.0000.0000.000