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: N235Q

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 OptAll
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 -4293304.41174
FMO2-HF: Nuclear repulsion 4170797.65192
FMO2-HF: Total energy -122506.759821
FMO2-MP2: Total energy -122861.838881


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.
2.0265.120.437-1.369-2.1630.001
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 : 0.028 / q_NPA : 0.011
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].
3A11SER00.0490.0103.6070.0181.644-0.001-0.750-0.8750.002
4A12ASP-1-0.939-0.9632.7670.8641.9130.438-0.429-1.058-0.002
5A13PHE00.0360.0093.9340.9911.4100.000-0.190-0.2300.001
6A14GLU-1-0.902-0.9645.863-1.493-1.4930.0000.0000.0000.000
7A15GLN0-0.097-0.0606.6110.6260.6260.0000.0000.0000.000
8A16LEU0-0.0110.0218.1830.2740.2740.0000.0000.0000.000
9A17PRO00.0210.02010.801-0.052-0.0520.0000.0000.0000.000
10A18ASP-1-0.824-0.94014.058-0.508-0.5080.0000.0000.0000.000
11A19ASP-1-0.813-0.87715.656-0.181-0.1810.0000.0000.0000.000
12A20VAL0-0.0060.00211.5050.0540.0540.0000.0000.0000.000
13A21ALA00.0070.00014.807-0.025-0.0250.0000.0000.0000.000
14A22ILE00.0110.00211.2510.0020.0020.0000.0000.0000.000
15A23SER0-0.045-0.02712.8020.0440.0440.0000.0000.0000.000
16A24ALA00.0190.01515.581-0.023-0.0230.0000.0000.0000.000
17A25ASN0-0.039-0.02618.8530.0430.0430.0000.0000.0000.000
18A26ILE0-0.033-0.01521.843-0.012-0.0120.0000.0000.0000.000
19A27ALA0-0.046-0.02125.5580.0010.0010.0000.0000.0000.000
20A28ASP-1-0.866-0.92127.6300.0020.0020.0000.0000.0000.000
21A29ILE0-0.062-0.04130.5300.0050.0050.0000.0000.0000.000
22A30GLU-1-0.765-0.84833.179-0.007-0.0070.0000.0000.0000.000
23A31GLU-1-0.851-0.89636.0810.0190.0190.0000.0000.0000.000
24A32LYS10.8810.93836.185-0.005-0.0050.0000.0000.0000.000
25A33ARG10.8100.86739.488-0.006-0.0060.0000.0000.0000.000
26A34GLY00.0280.00840.196-0.002-0.0020.0000.0000.0000.000
27A35PHE00.0310.00439.1900.0000.0000.0000.0000.0000.000
28A36THR00.000-0.01840.934-0.001-0.0010.0000.0000.0000.000
29A37SER0-0.0020.01741.2200.0000.0000.0000.0000.0000.000
30A38HIS0-0.090-0.05335.7210.0040.0040.0000.0000.0000.000
31A39PHE00.0960.03235.175-0.003-0.0030.0000.0000.0000.000
32A40VAL0-0.053-0.02331.8280.0050.0050.0000.0000.0000.000
33A41PHE0-0.020-0.00928.118-0.001-0.0010.0000.0000.0000.000
34A42VAL00.0280.02429.073-0.002-0.0020.0000.0000.0000.000
35A43ILE00.002-0.01422.8390.0050.0050.0000.0000.0000.000
36A44GLU-1-0.817-0.88422.360-0.066-0.0660.0000.0000.0000.000
37A45VAL0-0.006-0.01218.8730.0140.0140.0000.0000.0000.000
38A46LYS10.8640.92516.6480.1760.1760.0000.0000.0000.000
39A47THR00.0260.00915.9860.0200.0200.0000.0000.0000.000
40A48LYS10.8280.9259.9101.0021.0020.0000.0000.0000.000
41A49GLY00.0080.01313.836-0.031-0.0310.0000.0000.0000.000
42A50GLY0-0.053-0.01916.6270.0260.0260.0000.0000.0000.000
43A51SER0-0.0060.00218.1970.0310.0310.0000.0000.0000.000
44A52LYS10.8090.87419.9160.0750.0750.0000.0000.0000.000
45A53TYR0-0.038-0.02921.061-0.006-0.0060.0000.0000.0000.000
46A54LEU00.0150.00624.2040.0060.0060.0000.0000.0000.000
47A55ILE0-0.0200.00723.393-0.004-0.0040.0000.0000.0000.000
48A56TYR0-0.0010.00427.3450.0050.0050.0000.0000.0000.000
49A57ARG10.7910.88925.0570.0010.0010.0000.0000.0000.000
50A58ARG10.8990.94529.041-0.025-0.0250.0000.0000.0000.000
51A59TYR00.0780.01628.8440.0020.0020.0000.0000.0000.000
52A60ARG10.8320.87929.461-0.034-0.0340.0000.0000.0000.000
53A61GLN00.0700.03527.5870.0040.0040.0000.0000.0000.000
54A62PHE00.0420.02923.3570.0020.0020.0000.0000.0000.000
55A63HIS00.0160.00325.1240.0110.0110.0000.0000.0000.000
56A64ALA0-0.027-0.01027.0740.0070.0070.0000.0000.0000.000
57A65LEU00.0220.02020.3470.0020.0020.0000.0000.0000.000
58A66GLN0-0.047-0.03422.5660.0060.0060.0000.0000.0000.000
59A67SER00.011-0.00423.5270.0080.0080.0000.0000.0000.000
60A68LYS10.8410.92623.682-0.066-0.0660.0000.0000.0000.000
61A69LEU0-0.005-0.00418.0220.0050.0050.0000.0000.0000.000
62A70GLU-1-0.863-0.94621.3270.1880.1880.0000.0000.0000.000
63A71GLU-1-0.978-0.98223.4220.0960.0960.0000.0000.0000.000
64A72ARG10.7660.86019.435-0.097-0.0970.0000.0000.0000.000
65A73PHE0-0.033-0.03016.7470.0120.0120.0000.0000.0000.000
66A74GLY0-0.0270.00820.5280.0320.0320.0000.0000.0000.000
67A84CAF00.0410.02012.0180.0530.0530.0000.0000.0000.000
68A85THR0-0.059-0.04913.202-0.074-0.0740.0000.0000.0000.000
69A86LEU00.0290.03315.9670.0090.0090.0000.0000.0000.000
70A87PRO0-0.0130.01116.433-0.012-0.0120.0000.0000.0000.000
71A88THR00.006-0.00919.356-0.022-0.0220.0000.0000.0000.000
72A89LEU0-0.012-0.00923.132-0.002-0.0020.0000.0000.0000.000
73A90PRO00.0150.00325.305-0.005-0.0050.0000.0000.0000.000
74A91ALA00.0210.01328.154-0.010-0.0100.0000.0000.0000.000
75A92LYS10.8260.91029.483-0.116-0.1160.0000.0000.0000.000
76A93VAL00.0450.02034.183-0.003-0.0030.0000.0000.0000.000
77A94TYR00.014-0.00630.220-0.004-0.0040.0000.0000.0000.000
78A95VAL0-0.023-0.00736.310-0.002-0.0020.0000.0000.0000.000
79A96GLY00.0520.02540.0850.0000.0000.0000.0000.0000.000
80A97VAL0-0.0040.00741.425-0.001-0.0010.0000.0000.0000.000
81A98LYS10.8810.91439.998-0.026-0.0260.0000.0000.0000.000
82A99GLN0-0.0030.00937.9730.0000.0000.0000.0000.0000.000
83A100GLU-1-0.874-0.93336.6900.0500.0500.0000.0000.0000.000
84A101ILE0-0.035-0.00935.9860.0050.0050.0000.0000.0000.000
85A102ALA0-0.024-0.00233.3660.0060.0060.0000.0000.0000.000
86A103GLU-1-0.796-0.92331.9920.0370.0370.0000.0000.0000.000
87A104MET0-0.0030.01031.5410.0070.0070.0000.0000.0000.000
88A105ARG10.8040.89429.346-0.061-0.0610.0000.0000.0000.000
89A106ILE00.0210.02926.9860.0090.0090.0000.0000.0000.000
90A107PRO0-0.002-0.00825.2470.0060.0060.0000.0000.0000.000
91A108ALA00.0160.01023.7810.0130.0130.0000.0000.0000.000
92A109LEU0-0.0010.00323.3010.0150.0150.0000.0000.0000.000
93A110ASN00.0550.02421.518-0.002-0.0020.0000.0000.0000.000
94A111ALA0-0.0110.00119.3780.0090.0090.0000.0000.0000.000
95A112TYR00.0170.01818.4630.0270.0270.0000.0000.0000.000
96A113MET0-0.007-0.00318.2990.0150.0150.0000.0000.0000.000
97A114LYS10.9130.96215.289-0.096-0.0960.0000.0000.0000.000
98A115SER0-0.007-0.00213.7930.0470.0470.0000.0000.0000.000
99A116LEU0-0.013-0.00913.7610.0620.0620.0000.0000.0000.000
100A117LEU0-0.050-0.03113.0200.0210.0210.0000.0000.0000.000
101A118SER0-0.037-0.0159.661-0.042-0.0420.0000.0000.0000.000
102A119LEU0-0.071-0.0189.1360.2280.2280.0000.0000.0000.000
103A120PRO00.0410.0197.096-0.059-0.0590.0000.0000.0000.000
104A121VAL00.0600.0306.355-0.148-0.1480.0000.0000.0000.000
105A122TRP0-0.043-0.0278.790-0.113-0.1130.0000.0000.0000.000
106A123VAL0-0.028-0.01211.554-0.023-0.0230.0000.0000.0000.000
107A124LEU0-0.0180.0029.682-0.051-0.0510.0000.0000.0000.000
108A125MET0-0.038-0.02312.601-0.071-0.0710.0000.0000.0000.000
109A126ASP-1-0.807-0.89714.3070.0910.0910.0000.0000.0000.000
110A127GLU-1-0.923-0.95817.238-0.027-0.0270.0000.0000.0000.000
111A128ASP-1-0.777-0.86620.5760.0540.0540.0000.0000.0000.000
112A129VAL00.0070.00416.027-0.002-0.0020.0000.0000.0000.000
113A130ARG10.8270.89715.3920.1420.1420.0000.0000.0000.000
114A131ILE00.0140.00319.137-0.012-0.0120.0000.0000.0000.000
115A132PHE0-0.049-0.01221.281-0.002-0.0020.0000.0000.0000.000
116A133PHE00.037-0.00617.676-0.001-0.0010.0000.0000.0000.000
117A134TYR0-0.0020.01120.075-0.008-0.0080.0000.0000.0000.000
118A135GLN0-0.074-0.04222.8720.0070.0070.0000.0000.0000.000
119A136SER0-0.007-0.01926.152-0.005-0.0050.0000.0000.0000.000
120A137PRO00.0620.00429.041-0.002-0.0020.0000.0000.0000.000
121A138TYR00.0670.04232.476-0.001-0.0010.0000.0000.0000.000
122A139ASP-1-0.787-0.84028.365-0.013-0.0130.0000.0000.0000.000
123A140SER0-0.053-0.04030.905-0.002-0.0020.0000.0000.0000.000
124A141GLU-1-0.797-0.89332.146-0.026-0.0260.0000.0000.0000.000
125A142GLN0-0.009-0.02333.2300.0050.0050.0000.0000.0000.000
126A143VAL00.0090.02730.4890.0020.0020.0000.0000.0000.000
127A144PRO00.004-0.00833.8860.0010.0010.0000.0000.0000.000
128A145GLN0-0.0010.00937.2280.0030.0030.0000.0000.0000.000
129A146ALA00.0230.01035.2530.0020.0020.0000.0000.0000.000
130A147LEU00.008-0.00834.5040.0010.0010.0000.0000.0000.000
131A148ARG10.8960.95037.9170.0300.0300.0000.0000.0000.000
132A149ARG10.8610.91236.8030.0050.0050.0000.0000.0000.000
133A150LEU00.0050.01435.8590.0020.0020.0000.0000.0000.000
134A151ARG10.8670.94440.0790.0180.0180.0000.0000.0000.000
135A152PRO00.0830.06342.047-0.003-0.0030.0000.0000.0000.000
136A153ARG10.8760.92841.6460.0260.0260.0000.0000.0000.000
137A169ARG10.8470.91644.810-0.010-0.0100.0000.0000.0000.000
138A170MET0-0.048-0.00347.5600.0000.0000.0000.0000.0000.000
139A171ALA00.0070.00150.1000.0010.0010.0000.0000.0000.000
140A172ALA00.0490.01353.102-0.001-0.0010.0000.0000.0000.000
141A173PRO0-0.0250.00052.9070.0000.0000.0000.0000.0000.000
142A174ARG10.9360.97856.0160.0010.0010.0000.0000.0000.000
143A175ALA00.0150.00259.819-0.001-0.0010.0000.0000.0000.000
144A176GLU-1-0.898-0.95163.193-0.002-0.0020.0000.0000.0000.000
145A177ALA00.0010.01366.915-0.001-0.0010.0000.0000.0000.000
146A178LEU0-0.020-0.00569.8460.0000.0000.0000.0000.0000.000
147A179PHE0-0.031-0.02472.3470.0000.0000.0000.0000.0000.000
148A180ASP-1-0.803-0.89173.497-0.002-0.0020.0000.0000.0000.000
149A181PHE0-0.047-0.02170.290-0.001-0.0010.0000.0000.0000.000
150A182THR0-0.0080.00473.5240.0000.0000.0000.0000.0000.000
151A183GLY00.0140.00472.0440.0000.0000.0000.0000.0000.000
152A184ASN0-0.068-0.05872.7080.0000.0000.0000.0000.0000.000
153A185SER0-0.029-0.02870.2530.0000.0000.0000.0000.0000.000
154A186LYS10.9350.94670.2800.0040.0040.0000.0000.0000.000
155A187LEU00.0170.02463.4750.0000.0000.0000.0000.0000.000
156A188GLU-1-0.801-0.86166.240-0.008-0.0080.0000.0000.0000.000
157A189LEU0-0.043-0.01064.9420.0010.0010.0000.0000.0000.000
158A190ASN0-0.036-0.03168.1950.0000.0000.0000.0000.0000.000
159A191PHE0-0.037-0.01568.6530.0010.0010.0000.0000.0000.000
160A192LYS10.8820.92071.8670.0010.0010.0000.0000.0000.000
161A193ALA00.0120.00372.5260.0000.0000.0000.0000.0000.000
162A194GLY00.001-0.00471.7210.0010.0010.0000.0000.0000.000
163A195ASP-1-0.801-0.86568.8940.0000.0000.0000.0000.0000.000
164A196VAL0-0.039-0.02063.478-0.001-0.0010.0000.0000.0000.000
165A197ILE0-0.028-0.00263.0450.0010.0010.0000.0000.0000.000
166A198PHE00.007-0.00757.9730.0000.0000.0000.0000.0000.000
167A199LEU0-0.034-0.01657.5220.0000.0000.0000.0000.0000.000
168A200LEU0-0.020-0.00355.9030.0000.0000.0000.0000.0000.000
169A201SER00.0600.02254.579-0.001-0.0010.0000.0000.0000.000
170A202ARG10.9100.95955.5230.0140.0140.0000.0000.0000.000
171A203ILE0-0.0230.00756.499-0.001-0.0010.0000.0000.0000.000
172A204ASN00.014-0.01258.803-0.001-0.0010.0000.0000.0000.000
173A205LYS10.8640.92760.3150.0150.0150.0000.0000.0000.000
174A206ASP-1-0.820-0.90362.124-0.013-0.0130.0000.0000.0000.000
175A207TRP00.0140.02663.3350.0010.0010.0000.0000.0000.000
176A208LEU00.007-0.00159.530-0.001-0.0010.0000.0000.0000.000
177A209GLU-1-0.903-0.95457.226-0.007-0.0070.0000.0000.0000.000
178A210GLY00.018-0.00759.7280.0000.0000.0000.0000.0000.000
179A211THR0-0.026-0.02259.8460.0000.0000.0000.0000.0000.000
180A212VAL00.011-0.00362.6890.0000.0000.0000.0000.0000.000
181A213ARG10.8400.88265.1470.0000.0000.0000.0000.0000.000
182A214GLY00.0750.05463.7300.0000.0000.0000.0000.0000.000
183A215ALA0-0.0130.01064.6450.0000.0000.0000.0000.0000.000
184A216THR00.009-0.01660.6810.0000.0000.0000.0000.0000.000
185A217GLY00.0120.01863.4480.0000.0000.0000.0000.0000.000
186A218ILE0-0.015-0.00562.5110.0000.0000.0000.0000.0000.000
187A219PHE0-0.005-0.01062.3640.0010.0010.0000.0000.0000.000
188A220PRO00.0310.03465.354-0.001-0.0010.0000.0000.0000.000
189A221LEU00.014-0.01662.4450.0000.0000.0000.0000.0000.000
190A222SER0-0.008-0.01565.7840.0000.0000.0000.0000.0000.000
191A223PHE00.0130.00769.0240.0000.0000.0000.0000.0000.000
192A224VAL0-0.021-0.00464.6250.0010.0010.0000.0000.0000.000
193A225LYS10.9070.97364.4970.0040.0040.0000.0000.0000.000
194A226ILE00.0310.00459.5510.0010.0010.0000.0000.0000.000
195A227LEU0-0.091-0.04461.6340.0000.0000.0000.0000.0000.000
196A228LYS10.8070.89751.9970.0060.0060.0000.0000.0000.000
197A229ASP-1-0.784-0.88455.620-0.011-0.0110.0000.0000.0000.000
198A230PHE0-0.022-0.02952.3920.0010.0010.0000.0000.0000.000
199A231PRO0-0.039-0.02348.0450.0000.0000.0000.0000.0000.000
200A232GLU-1-0.880-0.92447.824-0.021-0.0210.0000.0000.0000.000
201A233GLU-1-0.804-0.89045.535-0.025-0.0250.0000.0000.0000.000
202A234ASP-1-0.938-0.97542.674-0.032-0.0320.0000.0000.0000.000
203A235ASP-1-0.880-0.92242.082-0.012-0.0120.0000.0000.0000.000
204A236PRO0-0.015-0.01338.7890.0010.0010.0000.0000.0000.000
205A237THR0-0.108-0.07940.7960.0030.0030.0000.0000.0000.000
206A238ASN0-0.0040.00239.362-0.003-0.0030.0000.0000.0000.000
207A239TRP00.007-0.01043.3560.0030.0030.0000.0000.0000.000
208A240LEU0-0.008-0.00645.6620.0000.0000.0000.0000.0000.000
209A241ARG10.8070.88247.5610.0040.0040.0000.0000.0000.000
210A242CYS0-0.061-0.02450.6180.0010.0010.0000.0000.0000.000
211A243TYR00.0240.01052.937-0.001-0.0010.0000.0000.0000.000
212A244TYR0-0.092-0.05756.0500.0020.0020.0000.0000.0000.000
213A245TYR0-0.041-0.04157.398-0.001-0.0010.0000.0000.0000.000
214A246GLU-1-0.859-0.92061.4580.0080.0080.0000.0000.0000.000
215A247ASP-1-0.880-0.93364.4180.0090.0090.0000.0000.0000.000
216A248THR0-0.057-0.03267.8850.0000.0000.0000.0000.0000.000
217A249ILE0-0.0150.00465.408-0.001-0.0010.0000.0000.0000.000
218A250SER00.0140.00861.6190.0010.0010.0000.0000.0000.000
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220A252ILE00.013-0.00555.8910.0000.0000.0000.0000.0000.000
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