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: JQ1Y9

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 OptHSide
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 -2168106.623076
FMO2-HF: Nuclear repulsion 2091467.619799
FMO2-HF: Total energy -76639.003278
FMO2-MP2: Total energy -76859.702725


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.
-11.835-6.68410.467-5.78-9.841-0.044
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 : -0.059 / q_NPA : -0.035
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].
3A3ILE00.0300.0513.7970.3121.868-0.026-0.682-0.8490.000
4A4VAL00.0070.0116.542-0.514-0.5140.0000.0000.0000.000
5A5ILE00.0220.00510.070-0.033-0.0330.0000.0000.0000.000
6A6ASN0-0.014-0.02613.132-0.151-0.1510.0000.0000.0000.000
7A7TYR0-0.013-0.02316.2550.0030.0030.0000.0000.0000.000
8A8LYS10.8070.89218.767-0.451-0.4510.0000.0000.0000.000
9A9THR00.0360.00521.723-0.019-0.0190.0000.0000.0000.000
10A10TYR0-0.0040.01720.700-0.007-0.0070.0000.0000.0000.000
11A11ASN00.006-0.00825.364-0.002-0.0020.0000.0000.0000.000
12A12GLU-1-0.940-0.98623.8010.2700.2700.0000.0000.0000.000
13A13SER00.0350.01121.4340.0250.0250.0000.0000.0000.000
14A14ILE0-0.0080.02023.202-0.003-0.0030.0000.0000.0000.000
15A15GLY00.0130.00826.163-0.012-0.0120.0000.0000.0000.000
16A16ASN00.028-0.01024.9550.0170.0170.0000.0000.0000.000
17A17ARG10.8520.92924.468-0.193-0.1930.0000.0000.0000.000
18A18GLY00.0810.03621.3640.0230.0230.0000.0000.0000.000
19A19LEU0-0.0140.00620.2110.0350.0350.0000.0000.0000.000
20A20GLU-1-0.827-0.91119.9190.1960.1960.0000.0000.0000.000
21A21ILE0-0.026-0.00416.7360.0120.0120.0000.0000.0000.000
22A22ALA0-0.0070.00815.7890.0600.0600.0000.0000.0000.000
23A23LYS10.9200.93614.800-0.150-0.1500.0000.0000.0000.000
24A24ILE0-0.052-0.00715.714-0.022-0.0220.0000.0000.0000.000
25A25ALA0-0.005-0.01912.0250.0100.0100.0000.0000.0000.000
26A26GLU-1-0.821-0.91810.8330.2390.2390.0000.0000.0000.000
27A27LYS10.8560.92211.392-0.226-0.2260.0000.0000.0000.000
28A28VAL0-0.016-0.01710.353-0.062-0.0620.0000.0000.0000.000
29A29SER0-0.066-0.0446.471-0.064-0.0640.0000.0000.0000.000
30A30GLU-1-0.947-0.9766.801-0.431-0.4310.0000.0000.0000.000
31A31GLU-1-0.966-0.9749.291-0.013-0.0130.0000.0000.0000.000
32A32SER0-0.041-0.0276.6880.0550.0550.0000.0000.0000.000
33A33GLY0-0.0150.0015.353-0.305-0.265-0.001-0.005-0.0350.000
34A34ILE0-0.069-0.0382.350-3.870-3.0783.979-1.272-3.499-0.007
35A35THR00.0010.0202.883-0.0930.4440.0730.103-0.7130.000
36A36ILE00.0000.0024.9921.0681.198-0.001-0.012-0.1170.000
37A37GLY00.0080.0068.052-0.356-0.3560.0000.0000.0000.000
38A38VAL00.001-0.00310.6580.0740.0740.0000.0000.0000.000
39A39ALA00.0300.01413.986-0.059-0.0590.0000.0000.0000.000
40A40PRO00.0440.01716.591-0.019-0.0190.0000.0000.0000.000
41A41GLN00.0420.01719.966-0.002-0.0020.0000.0000.0000.000
42A42PHE00.011-0.02023.455-0.007-0.0070.0000.0000.0000.000
43A43VAL0-0.033-0.01825.316-0.010-0.0100.0000.0000.0000.000
44A44ASP-1-0.818-0.91023.6350.2110.2110.0000.0000.0000.000
45A45LEU0-0.031-0.01220.3960.0060.0060.0000.0000.0000.000
46A46ARG10.9000.92221.557-0.103-0.1030.0000.0000.0000.000
47A47MET0-0.0240.01323.665-0.009-0.0090.0000.0000.0000.000
48A48ILE00.002-0.00617.780-0.009-0.0090.0000.0000.0000.000
49A49VAL0-0.0170.01018.3200.0020.0020.0000.0000.0000.000
50A50GLU-1-0.950-0.96719.2040.0990.0990.0000.0000.0000.000
51A51ASN0-0.116-0.06520.849-0.029-0.0290.0000.0000.0000.000
52A52VAL0-0.053-0.02414.939-0.006-0.0060.0000.0000.0000.000
53A53ASN0-0.035-0.00412.0660.0010.0010.0000.0000.0000.000
54A54ILE00.002-0.00310.0730.0060.0060.0000.0000.0000.000
55A55PRO0-0.046-0.0298.860-0.051-0.0510.0000.0000.0000.000
56A56VAL00.0430.04112.1830.0780.0780.0000.0000.0000.000
57A57TYR0-0.100-0.08010.3920.0050.0050.0000.0000.0000.000
58A58ALA00.0410.01116.3960.0010.0010.0000.0000.0000.000
59A59GLN0-0.044-0.03218.337-0.005-0.0050.0000.0000.0000.000
60A60HIS0-0.043-0.04520.1060.0100.0100.0000.0000.0000.000
61A61ILE00.0200.00121.605-0.008-0.0080.0000.0000.0000.000
62A62ASP-1-0.795-0.87524.1410.1440.1440.0000.0000.0000.000
63A63ASN0-0.001-0.00727.411-0.008-0.0080.0000.0000.0000.000
64A64ILE0-0.029-0.00628.481-0.007-0.0070.0000.0000.0000.000
65A65ASN00.008-0.00430.5110.0050.0050.0000.0000.0000.000
66A66PRO00.0180.00131.7070.0010.0010.0000.0000.0000.000
67A67GLY00.0350.01134.323-0.006-0.0060.0000.0000.0000.000
68A68SER0-0.059-0.02037.6650.0020.0020.0000.0000.0000.000
69A69HIS00.0160.01134.636-0.001-0.0010.0000.0000.0000.000
70A70THR00.0170.00235.3330.0040.0040.0000.0000.0000.000
71A71GLY0-0.0040.00734.2800.0010.0010.0000.0000.0000.000
72A72HIS0-0.058-0.02631.2320.0060.0060.0000.0000.0000.000
73A73ILE0-0.040-0.01525.193-0.003-0.0030.0000.0000.0000.000
74A74LEU0-0.015-0.00128.001-0.002-0.0020.0000.0000.0000.000
75A75ALA00.0710.01925.0450.0080.0080.0000.0000.0000.000
76A76GLU-1-0.829-0.95425.1410.0870.0870.0000.0000.0000.000
77A77ALA0-0.025-0.00527.408-0.003-0.0030.0000.0000.0000.000
78A78ILE00.0200.00821.4490.0080.0080.0000.0000.0000.000
79A79LYS10.8940.93921.775-0.059-0.0590.0000.0000.0000.000
80A80ASP-1-0.887-0.91623.3540.0860.0860.0000.0000.0000.000
81A81CYS0-0.087-0.04322.988-0.004-0.0040.0000.0000.0000.000
82A82GLY00.0420.02920.9980.0000.0000.0000.0000.0000.000
83A83CYS0-0.089-0.02718.1080.0190.0190.0000.0000.0000.000
84A84LYS10.8900.94010.890-0.357-0.3570.0000.0000.0000.000
85A85GLY00.0430.01115.449-0.034-0.0340.0000.0000.0000.000
86A86THR0-0.049-0.02316.116-0.003-0.0030.0000.0000.0000.000
87A87LEU0-0.0300.00513.9490.0090.0090.0000.0000.0000.000
88A88ILE0-0.006-0.01416.732-0.037-0.0370.0000.0000.0000.000
89A89ASN0-0.017-0.01318.1050.0000.0000.0000.0000.0000.000
90A90HIS00.0740.04716.986-0.022-0.0220.0000.0000.0000.000
91A91SER0-0.080-0.07019.377-0.039-0.0390.0000.0000.0000.000
92A92GLU-1-0.867-0.91621.5770.3370.3370.0000.0000.0000.000
93A93LYS10.8290.92122.977-0.203-0.2030.0000.0000.0000.000
94A94ARG10.9340.99121.701-0.225-0.2250.0000.0000.0000.000
95A95MET0-0.0200.00223.076-0.016-0.0160.0000.0000.0000.000
96A96LEU00.0040.01025.851-0.002-0.0020.0000.0000.0000.000
97A97LEU00.021-0.00425.5720.0040.0040.0000.0000.0000.000
98A98ALA00.020-0.00626.173-0.001-0.0010.0000.0000.0000.000
99A99ASP-1-0.840-0.91627.0900.1000.1000.0000.0000.0000.000
100A100ILE00.008-0.01121.1070.0030.0030.0000.0000.0000.000
101A101GLU-1-0.875-0.94022.5830.0520.0520.0000.0000.0000.000
102A102ALA00.0320.02424.363-0.008-0.0080.0000.0000.0000.000
103A103VAL0-0.016-0.00821.474-0.004-0.0040.0000.0000.0000.000
104A104ILE00.0550.03118.5860.0060.0060.0000.0000.0000.000
105A105ASN0-0.045-0.02521.148-0.019-0.0190.0000.0000.0000.000
106A106LYS10.8410.92623.981-0.087-0.0870.0000.0000.0000.000
107A107CYS0-0.034-0.01519.4270.0030.0030.0000.0000.0000.000
108A108LYS10.9490.99319.661-0.027-0.0270.0000.0000.0000.000
109A109ASN0-0.058-0.02720.605-0.018-0.0180.0000.0000.0000.000
110A110LEU0-0.0170.00022.670-0.006-0.0060.0000.0000.0000.000
111A111GLY0-0.034-0.01619.219-0.002-0.0020.0000.0000.0000.000
112A112LEU0-0.081-0.02817.7370.0130.0130.0000.0000.0000.000
113A113GLU-1-0.776-0.87110.5340.3880.3880.0000.0000.0000.000
114A114THR0-0.045-0.06314.8740.0310.0310.0000.0000.0000.000
115A115ILE00.0160.00310.197-0.010-0.0100.0000.0000.0000.000
116A116VAL0-0.031-0.01613.3120.0270.0270.0000.0000.0000.000
117A117CYS0-0.0200.00814.5870.0350.0350.0000.0000.0000.000
118A118THR00.0300.01315.132-0.065-0.0650.0000.0000.0000.000
119A119ASN00.015-0.00117.0590.0340.0340.0000.0000.0000.000
120A120ASN00.0310.02319.4790.0150.0150.0000.0000.0000.000
121A121ILE00.0980.05717.8860.0060.0060.0000.0000.0000.000
122A122ASN0-0.015-0.02119.145-0.023-0.0230.0000.0000.0000.000
123A123THR00.008-0.01319.633-0.015-0.0150.0000.0000.0000.000
124A124SER00.005-0.01915.7510.0140.0140.0000.0000.0000.000
125A125LYS10.8730.93217.336-0.034-0.0340.0000.0000.0000.000
126A126ALA0-0.028-0.00119.221-0.015-0.0150.0000.0000.0000.000
127A127VAL00.0390.00717.687-0.011-0.0110.0000.0000.0000.000
128A128ALA00.0170.02016.699-0.009-0.0090.0000.0000.0000.000
129A129ALA00.007-0.00417.699-0.023-0.0230.0000.0000.0000.000
130A130LEU0-0.072-0.03520.260-0.007-0.0070.0000.0000.0000.000
131A131SER0-0.057-0.01317.505-0.010-0.0100.0000.0000.0000.000
132A132PRO0-0.0090.01614.458-0.002-0.0020.0000.0000.0000.000
133A133ASP-1-0.796-0.87611.7850.0510.0510.0000.0000.0000.000
134A134CYS0-0.067-0.0318.741-0.023-0.0230.0000.0000.0000.000
135A135ILE00.0060.01110.2490.0350.0350.0000.0000.0000.000
136A136ALA00.0170.01310.6410.0500.0500.0000.0000.0000.000
137A137VAL0-0.017-0.01511.822-0.095-0.0950.0000.0000.0000.000
138A138GLU-1-0.821-0.91613.7020.4700.4700.0000.0000.0000.000
139A139PRO0-0.0160.01215.943-0.017-0.0170.0000.0000.0000.000
140A140PRO00.0230.00717.5180.0170.0170.0000.0000.0000.000
141A155GLU-1-0.988-0.99418.8660.2040.2040.0000.0000.0000.000
142A156VAL0-0.037-0.03217.387-0.022-0.0220.0000.0000.0000.000
143A157VAL00.0460.01711.3750.0100.0100.0000.0000.0000.000
144A158GLU-1-0.770-0.85512.9790.0140.0140.0000.0000.0000.000
145A159GLY0-0.009-0.01514.320-0.045-0.0450.0000.0000.0000.000
146A160THR00.001-0.01413.786-0.035-0.0350.0000.0000.0000.000
147A161VAL00.0120.0179.909-0.023-0.0230.0000.0000.0000.000
148A162ARG10.8410.89712.724-0.073-0.0730.0000.0000.0000.000
149A163ALA0-0.034-0.00215.679-0.012-0.0120.0000.0000.0000.000
150A164VAL00.013-0.00913.047-0.002-0.0020.0000.0000.0000.000
151A165LYS10.8330.9028.1780.4820.4820.0000.0000.0000.000
152A166GLU-1-0.872-0.91814.991-0.041-0.0410.0000.0000.0000.000
153A167ILE0-0.110-0.04618.2750.0030.0030.0000.0000.0000.000
154A168ASN00.024-0.00316.232-0.034-0.0340.0000.0000.0000.000
155A169LYS10.8120.90013.7880.3280.3280.0000.0000.0000.000
156A170ASP-1-0.879-0.91712.269-0.383-0.3830.0000.0000.0000.000
157A171VAL0-0.0090.01911.8270.0030.0030.0000.0000.0000.000
158A172LYS10.9210.9783.3971.3481.6010.002-0.058-0.1970.000
159A173VAL00.008-0.0017.7720.1650.1650.0000.0000.0000.000
160A174LEU0-0.020-0.0155.7470.0630.0630.0000.0000.0000.000
161A175CYS00.0020.0057.677-0.301-0.3010.0000.0000.0000.000
162A176GLY00.0580.0199.7410.2810.2810.0000.0000.0000.000
163A177ALA0-0.033-0.01712.331-0.117-0.1170.0000.0000.0000.000
164A178GLY0-0.039-0.00614.6520.0140.0140.0000.0000.0000.000
165A179ILE0-0.008-0.0139.8850.0350.0350.0000.0000.0000.000
166A180SER0-0.125-0.07313.975-0.044-0.0440.0000.0000.0000.000
167A181LYS10.7730.85815.101-0.483-0.4830.0000.0000.0000.000
168A182GLY00.0590.03411.4510.1140.1140.0000.0000.0000.000
169A183GLU-1-0.876-0.94310.8630.5550.5550.0000.0000.0000.000
170A184ASP-1-0.778-0.88011.7220.6970.6970.0000.0000.0000.000
171A185VAL0-0.042-0.0116.5540.1510.1510.0000.0000.0000.000
172A186LYS10.9010.9507.383-0.148-0.1480.0000.0000.0000.000
173A187ALA00.0320.0058.512-0.111-0.1110.0000.0000.0000.000
174A188ALA0-0.0220.0028.173-0.154-0.1540.0000.0000.0000.000
175A189LEU0-0.030-0.0273.329-0.389-0.0790.010-0.060-0.2610.000
176A190ASP-1-0.906-0.9456.203-0.379-0.3790.0000.0000.0000.000
177A191LEU0-0.067-0.0379.213-0.117-0.1170.0000.0000.0000.000
178A192GLY0-0.007-0.0088.718-0.015-0.0150.0000.0000.0000.000
179A193ALA0-0.029-0.0106.503-0.194-0.1940.0000.0000.0000.000
180A194GLU-1-0.818-0.9122.797-1.738-1.0330.183-0.131-0.7570.000
181A195GLY0-0.003-0.0232.088-5.001-5.5486.080-3.283-2.250-0.035
182A196VAL0-0.028-0.0093.709-1.208-1.0000.011-0.017-0.2020.000
183A197LEU0-0.0190.0027.075-0.136-0.1360.0000.0000.0000.000
184A198LEU00.0280.01710.390-0.176-0.1760.0000.0000.0000.000
185A199ALA00.0490.01713.457-0.037-0.0370.0000.0000.0000.000
186A200SER00.0110.00616.8230.0130.0130.0000.0000.0000.000
187A201GLY0-0.023-0.01316.613-0.050-0.0500.0000.0000.0000.000
188A202VAL0-0.001-0.00313.395-0.009-0.0090.0000.0000.0000.000
189A203VAL0-0.004-0.00216.854-0.053-0.0530.0000.0000.0000.000
190A204LYS10.9460.99019.668-0.437-0.4370.0000.0000.0000.000
191A205ALA0-0.032-0.02319.576-0.036-0.0360.0000.0000.0000.000
192A206LYS10.9660.98521.535-0.223-0.2230.0000.0000.0000.000
193A207ASN0-0.0060.00020.8150.0030.0030.0000.0000.0000.000
194A208VAL00.0580.01917.1370.0260.0260.0000.0000.0000.000
195A209GLU-1-0.731-0.83415.9470.2880.2880.0000.0000.0000.000
196A210GLU-1-0.837-0.92115.7650.3070.3070.0000.0000.0000.000
197A211ALA0-0.049-0.01816.2540.0240.0240.0000.0000.0000.000
198A212ILE00.0170.00210.6500.1100.1100.0000.0000.0000.000
199A213ARG10.8390.87411.150-0.089-0.0890.0000.0000.0000.000
200A214GLU-1-0.843-0.87612.7200.5250.5250.0000.0000.0000.000
201A215LEU0-0.148-0.0679.8700.0660.0660.0000.0000.0000.000
202A216ILE0-0.115-0.0897.4190.6060.6060.0000.0000.0000.000
203A217LYN00.1690.1362.851-1.988-0.8210.157-0.363-0.961-0.002