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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: ZY23N

Calculation Name: 5RVE-B-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: B

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2021-09-27

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 206
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613
Total energy (hartree)
FMO2-HF: Electronic energy -1786321.836094
FMO2-HF: Nuclear repulsion 1719939.66299
FMO2-HF: Total energy -66382.173104
FMO2-MP2: Total energy -66575.750655


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(B:1:SER )


Summations of interaction energy for fragment #1(B:1:SER )
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.
-2.2970.4920.008-1.292-1.5050.006
Interaction energy analysis for fragmet #1(B:1:SER )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : 0.005
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].
3B3VAL 00.0330.0093.444-0.7622.0270.008-1.292-1.5050.006
4B4ASN 0-0.005-0.0115.839-0.674-0.6740.0000.0000.0000.000
5B5SER 00.0130.0198.146-0.279-0.2790.0000.0000.0000.000
6B6PHE 0-0.009-0.01310.0950.1360.1360.0000.0000.0000.000
7B7SER 00.0210.00313.890-0.053-0.0530.0000.0000.0000.000
8B8GLY 00.0270.00715.7710.0520.0520.0000.0000.0000.000
9B9TYR 0-0.077-0.05716.6550.0280.0280.0000.0000.0000.000
10B10LEU 00.0250.02620.884-0.024-0.0240.0000.0000.0000.000
11B11LYS 10.8430.91822.8640.2030.2030.0000.0000.0000.000
12B12LEU 0-0.035-0.00324.8640.0060.0060.0000.0000.0000.000
13B13THR 00.031-0.01026.3390.0010.0010.0000.0000.0000.000
14B14ASP -1-0.871-0.94825.247-0.171-0.1710.0000.0000.0000.000
15B15ASN 0-0.048-0.02022.273-0.022-0.0220.0000.0000.0000.000
16B16VAL 00.0210.02422.1090.0100.0100.0000.0000.0000.000
17B17TYR 00.0010.00220.465-0.021-0.0210.0000.0000.0000.000
18B18ILE 00.0140.01022.6940.0220.0220.0000.0000.0000.000
19B19LYS 10.8380.89817.8600.0510.0510.0000.0000.0000.000
20B20ASN 0-0.040-0.00722.8650.0120.0120.0000.0000.0000.000
21B21ALA 00.014-0.01220.015-0.006-0.0060.0000.0000.0000.000
22B22ASP -1-0.771-0.86420.9600.1240.1240.0000.0000.0000.000
23B23ILE 00.0320.00218.7900.0090.0090.0000.0000.0000.000
24B24VAL 0-0.0010.00217.4890.0340.0340.0000.0000.0000.000
25B25GLU -1-0.946-0.97316.2000.1420.1420.0000.0000.0000.000
26B26GLU -1-0.776-0.86315.089-0.008-0.0080.0000.0000.0000.000
27B27ALA 0-0.0010.00213.4450.0040.0040.0000.0000.0000.000
28B28LYS 10.9150.96411.493-0.219-0.2190.0000.0000.0000.000
29B29LYS 10.7860.89210.4370.0980.0980.0000.0000.0000.000
30B30VAL 0-0.068-0.0309.584-0.035-0.0350.0000.0000.0000.000
31B31LYS 10.9570.9975.160-0.763-0.7630.0000.0000.0000.000
32B32PRO 00.0220.0308.0550.1650.1650.0000.0000.0000.000
33B33THR 00.0160.00410.0770.2510.2510.0000.0000.0000.000
34B34VAL 0-0.015-0.01510.7840.0280.0280.0000.0000.0000.000
35B35VAL 0-0.0100.00414.475-0.045-0.0450.0000.0000.0000.000
36B36VAL 0-0.012-0.00616.7060.0070.0070.0000.0000.0000.000
37B37ASN 00.004-0.02720.400-0.010-0.0100.0000.0000.0000.000
38B38ALA 0-0.0100.01922.920-0.011-0.0110.0000.0000.0000.000
39B39ALA 00.0300.03126.1830.0010.0010.0000.0000.0000.000
40B40ASN 00.023-0.00227.941-0.011-0.0110.0000.0000.0000.000
41B41VAL 00.0240.00930.5720.0080.0080.0000.0000.0000.000
42B42TYR 00.0370.01532.4270.0020.0020.0000.0000.0000.000
43B43LEU 0-0.037-0.00726.4620.0060.0060.0000.0000.0000.000
44B44LYS 10.8690.94329.068-0.105-0.1050.0000.0000.0000.000
45B45HIS 0-0.007-0.00525.730-0.018-0.0180.0000.0000.0000.000
46B46GLY 00.0340.02328.4750.0040.0040.0000.0000.0000.000
47B47GLY 00.0190.00130.4190.0020.0020.0000.0000.0000.000
48B48GLY 00.0110.00329.0600.0050.0050.0000.0000.0000.000
49B49VAL 00.0670.02923.1150.0090.0090.0000.0000.0000.000
50B50ALA 00.0160.02024.2380.0170.0170.0000.0000.0000.000
51B51GLY 0-0.0120.00725.0630.0160.0160.0000.0000.0000.000
52B52ALA 0-0.035-0.02723.5530.0110.0110.0000.0000.0000.000
53B53LEU 00.0150.00018.8570.0190.0190.0000.0000.0000.000
54B54ASN 00.0680.02120.8170.0400.0400.0000.0000.0000.000
55B55LYS 10.9250.96922.836-0.123-0.1230.0000.0000.0000.000
56B56ALA 00.0000.01818.5250.0090.0090.0000.0000.0000.000
57B57THR 0-0.045-0.01917.9180.0290.0290.0000.0000.0000.000
58B58ASN 0-0.018-0.01219.746-0.006-0.0060.0000.0000.0000.000
59B59ASN 0-0.018-0.01122.813-0.013-0.0130.0000.0000.0000.000
60B60ALA 00.0400.03120.496-0.011-0.0110.0000.0000.0000.000
61B61MET 00.0150.02219.789-0.015-0.0150.0000.0000.0000.000
62B62GLN 0-0.042-0.03622.482-0.016-0.0160.0000.0000.0000.000
63B63VAL 0-0.0090.00025.432-0.011-0.0110.0000.0000.0000.000
64B64GLU -1-0.712-0.83220.5850.2880.2880.0000.0000.0000.000
65B65SER 0-0.019-0.02124.833-0.012-0.0120.0000.0000.0000.000
66B66ASP -1-0.823-0.89226.6550.1140.1140.0000.0000.0000.000
67B67ASP -1-0.914-0.94727.4910.1480.1480.0000.0000.0000.000
68B68TYR 00.0440.00826.026-0.009-0.0090.0000.0000.0000.000
69B69ILE 0-0.028-0.01328.327-0.012-0.0120.0000.0000.0000.000
70B70ALA 0-0.0260.00131.625-0.009-0.0090.0000.0000.0000.000
71B71THR 0-0.040-0.00830.137-0.008-0.0080.0000.0000.0000.000
72B72ASN 0-0.088-0.05628.626-0.010-0.0100.0000.0000.0000.000
73B73GLY 0-0.0230.00132.378-0.008-0.0080.0000.0000.0000.000
74B74PRO 0-0.055-0.03132.5610.0060.0060.0000.0000.0000.000
75B75LEU 0-0.028-0.01227.603-0.004-0.0040.0000.0000.0000.000
76B76LYS 10.9980.99132.139-0.048-0.0480.0000.0000.0000.000
77B77VAL 00.0250.00032.5380.0040.0040.0000.0000.0000.000
78B78GLY 00.0030.01031.952-0.005-0.0050.0000.0000.0000.000
79B79GLY 00.0050.02329.886-0.004-0.0040.0000.0000.0000.000
80B80SER 0-0.044-0.05124.6830.0070.0070.0000.0000.0000.000
81B81CYS 0-0.0160.02224.634-0.005-0.0050.0000.0000.0000.000
82B82VAL 00.0170.01618.1810.0060.0060.0000.0000.0000.000
83B83LEU 0-0.0040.00819.934-0.006-0.0060.0000.0000.0000.000
84B84SER 00.0410.01816.4660.0580.0580.0000.0000.0000.000
85B85GLY 00.0150.01814.559-0.053-0.0530.0000.0000.0000.000
86B86HIS 0-0.026-0.02314.8640.0280.0280.0000.0000.0000.000
87B87ASN 0-0.061-0.04112.6180.0960.0960.0000.0000.0000.000
88B88LEU 0-0.028-0.01212.704-0.002-0.0020.0000.0000.0000.000
89B89ALA 00.0420.02611.053-0.014-0.0140.0000.0000.0000.000
90B90LYS 10.9200.9929.450-0.738-0.7380.0000.0000.0000.000
91B91HIS 00.013-0.00511.315-0.030-0.0300.0000.0000.0000.000
92B92CYS 0-0.029-0.01414.958-0.011-0.0110.0000.0000.0000.000
93B93LEU 0-0.0220.01017.998-0.014-0.0140.0000.0000.0000.000
94B94HIS 00.0430.00120.464-0.033-0.0330.0000.0000.0000.000
95B95VAL 00.0100.00123.607-0.009-0.0090.0000.0000.0000.000
96B96VAL 0-0.0300.01126.1980.0010.0010.0000.0000.0000.000
97B97GLY 00.0310.01729.891-0.008-0.0080.0000.0000.0000.000
98B98PRO 0-0.0020.01231.6020.0050.0050.0000.0000.0000.000
99B99ASN 00.0130.01234.732-0.004-0.0040.0000.0000.0000.000
100B100VAL 00.0800.03636.579-0.001-0.0010.0000.0000.0000.000
101B101ASN 0-0.043-0.01837.499-0.005-0.0050.0000.0000.0000.000
102B102LYS 10.7660.88136.370-0.054-0.0540.0000.0000.0000.000
103B103GLY 00.0050.01041.1830.0000.0000.0000.0000.0000.000
104B104GLU -1-0.826-0.86636.8320.0470.0470.0000.0000.0000.000
105B105ASP -1-0.814-0.91340.4740.0120.0120.0000.0000.0000.000
106B106ILE 00.0300.00036.4320.0020.0020.0000.0000.0000.000
107B107GLN 0-0.032-0.01737.2490.0010.0010.0000.0000.0000.000
108B108LEU 00.0220.00635.613-0.001-0.0010.0000.0000.0000.000
109B109LEU 0-0.036-0.01931.3000.0040.0040.0000.0000.0000.000
110B110LYS 10.8770.93131.6830.0200.0200.0000.0000.0000.000
111B111SER 00.0230.01331.262-0.001-0.0010.0000.0000.0000.000
112B112ALA 00.0350.01229.6060.0030.0030.0000.0000.0000.000
113B113TYR 00.020-0.01626.1280.0080.0080.0000.0000.0000.000
114B114GLU -1-0.878-0.91926.428-0.004-0.0040.0000.0000.0000.000
115B115ASN 0-0.028-0.00924.8370.0030.0030.0000.0000.0000.000
116B116PHE 00.031-0.00822.1090.0120.0120.0000.0000.0000.000
117B117ASN 0-0.038-0.01621.493-0.016-0.0160.0000.0000.0000.000
118B118GLN 0-0.0340.00922.027-0.014-0.0140.0000.0000.0000.000
119B119HIS 00.0030.00117.0880.0250.0250.0000.0000.0000.000
120B120GLU -1-0.838-0.90315.424-0.168-0.1680.0000.0000.0000.000
121B121VAL 0-0.016-0.01212.622-0.038-0.0380.0000.0000.0000.000
122B122LEU 0-0.0080.02715.0420.0730.0730.0000.0000.0000.000
123B123LEU 0-0.0060.01414.853-0.043-0.0430.0000.0000.0000.000
124B124ALA 00.006-0.00817.1740.0330.0330.0000.0000.0000.000
125B125PRO 0-0.0030.01220.830-0.017-0.0170.0000.0000.0000.000
126B126LEU 00.0100.00523.979-0.003-0.0030.0000.0000.0000.000
127B127LEU 00.0210.02225.7660.0080.0080.0000.0000.0000.000
128B128SER 00.009-0.02728.796-0.008-0.0080.0000.0000.0000.000
129B129ALA 00.0060.02130.054-0.004-0.0040.0000.0000.0000.000
130B130GLY 00.0330.01131.8090.0080.0080.0000.0000.0000.000
131B131ILE 0-0.007-0.01031.428-0.003-0.0030.0000.0000.0000.000
132B132PHE 0-0.080-0.02830.8080.0000.0000.0000.0000.0000.000
133B133GLY 00.0260.01134.631-0.003-0.0030.0000.0000.0000.000
134B134ALA 0-0.0150.00134.831-0.004-0.0040.0000.0000.0000.000
135B135ASP -1-0.810-0.91235.9630.0000.0000.0000.0000.0000.000
136B136PRO 0-0.048-0.02532.348-0.001-0.0010.0000.0000.0000.000
137B137ILE 00.015-0.00132.771-0.003-0.0030.0000.0000.0000.000
138B138HIS 00.0580.03334.588-0.007-0.0070.0000.0000.0000.000
139B139SER 0-0.025-0.03130.679-0.004-0.0040.0000.0000.0000.000
140B140LEU 0-0.015-0.00528.3310.0000.0000.0000.0000.0000.000
141B141ARG 10.8560.90030.6380.0340.0340.0000.0000.0000.000
142B142VAL 00.0200.01531.677-0.004-0.0040.0000.0000.0000.000
143B143CYS 0-0.0160.00326.281-0.001-0.0010.0000.0000.0000.000
144B144VAL 0-0.0080.00528.207-0.006-0.0060.0000.0000.0000.000
145B145ASP -1-0.758-0.83029.419-0.047-0.0470.0000.0000.0000.000
146B146THR 0-0.113-0.06429.0300.0010.0010.0000.0000.0000.000
147B147VAL 0-0.056-0.01523.2730.0010.0010.0000.0000.0000.000
148B148ARG 10.9200.96825.2730.0400.0400.0000.0000.0000.000
149B149THR 0-0.0240.01319.732-0.020-0.0200.0000.0000.0000.000
150B150ASN 0-0.031-0.00517.425-0.004-0.0040.0000.0000.0000.000
151B151VAL 00.0360.01218.2600.0240.0240.0000.0000.0000.000
152B152TYR 0-0.023-0.00916.402-0.028-0.0280.0000.0000.0000.000
153B153LEU 00.0240.00019.4270.0340.0340.0000.0000.0000.000
154B154ALA 00.0010.00020.011-0.015-0.0150.0000.0000.0000.000
155B155VAL 0-0.026-0.01822.0900.0110.0110.0000.0000.0000.000
156B156PHE 00.0230.01424.685-0.009-0.0090.0000.0000.0000.000
157B157ASP -1-0.793-0.89426.2180.0090.0090.0000.0000.0000.000
158B158LYS 10.8710.91729.0410.0280.0280.0000.0000.0000.000
159B159ASN 0-0.013-0.02730.128-0.010-0.0100.0000.0000.0000.000
160B160LEU 0-0.0080.00530.639-0.003-0.0030.0000.0000.0000.000
161B161TYR 0-0.016-0.01725.539-0.004-0.0040.0000.0000.0000.000
162B162ASP -1-0.760-0.85629.933-0.039-0.0390.0000.0000.0000.000
163B163LYS 10.9461.01132.7620.0050.0050.0000.0000.0000.000
164B164LEU 0-0.0370.00429.546-0.002-0.0020.0000.0000.0000.000
165B165VAL 00.0350.00528.982-0.004-0.0040.0000.0000.0000.000
166B166SER 0-0.064-0.03531.855-0.003-0.0030.0000.0000.0000.000
167B167SER 0-0.017-0.03035.430-0.001-0.0010.0000.0000.0000.000
168B168PHE 0-0.0170.00031.1430.0010.0010.0000.0000.0000.000
169B169LEU -1-0.876-0.89834.139-0.055-0.0550.0000.0000.0000.000
170B216HOH 0-0.067-0.04811.9110.0390.0390.0000.0000.0000.000
171B220HOH 0-0.025-0.02712.375-0.035-0.0350.0000.0000.0000.000
172B225HOH 0-0.006-0.01233.8060.0010.0010.0000.0000.0000.000
173B226HOH 0-0.039-0.03138.8730.0010.0010.0000.0000.0000.000
174B232HOH 0-0.061-0.05137.9550.0000.0000.0000.0000.0000.000
175B234HOH 0-0.042-0.03327.7200.0000.0000.0000.0000.0000.000
176B242HOH 0-0.019-0.02122.7010.0050.0050.0000.0000.0000.000
177B248HOH 0-0.011-0.01228.509-0.004-0.0040.0000.0000.0000.000
178B251HOH 0-0.011-0.03519.578-0.014-0.0140.0000.0000.0000.000
179B254HOH 0-0.025-0.03513.605-0.003-0.0030.0000.0000.0000.000
180B257HOH 0-0.036-0.02930.9970.0020.0020.0000.0000.0000.000
181B262HOH 0-0.041-0.03034.7510.0010.0010.0000.0000.0000.000
182B263HOH 0-0.049-0.05033.9450.0030.0030.0000.0000.0000.000
183B264HOH 00.0160.00423.9860.0060.0060.0000.0000.0000.000
184B268HOH 0-0.022-0.00927.293-0.001-0.0010.0000.0000.0000.000
185B271HOH 0-0.068-0.05129.183-0.003-0.0030.0000.0000.0000.000
186B277HOH 0-0.031-0.03023.1570.0060.0060.0000.0000.0000.000
187B278HOH 00.0230.00029.647-0.002-0.0020.0000.0000.0000.000
188B284HOH 00.001-0.00322.0930.0030.0030.0000.0000.0000.000
189B291HOH 0-0.022-0.02228.2380.0010.0010.0000.0000.0000.000
190B293HOH 0-0.018-0.03012.3550.0360.0360.0000.0000.0000.000
191B300HOH 00.0220.01428.172-0.002-0.0020.0000.0000.0000.000
192B303HOH 0-0.066-0.04837.0960.0000.0000.0000.0000.0000.000
193B306HOH 00.008-0.01428.082-0.003-0.0030.0000.0000.0000.000
194B311HOH 0-0.040-0.03134.023-0.002-0.0020.0000.0000.0000.000
195B314HOH 0-0.016-0.01015.2620.0150.0150.0000.0000.0000.000
196B320HOH 0-0.020-0.00329.6110.0030.0030.0000.0000.0000.000
197B323HOH 00.0020.00331.5210.0030.0030.0000.0000.0000.000
198B329HOH 00.000-0.01815.6680.0220.0220.0000.0000.0000.000
199B331HOH 00.003-0.01434.7420.0020.0020.0000.0000.0000.000
200B336HOH 00.0280.01831.9000.0010.0010.0000.0000.0000.000
201B340HOH 00.0170.00829.9310.0020.0020.0000.0000.0000.000
202B345HOH 00.0140.00428.311-0.002-0.0020.0000.0000.0000.000
203B346HOH 00.005-0.00530.532-0.002-0.0020.0000.0000.0000.000
204B352HOH 00.0400.02134.0930.0010.0010.0000.0000.0000.000
205B353HOH 0-0.014-0.02628.7510.0000.0000.0000.0000.0000.000
206B362HOH 0-0.030-0.02028.799-0.001-0.0010.0000.0000.0000.000