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: LZ539

Calculation Name: 5JD6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5JD6

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-20

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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2733964.829238
FMO2-HF: Nuclear repulsion 2647032.86348
FMO2-HF: Total energy -86931.965758
FMO2-MP2: Total energy -87185.022778


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:3:ASP)


Summations of interaction energy for fragment #1(A:3: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.
50.79159.4339.652-7.731-10.560.03
Interaction energy analysis for fragmet #1(A:3:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.921 / q_NPA : -0.989
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].
3A5LEU00.0190.0053.7930.4842.693-0.037-0.978-1.1930.002
4A6LYS10.8750.9526.182-37.582-37.5820.0000.0000.0000.000
5A7GLN0-0.018-0.0218.991-1.395-1.3950.0000.0000.0000.000
6A8GLU-1-0.859-0.91712.07422.82322.8230.0000.0000.0000.000
7A9GLY00.0110.00215.019-0.428-0.4280.0000.0000.0000.000
8A10LYS10.7880.87717.573-14.671-14.6710.0000.0000.0000.000
9A11PHE0-0.012-0.00413.8070.0180.0180.0000.0000.0000.000
10A12THR00.0270.01110.4950.2360.2360.0000.0000.0000.000
11A13TYR0-0.055-0.0328.067-1.220-1.2200.0000.0000.0000.000
12A14LEU00.0590.0523.277-7.239-4.3910.141-1.494-1.4950.012
13A15GLU-1-0.833-0.9413.82324.43924.7920.001-0.121-0.2330.000
14A16LYS10.9450.9901.908-45.100-43.3649.329-4.563-6.5010.011
15A17GLY00.0410.0273.716-6.173-6.0910.010-0.028-0.0640.000
16A18GLU-1-0.999-1.0077.07125.71825.7180.0000.0000.0000.000
17A19GLY0-0.0120.00310.208-1.477-1.4770.0000.0000.0000.000
18A20THR00.0360.01513.1720.3700.3700.0000.0000.0000.000
19A21PRO0-0.0080.01812.1221.6701.6700.0000.0000.0000.000
20A22ILE0-0.008-0.00611.293-1.678-1.6780.0000.0000.0000.000
21A23VAL0-0.046-0.01510.7452.7312.7310.0000.0000.0000.000
22A24ILE00.005-0.0028.930-2.021-2.0210.0000.0000.0000.000
23A25LEU0-0.034-0.02812.0590.3110.3110.0000.0000.0000.000
24A26HIS00.0400.01812.700-1.641-1.6410.0000.0000.0000.000
25A27GLY0-0.037-0.02814.684-1.180-1.1800.0000.0000.0000.000
26A28LEU0-0.057-0.04017.2080.3170.3170.0000.0000.0000.000
27A29MET0-0.002-0.00317.278-0.229-0.2290.0000.0000.0000.000
28A30GLY0-0.0290.00714.9610.1700.1700.0000.0000.0000.000
29A31GLY00.0760.04412.508-0.185-0.1850.0000.0000.0000.000
30A32LEU0-0.011-0.0267.1050.0010.0010.0000.0000.0000.000
31A33SER0-0.0120.0087.7241.8271.8270.0000.0000.0000.000
32A34ASN0-0.080-0.0529.311-2.591-2.5910.0000.0000.0000.000
33A35PHE00.056-0.0028.604-2.626-2.6260.0000.0000.0000.000
34A36ASP-1-0.791-0.8906.01344.34744.3470.0000.0000.0000.000
35A37GLY00.0110.0097.4050.3040.3040.0000.0000.0000.000
36A38VAL0-0.027-0.0209.558-0.987-0.9870.0000.0000.0000.000
37A39ILE0-0.008-0.0173.251-4.345-3.0090.209-0.544-1.0010.005
38A40ASP-1-0.868-0.9344.89346.04946.127-0.001-0.003-0.0730.000
39A41TYR0-0.118-0.0946.728-3.114-3.1140.0000.0000.0000.000
40A42PHE0-0.012-0.0229.654-1.267-1.2670.0000.0000.0000.000
41A43PRO00.0100.0175.327-2.154-2.1540.0000.0000.0000.000
42A44GLU-1-0.927-0.9546.66829.76529.7650.0000.0000.0000.000
43A45LYS10.7990.9009.878-23.266-23.2660.0000.0000.0000.000
44A46GLY00.0210.02511.795-1.428-1.4280.0000.0000.0000.000
45A47TYR0-0.052-0.04711.391-1.152-1.1520.0000.0000.0000.000
46A48LYS10.8790.9428.599-24.224-24.2240.0000.0000.0000.000
47A49VAL00.0310.0066.390-2.794-2.7940.0000.0000.0000.000
48A50LEU0-0.025-0.0266.4085.1415.1410.0000.0000.0000.000
49A51ILE00.0120.0096.224-4.058-4.0580.0000.0000.0000.000
50A52PRO0-0.026-0.0058.4851.2811.2810.0000.0000.0000.000
51A53GLU-1-0.815-0.91510.24027.57227.5720.0000.0000.0000.000
52A54LEU0-0.026-0.01113.012-1.880-1.8800.0000.0000.0000.000
53A55PRO00.0020.01416.579-0.196-0.1960.0000.0000.0000.000
54A56LEU00.012-0.01117.576-1.246-1.2460.0000.0000.0000.000
55A57TYR00.049-0.00520.872-0.841-0.8410.0000.0000.0000.000
56A58SER00.015-0.00221.072-0.482-0.4820.0000.0000.0000.000
57A59MET0-0.0010.02522.978-0.407-0.4070.0000.0000.0000.000
58A60SER0-0.018-0.01025.264-0.601-0.6010.0000.0000.0000.000
59A61LEU00.0260.00328.3480.1950.1950.0000.0000.0000.000
60A62LEU0-0.040-0.05530.2480.0160.0160.0000.0000.0000.000
61A63LYS11.0031.03227.192-11.867-11.8670.0000.0000.0000.000
62A64THR00.0050.02125.4110.4030.4030.0000.0000.0000.000
63A65SER0-0.009-0.00526.653-0.372-0.3720.0000.0000.0000.000
64A66VAL00.0850.03524.6840.3500.3500.0000.0000.0000.000
65A67GLY00.0310.01024.8010.3350.3350.0000.0000.0000.000
66A68THR0-0.136-0.08624.123-0.049-0.0490.0000.0000.0000.000
67A69PHE00.0100.01520.7080.2320.2320.0000.0000.0000.000
68A70ALA00.0770.04420.7040.6660.6660.0000.0000.0000.000
69A71ARG10.9310.95722.049-11.229-11.2290.0000.0000.0000.000
70A72TYR0-0.0050.00416.1180.0630.0630.0000.0000.0000.000
71A73LEU00.0450.02216.2250.5110.5110.0000.0000.0000.000
72A74LYS10.8410.92118.371-12.746-12.7460.0000.0000.0000.000
73A75GLU-1-0.833-0.90620.62914.39614.3960.0000.0000.0000.000
74A76PHE0-0.032-0.00811.0950.0710.0710.0000.0000.0000.000
75A77VAL00.015-0.00116.5340.7080.7080.0000.0000.0000.000
76A78ASP-1-0.824-0.91017.65413.86113.8610.0000.0000.0000.000
77A79PHE0-0.109-0.04514.145-0.318-0.3180.0000.0000.0000.000
78A80LYS10.8650.93410.685-25.868-25.8680.0000.0000.0000.000
79A81GLY0-0.0140.01516.2090.0870.0870.0000.0000.0000.000
80A82TYR0-0.027-0.01011.8690.1280.1280.0000.0000.0000.000
81A83GLU-1-0.895-0.95818.79412.93312.9330.0000.0000.0000.000
82A84ASN0-0.049-0.02920.255-0.674-0.6740.0000.0000.0000.000
83A85VAL0-0.010-0.00416.0330.8300.8300.0000.0000.0000.000
84A86ILE00.0310.03015.846-1.022-1.0220.0000.0000.0000.000
85A87LEU0-0.028-0.00315.3771.4551.4550.0000.0000.0000.000
86A88LEU00.0450.03512.826-0.883-0.8830.0000.0000.0000.000
87A89GLY0-0.0070.00215.0841.0391.0390.0000.0000.0000.000
88A90ASN00.0480.01416.454-0.273-0.2730.0000.0000.0000.000
89A91SER0-0.056-0.03118.322-0.268-0.2680.0000.0000.0000.000
90A92LEU0-0.018-0.02020.789-0.512-0.5120.0000.0000.0000.000
91A93GLY00.0660.03817.688-0.420-0.4200.0000.0000.0000.000
92A94GLY00.0570.00918.6610.0310.0310.0000.0000.0000.000
93A95HIS0-0.063-0.01220.618-0.266-0.2660.0000.0000.0000.000
94A96ILE0-0.055-0.03819.710-0.574-0.5740.0000.0000.0000.000
95A97ALA00.0590.02518.829-0.295-0.2950.0000.0000.0000.000
96A98LEU00.0560.03620.689-0.463-0.4630.0000.0000.0000.000
97A99LEU0-0.0380.01024.285-0.555-0.5550.0000.0000.0000.000
98A100ALA00.016-0.00121.736-0.458-0.4580.0000.0000.0000.000
99A101THR0-0.003-0.01922.504-0.306-0.3060.0000.0000.0000.000
100A102LYS10.8970.95624.837-10.730-10.7300.0000.0000.0000.000
101A103MET0-0.175-0.09326.682-0.377-0.3770.0000.0000.0000.000
102A104PHE0-0.006-0.02024.067-0.346-0.3460.0000.0000.0000.000
103A105PRO00.0440.03524.9140.5450.5450.0000.0000.0000.000
104A106GLU-1-0.926-0.97325.97611.45711.4570.0000.0000.0000.000
105A107ILE0-0.0180.01021.2350.1180.1180.0000.0000.0000.000
106A108VAL0-0.083-0.04320.9750.9470.9470.0000.0000.0000.000
107A109GLN0-0.0090.00819.869-1.050-1.0500.0000.0000.0000.000
108A110ALA00.0100.00420.512-0.542-0.5420.0000.0000.0000.000
109A111LEU0-0.037-0.01120.1860.8720.8720.0000.0000.0000.000
110A112VAL00.0170.00617.710-0.494-0.4940.0000.0000.0000.000
111A113ILE0-0.004-0.01519.0520.6910.6910.0000.0000.0000.000
112A114THR0-0.0060.00217.881-0.114-0.1140.0000.0000.0000.000
113A115GLY00.0780.05020.4040.6050.6050.0000.0000.0000.000
114A116SER0-0.056-0.02021.8820.3970.3970.0000.0000.0000.000
115A117SER0-0.025-0.01623.203-0.473-0.4730.0000.0000.0000.000
116A118GLY00.0450.00525.7860.2360.2360.0000.0000.0000.000
117A119LEU0-0.0260.00128.199-0.443-0.4430.0000.0000.0000.000
118A153LYS10.9340.94620.257-13.932-13.9320.0000.0000.0000.000
119A154GLU-1-0.848-0.95619.93912.83912.8390.0000.0000.0000.000
120A155ILE00.0170.03618.4480.0770.0770.0000.0000.0000.000
121A156VAL0-0.031-0.01620.779-0.288-0.2880.0000.0000.0000.000
122A157ASP-1-0.911-0.96322.25712.64912.6490.0000.0000.0000.000
123A158GLU-1-0.893-0.93719.09315.86515.8650.0000.0000.0000.000
124A159VAL0-0.107-0.05522.2690.0860.0860.0000.0000.0000.000
125A160TYR0-0.023-0.02625.004-0.658-0.6580.0000.0000.0000.000
126A161GLU-1-0.799-0.89722.83112.76912.7690.0000.0000.0000.000
127A162THR0-0.093-0.05625.442-0.141-0.1410.0000.0000.0000.000
128A163VAL0-0.064-0.02727.187-0.381-0.3810.0000.0000.0000.000
129A164SER0-0.003-0.00529.608-0.592-0.5920.0000.0000.0000.000
130A165ASP-1-0.864-0.92026.70811.86111.8610.0000.0000.0000.000
131A166ARG10.8830.96229.253-9.783-9.7830.0000.0000.0000.000
132A167ASN00.006-0.01929.572-0.456-0.4560.0000.0000.0000.000
133A168LYS10.9390.98522.287-13.966-13.9660.0000.0000.0000.000
134A169LEU00.0640.04327.8250.2380.2380.0000.0000.0000.000
135A170VAL00.0420.01130.205-0.023-0.0230.0000.0000.0000.000
136A171LYS10.9060.96626.073-12.129-12.1290.0000.0000.0000.000
137A172THR00.0530.02526.4890.3530.3530.0000.0000.0000.000
138A173LEU0-0.018-0.00927.597-0.035-0.0350.0000.0000.0000.000
139A174ALA0-0.060-0.02629.499-0.199-0.1990.0000.0000.0000.000
140A175ILE00.006-0.00123.608-0.167-0.1670.0000.0000.0000.000
141A176ALA00.0390.02627.746-0.048-0.0480.0000.0000.0000.000
142A177LYS10.9810.99329.571-9.163-9.1630.0000.0000.0000.000
143A178SER0-0.051-0.03129.133-0.122-0.1220.0000.0000.0000.000
144A179ALA00.004-0.01027.406-0.065-0.0650.0000.0000.0000.000
145A180ILE00.0260.01529.166-0.069-0.0690.0000.0000.0000.000
146A181ARG10.9100.96132.368-9.351-9.3510.0000.0000.0000.000
147A182HIS0-0.104-0.04529.924-0.346-0.3460.0000.0000.0000.000
148A183ASN00.0640.02830.6960.5680.5680.0000.0000.0000.000
149A184MET00.0710.03127.423-0.192-0.1920.0000.0000.0000.000
150A185ALA0-0.0020.01131.434-0.105-0.1050.0000.0000.0000.000
151A186LYS10.9120.95434.309-9.124-9.1240.0000.0000.0000.000
152A187ASP-1-0.910-0.97531.9289.5369.5360.0000.0000.0000.000
153A188LEU00.013-0.00329.1140.0510.0510.0000.0000.0000.000
154A189PRO00.0080.00832.4450.0810.0810.0000.0000.0000.000
155A190LYS10.9140.95334.354-9.132-9.1320.0000.0000.0000.000
156A191MET0-0.0110.02127.157-0.149-0.1490.0000.0000.0000.000
157A192LYS10.9100.92729.921-9.435-9.4350.0000.0000.0000.000
158A193THR00.0090.02325.389-0.008-0.0080.0000.0000.0000.000
159A194PRO00.0830.05825.058-0.076-0.0760.0000.0000.0000.000
160A195THR0-0.030-0.01624.0380.6950.6950.0000.0000.0000.000
161A196CYS0-0.0180.01521.526-0.484-0.4840.0000.0000.0000.000
162A197ILE0-0.010-0.01222.4710.5790.5790.0000.0000.0000.000
163A198ILE00.0500.03119.542-0.445-0.4450.0000.0000.0000.000
164A199TRP0-0.026-0.03822.6650.6320.6320.0000.0000.0000.000
165A200GLY00.0520.02924.244-0.124-0.1240.0000.0000.0000.000
166A201LYS10.9030.93125.010-10.719-10.7190.0000.0000.0000.000
167A202ASN0-0.032-0.00827.247-0.532-0.5320.0000.0000.0000.000
168A203ASP-1-0.748-0.86324.84013.10113.1010.0000.0000.0000.000
169A204ASN00.028-0.00127.273-0.664-0.6640.0000.0000.0000.000
170A205VAL0-0.047-0.01324.903-0.258-0.2580.0000.0000.0000.000
171A206THR0-0.088-0.05325.743-0.011-0.0110.0000.0000.0000.000
172A207PRO00.0580.04227.7820.3330.3330.0000.0000.0000.000
173A208PRO00.0060.00629.6830.1910.1910.0000.0000.0000.000
174A209GLU-1-0.824-0.92330.6729.5299.5290.0000.0000.0000.000
175A210VAL0-0.016-0.00928.814-0.055-0.0550.0000.0000.0000.000
176A211ALA0-0.0010.00328.1020.0970.0970.0000.0000.0000.000
177A212GLU-1-0.893-0.96229.3109.4399.4390.0000.0000.0000.000
178A213ASP-1-0.871-0.91132.6339.0499.0490.0000.0000.0000.000
179A214PHE0-0.035-0.03426.787-0.100-0.1000.0000.0000.0000.000
180A215LYS10.8820.94930.525-10.201-10.2010.0000.0000.0000.000
181A216ARG10.7920.88431.663-9.017-9.0170.0000.0000.0000.000
182A217LEU0-0.068-0.03033.297-0.213-0.2130.0000.0000.0000.000
183A218LEU0-0.0020.00227.631-0.118-0.1180.0000.0000.0000.000
184A219PRO0-0.071-0.00731.735-0.121-0.1210.0000.0000.0000.000
185A220ASP-1-0.835-0.91429.81410.71610.7160.0000.0000.0000.000
186A221ALA00.0330.01628.1020.4790.4790.0000.0000.0000.000
187A222ASP-1-0.842-0.90626.82210.87210.8720.0000.0000.0000.000
188A223LEU0-0.032-0.01726.6960.4290.4290.0000.0000.0000.000
189A224TYR00.0200.01024.597-0.200-0.2000.0000.0000.0000.000
190A225TRP0-0.005-0.02025.6970.2830.2830.0000.0000.0000.000
191A226ILE00.0300.01420.8800.1190.1190.0000.0000.0000.000
192A227ASP-1-0.862-0.94825.08310.57110.5710.0000.0000.0000.000
193A228LYS10.8940.96025.983-10.096-10.0960.0000.0000.0000.000
194A229CYS0-0.0420.01722.2560.7770.7770.0000.0000.0000.000
195A230GLY0-0.009-0.01023.172-0.531-0.5310.0000.0000.0000.000
196A231HIS10.7880.88321.862-13.957-13.9570.0000.0000.0000.000
197A232ALA00.0170.00017.0300.4620.4620.0000.0000.0000.000
198A233ALA00.0880.03218.1830.4250.4250.0000.0000.0000.000
199A234MET0-0.041-0.00513.5460.1700.1700.0000.0000.0000.000
200A235MET00.0110.00914.0551.2931.2930.0000.0000.0000.000
201A236GLU-1-0.886-0.94415.06614.37314.3730.0000.0000.0000.000
202A237HIS10.8700.92417.981-15.138-15.1380.0000.0000.0000.000
203A238PRO00.0610.04113.356-0.223-0.2230.0000.0000.0000.000
204A239GLU-1-0.940-0.98015.20315.78115.7810.0000.0000.0000.000
205A240GLU-1-0.889-0.95317.28413.69413.6940.0000.0000.0000.000
206A241PHE0-0.0170.00015.250-0.313-0.3130.0000.0000.0000.000
207A242ASN00.0300.00112.1170.3250.3250.0000.0000.0000.000
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209A244LEU00.000-0.00918.891-0.517-0.5170.0000.0000.0000.000
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