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: KGJR3

Calculation Name: 4J9J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4J9J

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X0C6

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 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 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2738439.659666
FMO2-HF: Nuclear repulsion 2651385.308817
FMO2-HF: Total energy -87054.350849
FMO2-MP2: Total energy -87310.371293


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:0:LEU)


Summations of interaction energy for fragment #1(A:0:LEU)
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.
-20.765-12.71718.228-8.527-17.749-0.062
Interaction energy analysis for fragmet #1(A:0:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.021 / q_NPA : -0.008
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].
3A2ASP-1-0.791-0.8893.735-6.345-4.372-0.009-0.943-1.0210.005
4A3LYS10.7730.8665.7911.7971.7970.0000.0000.0000.000
5A4VAL0-0.0010.0207.393-0.169-0.1690.0000.0000.0000.000
6A5ILE0-0.016-0.0049.6980.1710.1710.0000.0000.0000.000
7A6ILE0-0.043-0.02112.7580.0110.0110.0000.0000.0000.000
8A7ASN00.0430.02515.5370.0400.0400.0000.0000.0000.000
9A8THR00.0600.00719.1300.0090.0090.0000.0000.0000.000
10A9ALA00.0130.01817.1480.0170.0170.0000.0000.0000.000
11A10ALA00.0180.01618.606-0.002-0.0020.0000.0000.0000.000
12A11VAL0-0.018-0.01320.1570.0220.0220.0000.0000.0000.000
13A12GLU-1-0.885-0.90522.978-0.231-0.2310.0000.0000.0000.000
14A13ASN00.0210.02420.5500.0340.0340.0000.0000.0000.000
15A14PRO00.0820.04821.068-0.040-0.0400.0000.0000.0000.000
16A15SER0-0.072-0.05121.291-0.033-0.0330.0000.0000.0000.000
17A16LEU0-0.0060.00515.783-0.029-0.0290.0000.0000.0000.000
18A17ILE00.0050.00016.421-0.082-0.0820.0000.0000.0000.000
19A18THR0-0.003-0.00216.788-0.045-0.0450.0000.0000.0000.000
20A19GLN0-0.0120.00016.337-0.046-0.0460.0000.0000.0000.000
21A20ILE00.0170.05510.922-0.044-0.0440.0000.0000.0000.000
22A21ALA00.0120.01712.964-0.110-0.1100.0000.0000.0000.000
23A22GLN0-0.051-0.01915.2470.0330.0330.0000.0000.0000.000
24A23THR0-0.101-0.08711.3400.0900.0900.0000.0000.0000.000
25A24PHE0-0.009-0.0237.200-0.088-0.0880.0000.0000.0000.000
26A25GLY00.0130.02310.546-0.101-0.1010.0000.0000.0000.000
27A26SER00.049-0.02013.046-0.083-0.0830.0000.0000.0000.000
28A27GLN0-0.0110.00510.4390.1550.1550.0000.0000.0000.000
29A28ALA0-0.0040.0059.364-0.090-0.0900.0000.0000.0000.000
30A29VAL0-0.037-0.01910.820-0.101-0.1010.0000.0000.0000.000
31A30VAL00.0310.02412.9990.1130.1130.0000.0000.0000.000
32A31VAL00.0200.00115.085-0.007-0.0070.0000.0000.0000.000
33A32ALA0-0.035-0.02217.5820.0350.0350.0000.0000.0000.000
34A33ILE0-0.047-0.03119.2640.0200.0200.0000.0000.0000.000
35A34ASP-1-0.880-0.93523.014-0.251-0.2510.0000.0000.0000.000
36A35ALA0-0.003-0.02225.1900.0040.0040.0000.0000.0000.000
37A36LYS10.9340.96228.8570.1450.1450.0000.0000.0000.000
38A37ARG10.7810.86932.2760.1300.1300.0000.0000.0000.000
39A38VAL0-0.073-0.05334.9660.0050.0050.0000.0000.0000.000
40A39ASP-1-0.920-0.96037.691-0.103-0.1030.0000.0000.0000.000
41A40GLY00.0010.01040.6410.0000.0000.0000.0000.0000.000
42A41GLU-1-0.880-0.92737.393-0.132-0.1320.0000.0000.0000.000
43A42PHE0-0.020-0.01432.395-0.001-0.0010.0000.0000.0000.000
44A43MET0-0.0270.01432.409-0.005-0.0050.0000.0000.0000.000
45A44ALA00.0720.03527.000-0.004-0.0040.0000.0000.0000.000
46A45PHE0-0.071-0.02027.2770.0180.0180.0000.0000.0000.000
47A46THR00.0560.02723.739-0.014-0.0140.0000.0000.0000.000
48A47TYR0-0.130-0.13423.1960.0210.0210.0000.0000.0000.000
49A48SER00.004-0.00222.4250.0180.0180.0000.0000.0000.000
50A49GLY00.0600.02623.9700.0160.0160.0000.0000.0000.000
51A50LYS10.8470.93327.1570.1490.1490.0000.0000.0000.000
52A51LYS10.9901.00128.3640.1910.1910.0000.0000.0000.000
53A52ASN00.0410.01929.166-0.022-0.0220.0000.0000.0000.000
54A53THR0-0.053-0.04627.2280.0050.0050.0000.0000.0000.000
55A54GLY00.0130.01430.3700.0020.0020.0000.0000.0000.000
56A55ILE0-0.015-0.00228.4970.0030.0030.0000.0000.0000.000
57A56LEU00.0260.01031.570-0.003-0.0030.0000.0000.0000.000
58A57LEU0-0.002-0.01427.802-0.014-0.0140.0000.0000.0000.000
59A58ARG10.9250.95029.5800.1480.1480.0000.0000.0000.000
60A59ASP-1-0.825-0.91530.903-0.189-0.1890.0000.0000.0000.000
61A60TRP00.007-0.00322.353-0.009-0.0090.0000.0000.0000.000
62A61VAL00.0280.01425.674-0.025-0.0250.0000.0000.0000.000
63A62VAL00.0190.00725.836-0.019-0.0190.0000.0000.0000.000
64A63GLU-1-0.875-0.92825.688-0.290-0.2900.0000.0000.0000.000
65A64VAL0-0.005-0.02321.417-0.023-0.0230.0000.0000.0000.000
66A65GLU-1-0.795-0.87921.818-0.358-0.3580.0000.0000.0000.000
67A66LYS10.8740.94423.2810.2460.2460.0000.0000.0000.000
68A67ARG10.7980.90521.4610.3210.3210.0000.0000.0000.000
69A68GLY00.0420.02519.985-0.027-0.0270.0000.0000.0000.000
70A69ALA0-0.023-0.00917.662-0.076-0.0760.0000.0000.0000.000
71A70GLY00.0230.02116.3380.0380.0380.0000.0000.0000.000
72A71GLU-1-0.788-0.90415.316-0.654-0.6540.0000.0000.0000.000
73A72ILE0-0.0110.00418.355-0.030-0.0300.0000.0000.0000.000
74A73LEU0-0.042-0.00817.0800.0170.0170.0000.0000.0000.000
75A74LEU00.0160.01820.3030.0140.0140.0000.0000.0000.000
76A75ALA00.007-0.00323.3630.0120.0120.0000.0000.0000.000
77A76SER0-0.040-0.01125.3200.0080.0080.0000.0000.0000.000
78A85GLY0-0.014-0.02732.106-0.001-0.0010.0000.0000.0000.000
79A86TYR00.0240.00626.308-0.005-0.0050.0000.0000.0000.000
80A87ASP-1-0.747-0.86630.636-0.139-0.1390.0000.0000.0000.000
81A88THR00.041-0.00432.044-0.010-0.0100.0000.0000.0000.000
82A89GLU-1-0.858-0.90033.641-0.126-0.1260.0000.0000.0000.000
83A90MET0-0.0170.00829.810-0.008-0.0080.0000.0000.0000.000
84A91ILE0-0.018-0.01228.531-0.010-0.0100.0000.0000.0000.000
85A92ARG10.9600.98430.6230.1230.1230.0000.0000.0000.000
86A93PHE0-0.049-0.01232.281-0.001-0.0010.0000.0000.0000.000
87A94VAL00.010-0.01326.990-0.002-0.0020.0000.0000.0000.000
88A95ARG10.8090.90025.5390.2550.2550.0000.0000.0000.000
89A96PRO0-0.0250.00629.989-0.008-0.0080.0000.0000.0000.000
90A97LEU0-0.077-0.03330.2530.0020.0020.0000.0000.0000.000
91A98THR0-0.026-0.03025.554-0.018-0.0180.0000.0000.0000.000
92A99THR0-0.027-0.00425.8990.0080.0080.0000.0000.0000.000
93A100LEU0-0.0360.00020.624-0.009-0.0090.0000.0000.0000.000
94A101PRO00.0060.00618.5940.0320.0320.0000.0000.0000.000
95A102ILE0-0.0100.00421.235-0.026-0.0260.0000.0000.0000.000
96A103ILE0-0.017-0.01317.2910.0230.0230.0000.0000.0000.000
97A104ALA00.0300.01521.6510.0010.0010.0000.0000.0000.000
98A105SER0-0.029-0.03321.9940.0020.0020.0000.0000.0000.000
99A106GLY00.0110.01622.6500.0210.0210.0000.0000.0000.000
100A107GLY0-0.015-0.01124.6310.0040.0040.0000.0000.0000.000
101A108ALA0-0.053-0.01926.8150.0160.0160.0000.0000.0000.000
102A109GLY00.0440.00327.238-0.004-0.0040.0000.0000.0000.000
103A110LYS10.8350.90629.2410.0770.0770.0000.0000.0000.000
104A111MET00.0930.04429.281-0.009-0.0090.0000.0000.0000.000
105A112GLU-1-0.857-0.92231.848-0.076-0.0760.0000.0000.0000.000
106A113HIS00.0110.00831.643-0.004-0.0040.0000.0000.0000.000
107A114PHE0-0.009-0.02026.166-0.011-0.0110.0000.0000.0000.000
108A115LEU00.0080.00329.627-0.012-0.0120.0000.0000.0000.000
109A116GLU-1-0.884-0.93732.019-0.113-0.1130.0000.0000.0000.000
110A117ALA0-0.046-0.01727.876-0.006-0.0060.0000.0000.0000.000
111A118PHE0-0.024-0.02224.193-0.008-0.0080.0000.0000.0000.000
112A119LEU0-0.0430.00329.108-0.002-0.0020.0000.0000.0000.000
113A120ALA0-0.070-0.03731.3780.0020.0020.0000.0000.0000.000
114A121GLY00.018-0.00629.7820.0000.0000.0000.0000.0000.000
115A122ALA0-0.053-0.01125.309-0.016-0.0160.0000.0000.0000.000
116A123ASP-1-0.797-0.90322.277-0.283-0.2830.0000.0000.0000.000
117A124LYS10.7590.85615.7100.5900.5900.0000.0000.0000.000
118A125VAL0-0.0100.00821.7920.0110.0110.0000.0000.0000.000
119A126SER0-0.0050.00418.279-0.014-0.0140.0000.0000.0000.000
120A127ILE0-0.0050.00020.0040.0300.0300.0000.0000.0000.000
121A128ASN00.0500.00519.1070.0040.0040.0000.0000.0000.000
122A129THR00.0300.00320.4370.0190.0190.0000.0000.0000.000
123A130ALA00.0440.02223.4260.0140.0140.0000.0000.0000.000
124A131ALA00.0070.00620.8500.0080.0080.0000.0000.0000.000
125A132VAL00.001-0.00721.5710.0150.0150.0000.0000.0000.000
126A133GLU-1-0.900-0.93923.016-0.014-0.0140.0000.0000.0000.000
127A134ASN0-0.0110.00725.8910.0110.0110.0000.0000.0000.000
128A135PRO00.0880.03723.225-0.014-0.0140.0000.0000.0000.000
129A136SER0-0.050-0.03124.249-0.009-0.0090.0000.0000.0000.000
130A137LEU0-0.023-0.01025.402-0.008-0.0080.0000.0000.0000.000
131A138ILE00.0150.01419.669-0.014-0.0140.0000.0000.0000.000
132A139THR0-0.002-0.00523.368-0.008-0.0080.0000.0000.0000.000
133A140GLN0-0.024-0.00725.430-0.008-0.0080.0000.0000.0000.000
134A141ILE00.0220.06323.960-0.002-0.0020.0000.0000.0000.000
135A142ALA00.0010.00922.327-0.010-0.0100.0000.0000.0000.000
136A143GLN0-0.051-0.01723.9370.0030.0030.0000.0000.0000.000
137A144THR0-0.120-0.10627.1990.0070.0070.0000.0000.0000.000
138A145PHE0-0.005-0.02325.5470.0020.0020.0000.0000.0000.000
139A146GLY00.0280.03323.389-0.016-0.0160.0000.0000.0000.000
140A147SER00.049-0.00118.696-0.003-0.0030.0000.0000.0000.000
141A148GLN00.0040.00917.569-0.014-0.0140.0000.0000.0000.000
142A149ALA00.0010.01218.620-0.044-0.0440.0000.0000.0000.000
143A150VAL0-0.022-0.01519.6060.0100.0100.0000.0000.0000.000
144A151VAL00.0290.02215.097-0.028-0.0280.0000.0000.0000.000
145A152VAL00.011-0.00115.7590.0440.0440.0000.0000.0000.000
146A153ALA0-0.0130.00014.527-0.045-0.0450.0000.0000.0000.000
147A154ILE0-0.018-0.01312.4100.0670.0670.0000.0000.0000.000
148A155VAL0-0.001-0.01113.484-0.025-0.0250.0000.0000.0000.000
149A156ALA00.0250.01712.6460.0310.0310.0000.0000.0000.000
150A157LYS10.9090.93914.583-0.100-0.1000.0000.0000.0000.000
151A158ARG10.7150.7969.899-0.393-0.3930.0000.0000.0000.000
152A159VAL0-0.076-0.05816.262-0.045-0.0450.0000.0000.0000.000
153A160ASP-1-0.905-0.94319.6280.1660.1660.0000.0000.0000.000
154A161GLY0-0.0020.01617.7730.0070.0070.0000.0000.0000.000
155A162GLU-1-0.919-0.96115.9090.3370.3370.0000.0000.0000.000
156A163PHE0-0.019-0.01210.046-0.050-0.0500.0000.0000.0000.000
157A164MET00.0170.02514.476-0.005-0.0050.0000.0000.0000.000
158A165VAL00.0350.01415.860-0.019-0.0190.0000.0000.0000.000
159A166PHE0-0.036-0.01517.807-0.009-0.0090.0000.0000.0000.000
160A167THR00.011-0.00119.516-0.023-0.0230.0000.0000.0000.000
161A168TYR0-0.094-0.06522.223-0.001-0.0010.0000.0000.0000.000
162A169SER0-0.003-0.01121.6490.0010.0010.0000.0000.0000.000
163A170GLY00.033-0.00120.221-0.002-0.0020.0000.0000.0000.000
164A171LYS10.8880.95420.8390.0670.0670.0000.0000.0000.000
165A172LYS10.9830.99924.177-0.002-0.0020.0000.0000.0000.000
166A173ASN00.0490.02722.2580.0000.0000.0000.0000.0000.000
167A174THR0-0.067-0.05421.0210.0010.0010.0000.0000.0000.000
168A175GLY00.0300.02522.722-0.002-0.0020.0000.0000.0000.000
169A176ILE0-0.0110.00419.1600.0140.0140.0000.0000.0000.000
170A177LEU00.0620.01417.0650.0050.0050.0000.0000.0000.000
171A178LEU0-0.016-0.02110.458-0.026-0.0260.0000.0000.0000.000
172A179ARG10.8980.93813.146-0.391-0.3910.0000.0000.0000.000
173A180ASP-1-0.814-0.90814.1730.2660.2660.0000.0000.0000.000
174A181TRP00.0200.01215.958-0.022-0.0220.0000.0000.0000.000
175A182VAL00.0190.01010.537-0.052-0.0520.0000.0000.0000.000
176A183VAL00.0190.01213.744-0.039-0.0390.0000.0000.0000.000
177A184GLU-1-0.904-0.95415.7300.0430.0430.0000.0000.0000.000
178A185VAL0-0.020-0.02214.969-0.031-0.0310.0000.0000.0000.000
179A186GLU-1-0.778-0.88113.5140.0420.0420.0000.0000.0000.000
180A187LYS10.8900.95016.801-0.162-0.1620.0000.0000.0000.000
181A188ARG10.7910.91120.115-0.032-0.0320.0000.0000.0000.000
182A189GLY00.0560.03419.825-0.006-0.0060.0000.0000.0000.000
183A190ALA0-0.051-0.03416.470-0.027-0.0270.0000.0000.0000.000
184A191GLY00.0310.02515.9490.0170.0170.0000.0000.0000.000
185A192GLU-1-0.792-0.87412.328-0.873-0.8730.0000.0000.0000.000
186A193ILE00.0220.02010.1220.1340.1340.0000.0000.0000.000
187A194LEU0-0.0120.00310.598-0.196-0.1960.0000.0000.0000.000
188A195LEU00.0190.0166.9410.1590.1590.0000.0000.0000.000
189A196THR0-0.025-0.0309.982-0.127-0.1270.0000.0000.0000.000
190A197SER00.035-0.00310.1840.0580.0580.0000.0000.0000.000
191A198ILE0-0.068-0.01112.335-0.051-0.0510.0000.0000.0000.000
192A199ASP-1-0.793-0.88713.3430.1640.1640.0000.0000.0000.000
193A200ARG10.9700.98113.238-0.036-0.0360.0000.0000.0000.000
194A201VAL0-0.055-0.04613.371-0.012-0.0120.0000.0000.0000.000
195A202GLY00.1070.05610.0130.0730.0730.0000.0000.0000.000
196A203THR0-0.0030.02910.666-0.080-0.0800.0000.0000.0000.000
197A204LYS10.8100.86811.2090.3460.3460.0000.0000.0000.000
198A205SER0-0.031-0.00611.520-0.079-0.0790.0000.0000.0000.000
199A206GLY0-0.079-0.04010.160-0.091-0.0910.0000.0000.0000.000
200A207TYR00.015-0.0096.0220.0970.0970.0000.0000.0000.000
201A208ASP-1-0.681-0.8067.2860.5280.5280.0000.0000.0000.000
202A209THR00.0150.0023.185-0.0820.3160.032-0.095-0.3340.000
203A210GLU-1-0.906-0.9203.8861.2511.5760.005-0.119-0.211-0.001
204A211MET0-0.0200.0346.2410.1940.1940.0000.0000.0000.000
205A212ILE00.0110.0041.9730.543-1.3595.877-1.049-2.9260.002
206A213ARG10.9450.9692.253-3.235-1.6962.484-1.235-2.7890.000
207A214PHE0-0.041-0.0063.0860.345-0.4010.0790.892-0.2260.000
208A215VAL00.018-0.0116.179-0.107-0.1070.0000.0000.0000.000
209A216ARG10.7840.8752.745-0.4481.3190.829-0.658-1.9380.000
210A217PRO0-0.0200.0055.012-0.486-0.417-0.001-0.005-0.0620.000
211A218LEU0-0.089-0.0417.688-0.343-0.3430.0000.0000.0000.000
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