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: 3J6ZL

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 OptAll
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 -2172628.181529
FMO2-HF: Nuclear repulsion 2095988.357182
FMO2-HF: Total energy -76639.824347
FMO2-MP2: Total energy -76860.459678


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.
-21.027-15.75114.014-7.771-11.515-0.05
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 : -0.065 / q_NPA : -0.042
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].
3A3ILE00.0180.0343.8591.3112.503-0.013-0.486-0.6920.001
4A4VAL0-0.0030.0036.712-0.496-0.4960.0000.0000.0000.000
5A5ILE00.0180.00710.265-0.073-0.0730.0000.0000.0000.000
6A6ASN00.015-0.00213.344-0.144-0.1440.0000.0000.0000.000
7A7TYR0-0.033-0.03216.1620.0030.0030.0000.0000.0000.000
8A8LYS10.8210.89618.989-0.419-0.4190.0000.0000.0000.000
9A9THR00.0250.00321.620-0.018-0.0180.0000.0000.0000.000
10A10TYR0-0.0030.01520.654-0.009-0.0090.0000.0000.0000.000
11A11ASN0-0.013-0.01225.088-0.011-0.0110.0000.0000.0000.000
12A12GLU-1-0.905-0.97223.5740.2960.2960.0000.0000.0000.000
13A13SER00.007-0.00821.5510.0210.0210.0000.0000.0000.000
14A14ILE0-0.0240.01023.171-0.001-0.0010.0000.0000.0000.000
15A15GLY00.0360.01725.697-0.011-0.0110.0000.0000.0000.000
16A16ASN00.005-0.01824.4290.0210.0210.0000.0000.0000.000
17A17ARG10.8360.93724.331-0.222-0.2220.0000.0000.0000.000
18A18GLY00.1090.04520.7720.0290.0290.0000.0000.0000.000
19A19LEU0-0.0110.00619.7570.0440.0440.0000.0000.0000.000
20A20GLU-1-0.822-0.89820.0230.2680.2680.0000.0000.0000.000
21A21ILE0-0.035-0.01616.5120.0280.0280.0000.0000.0000.000
22A22ALA00.0030.00815.7970.0770.0770.0000.0000.0000.000
23A23LYS10.8950.92315.132-0.197-0.1970.0000.0000.0000.000
24A24ILE0-0.051-0.01615.728-0.016-0.0160.0000.0000.0000.000
25A25ALA0-0.014-0.02211.8710.0310.0310.0000.0000.0000.000
26A26GLU-1-0.830-0.92311.1020.3880.3880.0000.0000.0000.000
27A27LYS10.8590.93311.261-0.300-0.3000.0000.0000.0000.000
28A28VAL0-0.034-0.02710.802-0.053-0.0530.0000.0000.0000.000
29A29SER0-0.086-0.0446.521-0.029-0.0290.0000.0000.0000.000
30A30GLU-1-0.940-0.9826.934-0.247-0.2470.0000.0000.0000.000
31A31GLU-1-0.930-0.9799.3480.0960.0960.0000.0000.0000.000
32A32SER0-0.037-0.0226.5880.0300.0300.0000.0000.0000.000
33A33GLY0-0.0160.0115.165-0.296-0.237-0.001-0.010-0.0480.000
34A34ILE0-0.044-0.0262.237-5.021-3.3393.512-1.677-3.517-0.011
35A35THR0-0.0010.0143.065-0.954-0.4720.3750.277-1.134-0.001
36A36ILE00.0020.0035.0620.6760.768-0.001-0.009-0.0820.000
37A37GLY00.0480.0197.746-0.396-0.3960.0000.0000.0000.000
38A38VAL0-0.028-0.00910.7020.0800.0800.0000.0000.0000.000
39A39ALA00.0290.00913.951-0.066-0.0660.0000.0000.0000.000
40A40PRO00.0310.01216.776-0.020-0.0200.0000.0000.0000.000
41A41GLN00.0550.03120.029-0.004-0.0040.0000.0000.0000.000
42A42PHE00.000-0.01923.358-0.005-0.0050.0000.0000.0000.000
43A43VAL0-0.028-0.01025.275-0.009-0.0090.0000.0000.0000.000
44A44ASP-1-0.804-0.90623.3840.2370.2370.0000.0000.0000.000
45A45LEU0-0.047-0.01520.2310.0070.0070.0000.0000.0000.000
46A46ARG10.8960.91721.399-0.117-0.1170.0000.0000.0000.000
47A47MET0-0.0370.00523.521-0.004-0.0040.0000.0000.0000.000
48A48ILE00.0020.00517.7360.0000.0000.0000.0000.0000.000
49A49VAL00.0160.00618.3890.0000.0000.0000.0000.0000.000
50A50GLU-1-0.923-0.95519.7130.1290.1290.0000.0000.0000.000
51A51ASN0-0.129-0.07520.874-0.033-0.0330.0000.0000.0000.000
52A52VAL0-0.0280.00015.3160.0000.0000.0000.0000.0000.000
53A53ASN0-0.040-0.00811.964-0.013-0.0130.0000.0000.0000.000
54A54ILE0-0.0140.00010.2090.0320.0320.0000.0000.0000.000
55A55PRO0-0.052-0.0338.842-0.084-0.0840.0000.0000.0000.000
56A56VAL00.0320.02912.1470.0730.0730.0000.0000.0000.000
57A57TYR0-0.072-0.05610.5660.0020.0020.0000.0000.0000.000
58A58ALA00.0440.00916.4640.0060.0060.0000.0000.0000.000
59A59GLN0-0.056-0.04318.261-0.009-0.0090.0000.0000.0000.000
60A60HIS0-0.036-0.02919.9100.0080.0080.0000.0000.0000.000
61A61ILE00.0390.01821.676-0.004-0.0040.0000.0000.0000.000
62A62ASP-1-0.777-0.87524.0530.1360.1360.0000.0000.0000.000
63A63ASN00.004-0.00527.353-0.008-0.0080.0000.0000.0000.000
64A64ILE0-0.050-0.01328.829-0.008-0.0080.0000.0000.0000.000
65A65ASN00.0330.00830.5090.0040.0040.0000.0000.0000.000
66A66PRO00.018-0.00131.9380.0020.0020.0000.0000.0000.000
67A67GLY00.0240.01134.631-0.006-0.0060.0000.0000.0000.000
68A68SER0-0.039-0.01637.4490.0040.0040.0000.0000.0000.000
69A69HIS0-0.0040.00234.573-0.002-0.0020.0000.0000.0000.000
70A70THR00.0330.00134.9880.0050.0050.0000.0000.0000.000
71A71GLY0-0.0070.00434.1630.0000.0000.0000.0000.0000.000
72A72HIS0-0.055-0.01431.1040.0060.0060.0000.0000.0000.000
73A73ILE0-0.032-0.01825.045-0.003-0.0030.0000.0000.0000.000
74A74LEU0-0.0010.00427.469-0.001-0.0010.0000.0000.0000.000
75A75ALA00.0500.01224.9280.0080.0080.0000.0000.0000.000
76A76GLU-1-0.826-0.94624.9740.0850.0850.0000.0000.0000.000
77A77ALA0-0.0040.00326.7390.0010.0010.0000.0000.0000.000
78A78ILE00.0220.01121.1950.0120.0120.0000.0000.0000.000
79A79LYS10.8940.94021.975-0.056-0.0560.0000.0000.0000.000
80A80ASP-1-0.910-0.93123.4060.1020.1020.0000.0000.0000.000
81A81CYS0-0.085-0.04723.467-0.001-0.0010.0000.0000.0000.000
82A82GLY00.0340.01821.3990.0130.0130.0000.0000.0000.000
83A83CYS0-0.069-0.01818.3040.0250.0250.0000.0000.0000.000
84A84LYS10.8560.93010.461-0.370-0.3700.0000.0000.0000.000
85A85GLY00.0480.00115.574-0.028-0.0280.0000.0000.0000.000
86A86THR0-0.067-0.04416.6380.0110.0110.0000.0000.0000.000
87A87LEU00.0060.02014.014-0.002-0.0020.0000.0000.0000.000
88A88ILE00.0210.00616.649-0.035-0.0350.0000.0000.0000.000
89A89ASN0-0.026-0.02218.2360.0020.0020.0000.0000.0000.000
90A90HIS00.0600.03017.098-0.020-0.0200.0000.0000.0000.000
91A91SER0-0.051-0.06719.359-0.026-0.0260.0000.0000.0000.000
92A92GLU-1-0.878-0.91521.6720.3050.3050.0000.0000.0000.000
93A93LYS10.7750.88623.152-0.176-0.1760.0000.0000.0000.000
94A94ARG10.8720.95820.839-0.201-0.2010.0000.0000.0000.000
95A95MET0-0.023-0.00423.389-0.008-0.0080.0000.0000.0000.000
96A96LEU00.0020.01226.346-0.004-0.0040.0000.0000.0000.000
97A97LEU00.014-0.00625.7650.0020.0020.0000.0000.0000.000
98A98ALA00.0290.00326.449-0.003-0.0030.0000.0000.0000.000
99A99ASP-1-0.822-0.90927.1570.0810.0810.0000.0000.0000.000
100A100ILE0-0.009-0.00921.6870.0030.0030.0000.0000.0000.000
101A101GLU-1-0.855-0.91422.7940.0200.0200.0000.0000.0000.000
102A102ALA00.0420.02324.630-0.004-0.0040.0000.0000.0000.000
103A103VAL0-0.031-0.01921.894-0.002-0.0020.0000.0000.0000.000
104A104ILE00.0550.03318.6350.0080.0080.0000.0000.0000.000
105A105ASN0-0.077-0.04321.673-0.015-0.0150.0000.0000.0000.000
106A106LYS10.8320.92124.391-0.071-0.0710.0000.0000.0000.000
107A107CYS0-0.047-0.01819.5020.0060.0060.0000.0000.0000.000
108A108LYS10.9560.97419.518-0.001-0.0010.0000.0000.0000.000
109A109ASN0-0.049-0.02320.457-0.014-0.0140.0000.0000.0000.000
110A110LEU0-0.0120.00822.640-0.004-0.0040.0000.0000.0000.000
111A111GLY0-0.0210.00219.1000.0020.0020.0000.0000.0000.000
112A112LEU0-0.084-0.02817.8730.0160.0160.0000.0000.0000.000
113A113GLU-1-0.779-0.87110.6490.2670.2670.0000.0000.0000.000
114A114THR0-0.041-0.05914.9130.0390.0390.0000.0000.0000.000
115A115ILE00.010-0.00310.457-0.020-0.0200.0000.0000.0000.000
116A116VAL0-0.027-0.00813.5090.0330.0330.0000.0000.0000.000
117A117CYS0-0.0150.00514.9160.0190.0190.0000.0000.0000.000
118A118THR00.0160.01615.576-0.049-0.0490.0000.0000.0000.000
119A119ASN00.004-0.01017.2550.0320.0320.0000.0000.0000.000
120A120ASN00.0500.03519.8000.0150.0150.0000.0000.0000.000
121A121ILE00.0830.05018.228-0.004-0.0040.0000.0000.0000.000
122A122ASN0-0.011-0.01019.668-0.022-0.0220.0000.0000.0000.000
123A123THR00.019-0.01320.125-0.011-0.0110.0000.0000.0000.000
124A124SER0-0.009-0.01416.1540.0100.0100.0000.0000.0000.000
125A125LYS10.8610.91818.0210.0270.0270.0000.0000.0000.000
126A126ALA0-0.031-0.00819.605-0.011-0.0110.0000.0000.0000.000
127A127VAL00.010-0.00518.062-0.007-0.0070.0000.0000.0000.000
128A128ALA00.0240.01217.032-0.006-0.0060.0000.0000.0000.000
129A129ALA00.0180.00918.056-0.018-0.0180.0000.0000.0000.000
130A130LEU0-0.069-0.03420.841-0.005-0.0050.0000.0000.0000.000
131A131SER0-0.056-0.01417.844-0.004-0.0040.0000.0000.0000.000
132A132PRO0-0.0020.01615.0240.0000.0000.0000.0000.0000.000
133A133ASP-1-0.804-0.88012.237-0.014-0.0140.0000.0000.0000.000
134A134CYS0-0.098-0.0369.209-0.044-0.0440.0000.0000.0000.000
135A135ILE00.0110.00910.8010.0710.0710.0000.0000.0000.000
136A136ALA00.0170.00310.7360.0080.0080.0000.0000.0000.000
137A137VAL0-0.024-0.02011.937-0.047-0.0470.0000.0000.0000.000
138A138GLU-1-0.719-0.84913.9390.3790.3790.0000.0000.0000.000
139A139PRO0-0.0400.00416.3490.0020.0020.0000.0000.0000.000
140A140PRO0-0.011-0.02217.5810.0130.0130.0000.0000.0000.000
141A155GLU-1-0.966-0.97719.0950.1550.1550.0000.0000.0000.000
142A156VAL0-0.030-0.02017.473-0.018-0.0180.0000.0000.0000.000
143A157VAL00.0370.02111.2890.0140.0140.0000.0000.0000.000
144A158GLU-1-0.730-0.83013.499-0.100-0.1000.0000.0000.0000.000
145A159GLY00.009-0.00114.460-0.038-0.0380.0000.0000.0000.000
146A160THR00.004-0.01614.043-0.021-0.0210.0000.0000.0000.000
147A161VAL00.0040.01510.331-0.021-0.0210.0000.0000.0000.000
148A162ARG10.8210.88013.0760.0170.0170.0000.0000.0000.000
149A163ALA0-0.0180.00016.221-0.007-0.0070.0000.0000.0000.000
150A164VAL00.013-0.01013.3340.0100.0100.0000.0000.0000.000
151A165LYS10.8420.9148.7050.6380.6380.0000.0000.0000.000
152A166GLU-1-0.878-0.93115.674-0.086-0.0860.0000.0000.0000.000
153A167ILE0-0.093-0.03218.8000.0080.0080.0000.0000.0000.000
154A168ASN00.020-0.01016.644-0.029-0.0290.0000.0000.0000.000
155A169LYS10.7840.87914.1800.3610.3610.0000.0000.0000.000
156A170ASP-1-0.839-0.89812.351-0.435-0.4350.0000.0000.0000.000
157A171VAL0-0.0300.01111.792-0.019-0.0190.0000.0000.0000.000
158A172LYS10.9460.9863.6071.7151.8900.000-0.035-0.1400.000
159A173VAL0-0.009-0.0038.0500.1850.1850.0000.0000.0000.000
160A174LEU0-0.0220.0025.540-0.112-0.1120.0000.0000.0000.000
161A175CYS0-0.006-0.0047.729-0.180-0.1800.0000.0000.0000.000
162A176GLY00.0550.0189.8040.2440.2440.0000.0000.0000.000
163A177ALA0-0.053-0.02112.591-0.055-0.0550.0000.0000.0000.000
164A178GLY0-0.025-0.01514.0820.0380.0380.0000.0000.0000.000
165A179ILE0-0.013-0.0099.7970.0260.0260.0000.0000.0000.000
166A180SER0-0.143-0.08613.966-0.032-0.0320.0000.0000.0000.000
167A181LYS10.7710.86314.358-0.558-0.5580.0000.0000.0000.000
168A182GLY00.0790.04310.7140.1520.1520.0000.0000.0000.000
169A183GLU-1-0.879-0.93810.4100.6000.6000.0000.0000.0000.000
170A184ASP-1-0.746-0.86712.1380.6240.6240.0000.0000.0000.000
171A185VAL0-0.029-0.0126.1540.0380.0380.0000.0000.0000.000
172A186LYS10.8500.9437.125-0.380-0.3800.0000.0000.0000.000
173A187ALA00.0520.0208.754-0.176-0.1760.0000.0000.0000.000
174A188ALA0-0.022-0.0108.106-0.155-0.1550.0000.0000.0000.000
175A189LEU0-0.046-0.0243.372-0.459-0.1860.007-0.047-0.2320.000
176A190ASP-1-0.876-0.9476.380-0.441-0.4410.0000.0000.0000.000
177A191LEU0-0.090-0.0369.352-0.095-0.0950.0000.0000.0000.000
178A192GLY00.004-0.0038.9880.0240.0240.0000.0000.0000.000
179A193ALA0-0.034-0.0156.881-0.102-0.1020.0000.0000.0000.000
180A194GLU-1-0.814-0.9273.336-2.089-1.2010.019-0.356-0.550-0.002
181A195GLY00.011-0.0061.967-6.680-7.8437.539-3.787-2.589-0.041
182A196VAL0-0.0190.0013.539-1.427-1.2340.024-0.018-0.1980.000
183A197LEU0-0.0070.0047.0950.0020.0020.0000.0000.0000.000
184A198LEU00.0330.01610.411-0.167-0.1670.0000.0000.0000.000
185A199ALA00.0680.02213.322-0.041-0.0410.0000.0000.0000.000
186A200SER0-0.0010.01316.6760.0340.0340.0000.0000.0000.000
187A201GLY00.0220.01616.299-0.057-0.0570.0000.0000.0000.000
188A202VAL00.0170.00813.223-0.023-0.0230.0000.0000.0000.000
189A203VAL00.012-0.00216.702-0.061-0.0610.0000.0000.0000.000
190A204LYS10.9010.94719.296-0.480-0.4800.0000.0000.0000.000
191A205ALA0-0.047-0.00919.291-0.045-0.0450.0000.0000.0000.000
192A206LYS10.9370.94621.221-0.255-0.2550.0000.0000.0000.000
193A207ASN0-0.010-0.00720.163-0.002-0.0020.0000.0000.0000.000
194A208VAL00.0540.02316.4980.0320.0320.0000.0000.0000.000
195A209GLU-1-0.726-0.82716.0370.4070.4070.0000.0000.0000.000
196A210GLU-1-0.799-0.88515.2650.4360.4360.0000.0000.0000.000
197A211ALA0-0.041-0.01515.8420.0460.0460.0000.0000.0000.000
198A212ILE00.001-0.00210.1870.1240.1240.0000.0000.0000.000
199A213ARG10.7760.83911.181-0.182-0.1820.0000.0000.0000.000
200A214GLU-1-0.855-0.88512.9840.5860.5860.0000.0000.0000.000
201A215LEU0-0.027-0.01810.0220.0250.0250.0000.0000.0000.000
202A216ILE0-0.025-0.0027.4870.4480.4480.0000.0000.0000.000
203A217LYN0-0.012-0.0042.191-8.043-6.6402.553-1.623-2.3330.004