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: KGJ83

Calculation Name: 5HXG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5HXG

Chain ID: A

ChEMBL ID:

UniProt ID: A0A6C8

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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2515665.345638
FMO2-HF: Nuclear repulsion 2431987.763127
FMO2-HF: Total energy -83677.58251
FMO2-MP2: Total energy -83920.588826


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:2:ARG)


Summations of interaction energy for fragment #1(A:2:ARG)
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.
-16.546-17.50910.212-3.54-5.708-0.005
Interaction energy analysis for fragmet #1(A:2:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.941 / q_NPA : 0.955
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].
3A4PHE00.0570.0383.649-1.3500.475-0.053-0.526-1.2460.003
4A5PHE00.0200.0006.9370.5230.5230.0000.0000.0000.000
5A6MET0-0.0070.01710.3190.5490.5490.0000.0000.0000.000
6A7ALA00.0160.00612.6000.0410.0410.0000.0000.0000.000
7A8GLU-1-0.894-0.96015.462-15.121-15.1210.0000.0000.0000.000
8A9PRO0-0.026-0.01318.2980.2880.2880.0000.0000.0000.000
9A10ILE0-0.014-0.00321.9730.1990.1990.0000.0000.0000.000
10A11ARG10.8280.88824.71410.74110.7410.0000.0000.0000.000
11A12ALA00.0500.01428.0570.0980.0980.0000.0000.0000.000
12A13MET0-0.040-0.01231.6420.0470.0470.0000.0000.0000.000
13A14GLU-1-0.871-0.93333.971-7.622-7.6220.0000.0000.0000.000
14A15GLY0-0.0120.00631.1350.0450.0450.0000.0000.0000.000
15A16ASP-1-0.919-0.94830.460-8.927-8.9270.0000.0000.0000.000
16A17LEU0-0.072-0.04724.134-0.169-0.1690.0000.0000.0000.000
17A18LEU0-0.018-0.00927.4510.2180.2180.0000.0000.0000.000
18A19GLY00.0300.00724.8360.0410.0410.0000.0000.0000.000
19A20VAL0-0.052-0.01019.3120.0070.0070.0000.0000.0000.000
20A21GLU-1-0.781-0.86617.085-14.565-14.5650.0000.0000.0000.000
21A22ILE0-0.020-0.01013.192-0.458-0.4580.0000.0000.0000.000
22A23ILE0-0.030-0.00511.162-0.233-0.2330.0000.0000.0000.000
23A24THR0-0.023-0.0206.698-1.278-1.2780.0000.0000.0000.000
24A25HIS00.0180.0246.3910.7580.7580.0000.0000.0000.000
25A26PHE00.0110.0062.086-3.511-6.29910.265-3.014-4.462-0.008
26A39VAL00.0570.0137.6830.1290.1290.0000.0000.0000.000
27A40ILE00.0450.0318.125-0.378-0.3780.0000.0000.0000.000
28A41SER0-0.007-0.00410.261-0.044-0.0440.0000.0000.0000.000
29A42SER0-0.075-0.03711.4331.0041.0040.0000.0000.0000.000
30A43TRP0-0.0090.0035.493-1.004-1.0040.0000.0000.0000.000
31A44ASP-1-0.779-0.89411.462-21.981-21.9810.0000.0000.0000.000
32A45ASN00.051-0.00912.425-1.433-1.4330.0000.0000.0000.000
33A46SER0-0.0250.00112.184-0.517-0.5170.0000.0000.0000.000
34A47GLN0-0.012-0.0146.7061.0561.0560.0000.0000.0000.000
35A48LYS10.8530.9449.41418.33718.3370.0000.0000.0000.000
36A49ARG10.8800.95111.70318.69718.6970.0000.0000.0000.000
37A50ARG10.9160.9467.12430.87230.8720.0000.0000.0000.000
38A51PHE00.0180.0287.454-0.106-0.1060.0000.0000.0000.000
39A52LEU00.0520.0159.4130.6980.6980.0000.0000.0000.000
40A53LEU0-0.033-0.01412.7770.9610.9610.0000.0000.0000.000
41A54ASP-1-0.862-0.9198.124-29.999-29.9990.0000.0000.0000.000
42A55LEU00.0320.04211.4611.0901.0900.0000.0000.0000.000
43A56LEU00.001-0.00912.7401.2981.2980.0000.0000.0000.000
44A57ARG10.9400.96414.08420.28220.2820.0000.0000.0000.000
45A58THR00.010-0.00212.1530.6760.6760.0000.0000.0000.000
46A59ILE0-0.002-0.01014.6630.9470.9470.0000.0000.0000.000
47A60ALA00.001-0.01317.6630.9380.9380.0000.0000.0000.000
48A61ALA0-0.052-0.01017.4180.8680.8680.0000.0000.0000.000
49A62LYS10.8130.89617.69115.85215.8520.0000.0000.0000.000
50A63HIS0-0.031-0.02720.9390.9640.9640.0000.0000.0000.000
51A64GLY00.0310.01923.3970.4770.4770.0000.0000.0000.000
52A65TRP0-0.0040.00122.9840.5550.5550.0000.0000.0000.000
53A66PHE00.0500.00620.2660.2950.2950.0000.0000.0000.000
54A67LEU00.0020.00825.8240.4300.4300.0000.0000.0000.000
55A68ARG10.9100.95828.8459.9039.9030.0000.0000.0000.000
56A69HIS10.8220.90627.59610.64510.6450.0000.0000.0000.000
57A70GLY00.0360.04330.5460.1100.1100.0000.0000.0000.000
58A71LEU0-0.047-0.00625.5280.0340.0340.0000.0000.0000.000
59A72PHE00.0450.02623.915-0.119-0.1190.0000.0000.0000.000
60A73CYS0-0.077-0.04519.417-0.508-0.5080.0000.0000.0000.000
61A74ILE00.0230.02619.759-0.108-0.1080.0000.0000.0000.000
62A75VAL00.0200.00415.959-0.918-0.9180.0000.0000.0000.000
63A76ASN0-0.031-0.01215.8681.3671.3670.0000.0000.0000.000
64A77ILE0-0.025-0.01616.200-1.128-1.1280.0000.0000.0000.000
65A78ASP-1-0.739-0.89215.375-18.147-18.1470.0000.0000.0000.000
66A79ARG10.8900.91218.53912.20712.2070.0000.0000.0000.000
67A80GLY0-0.031-0.00517.8340.3280.3280.0000.0000.0000.000
68A81MET00.022-0.00112.7340.2740.2740.0000.0000.0000.000
69A82ALA00.0380.02917.6440.3380.3380.0000.0000.0000.000
70A83GLN0-0.010-0.00720.7390.4300.4300.0000.0000.0000.000
71A84LEU0-0.029-0.01315.5420.3130.3130.0000.0000.0000.000
72A85VAL00.0120.01919.7390.3340.3340.0000.0000.0000.000
73A86LEU0-0.017-0.01021.7110.5610.5610.0000.0000.0000.000
74A87GLN0-0.052-0.02122.9920.7540.7540.0000.0000.0000.000
75A88ASP-1-0.836-0.90918.590-16.116-16.1160.0000.0000.0000.000
76A89LYS10.9410.95821.41813.37813.3780.0000.0000.0000.000
77A90ASP-1-0.901-0.94718.797-14.876-14.8760.0000.0000.0000.000
78A91ILE0-0.026-0.02515.503-0.106-0.1060.0000.0000.0000.000
79A92ARG10.8740.94219.43911.98511.9850.0000.0000.0000.000
80A93ALA0-0.0190.00822.9890.3830.3830.0000.0000.0000.000
81A94LEU0-0.022-0.01317.8190.2150.2150.0000.0000.0000.000
82A95LEU00.0290.00620.3780.1920.1920.0000.0000.0000.000
83A96HIS0-0.035-0.02822.7420.6430.6430.0000.0000.0000.000
84A97ALA0-0.0230.00824.6190.4730.4730.0000.0000.0000.000
85A98MET0-0.081-0.02619.5560.1660.1660.0000.0000.0000.000
86A99LEU00.0280.00824.845-0.241-0.2410.0000.0000.0000.000
87A100PHE00.0260.02322.1350.1730.1730.0000.0000.0000.000
88A101VAL0-0.023-0.01120.466-0.267-0.2670.0000.0000.0000.000
89A102GLU-1-0.856-0.91222.737-10.711-10.7110.0000.0000.0000.000
90A103LEU0-0.008-0.00720.535-0.709-0.7090.0000.0000.0000.000
91A104GLN0-0.029-0.01919.9181.2441.2440.0000.0000.0000.000
92A105VAL0-0.024-0.01120.654-0.758-0.7580.0000.0000.0000.000
93A106ALA00.0430.02221.3430.2920.2920.0000.0000.0000.000
94A107GLU-1-0.740-0.91423.228-9.890-9.8900.0000.0000.0000.000
95A108HIS0-0.007-0.00620.0220.5120.5120.0000.0000.0000.000
96A109PHE0-0.069-0.02521.736-0.286-0.2860.0000.0000.0000.000
97A110SER0-0.029-0.02224.2820.0570.0570.0000.0000.0000.000
98A111CYS0-0.085-0.05026.8770.2170.2170.0000.0000.0000.000
99A112GLN00.0400.01627.658-0.507-0.5070.0000.0000.0000.000
100A113ASP-1-0.924-0.92430.294-9.064-9.0640.0000.0000.0000.000
101A114ASN0-0.041-0.01532.3730.2700.2700.0000.0000.0000.000
102A115VAL00.019-0.00935.4220.0910.0910.0000.0000.0000.000
103A116LEU0-0.043-0.02836.9530.0450.0450.0000.0000.0000.000
104A117VAL00.0280.01733.175-0.210-0.2100.0000.0000.0000.000
105A118ASP-1-0.728-0.85328.677-10.786-10.7860.0000.0000.0000.000
106A119PRO00.028-0.00331.511-0.069-0.0690.0000.0000.0000.000
107A120LEU0-0.035-0.01024.114-0.042-0.0420.0000.0000.0000.000
108A121ILE00.0340.02126.798-0.215-0.2150.0000.0000.0000.000
109A122HIS00.0080.00229.1430.1610.1610.0000.0000.0000.000
110A123ALA0-0.029-0.02428.9280.1150.1150.0000.0000.0000.000
111A124LEU0-0.021-0.02824.017-0.076-0.0760.0000.0000.0000.000
112A125HIS00.0370.02128.015-0.231-0.2310.0000.0000.0000.000
113A126LYS10.8880.96130.9549.1519.1510.0000.0000.0000.000
114A127GLN0-0.061-0.01927.216-0.025-0.0250.0000.0000.0000.000
115A128PRO00.0340.01928.2380.0990.0990.0000.0000.0000.000
116A129ASN0-0.076-0.03724.9210.1210.1210.0000.0000.0000.000
117A130PRO00.0490.03427.3130.0160.0160.0000.0000.0000.000
118A131LEU00.0090.00525.940-0.561-0.5610.0000.0000.0000.000
119A132TRP0-0.033-0.03724.3360.4760.4760.0000.0000.0000.000
120A133LEU0-0.039-0.01825.367-0.316-0.3160.0000.0000.0000.000
121A134GLY00.019-0.01522.7550.2160.2160.0000.0000.0000.000
122A135ASP-1-0.826-0.90923.312-12.084-12.0840.0000.0000.0000.000
123A136LEU00.0300.01725.2600.2620.2620.0000.0000.0000.000
124A137GLY0-0.023-0.01929.0010.0930.0930.0000.0000.0000.000
125A138VAL0-0.049-0.01525.2080.1840.1840.0000.0000.0000.000
126A139GLY0-0.036-0.00528.4080.1190.1190.0000.0000.0000.000
127A140ASN0-0.040-0.02125.2380.2600.2600.0000.0000.0000.000
128A141ALA0-0.0110.00129.146-0.099-0.0990.0000.0000.0000.000
129A142THR00.0230.01631.3600.1880.1880.0000.0000.0000.000
130A143ALA00.0570.02033.326-0.209-0.2090.0000.0000.0000.000
131A144ALA00.0150.01635.3330.0670.0670.0000.0000.0000.000
132A145PRO00.033-0.00331.3500.1370.1370.0000.0000.0000.000
133A146LEU00.0170.00933.342-0.016-0.0160.0000.0000.0000.000
134A147VAL0-0.031-0.02234.5960.1310.1310.0000.0000.0000.000
135A148CYS0-0.087-0.04036.7780.2510.2510.0000.0000.0000.000
136A149GLY00.0090.01336.5790.0390.0390.0000.0000.0000.000
137A150CYS0-0.086-0.03731.661-0.085-0.0850.0000.0000.0000.000
138A151PHE0-0.008-0.00127.835-0.220-0.2200.0000.0000.0000.000
139A152SER00.010-0.00330.0160.3380.3380.0000.0000.0000.000
140A153GLY00.0110.00028.9870.1920.1920.0000.0000.0000.000
141A154VAL0-0.008-0.01227.998-0.212-0.2120.0000.0000.0000.000
142A155LYS10.9140.96820.36013.14413.1440.0000.0000.0000.000
143A156LEU0-0.049-0.01626.904-0.013-0.0130.0000.0000.0000.000
144A157ASP-1-0.793-0.91025.553-11.086-11.0860.0000.0000.0000.000
145A158ARG10.9700.98119.27312.99612.9960.0000.0000.0000.000
146A159SER00.0320.01726.2060.3070.3070.0000.0000.0000.000
147A160PHE00.0080.01228.2880.4660.4660.0000.0000.0000.000
148A161PHE00.004-0.00829.1360.3440.3440.0000.0000.0000.000
149A162VAL00.001-0.00428.7670.3120.3120.0000.0000.0000.000
150A163SER0-0.066-0.02631.5770.3280.3280.0000.0000.0000.000
151A164GLN0-0.032-0.03534.1360.5080.5080.0000.0000.0000.000
152A165ILE0-0.0270.00533.5750.2490.2490.0000.0000.0000.000
153A166GLU-1-0.845-0.93535.983-7.529-7.5290.0000.0000.0000.000
154A167LYS10.8730.96238.8067.6337.6330.0000.0000.0000.000
155A168MET00.0500.01541.105-0.019-0.0190.0000.0000.0000.000
156A169THR0-0.023-0.02041.8760.0660.0660.0000.0000.0000.000
157A170PHE00.0470.03834.204-0.070-0.0700.0000.0000.0000.000
158A171PRO00.0590.00439.318-0.107-0.1070.0000.0000.0000.000
159A172LEU0-0.021-0.00641.2940.0000.0000.0000.0000.0000.000
160A173LEU0-0.0020.00935.427-0.006-0.0060.0000.0000.0000.000
161A174VAL00.0510.02635.837-0.123-0.1230.0000.0000.0000.000
162A175LYS10.9360.97638.0086.5346.5340.0000.0000.0000.000
163A176HIS0-0.056-0.04240.8880.1260.1260.0000.0000.0000.000
164A177ILE00.0150.00933.968-0.032-0.0320.0000.0000.0000.000
165A178ARG10.8310.90636.7707.6707.6700.0000.0000.0000.000
166A179HIS0-0.092-0.03238.1570.1520.1520.0000.0000.0000.000
167A180TYR0-0.038-0.01137.4250.1250.1250.0000.0000.0000.000
168A181CYS0-0.0260.00532.821-0.212-0.2120.0000.0000.0000.000
169A182ASP-1-0.794-0.86335.380-8.012-8.0120.0000.0000.0000.000
170A183LYS10.8680.93131.7438.5998.5990.0000.0000.0000.000
171A184ILE00.0530.01830.913-0.210-0.2100.0000.0000.0000.000
172A185VAL00.002-0.00425.2840.1630.1630.0000.0000.0000.000
173A186VAL00.0120.00227.984-0.043-0.0430.0000.0000.0000.000
174A187GLY00.0530.01523.799-0.108-0.1080.0000.0000.0000.000
175A188GLY0-0.059-0.03322.4040.2360.2360.0000.0000.0000.000
176A189GLN0-0.018-0.01523.3750.5180.5180.0000.0000.0000.000
177A190GLU-1-0.909-0.95223.507-11.188-11.1880.0000.0000.0000.000
178A191ASN0-0.011-0.01725.7180.2140.2140.0000.0000.0000.000
179A192ALA00.0610.01029.146-0.043-0.0430.0000.0000.0000.000
180A193ARG10.9270.98332.0908.4198.4190.0000.0000.0000.000
181A194TYR0-0.012-0.02031.5580.1440.1440.0000.0000.0000.000
182A195LEU00.0170.03030.5250.1110.1110.0000.0000.0000.000
183A196PRO00.0330.01234.4720.0770.0770.0000.0000.0000.000
184A197ALA00.0340.01737.2660.1340.1340.0000.0000.0000.000
185A198LEU0-0.034-0.02131.5320.0500.0500.0000.0000.0000.000
186A199LYS10.9160.93935.8177.4817.4810.0000.0000.0000.000
187A200THR0-0.071-0.02337.6670.1570.1570.0000.0000.0000.000
188A201ALA0-0.049-0.02537.6800.1200.1200.0000.0000.0000.000
189A202GLY0-0.0140.00038.4550.0480.0480.0000.0000.0000.000
190A203ILE0-0.054-0.02931.896-0.119-0.1190.0000.0000.0000.000
191A204TRP00.0010.01228.9660.0870.0870.0000.0000.0000.000
192A205ALA00.017-0.00428.5340.0300.0300.0000.0000.0000.000
193A206THR0-0.016-0.01127.558-0.046-0.0460.0000.0000.0000.000
194A207GLN00.025-0.01119.3330.3810.3810.0000.0000.0000.000
195A208GLY0-0.016-0.01321.5190.2250.2250.0000.0000.0000.000
196A209THR00.0470.02419.1290.0140.0140.0000.0000.0000.000
197A210LEU0-0.0260.00721.5520.1210.1210.0000.0000.0000.000
198A211PHE0-0.059-0.03323.4280.3090.3090.0000.0000.0000.000
199A212PRO00.0140.00220.114-0.451-0.4510.0000.0000.0000.000
200A213SER00.0070.00015.746-0.038-0.0380.0000.0000.0000.000
201A214VAL00.0050.01716.5810.0430.0430.0000.0000.0000.000
202A215ALA00.0750.02512.989-0.627-0.6270.0000.0000.0000.000
203A216LEU0-0.022-0.00813.4281.0701.0700.0000.0000.0000.000
204A217GLU-1-0.865-0.95811.578-21.706-21.7060.0000.0000.0000.000
205A218GLU-1-0.959-0.96815.290-15.168-15.1680.0000.0000.0000.000
206A219ILE00.0040.01518.1160.6970.6970.0000.0000.0000.000
207A220GLU-1-0.863-0.93519.828-13.324-13.3240.0000.0000.0000.000
208A221THR0-0.076-0.04320.5580.6330.6330.0000.0000.0000.000
209A222LEU0-0.030-0.00320.6460.4250.4250.0000.0000.0000.000
210A223LEU00.0340.01623.8020.3530.3530.0000.0000.0000.000
211A224LEU00.0450.04927.213-0.005-0.0050.0000.0000.0000.000