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: 17ZKZ

Calculation Name: 2FUK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FUK

Chain ID: A

ChEMBL ID:

UniProt ID: B0RM26

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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2589080.446667
FMO2-HF: Nuclear repulsion 2506607.960116
FMO2-HF: Total energy -82472.486551
FMO2-MP2: Total energy -82716.727808


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:3:ASN)


Summations of interaction energy for fragment #1(A:3:ASN)
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.
-29.987-30.84611.738-5.749-5.129-0.067
Interaction energy analysis for fragmet #1(A:3:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.045 / q_NPA : -0.045
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].
3A5LEU00.0150.0043.9060.7071.662-0.009-0.429-0.5160.002
4A6PHE00.027-0.0016.5450.0020.0020.0000.0000.0000.000
5A7PRO0-0.049-0.0059.2680.0490.0490.0000.0000.0000.000
6A8THR0-0.010-0.02612.2950.0420.0420.0000.0000.0000.000
7A9GLU-1-0.881-0.93415.568-0.101-0.1010.0000.0000.0000.000
8A10SER0-0.036-0.02715.906-0.038-0.0380.0000.0000.0000.000
9A11ALA0-0.026-0.00613.8290.0020.0020.0000.0000.0000.000
10A12ALA0-0.029-0.01813.2660.0020.0020.0000.0000.0000.000
11A13LEU0-0.028-0.0107.0120.0050.0050.0000.0000.0000.000
12A14THR0-0.007-0.0077.0960.2230.2230.0000.0000.0000.000
13A15LEU00.0040.0044.279-0.520-0.423-0.001-0.023-0.0730.000
14A16ASP-1-0.885-0.9301.773-29.964-32.01511.750-5.281-4.418-0.069
15A17GLY00.0400.0195.0241.2021.226-0.001-0.005-0.0180.000
16A18PRO0-0.020-0.0138.651-0.266-0.2660.0000.0000.0000.000
17A19VAL0-0.046-0.01711.1520.1060.1060.0000.0000.0000.000
18A20GLY0-0.010-0.0058.8350.1320.1320.0000.0000.0000.000
19A21PRO0-0.025-0.0197.069-0.075-0.0750.0000.0000.0000.000
20A22LEU00.0440.0348.1950.5330.5330.0000.0000.0000.000
21A23ASP-1-0.754-0.8329.212-1.140-1.1400.0000.0000.0000.000
22A24VAL0-0.008-0.0259.3380.1490.1490.0000.0000.0000.000
23A25ALA0-0.023-0.01411.831-0.020-0.0200.0000.0000.0000.000
24A26VAL00.0240.01211.9040.0300.0300.0000.0000.0000.000
25A27ASP-1-0.808-0.87215.197-0.285-0.2850.0000.0000.0000.000
26A28LEU00.0330.01817.2320.0180.0180.0000.0000.0000.000
27A29PRO0-0.015-0.00519.791-0.008-0.0080.0000.0000.0000.000
28A30GLU-1-0.871-0.92322.886-0.121-0.1210.0000.0000.0000.000
29A31PRO00.004-0.01226.0620.0100.0100.0000.0000.0000.000
30A32ASP-1-0.956-0.97227.934-0.040-0.0400.0000.0000.0000.000
31A33VAL0-0.057-0.01028.1060.0040.0040.0000.0000.0000.000
32A34ALA0-0.037-0.02228.0450.0030.0030.0000.0000.0000.000
33A35VAL00.0050.00022.247-0.005-0.0050.0000.0000.0000.000
34A36GLN0-0.013-0.01423.5610.0110.0110.0000.0000.0000.000
35A37PRO0-0.0030.00921.178-0.002-0.0020.0000.0000.0000.000
36A38VAL0-0.011-0.01020.3180.0030.0030.0000.0000.0000.000
37A39THR00.0060.00314.368-0.012-0.0120.0000.0000.0000.000
38A40ALA0-0.018-0.00517.7300.0050.0050.0000.0000.0000.000
39A41ILE00.0190.01414.334-0.019-0.0190.0000.0000.0000.000
40A42VAL0-0.059-0.02817.9090.0170.0170.0000.0000.0000.000
41A43CYS0-0.0050.01219.404-0.043-0.0430.0000.0000.0000.000
42A44HIS0-0.031-0.01618.983-0.002-0.0020.0000.0000.0000.000
43A45PRO0-0.036-0.01922.459-0.002-0.0020.0000.0000.0000.000
44A46LEU00.0630.02624.004-0.027-0.0270.0000.0000.0000.000
45A47SER00.0350.00620.7380.0160.0160.0000.0000.0000.000
46A48THR0-0.021-0.01323.453-0.017-0.0170.0000.0000.0000.000
47A49GLU-1-0.866-0.91626.562-0.235-0.2350.0000.0000.0000.000
48A50GLY0-0.036-0.00626.562-0.017-0.0170.0000.0000.0000.000
49A51GLY0-0.054-0.02124.1010.0160.0160.0000.0000.0000.000
50A52SER00.0490.01420.174-0.026-0.0260.0000.0000.0000.000
51A53MET00.0100.00514.2070.0740.0740.0000.0000.0000.000
52A54HIS00.0140.01018.7350.0580.0580.0000.0000.0000.000
53A55ASN0-0.031-0.01222.3030.0460.0460.0000.0000.0000.000
54A56LYS10.9750.97125.1890.2000.2000.0000.0000.0000.000
55A57VAL00.0250.02627.9500.0110.0110.0000.0000.0000.000
56A58VAL00.0200.02421.3560.0120.0120.0000.0000.0000.000
57A59THR00.008-0.00922.4510.0130.0130.0000.0000.0000.000
58A60MET0-0.069-0.02124.4470.0110.0110.0000.0000.0000.000
59A61ALA00.0270.00625.6800.0140.0140.0000.0000.0000.000
60A62ALA00.0370.02121.9080.0100.0100.0000.0000.0000.000
61A63ARG10.9420.96523.7570.1580.1580.0000.0000.0000.000
62A64ALA0-0.024-0.02126.2780.0130.0130.0000.0000.0000.000
63A65LEU00.0280.01723.1850.0130.0130.0000.0000.0000.000
64A66ARG10.8300.90622.3290.1570.1570.0000.0000.0000.000
65A67GLU-1-0.805-0.89224.698-0.093-0.0930.0000.0000.0000.000
66A68LEU0-0.090-0.03827.1100.0100.0100.0000.0000.0000.000
67A69GLY00.0250.02625.4740.0090.0090.0000.0000.0000.000
68A70ILE0-0.030-0.01721.2080.0070.0070.0000.0000.0000.000
69A71THR00.0320.02216.304-0.013-0.0130.0000.0000.0000.000
70A72VAL0-0.051-0.02218.5300.0040.0040.0000.0000.0000.000
71A73VAL00.0170.01513.024-0.021-0.0210.0000.0000.0000.000
72A74ARG10.7350.83115.7940.3560.3560.0000.0000.0000.000
73A75PHE00.0340.00913.035-0.027-0.0270.0000.0000.0000.000
74A76ASN0-0.015-0.02114.2640.1610.1610.0000.0000.0000.000
75A77PHE00.0420.01714.560-0.093-0.0930.0000.0000.0000.000
76A78ARG10.8460.90614.6490.6670.6670.0000.0000.0000.000
77A79SER0-0.129-0.05816.1070.1370.1370.0000.0000.0000.000
78A80VAL0-0.0280.00017.3080.0680.0680.0000.0000.0000.000
79A81GLY0-0.038-0.02516.737-0.064-0.0640.0000.0000.0000.000
80A82THR0-0.093-0.09313.8280.0820.0820.0000.0000.0000.000
81A83SER0-0.033-0.01312.474-0.216-0.2160.0000.0000.0000.000
82A84ALA0-0.0100.01011.7570.1600.1600.0000.0000.0000.000
83A85GLY00.0400.01413.5520.0500.0500.0000.0000.0000.000
84A86SER0-0.029-0.03016.0860.0450.0450.0000.0000.0000.000
85A87PHE0-0.016-0.01019.503-0.010-0.0100.0000.0000.0000.000
86A88ASP-1-0.863-0.93519.688-0.442-0.4420.0000.0000.0000.000
87A89HIS0-0.017-0.01422.1100.0300.0300.0000.0000.0000.000
88A90GLY00.0550.00622.8500.0320.0320.0000.0000.0000.000
89A91ASP-1-0.923-0.93322.034-0.274-0.2740.0000.0000.0000.000
90A92GLY00.018-0.00518.313-0.017-0.0170.0000.0000.0000.000
91A93GLU-1-0.786-0.91117.017-0.507-0.5070.0000.0000.0000.000
92A94GLN0-0.009-0.02417.8650.0120.0120.0000.0000.0000.000
93A95ASP-1-0.832-0.89215.200-0.521-0.5210.0000.0000.0000.000
94A96ASP-1-0.801-0.89213.056-0.898-0.8980.0000.0000.0000.000
95A97LEU0-0.026-0.01813.139-0.012-0.0120.0000.0000.0000.000
96A98ARG10.7820.86912.7760.4370.4370.0000.0000.0000.000
97A99ALA00.0310.0279.4540.0750.0750.0000.0000.0000.000
98A100VAL0-0.007-0.0049.4990.1870.1870.0000.0000.0000.000
99A101ALA00.010-0.00710.9690.1220.1220.0000.0000.0000.000
100A102GLU-1-0.888-0.93010.255-0.131-0.1310.0000.0000.0000.000
101A103TRP0-0.032-0.0194.553-0.245-0.129-0.001-0.011-0.1040.000
102A104VAL00.012-0.0097.866-0.003-0.0030.0000.0000.0000.000
103A105ARG10.8510.91110.8580.0490.0490.0000.0000.0000.000
104A106ALA0-0.035-0.0087.3150.0130.0130.0000.0000.0000.000
105A107GLN0-0.040-0.0216.598-0.155-0.1550.0000.0000.0000.000
106A108ARG10.7840.8779.514-0.036-0.0360.0000.0000.0000.000
107A109PRO00.0330.01812.160-0.017-0.0170.0000.0000.0000.000
108A110THR0-0.082-0.05014.7940.0010.0010.0000.0000.0000.000
109A111ASP-1-0.834-0.86416.800-0.008-0.0080.0000.0000.0000.000
110A112THR0-0.040-0.03918.1270.0030.0030.0000.0000.0000.000
111A113LEU00.0270.02115.760-0.010-0.0100.0000.0000.0000.000
112A114TRP0-0.027-0.03318.608-0.004-0.0040.0000.0000.0000.000
113A115LEU00.0280.00617.835-0.019-0.0190.0000.0000.0000.000
114A116ALA00.0180.00421.3500.0160.0160.0000.0000.0000.000
115A117GLY00.0580.03322.264-0.029-0.0290.0000.0000.0000.000
116A118PHE0-0.054-0.02424.3570.0210.0210.0000.0000.0000.000
117A119SER0-0.019-0.02026.300-0.021-0.0210.0000.0000.0000.000
118A120PHE00.0160.02221.9130.0120.0120.0000.0000.0000.000
119A121GLY00.0790.04022.888-0.008-0.0080.0000.0000.0000.000
120A122ALA0-0.073-0.01423.6650.0050.0050.0000.0000.0000.000
121A123TYR00.002-0.00526.2110.0150.0150.0000.0000.0000.000
122A124VAL00.0080.01920.3180.0090.0090.0000.0000.0000.000
123A125SER0-0.015-0.04421.7440.0100.0100.0000.0000.0000.000
124A126LEU0-0.046-0.01722.7160.0150.0150.0000.0000.0000.000
125A127ARG10.8290.90024.8890.1840.1840.0000.0000.0000.000
126A128ALA00.0360.01419.9230.0090.0090.0000.0000.0000.000
127A129ALA0-0.033-0.01421.5920.0140.0140.0000.0000.0000.000
128A130ALA00.0110.00623.1670.0150.0150.0000.0000.0000.000
129A131ALA0-0.0030.00820.3710.0130.0130.0000.0000.0000.000
130A132LEU0-0.029-0.00816.3100.0020.0020.0000.0000.0000.000
131A133GLU-1-0.906-0.93419.226-0.014-0.0140.0000.0000.0000.000
132A134PRO0-0.056-0.01720.9640.0120.0120.0000.0000.0000.000
133A135GLN00.0420.03221.8660.0040.0040.0000.0000.0000.000
134A136VAL0-0.038-0.01923.8690.0010.0010.0000.0000.0000.000
135A137LEU00.0280.01823.982-0.010-0.0100.0000.0000.0000.000
136A138ILE0-0.009-0.01225.5980.0090.0090.0000.0000.0000.000
137A139SER00.0130.00626.530-0.013-0.0130.0000.0000.0000.000
138A140ILE00.0090.00527.7710.0110.0110.0000.0000.0000.000
139A141ALA00.013-0.00529.928-0.015-0.0150.0000.0000.0000.000
140A142PRO00.0340.02230.688-0.012-0.0120.0000.0000.0000.000
141A143PRO00.0080.01029.8780.0090.0090.0000.0000.0000.000
142A144ALA00.0600.02632.968-0.003-0.0030.0000.0000.0000.000
143A145GLY0-0.0090.00035.6570.0010.0010.0000.0000.0000.000
144A146ARG10.8200.90633.5310.1490.1490.0000.0000.0000.000
145A147TRP00.0170.01028.119-0.011-0.0110.0000.0000.0000.000
146A148ASP-1-0.779-0.86031.072-0.132-0.1320.0000.0000.0000.000
147A149PHE0-0.024-0.02329.989-0.013-0.0130.0000.0000.0000.000
148A150SER0-0.063-0.04232.3470.0100.0100.0000.0000.0000.000
149A151ASP-1-0.865-0.93031.521-0.112-0.1120.0000.0000.0000.000
150A152VAL0-0.0050.00627.725-0.011-0.0110.0000.0000.0000.000
151A153GLN0-0.064-0.04228.0710.0140.0140.0000.0000.0000.000
152A154PRO00.0070.01227.262-0.002-0.0020.0000.0000.0000.000
153A155PRO00.0010.01025.8890.0090.0090.0000.0000.0000.000
154A156ALA00.0480.00228.426-0.003-0.0030.0000.0000.0000.000
155A157GLN0-0.080-0.02428.7100.0010.0010.0000.0000.0000.000
156A158TRP00.0560.01728.756-0.005-0.0050.0000.0000.0000.000
157A159LEU0-0.046-0.02229.9850.0060.0060.0000.0000.0000.000
158A160VAL00.0120.01130.694-0.012-0.0120.0000.0000.0000.000
159A161ILE0-0.017-0.01432.0220.0070.0070.0000.0000.0000.000
160A162GLN00.024-0.00233.860-0.016-0.0160.0000.0000.0000.000
161A163GLY0-0.0110.00836.5650.0060.0060.0000.0000.0000.000
162A164ASP-1-0.756-0.86038.626-0.090-0.0900.0000.0000.0000.000
163A165ALA0-0.018-0.00641.2540.0030.0030.0000.0000.0000.000
164A166ASP-1-0.789-0.88336.050-0.149-0.1490.0000.0000.0000.000
165A167GLU-1-0.919-0.95439.311-0.111-0.1110.0000.0000.0000.000
166A168ILE0-0.102-0.04933.950-0.004-0.0040.0000.0000.0000.000
167A169VAL0-0.080-0.03633.541-0.006-0.0060.0000.0000.0000.000
168A170ASP-1-0.817-0.90336.934-0.098-0.0980.0000.0000.0000.000
169A171PRO0-0.013-0.01539.6910.0000.0000.0000.0000.0000.000
170A172GLN0-0.033-0.02840.7250.0020.0020.0000.0000.0000.000
171A173ALA00.0330.02040.0010.0020.0020.0000.0000.0000.000
172A174VAL0-0.063-0.03336.291-0.001-0.0010.0000.0000.0000.000
173A175TYR0-0.072-0.08038.6650.0000.0000.0000.0000.0000.000
174A176ASP-1-0.807-0.89041.460-0.081-0.0810.0000.0000.0000.000
175A177TRP0-0.008-0.00132.594-0.001-0.0010.0000.0000.0000.000
176A178LEU0-0.024-0.01535.3320.0030.0030.0000.0000.0000.000
177A179GLU-1-0.957-0.97539.093-0.065-0.0650.0000.0000.0000.000
178A180THR0-0.096-0.05740.3190.0040.0040.0000.0000.0000.000
179A181LEU0-0.047-0.01235.4290.0010.0010.0000.0000.0000.000
180A182GLU-1-0.927-0.96838.725-0.054-0.0540.0000.0000.0000.000
181A183GLN0-0.098-0.06035.6350.0070.0070.0000.0000.0000.000
182A184GLN0-0.0120.00835.894-0.003-0.0030.0000.0000.0000.000
183A185PRO0-0.0020.02133.3590.0040.0040.0000.0000.0000.000
184A186THR0-0.020-0.01134.4750.0040.0040.0000.0000.0000.000
185A187LEU00.0180.01135.171-0.007-0.0070.0000.0000.0000.000
186A188VAL0-0.047-0.02836.3800.0050.0050.0000.0000.0000.000
187A189ARG10.9100.94437.9530.0750.0750.0000.0000.0000.000
188A190MET0-0.049-0.01936.5980.0020.0020.0000.0000.0000.000
189A191PRO00.0750.03440.511-0.003-0.0030.0000.0000.0000.000
190A192ASP-1-0.915-0.95342.747-0.082-0.0820.0000.0000.0000.000
191A193THR0-0.066-0.04037.594-0.003-0.0030.0000.0000.0000.000
192A194SER00.0280.01138.294-0.002-0.0020.0000.0000.0000.000
193A195HIS10.8450.90731.3340.1670.1670.0000.0000.0000.000
194A196PHE00.021-0.00130.046-0.008-0.0080.0000.0000.0000.000
195A197PHE00.0330.00432.281-0.002-0.0020.0000.0000.0000.000
196A198HIS00.0350.01735.268-0.003-0.0030.0000.0000.0000.000
197A199ARG10.8550.91637.0600.1220.1220.0000.0000.0000.000
198A200LYS10.9400.98137.1390.0960.0960.0000.0000.0000.000
199A201LEU00.0050.00630.8590.0010.0010.0000.0000.0000.000
200A202ILE0-0.0050.00533.578-0.002-0.0020.0000.0000.0000.000
201A203ASP-1-0.803-0.90535.970-0.090-0.0900.0000.0000.0000.000
202A204LEU00.0050.00630.6080.0030.0030.0000.0000.0000.000
203A205ARG10.8210.90630.7820.0980.0980.0000.0000.0000.000
204A206GLY00.0270.01432.8580.0040.0040.0000.0000.0000.000
205A207ALA00.004-0.00735.0690.0050.0050.0000.0000.0000.000
206A208LEU00.0010.00328.6940.0030.0030.0000.0000.0000.000
207A209GLN0-0.028-0.02830.3080.0090.0090.0000.0000.0000.000
208A210HIS0-0.045-0.01432.5570.0080.0080.0000.0000.0000.000
209A211GLY00.0170.00433.7840.0050.0050.0000.0000.0000.000
210A212VAL00.0420.02628.3520.0020.0020.0000.0000.0000.000
211A213ARG10.8650.94330.9850.0660.0660.0000.0000.0000.000
212A214ARG10.9070.93332.9990.0420.0420.0000.0000.0000.000
213A215TRP00.011-0.00229.4200.0040.0040.0000.0000.0000.000
214A216LEU0-0.0070.01527.4660.0000.0000.0000.0000.0000.000
215A217PRO0-0.0180.00524.8900.0050.0050.0000.0000.0000.000
216A218ALA00.0140.01427.3200.0090.0090.0000.0000.0000.000
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