Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

tag_button

FMODB ID: 8JZYY

Calculation Name: 2H6R-A-Xray311

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2H6R

Chain ID: A

ChEMBL ID:

UniProt ID: Q58923

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 206
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2178995.091464
FMO2-HF: Nuclear repulsion 2102168.207718
FMO2-HF: Total energy -76826.883746
FMO2-MP2: Total energy -77048.35266


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:1:MET )


Summations of interaction energy for fragment #1(A:1:MET )
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.
-11.025-10.14619.093-9.704-10.264-0.056
Interaction energy analysis for fragmet #1(A:1:MET )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.067 / q_NPA : -0.063
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].
3A3ILE 00.0430.0583.7970.4191.957-0.019-0.675-0.8440.000
4A4VAL 00.0050.0086.669-0.479-0.4790.0000.0000.0000.000
5A5ILE 00.0270.00510.088-0.020-0.0200.0000.0000.0000.000
6A6ASN 00.000-0.02613.258-0.131-0.1310.0000.0000.0000.000
7A7TYR 0-0.033-0.01016.0860.0080.0080.0000.0000.0000.000
8A8LYS 10.8320.93018.633-0.373-0.3730.0000.0000.0000.000
9A9THR 00.0320.00221.544-0.014-0.0140.0000.0000.0000.000
10A10TYR 00.0410.03520.806-0.006-0.0060.0000.0000.0000.000
11A11ASN 00.044-0.00425.4930.0050.0050.0000.0000.0000.000
12A12GLU -1-0.984-0.99824.1150.2440.2440.0000.0000.0000.000
13A13SER 0-0.029-0.01421.5520.0260.0260.0000.0000.0000.000
14A14ILE 00.0190.02523.324-0.004-0.0040.0000.0000.0000.000
15A15GLY 0-0.011-0.02026.281-0.009-0.0090.0000.0000.0000.000
16A16ASN 00.021-0.01425.1460.0140.0140.0000.0000.0000.000
17A17ARG 10.8820.95624.786-0.170-0.1700.0000.0000.0000.000
18A18GLY 00.0790.02621.4810.0230.0230.0000.0000.0000.000
19A19LEU 0-0.011-0.00820.3440.0300.0300.0000.0000.0000.000
20A20GLU -1-0.933-0.98620.2440.2040.2040.0000.0000.0000.000
21A21ILE 0-0.038-0.00816.7130.0160.0160.0000.0000.0000.000
22A22ALA 0-0.0070.01116.1210.0590.0590.0000.0000.0000.000
23A23LYS 11.0351.01215.123-0.146-0.1460.0000.0000.0000.000
24A24ILE 0-0.056-0.00416.012-0.014-0.0140.0000.0000.0000.000
25A25ALA 0-0.004-0.01912.2830.0160.0160.0000.0000.0000.000
26A26GLU -1-0.836-0.94311.1280.2700.2700.0000.0000.0000.000
27A27LYS 10.8440.91711.684-0.237-0.2370.0000.0000.0000.000
28A28VAL 0-0.038-0.03110.092-0.060-0.0600.0000.0000.0000.000
29A29SER 0-0.058-0.0316.879-0.042-0.0420.0000.0000.0000.000
30A30GLU -1-0.934-0.9697.039-0.242-0.2420.0000.0000.0000.000
31A31GLU -1-0.989-0.9839.513-0.023-0.0230.0000.0000.0000.000
32A32SER 0-0.072-0.0386.796-0.191-0.1910.0000.0000.0000.000
33A33GLY 00.0070.0125.466-0.260-0.2600.0000.0000.0000.000
34A34ILE 0-0.059-0.0352.575-4.170-1.9310.862-0.939-2.162-0.007
35A35THR 00.0010.0023.220-0.2760.2130.0310.000-0.5190.000
36A36ILE 00.0000.0045.3290.8290.9060.000-0.005-0.0720.000
37A37GLY 0-0.0030.0018.367-0.319-0.3190.0000.0000.0000.000
38A38VAL 0-0.0060.00010.8420.0590.0590.0000.0000.0000.000
39A39ALA 00.0220.01314.095-0.064-0.0640.0000.0000.0000.000
40A40PRO 00.0570.01716.591-0.018-0.0180.0000.0000.0000.000
41A41GLN 00.0780.03420.034-0.013-0.0130.0000.0000.0000.000
42A42PHE 00.008-0.02123.409-0.005-0.0050.0000.0000.0000.000
43A43VAL 0-0.041-0.02325.316-0.008-0.0080.0000.0000.0000.000
44A44ASP -1-0.800-0.88923.6580.1850.1850.0000.0000.0000.000
45A45LEU 0-0.035-0.01720.5490.0070.0070.0000.0000.0000.000
46A46ARG 10.9600.96521.750-0.086-0.0860.0000.0000.0000.000
47A47MET 0-0.0010.02823.875-0.003-0.0030.0000.0000.0000.000
48A48ILE 0-0.002-0.01218.065-0.004-0.0040.0000.0000.0000.000
49A49VAL 0-0.0170.00918.6610.0060.0060.0000.0000.0000.000
50A50GLU -1-0.965-0.96819.5430.0950.0950.0000.0000.0000.000
51A51ASN 0-0.115-0.06221.191-0.023-0.0230.0000.0000.0000.000
52A52VAL 0-0.053-0.02715.045-0.002-0.0020.0000.0000.0000.000
53A53ASN 0-0.0160.01212.6090.0040.0040.0000.0000.0000.000
54A54ILE 0-0.0020.00110.6880.0270.0270.0000.0000.0000.000
55A55PRO 0-0.040-0.0329.031-0.059-0.0590.0000.0000.0000.000
56A56VAL 00.0550.04612.3300.0560.0560.0000.0000.0000.000
57A57TYR 0-0.066-0.03910.376-0.001-0.0010.0000.0000.0000.000
58A58ALA 00.0270.00816.3960.0090.0090.0000.0000.0000.000
59A59GLN 0-0.070-0.04218.183-0.016-0.0160.0000.0000.0000.000
60A60HIS 0-0.046-0.06519.9440.0010.0010.0000.0000.0000.000
61A61ILE 00.0340.00421.277-0.003-0.0030.0000.0000.0000.000
62A62ASP -1-0.800-0.86424.0070.0880.0880.0000.0000.0000.000
63A63ASN 00.0150.00427.282-0.008-0.0080.0000.0000.0000.000
64A64ILE 0-0.036-0.01028.371-0.005-0.0050.0000.0000.0000.000
65A65ASN 0-0.013-0.01430.405-0.001-0.0010.0000.0000.0000.000
66A66PRO 00.010-0.00331.5490.0020.0020.0000.0000.0000.000
67A67GLY 00.0410.01334.162-0.005-0.0050.0000.0000.0000.000
68A68SER 0-0.066-0.02237.5500.0020.0020.0000.0000.0000.000
69A69HIS 00.0200.01134.475-0.002-0.0020.0000.0000.0000.000
70A70THR 00.016-0.00135.1950.0030.0030.0000.0000.0000.000
71A71GLY 0-0.0140.00034.1250.0010.0010.0000.0000.0000.000
72A72HIS 0-0.043-0.01131.0890.0040.0040.0000.0000.0000.000
73A73ILE 0-0.052-0.01224.970-0.001-0.0010.0000.0000.0000.000
74A74LEU 0-0.0010.00427.869-0.004-0.0040.0000.0000.0000.000
75A75ALA 00.0710.01724.8350.0080.0080.0000.0000.0000.000
76A76GLU -1-0.828-0.95724.9820.0480.0480.0000.0000.0000.000
77A77ALA 0-0.045-0.00727.2540.0000.0000.0000.0000.0000.000
78A78ILE 00.0160.00721.3170.0090.0090.0000.0000.0000.000
79A79LYS 10.9250.96021.795-0.032-0.0320.0000.0000.0000.000
80A80ASP -1-0.928-0.95423.2910.0660.0660.0000.0000.0000.000
81A81CYS 0-0.116-0.05823.0600.0010.0010.0000.0000.0000.000
82A82GLY 00.0440.03221.1190.0050.0050.0000.0000.0000.000
83A83CYS 0-0.094-0.03018.2150.0210.0210.0000.0000.0000.000
84A84LYS 10.9420.98910.423-0.295-0.2950.0000.0000.0000.000
85A85GLY 00.0530.00715.292-0.041-0.0410.0000.0000.0000.000
86A86THR 0-0.054-0.03016.0080.0180.0180.0000.0000.0000.000
87A87LEU 0-0.0290.00813.679-0.009-0.0090.0000.0000.0000.000
88A88ILE 0-0.006-0.00216.587-0.017-0.0170.0000.0000.0000.000
89A89ASN 0-0.010-0.01517.977-0.001-0.0010.0000.0000.0000.000
90A90HIS 00.1140.06116.861-0.021-0.0210.0000.0000.0000.000
91A91SER 0-0.093-0.04119.394-0.027-0.0270.0000.0000.0000.000
92A92GLU -1-0.863-0.93921.4000.2640.2640.0000.0000.0000.000
93A93LYS 10.8310.92222.832-0.143-0.1430.0000.0000.0000.000
94A94ARG 10.9460.98822.299-0.145-0.1450.0000.0000.0000.000
95A95MET 0-0.0060.02022.637-0.007-0.0070.0000.0000.0000.000
96A96LEU 0-0.0080.00025.730-0.003-0.0030.0000.0000.0000.000
97A97LEU 00.017-0.00425.2710.0000.0000.0000.0000.0000.000
98A98ALA 00.023-0.00426.094-0.005-0.0050.0000.0000.0000.000
99A99ASP -1-0.884-0.94526.9780.0490.0490.0000.0000.0000.000
100A100ILE 00.026-0.00720.8940.0010.0010.0000.0000.0000.000
101A101GLU -1-0.907-0.95022.499-0.012-0.0120.0000.0000.0000.000
102A102ALA 00.0330.02624.294-0.007-0.0070.0000.0000.0000.000
103A103VAL 0-0.034-0.01621.280-0.002-0.0020.0000.0000.0000.000
104A104ILE 00.0530.02918.5540.0050.0050.0000.0000.0000.000
105A105ASN 00.021-0.00221.075-0.016-0.0160.0000.0000.0000.000
106A106LYS 10.8600.93323.878-0.033-0.0330.0000.0000.0000.000
107A107CYS 0-0.030-0.01519.2580.0080.0080.0000.0000.0000.000
108A108LYS 10.9361.00319.4740.0400.0400.0000.0000.0000.000
109A109ASN 0-0.031-0.01720.452-0.016-0.0160.0000.0000.0000.000
110A110LEU 0-0.035-0.01522.5240.0010.0010.0000.0000.0000.000
111A111GLY 0-0.034-0.01819.0710.0060.0060.0000.0000.0000.000
112A112LEU 0-0.091-0.03817.5860.0140.0140.0000.0000.0000.000
113A113GLU -1-0.827-0.93810.0880.0940.0940.0000.0000.0000.000
114A114THR 0-0.053-0.04714.6910.0320.0320.0000.0000.0000.000
115A115ILE 00.0290.00910.773-0.038-0.0380.0000.0000.0000.000
116A116VAL 0-0.031-0.02113.1960.0520.0520.0000.0000.0000.000
117A117CYS 0-0.042-0.00614.4840.0130.0130.0000.0000.0000.000
118A118THR 00.0530.03215.109-0.041-0.0410.0000.0000.0000.000
119A119ASN 00.0380.01616.9520.0280.0280.0000.0000.0000.000
120A120ASN 00.0220.01219.3820.0160.0160.0000.0000.0000.000
121A121ILE 00.1340.08218.054-0.007-0.0070.0000.0000.0000.000
122A122ASN 0-0.044-0.05019.109-0.032-0.0320.0000.0000.0000.000
123A123THR 00.008-0.02019.431-0.011-0.0110.0000.0000.0000.000
124A124SER 0-0.001-0.03415.7610.0040.0040.0000.0000.0000.000
125A125LYS 10.9620.99217.3060.0030.0030.0000.0000.0000.000
126A126ALA 0-0.042-0.01319.209-0.010-0.0100.0000.0000.0000.000
127A127VAL 00.0480.00917.492-0.005-0.0050.0000.0000.0000.000
128A128ALA 00.0190.02116.791-0.013-0.0130.0000.0000.0000.000
129A129ALA 0-0.003-0.00517.686-0.020-0.0200.0000.0000.0000.000
130A130LEU 0-0.074-0.03320.0680.0000.0000.0000.0000.0000.000
131A131SER 0-0.064-0.01517.525-0.005-0.0050.0000.0000.0000.000
132A132PRO 0-0.0270.00214.5220.0070.0070.0000.0000.0000.000
133A133ASP -1-0.782-0.88311.555-0.133-0.1330.0000.0000.0000.000
134A134CYS 0-0.047-0.0238.642-0.103-0.1030.0000.0000.0000.000
135A135ILE 0-0.0150.00610.1960.1030.1030.0000.0000.0000.000
136A136ALA 00.0060.01010.5580.0070.0070.0000.0000.0000.000
137A137VAL 0-0.037-0.02311.748-0.050-0.0500.0000.0000.0000.000
138A138GLU -1-0.872-0.96213.5890.3600.3600.0000.0000.0000.000
139A139PRO 0-0.0270.00015.906-0.004-0.0040.0000.0000.0000.000
140A140PRO 00.008-0.01417.4260.0340.0340.0000.0000.0000.000
141A141NME 0-0.0150.07619.447-0.022-0.0220.0000.0000.0000.000
142A154ACE 00.003-0.06718.3820.0100.0100.0000.0000.0000.000
143A155GLU -1-0.941-0.97218.6180.1120.1120.0000.0000.0000.000
144A156VAL 0-0.048-0.03217.278-0.016-0.0160.0000.0000.0000.000
145A157VAL 00.0540.02511.2830.0000.0000.0000.0000.0000.000
146A158GLU -1-0.816-0.90812.980-0.053-0.0530.0000.0000.0000.000
147A159GLY 0-0.037-0.05314.349-0.055-0.0550.0000.0000.0000.000
148A160THR 0-0.021-0.01613.660-0.026-0.0260.0000.0000.0000.000
149A161VAL 00.0260.0249.977-0.037-0.0370.0000.0000.0000.000
150A162ARG 10.8980.96412.755-0.004-0.0040.0000.0000.0000.000
151A163ALA 0-0.0140.00315.738-0.004-0.0040.0000.0000.0000.000
152A164VAL 00.007-0.00713.3590.0080.0080.0000.0000.0000.000
153A165LYS 10.9230.9588.8810.7220.7220.0000.0000.0000.000
154A166GLU -1-0.958-0.96715.055-0.123-0.1230.0000.0000.0000.000
155A167ILE 0-0.122-0.03518.3330.0140.0140.0000.0000.0000.000
156A168ASN 00.027-0.00315.922-0.034-0.0340.0000.0000.0000.000
157A169LYS 10.9480.97413.9650.4070.4070.0000.0000.0000.000
158A170ASP -1-0.978-0.97112.231-0.484-0.4840.0000.0000.0000.000
159A171VAL 0-0.0160.01211.805-0.013-0.0130.0000.0000.0000.000
160A172LYS 10.9500.9854.1201.5581.6820.000-0.009-0.1140.000
161A173VAL 00.0170.0047.7950.2210.2210.0000.0000.0000.000
162A174LEU 0-0.018-0.0085.518-0.069-0.0690.0000.0000.0000.000
163A175CYS 00.0010.0067.567-0.170-0.1700.0000.0000.0000.000
164A176GLY 00.0620.0199.6040.2610.2610.0000.0000.0000.000
165A177ALA 0-0.030-0.01712.190-0.096-0.0960.0000.0000.0000.000
166A178GLY 0-0.044-0.01014.5440.0170.0170.0000.0000.0000.000
167A179ILE 00.0280.0049.9260.0310.0310.0000.0000.0000.000
168A180SER 0-0.129-0.06413.975-0.027-0.0270.0000.0000.0000.000
169A181LYS 10.8520.92015.140-0.469-0.4690.0000.0000.0000.000
170A182GLY 00.0830.05111.5250.1020.1020.0000.0000.0000.000
171A183GLU -1-0.942-0.98011.0670.5670.5670.0000.0000.0000.000
172A184ASP -1-0.825-0.91911.8900.6700.6700.0000.0000.0000.000
173A185VAL 0-0.048-0.0106.6870.1160.1160.0000.0000.0000.000
174A186LYS 10.9140.9587.536-0.261-0.2610.0000.0000.0000.000
175A187ALA 00.014-0.0068.631-0.122-0.1220.0000.0000.0000.000
176A188ALA 0-0.0160.0048.207-0.182-0.1820.0000.0000.0000.000
177A189LEU 0-0.024-0.0233.741-0.297-0.0840.002-0.031-0.1840.000
178A190ASP -1-0.904-0.9506.244-0.374-0.3740.0000.0000.0000.000
179A191LEU 0-0.075-0.0349.241-0.133-0.1330.0000.0000.0000.000
180A192GLY 0-0.032-0.0288.677-0.033-0.0330.0000.0000.0000.000
181A193ALA 0-0.040-0.0106.523-0.257-0.2570.0000.0000.0000.000
182A194GLU -1-0.894-0.9622.879-2.397-1.5350.157-0.226-0.793-0.001
183A195GLY 0-0.009-0.0332.023-7.095-7.9677.288-3.970-2.447-0.044
184A196VAL 0-0.036-0.0093.562-0.605-0.4100.0150.002-0.2100.000
185A197LEU 0-0.0180.0036.915-0.148-0.1480.0000.0000.0000.000
186A198LEU 00.0210.01710.217-0.148-0.1480.0000.0000.0000.000
187A199ALA 00.0490.01413.334-0.046-0.0460.0000.0000.0000.000
188A200SER 00.0040.00316.7460.0180.0180.0000.0000.0000.000
189A201GLY 0-0.015-0.01116.724-0.040-0.0400.0000.0000.0000.000
190A202VAL 00.0060.00513.554-0.002-0.0020.0000.0000.0000.000
191A203VAL 0-0.001-0.00416.978-0.048-0.0480.0000.0000.0000.000
192A204LYS 10.9480.98919.794-0.415-0.4150.0000.0000.0000.000
193A205ALA 0-0.048-0.03219.712-0.031-0.0310.0000.0000.0000.000
194A206LYS 10.9640.98721.652-0.215-0.2150.0000.0000.0000.000
195A207ASN 00.0200.01520.9580.0010.0010.0000.0000.0000.000
196A208VAL 00.0700.02217.1410.0280.0280.0000.0000.0000.000
197A209GLU -1-0.763-0.86916.0640.3190.3190.0000.0000.0000.000
198A210GLU -1-0.949-0.98115.8230.3350.3350.0000.0000.0000.000
199A211ALA 0-0.046-0.02216.3570.0300.0300.0000.0000.0000.000
200A212ILE 00.0170.00010.8090.1090.1090.0000.0000.0000.000
201A213ARG 10.9460.95711.240-0.102-0.1020.0000.0000.0000.000
202A214GLU -1-0.850-0.89512.7820.5070.5070.0000.0000.0000.000
203A215LEU 0-0.168-0.0979.9790.0710.0710.0000.0000.0000.000
204A216ILE 00.1230.0576.9000.7580.7580.0000.0000.0000.000
205A217LYN 00.1050.1484.065-0.728-0.4200.001-0.036-0.2720.000
206A218NME 0-0.158-0.1071.8632.156-2.13810.756-3.815-2.647-0.004