FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: Q8GGY

Calculation Name: 6YWM-A-Xray128

Preferred Name:

Target Type:

Ligand Name: 2-(n-morpholino)-ethanesulfonic acid

ligand 3-letter code: MES

PDB ID: 6YWM

Chain ID: A

ChEMBL ID:

UniProt ID: P0DTD1

Base Structure: X-ray

Registration Date: 2020-06-09

Reference: K. Kato Y. Handa, Y. Kawashima, K. Fukuzawa, C. Watanabe, T. Honma, , 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 Selected crystal waters in PDB
Procedure Manual calculation
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 206
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1866183.692253
FMO2-HF: Nuclear repulsion 1797358.816788
FMO2-HF: Total energy -68824.875466
FMO2-MP2: Total energy -69023.564478


3D Structure
Snapshot
 
Ligand structure

MES

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.
-138.611-136.34879.022-29.093-52.1900.061


Interactive mode: IFIE and PIEDA for fragment #173(A:201:MES )


Summations of interaction energy for fragment #173(A:201:MES )
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.
-138.611-136.34879.022-29.093-52.19-0.061
Interaction energy analysis for fragmet #173(A:201:MES )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.061 / q_NPA : 0.026
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].
1A1HIS 10.8490.91028.306-0.050-0.0500.0000.0000.0000.000
2A2MET 00.0410.02325.953-0.009-0.0090.0000.0000.0000.000
3A3VAL 00.0620.04123.558-0.018-0.0180.0000.0000.0000.000
4A4ASN 00.0260.01221.6710.0110.0110.0000.0000.0000.000
5A5SER 00.0180.01922.7420.0600.0600.0000.0000.0000.000
6A6PHE 00.0070.00917.121-0.014-0.0140.0000.0000.0000.000
7A7SER 00.018-0.00221.999-0.062-0.0620.0000.0000.0000.000
8A8GLY 00.004-0.00121.9520.0670.0670.0000.0000.0000.000
9A9TYR 0-0.066-0.04616.0660.1650.1650.0000.0000.0000.000
10A10LEU 00.0230.01720.109-0.203-0.2030.0000.0000.0000.000
11A11LYS 10.8210.91420.268-1.356-1.3560.0000.0000.0000.000
12A12LEU 0-0.0310.00516.959-0.048-0.0480.0000.0000.0000.000
13A13THR 00.0500.00320.574-0.108-0.1080.0000.0000.0000.000
14A14ASP -1-0.880-0.95522.8191.3871.3870.0000.0000.0000.000
15A15ASN 0-0.055-0.03719.141-0.149-0.1490.0000.0000.0000.000
16A16VAL 00.0130.01916.0510.1440.1440.0000.0000.0000.000
17A17TYR 00.0180.00417.651-0.214-0.2140.0000.0000.0000.000
18A18ILE 00.0140.01213.6720.4330.4330.0000.0000.0000.000
19A19LYS 10.8520.90815.389-2.042-2.0420.0000.0000.0000.000
20A20ASN 0-0.064-0.02514.8450.1200.1200.0000.0000.0000.000
21A21ALA 00.0190.00014.375-0.464-0.4640.0000.0000.0000.000
22A22ASP -1-0.841-0.92812.5301.7591.7590.0000.0000.0000.000
23A23ILE 00.0320.0168.890-0.376-0.3760.0000.0000.0000.000
24A24VAL 00.0060.00111.526-0.452-0.4520.0000.0000.0000.000
25A25GLU -1-0.891-0.95413.9970.2290.2290.0000.0000.0000.000
26A26GLU -1-0.828-0.87615.0841.4051.4050.0000.0000.0000.000
27A27ALA 00.0220.00614.866-0.109-0.1090.0000.0000.0000.000
28A28LYS 10.8720.94016.5410.3760.3760.0000.0000.0000.000
29A29LYS 10.8380.91719.445-0.882-0.8820.0000.0000.0000.000
30A30VAL 0-0.050-0.01319.074-0.060-0.0600.0000.0000.0000.000
31A31LYS 10.9320.97220.417-0.034-0.0340.0000.0000.0000.000
32A32PRO 0-0.0120.00416.714-0.004-0.0040.0000.0000.0000.000
33A33THR 0-0.010-0.02319.135-0.261-0.2610.0000.0000.0000.000
34A34VAL 00.000-0.00314.393-0.242-0.2420.0000.0000.0000.000
35A35VAL 0-0.0020.00711.4350.4260.4260.0000.0000.0000.000
36A36VAL 00.004-0.0018.184-0.676-0.6760.0000.0000.0000.000
37A37ASN 0-0.018-0.0324.702-0.183-0.056-0.001-0.008-0.1190.000
38A38ALA 0-0.0040.0172.669-1.2030.3052.246-1.349-2.4050.012
39A39ALA 00.0490.0172.174-27.040-26.5648.475-3.952-5.000-0.064
40A40ASN 00.037-0.0051.7181.7932.1218.155-2.817-5.667-0.031
41A41VAL 00.0370.0133.4292.4232.7070.0240.032-0.3400.000
42A42TYR 00.0100.0036.3641.6911.6910.0000.0000.0000.000
43A43LEU 0-0.0190.0075.3050.7790.7790.0000.0000.0000.000
44A44LYS 10.8530.9264.4778.5168.722-0.001-0.036-0.1690.000
45A45HIS 00.003-0.0152.479-16.056-14.3831.235-1.106-1.802-0.018
46A46GLY 00.0230.0063.2302.9643.3920.029-0.124-0.3330.000
47A47GLY 00.0190.0023.1433.2303.6390.013-0.085-0.3370.000
48A48GLY 0-0.0040.0103.183-7.997-6.9190.068-0.516-0.629-0.004
49A49VAL 00.0290.0054.450-1.931-1.4900.000-0.045-0.3960.000
50A50ALA 00.0370.0332.1110.2790.4542.063-0.734-1.503-0.004
51A51GLY 0-0.015-0.0074.0442.8142.9830.000-0.029-0.1400.000
52A52ALA 0-0.035-0.0135.7041.4631.4630.0000.0000.0000.000
53A53LEU 00.0420.0107.1530.5700.5700.0000.0000.0000.000
54A54ASN 00.0670.0207.5941.2181.2180.0000.0000.0000.000
55A55LYS 10.9320.9699.2274.5094.5090.0000.0000.0000.000
56A56ALA 00.0110.03111.4930.4380.4380.0000.0000.0000.000
57A57THR 0-0.0020.01412.1130.2940.2940.0000.0000.0000.000
58A58ASN 0-0.019-0.01514.2670.0670.0670.0000.0000.0000.000
59A59ASN 00.000-0.00111.660-0.400-0.4000.0000.0000.0000.000
60A60ALA 00.0150.01813.074-0.231-0.2310.0000.0000.0000.000
61A61MET 00.0190.0278.857-0.623-0.6230.0000.0000.0000.000
62A62GLN 0-0.029-0.0287.111-1.750-1.7500.0000.0000.0000.000
63A63VAL 0-0.0080.00310.230-0.046-0.0460.0000.0000.0000.000
64A64GLU -1-0.729-0.84613.468-2.591-2.5910.0000.0000.0000.000
65A65SER 0-0.012-0.0198.924-0.236-0.2360.0000.0000.0000.000
66A66ASP -1-0.819-0.89610.504-5.861-5.8610.0000.0000.0000.000
67A67ASP -1-0.918-0.94312.329-2.163-2.1630.0000.0000.0000.000
68A68TYR 00.023-0.00112.1930.2830.2830.0000.0000.0000.000
69A69ILE 0-0.030-0.0189.8830.2290.2290.0000.0000.0000.000
70A70ALA 0-0.048-0.02013.2650.2350.2350.0000.0000.0000.000
71A71THR 0-0.042-0.00516.4290.3260.3260.0000.0000.0000.000
72A72ASN 0-0.089-0.05415.7340.4590.4590.0000.0000.0000.000
73A73GLY 00.0220.03115.1540.1780.1780.0000.0000.0000.000
74A74PRO 0-0.050-0.03911.100-0.243-0.2430.0000.0000.0000.000
75A75LEU 0-0.037-0.0108.5540.6390.6390.0000.0000.0000.000
76A76LYS 10.9750.98911.1340.5180.5180.0000.0000.0000.000
77A77VAL 00.0280.0128.225-0.182-0.1820.0000.0000.0000.000
78A78GLY 00.0210.0138.9970.2970.2970.0000.0000.0000.000
79A79GLY 0-0.0140.00410.5150.3150.3150.0000.0000.0000.000
80A80SER 0-0.030-0.04810.1330.0390.0390.0000.0000.0000.000
81A81CYS 0-0.0430.00211.416-0.278-0.2780.0000.0000.0000.000
82A82VAL 00.0110.01212.174-0.088-0.0880.0000.0000.0000.000
83A83LEU 00.0120.01511.366-0.130-0.1300.0000.0000.0000.000
84A84SER 00.0550.02514.6840.4760.4760.0000.0000.0000.000
85A85GLY 0-0.021-0.00614.209-0.404-0.4040.0000.0000.0000.000
86A86HIS 0-0.053-0.05014.0020.2360.2360.0000.0000.0000.000
87A87ASN 0-0.045-0.03816.4600.1110.1110.0000.0000.0000.000
88A88LEU 0-0.023-0.00312.7500.2140.2140.0000.0000.0000.000
89A89ALA 00.0230.00915.6380.3220.3220.0000.0000.0000.000
90A90LYS 10.8940.98617.635-0.137-0.1370.0000.0000.0000.000
91A91HIS 00.0430.01316.367-0.292-0.2920.0000.0000.0000.000
92A92CYS 0-0.031-0.0209.8430.2940.2940.0000.0000.0000.000
93A93LEU 0-0.0330.00611.757-0.344-0.3440.0000.0000.0000.000
94A94HIS 00.0380.0047.697-1.042-1.0420.0000.0000.0000.000
95A95VAL 00.0200.0057.4490.0130.0130.0000.0000.0000.000
96A96VAL 0-0.0440.0045.193-0.265-0.2650.0000.0000.0000.000
97A97GLY 00.0660.0354.408-0.615-0.462-0.001-0.017-0.1350.000
98A98PRO 0-0.0160.0005.369-3.169-3.114-0.001-0.003-0.0510.000
99A99ASN 0-0.005-0.0095.3776.7766.7760.0000.0000.0000.000
100A100VAL 00.0590.0186.503-1.729-1.7290.0000.0000.0000.000
101A101ASN 0-0.024-0.0087.034-1.017-1.0170.0000.0000.0000.000
102A102LYS 10.8650.9438.4423.2503.2500.0000.0000.0000.000
103A103GLY 00.0180.01310.795-0.294-0.2940.0000.0000.0000.000
104A104GLU -1-0.868-0.9218.302-2.332-2.3320.0000.0000.0000.000
105A105ASP -1-0.786-0.90211.7082.8552.8550.0000.0000.0000.000
106A106ILE 00.0650.01510.7420.4100.4100.0000.0000.0000.000
107A107GLN 0-0.060-0.01211.6000.6860.6860.0000.0000.0000.000
108A108LEU 0-0.007-0.00910.633-0.048-0.0480.0000.0000.0000.000
109A109LEU 0-0.031-0.0196.7070.1850.1850.0000.0000.0000.000
110A110LYS 10.9210.9629.584-2.440-2.4400.0000.0000.0000.000
111A111SER 00.0070.00612.367-0.095-0.0950.0000.0000.0000.000
112A112ALA 00.0120.0027.897-0.405-0.4050.0000.0000.0000.000
113A113TYR 00.0360.0018.459-0.293-0.2930.0000.0000.0000.000
114A114GLU -1-0.857-0.92611.5391.4321.4320.0000.0000.0000.000
115A115ASN 0-0.048-0.00611.531-0.960-0.9600.0000.0000.0000.000
116A116PHE 00.0640.0109.239-0.300-0.3000.0000.0000.0000.000
117A117ASN 0-0.026-0.00514.597-0.223-0.2230.0000.0000.0000.000
118A118GLN 0-0.044-0.00917.484-0.264-0.2640.0000.0000.0000.000
119A119HIS 0-0.004-0.00416.363-0.247-0.2470.0000.0000.0000.000
120A120GLU -1-0.932-0.96519.2970.9290.9290.0000.0000.0000.000
121A121VAL 0-0.004-0.01419.4290.1490.1490.0000.0000.0000.000
122A122LEU 0-0.0220.02313.783-0.223-0.2230.0000.0000.0000.000
123A123LEU 0-0.0210.01112.9770.1780.1780.0000.0000.0000.000
124A124ALA 00.0170.00110.015-0.420-0.4200.0000.0000.0000.000
125A125PRO 0-0.0270.0025.653-0.386-0.3860.0000.0000.0000.000
126A126LEU 0-0.004-0.0067.093-0.461-0.4610.0000.0000.0000.000
127A127LEU 00.0110.0123.9666.3526.7870.005-0.110-0.3300.000
128A128SER 00.018-0.0222.326-8.213-7.3554.133-2.087-2.9030.020
129A129ALA 0-0.0020.0143.312-2.862-4.1360.5291.893-1.1480.001
130A130GLY 00.0110.0151.992-9.813-12.6887.358-1.976-2.5080.018
131A131ILE 0-0.029-0.0362.136-5.263-6.3193.8021.492-4.238-0.001
132A132PHE 0-0.033-0.0152.358-30.389-25.80113.191-5.261-12.518-0.031
133A133GLY 00.0340.0213.914-4.121-3.8720.014-0.047-0.2160.000
134A134ALA 00.0160.0165.190-3.223-3.215-0.001-0.002-0.0050.000
135A135ASP -1-0.817-0.9196.8807.9487.9480.0000.0000.0000.000
136A136PRO 0-0.005-0.0187.7810.4180.4180.0000.0000.0000.000
137A137ILE 00.0180.0109.322-0.112-0.1120.0000.0000.0000.000
138A138HIS 00.0050.01110.746-0.531-0.5310.0000.0000.0000.000
139A139SER 0-0.019-0.0256.946-1.501-1.5010.0000.0000.0000.000
140A140LEU 00.001-0.0039.950-0.494-0.4940.0000.0000.0000.000
141A141ARG 10.8880.93212.673-3.632-3.6320.0000.0000.0000.000
142A142VAL 00.0090.01211.641-0.514-0.5140.0000.0000.0000.000
143A143CYS 0-0.0130.00311.470-0.712-0.7120.0000.0000.0000.000
144A144VAL 0-0.031-0.01213.204-0.604-0.6040.0000.0000.0000.000
145A145ASP -1-0.765-0.83916.6632.5182.5180.0000.0000.0000.000
146A146THR 0-0.090-0.04514.494-0.478-0.4780.0000.0000.0000.000
147A147VAL 0-0.047-0.01213.805-0.372-0.3720.0000.0000.0000.000
148A148ARG 10.9080.94716.904-1.562-1.5620.0000.0000.0000.000
149A149THR 0-0.0170.01218.259-0.058-0.0580.0000.0000.0000.000
150A150ASN 0-0.045-0.01119.2200.2730.2730.0000.0000.0000.000
151A151VAL 00.0330.01113.490-0.062-0.0620.0000.0000.0000.000
152A152TYR 0-0.009-0.00415.8690.0010.0010.0000.0000.0000.000
153A153LEU 00.0340.00310.6010.1070.1070.0000.0000.0000.000
154A154ALA 0-0.012-0.00511.386-0.585-0.5850.0000.0000.0000.000
155A155VAL 0-0.0020.00710.0571.4071.4070.0000.0000.0000.000
156A156PHE 00.0190.00410.397-0.848-0.8480.0000.0000.0000.000
157A157ASP -1-0.803-0.90711.6442.9662.9660.0000.0000.0000.000
158A158LYS 10.9680.98713.462-1.383-1.3830.0000.0000.0000.000
159A159ASN 00.0490.02116.481-0.039-0.0390.0000.0000.0000.000
160A160LEU 00.0160.0159.562-0.031-0.0310.0000.0000.0000.000
161A161TYR 00.023-0.00314.0740.0580.0580.0000.0000.0000.000
162A162ASP -1-0.857-0.93615.3292.4112.4110.0000.0000.0000.000
163A163LYS 10.8370.92215.805-3.091-3.0910.0000.0000.0000.000
164A164LEU 0-0.022-0.00811.552-0.047-0.0470.0000.0000.0000.000
165A165VAL 00.0090.00616.039-0.149-0.1490.0000.0000.0000.000
166A166SER 0-0.035-0.02019.170-0.254-0.2540.0000.0000.0000.000
167A167SER 0-0.0050.00217.704-0.028-0.0280.0000.0000.0000.000
168A168PHE 00.008-0.00118.202-0.137-0.1370.0000.0000.0000.000
169A169LEU 0-0.056-0.03920.299-0.208-0.2080.0000.0000.0000.000
170A170GLU -1-0.928-0.96722.8041.9831.9830.0000.0000.0000.000
171A171MET 0-0.115-0.04322.203-0.139-0.1390.0000.0000.0000.000
172A172LYS 0-0.0240.00123.1280.1320.1320.0000.0000.0000.000
174A306HOH 00.0150.01721.5700.0440.0440.0000.0000.0000.000
175A309HOH 0-0.003-0.00213.076-0.218-0.2180.0000.0000.0000.000
176A313HOH 0-0.041-0.03716.567-0.003-0.0030.0000.0000.0000.000
177A315HOH 0-0.010-0.00717.575-0.075-0.0750.0000.0000.0000.000
178A318HOH 0-0.058-0.04219.5850.0460.0460.0000.0000.0000.000
179A319HOH 0-0.011-0.01116.5360.1150.1150.0000.0000.0000.000
180A321HOH 0-0.048-0.03121.539-0.057-0.0570.0000.0000.0000.000
181A324HOH 0-0.024-0.02416.7830.0940.0940.0000.0000.0000.000
182A329HOH 00.0330.02014.5350.0280.0280.0000.0000.0000.000
183A330HOH 0-0.020-0.00519.7040.0160.0160.0000.0000.0000.000
184A331HOH 0-0.030-0.03019.862-0.008-0.0080.0000.0000.0000.000
185A333HOH 0-0.020-0.0091.877-4.945-7.3346.650-2.250-2.0110.025
186A334HOH 0-0.002-0.01112.3340.1740.1740.0000.0000.0000.000
187A336HOH 00.006-0.00414.8600.0270.0270.0000.0000.0000.000
188A338HOH 0-0.002-0.01618.879-0.059-0.0590.0000.0000.0000.000
189A341HOH 0-0.008-0.01013.8150.0630.0630.0000.0000.0000.000
190A342HOH 0-0.034-0.02313.352-0.159-0.1590.0000.0000.0000.000
191A344HOH 0-0.012-0.0132.211-16.812-13.5173.249-3.239-3.304-0.020
192A346HOH 0-0.047-0.03314.881-0.147-0.1470.0000.0000.0000.000
193A347HOH 00.011-0.0051.644-18.463-26.58316.075-5.376-2.5780.050
194A349HOH 00.0120.00516.2290.0940.0940.0000.0000.0000.000
195A350HOH 0-0.039-0.0295.839-2.057-2.0570.0000.0000.0000.000
196A352HOH 0-0.004-0.02012.157-0.290-0.2900.0000.0000.0000.000
197A353HOH 0-0.019-0.01716.2410.0230.0230.0000.0000.0000.000
198A356HOH 0-0.011-0.01319.844-0.002-0.0020.0000.0000.0000.000
199A357HOH 00.003-0.00213.171-0.204-0.2040.0000.0000.0000.000
200A358HOH 0-0.019-0.0252.162-5.494-4.4601.713-1.341-1.405-0.014
201A360HOH 0-0.006-0.0127.4870.6190.6190.0000.0000.0000.000
202A363HOH 0-0.024-0.01319.528-0.105-0.1050.0000.0000.0000.000
203A368HOH 00.006-0.0095.506-2.071-2.0710.0000.0000.0000.000
204A369HOH 00.0330.01413.8220.0200.0200.0000.0000.0000.000
205A370HOH 00.0610.03722.6380.0140.0140.0000.0000.0000.000
206A380HOH 0-0.005-0.01715.256-0.132-0.1320.0000.0000.0000.000