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: QYNGY

Calculation Name: 4GK0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4GK0

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UI95

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 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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2415502.091372
FMO2-HF: Nuclear repulsion 2333915.53612
FMO2-HF: Total energy -81586.555252
FMO2-MP2: Total energy -81822.443739


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:9:LEU)


Summations of interaction energy for fragment #1(A:9:LEU)
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.
-3.348-8.67125.908-7.105-13.481-0.033
Interaction energy analysis for fragmet #1(A:9:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.021 / q_NPA : -0.014
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].
3A11PHE00.0000.0152.440-3.746-0.5642.189-1.758-3.613-0.023
4A12GLY00.0640.0224.5440.3440.394-0.001-0.011-0.0380.000
5A13GLN00.0550.0057.779-0.024-0.0240.0000.0000.0000.000
6A14VAL00.0610.04411.355-0.021-0.0210.0000.0000.0000.000
7A15VAL0-0.0240.0016.8470.0090.0090.0000.0000.0000.000
8A16ALA00.0200.0179.4030.0060.0060.0000.0000.0000.000
9A17ASP-1-0.857-0.94610.575-0.198-0.1980.0000.0000.0000.000
10A18VAL0-0.031-0.02012.2790.0260.0260.0000.0000.0000.000
11A19LEU0-0.022-0.0238.1600.0330.0330.0000.0000.0000.000
12A20CYS0-0.035-0.00212.8220.0320.0320.0000.0000.0000.000
13A21GLU-1-0.925-0.95515.596-0.168-0.1680.0000.0000.0000.000
14A22PHE0-0.037-0.02514.7700.0200.0200.0000.0000.0000.000
15A23LEU00.003-0.01913.9110.0210.0210.0000.0000.0000.000
16A24GLU-1-0.893-0.94317.734-0.127-0.1270.0000.0000.0000.000
17A25VAL0-0.071-0.05220.9640.0200.0200.0000.0000.0000.000
18A26ALA00.0070.01119.5550.0140.0140.0000.0000.0000.000
19A27VAL00.0240.01420.6730.0110.0110.0000.0000.0000.000
20A28HIS0-0.0050.00023.0340.0170.0170.0000.0000.0000.000
21A29LEU0-0.031-0.01224.5410.0090.0090.0000.0000.0000.000
22A30ILE00.0070.00721.9820.0080.0080.0000.0000.0000.000
23A31LEU00.0040.00126.2500.0090.0090.0000.0000.0000.000
24A32TYR0-0.038-0.02028.9320.0090.0090.0000.0000.0000.000
25A33VAL0-0.027-0.02328.7610.0050.0050.0000.0000.0000.000
26A34ARG10.7520.86428.4090.1060.1060.0000.0000.0000.000
27A35GLU-1-0.902-0.94831.443-0.071-0.0710.0000.0000.0000.000
28A36VAL0-0.0440.00229.7450.0030.0030.0000.0000.0000.000
29A37TYR0-0.008-0.00930.4970.0070.0070.0000.0000.0000.000
30A38PRO00.0370.01834.624-0.001-0.0010.0000.0000.0000.000
31A39VAL00.0670.00335.941-0.001-0.0010.0000.0000.0000.000
32A40GLY0-0.029-0.01237.028-0.001-0.0010.0000.0000.0000.000
33A41ILE0-0.0080.01133.4220.0020.0020.0000.0000.0000.000
34A42PHE0-0.0240.00229.854-0.003-0.0030.0000.0000.0000.000
35A43GLN0-0.011-0.00433.0610.0060.0060.0000.0000.0000.000
36A44LYS10.9420.98232.0590.0840.0840.0000.0000.0000.000
37A45ARG10.9840.97828.0120.1050.1050.0000.0000.0000.000
38A46LYS10.9160.93628.2430.1040.1040.0000.0000.0000.000
39A47LYS10.9511.00122.7830.1420.1420.0000.0000.0000.000
40A48TYR00.1270.06217.9250.0060.0060.0000.0000.0000.000
41A49ASN0-0.0030.00622.7290.0110.0110.0000.0000.0000.000
42A50VAL00.003-0.00824.2090.0100.0100.0000.0000.0000.000
43A51PRO0-0.133-0.06527.0420.0010.0010.0000.0000.0000.000
44A52VAL00.0770.04724.891-0.003-0.0030.0000.0000.0000.000
45A53GLN00.011-0.00228.2410.0100.0100.0000.0000.0000.000
46A54MET0-0.025-0.00725.048-0.007-0.0070.0000.0000.0000.000
47A55SER00.0360.01229.4560.0090.0090.0000.0000.0000.000
48A56CYS0-0.060-0.03131.255-0.002-0.0020.0000.0000.0000.000
49A57HIS00.0080.01433.5340.0020.0020.0000.0000.0000.000
50A58PRO00.0250.00032.539-0.004-0.0040.0000.0000.0000.000
51A59GLU-1-0.901-0.94531.798-0.066-0.0660.0000.0000.0000.000
52A60LEU00.0190.01529.451-0.004-0.0040.0000.0000.0000.000
53A61ASN0-0.033-0.04228.202-0.008-0.0080.0000.0000.0000.000
54A62GLN00.0040.03026.936-0.004-0.0040.0000.0000.0000.000
55A63TYR00.0670.04125.558-0.008-0.0080.0000.0000.0000.000
56A64ILE0-0.030-0.00222.966-0.009-0.0090.0000.0000.0000.000
57A65GLN00.000-0.01022.417-0.008-0.0080.0000.0000.0000.000
58A66ASP-1-0.866-0.94121.954-0.104-0.1040.0000.0000.0000.000
59A67THR0-0.031-0.03419.975-0.008-0.0080.0000.0000.0000.000
60A68LEU0-0.016-0.00917.124-0.016-0.0160.0000.0000.0000.000
61A69HIS0-0.049-0.01717.036-0.036-0.0360.0000.0000.0000.000
62A70CYS0-0.0080.01417.7710.0000.0000.0000.0000.0000.000
63A71VAL00.0030.00213.223-0.011-0.0110.0000.0000.0000.000
64A72LYS10.9790.99113.0710.1710.1710.0000.0000.0000.000
65A73PRO00.0080.00811.713-0.068-0.0680.0000.0000.0000.000
66A74LEU00.001-0.00911.016-0.028-0.0280.0000.0000.0000.000
67A75LEU0-0.0170.0028.362-0.138-0.1380.0000.0000.0000.000
68A76GLU-1-0.901-0.9516.778-0.449-0.4490.0000.0000.0000.000
69A77LYS10.8240.9266.608-0.050-0.0500.0000.0000.0000.000
70A78ASN0-0.040-0.0202.399-0.421-0.4722.626-0.604-1.971-0.006
71A79ASP-1-0.792-0.9055.178-0.614-0.588-0.001-0.005-0.0200.000
72A80VAL0-0.043-0.0328.0210.1320.1320.0000.0000.0000.000
73A81GLU-1-0.952-0.9608.489-0.351-0.3510.0000.0000.0000.000
74A82LYS10.9360.96810.0490.2310.2310.0000.0000.0000.000
75A83VAL00.0040.01913.1380.0110.0110.0000.0000.0000.000
76A84VAL0-0.010-0.01615.402-0.001-0.0010.0000.0000.0000.000
77A85VAL00.0050.01918.8480.0100.0100.0000.0000.0000.000
78A86VAL0-0.006-0.00722.0560.0010.0010.0000.0000.0000.000
79A87ILE00.0060.00624.7750.0040.0040.0000.0000.0000.000
80A88LEU00.004-0.00128.3100.0000.0000.0000.0000.0000.000
81A89ASP-1-0.737-0.87931.043-0.068-0.0680.0000.0000.0000.000
82A90LYS10.9700.97234.6460.0520.0520.0000.0000.0000.000
83A91GLU-1-1.004-1.00137.650-0.055-0.0550.0000.0000.0000.000
84A92HIS0-0.005-0.01133.464-0.001-0.0010.0000.0000.0000.000
85A93ARG10.9370.98232.5900.0610.0610.0000.0000.0000.000
86A94PRO00.0340.02027.700-0.001-0.0010.0000.0000.0000.000
87A95VAL0-0.018-0.00729.8670.0040.0040.0000.0000.0000.000
88A96GLU-1-0.717-0.84827.173-0.107-0.1070.0000.0000.0000.000
89A97LYS10.8620.93422.1770.1300.1300.0000.0000.0000.000
90A98PHE00.0210.00321.231-0.004-0.0040.0000.0000.0000.000
91A99VAL0-0.0050.00416.091-0.009-0.0090.0000.0000.0000.000
92A100PHE0-0.011-0.01713.958-0.005-0.0050.0000.0000.0000.000
93A101GLU-1-0.869-0.92211.424-0.325-0.3250.0000.0000.0000.000
94A102ILE00.009-0.0056.607-0.032-0.0320.0000.0000.0000.000
95A103THR00.006-0.0076.3200.0310.0310.0000.0000.0000.000
96A104GLN0-0.012-0.0092.0403.461-6.05821.083-4.577-6.987-0.004
97A105PRO0-0.0260.0003.700-0.1550.1520.0090.002-0.3180.001
98A106PRO00.0310.0014.459-0.612-0.444-0.001-0.010-0.1570.000
99A107LEU0-0.0010.0076.2840.0640.0640.0000.0000.0000.000
100A108LEU00.0200.0018.4470.0880.0880.0000.0000.0000.000
101A109SER0-0.016-0.01311.885-0.004-0.0040.0000.0000.0000.000
102A110ILE0-0.022-0.0018.3470.0100.0100.0000.0000.0000.000
103A111SER0-0.008-0.01511.9200.0300.0300.0000.0000.0000.000
104A112SER0-0.023-0.00811.2290.0440.0440.0000.0000.0000.000
105A113ASP-1-0.868-0.90913.264-0.252-0.2520.0000.0000.0000.000
106A114SER00.0360.03011.714-0.063-0.0630.0000.0000.0000.000
107A115LEU00.011-0.0228.5080.0380.0380.0000.0000.0000.000
108A116LEU00.011-0.02010.9290.0460.0460.0000.0000.0000.000
109A117SER0-0.032-0.02413.7080.0490.0490.0000.0000.0000.000
110A118HIS00.0310.01615.5680.0350.0350.0000.0000.0000.000
111A119VAL00.0090.03114.439-0.004-0.0040.0000.0000.0000.000
112A120GLU-1-0.860-0.94216.195-0.209-0.2090.0000.0000.0000.000
113A121GLN0-0.032-0.01919.3340.0110.0110.0000.0000.0000.000
114A122LEU0-0.008-0.01313.1760.0010.0010.0000.0000.0000.000
115A123LEU0-0.0020.00013.418-0.004-0.0040.0000.0000.0000.000
116A124ALA00.0310.01917.2090.0160.0160.0000.0000.0000.000
117A125ALA0-0.033-0.01819.0400.0160.0160.0000.0000.0000.000
118A126PHE00.008-0.00614.2790.0120.0120.0000.0000.0000.000
119A127ILE00.0190.01519.7430.0150.0150.0000.0000.0000.000
120A128LEU0-0.019-0.01222.4430.0140.0140.0000.0000.0000.000
121A129LYS10.8870.94421.9450.1630.1630.0000.0000.0000.000
122A130ILE00.0430.01820.7120.0070.0070.0000.0000.0000.000
123A131SER0-0.070-0.03924.7870.0100.0100.0000.0000.0000.000
124A132VAL0-0.028-0.01127.8060.0070.0070.0000.0000.0000.000
125A133CYS0-0.050-0.01226.3020.0030.0030.0000.0000.0000.000
126A134ASP-1-0.828-0.92828.351-0.096-0.0960.0000.0000.0000.000
127A135ALA0-0.060-0.02431.6820.0050.0050.0000.0000.0000.000
128A136VAL0-0.091-0.04727.9580.0020.0020.0000.0000.0000.000
129A137LEU0-0.067-0.01227.308-0.003-0.0030.0000.0000.0000.000
130A138ASP-1-0.874-0.92131.342-0.076-0.0760.0000.0000.0000.000
131A139HIS0-0.082-0.05633.555-0.005-0.0050.0000.0000.0000.000
132A140ASN0-0.027-0.03030.6990.0010.0010.0000.0000.0000.000
133A141PRO00.001-0.00235.0020.0030.0030.0000.0000.0000.000
134A142PRO00.0220.00336.962-0.002-0.0020.0000.0000.0000.000
135A143GLY0-0.039-0.03938.1480.0020.0020.0000.0000.0000.000
136A144CYS0-0.0430.00432.5870.0000.0000.0000.0000.0000.000
137A145THR00.0120.01532.071-0.001-0.0010.0000.0000.0000.000
138A146PHE0-0.010-0.02624.958-0.004-0.0040.0000.0000.0000.000
139A147THR00.0270.03025.2100.0020.0020.0000.0000.0000.000
140A148VAL00.0150.00219.658-0.008-0.0080.0000.0000.0000.000
141A149LEU00.0010.00720.0420.0060.0060.0000.0000.0000.000
142A150VAL00.006-0.00214.194-0.022-0.0220.0000.0000.0000.000
143A151HIS00.0070.01014.3010.0170.0170.0000.0000.0000.000
144A152THR0-0.032-0.04712.138-0.037-0.0370.0000.0000.0000.000
145A153ARG10.8400.9395.2070.6930.6930.0000.0000.0000.000
146A154GLU-1-0.896-0.9469.374-0.208-0.2080.0000.0000.0000.000
147A155ALA00.0040.01312.329-0.004-0.0040.0000.0000.0000.000
148A156ALA0-0.038-0.02613.0670.0340.0340.0000.0000.0000.000
149A157THR00.0740.02315.066-0.017-0.0170.0000.0000.0000.000
150A158ARG10.8870.9358.5980.2440.2440.0000.0000.0000.000
151A159ASN00.0000.00712.628-0.032-0.0320.0000.0000.0000.000
152A160MET00.0390.01115.243-0.002-0.0020.0000.0000.0000.000
153A161GLU-1-0.932-0.96917.8500.0170.0170.0000.0000.0000.000
154A162LYS10.8880.93411.2070.0870.0870.0000.0000.0000.000
155A163ILE0-0.0020.01716.703-0.007-0.0070.0000.0000.0000.000
156A164GLN0-0.0160.01818.307-0.002-0.0020.0000.0000.0000.000
157A165VAL0-0.023-0.02719.5970.0150.0150.0000.0000.0000.000
158A166ILE0-0.0120.00622.2780.0080.0080.0000.0000.0000.000
159A167LYS10.9410.96025.2280.0280.0280.0000.0000.0000.000
160A168ASP-1-0.901-0.96028.352-0.050-0.0500.0000.0000.0000.000
161A169PHE0-0.077-0.02623.362-0.001-0.0010.0000.0000.0000.000
162A170PRO00.0190.00624.742-0.007-0.0070.0000.0000.0000.000
163A171TRP0-0.033-0.02119.401-0.013-0.0130.0000.0000.0000.000
164A172ILE0-0.008-0.01423.9360.0110.0110.0000.0000.0000.000
165A173LEU0-0.066-0.03920.865-0.011-0.0110.0000.0000.0000.000
166A174ALA00.0300.02422.7300.0060.0060.0000.0000.0000.000
167A175ASP-1-0.888-0.95224.437-0.071-0.0710.0000.0000.0000.000
168A176GLU-1-0.894-0.96725.702-0.091-0.0910.0000.0000.0000.000
169A177GLN0-0.085-0.02427.5810.0020.0020.0000.0000.0000.000
170A178ASP-1-0.880-0.93125.698-0.090-0.0900.0000.0000.0000.000
171A179VAL0-0.034-0.02922.699-0.011-0.0110.0000.0000.0000.000
172A180HIS0-0.0060.01825.347-0.009-0.0090.0000.0000.0000.000
173A181MET0-0.039-0.01226.4200.0020.0020.0000.0000.0000.000
174A182HIS0-0.024-0.01928.887-0.001-0.0010.0000.0000.0000.000
175A183ASP-1-0.893-0.94631.523-0.074-0.0740.0000.0000.0000.000
176A184PRO00.0120.00826.6380.0000.0000.0000.0000.0000.000
177A185ARG10.8700.92728.5110.0840.0840.0000.0000.0000.000
178A186LEU00.0120.00821.350-0.005-0.0050.0000.0000.0000.000
179A187ILE00.0110.00924.6560.0040.0040.0000.0000.0000.000
180A188PRO0-0.013-0.01521.008-0.011-0.0110.0000.0000.0000.000
181A189LEU0-0.0310.00520.6860.0080.0080.0000.0000.0000.000
182A190LYS10.8890.93017.6820.2230.2230.0000.0000.0000.000
183A191THR00.0170.01314.081-0.010-0.0100.0000.0000.0000.000
184A192MET0-0.078-0.02110.9060.0220.0220.0000.0000.0000.000
185A193THR0-0.003-0.0169.696-0.048-0.0480.0000.0000.0000.000
186A194SER0-0.027-0.0488.5710.0220.0220.0000.0000.0000.000
187A195ASP-1-0.897-0.9537.991-0.566-0.5660.0000.0000.0000.000
188A196ILE0-0.034-0.0084.561-0.234-0.076-0.001-0.007-0.1500.000
189A197LEU00.0180.0053.693-1.133-0.7770.005-0.135-0.227-0.001
190A198LYS10.9501.0125.9910.5880.5880.0000.0000.0000.000
191A199MET0-0.0130.0128.3730.0030.0030.0000.0000.0000.000
192A200GLN0-0.051-0.03610.8700.0470.0470.0000.0000.0000.000
193A201LEU00.0060.01614.229-0.004-0.0040.0000.0000.0000.000
194A202TYR0-0.010-0.02216.2450.0060.0060.0000.0000.0000.000
195A203VAL00.0350.02920.185-0.005-0.0050.0000.0000.0000.000
196A204GLU-1-0.912-0.95722.115-0.143-0.1430.0000.0000.0000.000
197A205GLU-1-0.821-0.92824.899-0.097-0.0970.0000.0000.0000.000
198A206ARG10.8300.90428.6050.0780.0780.0000.0000.0000.000
199A207ALA00.0000.01531.4630.0010.0010.0000.0000.0000.000
200A208HIS0-0.035-0.01233.9500.0050.0050.0000.0000.0000.000
201A209LYS10.8360.94230.9160.0970.0970.0000.0000.0000.000