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

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FMODB ID: NN48Q

Calculation Name: 2H6R-A-Xray372

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: 2023-09-24

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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2166973.199516
FMO2-HF: Nuclear repulsion 2090336.19212
FMO2-HF: Total energy -76637.007396
FMO2-MP2: Total energy -76857.81009


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.
-13.21-7.2828.033-5.852-8.107-0.05
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 : -0.052 / q_NPA : -0.038
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].
3A3ILE00.0330.0533.7970.4321.980-0.027-0.677-0.8440.000
4A4VAL00.0110.0116.585-0.420-0.4200.0000.0000.0000.000
5A5ILE00.0270.00510.109-0.014-0.0140.0000.0000.0000.000
6A6ASN00.000-0.02513.175-0.117-0.1170.0000.0000.0000.000
7A7TYR0-0.032-0.00916.1320.0060.0060.0000.0000.0000.000
8A8LYS10.8320.93018.699-0.360-0.3600.0000.0000.0000.000
9A9THR00.0310.00221.611-0.012-0.0120.0000.0000.0000.000
10A10TYR00.0410.03620.874-0.006-0.0060.0000.0000.0000.000
11A11ASN00.043-0.00525.4110.0050.0050.0000.0000.0000.000
12A12GLU-1-0.983-0.99924.0330.2280.2280.0000.0000.0000.000
13A13SER0-0.030-0.01521.4670.0230.0230.0000.0000.0000.000
14A14ILE00.0240.02723.238-0.002-0.0020.0000.0000.0000.000
15A15GLY0-0.015-0.02126.194-0.009-0.0090.0000.0000.0000.000
16A16ASN00.023-0.01325.0590.0140.0140.0000.0000.0000.000
17A17ARG10.8820.95524.785-0.162-0.1620.0000.0000.0000.000
18A18GLY00.0770.02721.3940.0200.0200.0000.0000.0000.000
19A19LEU0-0.011-0.00820.2570.0280.0280.0000.0000.0000.000
20A20GLU-1-0.933-0.98720.2430.1890.1890.0000.0000.0000.000
21A21ILE0-0.038-0.00816.6280.0120.0120.0000.0000.0000.000
22A22ALA0-0.0080.01016.1190.0520.0520.0000.0000.0000.000
23A23LYS11.0371.01315.121-0.137-0.1370.0000.0000.0000.000
24A24ILE0-0.056-0.00416.010-0.016-0.0160.0000.0000.0000.000
25A25ALA0-0.004-0.01912.2610.0080.0080.0000.0000.0000.000
26A26GLU-1-0.836-0.94311.1260.2580.2580.0000.0000.0000.000
27A27LYS10.8440.91611.682-0.203-0.2030.0000.0000.0000.000
28A28VAL0-0.036-0.03010.090-0.057-0.0570.0000.0000.0000.000
29A29SER0-0.057-0.0316.877-0.046-0.0460.0000.0000.0000.000
30A30GLU-1-0.932-0.9697.037-0.214-0.2140.0000.0000.0000.000
31A31GLU-1-0.995-0.9849.512-0.044-0.0440.0000.0000.0000.000
32A32SER0-0.067-0.0376.798-0.175-0.1750.0000.0000.0000.000
33A33GLY00.0030.0115.464-0.243-0.2430.0000.0000.0000.000
34A34ILE0-0.054-0.0272.573-3.951-1.7960.848-0.888-2.115-0.006
35A35THR00.0000.0023.219-0.3600.1300.0300.000-0.5200.000
36A36ILE0-0.0040.0035.3280.7010.782-0.001-0.005-0.0750.000
37A37GLY0-0.0020.0028.284-0.271-0.2710.0000.0000.0000.000
38A38VAL0-0.0070.00010.7580.0520.0520.0000.0000.0000.000
39A39ALA00.0250.01414.009-0.052-0.0520.0000.0000.0000.000
40A40PRO00.0550.01716.591-0.018-0.0180.0000.0000.0000.000
41A41GLN00.0780.03519.993-0.010-0.0100.0000.0000.0000.000
42A42PHE00.008-0.02223.457-0.004-0.0040.0000.0000.0000.000
43A43VAL0-0.041-0.02425.316-0.007-0.0070.0000.0000.0000.000
44A44ASP-1-0.802-0.88823.5730.1800.1800.0000.0000.0000.000
45A45LEU0-0.034-0.01620.5490.0070.0070.0000.0000.0000.000
46A46ARG10.9610.96621.750-0.093-0.0930.0000.0000.0000.000
47A47MET0-0.0050.02623.875-0.004-0.0040.0000.0000.0000.000
48A48ILE0-0.003-0.01318.064-0.005-0.0050.0000.0000.0000.000
49A49VAL0-0.0160.00918.6610.0060.0060.0000.0000.0000.000
50A50GLU-1-0.965-0.96919.5420.1010.1010.0000.0000.0000.000
51A51ASN0-0.113-0.06121.190-0.023-0.0230.0000.0000.0000.000
52A52VAL0-0.054-0.02615.044-0.003-0.0030.0000.0000.0000.000
53A53ASN0-0.0160.01112.6100.0080.0080.0000.0000.0000.000
54A54ILE0-0.0040.00110.6870.0260.0260.0000.0000.0000.000
55A55PRO0-0.038-0.0319.031-0.055-0.0550.0000.0000.0000.000
56A56VAL00.0550.04612.3300.0490.0490.0000.0000.0000.000
57A57TYR0-0.070-0.04010.3740.0040.0040.0000.0000.0000.000
58A58ALA00.0300.01016.3960.0050.0050.0000.0000.0000.000
59A59GLN0-0.068-0.04318.238-0.013-0.0130.0000.0000.0000.000
60A60HIS0-0.045-0.06520.0020.0030.0030.0000.0000.0000.000
61A61ILE00.0300.00421.320-0.003-0.0030.0000.0000.0000.000
62A62ASP-1-0.798-0.86324.0540.0960.0960.0000.0000.0000.000
63A63ASN00.0180.00527.327-0.006-0.0060.0000.0000.0000.000
64A64ILE0-0.038-0.01128.408-0.005-0.0050.0000.0000.0000.000
65A65ASN0-0.015-0.01430.4400.0010.0010.0000.0000.0000.000
66A66PRO00.010-0.00331.5490.0010.0010.0000.0000.0000.000
67A67GLY00.0410.01234.162-0.005-0.0050.0000.0000.0000.000
68A68SER0-0.065-0.02137.5890.0020.0020.0000.0000.0000.000
69A69HIS00.0200.01234.521-0.002-0.0020.0000.0000.0000.000
70A70THR00.015-0.00135.2430.0030.0030.0000.0000.0000.000
71A71GLY0-0.0140.00034.1810.0000.0000.0000.0000.0000.000
72A72HIS0-0.043-0.01131.1400.0030.0030.0000.0000.0000.000
73A73ILE0-0.052-0.01125.021-0.001-0.0010.0000.0000.0000.000
74A74LEU00.0010.00527.915-0.003-0.0030.0000.0000.0000.000
75A75ALA00.0670.01624.8350.0080.0080.0000.0000.0000.000
76A76GLU-1-0.827-0.95724.9820.0620.0620.0000.0000.0000.000
77A77ALA0-0.045-0.00627.2540.0000.0000.0000.0000.0000.000
78A78ILE00.0160.00821.3170.0080.0080.0000.0000.0000.000
79A79LYS10.9260.96021.795-0.053-0.0530.0000.0000.0000.000
80A80ASP-1-0.931-0.95523.2910.0760.0760.0000.0000.0000.000
81A81CYS0-0.115-0.05823.060-0.001-0.0010.0000.0000.0000.000
82A82GLY00.0430.03221.1190.0040.0040.0000.0000.0000.000
83A83CYS0-0.089-0.02918.2160.0200.0200.0000.0000.0000.000
84A84LYS10.9410.98910.423-0.361-0.3610.0000.0000.0000.000
85A85GLY00.0510.00715.292-0.035-0.0350.0000.0000.0000.000
86A86THR0-0.061-0.03316.0490.0110.0110.0000.0000.0000.000
87A87LEU0-0.0220.01113.738-0.005-0.0050.0000.0000.0000.000
88A88ILE0-0.007-0.00216.639-0.020-0.0200.0000.0000.0000.000
89A89ASN0-0.007-0.01418.023-0.001-0.0010.0000.0000.0000.000
90A90HIS00.1120.06016.933-0.020-0.0200.0000.0000.0000.000
91A91SER0-0.092-0.04119.449-0.028-0.0280.0000.0000.0000.000
92A92GLU-1-0.863-0.94021.4620.2580.2580.0000.0000.0000.000
93A93LYS10.8320.92322.887-0.148-0.1480.0000.0000.0000.000
94A94ARG10.9460.98722.346-0.147-0.1470.0000.0000.0000.000
95A95MET0-0.0070.02122.680-0.008-0.0080.0000.0000.0000.000
96A96LEU0-0.0100.00025.773-0.003-0.0030.0000.0000.0000.000
97A97LEU00.018-0.00425.2940.0010.0010.0000.0000.0000.000
98A98ALA00.024-0.00526.120-0.003-0.0030.0000.0000.0000.000
99A99ASP-1-0.883-0.94527.0150.0590.0590.0000.0000.0000.000
100A100ILE00.028-0.00620.9230.0020.0020.0000.0000.0000.000
101A101GLU-1-0.912-0.95222.5260.0080.0080.0000.0000.0000.000
102A102ALA00.0330.02624.316-0.006-0.0060.0000.0000.0000.000
103A103VAL0-0.034-0.01621.314-0.002-0.0020.0000.0000.0000.000
104A104ILE00.0570.03018.5770.0060.0060.0000.0000.0000.000
105A105ASN00.020-0.00321.097-0.012-0.0120.0000.0000.0000.000
106A106LYS10.8600.93323.878-0.047-0.0470.0000.0000.0000.000
107A107CYS0-0.031-0.01419.2590.0070.0070.0000.0000.0000.000
108A108LYS10.9391.00219.4740.0160.0160.0000.0000.0000.000
109A109ASN0-0.033-0.01720.452-0.014-0.0140.0000.0000.0000.000
110A110LEU0-0.035-0.01422.5230.0000.0000.0000.0000.0000.000
111A111GLY0-0.035-0.01919.0710.0050.0050.0000.0000.0000.000
112A112LEU0-0.090-0.03717.5860.0150.0150.0000.0000.0000.000
113A113GLU-1-0.827-0.93710.0880.1780.1780.0000.0000.0000.000
114A114THR0-0.049-0.04514.6910.0250.0250.0000.0000.0000.000
115A115ILE00.0270.00810.824-0.031-0.0310.0000.0000.0000.000
116A116VAL0-0.032-0.02013.2360.0420.0420.0000.0000.0000.000
117A117CYS0-0.046-0.00914.5200.0050.0050.0000.0000.0000.000
118A118THR00.0590.03615.141-0.044-0.0440.0000.0000.0000.000
119A119ASN00.0330.01416.9920.0270.0270.0000.0000.0000.000
120A120ASN00.0190.01119.4180.0140.0140.0000.0000.0000.000
121A121ILE00.1320.08118.067-0.003-0.0030.0000.0000.0000.000
122A122ASN0-0.045-0.05119.122-0.029-0.0290.0000.0000.0000.000
123A123THR00.003-0.02219.449-0.011-0.0110.0000.0000.0000.000
124A124SER00.008-0.02915.7720.0060.0060.0000.0000.0000.000
125A125LYS10.9580.99017.315-0.006-0.0060.0000.0000.0000.000
126A126ALA0-0.040-0.01319.211-0.010-0.0100.0000.0000.0000.000
127A127VAL00.0510.01117.509-0.005-0.0050.0000.0000.0000.000
128A128ALA00.0130.01716.793-0.009-0.0090.0000.0000.0000.000
129A129ALA0-0.001-0.00417.688-0.018-0.0180.0000.0000.0000.000
130A130LEU0-0.074-0.03320.080-0.001-0.0010.0000.0000.0000.000
131A131SER0-0.063-0.01517.522-0.004-0.0040.0000.0000.0000.000
132A132PRO0-0.0270.00214.5330.0060.0060.0000.0000.0000.000
133A133ASP-1-0.782-0.88411.555-0.066-0.0660.0000.0000.0000.000
134A134CYS0-0.047-0.0238.661-0.084-0.0840.0000.0000.0000.000
135A135ILE0-0.0190.00610.2170.0810.0810.0000.0000.0000.000
136A136ALA00.0080.01110.5870.0140.0140.0000.0000.0000.000
137A137VAL0-0.032-0.02211.786-0.058-0.0580.0000.0000.0000.000
138A138GLU-1-0.867-0.96113.6320.3610.3610.0000.0000.0000.000
139A139PRO0-0.0300.00015.941-0.006-0.0060.0000.0000.0000.000
140A140PRO00.0240.01017.4630.0130.0130.0000.0000.0000.000
141A155GLU-1-0.970-0.99218.6810.1460.1460.0000.0000.0000.000
142A156VAL0-0.054-0.03317.281-0.018-0.0180.0000.0000.0000.000
143A157VAL00.0620.03111.2920.0010.0010.0000.0000.0000.000
144A158GLU-1-0.815-0.90712.981-0.050-0.0500.0000.0000.0000.000
145A159GLY0-0.039-0.05414.340-0.049-0.0490.0000.0000.0000.000
146A160THR0-0.016-0.01513.670-0.025-0.0250.0000.0000.0000.000
147A161VAL00.0260.0249.969-0.029-0.0290.0000.0000.0000.000
148A162ARG10.8950.96212.743-0.004-0.0040.0000.0000.0000.000
149A163ALA0-0.0140.00315.715-0.004-0.0040.0000.0000.0000.000
150A164VAL00.007-0.00613.3570.0080.0080.0000.0000.0000.000
151A165LYS10.9210.9578.8400.6520.6520.0000.0000.0000.000
152A166GLU-1-0.958-0.96615.028-0.109-0.1090.0000.0000.0000.000
153A167ILE0-0.119-0.03418.3130.0110.0110.0000.0000.0000.000
154A168ASN00.027-0.00215.904-0.028-0.0280.0000.0000.0000.000
155A169LYS10.9480.97413.9660.3700.3700.0000.0000.0000.000
156A170ASP-1-0.979-0.97112.231-0.416-0.4160.0000.0000.0000.000
157A171VAL0-0.0160.01211.805-0.005-0.0050.0000.0000.0000.000
158A172LYS10.9500.9864.1191.2891.413-0.001-0.008-0.1140.000
159A173VAL00.0140.0027.7880.1960.1960.0000.0000.0000.000
160A174LEU0-0.018-0.0085.552-0.036-0.0360.0000.0000.0000.000
161A175CYS00.0040.0077.610-0.201-0.2010.0000.0000.0000.000
162A176GLY00.0610.0179.6570.2500.2500.0000.0000.0000.000
163A177ALA0-0.035-0.01912.245-0.093-0.0930.0000.0000.0000.000
164A178GLY0-0.037-0.00414.5870.0150.0150.0000.0000.0000.000
165A179ILE00.0280.0039.9260.0280.0280.0000.0000.0000.000
166A180SER0-0.124-0.06313.975-0.023-0.0230.0000.0000.0000.000
167A181LYS10.8470.91815.140-0.409-0.4090.0000.0000.0000.000
168A182GLY00.0780.05011.5030.0940.0940.0000.0000.0000.000
169A183GLU-1-0.940-0.98010.9900.4720.4720.0000.0000.0000.000
170A184ASP-1-0.821-0.91811.8270.5980.5980.0000.0000.0000.000
171A185VAL0-0.049-0.0116.6210.1180.1180.0000.0000.0000.000
172A186LYS10.9150.9587.479-0.133-0.1330.0000.0000.0000.000
173A187ALA00.013-0.0078.585-0.108-0.1080.0000.0000.0000.000
174A188ALA0-0.0170.0048.168-0.161-0.1610.0000.0000.0000.000
175A189LEU0-0.022-0.0223.679-0.295-0.0770.002-0.031-0.1880.000
176A190ASP-1-0.905-0.9506.228-0.445-0.4450.0000.0000.0000.000
177A191LEU0-0.075-0.0349.228-0.110-0.1100.0000.0000.0000.000
178A192GLY0-0.032-0.0288.693-0.016-0.0160.0000.0000.0000.000
179A193ALA0-0.038-0.0106.517-0.227-0.2270.0000.0000.0000.000
180A194GLU-1-0.895-0.9622.845-2.179-1.3680.163-0.180-0.794-0.001
181A195GLY0-0.010-0.0332.042-6.325-7.1406.881-3.690-2.376-0.040
182A196VAL0-0.038-0.0103.617-0.797-0.5960.013-0.008-0.2060.000
183A197LEU0-0.0180.0026.977-0.145-0.1450.0000.0000.0000.000
184A198LEU00.0240.01910.283-0.141-0.1410.0000.0000.0000.000
185A199ALA00.0460.01313.401-0.038-0.0380.0000.0000.0000.000
186A200SER00.0020.00316.8140.0150.0150.0000.0000.0000.000
187A201GLY0-0.015-0.01216.672-0.040-0.0400.0000.0000.0000.000
188A202VAL00.0060.00513.478-0.005-0.0050.0000.0000.0000.000
189A203VAL00.003-0.00316.903-0.043-0.0430.0000.0000.0000.000
190A204LYS10.9430.98819.714-0.379-0.3790.0000.0000.0000.000
191A205ALA0-0.047-0.03219.640-0.029-0.0290.0000.0000.0000.000
192A206LYS10.9650.98721.582-0.193-0.1930.0000.0000.0000.000
193A207ASN00.0210.01520.9210.0010.0010.0000.0000.0000.000
194A208VAL00.0690.02217.0630.0230.0230.0000.0000.0000.000
195A209GLU-1-0.765-0.86916.0660.2740.2740.0000.0000.0000.000
196A210GLU-1-0.950-0.98115.7900.2790.2790.0000.0000.0000.000
197A211ALA0-0.043-0.02116.2960.0230.0230.0000.0000.0000.000
198A212ILE00.0190.00110.7380.0960.0960.0000.0000.0000.000
199A213ARG10.9440.95511.184-0.076-0.0760.0000.0000.0000.000
200A214GLU-1-0.849-0.89512.7480.4230.4230.0000.0000.0000.000
201A215LEU0-0.177-0.1029.9280.0550.0550.0000.0000.0000.000
202A216ILE0-0.076-0.0626.9010.5710.5710.0000.0000.0000.000
203A217LYN00.1590.1413.066-1.265-0.1500.125-0.365-0.875-0.003