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: K9943

Calculation Name: 5F5U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5F5U

Chain ID: A

ChEMBL ID:

UniProt ID: G0S6R0

Base Structure: X-ray

Registration Date: 2023-06-21

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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2157017.156919
FMO2-HF: Nuclear repulsion 2081266.88258
FMO2-HF: Total energy -75750.274339
FMO2-MP2: Total energy -75972.428388


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:22:GLY)


Summations of interaction energy for fragment #1(A:22: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.
0.751.59-0.007-0.381-0.4510.001
Interaction energy analysis for fragmet #1(A:22:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.014 / q_NPA : -0.018
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].
3A24LEU0-0.017-0.0213.872-0.5180.322-0.007-0.381-0.4510.001
4A25ALA0-0.028-0.0096.7220.3540.3540.0000.0000.0000.000
5A26PRO00.0160.0069.664-0.036-0.0360.0000.0000.0000.000
6A27ASN0-0.0180.00313.019-0.044-0.0440.0000.0000.0000.000
7A28GLY00.0480.01012.077-0.082-0.0820.0000.0000.0000.000
8A29LEU0-0.054-0.01111.369-0.051-0.0510.0000.0000.0000.000
9A30ASN00.0700.0306.064-0.211-0.2110.0000.0000.0000.000
10A31PRO00.1090.0505.6560.2920.2920.0000.0000.0000.000
11A32ALA0-0.016-0.0046.3290.2050.2050.0000.0000.0000.000
12A33THR0-0.147-0.0998.1200.0740.0740.0000.0000.0000.000
13A34ILE00.0180.03110.9820.0480.0480.0000.0000.0000.000
14A35MET0-0.0050.02112.8860.0490.0490.0000.0000.0000.000
15A36GLU-1-0.720-0.83314.370-0.114-0.1140.0000.0000.0000.000
16A37LYS10.8490.90315.7670.0880.0880.0000.0000.0000.000
17A38ALA00.0640.02716.7710.0180.0180.0000.0000.0000.000
18A39VAL0-0.023-0.00217.6780.0170.0170.0000.0000.0000.000
19A40ARG10.9330.95811.7350.1550.1550.0000.0000.0000.000
20A41GLU-1-0.838-0.89015.724-0.021-0.0210.0000.0000.0000.000
21A42ARG10.8760.91018.1140.0190.0190.0000.0000.0000.000
22A43ILE0-0.038-0.01016.2030.0090.0090.0000.0000.0000.000
23A44VAL00.0000.02014.4300.0150.0150.0000.0000.0000.000
24A45GLU-1-0.845-0.91517.5210.0200.0200.0000.0000.0000.000
25A46SER0-0.088-0.04420.3020.0020.0020.0000.0000.0000.000
26A47TYR00.0240.00221.7640.0080.0080.0000.0000.0000.000
27A48PHE00.0290.00520.8490.0080.0080.0000.0000.0000.000
28A49TRP00.030-0.00112.2370.0030.0030.0000.0000.0000.000
29A50LYS10.8570.91818.751-0.057-0.0570.0000.0000.0000.000
30A51GLU-1-0.883-0.93120.5650.0960.0960.0000.0000.0000.000
31A52GLN0-0.024-0.02422.0260.0160.0160.0000.0000.0000.000
32A53CYS0-0.038-0.00716.4630.0010.0010.0000.0000.0000.000
33A54PHE00.0560.03716.4260.0500.0500.0000.0000.0000.000
34A55GLY0-0.024-0.00216.885-0.015-0.0150.0000.0000.0000.000
35A56VAL0-0.096-0.04616.0550.0340.0340.0000.0000.0000.000
36A57ASN00.0370.02214.5690.0470.0470.0000.0000.0000.000
37A58GLU-1-0.816-0.93212.4510.4590.4590.0000.0000.0000.000
38A59ALA00.0250.02616.471-0.043-0.0430.0000.0000.0000.000
39A60ASP-1-0.745-0.87919.1410.2350.2350.0000.0000.0000.000
40A61ILE0-0.062-0.01815.383-0.025-0.0250.0000.0000.0000.000
41A62VAL0-0.018-0.01319.264-0.027-0.0270.0000.0000.0000.000
42A63ASP-1-0.869-0.92422.5780.1310.1310.0000.0000.0000.000
43A64ARG10.8520.90720.723-0.176-0.1760.0000.0000.0000.000
44A65VAL0-0.024-0.02421.626-0.017-0.0170.0000.0000.0000.000
45A66VAL0-0.010-0.00324.237-0.013-0.0130.0000.0000.0000.000
46A67GLU-1-0.825-0.88525.5120.1070.1070.0000.0000.0000.000
47A68HIS0-0.027-0.01824.814-0.016-0.0160.0000.0000.0000.000
48A69VAL0-0.064-0.00923.379-0.009-0.0090.0000.0000.0000.000
49A70ARG10.8340.89826.509-0.063-0.0630.0000.0000.0000.000
50A71PHE0-0.076-0.04927.370-0.004-0.0040.0000.0000.0000.000
51A72VAL00.0520.05025.6900.0050.0050.0000.0000.0000.000
52A73GLY00.0730.00425.003-0.004-0.0040.0000.0000.0000.000
53A74GLY00.0380.03522.8300.0040.0040.0000.0000.0000.000
54A75VAL0-0.024-0.00222.4040.0080.0080.0000.0000.0000.000
55A76THR0-0.087-0.05424.868-0.004-0.0040.0000.0000.0000.000
56A77GLY00.0310.01128.5370.0030.0030.0000.0000.0000.000
57A78VAL00.0540.01430.965-0.002-0.0020.0000.0000.0000.000
58A79THR00.0020.00029.584-0.003-0.0030.0000.0000.0000.000
59A80GLN00.0030.02025.5760.0010.0010.0000.0000.0000.000
60A81LYS10.9810.98925.414-0.044-0.0440.0000.0000.0000.000
61A82PRO00.0280.02321.208-0.005-0.0050.0000.0000.0000.000
62A83SER0-0.034-0.03023.2540.0110.0110.0000.0000.0000.000
63A84PRO00.0460.01622.0190.0020.0020.0000.0000.0000.000
64A85PHE00.0560.02320.8560.0120.0120.0000.0000.0000.000
65A86LEU0-0.0030.00918.1330.0040.0040.0000.0000.0000.000
66A87CYS0-0.055-0.02317.351-0.001-0.0010.0000.0000.0000.000
67A88LEU00.0400.01516.1020.0200.0200.0000.0000.0000.000
68A89ALA00.0180.01415.4300.0210.0210.0000.0000.0000.000
69A90PHE0-0.004-0.01510.877-0.002-0.0020.0000.0000.0000.000
70A91LYS10.8390.92011.371-0.350-0.3500.0000.0000.0000.000
71A92LEU00.0410.02411.2250.0760.0760.0000.0000.0000.000
72A93LEU0-0.040-0.0179.4210.0100.0100.0000.0000.0000.000
73A94GLN0-0.056-0.0327.032-0.121-0.1210.0000.0000.0000.000
74A95LEU0-0.057-0.0256.6500.2850.2850.0000.0000.0000.000
75A96ALA0-0.050-0.0066.3340.1280.1280.0000.0000.0000.000
76A97PRO00.0160.0168.3500.0370.0370.0000.0000.0000.000
77A98GLY00.0560.02511.802-0.081-0.0810.0000.0000.0000.000
78A99ASP-1-0.765-0.88413.989-0.024-0.0240.0000.0000.0000.000
79A100ASP-1-0.905-0.94316.6100.1820.1820.0000.0000.0000.000
80A101ILE00.0710.03614.618-0.016-0.0160.0000.0000.0000.000
81A102LEU0-0.024-0.00514.631-0.019-0.0190.0000.0000.0000.000
82A103LYS10.8590.91718.484-0.057-0.0570.0000.0000.0000.000
83A104GLU-1-0.872-0.93221.3580.0960.0960.0000.0000.0000.000
84A105TYR0-0.082-0.07816.678-0.007-0.0070.0000.0000.0000.000
85A106LEU0-0.0190.00021.616-0.008-0.0080.0000.0000.0000.000
86A107TYR00.0230.01823.901-0.008-0.0080.0000.0000.0000.000
87A108PHE00.1000.05226.510-0.005-0.0050.0000.0000.0000.000
88A109GLY00.0350.01425.2160.0000.0000.0000.0000.0000.000
89A110GLY00.0120.01326.020-0.004-0.0040.0000.0000.0000.000
90A111GLU-1-0.794-0.88227.3080.0290.0290.0000.0000.0000.000
91A112LYS10.7580.90229.698-0.075-0.0750.0000.0000.0000.000
92A113PHE0-0.007-0.01526.991-0.003-0.0030.0000.0000.0000.000
93A114LYS10.9200.96027.142-0.027-0.0270.0000.0000.0000.000
94A115TYR0-0.002-0.02825.774-0.006-0.0060.0000.0000.0000.000
95A116LEU00.0140.03020.729-0.003-0.0030.0000.0000.0000.000
96A117ARG10.7970.86422.308-0.029-0.0290.0000.0000.0000.000
97A118ALA00.0000.00523.421-0.007-0.0070.0000.0000.0000.000
98A119LEU0-0.039-0.01617.998-0.012-0.0120.0000.0000.0000.000
99A120ALA00.0490.01818.509-0.007-0.0070.0000.0000.0000.000
100A121ALA00.0340.01819.018-0.014-0.0140.0000.0000.0000.000
101A122PHE0-0.018-0.02218.496-0.016-0.0160.0000.0000.0000.000
102A123TYR00.005-0.01710.092-0.049-0.0490.0000.0000.0000.000
103A124ILE00.0430.03015.483-0.035-0.0350.0000.0000.0000.000
104A125ARG10.8280.90917.4500.0830.0830.0000.0000.0000.000
105A126LEU0-0.059-0.03114.713-0.022-0.0220.0000.0000.0000.000
106A127THR0-0.026-0.01711.698-0.040-0.0400.0000.0000.0000.000
107A128ARG10.8780.92512.145-0.004-0.0040.0000.0000.0000.000
108A129PRO00.0300.00716.094-0.008-0.0080.0000.0000.0000.000
109A130ASP-1-0.728-0.83418.816-0.115-0.1150.0000.0000.0000.000
110A131LYS10.9731.00022.1590.0700.0700.0000.0000.0000.000
111A132GLU-1-0.914-0.95918.260-0.100-0.1000.0000.0000.0000.000
112A133VAL0-0.041-0.01719.8080.0170.0170.0000.0000.0000.000
113A134TYR0-0.001-0.02422.2430.0140.0140.0000.0000.0000.000
114A135THR0-0.011-0.02924.9090.0100.0100.0000.0000.0000.000
115A136LEU0-0.036-0.00920.5320.0110.0110.0000.0000.0000.000
116A137LEU0-0.039-0.02621.8740.0110.0110.0000.0000.0000.000
117A138GLU-1-0.742-0.84525.911-0.035-0.0350.0000.0000.0000.000
118A139PRO00.0190.01328.3150.0020.0020.0000.0000.0000.000
119A140PHE0-0.024-0.01825.3480.0050.0050.0000.0000.0000.000
120A141LEU0-0.018-0.01230.3330.0010.0010.0000.0000.0000.000
121A142GLU-1-0.775-0.87332.612-0.007-0.0070.0000.0000.0000.000
122A143ASP-1-0.788-0.84730.8480.0240.0240.0000.0000.0000.000
123A144ARG11.0061.00633.453-0.009-0.0090.0000.0000.0000.000
124A145ARG10.6850.80030.036-0.029-0.0290.0000.0000.0000.000
125A146LYS10.9540.98633.761-0.012-0.0120.0000.0000.0000.000
126A147LEU0-0.0170.00128.8470.0060.0060.0000.0000.0000.000
127A148ARG10.9070.95731.872-0.027-0.0270.0000.0000.0000.000
128A149ARG10.8730.92928.8530.0160.0160.0000.0000.0000.000
129A150LYS10.8720.92129.474-0.014-0.0140.0000.0000.0000.000
130A151GLY00.0240.00528.862-0.001-0.0010.0000.0000.0000.000
131A152LYS10.9780.99029.1120.0410.0410.0000.0000.0000.000
132A153ASN00.0160.00832.2350.0000.0000.0000.0000.0000.000
133A154GLY00.0730.06134.3400.0020.0020.0000.0000.0000.000
134A155THR0-0.085-0.06833.5670.0040.0040.0000.0000.0000.000
135A156SER00.0260.02634.579-0.001-0.0010.0000.0000.0000.000
136A157LEU0-0.031-0.01534.9740.0030.0030.0000.0000.0000.000
137A158THR0-0.031-0.03330.942-0.003-0.0030.0000.0000.0000.000
138A159TYR00.0200.00033.6650.0060.0060.0000.0000.0000.000
139A160MET0-0.043-0.01227.107-0.003-0.0030.0000.0000.0000.000
140A161ASP-1-0.814-0.90229.896-0.006-0.0060.0000.0000.0000.000
141A162GLU-1-0.760-0.86531.574-0.010-0.0100.0000.0000.0000.000
142A163PHE0-0.068-0.04223.605-0.004-0.0040.0000.0000.0000.000
143A164ILE00.007-0.00525.683-0.005-0.0050.0000.0000.0000.000
144A165ASP-1-0.777-0.89427.595-0.040-0.0400.0000.0000.0000.000
145A166ASP-1-0.834-0.89727.627-0.032-0.0320.0000.0000.0000.000
146A167LEU0-0.095-0.04721.875-0.008-0.0080.0000.0000.0000.000
147A168LEU0-0.0040.00324.617-0.013-0.0130.0000.0000.0000.000
148A169THR0-0.022-0.00426.734-0.006-0.0060.0000.0000.0000.000
149A170LYS10.7880.90327.2940.0360.0360.0000.0000.0000.000
150A171ASP-1-0.748-0.85924.483-0.098-0.0980.0000.0000.0000.000
151A172ARG10.7500.84721.0920.0700.0700.0000.0000.0000.000
152A173VAL00.0630.04022.7900.0100.0100.0000.0000.0000.000
153A174CYS0-0.079-0.02321.754-0.003-0.0030.0000.0000.0000.000
154A175SER0-0.052-0.03421.4420.0040.0040.0000.0000.0000.000
155A176THR00.0430.02716.7280.0000.0000.0000.0000.0000.000
156A177SER0-0.032-0.04319.0000.0110.0110.0000.0000.0000.000
157A178LEU0-0.053-0.01318.525-0.018-0.0180.0000.0000.0000.000
158A179TRP00.0170.01317.371-0.004-0.0040.0000.0000.0000.000
159A180LYS10.8630.90619.6300.1180.1180.0000.0000.0000.000
160A181MET00.0010.02221.734-0.013-0.0130.0000.0000.0000.000
161A182ARG10.8460.89723.5300.1350.1350.0000.0000.0000.000
162A183ARG10.8690.90826.5030.0740.0740.0000.0000.0000.000
163A184ARG10.7490.82329.5910.0400.0400.0000.0000.0000.000
164A185ASP-1-0.699-0.82930.557-0.065-0.0650.0000.0000.0000.000
165A186ILE0-0.032-0.01429.752-0.002-0.0020.0000.0000.0000.000
166A187LEU0-0.050-0.03726.045-0.006-0.0060.0000.0000.0000.000
167A188GLU-1-0.855-0.91529.974-0.044-0.0440.0000.0000.0000.000
168A189ASP-1-0.899-0.95033.438-0.054-0.0540.0000.0000.0000.000
169A190LEU0-0.143-0.07629.193-0.002-0.0020.0000.0000.0000.000
170A191ASP-1-0.915-0.94631.496-0.048-0.0480.0000.0000.0000.000
171A192LEU0-0.105-0.04526.281-0.003-0.0030.0000.0000.0000.000
172A193LEU0-0.109-0.07028.203-0.001-0.0010.0000.0000.0000.000
173A194GLU-1-0.824-0.90230.577-0.027-0.0270.0000.0000.0000.000
174A195PRO00.0370.02733.254-0.002-0.0020.0000.0000.0000.000
175A196ARG10.7630.88332.9000.0210.0210.0000.0000.0000.000
176A197VAL00.0370.02735.3860.0010.0010.0000.0000.0000.000
177A198SER00.002-0.01437.2260.0010.0010.0000.0000.0000.000
178A199PRO0-0.016-0.01239.0390.0000.0000.0000.0000.0000.000
179A200LEU00.000-0.00641.3910.0010.0010.0000.0000.0000.000
180A201GLY00.0310.02642.0640.0000.0000.0000.0000.0000.000
181A202SER00.0180.01143.3430.0000.0000.0000.0000.0000.000
182A203LEU0-0.077-0.03045.8950.0010.0010.0000.0000.0000.000
183A204GLU-1-0.901-0.97145.757-0.013-0.0130.0000.0000.0000.000
184A205ASP-1-0.899-0.94946.541-0.017-0.0170.0000.0000.0000.000
185A206ILE0-0.045-0.03048.9680.0000.0000.0000.0000.0000.000
186A207LEU0-0.104-0.04949.7470.0010.0010.0000.0000.0000.000
187A208GLU-1-0.981-0.97348.575-0.019-0.0190.0000.0000.0000.000
188A209GLU-1-1.078-1.02652.391-0.011-0.0110.0000.0000.0000.000