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

tag_button

FMODB ID: 49LVN

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 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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2419588.129633
FMO2-HF: Nuclear repulsion 2337999.321217
FMO2-HF: Total energy -81588.808416
FMO2-MP2: Total energy -81824.835727


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.
-10.273-2.3747.602-5.024-10.479-0.029
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 : 0.023 / q_NPA : 0.027
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].
3A11PHE00.0070.0092.587-3.8510.1001.848-2.158-3.642-0.011
4A12GLY00.0890.0364.3950.0240.063-0.001-0.010-0.0270.000
5A13GLN0-0.051-0.0328.0470.0420.0420.0000.0000.0000.000
6A14VAL00.0620.02211.4210.0060.0060.0000.0000.0000.000
7A15VAL00.0020.0066.9030.0360.0360.0000.0000.0000.000
8A16ALA00.0250.02310.0580.0270.0270.0000.0000.0000.000
9A17ASP-1-0.807-0.89411.246-0.283-0.2830.0000.0000.0000.000
10A18VAL0-0.0010.00112.7050.0330.0330.0000.0000.0000.000
11A19LEU0-0.005-0.0078.8870.0300.0300.0000.0000.0000.000
12A20CYS0-0.034-0.00913.4260.0280.0280.0000.0000.0000.000
13A21GLU-1-0.821-0.87516.494-0.163-0.1630.0000.0000.0000.000
14A22PHE00.015-0.00415.4650.0260.0260.0000.0000.0000.000
15A23LEU00.005-0.01014.6160.0210.0210.0000.0000.0000.000
16A24GLU-1-0.800-0.89118.571-0.140-0.1400.0000.0000.0000.000
17A25VAL0-0.047-0.03621.6070.0180.0180.0000.0000.0000.000
18A26ALA0-0.007-0.00120.0530.0140.0140.0000.0000.0000.000
19A27VAL00.0210.01721.3110.0120.0120.0000.0000.0000.000
20A28HIS0-0.004-0.00723.7570.0190.0190.0000.0000.0000.000
21A29LEU0-0.027-0.01525.3190.0100.0100.0000.0000.0000.000
22A30ILE0-0.0010.00322.4220.0080.0080.0000.0000.0000.000
23A31LEU0-0.021-0.01326.8050.0090.0090.0000.0000.0000.000
24A32TYR0-0.046-0.02329.4360.0080.0080.0000.0000.0000.000
25A33VAL0-0.032-0.02629.3950.0050.0050.0000.0000.0000.000
26A34ARG10.7630.84428.7600.0830.0830.0000.0000.0000.000
27A35GLU-1-0.896-0.93931.826-0.061-0.0610.0000.0000.0000.000
28A36VAL0-0.0260.00530.0340.0020.0020.0000.0000.0000.000
29A37TYR00.0220.00230.805-0.001-0.0010.0000.0000.0000.000
30A38PRO00.0070.01335.0930.0010.0010.0000.0000.0000.000
31A39VAL00.0740.00636.046-0.002-0.0020.0000.0000.0000.000
32A40GLY0-0.023-0.00737.448-0.001-0.0010.0000.0000.0000.000
33A41ILE0-0.0240.00334.0970.0010.0010.0000.0000.0000.000
34A42PHE0-0.027-0.00930.472-0.005-0.0050.0000.0000.0000.000
35A43GLN0-0.019-0.01033.5680.0030.0030.0000.0000.0000.000
36A44LYS10.9510.99032.6720.0680.0680.0000.0000.0000.000
37A45ARG10.9480.97327.8900.1160.1160.0000.0000.0000.000
38A46LYS10.8390.89328.4990.0920.0920.0000.0000.0000.000
39A47LYS10.8430.92922.6660.1650.1650.0000.0000.0000.000
40A48TYR00.026-0.02118.5160.0060.0060.0000.0000.0000.000
41A49ASN00.0210.01122.5520.0100.0100.0000.0000.0000.000
42A50VAL00.0240.03324.2190.0120.0120.0000.0000.0000.000
43A51PRO0-0.096-0.06027.064-0.002-0.0020.0000.0000.0000.000
44A52VAL00.0400.02525.322-0.003-0.0030.0000.0000.0000.000
45A53GLN00.0190.00628.7350.0050.0050.0000.0000.0000.000
46A54MET0-0.026-0.00225.231-0.006-0.0060.0000.0000.0000.000
47A55SER00.0520.02329.9470.0100.0100.0000.0000.0000.000
48A56CYS0-0.059-0.03131.700-0.003-0.0030.0000.0000.0000.000
49A57HIS00.0290.02934.3440.0000.0000.0000.0000.0000.000
50A58PRO00.013-0.01033.209-0.006-0.0060.0000.0000.0000.000
51A59GLU-1-0.907-0.94432.270-0.096-0.0960.0000.0000.0000.000
52A60LEU00.0070.01229.475-0.007-0.0070.0000.0000.0000.000
53A61ASN0-0.022-0.03528.642-0.007-0.0070.0000.0000.0000.000
54A62GLN0-0.046-0.02227.421-0.005-0.0050.0000.0000.0000.000
55A63TYR00.0650.03825.985-0.009-0.0090.0000.0000.0000.000
56A64ILE0-0.0170.00323.409-0.014-0.0140.0000.0000.0000.000
57A65GLN0-0.020-0.01522.874-0.014-0.0140.0000.0000.0000.000
58A66ASP-1-0.830-0.91222.385-0.180-0.1800.0000.0000.0000.000
59A67THR0-0.015-0.01420.542-0.018-0.0180.0000.0000.0000.000
60A68LEU0-0.019-0.01617.742-0.027-0.0270.0000.0000.0000.000
61A69HIS0-0.033-0.01917.592-0.045-0.0450.0000.0000.0000.000
62A70CYS0-0.031-0.00218.244-0.020-0.0200.0000.0000.0000.000
63A71VAL00.0290.01414.261-0.034-0.0340.0000.0000.0000.000
64A72LYS10.9010.94413.8360.2400.2400.0000.0000.0000.000
65A73PRO00.0210.00712.358-0.093-0.0930.0000.0000.0000.000
66A74LEU0-0.0030.01511.726-0.113-0.1130.0000.0000.0000.000
67A75LEU00.0050.0009.040-0.193-0.1930.0000.0000.0000.000
68A76GLU-1-0.863-0.9187.665-0.902-0.9020.0000.0000.0000.000
69A77LYS10.7940.8776.6520.7770.7770.0000.0000.0000.000
70A78ASN0-0.064-0.0252.782-1.1760.2430.472-0.639-1.252-0.006
71A79ASP-1-0.718-0.8335.656-1.170-1.1700.0000.0000.0000.000
72A80VAL0-0.043-0.0208.4530.1800.1800.0000.0000.0000.000
73A81GLU-1-0.898-0.9268.733-0.289-0.2890.0000.0000.0000.000
74A82LYS10.8220.88210.5960.2220.2220.0000.0000.0000.000
75A83VAL0-0.0030.01413.474-0.010-0.0100.0000.0000.0000.000
76A84VAL0-0.012-0.01415.7810.0160.0160.0000.0000.0000.000
77A85VAL00.0190.02019.3280.0020.0020.0000.0000.0000.000
78A86VAL0-0.0040.00522.4600.0090.0090.0000.0000.0000.000
79A87ILE00.004-0.00325.1820.0000.0000.0000.0000.0000.000
80A88LEU00.0170.01228.7500.0030.0030.0000.0000.0000.000
81A89ASP-1-0.691-0.86131.599-0.062-0.0620.0000.0000.0000.000
82A90LYS10.9610.98835.2700.0500.0500.0000.0000.0000.000
83A91GLU-1-0.955-0.97438.154-0.055-0.0550.0000.0000.0000.000
84A92HIS0-0.005-0.01033.962-0.002-0.0020.0000.0000.0000.000
85A93ARG10.8610.92532.9750.0530.0530.0000.0000.0000.000
86A94PRO00.0340.02528.3220.0010.0010.0000.0000.0000.000
87A95VAL0-0.018-0.01030.4430.0070.0070.0000.0000.0000.000
88A96GLU-1-0.719-0.83827.371-0.082-0.0820.0000.0000.0000.000
89A97LYS10.8550.93223.1910.0980.0980.0000.0000.0000.000
90A98PHE00.0270.01521.6480.0030.0030.0000.0000.0000.000
91A99VAL0-0.017-0.00116.757-0.019-0.0190.0000.0000.0000.000
92A100PHE00.022-0.00714.8320.0080.0080.0000.0000.0000.000
93A101GLU-1-0.811-0.88211.928-0.194-0.1940.0000.0000.0000.000
94A102ILE00.0110.0007.2570.0020.0020.0000.0000.0000.000
95A103THR00.0090.0076.613-0.022-0.0220.0000.0000.0000.000
96A104GLN00.0340.0212.327-2.990-1.7935.266-1.867-4.596-0.010
97A105PRO0-0.0380.0034.044-0.0380.2320.001-0.044-0.2280.000
98A106PRO00.0360.0144.527-0.395-0.222-0.001-0.010-0.1620.000
99A107LEU00.0310.0166.102-0.151-0.1510.0000.0000.0000.000
100A108LEU0-0.022-0.0117.8110.0830.0830.0000.0000.0000.000
101A109SER0-0.021-0.02911.261-0.052-0.0520.0000.0000.0000.000
102A110ILE0-0.033-0.0086.848-0.003-0.0030.0000.0000.0000.000
103A111SER00.0250.00611.0280.0110.0110.0000.0000.0000.000
104A112SER0-0.065-0.0219.9500.0260.0260.0000.0000.0000.000
105A113ASP-1-0.798-0.89812.660-0.112-0.1120.0000.0000.0000.000
106A114SER0-0.047-0.03112.171-0.042-0.0420.0000.0000.0000.000
107A115LEU0-0.027-0.0347.9460.0120.0120.0000.0000.0000.000
108A116LEU00.004-0.02311.1180.0220.0220.0000.0000.0000.000
109A117SER0-0.019-0.00513.5990.0280.0280.0000.0000.0000.000
110A118HIS0-0.043-0.01915.6070.0210.0210.0000.0000.0000.000
111A119VAL00.0170.02514.404-0.004-0.0040.0000.0000.0000.000
112A120GLU-1-0.883-0.95416.371-0.149-0.1490.0000.0000.0000.000
113A121GLN00.0210.00919.204-0.004-0.0040.0000.0000.0000.000
114A122LEU0-0.039-0.01513.0160.0050.0050.0000.0000.0000.000
115A123LEU00.0110.01213.872-0.001-0.0010.0000.0000.0000.000
116A124ALA00.0280.00917.5360.0090.0090.0000.0000.0000.000
117A125ALA0-0.013-0.01119.5490.0100.0100.0000.0000.0000.000
118A126PHE0-0.022-0.01614.6230.0080.0080.0000.0000.0000.000
119A127ILE00.0260.01820.2660.0090.0090.0000.0000.0000.000
120A128LEU0-0.0040.00222.8650.0090.0090.0000.0000.0000.000
121A129LYS10.8550.91422.8780.0940.0940.0000.0000.0000.000
122A130ILE00.0360.02021.2010.0040.0040.0000.0000.0000.000
123A131SER0-0.054-0.04725.3330.0060.0060.0000.0000.0000.000
124A132VAL0-0.0360.00028.2220.0050.0050.0000.0000.0000.000
125A133CYS0-0.078-0.02726.6200.0030.0030.0000.0000.0000.000
126A134ASP-1-0.823-0.93028.676-0.068-0.0680.0000.0000.0000.000
127A135ALA0-0.044-0.01232.2180.0040.0040.0000.0000.0000.000
128A136VAL0-0.127-0.06628.5460.0040.0040.0000.0000.0000.000
129A137LEU0-0.029-0.00627.408-0.002-0.0020.0000.0000.0000.000
130A138ASP-1-0.868-0.92531.704-0.048-0.0480.0000.0000.0000.000
131A139HIS0-0.080-0.04133.935-0.004-0.0040.0000.0000.0000.000
132A140ASN0-0.022-0.01731.0250.0030.0030.0000.0000.0000.000
133A141PRO00.005-0.00835.4000.0020.0020.0000.0000.0000.000
134A142PRO00.0320.02537.507-0.003-0.0030.0000.0000.0000.000
135A143GLY0-0.029-0.03138.8980.0020.0020.0000.0000.0000.000
136A144CYS0-0.055-0.00633.3650.0000.0000.0000.0000.0000.000
137A145THR0-0.0100.00132.831-0.002-0.0020.0000.0000.0000.000
138A146PHE0-0.001-0.02125.401-0.001-0.0010.0000.0000.0000.000
139A147THR00.0420.03325.286-0.003-0.0030.0000.0000.0000.000
140A148VAL0-0.013-0.01719.918-0.003-0.0030.0000.0000.0000.000
141A149LEU0-0.0010.01820.508-0.004-0.0040.0000.0000.0000.000
142A150VAL0-0.006-0.01914.907-0.017-0.0170.0000.0000.0000.000
143A151HIS00.0310.02915.0750.0040.0040.0000.0000.0000.000
144A152THR00.011-0.02012.415-0.034-0.0340.0000.0000.0000.000
145A153ARG10.7880.8796.1360.7930.7930.0000.0000.0000.000
146A154GLU-1-0.849-0.91510.089-0.446-0.4460.0000.0000.0000.000
147A155ALA00.0060.00812.017-0.016-0.0160.0000.0000.0000.000
148A156ALA00.0110.00913.3100.0400.0400.0000.0000.0000.000
149A157THR0-0.028-0.04115.334-0.018-0.0180.0000.0000.0000.000
150A158ARG10.8210.8828.8670.8200.8200.0000.0000.0000.000
151A159ASN0-0.016-0.01112.406-0.087-0.0870.0000.0000.0000.000
152A160MET00.0290.00615.4970.0140.0140.0000.0000.0000.000
153A161GLU-1-0.880-0.92817.926-0.257-0.2570.0000.0000.0000.000
154A162LYS10.7680.87910.8790.8230.8230.0000.0000.0000.000
155A163ILE0-0.0140.01417.6710.0040.0040.0000.0000.0000.000
156A164GLN00.0100.01519.1060.0110.0110.0000.0000.0000.000
157A165VAL0-0.063-0.03219.6340.0190.0190.0000.0000.0000.000
158A166ILE0-0.024-0.00722.6620.0110.0110.0000.0000.0000.000
159A167LYS10.9240.95525.7020.1230.1230.0000.0000.0000.000
160A168ASP-1-0.896-0.95529.024-0.117-0.1170.0000.0000.0000.000
161A169PHE0-0.031-0.00624.1560.0060.0060.0000.0000.0000.000
162A170PRO0-0.036-0.01125.503-0.014-0.0140.0000.0000.0000.000
163A171TRP00.029-0.00920.263-0.003-0.0030.0000.0000.0000.000
164A172ILE0-0.016-0.01824.5110.0060.0060.0000.0000.0000.000
165A173LEU0-0.046-0.02720.892-0.015-0.0150.0000.0000.0000.000
166A174ALA00.0260.02223.3150.0100.0100.0000.0000.0000.000
167A175ASP-1-0.890-0.95725.112-0.090-0.0900.0000.0000.0000.000
168A176GLU-1-0.908-0.95926.821-0.082-0.0820.0000.0000.0000.000
169A177GLN0-0.110-0.06228.2550.0080.0080.0000.0000.0000.000
170A178ASP-1-0.855-0.91526.179-0.112-0.1120.0000.0000.0000.000
171A179VAL0-0.039-0.02523.168-0.008-0.0080.0000.0000.0000.000
172A180HIS00.0040.00725.685-0.001-0.0010.0000.0000.0000.000
173A181MET0-0.070-0.02527.410-0.002-0.0020.0000.0000.0000.000
174A182HIS00.0090.00030.0010.0020.0020.0000.0000.0000.000
175A183ASP-1-0.836-0.89732.196-0.042-0.0420.0000.0000.0000.000
176A184PRO00.0470.02727.387-0.001-0.0010.0000.0000.0000.000
177A185ARG10.7810.86729.2220.0460.0460.0000.0000.0000.000
178A186LEU00.0110.00422.140-0.006-0.0060.0000.0000.0000.000
179A187ILE00.0190.01625.2580.0060.0060.0000.0000.0000.000
180A188PRO0-0.014-0.01521.385-0.011-0.0110.0000.0000.0000.000
181A189LEU0-0.0270.00921.3750.0060.0060.0000.0000.0000.000
182A190LYS10.8840.94617.6180.1360.1360.0000.0000.0000.000
183A191THR00.0220.01614.410-0.015-0.0150.0000.0000.0000.000
184A192MET0-0.060-0.01110.2870.0300.0300.0000.0000.0000.000
185A193THR0-0.035-0.0489.390-0.008-0.0080.0000.0000.0000.000
186A194SER00.0050.0018.9020.0200.0200.0000.0000.0000.000
187A195ASP-1-0.822-0.9037.882-0.324-0.3240.0000.0000.0000.000
188A196ILE0-0.0070.0003.793-0.323-0.0260.002-0.036-0.2630.000
189A197LEU0-0.001-0.0033.537-0.906-0.3530.015-0.260-0.309-0.002
190A198LYS10.9550.9926.1610.2390.2390.0000.0000.0000.000
191A199MET0-0.0210.0008.864-0.046-0.0460.0000.0000.0000.000
192A200GLN0-0.029-0.03911.4560.0500.0500.0000.0000.0000.000
193A201LEU0-0.0060.02314.760-0.010-0.0100.0000.0000.0000.000
194A202TYR0-0.033-0.03217.1980.0150.0150.0000.0000.0000.000
195A203VAL00.0310.02320.566-0.012-0.0120.0000.0000.0000.000
196A204GLU-1-0.811-0.89521.842-0.100-0.1000.0000.0000.0000.000
197A205GLU-1-0.804-0.91825.355-0.071-0.0710.0000.0000.0000.000
198A206ARG10.7670.85329.0900.0660.0660.0000.0000.0000.000
199A207ALA0-0.020-0.00132.0530.0010.0010.0000.0000.0000.000
200A208HIS0-0.073-0.03334.5640.0060.0060.0000.0000.0000.000
201A209LYS10.8720.95631.4680.0690.0690.0000.0000.0000.000