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: K9G43

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 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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2153739.1639
FMO2-HF: Nuclear repulsion 2072925.224191
FMO2-HF: Total energy -80813.939708
FMO2-MP2: Total energy -81050.540259


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.
-42.729-46.88949.418-17.427-27.832-0.088
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 : 0.072
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].
3A3LEU00.0780.0252.514-2.821-0.2541.104-1.703-1.968-0.012
4A4ALA00.0280.0105.1570.6110.758-0.001-0.008-0.1380.000
5A5ASP-1-0.824-0.9012.298-0.7671.8042.496-2.131-2.936-0.013
6A6LEU00.0570.0292.8300.9231.8536.249-2.465-4.713-0.008
7A7SER0-0.054-0.0333.5730.760-2.5190.0403.813-0.575-0.001
8A8LYS10.9490.9657.081-1.734-1.7340.0000.0000.0000.000
9A9ARG10.7560.8002.126-9.744-21.51223.885-7.150-4.9670.039
10A10SER0-0.005-0.0286.467-1.152-1.1520.0000.0000.0000.000
11A11GLY0-0.0020.0157.908-0.431-0.4310.0000.0000.0000.000
12A12VAL0-0.0110.0079.755-0.291-0.2910.0000.0000.0000.000
13A13SER00.0600.04710.2160.1810.1810.0000.0000.0000.000
14A14THR00.0830.0169.739-0.068-0.0680.0000.0000.0000.000
15A15ALA0-0.028-0.00410.765-0.130-0.1300.0000.0000.0000.000
16A16THR0-0.009-0.01813.649-0.095-0.0950.0000.0000.0000.000
17A17ILE00.0020.0207.216-0.074-0.0740.0000.0000.0000.000
18A18LYN00.0310.02311.203-0.156-0.1560.0000.0000.0000.000
19A19TYR0-0.105-0.07813.025-0.044-0.0440.0000.0000.0000.000
20A20TYR00.0680.01511.8430.0100.0100.0000.0000.0000.000
21A21LEU0-0.0160.0049.054-0.052-0.0520.0000.0000.0000.000
22A22ARG10.8820.94413.0390.0960.0960.0000.0000.0000.000
23A23GLU-1-0.794-0.85616.562-0.166-0.1660.0000.0000.0000.000
24A24GLY00.0010.00415.3060.0150.0150.0000.0000.0000.000
25A25LEU0-0.0210.00314.277-0.036-0.0360.0000.0000.0000.000
26A26LEU0-0.031-0.0106.896-0.046-0.0460.0000.0000.0000.000
27A27PRO00.0790.0389.8750.0450.0450.0000.0000.0000.000
28A28PRO00.0130.0029.122-0.223-0.2230.0000.0000.0000.000
29A29GLY0-0.0130.0097.200-0.172-0.1720.0000.0000.0000.000
30A39TYR0-0.013-0.0102.4060.1111.6880.956-0.667-1.8670.000
31A40ASP-1-0.856-0.9461.918-18.746-18.2758.754-4.656-4.569-0.059
32A41GLU-1-0.752-0.8702.464-8.433-7.2074.740-2.023-3.943-0.033
33A42ASP-1-0.753-0.8363.627-0.732-0.6960.0010.127-0.1640.000
34A43HIS00.0220.0203.171-0.999-0.6160.021-0.062-0.3410.000
35A44LEU0-0.065-0.0372.2430.9651.7891.171-0.454-1.542-0.001
36A45ARG10.8220.8844.0462.7522.9070.002-0.048-0.1090.000
37A46ARG10.7870.8557.2341.3581.3580.0000.0000.0000.000
38A47LEU0-0.033-0.0206.7050.3850.3850.0000.0000.0000.000
39A48ARG10.8720.9187.747-0.543-0.5430.0000.0000.0000.000
40A49LEU00.0280.04010.0500.1020.1020.0000.0000.0000.000
41A50VAL00.0180.00311.9070.0780.0780.0000.0000.0000.000
42A51ARG10.8250.89912.012-0.158-0.1580.0000.0000.0000.000
43A52ALA00.0220.02114.1340.0290.0290.0000.0000.0000.000
44A53LEU00.0720.02716.1220.0210.0210.0000.0000.0000.000
45A54ILE0-0.032-0.00316.4260.0240.0240.0000.0000.0000.000
46A55GLN0-0.032-0.02316.3790.0510.0510.0000.0000.0000.000
47A56VAL0-0.0260.00218.5610.0160.0160.0000.0000.0000.000
48A57GLY00.0460.01820.323-0.005-0.0050.0000.0000.0000.000
49A58LYS10.8110.91721.9520.0400.0400.0000.0000.0000.000
50A59VAL00.0170.01720.892-0.001-0.0010.0000.0000.0000.000
51A60PRO00.0130.00221.7270.0060.0060.0000.0000.0000.000
52A61VAL00.0310.00318.614-0.020-0.0200.0000.0000.0000.000
53A62ALA0-0.013-0.01620.611-0.032-0.0320.0000.0000.0000.000
54A63THR00.0520.03223.102-0.012-0.0120.0000.0000.0000.000
55A64ALA00.0200.00318.123-0.020-0.0200.0000.0000.0000.000
56A65ARG10.8140.89118.5670.1810.1810.0000.0000.0000.000
57A66GLU-1-0.872-0.90719.630-0.249-0.2490.0000.0000.0000.000
58A67VAL0-0.014-0.00418.885-0.026-0.0260.0000.0000.0000.000
59A68LEU0-0.026-0.03114.409-0.027-0.0270.0000.0000.0000.000
60A69GLY00.0220.02117.289-0.061-0.0610.0000.0000.0000.000
61A70HIS0-0.032-0.03219.662-0.033-0.0330.0000.0000.0000.000
62A71VAL0-0.050-0.02714.768-0.004-0.0040.0000.0000.0000.000
63A72ASP-1-0.807-0.87614.290-0.937-0.9370.0000.0000.0000.000
64A73ASP-1-0.838-0.88617.083-0.367-0.3670.0000.0000.0000.000
65A74ASP-1-0.956-0.97919.909-0.470-0.4700.0000.0000.0000.000
66A75SER0-0.101-0.06821.6130.0350.0350.0000.0000.0000.000
67A76LEU0-0.0080.00324.4930.0330.0330.0000.0000.0000.000
68A77GLY00.0150.00324.059-0.034-0.0340.0000.0000.0000.000
69A78ARG10.9030.92118.5090.5030.5030.0000.0000.0000.000
70A79THR00.0040.00223.203-0.005-0.0050.0000.0000.0000.000
71A80VAL00.0380.02026.1210.0120.0120.0000.0000.0000.000
72A81ARG10.8240.92818.4270.5180.5180.0000.0000.0000.000
73A82LEU00.0010.00421.500-0.004-0.0040.0000.0000.0000.000
74A83GLY00.0180.01623.3310.0120.0120.0000.0000.0000.000
75A84ALA00.0240.00725.0500.0120.0120.0000.0000.0000.000
76A85ALA00.014-0.00520.5420.0110.0110.0000.0000.0000.000
77A86LEU0-0.034-0.02722.5730.0140.0140.0000.0000.0000.000
78A87TRP0-0.019-0.02424.3020.0210.0210.0000.0000.0000.000
79A88ALA00.0220.03124.0220.0140.0140.0000.0000.0000.000
80A89LEU0-0.061-0.02621.0950.0060.0060.0000.0000.0000.000
81A90PRO0-0.044-0.03624.6050.0080.0080.0000.0000.0000.000
82A91GLN00.0000.00127.6370.0060.0060.0000.0000.0000.000
83A92ASP-1-0.873-0.89530.939-0.067-0.0670.0000.0000.0000.000
84A93ALA0-0.025-0.02334.512-0.006-0.0060.0000.0000.0000.000
85A94GLU-1-0.799-0.87337.402-0.096-0.0960.0000.0000.0000.000
86A95PRO0-0.022-0.00339.7140.0050.0050.0000.0000.0000.000
87A96ASP-1-0.875-0.93842.886-0.053-0.0530.0000.0000.0000.000
88A97GLU-1-0.802-0.89243.195-0.072-0.0720.0000.0000.0000.000
89A98ALA0-0.060-0.02147.1360.0010.0010.0000.0000.0000.000
90A99ASP-1-0.781-0.86248.519-0.041-0.0410.0000.0000.0000.000
91A100PRO0-0.006-0.01150.034-0.002-0.0020.0000.0000.0000.000
92A101ALA0-0.007-0.00549.100-0.001-0.0010.0000.0000.0000.000
93A102VAL00.0210.01144.660-0.001-0.0010.0000.0000.0000.000
94A103ALA00.0040.00346.665-0.003-0.0030.0000.0000.0000.000
95A104ALA0-0.035-0.02248.858-0.002-0.0020.0000.0000.0000.000
96A105ALA00.0190.00744.460-0.001-0.0010.0000.0000.0000.000
97A106ARG10.8350.88240.6090.0760.0760.0000.0000.0000.000
98A107VAL0-0.028-0.00344.845-0.003-0.0030.0000.0000.0000.000
99A108GLU-1-0.791-0.87245.934-0.048-0.0480.0000.0000.0000.000
100A109VAL00.005-0.00439.786-0.001-0.0010.0000.0000.0000.000
101A110ASP-1-0.848-0.89741.838-0.084-0.0840.0000.0000.0000.000
102A111ARG10.8580.90143.4750.0500.0500.0000.0000.0000.000
103A112LEU0-0.022-0.00440.0450.0000.0000.0000.0000.0000.000
104A113LEU0-0.031-0.02437.169-0.003-0.0030.0000.0000.0000.000
105A114GLU-1-0.868-0.90740.569-0.073-0.0730.0000.0000.0000.000
106A115LEU0-0.064-0.03543.5040.0000.0000.0000.0000.0000.000
107A116LEU0-0.068-0.02438.0930.0020.0020.0000.0000.0000.000
108A117GLY00.0160.02039.241-0.004-0.0040.0000.0000.0000.000
109A118TRP0-0.075-0.03235.208-0.008-0.0080.0000.0000.0000.000
110A119GLU-1-0.802-0.91537.202-0.095-0.0950.0000.0000.0000.000
111A120THR0-0.002-0.00132.412-0.001-0.0010.0000.0000.0000.000
112A121SER0-0.052-0.03534.097-0.009-0.0090.0000.0000.0000.000
113A122ARG10.7100.80335.3380.0850.0850.0000.0000.0000.000
114A123GLU-1-0.924-0.95936.169-0.136-0.1360.0000.0000.0000.000
115A124LEU0-0.045-0.02531.162-0.003-0.0030.0000.0000.0000.000
116A125ALA00.0250.01835.246-0.001-0.0010.0000.0000.0000.000
117A126PRO0-0.077-0.03837.7850.0030.0030.0000.0000.0000.000
118A127LEU0-0.036-0.01934.3810.0000.0000.0000.0000.0000.000
119A128SER00.0030.01632.591-0.004-0.0040.0000.0000.0000.000
120A129PRO00.0040.00930.5850.0100.0100.0000.0000.0000.000
121A130VAL00.0540.01829.5090.0090.0090.0000.0000.0000.000
122A131HIS00.0080.01332.7970.0090.0090.0000.0000.0000.000
123A132ARG10.8290.89433.4920.1070.1070.0000.0000.0000.000
124A133SER0-0.034-0.05533.9020.0040.0040.0000.0000.0000.000
125A134LEU0-0.0170.00136.2530.0080.0080.0000.0000.0000.000
126A135VAL00.007-0.00337.8710.0060.0060.0000.0000.0000.000
127A136VAL00.0140.00439.0980.0060.0060.0000.0000.0000.000
128A137ALA0-0.025-0.00938.6980.0050.0050.0000.0000.0000.000
129A138VAL00.0220.00240.8020.0050.0050.0000.0000.0000.000
130A139ALA0-0.0040.00243.5510.0030.0030.0000.0000.0000.000
131A140ALA0-0.056-0.03143.3460.0030.0030.0000.0000.0000.000
132A141LEU0-0.012-0.00742.6710.0040.0040.0000.0000.0000.000
133A142ARG10.8620.91946.3820.0460.0460.0000.0000.0000.000
134A143ARG10.8070.89046.3720.0420.0420.0000.0000.0000.000
135A144LEU0-0.080-0.04047.7720.0020.0020.0000.0000.0000.000
136A145ASP-1-0.917-0.95051.133-0.024-0.0240.0000.0000.0000.000
137A146TYR0-0.027-0.00648.6030.0010.0010.0000.0000.0000.000
138A147PRO0-0.025-0.00549.841-0.002-0.0020.0000.0000.0000.000
139A148TRP00.012-0.00941.412-0.001-0.0010.0000.0000.0000.000
140A149ASP-1-0.858-0.93247.534-0.041-0.0410.0000.0000.0000.000
141A150ALA00.0060.00045.0530.0000.0000.0000.0000.0000.000
142A151GLU-1-0.844-0.93745.329-0.049-0.0490.0000.0000.0000.000
143A152LEU0-0.082-0.02445.1950.0010.0010.0000.0000.0000.000
144A153MET0-0.024-0.01741.9670.0000.0000.0000.0000.0000.000
145A154ALA00.0580.03241.506-0.002-0.0020.0000.0000.0000.000
146A155PRO0-0.024-0.02040.966-0.003-0.0030.0000.0000.0000.000
147A156TYR0-0.008-0.00638.9830.0010.0010.0000.0000.0000.000
148A157GLY00.0340.02837.142-0.003-0.0030.0000.0000.0000.000
149A158GLU-1-0.767-0.88635.876-0.083-0.0830.0000.0000.0000.000
150A159LEU0-0.054-0.01335.517-0.002-0.0020.0000.0000.0000.000
151A160MET0-0.022-0.02032.9960.0000.0000.0000.0000.0000.000
152A161MET00.0140.02031.474-0.010-0.0100.0000.0000.0000.000
153A162GLU-1-0.865-0.91831.000-0.059-0.0590.0000.0000.0000.000
154A163VAL0-0.049-0.01028.1580.0020.0020.0000.0000.0000.000
155A164ALA00.0380.01327.086-0.006-0.0060.0000.0000.0000.000
156A165ARG10.8170.89426.2270.0750.0750.0000.0000.0000.000
157A166ARG10.8560.91025.8230.0430.0430.0000.0000.0000.000
158A167ASP-1-0.900-0.95323.333-0.088-0.0880.0000.0000.0000.000
159A168LEU0-0.029-0.02121.550-0.022-0.0220.0000.0000.0000.000
160A169ASP-1-0.887-0.94421.234-0.152-0.1520.0000.0000.0000.000
161A170PHE0-0.032-0.01117.517-0.005-0.0050.0000.0000.0000.000
162A171MET0-0.046-0.01714.9090.0020.0020.0000.0000.0000.000
163A172GLU-1-0.786-0.90616.551-0.401-0.4010.0000.0000.0000.000
164A173THR0-0.090-0.05418.020-0.011-0.0110.0000.0000.0000.000
165A174HIS0-0.047-0.02013.946-0.002-0.0020.0000.0000.0000.000
166A175ALA0-0.061-0.03812.4370.0030.0030.0000.0000.0000.000
167A176SER0-0.001-0.01813.236-0.096-0.0960.0000.0000.0000.000
168A177GLU-1-0.943-0.95310.456-0.708-0.7080.0000.0000.0000.000
169A178ALA0-0.037-0.01511.039-0.195-0.1950.0000.0000.0000.000
170A179GLU-1-0.742-0.86111.994-0.499-0.4990.0000.0000.0000.000
171A180LYS10.8140.88614.1420.4950.4950.0000.0000.0000.000
172A181VAL0-0.0020.00217.4810.0620.0620.0000.0000.0000.000
173A182GLU-1-0.813-0.89611.350-0.990-0.9900.0000.0000.0000.000
174A183MET0-0.081-0.01515.1610.0840.0840.0000.0000.0000.000
175A184ALA00.0490.01916.2640.0600.0600.0000.0000.0000.000
176A185VAL00.008-0.00617.7880.0440.0440.0000.0000.0000.000
177A186ALA0-0.016-0.01715.4080.0420.0420.0000.0000.0000.000
178A187ALA00.0040.00217.4620.0490.0490.0000.0000.0000.000
179A188ALA0-0.0050.01320.5000.0290.0290.0000.0000.0000.000
180A189VAL0-0.035-0.02419.6150.0240.0240.0000.0000.0000.000
181A190LEU0-0.062-0.02016.6320.0310.0310.0000.0000.0000.000
182A191PHE00.0920.02819.4360.0300.0300.0000.0000.0000.000
183A192GLN00.0000.00623.4930.0250.0250.0000.0000.0000.000
184A193PRO0-0.036-0.02724.1060.0080.0080.0000.0000.0000.000
185A194VAL00.0210.01324.1540.0070.0070.0000.0000.0000.000
186A195LEU00.0630.03726.3430.0060.0060.0000.0000.0000.000
187A196ARG10.9620.98829.1380.0090.0090.0000.0000.0000.000
188A197ALA0-0.050-0.02729.8160.0030.0030.0000.0000.0000.000
189A198LEU00.0160.00328.7450.0030.0030.0000.0000.0000.000
190A199HIS00.0160.01432.5050.0000.0000.0000.0000.0000.000
191A200ARG10.8110.88834.726-0.013-0.0130.0000.0000.0000.000
192A201LEU00.0180.01334.4590.0010.0010.0000.0000.0000.000
193A202ALA00.0170.01236.6060.0010.0010.0000.0000.0000.000
194A203GLN00.0140.00338.395-0.004-0.0040.0000.0000.0000.000
195A204GLU-1-0.875-0.91339.5130.0220.0220.0000.0000.0000.000
196A205GLU-1-0.784-0.88040.4940.0190.0190.0000.0000.0000.000
197A206GLU-1-0.806-0.88042.250-0.001-0.0010.0000.0000.0000.000
198A207SER0-0.037-0.04444.287-0.002-0.0020.0000.0000.0000.000
199A208ALA0-0.017-0.00745.2460.0000.0000.0000.0000.0000.000
200A209ARG10.7370.84541.683-0.009-0.0090.0000.0000.0000.000
201A210ARG10.7970.88746.7980.0050.0050.0000.0000.0000.000
202A211TYR0-0.052-0.03247.969-0.002-0.0020.0000.0000.0000.000
203A212GLY00.0180.04250.3690.0000.0000.0000.0000.0000.000
204A213ILE0-0.051-0.03745.382-0.001-0.0010.0000.0000.0000.000
205A214GLU-1-0.956-0.96848.2500.0230.0230.0000.0000.0000.000
206A215LEU0-0.049-0.03044.5310.0010.0010.0000.0000.0000.000
207A216GLU-1-0.979-0.98049.0110.0280.0280.0000.0000.0000.000