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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: Q111Y

Calculation Name: 5RVE-A-Xray89

Preferred Name:

Target Type:

Ligand Name: {[(2s)-1-oxo-1-(2-oxoimidazolidin-1-yl)propan-2-yl]sulfanyl}acetic acid

ligand 3-letter code: W8A

PDB ID: 5RVE

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 W8A=-1
Software ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613
Total energy (hartree)
FMO2-HF: Electronic energy -1799806.936165
FMO2-HF: Nuclear repulsion 1733427.588769
FMO2-HF: Total energy -66379.347397
FMO2-MP2: Total energy -66572.892046


3D Structure
Snapshot
 
Ligand structure

W8A

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.
-152.380-151.36076.790-29.273-48.539-0.173


Interactive mode: IFIE and PIEDA for fragment #204(A:201:W8A )


Summations of interaction energy for fragment #204(A:201:W8A )
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.
-152.38-151.3676.79-29.273-48.5390.173
Interaction energy analysis for fragmet #204(A:201:W8A )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.828 / q_NPA : -0.872
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 00.012-0.00723.9530.0760.0760.0000.0000.0000.000
2A4ASN 0-0.016-0.01818.6410.2920.2920.0000.0000.0000.000
3A5SER 00.0280.00617.797-0.166-0.1660.0000.0000.0000.000
4A6PHE 0-0.0390.00612.1610.3800.3800.0000.0000.0000.000
5A7SER 00.0300.00915.250-0.479-0.4790.0000.0000.0000.000
6A8GLY 00.003-0.00914.8281.3451.3450.0000.0000.0000.000
7A9TYR 0-0.051-0.03610.4731.6201.6200.0000.0000.0000.000
8A10LEU 0-0.0100.00713.301-1.917-1.9170.0000.0000.0000.000
9A11LYS 10.8010.89114.209-14.676-14.6760.0000.0000.0000.000
10A12LEU 0-0.053-0.01911.518-0.166-0.1660.0000.0000.0000.000
11A13THR 00.0250.00016.059-0.787-0.7870.0000.0000.0000.000
12A14ASP -1-0.875-0.91518.69513.93613.9360.0000.0000.0000.000
13A15ASN 0-0.004-0.00517.030-0.388-0.3880.0000.0000.0000.000
14A16VAL 00.0070.01612.5640.9140.9140.0000.0000.0000.000
15A17TYR 00.0300.02213.461-1.107-1.1070.0000.0000.0000.000
16A18ILE 00.0290.0157.4782.4702.4700.0000.0000.0000.000
17A19LYS 10.8260.8988.617-27.919-27.9190.0000.0000.0000.000
18A20ASN 00.0170.0146.6819.4849.4840.0000.0000.0000.000
19A21ALA 0-0.043-0.0336.586-6.504-6.5040.0000.0000.0000.000
20A22ASP -1-0.811-0.9013.82831.86632.1360.000-0.040-0.2300.000
21A23ILE 00.0370.0042.583-4.154-2.7910.303-0.391-1.2760.001
22A24VAL 00.0320.0234.664-2.266-2.163-0.001-0.008-0.0950.000
23A25GLU -1-0.833-0.9006.71217.43617.4360.0000.0000.0000.000
24A26GLU -1-0.774-0.8547.58221.79421.7940.0000.0000.0000.000
25A27ALA 0-0.023-0.0238.502-1.603-1.6030.0000.0000.0000.000
26A28LYS 10.8160.89810.368-19.483-19.4830.0000.0000.0000.000
27A29LYS 10.8180.90612.137-21.180-21.1800.0000.0000.0000.000
28A30VAL 0-0.047-0.02813.195-0.895-0.8950.0000.0000.0000.000
29A31LYS 10.8700.95914.067-16.053-16.0530.0000.0000.0000.000
30A32PRO 00.0070.02312.103-0.694-0.6940.0000.0000.0000.000
31A33THR 00.028-0.01015.428-0.344-0.3440.0000.0000.0000.000
32A34VAL 0-0.021-0.01713.336-0.423-0.4230.0000.0000.0000.000
33A35VAL 00.0090.0108.7800.9100.9100.0000.0000.0000.000
34A36VAL 00.0080.0007.360-1.284-1.2840.0000.0000.0000.000
35A37ASN 00.003-0.0207.1095.0775.0770.0000.0000.0000.000
36A38ALA 0-0.0250.0073.631-1.434-1.2350.006-0.046-0.1590.000
37A39ALA 00.0350.0295.6750.2430.2430.0000.0000.0000.000
38A40ASN 0-0.008-0.0279.197-0.853-0.8530.0000.0000.0000.000
39A41VAL 00.0380.01811.628-0.389-0.3890.0000.0000.0000.000
40A42TYR 00.0040.00315.112-0.650-0.6500.0000.0000.0000.000
41A43LEU 0-0.0050.01013.406-0.325-0.3250.0000.0000.0000.000
42A44LYS 10.9761.00513.811-15.330-15.3300.0000.0000.0000.000
43A45HIS 00.0260.0159.8783.0173.0170.0000.0000.0000.000
44A46GLY 00.0390.0309.983-0.424-0.4240.0000.0000.0000.000
45A47GLY 00.0250.0016.557-1.216-1.2160.0000.0000.0000.000
46A48GLY 00.0410.0332.3310.8711.2761.219-0.433-1.1910.001
47A49VAL 00.0140.0232.373-11.509-10.1056.607-1.610-6.4010.012
48A50ALA 00.0590.0343.617-4.916-4.4420.013-0.004-0.4830.000
49A51GLY 0-0.020-0.0015.992-2.563-2.5630.0000.0000.0000.000
50A52ALA 0-0.006-0.0033.181-2.427-2.1160.047-0.080-0.2780.000
51A53LEU 00.0300.0035.115-1.843-1.737-0.001-0.004-0.1010.000
52A54ASN 00.0570.0067.394-2.125-2.1250.0000.0000.0000.000
53A55LYS 10.9570.9878.442-18.566-18.5660.0000.0000.0000.000
54A56ALA 0-0.032-0.0078.767-1.138-1.1380.0000.0000.0000.000
55A57THR 0-0.043-0.01110.590-0.904-0.9040.0000.0000.0000.000
56A58ASN 0-0.042-0.02913.203-0.720-0.7200.0000.0000.0000.000
57A59ASN 00.0000.00213.696-0.084-0.0840.0000.0000.0000.000
58A60ALA 00.0290.02415.114-0.278-0.2780.0000.0000.0000.000
59A61MET 00.0170.01911.0240.2410.2410.0000.0000.0000.000
60A62GLN 0-0.048-0.03013.9920.9850.9850.0000.0000.0000.000
61A63VAL 00.0160.01815.798-0.354-0.3540.0000.0000.0000.000
62A64GLU -1-0.723-0.83717.75114.14314.1430.0000.0000.0000.000
63A65SER 00.002-0.00515.9290.1210.1210.0000.0000.0000.000
64A66ASP -1-0.860-0.92318.21913.51613.5160.0000.0000.0000.000
65A67ASP -1-0.893-0.91520.46310.73510.7350.0000.0000.0000.000
66A68TYR 00.0440.01019.185-0.248-0.2480.0000.0000.0000.000
67A69ILE 0-0.039-0.02417.790-0.258-0.2580.0000.0000.0000.000
68A70ALA 0-0.032-0.00321.640-0.323-0.3230.0000.0000.0000.000
69A71THR 0-0.043-0.00824.894-0.530-0.5300.0000.0000.0000.000
70A72ASN 0-0.092-0.05522.569-0.547-0.5470.0000.0000.0000.000
71A73GLY 00.0180.02723.323-0.058-0.0580.0000.0000.0000.000
72A74PRO 0-0.068-0.04119.2420.4340.4340.0000.0000.0000.000
73A75LEU 0-0.0060.00014.255-0.322-0.3220.0000.0000.0000.000
74A76LYS 10.9820.98517.900-12.623-12.6230.0000.0000.0000.000
75A77VAL 00.0290.00413.0890.6870.6870.0000.0000.0000.000
76A78GLY 00.0070.01513.593-0.765-0.7650.0000.0000.0000.000
77A79GLY 0-0.026-0.00514.801-0.296-0.2960.0000.0000.0000.000
78A80SER 0-0.015-0.03913.7271.0581.0580.0000.0000.0000.000
79A81CYS 0-0.0440.00514.833-0.773-0.7730.0000.0000.0000.000
80A82VAL 00.0100.01015.3091.0561.0560.0000.0000.0000.000
81A83LEU 00.0020.00716.112-0.773-0.7730.0000.0000.0000.000
82A84SER 00.0290.01317.6020.4560.4560.0000.0000.0000.000
83A85GLY 0-0.0080.00914.7770.8580.8580.0000.0000.0000.000
84A86HIS 0-0.032-0.03314.7130.2110.2110.0000.0000.0000.000
85A87ASN 0-0.021-0.02414.0170.0080.0080.0000.0000.0000.000
86A88LEU 0-0.020-0.0219.5980.0760.0760.0000.0000.0000.000
87A89ALA 0-0.007-0.00213.0960.6570.6570.0000.0000.0000.000
88A90LYS 10.8490.94515.002-13.194-13.1940.0000.0000.0000.000
89A91HIS 00.0250.00917.056-1.034-1.0340.0000.0000.0000.000
90A92CYS 0-0.0090.00011.9901.5651.5650.0000.0000.0000.000
91A93LEU 0-0.0370.00212.467-1.022-1.0220.0000.0000.0000.000
92A94HIS 00.0510.00510.7173.2413.2410.0000.0000.0000.000
93A95VAL 00.0180.0039.230-1.643-1.6430.0000.0000.0000.000
94A96VAL 0-0.0280.0138.9682.1002.1000.0000.0000.0000.000
95A97GLY 00.0460.0268.695-1.245-1.2450.0000.0000.0000.000
96A98PRO 0-0.0070.0059.622-0.035-0.0350.0000.0000.0000.000
97A99ASN 0-0.015-0.0039.2062.3922.3920.0000.0000.0000.000
98A100VAL 00.0580.0169.988-1.922-1.9220.0000.0000.0000.000
99A101ASN 0-0.061-0.0379.492-2.801-2.8010.0000.0000.0000.000
100A102LYS 10.8050.90512.128-20.592-20.5920.0000.0000.0000.000
101A103GLY 0-0.0100.00614.693-1.012-1.0120.0000.0000.0000.000
102A104GLU -1-0.783-0.84112.88318.66818.6680.0000.0000.0000.000
103A105ASP -1-0.829-0.91914.84716.17516.1750.0000.0000.0000.000
104A106ILE 00.0520.01111.0610.7270.7270.0000.0000.0000.000
105A107GLN 00.0100.00413.9851.0281.0280.0000.0000.0000.000
106A108LEU 0-0.046-0.02614.6130.0300.0300.0000.0000.0000.000
107A109LEU 0-0.021-0.0128.3510.4790.4790.0000.0000.0000.000
108A110LYS 10.8930.93612.272-15.563-15.5630.0000.0000.0000.000
109A111SER 00.0190.00114.750-0.041-0.0410.0000.0000.0000.000
110A112ALA 00.0250.01211.058-0.180-0.1800.0000.0000.0000.000
111A113TYR 00.027-0.0037.2060.6760.6760.0000.0000.0000.000
112A114GLU -1-0.815-0.86612.50714.53014.5300.0000.0000.0000.000
113A115ASN 0-0.065-0.02213.755-1.506-1.5060.0000.0000.0000.000
114A116PHE 00.0470.0008.377-0.313-0.3130.0000.0000.0000.000
115A117ASN 0-0.021-0.00414.688-0.408-0.4080.0000.0000.0000.000
116A118GLN 0-0.0420.00517.929-1.160-1.1600.0000.0000.0000.000
117A119HIS 0-0.040-0.02916.514-0.455-0.4550.0000.0000.0000.000
118A120GLU -1-0.879-0.93518.20213.35213.3520.0000.0000.0000.000
119A121VAL 00.006-0.01016.1130.3260.3260.0000.0000.0000.000
120A122LEU 0-0.0400.02212.521-0.333-0.3330.0000.0000.0000.000
121A123LEU 0-0.0170.0138.3540.3030.3030.0000.0000.0000.000
122A124ALA 00.016-0.0107.730-1.248-1.2480.0000.0000.0000.000
123A125PRO 00.0020.0202.3721.0202.3690.986-0.603-1.7310.000
124A126LEU 00.0230.0073.341-9.719-8.7280.023-0.205-0.8090.000
125A127LEU 00.0000.0072.711-0.2631.2930.543-0.869-1.229-0.012
126A128SER 00.004-0.0325.284-0.640-0.552-0.001-0.003-0.0840.000
127A129ALA 00.0110.0322.609-2.513-1.6500.821-0.388-1.2960.002
128A130GLY 00.0880.0323.0490.9012.5003.041-2.103-2.538-0.001
129A131ILE 0-0.002-0.0193.666-7.139-9.3350.0852.757-0.6460.001
130A132PHE 0-0.071-0.0054.938-5.368-5.3680.0000.0000.0000.000
131A133GLY 00.0230.0186.687-3.426-3.4260.0000.0000.0000.000
132A134ALA 00.0020.0097.488-2.444-2.4440.0000.0000.0000.000
133A135ASP -1-0.789-0.9027.66332.35132.3510.0000.0000.0000.000
134A136PRO 00.000-0.0115.324-0.828-0.718-0.001-0.010-0.0980.000
135A137ILE 00.0250.0107.354-0.040-0.0400.0000.0000.0000.000
136A138HIS 00.0290.02010.743-1.478-1.4780.0000.0000.0000.000
137A139SER 0-0.009-0.0246.225-1.562-1.5620.0000.0000.0000.000
138A140LEU 0-0.0060.0018.732-0.924-0.9240.0000.0000.0000.000
139A141ARG 10.8430.9179.945-20.776-20.7760.0000.0000.0000.000
140A142VAL 0-0.0020.00411.497-1.457-1.4570.0000.0000.0000.000
141A143CYS 0-0.0180.0099.731-1.964-1.9640.0000.0000.0000.000
142A144VAL 00.0210.01911.856-1.421-1.4210.0000.0000.0000.000
143A145ASP -1-0.804-0.89514.85016.36816.3680.0000.0000.0000.000
144A146THR 0-0.131-0.07314.508-1.621-1.6210.0000.0000.0000.000
145A147VAL 0-0.047-0.01012.527-0.869-0.8690.0000.0000.0000.000
146A148ARG 10.9100.96015.862-14.532-14.5320.0000.0000.0000.000
147A149THR 0-0.0340.00617.363-0.323-0.3230.0000.0000.0000.000
148A150ASN 0-0.0230.00017.1450.8390.8390.0000.0000.0000.000
149A151VAL 00.0150.00111.0290.1910.1910.0000.0000.0000.000
150A152TYR 00.0140.01911.909-0.474-0.4740.0000.0000.0000.000
151A153LEU 00.017-0.0077.1721.0591.0590.0000.0000.0000.000
152A154ALA 0-0.021-0.0155.264-2.614-2.6140.0000.0000.0000.000
153A155VAL 0-0.0090.0042.7266.3559.9001.783-2.044-3.2840.024
154A156PHE 0-0.039-0.0271.878-34.162-33.96619.543-7.354-12.3850.040
155A157ASP -1-0.820-0.9181.83819.31916.5499.466-2.975-3.7210.038
156A158LYS 10.8750.9183.856-26.468-26.1700.005-0.065-0.2390.001
157A159ASN 0-0.051-0.0297.066-1.682-1.6820.0000.0000.0000.000
158A160LEU 00.000-0.0032.533-7.731-5.9981.192-1.152-1.7730.017
159A161TYR 0-0.007-0.0065.277-4.826-4.8260.0000.0000.0000.000
160A162ASP -1-0.779-0.8656.57723.08423.0840.0000.0000.0000.000
161A163LYS 10.9390.9858.698-31.273-31.2730.0000.0000.0000.000
162A164LEU 0-0.038-0.0135.588-2.011-2.0110.0000.0000.0000.000
163A165VAL 00.0090.0109.568-2.251-2.2510.0000.0000.0000.000
164A166SER 0-0.042-0.02812.166-2.295-2.2950.0000.0000.0000.000
165A167SER 0-0.104-0.07112.170-1.362-1.3620.0000.0000.0000.000
166A168PHE 00.0000.00613.499-0.235-0.2350.0000.0000.0000.000
167A169LEU -1-0.834-0.87915.16616.12616.1260.0000.0000.0000.000
168A308HOH 0-0.042-0.0286.1701.6031.6240.000-0.001-0.0200.000
169A315HOH 0-0.008-0.02120.0030.1260.1260.0000.0000.0000.000
170A336HOH 0-0.078-0.06521.8000.0910.0910.0000.0000.0000.000
171A338HOH 0-0.053-0.03812.123-0.226-0.2260.0000.0000.0000.000
172A344HOH 0-0.021-0.02322.099-0.027-0.0270.0000.0000.0000.000
173A350HOH 0-0.039-0.03518.051-0.214-0.2140.0000.0000.0000.000
174A357HOH 0-0.007-0.0117.4351.0871.0870.0000.0000.0000.000
175A365HOH 0-0.014-0.03515.5500.4190.4190.0000.0000.0000.000
176A368HOH 0-0.032-0.03810.6500.0390.0390.0000.0000.0000.000
177A376HOH 0-0.059-0.03922.307-0.149-0.1490.0000.0000.0000.000
178A377HOH 0-0.033-0.0451.601-20.687-30.99620.137-6.777-3.0510.040
179A378HOH 00.0150.00316.954-0.089-0.0890.0000.0000.0000.000
180A382HOH 0-0.028-0.01717.5260.2090.2090.0000.0000.0000.000
181A384HOH 0-0.041-0.0258.032-0.420-0.4200.0000.0000.0000.000
182A385HOH 0-0.015-0.0099.7890.0040.0040.0000.0000.0000.000
183A386HOH 0-0.007-0.01617.810-0.324-0.3240.0000.0000.0000.000
184A389HOH 0-0.018-0.0049.490-0.567-0.5670.0000.0000.0000.000
185A390HOH 00.0260.0025.2921.5711.5710.0000.0000.0000.000
186A401HOH 0-0.017-0.02514.605-0.338-0.3380.0000.0000.0000.000
187A403HOH 0-0.020-0.03823.1770.2060.2060.0000.0000.0000.000
188A404HOH 00.0210.01211.4541.0001.0000.0000.0000.0000.000
189A407HOH 0-0.009-0.0124.572-1.385-1.3280.000-0.012-0.0450.000
190A409HOH 0-0.079-0.06718.901-0.328-0.3280.0000.0000.0000.000
191A411HOH 0-0.020-0.02118.017-0.391-0.3910.0000.0000.0000.000
192A417HOH 00.002-0.00218.0040.2230.2230.0000.0000.0000.000
193A421HOH 0-0.029-0.01919.7870.1290.1290.0000.0000.0000.000
194A425HOH 0-0.039-0.0309.232-0.434-0.4340.0000.0000.0000.000
195A428HOH 00.011-0.01510.9210.4890.4890.0000.0000.0000.000
196A429HOH 00.0300.01217.7220.0890.0890.0000.0000.0000.000
197A431HOH 0-0.017-0.01712.768-0.406-0.4060.0000.0000.0000.000
198A432HOH 0-0.059-0.05712.675-0.154-0.1540.0000.0000.0000.000
199A434HOH 00.0320.01821.8910.2660.2660.0000.0000.0000.000
200A436HOH 0-0.031-0.0272.636-2.262-1.2811.597-1.042-1.537-0.013
201A463HOH 00.001-0.0181.840-12.335-14.5148.274-3.176-2.9200.030
202A465HOH 0-0.003-0.00419.386-0.259-0.2590.0000.0000.0000.000
203A466HOH 0-0.0120.0022.5221.3361.7881.103-0.635-0.919-0.008