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: 8NJ3Y

Calculation Name: 2DYB-A-Xray372

Preferred Name:

Target Type:

Ligand Name: s-dimethylarsinoyl-cysteine

ligand 3-letter code: CAF

PDB ID: 2DYB

Chain ID: A

ChEMBL ID:

UniProt ID: Q15080

Base Structure: X-ray

Registration Date: 2023-09-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 298
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4287362.685659
FMO2-HF: Nuclear repulsion 4164857.433997
FMO2-HF: Total energy -122505.251663
FMO2-MP2: Total energy -122860.443681


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(A:9:ALA)


Summations of interaction energy for fragment #1(A:9:ALA)
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.
2.3575.3272.936-2.521-3.383-0.002
Interaction energy analysis for fragmet #1(A:9:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : 0.001
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].
3A11SER00.0400.0083.799-0.1081.539-0.003-0.719-0.9250.003
4A12ASP-1-0.950-0.9892.1071.5682.2602.934-1.546-2.079-0.005
5A13PHE00.0370.0203.6511.1951.7920.006-0.252-0.3510.000
6A14GLU-1-0.877-0.9545.360-1.752-1.718-0.001-0.004-0.0280.000
7A15GLN0-0.071-0.0266.3690.5300.5300.0000.0000.0000.000
8A16LEU0-0.070-0.0147.6360.2600.2600.0000.0000.0000.000
9A17PRO00.001-0.00410.447-0.061-0.0610.0000.0000.0000.000
10A18ASP-1-0.802-0.92513.280-0.427-0.4270.0000.0000.0000.000
11A19ASP-1-0.835-0.88715.279-0.125-0.1250.0000.0000.0000.000
12A20VAL00.0170.01011.0720.0550.0550.0000.0000.0000.000
13A21ALA0-0.004-0.00414.155-0.024-0.0240.0000.0000.0000.000
14A22ILE00.0150.00610.7900.0230.0230.0000.0000.0000.000
15A23SER0-0.043-0.03612.9490.0510.0510.0000.0000.0000.000
16A24ALA00.0320.02415.761-0.029-0.0290.0000.0000.0000.000
17A25ASN0-0.018-0.01218.4440.0400.0400.0000.0000.0000.000
18A26ILE0-0.022-0.01821.530-0.013-0.0130.0000.0000.0000.000
19A27ALA0-0.029-0.01125.2440.0000.0000.0000.0000.0000.000
20A28ASP-1-0.848-0.91727.5720.0270.0270.0000.0000.0000.000
21A29ILE0-0.064-0.02230.5080.0060.0060.0000.0000.0000.000
22A30GLU-1-0.801-0.87933.1190.0130.0130.0000.0000.0000.000
23A31GLU-1-0.867-0.91135.9330.0350.0350.0000.0000.0000.000
24A32LYS10.9050.96235.561-0.024-0.0240.0000.0000.0000.000
25A33ARG10.8220.87339.042-0.022-0.0220.0000.0000.0000.000
26A34GLY00.0350.02740.053-0.003-0.0030.0000.0000.0000.000
27A35PHE00.020-0.00438.843-0.001-0.0010.0000.0000.0000.000
28A36THR00.006-0.00540.666-0.001-0.0010.0000.0000.0000.000
29A37SER0-0.0100.02140.9310.0010.0010.0000.0000.0000.000
30A38HIS0-0.096-0.06135.3200.0050.0050.0000.0000.0000.000
31A39PHE00.0800.03134.949-0.003-0.0030.0000.0000.0000.000
32A40VAL0-0.045-0.01831.0680.0050.0050.0000.0000.0000.000
33A41PHE0-0.011-0.02328.0300.0000.0000.0000.0000.0000.000
34A42VAL00.0200.00428.457-0.001-0.0010.0000.0000.0000.000
35A43ILE00.0110.00922.4170.0030.0030.0000.0000.0000.000
36A44GLU-1-0.794-0.88022.534-0.020-0.0200.0000.0000.0000.000
37A45VAL0-0.021-0.01618.3900.0130.0130.0000.0000.0000.000
38A46LYS10.8860.95616.7290.1050.1050.0000.0000.0000.000
39A47THR00.006-0.00315.5680.0230.0230.0000.0000.0000.000
40A48LYS10.8860.9759.7050.8550.8550.0000.0000.0000.000
41A49GLY00.005-0.00513.474-0.031-0.0310.0000.0000.0000.000
42A50GLY0-0.053-0.01816.6540.0070.0070.0000.0000.0000.000
43A51SER0-0.047-0.01518.0800.0210.0210.0000.0000.0000.000
44A52LYS10.8070.86520.0290.0330.0330.0000.0000.0000.000
45A53TYR0-0.050-0.03820.586-0.009-0.0090.0000.0000.0000.000
46A54LEU00.0080.00824.0490.0090.0090.0000.0000.0000.000
47A55ILE0-0.0260.01022.677-0.006-0.0060.0000.0000.0000.000
48A56TYR0-0.020-0.01526.6350.0050.0050.0000.0000.0000.000
49A57ARG10.8080.89924.558-0.038-0.0380.0000.0000.0000.000
50A58ARG10.8980.94928.530-0.047-0.0470.0000.0000.0000.000
51A59TYR00.0970.02728.7330.0030.0030.0000.0000.0000.000
52A60ARG10.8080.87029.108-0.052-0.0520.0000.0000.0000.000
53A61GLN00.0620.02827.5820.0020.0020.0000.0000.0000.000
54A62PHE00.0480.03122.7040.0010.0010.0000.0000.0000.000
55A63HIS00.0090.00225.1560.0120.0120.0000.0000.0000.000
56A64ALA0-0.036-0.02226.8330.0070.0070.0000.0000.0000.000
57A65LEU00.0230.02920.313-0.001-0.0010.0000.0000.0000.000
58A66GLN0-0.028-0.02022.6580.0100.0100.0000.0000.0000.000
59A67SER0-0.002-0.01123.7350.0060.0060.0000.0000.0000.000
60A68LYS10.8740.94523.833-0.096-0.0960.0000.0000.0000.000
61A69LEU0-0.033-0.03018.2630.0070.0070.0000.0000.0000.000
62A70GLU-1-0.893-0.96521.4600.2210.2210.0000.0000.0000.000
63A71GLU-1-0.990-0.97623.3150.1180.1180.0000.0000.0000.000
64A72ARG10.7920.86919.754-0.137-0.1370.0000.0000.0000.000
65A73PHE0-0.041-0.03117.2730.0070.0070.0000.0000.0000.000
66A74GLY0-0.0010.02320.7820.0320.0320.0000.0000.0000.000
67A84CAF00.0220.01312.0510.0410.0410.0000.0000.0000.000
68A85THR0-0.051-0.04413.560-0.088-0.0880.0000.0000.0000.000
69A86LEU00.0430.03116.0840.0240.0240.0000.0000.0000.000
70A87PRO0-0.0300.01116.442-0.024-0.0240.0000.0000.0000.000
71A88THR00.0220.00119.311-0.022-0.0220.0000.0000.0000.000
72A89LEU0-0.043-0.01722.989-0.003-0.0030.0000.0000.0000.000
73A90PRO0-0.005-0.00525.388-0.006-0.0060.0000.0000.0000.000
74A91ALA00.0140.01928.068-0.007-0.0070.0000.0000.0000.000
75A92LYS10.8350.89730.082-0.135-0.1350.0000.0000.0000.000
76A93VAL00.0680.03734.459-0.002-0.0020.0000.0000.0000.000
77A94TYR00.0280.00229.846-0.004-0.0040.0000.0000.0000.000
78A95VAL0-0.007-0.01536.759-0.002-0.0020.0000.0000.0000.000
79A96GLY00.0710.04340.3510.0000.0000.0000.0000.0000.000
80A97VAL0-0.0210.00841.380-0.001-0.0010.0000.0000.0000.000
81A98LYS10.9040.92939.884-0.039-0.0390.0000.0000.0000.000
82A99GLN00.017-0.00538.0270.0010.0010.0000.0000.0000.000
83A100GLU-1-0.871-0.92436.7820.0680.0680.0000.0000.0000.000
84A101ILE0-0.066-0.02136.0280.0050.0050.0000.0000.0000.000
85A102ALA0-0.053-0.03433.6060.0070.0070.0000.0000.0000.000
86A103GLU-1-0.818-0.92832.2440.0590.0590.0000.0000.0000.000
87A104MET0-0.0140.00631.8920.0080.0080.0000.0000.0000.000
88A105ARG10.8530.92729.611-0.083-0.0830.0000.0000.0000.000
89A106ILE00.0400.03726.9800.0110.0110.0000.0000.0000.000
90A107PRO00.0280.01325.3180.0110.0110.0000.0000.0000.000
91A108ALA0-0.034-0.00924.0300.0170.0170.0000.0000.0000.000
92A109LEU00.005-0.00123.5160.0190.0190.0000.0000.0000.000
93A110ASN0-0.018-0.01021.1220.0080.0080.0000.0000.0000.000
94A111ALA00.0000.00619.6050.0200.0200.0000.0000.0000.000
95A112TYR00.0300.02018.6220.0350.0350.0000.0000.0000.000
96A113MET00.0170.02217.9820.0230.0230.0000.0000.0000.000
97A114LYS10.9420.98015.225-0.163-0.1630.0000.0000.0000.000
98A115SER00.0090.00813.7790.0640.0640.0000.0000.0000.000
99A116LEU00.006-0.00313.3680.0810.0810.0000.0000.0000.000
100A117LEU0-0.061-0.04412.7400.0240.0240.0000.0000.0000.000
101A118SER0-0.059-0.0389.643-0.006-0.0060.0000.0000.0000.000
102A119LEU0-0.088-0.0238.7590.2660.2660.0000.0000.0000.000
103A120PRO00.0420.0187.4500.0190.0190.0000.0000.0000.000
104A121VAL00.0880.0505.929-0.205-0.2050.0000.0000.0000.000
105A122TRP0-0.020-0.0248.608-0.145-0.1450.0000.0000.0000.000
106A123VAL0-0.025-0.01411.527-0.057-0.0570.0000.0000.0000.000
107A124LEU0-0.0180.0049.682-0.066-0.0660.0000.0000.0000.000
108A125MET0-0.058-0.02912.684-0.077-0.0770.0000.0000.0000.000
109A126ASP-1-0.798-0.88214.4220.1210.1210.0000.0000.0000.000
110A127GLU-1-0.898-0.93717.4630.0060.0060.0000.0000.0000.000
111A128ASP-1-0.770-0.86620.5060.0860.0860.0000.0000.0000.000
112A129VAL0-0.003-0.00616.0060.0020.0020.0000.0000.0000.000
113A130ARG10.7970.87615.2980.0770.0770.0000.0000.0000.000
114A131ILE00.013-0.01318.752-0.010-0.0100.0000.0000.0000.000
115A132PHE0-0.046-0.00520.915-0.004-0.0040.0000.0000.0000.000
116A133PHE00.028-0.01417.5170.0000.0000.0000.0000.0000.000
117A134TYR00.0020.03019.837-0.007-0.0070.0000.0000.0000.000
118A135GLN0-0.054-0.03022.4810.0040.0040.0000.0000.0000.000
119A136SER00.006-0.02825.535-0.006-0.0060.0000.0000.0000.000
120A137PRO00.0380.00128.6000.0000.0000.0000.0000.0000.000
121A138TYR00.0870.05631.983-0.001-0.0010.0000.0000.0000.000
122A139ASP-1-0.791-0.83527.8390.0180.0180.0000.0000.0000.000
123A140SER0-0.049-0.03930.283-0.002-0.0020.0000.0000.0000.000
124A141GLU-1-0.825-0.91631.617-0.008-0.0080.0000.0000.0000.000
125A142GLN0-0.019-0.03132.7490.0050.0050.0000.0000.0000.000
126A143VAL0-0.0020.02330.2570.0010.0010.0000.0000.0000.000
127A144PRO0-0.016-0.01233.6550.0010.0010.0000.0000.0000.000
128A145GLN00.0120.00736.7690.0020.0020.0000.0000.0000.000
129A146ALA00.0380.02435.2760.0010.0010.0000.0000.0000.000
130A147LEU00.0030.00234.4160.0010.0010.0000.0000.0000.000
131A148ARG10.9120.95837.9570.0150.0150.0000.0000.0000.000
132A149ARG10.8840.92037.033-0.014-0.0140.0000.0000.0000.000
133A150LEU0-0.023-0.01135.9360.0010.0010.0000.0000.0000.000
134A151ARG10.9280.96040.0840.0040.0040.0000.0000.0000.000
135A152PRO00.0280.04641.963-0.003-0.0030.0000.0000.0000.000
136A153ARG10.9200.95641.6320.0110.0110.0000.0000.0000.000
137A169ARG10.8620.92544.620-0.023-0.0230.0000.0000.0000.000
138A170MET0-0.022-0.01346.852-0.001-0.0010.0000.0000.0000.000
139A171ALA0-0.0160.00349.9690.0010.0010.0000.0000.0000.000
140A172ALA00.0670.03052.739-0.001-0.0010.0000.0000.0000.000
141A173PRO0-0.015-0.00952.7990.0000.0000.0000.0000.0000.000
142A174ARG10.9420.98555.890-0.007-0.0070.0000.0000.0000.000
143A175ALA0-0.006-0.00959.629-0.001-0.0010.0000.0000.0000.000
144A176GLU-1-0.913-0.94462.9370.0040.0040.0000.0000.0000.000
145A177ALA00.0050.01666.603-0.001-0.0010.0000.0000.0000.000
146A178LEU0-0.033-0.01569.2790.0000.0000.0000.0000.0000.000
147A179PHE0-0.015-0.03671.9010.0000.0000.0000.0000.0000.000
148A180ASP-1-0.821-0.88873.3040.0020.0020.0000.0000.0000.000
149A181PHE0-0.027-0.01270.273-0.001-0.0010.0000.0000.0000.000
150A182THR0-0.034-0.01273.5870.0000.0000.0000.0000.0000.000
151A183GLY00.0060.00272.0310.0000.0000.0000.0000.0000.000
152A184ASN0-0.055-0.04672.3810.0000.0000.0000.0000.0000.000
153A185SER0-0.039-0.03170.1450.0000.0000.0000.0000.0000.000
154A186LYS10.9260.94669.8660.0000.0000.0000.0000.0000.000
155A187LEU00.0230.01363.3690.0000.0000.0000.0000.0000.000
156A188GLU-1-0.824-0.87666.185-0.003-0.0030.0000.0000.0000.000
157A189LEU0-0.031-0.00764.6200.0010.0010.0000.0000.0000.000
158A190ASN0-0.009-0.00968.1200.0000.0000.0000.0000.0000.000
159A191PHE0-0.032-0.01868.4830.0010.0010.0000.0000.0000.000
160A192LYS10.9000.93771.518-0.003-0.0030.0000.0000.0000.000
161A193ALA00.0070.00172.1240.0000.0000.0000.0000.0000.000
162A194GLY00.0070.00671.3730.0000.0000.0000.0000.0000.000
163A195ASP-1-0.803-0.87068.5280.0050.0050.0000.0000.0000.000
164A196VAL0-0.037-0.02163.0810.0000.0000.0000.0000.0000.000
165A197ILE0-0.025-0.00162.6160.0010.0010.0000.0000.0000.000
166A198PHE00.006-0.00657.8630.0000.0000.0000.0000.0000.000
167A199LEU0-0.034-0.03257.0610.0000.0000.0000.0000.0000.000
168A200LEU0-0.038-0.00955.5040.0010.0010.0000.0000.0000.000
169A201SER00.027-0.00254.2480.0000.0000.0000.0000.0000.000
170A202ARG10.9270.98054.9580.0060.0060.0000.0000.0000.000
171A203ILE0-0.0160.01156.2810.0000.0000.0000.0000.0000.000
172A204ASN00.016-0.01357.965-0.001-0.0010.0000.0000.0000.000
173A205LYS10.8560.92260.0830.0100.0100.0000.0000.0000.000
174A206ASP-1-0.835-0.92361.829-0.008-0.0080.0000.0000.0000.000
175A207TRP0-0.0010.01862.9780.0010.0010.0000.0000.0000.000
176A208LEU00.011-0.00459.332-0.001-0.0010.0000.0000.0000.000
177A209GLU-1-0.908-0.93557.1570.0000.0000.0000.0000.0000.000
178A210GLY00.0350.01159.2130.0000.0000.0000.0000.0000.000
179A211THR0-0.048-0.03759.4390.0000.0000.0000.0000.0000.000
180A212VAL00.000-0.02062.3210.0000.0000.0000.0000.0000.000
181A213ARG10.8840.90664.720-0.006-0.0060.0000.0000.0000.000
182A214GLY00.0270.03363.9640.0000.0000.0000.0000.0000.000
183A215ALA0-0.0220.00664.8010.0000.0000.0000.0000.0000.000
184A216THR00.0190.00660.2010.0000.0000.0000.0000.0000.000
185A217GLY00.0120.01563.2510.0000.0000.0000.0000.0000.000
186A218ILE0-0.002-0.00662.2550.0000.0000.0000.0000.0000.000
187A219PHE0-0.007-0.01462.3060.0000.0000.0000.0000.0000.000
188A220PRO00.0410.03665.303-0.001-0.0010.0000.0000.0000.000
189A221LEU00.004-0.01261.9340.0000.0000.0000.0000.0000.000
190A222SER0-0.006-0.01565.4760.0000.0000.0000.0000.0000.000
191A223PHE0-0.016-0.00868.7150.0000.0000.0000.0000.0000.000
192A224VAL00.0260.01864.2340.0010.0010.0000.0000.0000.000
193A225LYS10.9210.98763.588-0.002-0.0020.0000.0000.0000.000
194A226ILE00.004-0.01058.9760.0010.0010.0000.0000.0000.000
195A227LEU0-0.072-0.04061.2500.0000.0000.0000.0000.0000.000
196A228LYS10.8230.91051.597-0.004-0.0040.0000.0000.0000.000
197A229ASP-1-0.798-0.89954.962-0.003-0.0030.0000.0000.0000.000
198A230PHE0-0.019-0.02452.2140.0010.0010.0000.0000.0000.000
199A231PRO0-0.042-0.01747.7820.0000.0000.0000.0000.0000.000
200A232GLU-1-0.879-0.92747.654-0.010-0.0100.0000.0000.0000.000
201A233GLU-1-0.817-0.90845.544-0.012-0.0120.0000.0000.0000.000
202A234ASP-1-0.951-0.98542.328-0.018-0.0180.0000.0000.0000.000
203A235ASP-1-0.899-0.91741.8950.0030.0030.0000.0000.0000.000
204A236PRO0-0.010-0.01538.5550.0000.0000.0000.0000.0000.000
205A237THR0-0.114-0.07140.3690.0040.0040.0000.0000.0000.000
206A238ASN0-0.020-0.01139.114-0.004-0.0040.0000.0000.0000.000
207A239TRP0-0.003-0.02043.2160.0020.0020.0000.0000.0000.000
208A240LEU0-0.0080.00145.4340.0000.0000.0000.0000.0000.000
209A241ARG10.8330.88747.216-0.006-0.0060.0000.0000.0000.000
210A242CYS0-0.052-0.01550.5730.0020.0020.0000.0000.0000.000
211A243TYR00.0110.00052.868-0.001-0.0010.0000.0000.0000.000
212A244TYR0-0.089-0.05656.2230.0020.0020.0000.0000.0000.000
213A245TYR0-0.019-0.03857.294-0.001-0.0010.0000.0000.0000.000
214A246GLU-1-0.903-0.93761.0030.0140.0140.0000.0000.0000.000
215A247ASP-1-0.885-0.93063.9810.0150.0150.0000.0000.0000.000
216A248THR0-0.052-0.02267.5000.0000.0000.0000.0000.0000.000
217A249ILE00.001-0.00365.182-0.001-0.0010.0000.0000.0000.000
218A250SER00.0290.00661.5180.0010.0010.0000.0000.0000.000
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