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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: N111Q

Calculation Name: 5RTY-A-Xray89

Preferred Name:

Target Type:

Ligand Name: 4-hydroxybenzamide

ligand 3-letter code: HBD

PDB ID: 5RTY

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 214
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613
Total energy (hartree)
FMO2-HF: Electronic energy -1811781.205551
FMO2-HF: Nuclear repulsion 1745283.507567
FMO2-HF: Total energy -66497.697984
FMO2-MP2: Total energy -66692.365939


3D Structure
Snapshot
 
Ligand structure

HBD

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.
-70.287-65.46542.008-18.454-28.3770.054


Interactive mode: IFIE and PIEDA for fragment #214(A:201:HBD )


Summations of interaction energy for fragment #214(A:201:HBD )
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.
-70.287-65.46542.008-18.454-28.377-0.054
Interaction energy analysis for fragmet #214(A:201:HBD )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.054 / q_NPA : -0.053
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 00.012-0.00624.574-0.001-0.0010.0000.0000.0000.000
2A4ASN 0-0.014-0.01719.364-0.057-0.0570.0000.0000.0000.000
3A5SER 00.0290.00518.4430.0270.0270.0000.0000.0000.000
4A6PHE 0-0.0420.00412.765-0.110-0.1100.0000.0000.0000.000
5A7SER 00.0280.01115.9830.1150.1150.0000.0000.0000.000
6A8GLY 00.012-0.00515.552-0.217-0.2170.0000.0000.0000.000
7A9TYR 0-0.067-0.04311.323-0.186-0.1860.0000.0000.0000.000
8A10LEU 00.0110.01615.5730.1620.1620.0000.0000.0000.000
9A11LYS 10.8070.89516.6960.6130.6130.0000.0000.0000.000
10A12LEU 0-0.069-0.02714.4160.0370.0370.0000.0000.0000.000
11A13THR 00.026-0.00118.8310.0610.0610.0000.0000.0000.000
12A14ASP -1-0.864-0.90521.281-0.579-0.5790.0000.0000.0000.000
13A15ASN 0-0.006-0.01019.5370.0130.0130.0000.0000.0000.000
14A16VAL 00.0110.02014.759-0.104-0.1040.0000.0000.0000.000
15A17TYR 00.0390.02615.4520.0930.0930.0000.0000.0000.000
16A18ILE 00.0190.01010.464-0.254-0.2540.0000.0000.0000.000
17A19LYS 10.8340.90210.7602.6722.6720.0000.0000.0000.000
18A20ASN 0-0.062-0.0278.290-0.233-0.2330.0000.0000.0000.000
19A21ALA 00.0170.0027.4540.4930.4930.0000.0000.0000.000
20A22ASP -1-0.773-0.8781.879-37.863-39.60613.071-5.482-5.846-0.068
21A23ILE 00.002-0.0202.6180.5811.7010.348-0.270-1.198-0.001
22A24VAL 0-0.0020.0042.9582.5873.6720.187-0.350-0.9220.002
23A25GLU -1-0.818-0.8975.000-1.546-1.448-0.001-0.004-0.0930.000
24A26GLU -1-0.760-0.8397.206-1.621-1.6210.0000.0000.0000.000
25A27ALA 0-0.004-0.0038.4110.6940.6940.0000.0000.0000.000
26A28LYS 10.8320.9077.5672.8742.8740.0000.0000.0000.000
27A29LYS 10.8290.91611.2622.4942.4940.0000.0000.0000.000
28A30VAL 0-0.045-0.03112.9420.2150.2150.0000.0000.0000.000
29A31LYS 10.8750.96313.8091.2131.2130.0000.0000.0000.000
30A32PRO 00.0010.01612.5740.1470.1470.0000.0000.0000.000
31A33THR 00.031-0.00415.8040.0570.0570.0000.0000.0000.000
32A34VAL 0-0.015-0.01414.3800.0950.0950.0000.0000.0000.000
33A35VAL 00.0120.0119.034-0.209-0.2090.0000.0000.0000.000
34A36VAL 0-0.006-0.0059.9840.2970.2970.0000.0000.0000.000
35A37ASN 00.004-0.0228.370-0.431-0.4310.0000.0000.0000.000
36A38ALA 0-0.0250.0096.8670.0320.0320.0000.0000.0000.000
37A39ALA 00.0350.0258.8100.6300.6300.0000.0000.0000.000
38A40ASN 00.002-0.01611.977-0.142-0.1420.0000.0000.0000.000
39A41VAL 00.0450.01914.254-0.060-0.0600.0000.0000.0000.000
40A42TYR 0-0.006-0.00517.474-0.052-0.0520.0000.0000.0000.000
41A43LEU 00.0000.01415.4090.0030.0030.0000.0000.0000.000
42A44LYS 10.9761.00415.220-0.913-0.9130.0000.0000.0000.000
43A45HIS 00.0220.01310.6830.3290.3290.0000.0000.0000.000
44A46GLY 00.0480.03910.4450.2050.2050.0000.0000.0000.000
45A47GLY 00.0400.0136.6540.3700.3700.0000.0000.0000.000
46A48GLY 0-0.0080.0083.365-1.476-0.9250.083-0.262-0.3720.002
47A49VAL 00.0200.0042.282-1.3310.8193.003-1.260-3.8930.010
48A50ALA 00.0320.0244.266-1.531-1.2210.018-0.017-0.3100.001
49A51GLY 0-0.026-0.0036.889-0.519-0.5190.0000.0000.0000.000
50A52ALA 00.0160.0172.681-2.273-1.3493.056-1.330-2.6500.013
51A53LEU 00.0310.0054.735-2.213-1.9980.000-0.042-0.1730.000
52A54ASN 00.0530.0047.185-0.494-0.4940.0000.0000.0000.000
53A55LYS 10.9691.0016.011-3.810-3.8100.0000.0000.0000.000
54A56ALA 0-0.032-0.0066.709-0.325-0.3250.0000.0000.0000.000
55A57THR 0-0.058-0.0188.578-0.201-0.2010.0000.0000.0000.000
56A58ASN 0-0.040-0.02611.4370.0740.0740.0000.0000.0000.000
57A59ASN 00.0020.00412.5520.1680.1680.0000.0000.0000.000
58A60ALA 00.0340.02514.289-0.010-0.0100.0000.0000.0000.000
59A61MET 0-0.0010.00910.7400.0530.0530.0000.0000.0000.000
60A62GLN 0-0.056-0.02914.2970.1870.1870.0000.0000.0000.000
61A63VAL 00.0320.02715.999-0.031-0.0310.0000.0000.0000.000
62A64GLU -1-0.731-0.84517.719-0.145-0.1450.0000.0000.0000.000
63A65SER 00.006-0.00616.438-0.035-0.0350.0000.0000.0000.000
64A66ASP -1-0.817-0.89818.8300.5910.5910.0000.0000.0000.000
65A67ASP -1-0.821-0.85921.3280.0970.0970.0000.0000.0000.000
66A68TYR 00.011-0.01421.068-0.037-0.0370.0000.0000.0000.000
67A69ILE 0-0.042-0.02620.161-0.017-0.0170.0000.0000.0000.000
68A70ALA 0-0.027-0.00223.572-0.010-0.0100.0000.0000.0000.000
69A71THR 0-0.039-0.00626.435-0.017-0.0170.0000.0000.0000.000
70A72ASN 0-0.086-0.05124.947-0.035-0.0350.0000.0000.0000.000
71A73GLY 00.0270.02825.986-0.009-0.0090.0000.0000.0000.000
72A74PRO 0-0.040-0.02122.052-0.008-0.0080.0000.0000.0000.000
73A75LEU 0-0.021-0.00517.310-0.045-0.0450.0000.0000.0000.000
74A76LYS 10.9340.95321.1110.0030.0030.0000.0000.0000.000
75A77VAL 00.0400.01216.862-0.017-0.0170.0000.0000.0000.000
76A78GLY 00.0150.02017.248-0.026-0.0260.0000.0000.0000.000
77A79GLY 0-0.030-0.01018.444-0.074-0.0740.0000.0000.0000.000
78A80SER 0-0.017-0.04317.124-0.015-0.0150.0000.0000.0000.000
79A81CYS 0-0.0330.01017.5400.0310.0310.0000.0000.0000.000
80A82VAL 00.0090.00717.446-0.060-0.0600.0000.0000.0000.000
81A83LEU 00.0080.01317.1390.0630.0630.0000.0000.0000.000
82A84SER 00.0220.00817.950-0.153-0.1530.0000.0000.0000.000
83A85GLY 0-0.0100.00814.4990.0040.0040.0000.0000.0000.000
84A86HIS 0-0.029-0.03314.202-0.118-0.1180.0000.0000.0000.000
85A87ASN 0-0.027-0.02511.971-0.033-0.0330.0000.0000.0000.000
86A88LEU 0-0.010-0.0148.805-0.188-0.1880.0000.0000.0000.000
87A89ALA 0-0.009-0.00712.464-0.240-0.2400.0000.0000.0000.000
88A90LYS 10.8490.94414.8890.6010.6010.0000.0000.0000.000
89A91HIS 00.0340.01617.1830.1130.1130.0000.0000.0000.000
90A92CYS 0-0.013-0.00412.503-0.236-0.2360.0000.0000.0000.000
91A93LEU 0-0.0370.00113.8140.1640.1640.0000.0000.0000.000
92A94HIS 00.0530.00512.927-0.064-0.0640.0000.0000.0000.000
93A95VAL 00.0110.00212.5720.0620.0620.0000.0000.0000.000
94A96VAL 0-0.0390.00712.4300.0860.0860.0000.0000.0000.000
95A97GLY 00.0590.03512.410-0.091-0.0910.0000.0000.0000.000
96A98PRO 0-0.0110.00313.4060.1600.1600.0000.0000.0000.000
97A99ASN 0-0.027-0.01312.0040.0380.0380.0000.0000.0000.000
98A100VAL 00.0680.02713.417-0.060-0.0600.0000.0000.0000.000
99A101ASN 0-0.059-0.02911.199-0.189-0.1890.0000.0000.0000.000
100A102LYS 10.8170.90914.773-0.876-0.8760.0000.0000.0000.000
101A103GLY 00.0020.01017.640-0.056-0.0560.0000.0000.0000.000
102A104GLU -1-0.786-0.84216.5130.4890.4890.0000.0000.0000.000
103A105ASP -1-0.817-0.91318.6590.1000.1000.0000.0000.0000.000
104A106ILE 00.0510.01214.947-0.011-0.0110.0000.0000.0000.000
105A107GLN 0-0.0020.00018.004-0.084-0.0840.0000.0000.0000.000
106A108LEU 0-0.045-0.02518.595-0.043-0.0430.0000.0000.0000.000
107A109LEU 0-0.031-0.01912.413-0.030-0.0300.0000.0000.0000.000
108A110LYS 10.8730.93216.3180.2160.2160.0000.0000.0000.000
109A111SER 00.029-0.01018.799-0.049-0.0490.0000.0000.0000.000
110A112ALA 00.0260.01114.737-0.025-0.0250.0000.0000.0000.000
111A113TYR 00.0250.00011.010-0.175-0.1750.0000.0000.0000.000
112A114GLU -1-0.858-0.91416.156-0.293-0.2930.0000.0000.0000.000
113A115ASN 0-0.059-0.02617.1160.0130.0130.0000.0000.0000.000
114A116PHE 00.0460.00111.319-0.044-0.0440.0000.0000.0000.000
115A117ASN 0-0.0090.00717.518-0.057-0.0570.0000.0000.0000.000
116A118GLN 0-0.0210.01820.6730.0390.0390.0000.0000.0000.000
117A119HIS 0-0.035-0.02218.374-0.033-0.0330.0000.0000.0000.000
118A120GLU -1-0.871-0.92920.003-0.559-0.5590.0000.0000.0000.000
119A121VAL 00.006-0.01316.986-0.036-0.0360.0000.0000.0000.000
120A122LEU 0-0.0320.02713.7380.0210.0210.0000.0000.0000.000
121A123LEU 0-0.0160.0138.888-0.041-0.0410.0000.0000.0000.000
122A124ALA 00.027-0.0028.8840.1400.1400.0000.0000.0000.000
123A125PRO 0-0.0400.0014.560-0.779-0.712-0.001-0.009-0.0580.000
124A126LEU 00.0200.0045.7770.8840.8840.0000.0000.0000.000
125A127LEU 00.0150.0266.7580.3410.3410.0000.0000.0000.000
126A128SER 00.032-0.0129.189-0.056-0.0560.0000.0000.0000.000
127A129ALA 0-0.0080.0175.7780.1750.1750.0000.0000.0000.000
128A130GLY 00.0410.0314.4230.7280.841-0.001-0.028-0.0840.000
129A131ILE 00.013-0.0084.860-0.861-0.8610.0000.0000.0000.000
130A132PHE 0-0.068-0.0237.148-0.459-0.4590.0000.0000.0000.000
131A133GLY 00.0260.0209.202-0.299-0.2990.0000.0000.0000.000
132A134ALA 00.0000.00510.646-0.160-0.1600.0000.0000.0000.000
133A135ASP -1-0.792-0.89410.746-0.034-0.0340.0000.0000.0000.000
134A136PRO 0-0.013-0.0218.156-0.125-0.1250.0000.0000.0000.000
135A137ILE 00.013-0.00210.193-0.210-0.2100.0000.0000.0000.000
136A138HIS 00.0530.03113.508-0.088-0.0880.0000.0000.0000.000
137A139SER 0-0.012-0.02410.262-0.133-0.1330.0000.0000.0000.000
138A140LEU 0-0.018-0.00811.760-0.105-0.1050.0000.0000.0000.000
139A141ARG 10.8480.92013.0620.4450.4450.0000.0000.0000.000
140A142VAL 00.0130.01315.4200.0090.0090.0000.0000.0000.000
141A143CYS 0-0.045-0.00413.166-0.035-0.0350.0000.0000.0000.000
142A144VAL 00.0140.01115.3170.0140.0140.0000.0000.0000.000
143A145ASP -1-0.805-0.89617.955-0.373-0.3730.0000.0000.0000.000
144A146THR 0-0.117-0.06118.1840.0900.0900.0000.0000.0000.000
145A147VAL 0-0.062-0.02215.6570.0340.0340.0000.0000.0000.000
146A148ARG 10.9490.98719.0600.3800.3800.0000.0000.0000.000
147A149THR 0-0.044-0.00319.4900.0030.0030.0000.0000.0000.000
148A150ASN 0-0.0140.00319.002-0.041-0.0410.0000.0000.0000.000
149A151VAL 00.0150.00612.880-0.064-0.0640.0000.0000.0000.000
150A152TYR 00.0250.02112.8850.0950.0950.0000.0000.0000.000
151A153LEU 00.021-0.0039.338-0.347-0.3470.0000.0000.0000.000
152A154ALA 00.0260.0126.0420.1700.1700.0000.0000.0000.000
153A155VAL 0-0.0120.0045.197-1.963-1.9630.0000.0000.0000.000
154A156PHE 00.0110.0112.728-2.6451.4374.336-1.731-6.6870.008
155A157ASP -1-0.854-0.9234.8240.6920.8930.000-0.018-0.1820.000
156A158LYS 10.8890.9297.1420.9320.9320.0000.0000.0000.000
157A159ASN 0-0.011-0.00810.6150.0960.0960.0000.0000.0000.000
158A160LEU 0-0.002-0.0106.4210.0530.0530.0000.0000.0000.000
159A161TYR 0-0.014-0.0089.4130.0210.0210.0000.0000.0000.000
160A162ASP -1-0.779-0.86710.562-0.838-0.8380.0000.0000.0000.000
161A163LYS 10.9501.00212.9160.3040.3040.0000.0000.0000.000
162A164LEU 0-0.034-0.0118.9560.0400.0400.0000.0000.0000.000
163A165VAL 00.0020.00613.3680.0520.0520.0000.0000.0000.000
164A166SER 0-0.062-0.04715.8710.1000.1000.0000.0000.0000.000
165A167SER 0-0.078-0.05716.1140.0730.0730.0000.0000.0000.000
166A168PHE 0-0.0040.00216.5230.0210.0210.0000.0000.0000.000
167A169LEU -1-0.830-0.87618.533-0.444-0.4440.0000.0000.0000.000
168A301HOH 0-0.005-0.0123.176-3.632-2.8070.080-0.474-0.431-0.004
169A302HOH 00.0300.0141.941-8.021-8.8066.144-2.721-2.6380.025
170A307HOH 00.0290.02823.825-0.001-0.0010.0000.0000.0000.000
171A311HOH 0-0.065-0.05127.2190.0100.0100.0000.0000.0000.000
172A326HOH 0-0.075-0.06122.243-0.019-0.0190.0000.0000.0000.000
173A327HOH 0-0.042-0.03224.4010.0080.0080.0000.0000.0000.000
174A343HOH 0-0.049-0.03612.157-0.010-0.0100.0000.0000.0000.000
175A345HOH 0-0.008-0.0103.7981.1841.2480.000-0.011-0.0540.000
176A348HOH 0-0.026-0.0253.9030.6850.7470.000-0.014-0.0490.000
177A350HOH 00.007-0.0058.294-0.183-0.1830.0000.0000.0000.000
178A352HOH 0-0.020-0.02224.4680.0100.0100.0000.0000.0000.000
179A353HOH 0-0.026-0.00612.4400.0300.0300.0000.0000.0000.000
180A355HOH 0-0.054-0.04321.7560.0100.0100.0000.0000.0000.000
181A360HOH 0-0.014-0.03515.4920.0150.0150.0000.0000.0000.000
182A362HOH 0-0.057-0.03625.3860.0020.0020.0000.0000.0000.000
183A363HOH 0-0.009-0.01310.9620.0050.0050.0000.0000.0000.000
184A368HOH 0-0.039-0.02410.0210.0440.0440.0000.0000.0000.000
185A373HOH 0-0.027-0.0218.5330.0130.0130.0000.0000.0000.000
186A374HOH 0-0.004-0.00623.647-0.014-0.0140.0000.0000.0000.000
187A377HOH 0-0.017-0.0108.9630.0000.0000.0000.0000.0000.000
188A382HOH 00.0130.00119.822-0.016-0.0160.0000.0000.0000.000
189A386HOH 00.013-0.0024.362-0.758-0.6970.000-0.024-0.0370.000
190A394HOH 0-0.029-0.01820.377-0.015-0.0150.0000.0000.0000.000
191A395HOH 0-0.029-0.03714.1900.0610.0610.0000.0000.0000.000
192A398HOH 0-0.010-0.0138.399-0.345-0.3450.0000.0000.0000.000
193A399HOH 0-0.007-0.01618.7220.0250.0250.0000.0000.0000.000
194A400HOH 00.001-0.0095.3900.2870.2870.0000.0000.0000.000
195A402HOH 0-0.019-0.01921.1720.0270.0270.0000.0000.0000.000
196A404HOH 0-0.078-0.06722.3150.0080.0080.0000.0000.0000.000
197A410HOH 00.003-0.00220.594-0.029-0.0290.0000.0000.0000.000
198A412HOH 0-0.006-0.0086.3200.1450.1450.0000.0000.0000.000
199A413HOH 0-0.017-0.02515.3390.0170.0170.0000.0000.0000.000
200A419HOH 0-0.062-0.05915.8960.0310.0310.0000.0000.0000.000
201A420HOH 0-0.024-0.04125.336-0.017-0.0170.0000.0000.0000.000
202A421HOH 00.013-0.01212.622-0.029-0.0290.0000.0000.0000.000
203A427HOH 00.0000.00123.4030.0050.0050.0000.0000.0000.000
204A430HOH 0-0.020-0.01815.584-0.015-0.0150.0000.0000.0000.000
205A431HOH 00.0220.01013.709-0.114-0.1140.0000.0000.0000.000
206A434HOH 00.0340.01924.434-0.020-0.0200.0000.0000.0000.000
207A437HOH 00.0230.01021.4650.0080.0080.0000.0000.0000.000
208A455HOH 0-0.019-0.0264.029-0.675-0.4900.001-0.075-0.1110.000
209A457HOH 00.0210.01322.7850.0130.0130.0000.0000.0000.000
210A458HOH 0-0.032-0.02518.3670.0200.0200.0000.0000.0000.000
211A470HOH 0-0.015-0.0031.749-12.271-17.03411.684-4.332-2.589-0.042
212A472HOH 00.0430.03025.2470.0120.0120.0000.0000.0000.000
213A488HOH 0-0.035-0.0289.8510.0330.0330.0000.0000.0000.000