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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: LJJJ9

Calculation Name: 5RTV-A-Xray89

Preferred Name:

Target Type:

Ligand Name: 3-hydroxy-2-methylbenzoic acid

ligand 3-letter code: PF0

PDB ID: 5RTV

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 208
LigandCharge PF0=-1
Software ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613
Total energy (hartree)
FMO2-HF: Electronic energy -1791915.955549
FMO2-HF: Nuclear repulsion 1725816.097992
FMO2-HF: Total energy -66099.857557
FMO2-MP2: Total energy -66293.526067


3D Structure
Snapshot
 
Ligand structure

PF0

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.
-121.413-114.82637.841-15.609-28.821-0.173


Interactive mode: IFIE and PIEDA for fragment #208(A:201:PF0 )


Summations of interaction energy for fragment #208(A:201:PF0 )
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.
-121.413-114.82637.841-15.609-28.8210.173
Interaction energy analysis for fragmet #208(A:201:PF0 )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.827 / q_NPA : -0.905
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 00.009-0.00824.2080.0560.0560.0000.0000.0000.000
2A4ASN 0-0.012-0.01519.2020.3020.3020.0000.0000.0000.000
3A5SER 00.0250.00319.631-0.249-0.2490.0000.0000.0000.000
4A6PHE 0-0.0410.00613.5020.5020.5020.0000.0000.0000.000
5A7SER 00.0240.00715.986-0.623-0.6230.0000.0000.0000.000
6A8GLY 00.002-0.01015.0521.4371.4370.0000.0000.0000.000
7A9TYR 0-0.048-0.03310.3801.6001.6000.0000.0000.0000.000
8A10LEU 00.0000.01213.330-1.796-1.7960.0000.0000.0000.000
9A11LYS 10.8030.89314.129-14.356-14.3560.0000.0000.0000.000
10A12LEU 0-0.043-0.01010.724-0.250-0.2500.0000.0000.0000.000
11A13THR 00.0290.00515.384-0.816-0.8160.0000.0000.0000.000
12A14ASP -1-0.865-0.89517.91813.75513.7550.0000.0000.0000.000
13A15ASN 0-0.004-0.00716.997-0.382-0.3820.0000.0000.0000.000
14A16VAL 00.0080.01811.9331.0051.0050.0000.0000.0000.000
15A17TYR 00.0350.02313.241-1.177-1.1770.0000.0000.0000.000
16A18ILE 00.0270.0116.7162.4442.4440.0000.0000.0000.000
17A19LYS 10.8280.9018.598-28.508-28.5080.0000.0000.0000.000
18A20ASN 0-0.054-0.0276.3601.1931.1930.0000.0000.0000.000
19A21ALA 0-0.012-0.0186.287-5.555-5.5550.0000.0000.0000.000
20A22ASP -1-0.816-0.9015.72647.46447.4640.0000.0000.0000.000
21A23ILE 00.036-0.0025.893-5.490-5.4900.0000.0000.0000.000
22A24VAL 00.0290.0177.722-5.014-5.0140.0000.0000.0000.000
23A25GLU -1-0.837-0.90410.21819.93219.9320.0000.0000.0000.000
24A26GLU -1-0.770-0.85110.30722.14222.1420.0000.0000.0000.000
25A27ALA 0-0.017-0.01611.759-2.294-2.2940.0000.0000.0000.000
26A28LYS 10.8210.89813.598-23.441-23.4410.0000.0000.0000.000
27A29LYS 10.8160.91014.147-22.956-22.9560.0000.0000.0000.000
28A30VAL 0-0.045-0.03115.203-1.109-1.1090.0000.0000.0000.000
29A31LYS 10.8670.95917.083-17.615-17.6150.0000.0000.0000.000
30A32PRO 00.0090.02114.360-0.878-0.8780.0000.0000.0000.000
31A33THR 00.022-0.01117.672-0.245-0.2450.0000.0000.0000.000
32A34VAL 0-0.018-0.01515.556-0.411-0.4110.0000.0000.0000.000
33A35VAL 00.0140.01410.9780.8810.8810.0000.0000.0000.000
34A36VAL 00.004-0.0039.933-1.372-1.3720.0000.0000.0000.000
35A37ASN 00.006-0.0189.6035.8475.8470.0000.0000.0000.000
36A38ALA 0-0.0040.0246.943-1.753-1.7530.0000.0000.0000.000
37A39ALA 00.0130.0168.9780.5690.5690.0000.0000.0000.000
38A40ASN 00.029-0.00212.226-1.087-1.0870.0000.0000.0000.000
39A41VAL 00.0400.01014.448-0.141-0.1410.0000.0000.0000.000
40A42TYR 0-0.0030.00017.906-0.625-0.6250.0000.0000.0000.000
41A43LEU 0-0.0040.01016.225-0.272-0.2720.0000.0000.0000.000
42A44LYS 10.9761.00516.734-15.835-15.8350.0000.0000.0000.000
43A45HIS 00.0250.02313.0082.9522.9520.0000.0000.0000.000
44A46GLY 00.0500.03713.448-0.078-0.0780.0000.0000.0000.000
45A47GLY 00.0280.00510.139-0.913-0.9130.0000.0000.0000.000
46A48GLY 00.0390.0285.6830.3500.3500.0000.0000.0000.000
47A49VAL 00.0850.0403.544-3.498-2.7600.022-0.213-0.5480.001
48A50ALA 00.0250.0235.902-4.506-4.5060.0000.0000.0000.000
49A51GLY 0-0.0160.0039.321-2.733-2.7330.0000.0000.0000.000
50A52ALA 00.0040.0037.579-2.860-2.8600.0000.0000.0000.000
51A53LEU 00.018-0.0038.786-2.668-2.6680.0000.0000.0000.000
52A54ASN 00.0530.00411.019-2.849-2.8490.0000.0000.0000.000
53A55LYS 10.9600.98913.042-22.236-22.2360.0000.0000.0000.000
54A56ALA 0-0.030-0.00212.968-1.581-1.5810.0000.0000.0000.000
55A57THR 0-0.055-0.01614.870-1.378-1.3780.0000.0000.0000.000
56A58ASN 0-0.040-0.02717.480-0.968-0.9680.0000.0000.0000.000
57A59ASN 0-0.0030.00217.909-0.146-0.1460.0000.0000.0000.000
58A60ALA 00.0270.02219.192-0.432-0.4320.0000.0000.0000.000
59A61MET 00.0090.01513.5190.1960.1960.0000.0000.0000.000
60A62GLN 0-0.053-0.02917.2440.9970.9970.0000.0000.0000.000
61A63VAL 00.0250.02319.021-0.473-0.4730.0000.0000.0000.000
62A64GLU -1-0.730-0.84320.30315.03415.0340.0000.0000.0000.000
63A65SER 00.005-0.00918.4190.0390.0390.0000.0000.0000.000
64A66ASP -1-0.814-0.89520.77714.19014.1900.0000.0000.0000.000
65A67ASP -1-0.828-0.86523.32811.08911.0890.0000.0000.0000.000
66A68TYR 00.012-0.01222.304-0.277-0.2770.0000.0000.0000.000
67A69ILE 0-0.042-0.02720.827-0.332-0.3320.0000.0000.0000.000
68A70ALA 0-0.032-0.00224.549-0.379-0.3790.0000.0000.0000.000
69A71THR 0-0.041-0.00827.745-0.574-0.5740.0000.0000.0000.000
70A72ASN 0-0.078-0.04425.628-0.609-0.6090.0000.0000.0000.000
71A73GLY 00.0220.02426.236-0.089-0.0890.0000.0000.0000.000
72A74PRO 0-0.044-0.02321.8870.4720.4720.0000.0000.0000.000
73A75LEU 0-0.0050.00517.166-0.358-0.3580.0000.0000.0000.000
74A76LYS 10.9640.97620.266-12.660-12.6600.0000.0000.0000.000
75A77VAL 00.0310.00615.0880.7040.7040.0000.0000.0000.000
76A78GLY 00.0200.02315.433-0.780-0.7800.0000.0000.0000.000
77A79GLY 0-0.033-0.01116.387-0.277-0.2770.0000.0000.0000.000
78A80SER 0-0.011-0.03716.0621.0811.0810.0000.0000.0000.000
79A81CYS 0-0.0350.00817.609-0.791-0.7910.0000.0000.0000.000
80A82VAL 00.0110.01018.2681.1361.1360.0000.0000.0000.000
81A83LEU 00.0020.00818.829-0.834-0.8340.0000.0000.0000.000
82A84SER 00.0260.01119.9030.5130.5130.0000.0000.0000.000
83A85GLY 0-0.0090.00917.2690.9710.9710.0000.0000.0000.000
84A86HIS 0-0.034-0.03517.6190.4600.4600.0000.0000.0000.000
85A87ASN 0-0.021-0.02417.874-0.081-0.0810.0000.0000.0000.000
86A88LEU 0-0.015-0.01812.8390.1940.1940.0000.0000.0000.000
87A89ALA 0-0.007-0.00215.7940.7050.7050.0000.0000.0000.000
88A90LYS 10.8440.94217.822-13.811-13.8110.0000.0000.0000.000
89A91HIS 00.0330.01319.312-1.126-1.1260.0000.0000.0000.000
90A92CYS 0-0.011-0.00214.2491.7791.7790.0000.0000.0000.000
91A93LEU 0-0.0330.00514.789-1.178-1.1780.0000.0000.0000.000
92A94HIS 00.0500.00413.7303.3623.3620.0000.0000.0000.000
93A95VAL 00.011-0.00111.611-1.802-1.8020.0000.0000.0000.000
94A96VAL 0-0.0450.00511.6192.1362.1360.0000.0000.0000.000
95A97GLY 00.0580.03010.287-1.255-1.2550.0000.0000.0000.000
96A98PRO 0-0.0130.00111.325-0.032-0.0320.0000.0000.0000.000
97A99ASN 0-0.027-0.01110.9111.9961.9960.0000.0000.0000.000
98A100VAL 00.0560.02110.067-1.715-1.7150.0000.0000.0000.000
99A101ASN 0-0.054-0.0258.908-2.542-2.5420.0000.0000.0000.000
100A102LYS 10.8070.90512.811-20.068-20.0680.0000.0000.0000.000
101A103GLY 0-0.0040.00515.168-0.892-0.8920.0000.0000.0000.000
102A104GLU -1-0.795-0.84815.04618.27218.2720.0000.0000.0000.000
103A105ASP -1-0.817-0.91315.56715.41415.4140.0000.0000.0000.000
104A106ILE 00.0520.01410.5530.7220.7220.0000.0000.0000.000
105A107GLN 00.002-0.00114.0451.0601.0600.0000.0000.0000.000
106A108LEU 0-0.048-0.02715.7820.0310.0310.0000.0000.0000.000
107A109LEU 0-0.027-0.0168.8260.5640.5640.0000.0000.0000.000
108A110LYS 10.8890.93712.947-15.043-15.0430.0000.0000.0000.000
109A111SER 00.022-0.01715.3240.1320.1320.0000.0000.0000.000
110A112ALA 00.0300.01512.434-0.108-0.1080.0000.0000.0000.000
111A113TYR 00.022-0.0057.3570.8420.8420.0000.0000.0000.000
112A114GLU -1-0.819-0.86513.64614.27714.2770.0000.0000.0000.000
113A115ASN 0-0.068-0.02515.560-1.396-1.3960.0000.0000.0000.000
114A116PHE 00.047-0.0019.703-0.170-0.1700.0000.0000.0000.000
115A117ASN 0-0.017-0.00116.067-0.359-0.3590.0000.0000.0000.000
116A118GLN 0-0.0420.00519.421-1.135-1.1350.0000.0000.0000.000
117A119HIS 0-0.042-0.02818.179-0.347-0.3470.0000.0000.0000.000
118A120GLU -1-0.876-0.93419.45013.48013.4800.0000.0000.0000.000
119A121VAL 00.006-0.01117.1750.2640.2640.0000.0000.0000.000
120A122LEU 0-0.0360.02614.028-0.200-0.2000.0000.0000.0000.000
121A123LEU 0-0.0200.0119.6800.2030.2030.0000.0000.0000.000
122A124ALA 00.015-0.0109.224-0.975-0.9750.0000.0000.0000.000
123A125PRO 00.0020.0214.1612.0222.3630.000-0.020-0.3210.000
124A126LEU 00.0190.0052.906-9.224-8.2400.386-0.251-1.1180.000
125A127LEU 00.0010.0123.8492.8373.1280.004-0.096-0.199-0.001
126A128SER 00.022-0.0186.340-0.819-0.8190.0000.0000.0000.000
127A129ALA 0-0.0270.0102.426-3.381-2.5751.642-0.781-1.6670.006
128A130GLY 00.0440.0252.189-3.628-2.6756.132-2.930-4.1550.025
129A131ILE 0-0.015-0.0323.421-6.943-8.7670.2032.624-1.0030.004
130A132PHE 0-0.064-0.0156.665-4.774-4.7740.0000.0000.0000.000
131A133GLY 00.0440.0276.535-3.006-3.0060.0000.0000.0000.000
132A134ALA 0-0.012-0.0026.886-2.138-2.1380.0000.0000.0000.000
133A135ASP -1-0.789-0.9015.08028.87328.905-0.001-0.002-0.0290.000
134A136PRO 00.001-0.0132.712-2.287-0.4630.462-0.703-1.5820.006
135A137ILE 00.002-0.0034.707-0.481-0.354-0.001-0.011-0.1140.000
136A138HIS 00.0420.0268.136-1.220-1.2200.0000.0000.0000.000
137A139SER 0-0.007-0.0225.488-1.348-1.3480.0000.0000.0000.000
138A140LEU 0-0.0080.0027.208-0.706-0.7060.0000.0000.0000.000
139A141ARG 10.8410.9148.535-19.379-19.3790.0000.0000.0000.000
140A142VAL 00.0120.01311.098-1.260-1.2600.0000.0000.0000.000
141A143CYS 0-0.0290.0059.714-1.690-1.6900.0000.0000.0000.000
142A144VAL 00.0170.01711.797-1.236-1.2360.0000.0000.0000.000
143A145ASP -1-0.806-0.89714.28915.62015.6200.0000.0000.0000.000
144A146THR 0-0.127-0.07014.928-1.507-1.5070.0000.0000.0000.000
145A147VAL 0-0.045-0.00913.286-0.776-0.7760.0000.0000.0000.000
146A148ARG 10.9120.96116.527-14.331-14.3310.0000.0000.0000.000
147A149THR 0-0.0350.00618.319-0.340-0.3400.0000.0000.0000.000
148A150ASN 0-0.0180.00017.4560.7300.7300.0000.0000.0000.000
149A151VAL 00.0120.00011.2870.3450.3450.0000.0000.0000.000
150A152TYR 00.0220.02412.077-0.642-0.6420.0000.0000.0000.000
151A153LEU 00.013-0.0126.9621.5741.5740.0000.0000.0000.000
152A154ALA 0-0.014-0.0116.063-2.692-2.6920.0000.0000.0000.000
153A155VAL 0-0.0010.0122.4099.21012.3662.261-2.132-3.2850.023
154A156PHE 00.0050.0051.931-30.338-29.9737.995-2.907-5.4530.049
155A157ASP -1-0.866-0.9333.03722.07924.5420.501-1.216-1.7480.009
156A158LYS 10.8500.9034.739-25.490-25.3240.001-0.028-0.1400.000
157A159ASN 00.0310.0067.896-2.842-2.8420.0000.0000.0000.000
158A160LEU 0-0.046-0.0212.726-4.629-3.4572.866-0.729-3.3090.008
159A161TYR 00.0080.0066.836-2.671-2.6710.0000.0000.0000.000
160A162ASP -1-0.761-0.8567.58822.10422.1040.0000.0000.0000.000
161A163LYS 10.9320.9847.410-26.436-26.4360.0000.0000.0000.000
162A164LEU 0-0.034-0.0094.451-1.521-1.407-0.001-0.006-0.1080.000
163A165VAL 00.0130.0119.100-1.675-1.6750.0000.0000.0000.000
164A166SER 0-0.052-0.03511.998-1.915-1.9150.0000.0000.0000.000
165A167SER 0-0.105-0.07111.623-1.092-1.0920.0000.0000.0000.000
166A168PHE 00.0030.00812.105-0.142-0.1420.0000.0000.0000.000
167A169LEU -1-0.834-0.87814.09715.26615.2660.0000.0000.0000.000
168A306HOH 0-0.065-0.05129.599-0.020-0.0200.0000.0000.0000.000
169A310HOH 00.0290.02821.1260.2980.2980.0000.0000.0000.000
170A313HOH 0-0.040-0.0253.229-0.6120.1370.037-0.437-0.350-0.003
171A318HOH 0-0.008-0.02120.8020.1190.1190.0000.0000.0000.000
172A333HOH 0-0.074-0.06024.3420.0850.0850.0000.0000.0000.000
173A342HOH 0-0.021-0.00412.207-0.544-0.5440.0000.0000.0000.000
174A344HOH 0-0.050-0.03615.735-0.303-0.3030.0000.0000.0000.000
175A345HOH 0-0.048-0.03819.431-0.235-0.2350.0000.0000.0000.000
176A349HOH 00.008-0.00518.611-0.257-0.2570.0000.0000.0000.000
177A350HOH 0-0.021-0.02324.165-0.024-0.0240.0000.0000.0000.000
178A352HOH 0-0.029-0.03712.9600.0520.0520.0000.0000.0000.000
179A355HOH 0-0.013-0.03617.8610.4480.4480.0000.0000.0000.000
180A365HOH 0-0.013-0.01110.0570.9420.9420.0000.0000.0000.000
181A370HOH 0-0.028-0.01816.9890.2030.2030.0000.0000.0000.000
182A375HOH 0-0.060-0.03825.016-0.160-0.1600.0000.0000.0000.000
183A376HOH 00.0140.00219.455-0.076-0.0760.0000.0000.0000.000
184A382HOH 0-0.017-0.01013.5840.1380.1380.0000.0000.0000.000
185A384HOH 0-0.019-0.02716.310-0.325-0.3250.0000.0000.0000.000
186A388HOH 0-0.004-0.00423.7470.1980.1980.0000.0000.0000.000
187A393HOH 00.012-0.0067.8050.9750.9750.0000.0000.0000.000
188A397HOH 0-0.008-0.01619.400-0.346-0.3460.0000.0000.0000.000
189A399HOH 00.0240.01411.6571.0311.0310.0000.0000.0000.000
190A401HOH 0-0.039-0.0511.711-22.333-28.20315.332-5.771-3.6920.046
191A403HOH 0-0.080-0.06717.993-0.289-0.2890.0000.0000.0000.000
192A405HOH 0-0.021-0.02118.060-0.366-0.3660.0000.0000.0000.000
193A406HOH 0-0.023-0.04022.8400.1960.1960.0000.0000.0000.000
194A410HOH 00.004-0.00120.4370.2290.2290.0000.0000.0000.000
195A413HOH 00.016-0.01413.3700.4790.4790.0000.0000.0000.000
196A418HOH 0-0.030-0.01920.1220.1070.1070.0000.0000.0000.000
197A422HOH 0-0.019-0.01710.511-0.323-0.3230.0000.0000.0000.000
198A425HOH 00.0250.01120.6160.0550.0550.0000.0000.0000.000
199A426HOH 0-0.009-0.01013.340-0.689-0.6890.0000.0000.0000.000
200A428HOH 0-0.007-0.01220.1870.1280.1280.0000.0000.0000.000
201A431HOH 0-0.058-0.04010.675-0.227-0.2270.0000.0000.0000.000
202A432HOH 0-0.060-0.05515.210-0.108-0.1080.0000.0000.0000.000
203A433HOH 0-0.027-0.0206.692-1.079-1.0790.0000.0000.0000.000
204A438HOH 00.0050.0017.6302.2402.2400.0000.0000.0000.000
205A453HOH 0-0.035-0.02622.2860.1480.1480.0000.0000.0000.000
206A454HOH 0-0.001-0.00319.576-0.232-0.2320.0000.0000.0000.000
207A488HOH 0-0.033-0.02815.430-0.019-0.0190.0000.0000.0000.000