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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: 3JV4L

Calculation Name: 2IWR-A-Xray372

Preferred Name:

Target Type:

Ligand Name: s-dimethylarsinoyl-cysteine

ligand 3-letter code: CAF

PDB ID: 2IWR

Chain ID: A

ChEMBL ID:

UniProt ID: Q99490

Base Structure: X-ray

Registration Date: 2023-09-23

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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1872480.016562
FMO2-HF: Nuclear repulsion 1799384.436177
FMO2-HF: Total energy -73095.580385
FMO2-MP2: Total energy -73295.738105


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:64:SER)


Summations of interaction energy for fragment #1(A:64: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.
-18.645-14.7856.124-4.538-5.4460.039
Interaction energy analysis for fragmet #1(A:64:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.044 / q_NPA : 0.021
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].
3A66ARG10.9110.9452.147-19.161-15.3446.125-4.535-5.4070.039
4A67SER00.0090.0095.3800.0650.108-0.001-0.003-0.0390.000
5A68ILE00.0340.0279.0700.2090.2090.0000.0000.0000.000
6A69PRO0-0.028-0.00911.8090.0240.0240.0000.0000.0000.000
7A70GLU-1-0.821-0.89014.556-0.429-0.4290.0000.0000.0000.000
8A71LEU0-0.049-0.01917.8970.0600.0600.0000.0000.0000.000
9A72ARG10.8180.90619.6270.2870.2870.0000.0000.0000.000
10A73LEU00.0140.00624.4190.0270.0270.0000.0000.0000.000
11A74GLY00.0340.02027.362-0.008-0.0080.0000.0000.0000.000
12A75VAL0-0.024-0.01830.7450.0070.0070.0000.0000.0000.000
13A76LEU00.0000.00333.8110.0010.0010.0000.0000.0000.000
14A77GLY00.1010.03237.4640.0040.0040.0000.0000.0000.000
15A78ASP-1-0.801-0.87140.815-0.089-0.0890.0000.0000.0000.000
16A79ALA00.0140.03142.540-0.005-0.0050.0000.0000.0000.000
17A80ARG10.8380.86043.9960.0660.0660.0000.0000.0000.000
18A81SER0-0.028-0.03241.406-0.003-0.0030.0000.0000.0000.000
19A82GLY00.0600.05441.2660.0000.0000.0000.0000.0000.000
20A83LYS10.8420.92236.9740.1130.1130.0000.0000.0000.000
21A84SER0-0.014-0.03135.989-0.006-0.0060.0000.0000.0000.000
22A85SER00.008-0.00936.025-0.008-0.0080.0000.0000.0000.000
23A86LEU0-0.042-0.01534.122-0.006-0.0060.0000.0000.0000.000
24A87ILE0-0.013-0.01030.813-0.009-0.0090.0000.0000.0000.000
25A88HIS00.0090.00131.518-0.021-0.0210.0000.0000.0000.000
26A89ARG10.8410.94932.7650.1350.1350.0000.0000.0000.000
27A90PHE0-0.014-0.00725.135-0.010-0.0100.0000.0000.0000.000
28A91LEU0-0.053-0.02626.644-0.019-0.0190.0000.0000.0000.000
29A92THR0-0.0030.00528.370-0.013-0.0130.0000.0000.0000.000
30A93GLY0-0.0090.01031.0220.0010.0010.0000.0000.0000.000
31A94SER0-0.091-0.05332.3250.0160.0160.0000.0000.0000.000
32A95TYR00.032-0.00835.773-0.003-0.0030.0000.0000.0000.000
33A96GLN00.0470.03038.6090.0080.0080.0000.0000.0000.000
34A97VAL0-0.0150.01640.346-0.002-0.0020.0000.0000.0000.000
35A98LEU00.000-0.00137.760-0.002-0.0020.0000.0000.0000.000
36A99GLU-1-0.839-0.90941.249-0.102-0.1020.0000.0000.0000.000
37A100LYS10.7710.87436.3570.1610.1610.0000.0000.0000.000
38A101THR0-0.061-0.04933.9490.0030.0030.0000.0000.0000.000
39A102GLU-1-0.838-0.92035.252-0.174-0.1740.0000.0000.0000.000
40A103SER0-0.039-0.02631.734-0.011-0.0110.0000.0000.0000.000
41A104GLU-1-0.798-0.86332.769-0.167-0.1670.0000.0000.0000.000
42A105GLN0-0.059-0.03625.8370.0180.0180.0000.0000.0000.000
43A106TYR00.0400.02326.892-0.007-0.0070.0000.0000.0000.000
44A107LYS10.8360.90318.3550.6290.6290.0000.0000.0000.000
45A108LYS10.8510.91922.1420.2710.2710.0000.0000.0000.000
46A109GLU-1-0.829-0.90316.119-0.665-0.6650.0000.0000.0000.000
47A110MET0-0.033-0.00118.3500.0570.0570.0000.0000.0000.000
48A111LEU0-0.0100.00516.185-0.042-0.0420.0000.0000.0000.000
49A112VAL00.015-0.00117.7770.0350.0350.0000.0000.0000.000
50A113ASP-1-0.838-0.90317.749-0.035-0.0350.0000.0000.0000.000
51A114GLY00.0020.00817.5110.0340.0340.0000.0000.0000.000
52A115GLN0-0.0030.00411.3170.0440.0440.0000.0000.0000.000
53A116THR0-0.006-0.00812.4960.0540.0540.0000.0000.0000.000
54A117HIS0-0.002-0.01913.471-0.037-0.0370.0000.0000.0000.000
55A118LEU0-0.002-0.00516.079-0.011-0.0110.0000.0000.0000.000
56A119VAL00.0100.00817.9010.0360.0360.0000.0000.0000.000
57A120LEU0-0.026-0.01020.692-0.017-0.0170.0000.0000.0000.000
58A121ILE00.0080.00023.7040.0270.0270.0000.0000.0000.000
59A122ARG10.8070.87427.4660.1570.1570.0000.0000.0000.000
60A123GLU-1-0.716-0.82530.638-0.138-0.1380.0000.0000.0000.000
61A124GLU-1-0.761-0.87634.277-0.142-0.1420.0000.0000.0000.000
62A125ALA0-0.012-0.01637.0850.0030.0030.0000.0000.0000.000
63A126GLY0-0.001-0.01640.4210.0060.0060.0000.0000.0000.000
64A127ALA0-0.034-0.00740.684-0.001-0.0010.0000.0000.0000.000
65A128PRO0-0.0160.00436.763-0.005-0.0050.0000.0000.0000.000
66A129ASP-1-0.750-0.86934.752-0.126-0.1260.0000.0000.0000.000
67A130ALA00.0350.01935.776-0.001-0.0010.0000.0000.0000.000
68A131LYS10.8260.91128.5620.1600.1600.0000.0000.0000.000
69A132PHE00.0300.01230.939-0.009-0.0090.0000.0000.0000.000
70A133SER0-0.016-0.01931.170-0.002-0.0020.0000.0000.0000.000
71A134GLY0-0.009-0.00130.3330.0050.0050.0000.0000.0000.000
72A135TRP0-0.101-0.06425.636-0.003-0.0030.0000.0000.0000.000
73A136ALA00.0160.01126.214-0.015-0.0150.0000.0000.0000.000
74A137ASP-1-0.801-0.87222.814-0.203-0.2030.0000.0000.0000.000
75A138ALA0-0.016-0.02625.9360.0190.0190.0000.0000.0000.000
76A139VAL0-0.012-0.00628.728-0.011-0.0110.0000.0000.0000.000
77A140ILE0-0.0200.00029.8250.0110.0110.0000.0000.0000.000
78A141PHE00.0420.01133.626-0.003-0.0030.0000.0000.0000.000
79A142VAL0-0.036-0.02036.6660.0010.0010.0000.0000.0000.000
80A143PHE0-0.011-0.01339.3440.0020.0020.0000.0000.0000.000
81A144SER00.027-0.00443.066-0.002-0.0020.0000.0000.0000.000
82A145LEU0-0.013-0.01644.1790.0040.0040.0000.0000.0000.000
83A146GLU-1-0.725-0.78247.259-0.067-0.0670.0000.0000.0000.000
84A147ASP-1-0.809-0.87949.279-0.063-0.0630.0000.0000.0000.000
85A148GLU-1-0.722-0.82049.323-0.052-0.0520.0000.0000.0000.000
86A149ASN0-0.048-0.04450.3240.0010.0010.0000.0000.0000.000
87A150SER0-0.040-0.03445.426-0.003-0.0030.0000.0000.0000.000
88A151PHE0-0.024-0.02045.332-0.002-0.0020.0000.0000.0000.000
89A152GLN00.004-0.02646.095-0.001-0.0010.0000.0000.0000.000
90A153ALA0-0.063-0.02545.1690.0000.0000.0000.0000.0000.000
91A154VAL00.0130.01440.943-0.002-0.0020.0000.0000.0000.000
92A155SER00.0110.00342.837-0.001-0.0010.0000.0000.0000.000
93A156ARG10.9300.98344.8130.0690.0690.0000.0000.0000.000
94A157LEU0-0.0010.00640.5260.0000.0000.0000.0000.0000.000
95A158HIS00.0150.00738.214-0.003-0.0030.0000.0000.0000.000
96A159GLY00.0590.04140.3180.0010.0010.0000.0000.0000.000
97A160GLN0-0.012-0.00641.677-0.001-0.0010.0000.0000.0000.000
98A161LEU00.0130.00434.102-0.002-0.0020.0000.0000.0000.000
99A162SER0-0.020-0.02337.245-0.001-0.0010.0000.0000.0000.000
100A163SER0-0.065-0.04938.7030.0010.0010.0000.0000.0000.000
101A164LEU0-0.055-0.01237.3680.0010.0010.0000.0000.0000.000
102A165ARG10.8220.91930.1090.0760.0760.0000.0000.0000.000
103A166GLY00.0210.01534.7820.0010.0010.0000.0000.0000.000
104A167GLU-1-0.889-0.96635.060-0.049-0.0490.0000.0000.0000.000
105A168GLY0-0.040-0.01533.6180.0040.0040.0000.0000.0000.000
106A169ARG10.9180.96426.7990.1160.1160.0000.0000.0000.000
107A170GLY00.0260.03129.465-0.003-0.0030.0000.0000.0000.000
108A171GLY0-0.008-0.00230.876-0.005-0.0050.0000.0000.0000.000
109A172LEU00.0190.00929.614-0.007-0.0070.0000.0000.0000.000
110A173ALA0-0.0120.00128.1110.0090.0090.0000.0000.0000.000
111A174LEU00.0110.01330.066-0.011-0.0110.0000.0000.0000.000
112A175ALA0-0.021-0.01832.7530.0050.0050.0000.0000.0000.000
113A176LEU00.0130.01434.533-0.002-0.0020.0000.0000.0000.000
114A177VAL00.007-0.01035.4440.0030.0030.0000.0000.0000.000
115A178GLY00.0460.02738.6960.0000.0000.0000.0000.0000.000
116A179THR0-0.037-0.04439.7620.0010.0010.0000.0000.0000.000
117A180GLN00.012-0.03542.1320.0020.0020.0000.0000.0000.000
118A181ASP-1-0.816-0.89241.388-0.100-0.1000.0000.0000.0000.000
119A182ARG10.8260.91644.5520.0910.0910.0000.0000.0000.000
120A183ILE0-0.037-0.00447.3010.0040.0040.0000.0000.0000.000
121A184SER0-0.018-0.00649.9990.0000.0000.0000.0000.0000.000
122A185ALA0-0.004-0.01553.2040.0020.0020.0000.0000.0000.000
123A186SER0-0.0040.00455.7540.0020.0020.0000.0000.0000.000
124A187SER0-0.052-0.04252.5400.0010.0010.0000.0000.0000.000
125A188PRO00.0430.02852.938-0.002-0.0020.0000.0000.0000.000
126A189ARG10.7920.85446.1820.0560.0560.0000.0000.0000.000
127A190VAL00.0170.00851.4580.0030.0030.0000.0000.0000.000
128A191VAL0-0.034-0.00447.0510.0030.0030.0000.0000.0000.000
129A192GLY00.0350.02248.861-0.001-0.0010.0000.0000.0000.000
130A193ASP-1-0.780-0.88346.017-0.042-0.0420.0000.0000.0000.000
131A194ALA0-0.019-0.01546.4230.0000.0000.0000.0000.0000.000
132A195ARG10.8360.88448.2200.0480.0480.0000.0000.0000.000
133A196ALA00.0340.03043.673-0.001-0.0010.0000.0000.0000.000
134A197ARG10.8750.91242.9820.0360.0360.0000.0000.0000.000
135A198ALA00.0080.01443.6750.0010.0010.0000.0000.0000.000
136A199LEU00.0790.04142.8280.0010.0010.0000.0000.0000.000
137A200CAF0-0.075-0.02437.675-0.004-0.0040.0000.0000.0000.000
138A201ALA0-0.015-0.01140.0160.0000.0000.0000.0000.0000.000
139A202ASP-1-0.901-0.95141.850-0.035-0.0350.0000.0000.0000.000
140A203MET0-0.043-0.01138.533-0.001-0.0010.0000.0000.0000.000
141A204LYS10.8960.94737.7660.0350.0350.0000.0000.0000.000
142A205ARG10.9000.93429.1090.0260.0260.0000.0000.0000.000
143A206CYS0-0.0140.04633.401-0.009-0.0090.0000.0000.0000.000
144A207SER0-0.003-0.02233.7590.0080.0080.0000.0000.0000.000
145A208TYR0-0.021-0.04135.953-0.006-0.0060.0000.0000.0000.000
146A209TYR0-0.053-0.06332.2320.0000.0000.0000.0000.0000.000
147A210GLU-1-0.749-0.81138.161-0.062-0.0620.0000.0000.0000.000
148A211THR00.0070.00636.201-0.002-0.0020.0000.0000.0000.000
149A212CAF0-0.0150.01139.0370.0030.0030.0000.0000.0000.000
150A213ALA00.0320.01237.520-0.004-0.0040.0000.0000.0000.000
151A214THR0-0.001-0.02738.369-0.007-0.0070.0000.0000.0000.000
152A215TYR0-0.016-0.02639.785-0.004-0.0040.0000.0000.0000.000
153A216GLY00.0120.00835.852-0.004-0.0040.0000.0000.0000.000
154A217LEU0-0.025-0.00235.140-0.004-0.0040.0000.0000.0000.000
155A218ASN0-0.009-0.04234.3550.0000.0000.0000.0000.0000.000
156A219VAL00.0160.02431.802-0.002-0.0020.0000.0000.0000.000
157A220ASP-1-0.796-0.92027.465-0.214-0.2140.0000.0000.0000.000
158A221ARG10.8080.90028.3320.0760.0760.0000.0000.0000.000
159A222VAL00.0140.01829.6720.0030.0030.0000.0000.0000.000
160A223PHE00.0340.00826.7860.0020.0020.0000.0000.0000.000
161A224GLN0-0.029-0.01822.2400.0090.0090.0000.0000.0000.000
162A225GLU-1-0.731-0.82225.222-0.078-0.0780.0000.0000.0000.000
163A226VAL0-0.015-0.00727.3010.0110.0110.0000.0000.0000.000
164A227ALA00.0240.01222.1570.0020.0020.0000.0000.0000.000
165A228GLN00.021-0.01022.064-0.016-0.0160.0000.0000.0000.000
166A229LYS10.8070.89723.8820.0960.0960.0000.0000.0000.000
167A230VAL00.0030.01222.0300.0160.0160.0000.0000.0000.000
168A231VAL00.0020.00518.7760.0160.0160.0000.0000.0000.000
169A232THR0-0.044-0.04521.1560.0340.0340.0000.0000.0000.000
170A233LEU0-0.063-0.02223.8500.0210.0210.0000.0000.0000.000
171A234ARG10.8290.88418.3450.2300.2300.0000.0000.0000.000
172A235LYS10.8890.94719.2980.0050.0050.0000.0000.0000.000
173A236GLN00.0120.00721.6500.0120.0120.0000.0000.0000.000
174A237GLN0-0.017-0.02123.9510.0030.0030.0000.0000.0000.000
175A238GLN0-0.050-0.01218.2540.0210.0210.0000.0000.0000.000
176A239LEU0-0.0260.00821.4170.0240.0240.0000.0000.0000.000