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: QYV2Y

Calculation Name: 2DG6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2DG6

Chain ID: A

ChEMBL ID:

UniProt ID: O86531

Base Structure: X-ray

Registration Date: 2023-06-22

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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2150813.873548
FMO2-HF: Nuclear repulsion 2070000.371785
FMO2-HF: Total energy -80813.501763
FMO2-MP2: Total energy -81050.204048


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.
-44.885-49.84252.61-19.957-27.696-0.092
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 : 0.002 / 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].
3A3LEU00.0930.0382.311-2.550-0.9612.537-1.795-2.330-0.015
4A4ALA00.0310.0125.0770.7240.882-0.001-0.010-0.1460.000
5A5ASP-1-0.828-0.9062.259-0.6041.9132.370-1.981-2.907-0.012
6A6LEU00.0510.0262.8110.4992.3833.894-1.952-3.826-0.004
7A7SER0-0.046-0.0233.758-0.058-1.8660.0322.235-0.458-0.001
8A8LYS10.9520.9657.161-1.687-1.6870.0000.0000.0000.000
9A9ARG10.7600.7972.121-10.273-23.90026.434-7.501-5.3070.036
10A10SER0-0.021-0.0306.722-1.073-1.0730.0000.0000.0000.000
11A11GLY0-0.0140.0108.074-0.426-0.4260.0000.0000.0000.000
12A12VAL0-0.0170.0049.824-0.289-0.2890.0000.0000.0000.000
13A13SER00.0620.04210.4590.1290.1290.0000.0000.0000.000
14A14THR00.0710.01010.227-0.030-0.0300.0000.0000.0000.000
15A15ALA0-0.043-0.00411.149-0.128-0.1280.0000.0000.0000.000
16A16THR00.000-0.02813.830-0.089-0.0890.0000.0000.0000.000
17A17ILE00.0310.0357.588-0.080-0.0800.0000.0000.0000.000
18A18LYN00.0410.03511.557-0.149-0.1490.0000.0000.0000.000
19A19TYR0-0.101-0.07413.189-0.044-0.0440.0000.0000.0000.000
20A20TYR00.0790.02411.8310.0220.0220.0000.0000.0000.000
21A21LEU0-0.043-0.0119.285-0.028-0.0280.0000.0000.0000.000
22A22ARG10.8840.94013.1710.1560.1560.0000.0000.0000.000
23A23GLU-1-0.811-0.87316.478-0.186-0.1860.0000.0000.0000.000
24A24GLY00.0030.00516.0000.0250.0250.0000.0000.0000.000
25A25LEU0-0.031-0.00314.234-0.042-0.0420.0000.0000.0000.000
26A26LEU0-0.033-0.0156.986-0.045-0.0450.0000.0000.0000.000
27A27PRO00.0850.0439.7430.0520.0520.0000.0000.0000.000
28A28PRO00.0210.0039.451-0.229-0.2290.0000.0000.0000.000
29A29GLY0-0.0170.0007.876-0.203-0.2030.0000.0000.0000.000
30A39TYR0-0.069-0.0462.500-0.0511.6140.913-0.705-1.8730.001
31A40ASP-1-0.757-0.8781.901-20.099-20.44010.555-5.327-4.887-0.066
32A41GLU-1-0.782-0.8872.406-8.492-6.6764.368-2.495-3.690-0.030
33A42ASP-1-0.785-0.8693.574-0.745-0.7440.0010.181-0.1830.000
34A43HIS00.0230.0223.238-0.722-0.3620.014-0.063-0.3120.000
35A44LEU0-0.082-0.0442.1971.0791.7501.490-0.498-1.662-0.001
36A45ARG10.8720.9204.0422.8533.0110.003-0.046-0.1150.000
37A46ARG10.7680.8567.1121.4051.4050.0000.0000.0000.000
38A47LEU0-0.013-0.0166.9670.3930.3930.0000.0000.0000.000
39A48ARG10.8880.9247.440-0.578-0.5780.0000.0000.0000.000
40A49LEU00.0390.04510.0200.1140.1140.0000.0000.0000.000
41A50VAL00.0220.00811.9600.0860.0860.0000.0000.0000.000
42A51ARG10.8230.89411.953-0.109-0.1090.0000.0000.0000.000
43A52ALA00.0190.02214.2500.0380.0380.0000.0000.0000.000
44A53LEU00.0600.02216.1850.0210.0210.0000.0000.0000.000
45A54ILE0-0.032-0.01116.7670.0240.0240.0000.0000.0000.000
46A55GLN0-0.041-0.01816.2800.0530.0530.0000.0000.0000.000
47A56VAL0-0.0110.00318.6080.0120.0120.0000.0000.0000.000
48A57GLY00.0480.02220.392-0.002-0.0020.0000.0000.0000.000
49A58LYS10.8160.92222.1120.0410.0410.0000.0000.0000.000
50A59VAL00.0150.01521.019-0.003-0.0030.0000.0000.0000.000
51A60PRO00.0130.00621.9110.0040.0040.0000.0000.0000.000
52A61VAL00.0390.00619.096-0.020-0.0200.0000.0000.0000.000
53A62ALA0-0.021-0.01820.990-0.032-0.0320.0000.0000.0000.000
54A63THR00.0530.02623.352-0.011-0.0110.0000.0000.0000.000
55A64ALA00.0160.00318.255-0.020-0.0200.0000.0000.0000.000
56A65ARG10.8110.89518.8130.2080.2080.0000.0000.0000.000
57A66GLU-1-0.869-0.91319.886-0.260-0.2600.0000.0000.0000.000
58A67VAL0-0.0070.00019.024-0.023-0.0230.0000.0000.0000.000
59A68LEU0-0.027-0.03214.455-0.025-0.0250.0000.0000.0000.000
60A69GLY00.0230.02317.506-0.058-0.0580.0000.0000.0000.000
61A70HIS0-0.017-0.01819.757-0.030-0.0300.0000.0000.0000.000
62A71VAL0-0.042-0.03215.292-0.004-0.0040.0000.0000.0000.000
63A72ASP-1-0.833-0.87814.625-0.960-0.9600.0000.0000.0000.000
64A73ASP-1-0.829-0.87817.425-0.365-0.3650.0000.0000.0000.000
65A74ASP-1-0.972-0.99119.747-0.496-0.4960.0000.0000.0000.000
66A75SER0-0.090-0.06321.6380.0340.0340.0000.0000.0000.000
67A76LEU0-0.013-0.00324.4510.0390.0390.0000.0000.0000.000
68A77GLY00.0040.00024.212-0.032-0.0320.0000.0000.0000.000
69A78ARG10.9340.94518.7100.4870.4870.0000.0000.0000.000
70A79THR0-0.015-0.01123.391-0.004-0.0040.0000.0000.0000.000
71A80VAL00.0310.02026.2300.0140.0140.0000.0000.0000.000
72A81ARG10.8510.95618.4320.5320.5320.0000.0000.0000.000
73A82LEU0-0.003-0.00521.229-0.004-0.0040.0000.0000.0000.000
74A83GLY00.0140.01523.1920.0120.0120.0000.0000.0000.000
75A84ALA00.0140.00325.1660.0130.0130.0000.0000.0000.000
76A85ALA00.009-0.00420.7060.0090.0090.0000.0000.0000.000
77A86LEU0-0.017-0.02122.5600.0150.0150.0000.0000.0000.000
78A87TRP0-0.022-0.02324.2380.0190.0190.0000.0000.0000.000
79A88ALA00.0340.04824.1010.0140.0140.0000.0000.0000.000
80A89LEU0-0.079-0.03721.0700.0070.0070.0000.0000.0000.000
81A90PRO0-0.049-0.03624.6170.0090.0090.0000.0000.0000.000
82A91GLN00.0130.00627.7350.0080.0080.0000.0000.0000.000
83A92ASP-1-0.875-0.90030.960-0.070-0.0700.0000.0000.0000.000
84A93ALA0-0.047-0.03434.473-0.005-0.0050.0000.0000.0000.000
85A94GLU-1-0.851-0.91937.668-0.100-0.1000.0000.0000.0000.000
86A95PRO0-0.016-0.00539.6990.0040.0040.0000.0000.0000.000
87A96ASP-1-0.868-0.93242.944-0.056-0.0560.0000.0000.0000.000
88A97GLU-1-0.805-0.89043.572-0.072-0.0720.0000.0000.0000.000
89A98ALA0-0.047-0.00947.3480.0010.0010.0000.0000.0000.000
90A99ASP-1-0.784-0.87248.737-0.041-0.0410.0000.0000.0000.000
91A100PRO00.008-0.00650.235-0.002-0.0020.0000.0000.0000.000
92A101ALA0-0.011-0.01249.549-0.001-0.0010.0000.0000.0000.000
93A102VAL00.0000.00044.850-0.001-0.0010.0000.0000.0000.000
94A103ALA00.0140.01446.720-0.003-0.0030.0000.0000.0000.000
95A104ALA0-0.020-0.01848.730-0.002-0.0020.0000.0000.0000.000
96A105ALA00.0180.01044.645-0.001-0.0010.0000.0000.0000.000
97A106ARG10.8310.87840.8880.0780.0780.0000.0000.0000.000
98A107VAL0-0.041-0.01144.960-0.003-0.0030.0000.0000.0000.000
99A108GLU-1-0.792-0.87146.311-0.050-0.0500.0000.0000.0000.000
100A109VAL0-0.006-0.00740.074-0.001-0.0010.0000.0000.0000.000
101A110ASP-1-0.850-0.90842.100-0.083-0.0830.0000.0000.0000.000
102A111ARG10.8810.90843.6590.0510.0510.0000.0000.0000.000
103A112LEU0-0.0140.00040.1560.0000.0000.0000.0000.0000.000
104A113LEU0-0.035-0.02137.306-0.002-0.0020.0000.0000.0000.000
105A114GLU-1-0.879-0.91440.606-0.072-0.0720.0000.0000.0000.000
106A115LEU0-0.068-0.03943.4750.0000.0000.0000.0000.0000.000
107A116LEU0-0.065-0.03238.0220.0010.0010.0000.0000.0000.000
108A117GLY00.0330.03339.184-0.003-0.0030.0000.0000.0000.000
109A118TRP0-0.101-0.04335.104-0.009-0.0090.0000.0000.0000.000
110A119GLU-1-0.789-0.92837.138-0.094-0.0940.0000.0000.0000.000
111A120THR00.0140.01731.873-0.002-0.0020.0000.0000.0000.000
112A121SER0-0.027-0.02634.111-0.008-0.0080.0000.0000.0000.000
113A122ARG10.7290.83435.2980.0830.0830.0000.0000.0000.000
114A123GLU-1-0.946-0.96636.305-0.133-0.1330.0000.0000.0000.000
115A124LEU0-0.073-0.03731.035-0.004-0.0040.0000.0000.0000.000
116A125ALA00.0020.00335.130-0.001-0.0010.0000.0000.0000.000
117A126PRO0-0.062-0.02437.5680.0030.0030.0000.0000.0000.000
118A127LEU0-0.016-0.01534.4240.0010.0010.0000.0000.0000.000
119A128SER0-0.0020.01532.628-0.004-0.0040.0000.0000.0000.000
120A129PRO00.0100.01030.6140.0100.0100.0000.0000.0000.000
121A130VAL00.0440.01629.2630.0080.0080.0000.0000.0000.000
122A131HIS0-0.0010.00432.5500.0090.0090.0000.0000.0000.000
123A132ARG10.8780.92834.0500.1120.1120.0000.0000.0000.000
124A133SER0-0.008-0.03734.1420.0050.0050.0000.0000.0000.000
125A134LEU0-0.0200.00936.3660.0080.0080.0000.0000.0000.000
126A135VAL0-0.004-0.00637.9290.0070.0070.0000.0000.0000.000
127A136VAL0-0.002-0.00839.0870.0060.0060.0000.0000.0000.000
128A137ALA0-0.034-0.01738.5470.0050.0050.0000.0000.0000.000
129A138VAL00.010-0.00440.6640.0050.0050.0000.0000.0000.000
130A139ALA00.0200.00543.4000.0040.0040.0000.0000.0000.000
131A140ALA0-0.046-0.01543.5560.0030.0030.0000.0000.0000.000
132A141LEU00.0090.00542.8000.0040.0040.0000.0000.0000.000
133A142ARG10.9120.95146.5600.0440.0440.0000.0000.0000.000
134A143ARG10.8300.91346.5720.0430.0430.0000.0000.0000.000
135A144LEU0-0.098-0.04847.5880.0020.0020.0000.0000.0000.000
136A145ASP-1-0.930-0.96151.009-0.025-0.0250.0000.0000.0000.000
137A146TYR0-0.037-0.01048.6150.0020.0020.0000.0000.0000.000
138A147PRO0-0.031-0.01849.642-0.003-0.0030.0000.0000.0000.000
139A148TRP00.011-0.01141.401-0.001-0.0010.0000.0000.0000.000
140A149ASP-1-0.867-0.94647.292-0.041-0.0410.0000.0000.0000.000
141A150ALA0-0.0020.00645.0980.0000.0000.0000.0000.0000.000
142A151GLU-1-0.871-0.95345.242-0.047-0.0470.0000.0000.0000.000
143A152LEU0-0.086-0.01745.0790.0010.0010.0000.0000.0000.000
144A153MET0-0.016-0.01741.7610.0000.0000.0000.0000.0000.000
145A154ALA00.0390.02441.313-0.002-0.0020.0000.0000.0000.000
146A155PRO00.002-0.00440.892-0.002-0.0020.0000.0000.0000.000
147A156TYR0-0.015-0.00738.8790.0010.0010.0000.0000.0000.000
148A157GLY00.0220.01536.967-0.002-0.0020.0000.0000.0000.000
149A158GLU-1-0.886-0.95135.882-0.074-0.0740.0000.0000.0000.000
150A159LEU0-0.050-0.01835.587-0.002-0.0020.0000.0000.0000.000
151A160MET0-0.030-0.02732.9020.0000.0000.0000.0000.0000.000
152A161MET00.0200.02331.366-0.010-0.0100.0000.0000.0000.000
153A162GLU-1-0.875-0.92230.982-0.052-0.0520.0000.0000.0000.000
154A163VAL0-0.049-0.02428.3450.0000.0000.0000.0000.0000.000
155A164ALA00.0390.02327.103-0.005-0.0050.0000.0000.0000.000
156A165ARG10.9390.96325.9950.0770.0770.0000.0000.0000.000
157A166ARG10.8600.91825.8310.0380.0380.0000.0000.0000.000
158A167ASP-1-0.914-0.94722.983-0.081-0.0810.0000.0000.0000.000
159A168LEU0-0.020-0.03321.417-0.016-0.0160.0000.0000.0000.000
160A169ASP-1-0.884-0.92621.051-0.147-0.1470.0000.0000.0000.000
161A170PHE0-0.041-0.02317.296-0.004-0.0040.0000.0000.0000.000
162A171MET0-0.066-0.03515.0440.0080.0080.0000.0000.0000.000
163A172GLU-1-0.801-0.90316.279-0.371-0.3710.0000.0000.0000.000
164A173THR0-0.060-0.03117.677-0.014-0.0140.0000.0000.0000.000
165A174HIS0-0.048-0.01913.388-0.010-0.0100.0000.0000.0000.000
166A175ALA0-0.070-0.04312.159-0.001-0.0010.0000.0000.0000.000
167A176SER00.008-0.01613.107-0.077-0.0770.0000.0000.0000.000
168A177GLU-1-0.960-0.95210.134-0.700-0.7000.0000.0000.0000.000
169A178ALA0-0.055-0.03010.776-0.220-0.2200.0000.0000.0000.000
170A179GLU-1-0.747-0.87411.738-0.533-0.5330.0000.0000.0000.000
171A180LYS10.8140.88213.8030.4710.4710.0000.0000.0000.000
172A181VAL00.0100.00417.2980.0610.0610.0000.0000.0000.000
173A182GLU-1-0.830-0.90210.978-1.106-1.1060.0000.0000.0000.000
174A183MET0-0.065-0.01515.1450.0810.0810.0000.0000.0000.000
175A184ALA00.020-0.00116.0980.0640.0640.0000.0000.0000.000
176A185VAL00.014-0.00317.7430.0450.0450.0000.0000.0000.000
177A186ALA0-0.009-0.01015.4660.0440.0440.0000.0000.0000.000
178A187ALA0-0.001-0.00617.5020.0520.0520.0000.0000.0000.000
179A188ALA00.0050.02320.2050.0300.0300.0000.0000.0000.000
180A189VAL0-0.038-0.02419.8040.0240.0240.0000.0000.0000.000
181A190LEU0-0.074-0.02216.6790.0320.0320.0000.0000.0000.000
182A191PHE00.0850.02219.2150.0300.0300.0000.0000.0000.000
183A192GLN00.0270.01323.5630.0210.0210.0000.0000.0000.000
184A193PRO0-0.022-0.02124.2480.0090.0090.0000.0000.0000.000
185A194VAL00.0160.00624.1860.0080.0080.0000.0000.0000.000
186A195LEU00.0760.04426.3660.0070.0070.0000.0000.0000.000
187A196ARG10.9530.98829.1100.0060.0060.0000.0000.0000.000
188A197ALA0-0.063-0.03429.8190.0020.0020.0000.0000.0000.000
189A198LEU00.0290.01128.6990.0030.0030.0000.0000.0000.000
190A199HIS00.0230.02232.4260.0010.0010.0000.0000.0000.000
191A200ARG10.9140.94034.753-0.012-0.0120.0000.0000.0000.000
192A201LEU00.0230.02034.3200.0010.0010.0000.0000.0000.000
193A202ALA00.0200.01836.5450.0010.0010.0000.0000.0000.000
194A203GLN0-0.003-0.00438.237-0.004-0.0040.0000.0000.0000.000
195A204GLU-1-0.965-0.96240.0420.0260.0260.0000.0000.0000.000
196A205GLU-1-0.795-0.88740.2270.0240.0240.0000.0000.0000.000
197A206GLU-1-0.803-0.89442.0460.0030.0030.0000.0000.0000.000
198A207SER0-0.056-0.05244.165-0.002-0.0020.0000.0000.0000.000
199A208ALA0-0.014-0.00345.2280.0000.0000.0000.0000.0000.000
200A209ARG10.7430.85941.924-0.014-0.0140.0000.0000.0000.000
201A210ARG10.7950.88446.8380.0020.0020.0000.0000.0000.000
202A211TYR0-0.054-0.03547.964-0.002-0.0020.0000.0000.0000.000
203A212GLY00.0150.03849.9900.0000.0000.0000.0000.0000.000
204A213ILE0-0.047-0.03445.474-0.001-0.0010.0000.0000.0000.000
205A214GLU-1-0.962-0.97148.3380.0260.0260.0000.0000.0000.000
206A215LEU0-0.049-0.02044.2970.0000.0000.0000.0000.0000.000
207A216GLU-1-0.968-0.98448.5600.0290.0290.0000.0000.0000.000