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: G6KK1

Calculation Name: 3WOH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WOH

Chain ID: A

ChEMBL ID:

UniProt ID: K9M8L2

Base Structure: X-ray

Registration Date: 2023-09-20

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 235
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2642430.408892
FMO2-HF: Nuclear repulsion 2555749.557123
FMO2-HF: Total energy -86680.851769
FMO2-MP2: Total energy -86930.08948


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:5:GLY)


Summations of interaction energy for fragment #1(A:5:GLY)
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.
-2.1950.2943.275-2.199-3.568-0.003
Interaction energy analysis for fragmet #1(A:5:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : -0.008
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].
3A7LEU0-0.033-0.0223.805-0.9580.752-0.013-0.887-0.811-0.001
4A8SER0-0.047-0.0354.463-0.280-0.138-0.001-0.024-0.1180.000
5A9GLY00.0300.0285.692-0.652-0.6520.0000.0000.0000.000
6A10LYS10.8320.9127.817-0.734-0.7340.0000.0000.0000.000
7A11VAL00.0170.0199.8720.1860.1860.0000.0000.0000.000
8A12ALA00.001-0.00411.315-0.098-0.0980.0000.0000.0000.000
9A13LEU0-0.016-0.00113.253-0.008-0.0080.0000.0000.0000.000
10A14VAL00.0080.00614.440-0.031-0.0310.0000.0000.0000.000
11A15THR00.0300.02017.382-0.012-0.0120.0000.0000.0000.000
12A16GLY00.0270.00420.964-0.012-0.0120.0000.0000.0000.000
13A17GLY00.0090.00018.499-0.013-0.0130.0000.0000.0000.000
14A18SER00.0070.00018.6460.0030.0030.0000.0000.0000.000
15A19ARG10.8990.91721.282-0.054-0.0540.0000.0000.0000.000
16A20GLY00.0560.03920.8490.0030.0030.0000.0000.0000.000
17A21LEU00.0490.01119.0130.0000.0000.0000.0000.0000.000
18A22GLY00.0670.04017.4330.0010.0010.0000.0000.0000.000
19A23ARG10.8910.93516.414-0.007-0.0070.0000.0000.0000.000
20A24ALA00.0060.00314.6630.0130.0130.0000.0000.0000.000
21A25MET0-0.037-0.01512.905-0.009-0.0090.0000.0000.0000.000
22A26ALA00.0150.01111.7970.0400.0400.0000.0000.0000.000
23A27LEU00.0220.00210.7480.0880.0880.0000.0000.0000.000
24A28ARG10.7740.8607.3310.6000.6000.0000.0000.0000.000
25A29LEU00.0260.0057.069-0.090-0.0900.0000.0000.0000.000
26A30ALA00.0440.0256.3940.4910.4910.0000.0000.0000.000
27A31ARG10.8890.9505.3680.9610.9610.0000.0000.0000.000
28A32ASP-1-0.788-0.8552.901-3.536-2.5500.119-0.417-0.688-0.003
29A33GLY00.0480.0332.6303.3983.5123.096-1.465-1.745-0.001
30A34ALA0-0.038-0.0103.600-1.051-1.5140.0740.594-0.2060.002
31A35ALA00.0190.0097.349-0.172-0.1720.0000.0000.0000.000
32A36VAL0-0.034-0.0249.816-0.157-0.1570.0000.0000.0000.000
33A37ALA00.0180.01012.521-0.062-0.0620.0000.0000.0000.000
34A38ILE0-0.037-0.01215.553-0.034-0.0340.0000.0000.0000.000
35A39VAL00.017-0.00117.897-0.011-0.0110.0000.0000.0000.000
36A40TYR0-0.086-0.08221.333-0.011-0.0110.0000.0000.0000.000
37A41VAL00.0830.04624.1000.0020.0020.0000.0000.0000.000
38A42SER0-0.036-0.03725.725-0.002-0.0020.0000.0000.0000.000
39A43ASP-1-0.758-0.83226.7430.0670.0670.0000.0000.0000.000
40A44ASP-1-0.750-0.84725.2850.1070.1070.0000.0000.0000.000
41A45SER0-0.043-0.03324.2150.0100.0100.0000.0000.0000.000
42A46SER00.004-0.01822.5230.0030.0030.0000.0000.0000.000
43A47ALA0-0.0020.01920.6070.0080.0080.0000.0000.0000.000
44A48LYS10.8920.94019.458-0.163-0.1630.0000.0000.0000.000
45A49GLU-1-0.854-0.88219.5250.0650.0650.0000.0000.0000.000
46A50THR0-0.004-0.02015.634-0.003-0.0030.0000.0000.0000.000
47A51GLN0-0.057-0.04515.1560.0120.0120.0000.0000.0000.000
48A52GLY00.0480.02614.7590.0310.0310.0000.0000.0000.000
49A53GLU-1-0.866-0.90414.1010.0300.0300.0000.0000.0000.000
50A54ILE0-0.019-0.0149.748-0.011-0.0110.0000.0000.0000.000
51A55GLU-1-0.807-0.87210.5450.3140.3140.0000.0000.0000.000
52A56ARG10.8050.88812.461-0.055-0.0550.0000.0000.0000.000
53A57LEU0-0.084-0.0417.914-0.055-0.0550.0000.0000.0000.000
54A58GLY00.0020.0048.409-0.074-0.0740.0000.0000.0000.000
55A59GLY00.0060.0136.9730.1710.1710.0000.0000.0000.000
56A60THR0-0.003-0.0127.906-0.124-0.1240.0000.0000.0000.000
57A61ALA00.0330.01010.2660.0670.0670.0000.0000.0000.000
58A62ARG10.8130.90113.175-0.375-0.3750.0000.0000.0000.000
59A63SER00.005-0.00416.9450.0000.0000.0000.0000.0000.000
60A64TYR0-0.073-0.07518.317-0.001-0.0010.0000.0000.0000.000
61A65ARG10.8710.92923.004-0.093-0.0930.0000.0000.0000.000
62A66CYS0-0.080-0.04925.7780.0010.0010.0000.0000.0000.000
63A67ASP-1-0.771-0.86427.4110.0640.0640.0000.0000.0000.000
64A68VAL0-0.044-0.02125.9010.0070.0070.0000.0000.0000.000
65A69SER0-0.022-0.02428.957-0.004-0.0040.0000.0000.0000.000
66A70ASP-1-0.831-0.90732.3340.0710.0710.0000.0000.0000.000
67A71ALA00.0210.01632.1480.0040.0040.0000.0000.0000.000
68A72GLU-1-0.805-0.88031.2290.0890.0890.0000.0000.0000.000
69A73GLN0-0.049-0.02829.9880.0110.0110.0000.0000.0000.000
70A74VAL00.0760.03826.2680.0110.0110.0000.0000.0000.000
71A75THR0-0.030-0.05326.4580.0150.0150.0000.0000.0000.000
72A76ARG10.8640.93927.225-0.085-0.0850.0000.0000.0000.000
73A77CYS00.0120.02423.3920.0130.0130.0000.0000.0000.000
74A78VAL00.0600.02422.1560.0190.0190.0000.0000.0000.000
75A79LYS10.9140.95922.318-0.099-0.0990.0000.0000.0000.000
76A80ALA00.0110.02123.8360.0060.0060.0000.0000.0000.000
77A81VAL00.0180.01117.5860.0160.0160.0000.0000.0000.000
78A82THR0-0.066-0.05318.8660.0350.0350.0000.0000.0000.000
79A83ALA0-0.056-0.01820.6380.0070.0070.0000.0000.0000.000
80A84ASP-1-0.851-0.89018.5110.2640.2640.0000.0000.0000.000
81A85LEU0-0.073-0.03413.6600.0400.0400.0000.0000.0000.000
82A86GLY00.0410.02615.4130.0530.0530.0000.0000.0000.000
83A87PRO0-0.051-0.03317.441-0.015-0.0150.0000.0000.0000.000
84A88VAL00.0460.01715.9700.0270.0270.0000.0000.0000.000
85A89ASP-1-0.849-0.90513.0460.4120.4120.0000.0000.0000.000
86A90ILE0-0.0030.00410.280-0.059-0.0590.0000.0000.0000.000
87A91LEU0-0.023-0.00714.6320.0260.0260.0000.0000.0000.000
88A92VAL00.0160.01014.614-0.033-0.0330.0000.0000.0000.000
89A93ASN0-0.018-0.02417.7580.0160.0160.0000.0000.0000.000
90A94ASN00.009-0.01919.731-0.029-0.0290.0000.0000.0000.000
91A95ALA0-0.053-0.00621.731-0.007-0.0070.0000.0000.0000.000
92A96GLY00.0460.00624.784-0.006-0.0060.0000.0000.0000.000
93A97ILE0-0.052-0.01427.9890.0010.0010.0000.0000.0000.000
94A98ILE00.0360.01929.237-0.002-0.0020.0000.0000.0000.000
95A99ARG10.8190.88833.018-0.024-0.0240.0000.0000.0000.000
96A100ASP-1-0.857-0.90535.9630.0050.0050.0000.0000.0000.000
97A101GLY00.0350.00938.4760.0010.0010.0000.0000.0000.000
98A102LEU00.0100.00142.242-0.001-0.0010.0000.0000.0000.000
99A103ALA00.0320.00444.3400.0010.0010.0000.0000.0000.000
100A104ALA0-0.0180.00245.2660.0010.0010.0000.0000.0000.000
101A105SER0-0.083-0.05145.7170.0000.0000.0000.0000.0000.000
102A106ILE0-0.044-0.00940.7030.0010.0010.0000.0000.0000.000
103A107LYS10.8960.93443.324-0.019-0.0190.0000.0000.0000.000
104A108ASP-1-0.857-0.93042.6830.0200.0200.0000.0000.0000.000
105A109GLU-1-0.806-0.89641.3830.0230.0230.0000.0000.0000.000
106A110ASP-1-0.811-0.90638.8790.0210.0210.0000.0000.0000.000
107A111TYR00.0100.00837.8960.0000.0000.0000.0000.0000.000
108A112ASP-1-0.805-0.89937.6630.0340.0340.0000.0000.0000.000
109A113ALA0-0.0260.01035.6160.0040.0040.0000.0000.0000.000
110A114VAL0-0.0300.01333.3670.0040.0040.0000.0000.0000.000
111A115MET00.0490.03532.7150.0030.0030.0000.0000.0000.000
112A116ASN0-0.059-0.07233.0910.0070.0070.0000.0000.0000.000
113A117THR0-0.017-0.03629.3800.0040.0040.0000.0000.0000.000
114A118ASN0-0.068-0.04928.2490.0040.0040.0000.0000.0000.000
115A119LEU0-0.0120.00928.341-0.001-0.0010.0000.0000.0000.000
116A120LYS10.8570.93229.563-0.047-0.0470.0000.0000.0000.000
117A121GLY00.0860.03727.8670.0050.0050.0000.0000.0000.000
118A122ALA0-0.0010.00625.3090.0100.0100.0000.0000.0000.000
119A123PHE00.020-0.00126.2850.0060.0060.0000.0000.0000.000
120A124LEU0-0.043-0.00628.6480.0040.0040.0000.0000.0000.000
121A125PHE00.044-0.00322.6980.0080.0080.0000.0000.0000.000
122A126ILE00.0110.01523.6000.0140.0140.0000.0000.0000.000
123A127LYS10.8620.91425.118-0.075-0.0750.0000.0000.0000.000
124A128ALA0-0.058-0.02625.5790.0010.0010.0000.0000.0000.000
125A129CYS0-0.034-0.00921.4770.0170.0170.0000.0000.0000.000
126A130TYR0-0.062-0.05023.4000.0100.0100.0000.0000.0000.000
127A131PHE00.0340.00025.3030.0000.0000.0000.0000.0000.000
128A132GLY0-0.026-0.00222.704-0.001-0.0010.0000.0000.0000.000
129A133PHE00.0570.02017.9120.0020.0020.0000.0000.0000.000
130A134ILE00.0350.02521.917-0.007-0.0070.0000.0000.0000.000
131A135ARG10.9060.95824.314-0.137-0.1370.0000.0000.0000.000
132A136LYS10.7760.86215.840-0.335-0.3350.0000.0000.0000.000
133A137ARG10.8700.95220.474-0.081-0.0810.0000.0000.0000.000
134A138SER00.0510.02916.536-0.012-0.0120.0000.0000.0000.000
135A139GLY00.0590.02216.5780.0200.0200.0000.0000.0000.000
136A140SER0-0.081-0.05015.368-0.040-0.0400.0000.0000.0000.000
137A141ILE00.0140.01216.8930.0360.0360.0000.0000.0000.000
138A142ILE00.003-0.00415.087-0.023-0.0230.0000.0000.0000.000
139A143ASN00.012-0.01218.9120.0230.0230.0000.0000.0000.000
140A144ILE00.0050.00518.617-0.016-0.0160.0000.0000.0000.000
141A145SER0-0.014-0.03222.6560.0030.0030.0000.0000.0000.000
142A146SER00.0140.02326.095-0.007-0.0070.0000.0000.0000.000
143A147VAL00.0670.02127.3880.0020.0020.0000.0000.0000.000
144A148SER00.0030.00529.6070.0020.0020.0000.0000.0000.000
145A149GLY0-0.013-0.01330.8680.0020.0020.0000.0000.0000.000
146A150VAL0-0.079-0.03528.6090.0010.0010.0000.0000.0000.000
147A151PHE0-0.023-0.01931.839-0.001-0.0010.0000.0000.0000.000
148A152GLY00.0160.03034.7310.0010.0010.0000.0000.0000.000
149A153SER0-0.001-0.04834.955-0.002-0.0020.0000.0000.0000.000
150A154ALA0-0.011-0.00337.4800.0030.0030.0000.0000.0000.000
151A155GLY0-0.0010.00439.5460.0000.0000.0000.0000.0000.000
152A156GLN00.0470.02633.328-0.001-0.0010.0000.0000.0000.000
153A157ALA00.0040.00436.6590.0020.0020.0000.0000.0000.000
154A158ASN00.0100.02437.5090.0010.0010.0000.0000.0000.000
155A159TYR00.0600.02128.4470.0030.0030.0000.0000.0000.000
156A160ALA00.0220.01032.8380.0010.0010.0000.0000.0000.000
157A161SER0-0.008-0.01933.914-0.001-0.0010.0000.0000.0000.000
158A162ALA00.0140.00632.3770.0010.0010.0000.0000.0000.000
159A163LYS10.8360.93325.851-0.030-0.0300.0000.0000.0000.000
160A164ALA00.0420.02929.971-0.001-0.0010.0000.0000.0000.000
161A165GLY0-0.004-0.00532.2450.0000.0000.0000.0000.0000.000
162A166LEU0-0.024-0.00325.1800.0030.0030.0000.0000.0000.000
163A167ILE00.0080.01927.8480.0020.0020.0000.0000.0000.000
164A168GLY00.0060.00529.145-0.001-0.0010.0000.0000.0000.000
165A169LEU0-0.0040.00727.5960.0000.0000.0000.0000.0000.000
166A170THR0-0.012-0.03024.2590.0050.0050.0000.0000.0000.000
167A171LYS10.9030.95426.8130.0090.0090.0000.0000.0000.000
168A172SER0-0.053-0.02729.258-0.002-0.0020.0000.0000.0000.000
169A173ILE00.0340.00325.1330.0000.0000.0000.0000.0000.000
170A174ALA0-0.0230.00725.3690.0030.0030.0000.0000.0000.000
171A175LYS10.9320.96026.358-0.006-0.0060.0000.0000.0000.000
172A176GLU-1-0.869-0.90629.2220.0480.0480.0000.0000.0000.000
173A177LEU0-0.007-0.00424.3550.0050.0050.0000.0000.0000.000
174A178ALA00.0350.03125.4580.0030.0030.0000.0000.0000.000
175A179GLU-1-0.935-0.96925.9480.0180.0180.0000.0000.0000.000
176A180ARG10.7720.87725.683-0.058-0.0580.0000.0000.0000.000
177A181ASN0-0.044-0.02819.1870.0000.0000.0000.0000.0000.000
178A182VAL0-0.0270.00320.3870.0140.0140.0000.0000.0000.000
179A183ARG10.8150.91814.205-0.029-0.0290.0000.0000.0000.000
180A184CYS0-0.038-0.00420.4470.0220.0220.0000.0000.0000.000
181A185ASN00.006-0.01319.170-0.021-0.0210.0000.0000.0000.000
182A186ALA00.0030.00021.7720.0140.0140.0000.0000.0000.000
183A187VAL00.0000.00918.062-0.013-0.0130.0000.0000.0000.000
184A188ALA00.0480.00821.5180.0110.0110.0000.0000.0000.000
185A189PRO0-0.011-0.00521.967-0.009-0.0090.0000.0000.0000.000
186A190GLY00.0430.02224.3450.0060.0060.0000.0000.0000.000
187A191LEU0-0.024-0.00727.2320.0050.0050.0000.0000.0000.000
188A192ILE0-0.054-0.01322.230-0.009-0.0090.0000.0000.0000.000
189A193ALA00.0100.02624.5050.0070.0070.0000.0000.0000.000
190A194THR0-0.061-0.07622.892-0.012-0.0120.0000.0000.0000.000
191A195ASP-1-0.897-0.92024.8930.0060.0060.0000.0000.0000.000
192A206ARG10.8760.91235.1190.0260.0260.0000.0000.0000.000
193A207LEU0-0.018-0.02930.6700.0000.0000.0000.0000.0000.000
194A208ASP-1-0.821-0.87834.160-0.033-0.0330.0000.0000.0000.000
195A209PRO00.0020.00834.444-0.001-0.0010.0000.0000.0000.000
196A210VAL0-0.0050.00229.413-0.002-0.0020.0000.0000.0000.000
197A211PRO00.0280.02131.356-0.001-0.0010.0000.0000.0000.000
198A212MET0-0.046-0.01624.780-0.003-0.0030.0000.0000.0000.000
199A213ARG10.9150.95930.0210.0510.0510.0000.0000.0000.000
200A214ARG10.7570.84822.0400.1070.1070.0000.0000.0000.000
201A215PHE00.0540.02426.5450.0010.0010.0000.0000.0000.000
202A216GLY00.0140.00623.317-0.010-0.0100.0000.0000.0000.000
203A217ARG10.8370.87517.3780.1600.1600.0000.0000.0000.000
204A218PRO00.015-0.00317.946-0.005-0.0050.0000.0000.0000.000
205A219ASP-1-0.792-0.88414.198-0.156-0.1560.0000.0000.0000.000
206A220GLU-1-0.755-0.82914.603-0.154-0.1540.0000.0000.0000.000
207A221VAL00.0180.00616.755-0.007-0.0070.0000.0000.0000.000
208A222ALA0-0.005-0.00112.9520.0050.0050.0000.0000.0000.000
209A223GLY00.0040.00111.828-0.003-0.0030.0000.0000.0000.000
210A224LEU00.0020.01212.722-0.026-0.0260.0000.0000.0000.000
211A225VAL00.000-0.01313.3620.0100.0100.0000.0000.0000.000
212A226ALA00.0090.0078.8440.0490.0490.0000.0000.0000.000
213A227PHE00.0010.00810.6460.0120.0120.0000.0000.0000.000
214A228LEU00.0000.00512.5510.0170.0170.0000.0000.0000.000
215A229ALA0-0.0080.01811.0960.0320.0320.0000.0000.0000.000
216A230GLY00.0270.01210.1580.0520.0520.0000.0000.0000.000
217A231ASP-1-0.831-0.90510.7930.0350.0350.0000.0000.0000.000
218A232GLU-1-0.908-0.94711.103-0.485-0.4850.0000.0000.0000.000
219A233SER0-0.034-0.01913.8820.0400.0400.0000.0000.0000.000
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