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FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: ZYYYN

Calculation Name: 5RTZ-A-Xray89

Preferred Name:

Target Type:

Ligand Name: 3-fluoro-4-hydroxybenzoic acid

ligand 3-letter code: FHB

PDB ID: 5RTZ

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2021-10-07

Reference: T. Ohyama, K. Kamisaka, C. Watanabe, T. Honma et. al., FMO-based interaction energy analysis of SARS-Cov-2 related protein and ligand complexes, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHLSideSolv
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water Waters within average of the temperature factors of receptor.
Procedure Auto-FMO protocol ver. 1.20200406
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 204
LigandCharge FHB=-1
Software ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613
Total energy (hartree)
FMO2-HF: Electronic energy -1781295.464351
FMO2-HF: Nuclear repulsion 1715439.879892
FMO2-HF: Total energy -65855.584459
FMO2-MP2: Total energy -66048.520417


3D Structure
Snapshot
 
Ligand structure

FHB

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.
-177.726-186.38270.048-30.486-30.906-0.181


Interactive mode: IFIE and PIEDA for fragment #204(A:201:FHB )


Summations of interaction energy for fragment #204(A:201:FHB )
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.
-177.726-186.38270.048-30.486-30.9060.181
Interaction energy analysis for fragmet #204(A:201:FHB )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.820 / q_NPA : -0.858
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].
1A3VAL 00.009-0.00824.1100.0590.0590.0000.0000.0000.000
2A4ASN 0-0.011-0.01518.8190.2550.2550.0000.0000.0000.000
3A5SER 00.0270.00518.080-0.228-0.2280.0000.0000.0000.000
4A6PHE 0-0.0400.00612.2780.3240.3240.0000.0000.0000.000
5A7SER 00.0230.00715.506-0.532-0.5320.0000.0000.0000.000
6A8GLY 00.008-0.00715.0761.0521.0520.0000.0000.0000.000
7A9TYR 0-0.052-0.03510.7731.1931.1930.0000.0000.0000.000
8A10LEU 0-0.0040.01015.027-1.352-1.3520.0000.0000.0000.000
9A11LYS 10.8080.89415.936-13.165-13.1650.0000.0000.0000.000
10A12LEU 0-0.060-0.02313.553-0.209-0.2090.0000.0000.0000.000
11A13THR 00.0230.00017.957-0.589-0.5890.0000.0000.0000.000
12A14ASP -1-0.871-0.91120.30612.72612.7260.0000.0000.0000.000
13A15ASN 0-0.006-0.00718.472-0.436-0.4360.0000.0000.0000.000
14A16VAL 00.0070.01613.7100.9340.9340.0000.0000.0000.000
15A17TYR 00.0360.02414.573-1.165-1.1650.0000.0000.0000.000
16A18ILE 00.0290.0179.6112.1652.1650.0000.0000.0000.000
17A19LYS 10.8440.90510.141-23.171-23.1710.0000.0000.0000.000
18A20ASN 0-0.043-0.0178.0490.8770.8770.0000.0000.0000.000
19A21ALA 0-0.003-0.0157.026-3.152-3.1520.0000.0000.0000.000
20A22ASP -1-0.806-0.9122.45020.03423.7851.434-2.405-2.780-0.033
21A23ILE 00.0320.0082.374-4.065-2.9070.767-0.439-1.4860.002
22A24VAL 00.0010.0063.706-1.821-1.5270.002-0.052-0.2430.000
23A25GLU -1-0.809-0.8925.72118.24518.2450.0000.0000.0000.000
24A26GLU -1-0.773-0.8467.29019.27319.2730.0000.0000.0000.000
25A27ALA 0-0.011-0.0148.283-1.483-1.4830.0000.0000.0000.000
26A28LYS 10.8220.9028.940-20.548-20.5480.0000.0000.0000.000
27A29LYS 10.8170.90611.729-19.542-19.5420.0000.0000.0000.000
28A30VAL 0-0.045-0.02913.018-0.876-0.8760.0000.0000.0000.000
29A31LYS 10.8700.95913.860-16.525-16.5250.0000.0000.0000.000
30A32PRO 00.0090.02112.330-0.742-0.7420.0000.0000.0000.000
31A33THR 00.026-0.00815.630-0.092-0.0920.0000.0000.0000.000
32A34VAL 0-0.018-0.01614.048-0.245-0.2450.0000.0000.0000.000
33A35VAL 00.0130.0138.9090.5170.5170.0000.0000.0000.000
34A36VAL 0-0.003-0.0059.461-1.034-1.0340.0000.0000.0000.000
35A37ASN 00.006-0.0198.2246.9216.9210.0000.0000.0000.000
36A38ALA 0-0.0260.0095.814-2.128-2.1280.0000.0000.0000.000
37A39ALA 00.0360.0267.7880.9620.9620.0000.0000.0000.000
38A40ASN 0-0.003-0.02210.897-1.586-1.5860.0000.0000.0000.000
39A41VAL 00.0420.02013.033-0.464-0.4640.0000.0000.0000.000
40A42TYR 0-0.003-0.00116.355-0.883-0.8830.0000.0000.0000.000
41A43LEU 0-0.0040.01014.699-0.371-0.3710.0000.0000.0000.000
42A44LYS 10.9711.00214.451-18.215-18.2150.0000.0000.0000.000
43A45HIS 00.0380.02210.4324.1814.1810.0000.0000.0000.000
44A46GLY 00.0420.0299.969-0.271-0.2710.0000.0000.0000.000
45A47GLY 00.0170.0056.148-1.396-1.3960.0000.0000.0000.000
46A48GLY 00.0140.0162.672-1.764-0.3830.886-1.029-1.2370.008
47A49VAL 00.0190.0082.684-9.919-6.8873.897-1.524-5.4050.019
48A50ALA 00.0400.0344.378-8.470-8.0780.020-0.041-0.3720.001
49A51GLY 0-0.0030.0066.496-4.243-4.2430.0000.0000.0000.000
50A52ALA 00.0000.0082.976-6.294-5.0360.486-0.615-1.1290.005
51A53LEU 00.023-0.0074.915-4.685-4.529-0.001-0.009-0.1460.000
52A54ASN 00.045-0.0047.393-3.781-3.7810.0000.0000.0000.000
53A55LYS 10.9600.9927.599-24.423-24.4230.0000.0000.0000.000
54A56ALA 0-0.038-0.0097.611-1.946-1.9460.0000.0000.0000.000
55A57THR 0-0.053-0.0159.542-1.565-1.5650.0000.0000.0000.000
56A58ASN 0-0.041-0.02812.382-0.936-0.9360.0000.0000.0000.000
57A59ASN 0-0.002-0.00113.2770.0320.0320.0000.0000.0000.000
58A60ALA 00.0340.02814.830-0.372-0.3720.0000.0000.0000.000
59A61MET 00.0080.01310.9750.4000.4000.0000.0000.0000.000
60A62GLN 0-0.042-0.02514.3501.4451.4450.0000.0000.0000.000
61A63VAL 00.0200.02016.075-0.492-0.4920.0000.0000.0000.000
62A64GLU -1-0.726-0.84017.95615.75915.7590.0000.0000.0000.000
63A65SER 00.003-0.01116.7070.0770.0770.0000.0000.0000.000
64A66ASP -1-0.858-0.91819.05415.76215.7620.0000.0000.0000.000
65A67ASP -1-0.832-0.86721.13411.73511.7350.0000.0000.0000.000
66A68TYR 00.0380.00920.972-0.383-0.3830.0000.0000.0000.000
67A69ILE 0-0.039-0.02619.318-0.372-0.3720.0000.0000.0000.000
68A70ALA 0-0.029-0.00123.094-0.422-0.4220.0000.0000.0000.000
69A71THR 0-0.045-0.01026.348-0.656-0.6560.0000.0000.0000.000
70A72ASN 0-0.091-0.05424.424-0.724-0.7240.0000.0000.0000.000
71A73GLY 00.0130.02224.927-0.114-0.1140.0000.0000.0000.000
72A74PRO 0-0.062-0.03720.8330.5080.5080.0000.0000.0000.000
73A75LEU 0-0.0050.00116.257-0.502-0.5020.0000.0000.0000.000
74A76LYS 10.9760.98119.877-13.455-13.4550.0000.0000.0000.000
75A77VAL 00.0340.00815.3330.8140.8140.0000.0000.0000.000
76A78GLY 00.0100.01815.843-1.013-1.0130.0000.0000.0000.000
77A79GLY 0-0.026-0.00617.158-0.490-0.4900.0000.0000.0000.000
78A80SER 0-0.017-0.04216.1881.3111.3110.0000.0000.0000.000
79A81CYS 0-0.0440.00517.221-0.899-0.8990.0000.0000.0000.000
80A82VAL 00.0110.00917.3621.2631.2630.0000.0000.0000.000
81A83LEU 00.0020.00917.311-0.853-0.8530.0000.0000.0000.000
82A84SER 00.0250.00918.0710.3340.3340.0000.0000.0000.000
83A85GLY 0-0.0100.00914.6071.1261.1260.0000.0000.0000.000
84A86HIS 0-0.028-0.03114.3390.2370.2370.0000.0000.0000.000
85A87ASN 0-0.028-0.02712.905-0.089-0.0890.0000.0000.0000.000
86A88LEU 0-0.009-0.0149.011-0.074-0.0740.0000.0000.0000.000
87A89ALA 0-0.009-0.00512.7290.4050.4050.0000.0000.0000.000
88A90LYS 10.8420.94114.877-13.531-13.5310.0000.0000.0000.000
89A91HIS 00.0310.01317.160-1.092-1.0920.0000.0000.0000.000
90A92CYS 0-0.012-0.00212.5261.6571.6570.0000.0000.0000.000
91A93LEU 0-0.0320.00613.605-1.065-1.0650.0000.0000.0000.000
92A94HIS 00.0520.00312.7754.1554.1550.0000.0000.0000.000
93A95VAL 00.0120.00111.794-2.158-2.1580.0000.0000.0000.000
94A96VAL 0-0.0370.00911.3192.9962.9960.0000.0000.0000.000
95A97GLY 00.0590.03610.999-1.881-1.8810.0000.0000.0000.000
96A98PRO 0-0.0140.00211.9740.3130.3130.0000.0000.0000.000
97A99ASN 0-0.016-0.00710.9302.3272.3270.0000.0000.0000.000
98A100VAL 00.0660.02811.911-2.252-2.2520.0000.0000.0000.000
99A101ASN 0-0.053-0.02310.470-3.362-3.3620.0000.0000.0000.000
100A102LYS 10.8080.90413.561-23.580-23.5800.0000.0000.0000.000
101A103GLY 0-0.0030.00516.453-1.092-1.0920.0000.0000.0000.000
102A104GLU -1-0.792-0.84614.98620.80520.8050.0000.0000.0000.000
103A105ASP -1-0.821-0.91517.11316.33916.3390.0000.0000.0000.000
104A106ILE 00.0520.01413.6330.8260.8260.0000.0000.0000.000
105A107GLN 00.0000.00016.6970.9540.9540.0000.0000.0000.000
106A108LEU 0-0.041-0.02417.097-0.019-0.0190.0000.0000.0000.000
107A109LEU 0-0.023-0.01511.3830.6530.6530.0000.0000.0000.000
108A110LYS 10.8720.93115.145-15.041-15.0410.0000.0000.0000.000
109A111SER 00.0250.00617.801-0.058-0.0580.0000.0000.0000.000
110A112ALA 00.0310.01313.649-0.137-0.1370.0000.0000.0000.000
111A113TYR 00.023-0.0039.9410.8560.8560.0000.0000.0000.000
112A114GLU -1-0.862-0.92015.09514.66814.6680.0000.0000.0000.000
113A115ASN 0-0.057-0.02016.160-1.535-1.5350.0000.0000.0000.000
114A116PHE 00.044-0.00210.257-0.226-0.2260.0000.0000.0000.000
115A117ASN 0-0.029-0.00716.550-0.668-0.6680.0000.0000.0000.000
116A118GLN 0-0.0380.00519.853-1.216-1.2160.0000.0000.0000.000
117A119HIS 0-0.043-0.02917.978-0.425-0.4250.0000.0000.0000.000
118A120GLU -1-0.874-0.93219.47412.95112.9510.0000.0000.0000.000
119A121VAL 00.003-0.01316.5120.1330.1330.0000.0000.0000.000
120A122LEU 0-0.0330.02613.328-0.031-0.0310.0000.0000.0000.000
121A123LEU 0-0.0190.0118.391-0.050-0.0500.0000.0000.0000.000
122A124ALA 00.017-0.0098.467-0.289-0.2890.0000.0000.0000.000
123A125PRO 0-0.0110.0193.725-0.3000.3230.016-0.202-0.4370.001
124A126LEU 00.0130.0034.650-7.473-7.458-0.001-0.013-0.0020.000
125A127LEU 0-0.0090.0045.7927.8617.8610.0000.0000.0000.000
126A128SER 00.027-0.0197.807-2.333-2.3330.0000.0000.0000.000
127A129ALA 0-0.0140.0084.851-3.823-3.800-0.001-0.009-0.0130.000
128A130GLY 00.0590.0393.3745.2336.0780.032-0.404-0.4730.003
129A131ILE 0-0.023-0.0294.286-11.725-11.4440.000-0.085-0.1960.000
130A132PHE 0-0.051-0.0136.013-7.279-7.2790.0000.0000.0000.000
131A133GLY 00.0190.0187.852-4.395-4.3950.0000.0000.0000.000
132A134ALA 0-0.0020.0019.213-3.374-3.3740.0000.0000.0000.000
133A135ASP -1-0.802-0.9029.57227.78627.7860.0000.0000.0000.000
134A136PRO 0-0.009-0.0187.648-0.242-0.2420.0000.0000.0000.000
135A137ILE 00.0160.0089.609-0.325-0.3250.0000.0000.0000.000
136A138HIS 00.0410.02312.866-1.297-1.2970.0000.0000.0000.000
137A139SER 0-0.005-0.0199.322-1.458-1.4580.0000.0000.0000.000
138A140LEU 0-0.017-0.00610.870-0.529-0.5290.0000.0000.0000.000
139A141ARG 10.8470.91912.101-18.029-18.0290.0000.0000.0000.000
140A142VAL 00.0150.01414.430-1.114-1.1140.0000.0000.0000.000
141A143CYS 0-0.0320.00111.553-1.531-1.5310.0000.0000.0000.000
142A144VAL 00.0190.01614.237-1.164-1.1640.0000.0000.0000.000
143A145ASP -1-0.813-0.89716.88114.96314.9630.0000.0000.0000.000
144A146THR 0-0.119-0.06517.070-1.285-1.2850.0000.0000.0000.000
145A147VAL 0-0.055-0.01714.507-0.731-0.7310.0000.0000.0000.000
146A148ARG 10.9360.97617.917-14.310-14.3100.0000.0000.0000.000
147A149THR 0-0.0390.00318.689-0.396-0.3960.0000.0000.0000.000
148A150ASN 0-0.023-0.00218.2980.5490.5490.0000.0000.0000.000
149A151VAL 00.0220.00711.8780.4040.4040.0000.0000.0000.000
150A152TYR 00.0210.02312.359-0.757-0.7570.0000.0000.0000.000
151A153LEU 00.021-0.0068.3351.6861.6860.0000.0000.0000.000
152A154ALA 0-0.012-0.0075.475-2.649-2.6490.0000.0000.0000.000
153A155VAL 00.002-0.0064.54311.42211.832-0.001-0.020-0.3890.000
154A156PHE 00.0170.0032.605-12.794-8.4414.802-2.253-6.9020.008
155A157ASP -1-0.814-0.9134.57925.17725.3640.001-0.054-0.1350.000
156A158LYS 10.8710.9227.637-20.798-20.7980.0000.0000.0000.000
157A159ASN 0-0.034-0.02310.875-0.986-0.9860.0000.0000.0000.000
158A160LEU 00.007-0.0026.165-1.066-1.0660.0000.0000.0000.000
159A161TYR 0-0.017-0.0079.209-1.521-1.5210.0000.0000.0000.000
160A162ASP -1-0.772-0.86110.30518.90218.9020.0000.0000.0000.000
161A163LYS 10.9480.99012.768-24.701-24.7010.0000.0000.0000.000
162A164LEU 0-0.040-0.0138.280-0.825-0.8250.0000.0000.0000.000
163A165VAL 00.0100.00912.822-1.120-1.1200.0000.0000.0000.000
164A166SER 0-0.051-0.03615.329-1.397-1.3970.0000.0000.0000.000
165A167SER 0-0.106-0.07215.582-0.783-0.7830.0000.0000.0000.000
166A168PHE 0-0.008-0.00115.6160.0770.0770.0000.0000.0000.000
167A169LEU -1-0.888-0.92917.81314.18014.1800.0000.0000.0000.000
168A303HOH 0-0.065-0.05127.304-0.014-0.0140.0000.0000.0000.000
169A317HOH 0-0.009-0.0129.137-0.996-0.9960.0000.0000.0000.000
170A337HOH 0-0.052-0.03812.082-0.346-0.3460.0000.0000.0000.000
171A339HOH 0-0.075-0.06122.5550.0740.0740.0000.0000.0000.000
172A345HOH 0-0.006-0.0181.661-24.659-33.99219.151-6.420-3.3980.053
173A347HOH 0-0.055-0.04420.708-0.243-0.2430.0000.0000.0000.000
174A349HOH 0-0.026-0.00611.045-0.681-0.6810.0000.0000.0000.000
175A350HOH 0-0.021-0.02224.196-0.007-0.0070.0000.0000.0000.000
176A355HOH 00.009-0.0046.870-0.135-0.1350.0000.0000.0000.000
177A358HOH 0-0.011-0.0149.5921.3761.3760.0000.0000.0000.000
178A362HOH 0-0.013-0.03415.7010.5610.5610.0000.0000.0000.000
179A366HOH 0-0.037-0.0228.964-0.756-0.7560.0000.0000.0000.000
180A374HOH 00.0160.00319.343-0.117-0.1170.0000.0000.0000.000
181A378HOH 0-0.035-0.0247.6001.7021.7020.0000.0000.0000.000
182A379HOH 0-0.058-0.03924.166-0.182-0.1820.0000.0000.0000.000
183A384HOH 0-0.027-0.03512.6980.1860.1860.0000.0000.0000.000
184A385HOH 0-0.029-0.01719.2910.1080.1080.0000.0000.0000.000
185A394HOH 0-0.008-0.01618.327-0.350-0.3500.0000.0000.0000.000
186A397HOH 0-0.041-0.0331.686-16.169-23.30713.602-4.282-2.1820.049
187A402HOH 0-0.019-0.02614.938-0.339-0.3390.0000.0000.0000.000
188A404HOH 0-0.005-0.0143.619-4.901-4.4160.006-0.316-0.1740.002
189A405HOH 0-0.023-0.04024.4360.1520.1520.0000.0000.0000.000
190A407HOH 0-0.016-0.0109.0040.0210.0210.0000.0000.0000.000
191A409HOH 0-0.022-0.02020.037-0.317-0.3170.0000.0000.0000.000
192A410HOH 0-0.006-0.0115.337-1.906-1.9060.0000.0000.0000.000
193A412HOH 00.003-0.00220.2070.1960.1960.0000.0000.0000.000
194A417HOH 00.0000.00222.2800.2010.2010.0000.0000.0000.000
195A420HOH 00.011-0.01411.9280.5330.5330.0000.0000.0000.000
196A423HOH 0-0.060-0.05614.487-0.086-0.0860.0000.0000.0000.000
197A424HOH 0-0.019-0.01914.747-0.287-0.2870.0000.0000.0000.000
198A425HOH 00.0290.01220.0260.0910.0910.0000.0000.0000.000
199A436HOH 00.0320.01823.4040.2000.2000.0000.0000.0000.000
200A438HOH 00.013-0.0151.565-24.038-36.57424.868-9.218-3.1140.055
201A458HOH 00.0190.01121.645-0.107-0.1070.0000.0000.0000.000
202A466HOH 0-0.021-0.0213.106-7.791-6.0840.082-1.096-0.6930.008
203A487HOH 0-0.036-0.02910.724-0.059-0.0590.0000.0000.0000.000