Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: GY5K1

Calculation Name: 3DV8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DV8

Chain ID: A

ChEMBL ID:

UniProt ID: A5ZWV4

Base Structure: X-ray

Registration Date: 2023-09-27

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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2584724.047459
FMO2-HF: Nuclear repulsion 2496079.549766
FMO2-HF: Total energy -88644.497693
FMO2-MP2: Total energy -88898.492904


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:4:GLU)


Summations of interaction energy for fragment #1(A:4:GLU)
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.
8.97817.5560.926-3.306-6.1970.012
Interaction energy analysis for fragmet #1(A:4:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.951 / q_NPA : -0.979
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].
3A6TYR00.0230.0003.285-7.695-4.8220.056-1.401-1.5280.009
4A7PHE00.0340.0223.239-5.533-4.6500.062-0.247-0.6980.001
5A8PRO00.0190.0044.7880.8230.862-0.001-0.006-0.0310.000
6A9LEU00.0370.0237.579-1.029-1.0290.0000.0000.0000.000
7A10TRP00.0250.0023.109-3.821-0.9790.785-0.784-2.843-0.004
8A11ASN0-0.067-0.0545.5900.9300.9300.0000.0000.0000.000
9A12ASP-1-0.889-0.9258.34219.37619.3760.0000.0000.0000.000
10A13LEU0-0.088-0.0176.669-1.212-1.2120.0000.0000.0000.000
11A14ASN00.0360.01310.0791.3931.3930.0000.0000.0000.000
12A15THR00.027-0.0119.9062.1352.1350.0000.0000.0000.000
13A16ALA0-0.001-0.00210.1031.9711.9710.0000.0000.0000.000
14A17GLN00.0370.01210.5791.2041.2040.0000.0000.0000.000
15A18LYS10.9380.9825.874-32.339-32.3390.0000.0000.0000.000
16A19LYS10.9320.9706.272-20.751-20.7510.0000.0000.0000.000
17A20LEU0-0.0080.0098.3310.4930.4930.0000.0000.0000.000
18A21ILE00.0190.0026.097-1.085-1.0850.0000.0000.0000.000
19A22SER0-0.024-0.0103.162-7.412-6.1980.021-0.748-0.4870.006
20A23ASP-1-0.890-0.9565.70233.16133.201-0.001-0.001-0.0380.000
21A24ASN0-0.105-0.0508.729-4.040-4.0400.0000.0000.0000.000
22A25LEU0-0.0110.0073.764-2.358-2.1560.002-0.037-0.1670.000
23A26ILE0-0.0150.0128.354-0.614-0.6140.0000.0000.0000.000
24A27THR0-0.017-0.0179.1551.6091.6090.0000.0000.0000.000
25A28GLN00.002-0.01210.738-1.162-1.1620.0000.0000.0000.000
26A29HIS0-0.035-0.01013.132-0.451-0.4510.0000.0000.0000.000
27A30VAL0-0.030-0.01615.390-0.895-0.8950.0000.0000.0000.000
28A31LYS10.9950.99617.879-12.874-12.8740.0000.0000.0000.000
29A32LYS10.9470.97421.047-11.632-11.6320.0000.0000.0000.000
30A33GLY0-0.022-0.01422.761-0.408-0.4080.0000.0000.0000.000
31A34THR0-0.068-0.02421.274-0.403-0.4030.0000.0000.0000.000
32A35ILE00.0180.01122.0770.3950.3950.0000.0000.0000.000
33A36ILE0-0.051-0.03816.3460.1250.1250.0000.0000.0000.000
34A37HIS0-0.022-0.00819.5230.8050.8050.0000.0000.0000.000
35A38ASN00.0070.00721.384-0.378-0.3780.0000.0000.0000.000
36A39GLY00.0460.01924.937-0.317-0.3170.0000.0000.0000.000
37A40ASN0-0.029-0.03324.8560.6280.6280.0000.0000.0000.000
38A41MET0-0.098-0.02926.698-0.153-0.1530.0000.0000.0000.000
39A42ASP-1-0.880-0.92221.48512.67412.6740.0000.0000.0000.000
40A43CYS0-0.058-0.03920.369-0.306-0.3060.0000.0000.0000.000
41A44THR00.0350.03016.3900.4360.4360.0000.0000.0000.000
42A45GLY00.0600.01014.1310.5310.5310.0000.0000.0000.000
43A46LEU0-0.0440.01211.177-0.706-0.7060.0000.0000.0000.000
44A47LEU0-0.0070.00110.7691.2431.2430.0000.0000.0000.000
45A48LEU0-0.0270.0004.243-0.366-0.2370.001-0.034-0.0970.000
46A49VAL00.0320.0148.4411.0171.0170.0000.0000.0000.000
47A50LYS10.9260.9816.819-29.152-29.1520.0000.0000.0000.000
48A51SER00.002-0.0188.515-0.638-0.6380.0000.0000.0000.000
49A52GLY00.000-0.00512.159-0.214-0.2140.0000.0000.0000.000
50A53GLN0-0.013-0.02615.4790.0070.0070.0000.0000.0000.000
51A54LEU0-0.0090.00414.867-0.338-0.3380.0000.0000.0000.000
52A55ARG10.8110.91118.692-10.770-10.7700.0000.0000.0000.000
53A56THR00.0250.01120.2130.0520.0520.0000.0000.0000.000
54A57TYR0-0.059-0.04422.670-0.426-0.4260.0000.0000.0000.000
55A58ILE00.0210.01826.4390.1600.1600.0000.0000.0000.000
56A59LEU00.0220.00429.336-0.138-0.1380.0000.0000.0000.000
57A60SER0-0.036-0.00932.274-0.009-0.0090.0000.0000.0000.000
58A61ASP-1-0.854-0.94535.8587.6467.6460.0000.0000.0000.000
59A62GLU-1-1.022-1.00037.9186.9856.9850.0000.0000.0000.000
60A63GLY0-0.033-0.01735.729-0.078-0.0780.0000.0000.0000.000
61A64ARG10.8520.94035.735-7.587-7.5870.0000.0000.0000.000
62A65GLU-1-0.794-0.90230.7259.7039.7030.0000.0000.0000.000
63A66ILE0-0.025-0.02630.984-0.274-0.2740.0000.0000.0000.000
64A67THR0-0.017-0.03525.2370.1810.1810.0000.0000.0000.000
65A68LEU0-0.058-0.02224.823-0.201-0.2010.0000.0000.0000.000
66A69TYR00.025-0.00218.9210.1400.1400.0000.0000.0000.000
67A70ARG10.7830.88720.733-11.589-11.5890.0000.0000.0000.000
68A71LEU0-0.056-0.00615.0800.1550.1550.0000.0000.0000.000
69A72PHE00.018-0.00315.727-0.469-0.4690.0000.0000.0000.000
70A73ASP-1-0.788-0.90511.83919.76119.7610.0000.0000.0000.000
71A74MET0-0.088-0.0548.755-0.183-0.1830.0000.0000.0000.000
72A75ASP-1-0.826-0.8809.93617.52417.5240.0000.0000.0000.000
73A76MET0-0.027-0.0078.8171.9511.9510.0000.0000.0000.000
74A77CYS0-0.050-0.01511.658-1.914-1.9140.0000.0000.0000.000
75A78LEU00.0460.01013.7040.6840.6840.0000.0000.0000.000
76A79LEU00.025-0.00215.956-0.109-0.1090.0000.0000.0000.000
77A80SER00.0900.04615.218-0.653-0.6530.0000.0000.0000.000
78A81ALA0-0.037-0.00215.863-0.009-0.0090.0000.0000.0000.000
79A82SER00.038-0.02317.953-0.243-0.2430.0000.0000.0000.000
80A84ILE0-0.079-0.03717.037-0.434-0.4340.0000.0000.0000.000
81A85MET0-0.035-0.01519.278-0.066-0.0660.0000.0000.0000.000
82A86ARG10.9350.96423.414-11.327-11.3270.0000.0000.0000.000
83A87SER00.0200.00627.027-0.271-0.2710.0000.0000.0000.000
84A88ILE0-0.0160.01922.950-0.227-0.2270.0000.0000.0000.000
85A89GLN0-0.067-0.04826.434-0.165-0.1650.0000.0000.0000.000
86A90PHE0-0.0010.00624.662-0.312-0.3120.0000.0000.0000.000
87A91GLU-1-0.865-0.92726.55710.20610.2060.0000.0000.0000.000
88A92VAL0-0.043-0.02622.559-0.199-0.1990.0000.0000.0000.000
89A93THR00.0160.01024.5390.1910.1910.0000.0000.0000.000
90A94ILE0-0.026-0.01718.2360.0840.0840.0000.0000.0000.000
91A95GLU-1-0.824-0.91221.43011.28611.2860.0000.0000.0000.000
92A96ALA00.0100.01919.0990.2400.2400.0000.0000.0000.000
93A97GLU-1-0.755-0.86420.42611.28711.2870.0000.0000.0000.000
94A98LYS10.7610.85619.577-13.193-13.1930.0000.0000.0000.000
95A99ASP-1-0.871-0.93118.69313.95513.9550.0000.0000.0000.000
96A100THR0-0.045-0.03013.4690.1790.1790.0000.0000.0000.000
97A101ASP-1-0.899-0.91910.85220.75420.7540.0000.0000.0000.000
98A102LEU0-0.016-0.02610.2020.7840.7840.0000.0000.0000.000
99A103TRP00.0230.0124.4061.6472.0030.001-0.048-0.3080.000
100A104ILE0-0.003-0.0068.162-1.244-1.2440.0000.0000.0000.000
101A105ILE0-0.0050.0076.8601.6051.6050.0000.0000.0000.000
102A106PRO00.0350.01210.029-1.660-1.6600.0000.0000.0000.000
103A107ALA00.0880.03213.7660.3270.3270.0000.0000.0000.000
104A108GLU-1-0.938-0.97216.18516.68416.6840.0000.0000.0000.000
105A109ILE00.0030.00212.018-0.326-0.3260.0000.0000.0000.000
106A110TYR0-0.012-0.01910.7020.4980.4980.0000.0000.0000.000
107A111LYS10.9370.96413.895-13.571-13.5710.0000.0000.0000.000
108A112GLY0-0.027-0.01417.434-0.650-0.6500.0000.0000.0000.000
109A113ILE00.0140.00611.284-0.441-0.4410.0000.0000.0000.000
110A114MET0-0.037-0.01715.594-0.666-0.6660.0000.0000.0000.000
111A115LYS10.8840.95417.130-13.418-13.4180.0000.0000.0000.000
112A116ASP-1-0.908-0.95218.52213.88713.8870.0000.0000.0000.000
113A117SER0-0.046-0.01714.412-0.413-0.4130.0000.0000.0000.000
114A118ALA00.0680.02717.514-0.008-0.0080.0000.0000.0000.000
115A119PRO00.0230.01014.379-0.120-0.1200.0000.0000.0000.000
116A120VAL00.0480.02411.7280.2680.2680.0000.0000.0000.000
117A121ALA0-0.019-0.00214.227-0.018-0.0180.0000.0000.0000.000
118A122ASN00.015-0.00817.813-0.321-0.3210.0000.0000.0000.000
119A123TYR00.019-0.00310.743-0.156-0.1560.0000.0000.0000.000
120A124THR00.018-0.00315.1120.3160.3160.0000.0000.0000.000
121A125ASN0-0.032-0.01316.435-0.240-0.2400.0000.0000.0000.000
122A126GLU-1-0.870-0.93216.68612.89312.8930.0000.0000.0000.000
123A127LEU0-0.0410.00913.201-0.211-0.2110.0000.0000.0000.000
124A128MET0-0.029-0.02916.911-0.590-0.5900.0000.0000.0000.000
125A129ALA00.0280.01120.198-0.500-0.5000.0000.0000.0000.000
126A130THR0-0.0030.00718.092-0.461-0.4610.0000.0000.0000.000
127A131ARG10.8750.95915.064-15.949-15.9490.0000.0000.0000.000
128A132PHE0-0.055-0.02321.477-0.532-0.5320.0000.0000.0000.000
129A133SER0-0.005-0.03323.883-0.571-0.5710.0000.0000.0000.000
130A134ASP-1-0.877-0.93621.16412.49112.4910.0000.0000.0000.000
131A135VAL00.001-0.01824.747-0.415-0.4150.0000.0000.0000.000
132A136MET0-0.048-0.01727.244-0.528-0.5280.0000.0000.0000.000
133A137TRP00.0430.03127.589-0.350-0.3500.0000.0000.0000.000
134A138LEU0-0.0020.00728.602-0.358-0.3580.0000.0000.0000.000
135A139ILE0-0.011-0.00530.584-0.335-0.3350.0000.0000.0000.000
136A140GLU-1-0.931-0.97032.6698.5868.5860.0000.0000.0000.000
137A141GLN0-0.039-0.02231.807-0.306-0.3060.0000.0000.0000.000
138A142ILE0-0.050-0.03933.138-0.259-0.2590.0000.0000.0000.000
139A143MET0-0.048-0.00936.330-0.281-0.2810.0000.0000.0000.000
140A144TRP00.0040.00537.362-0.311-0.3110.0000.0000.0000.000
141A145LYS10.8090.91435.859-7.993-7.9930.0000.0000.0000.000
142A146SER00.011-0.01639.2750.0410.0410.0000.0000.0000.000
143A147LEU00.023-0.00738.3690.1210.1210.0000.0000.0000.000
144A148ASP-1-0.791-0.89539.2777.1237.1230.0000.0000.0000.000
145A149LYS10.9170.97038.618-6.919-6.9190.0000.0000.0000.000
146A150ARG10.9030.96733.435-8.188-8.1880.0000.0000.0000.000
147A151VAL0-0.0070.00334.6050.2370.2370.0000.0000.0000.000
148A152ALA0-0.015-0.01235.4330.1680.1680.0000.0000.0000.000
149A153SER0-0.001-0.00931.5890.1340.1340.0000.0000.0000.000
150A154PHE00.0230.02128.7500.1330.1330.0000.0000.0000.000
151A155LEU0-0.039-0.02730.8060.1960.1960.0000.0000.0000.000
152A156LEU00.0080.01831.9460.0990.0990.0000.0000.0000.000
153A157GLU-1-0.880-0.92925.02811.21711.2170.0000.0000.0000.000
154A158GLU-1-0.855-0.95926.54811.04811.0480.0000.0000.0000.000
155A159THR0-0.089-0.04827.6150.1590.1590.0000.0000.0000.000
156A160SER0-0.042-0.01726.0490.0590.0590.0000.0000.0000.000
157A161ILE0-0.059-0.01622.0180.2940.2940.0000.0000.0000.000
158A162GLU-1-0.895-0.94023.36611.84611.8460.0000.0000.0000.000
159A163GLY0-0.0030.01925.8710.0130.0130.0000.0000.0000.000
160A164THR0-0.044-0.03127.043-0.393-0.3930.0000.0000.0000.000
161A165ASN0-0.003-0.00530.5510.1470.1470.0000.0000.0000.000
162A166GLU-1-0.939-0.97032.9938.0268.0260.0000.0000.0000.000
163A167LEU00.0720.04030.2500.2140.2140.0000.0000.0000.000
164A168LYS10.9190.94731.469-9.288-9.2880.0000.0000.0000.000
165A169ILE00.0660.03830.1680.1350.1350.0000.0000.0000.000
166A170THR0-0.0030.01533.223-0.216-0.2160.0000.0000.0000.000
167A171HIS00.0560.03235.242-0.003-0.0030.0000.0000.0000.000
168A172GLU-1-0.864-0.95036.0517.8037.8030.0000.0000.0000.000
169A173THR00.0330.02130.0850.1190.1190.0000.0000.0000.000
170A174ILE00.0020.01032.0820.1210.1210.0000.0000.0000.000
171A175ALA0-0.066-0.04833.9630.0360.0360.0000.0000.0000.000
172A176ASN00.0330.01131.728-0.266-0.2660.0000.0000.0000.000
173A177HIS00.0380.06726.3920.0980.0980.0000.0000.0000.000
174A178LEU0-0.037-0.01830.9420.0420.0420.0000.0000.0000.000
175A179GLY00.0860.06333.724-0.137-0.1370.0000.0000.0000.000
176A180SER0-0.101-0.05535.424-0.338-0.3380.0000.0000.0000.000
177A181HIS00.0890.03138.1820.0730.0730.0000.0000.0000.000
178A182ARG11.0060.99839.846-7.079-7.0790.0000.0000.0000.000
179A183GLU-1-0.966-0.98140.8046.4036.4030.0000.0000.0000.000
180A184VAL0-0.004-0.00742.422-0.122-0.1220.0000.0000.0000.000
181A185ILE00.0200.02337.777-0.068-0.0680.0000.0000.0000.000
182A186THR0-0.018-0.05840.970-0.048-0.0480.0000.0000.0000.000
183A187ARG10.9030.95643.266-6.427-6.4270.0000.0000.0000.000
184A188MET00.0020.02541.469-0.139-0.1390.0000.0000.0000.000
185A189LEU00.0200.01238.306-0.038-0.0380.0000.0000.0000.000
186A190ARG10.9300.95242.518-6.510-6.5100.0000.0000.0000.000
187A191TYR00.0270.02945.242-0.122-0.1220.0000.0000.0000.000
188A192PHE00.0300.00339.116-0.058-0.0580.0000.0000.0000.000
189A193GLN0-0.029-0.01244.4190.0390.0390.0000.0000.0000.000
190A194VAL0-0.059-0.02645.813-0.069-0.0690.0000.0000.0000.000
191A195GLU-1-0.931-0.95346.5226.0326.0320.0000.0000.0000.000
192A196GLY0-0.018-0.01446.5010.0230.0230.0000.0000.0000.000
193A197LEU0-0.010-0.00241.5110.1000.1000.0000.0000.0000.000
194A198VAL00.000-0.00139.1710.2140.2140.0000.0000.0000.000
195A199LYS10.9860.99041.094-7.322-7.3220.0000.0000.0000.000
196A200LEU0-0.033-0.01040.8830.1950.1950.0000.0000.0000.000
197A201SER0-0.037-0.01941.200-0.167-0.1670.0000.0000.0000.000
198A202ARG10.9710.96041.280-6.785-6.7850.0000.0000.0000.000
199A203GLY00.0100.01838.2190.0810.0810.0000.0000.0000.000
200A204LYS10.8570.93636.360-7.741-7.7410.0000.0000.0000.000
201A205ILE00.0240.02335.942-0.299-0.2990.0000.0000.0000.000
202A206THR0-0.041-0.01836.2240.1440.1440.0000.0000.0000.000
203A207ILE00.0290.00634.832-0.262-0.2620.0000.0000.0000.000
204A208LEU0-0.067-0.03137.8600.0350.0350.0000.0000.0000.000
205A209ASP-1-0.826-0.92440.9647.0687.0680.0000.0000.0000.000
206A210SER00.0440.00834.7010.0240.0240.0000.0000.0000.000
207A211LYS11.0041.01437.386-6.877-6.8770.0000.0000.0000.000
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209A213LEU00.0060.01636.829-0.064-0.0640.0000.0000.0000.000
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