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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: JQ9R9

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 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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1867700.524946
FMO2-HF: Nuclear repulsion 1794605.616333
FMO2-HF: Total energy -73094.908613
FMO2-MP2: Total energy -73295.192186


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.
-2.50.3480.05-1.48-1.4180.003
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 : 0.025 / q_NPA : 0.013
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].
3A66ARG10.9650.9743.251-2.3830.4650.050-1.480-1.4180.003
4A67SER00.0030.0065.783-0.207-0.2070.0000.0000.0000.000
5A68ILE00.0280.0168.8550.0520.0520.0000.0000.0000.000
6A69PRO0-0.024-0.00412.1440.0230.0230.0000.0000.0000.000
7A70GLU-1-0.832-0.89714.585-0.214-0.2140.0000.0000.0000.000
8A71LEU0-0.059-0.02717.8420.0480.0480.0000.0000.0000.000
9A72ARG10.8480.92719.2210.0600.0600.0000.0000.0000.000
10A73LEU00.0130.00724.3560.0170.0170.0000.0000.0000.000
11A74GLY00.0220.01127.556-0.010-0.0100.0000.0000.0000.000
12A75VAL0-0.034-0.02330.7860.0040.0040.0000.0000.0000.000
13A76LEU00.0140.01333.9800.0000.0000.0000.0000.0000.000
14A77GLY00.1010.02737.5180.0010.0010.0000.0000.0000.000
15A78ASP-1-0.795-0.87040.945-0.045-0.0450.0000.0000.0000.000
16A79ALA00.0060.02443.090-0.003-0.0030.0000.0000.0000.000
17A80ARG10.8050.86544.5710.0360.0360.0000.0000.0000.000
18A81SER0-0.023-0.02241.766-0.002-0.0020.0000.0000.0000.000
19A82GLY00.0680.04541.8590.0000.0000.0000.0000.0000.000
20A83LYS10.8620.92337.3610.0570.0570.0000.0000.0000.000
21A84SER0-0.011-0.03036.606-0.004-0.0040.0000.0000.0000.000
22A85SER0-0.001-0.01836.609-0.006-0.0060.0000.0000.0000.000
23A86LEU0-0.033-0.00534.937-0.006-0.0060.0000.0000.0000.000
24A87ILE0-0.003-0.00531.185-0.007-0.0070.0000.0000.0000.000
25A88HIS00.0260.01532.269-0.012-0.0120.0000.0000.0000.000
26A89ARG10.8730.96433.4610.0950.0950.0000.0000.0000.000
27A90PHE0-0.001-0.00126.396-0.010-0.0100.0000.0000.0000.000
28A91LEU0-0.056-0.02527.387-0.015-0.0150.0000.0000.0000.000
29A92THR0-0.009-0.00228.977-0.013-0.0130.0000.0000.0000.000
30A93GLY0-0.0140.00931.645-0.003-0.0030.0000.0000.0000.000
31A94SER0-0.095-0.05633.2940.0090.0090.0000.0000.0000.000
32A95TYR00.017-0.00736.652-0.001-0.0010.0000.0000.0000.000
33A96GLN00.0530.03239.0660.0050.0050.0000.0000.0000.000
34A97VAL0-0.0100.01641.0190.0010.0010.0000.0000.0000.000
35A98LEU0-0.0060.00038.087-0.001-0.0010.0000.0000.0000.000
36A99GLU-1-0.875-0.93042.088-0.059-0.0590.0000.0000.0000.000
37A100LYS10.8080.91135.7700.0930.0930.0000.0000.0000.000
38A101THR0-0.060-0.04734.0560.0000.0000.0000.0000.0000.000
39A102GLU-1-0.896-0.94935.569-0.114-0.1140.0000.0000.0000.000
40A103SER0-0.033-0.01331.448-0.005-0.0050.0000.0000.0000.000
41A104GLU-1-0.821-0.88831.787-0.086-0.0860.0000.0000.0000.000
42A105GLN0-0.066-0.03324.9840.0180.0180.0000.0000.0000.000
43A106TYR00.0610.03127.026-0.007-0.0070.0000.0000.0000.000
44A107LYS10.8970.94318.5460.4020.4020.0000.0000.0000.000
45A108LYS10.8820.93922.5430.1770.1770.0000.0000.0000.000
46A109GLU-1-0.868-0.92516.531-0.454-0.4540.0000.0000.0000.000
47A110MET0-0.032-0.01119.5180.0230.0230.0000.0000.0000.000
48A111LEU00.0020.00817.029-0.009-0.0090.0000.0000.0000.000
49A112VAL0-0.009-0.02219.1410.0240.0240.0000.0000.0000.000
50A113ASP-1-0.862-0.92619.5280.0110.0110.0000.0000.0000.000
51A114GLY0-0.0100.00518.6970.0160.0160.0000.0000.0000.000
52A115GLN00.0030.00712.6980.0040.0040.0000.0000.0000.000
53A116THR0-0.024-0.01313.9060.0410.0410.0000.0000.0000.000
54A117HIS0-0.002-0.00914.8490.0390.0390.0000.0000.0000.000
55A118LEU0-0.0040.00116.590-0.029-0.0290.0000.0000.0000.000
56A119VAL0-0.008-0.01018.2380.0380.0380.0000.0000.0000.000
57A120LEU0-0.013-0.00520.530-0.014-0.0140.0000.0000.0000.000
58A121ILE0-0.004-0.01123.7390.0180.0180.0000.0000.0000.000
59A122ARG10.8210.88627.5350.0720.0720.0000.0000.0000.000
60A123GLU-1-0.714-0.84430.380-0.072-0.0720.0000.0000.0000.000
61A124GLU-1-0.790-0.88734.058-0.059-0.0590.0000.0000.0000.000
62A125ALA00.000-0.01436.4840.0010.0010.0000.0000.0000.000
63A126GLY00.004-0.01039.7930.0020.0020.0000.0000.0000.000
64A127ALA0-0.054-0.01840.2710.0000.0000.0000.0000.0000.000
65A128PRO0-0.0090.01036.822-0.002-0.0020.0000.0000.0000.000
66A129ASP-1-0.799-0.89334.957-0.042-0.0420.0000.0000.0000.000
67A130ALA00.0550.00835.4810.0000.0000.0000.0000.0000.000
68A131LYS10.8860.95128.2540.0460.0460.0000.0000.0000.000
69A132PHE00.0460.03130.7640.0000.0000.0000.0000.0000.000
70A133SER0-0.034-0.02831.1360.0020.0020.0000.0000.0000.000
71A134GLY0-0.012-0.00230.4340.0060.0060.0000.0000.0000.000
72A135TRP0-0.125-0.07324.9860.0090.0090.0000.0000.0000.000
73A136ALA00.0130.00926.191-0.003-0.0030.0000.0000.0000.000
74A137ASP-1-0.824-0.89723.186-0.020-0.0200.0000.0000.0000.000
75A138ALA0-0.015-0.02126.4730.0100.0100.0000.0000.0000.000
76A139VAL0-0.009-0.00629.141-0.008-0.0080.0000.0000.0000.000
77A140ILE0-0.0140.00530.5300.0060.0060.0000.0000.0000.000
78A141PHE00.0290.00834.200-0.003-0.0030.0000.0000.0000.000
79A142VAL0-0.021-0.01337.3080.0000.0000.0000.0000.0000.000
80A143PHE0-0.006-0.01039.9410.0020.0020.0000.0000.0000.000
81A144SER00.0350.00243.678-0.002-0.0020.0000.0000.0000.000
82A145LEU0-0.015-0.01745.2600.0030.0030.0000.0000.0000.000
83A146GLU-1-0.719-0.79548.090-0.039-0.0390.0000.0000.0000.000
84A147ASP-1-0.828-0.90049.548-0.033-0.0330.0000.0000.0000.000
85A148GLU-1-0.702-0.81349.809-0.022-0.0220.0000.0000.0000.000
86A149ASN0-0.024-0.02650.8280.0030.0030.0000.0000.0000.000
87A150SER0-0.040-0.04045.7990.0000.0000.0000.0000.0000.000
88A151PHE0-0.019-0.01845.8380.0000.0000.0000.0000.0000.000
89A152GLN0-0.020-0.02746.7070.0020.0020.0000.0000.0000.000
90A153ALA0-0.072-0.03745.7060.0020.0020.0000.0000.0000.000
91A154VAL00.0090.01641.3680.0000.0000.0000.0000.0000.000
92A155SER00.0420.01942.9460.0010.0010.0000.0000.0000.000
93A156ARG10.9360.98344.7310.0280.0280.0000.0000.0000.000
94A157LEU0-0.0060.00440.5600.0010.0010.0000.0000.0000.000
95A158HIS00.010-0.00338.6440.0000.0000.0000.0000.0000.000
96A159GLY00.0430.03140.4570.0030.0030.0000.0000.0000.000
97A160GLN00.002-0.00841.6350.0000.0000.0000.0000.0000.000
98A161LEU00.0050.00534.2500.0010.0010.0000.0000.0000.000
99A162SER0-0.021-0.02437.4140.0030.0030.0000.0000.0000.000
100A163SER0-0.052-0.03138.8260.0030.0030.0000.0000.0000.000
101A164LEU0-0.076-0.02337.1100.0020.0020.0000.0000.0000.000
102A165ARG10.8590.93330.002-0.006-0.0060.0000.0000.0000.000
103A166GLY00.0120.01434.7030.0040.0040.0000.0000.0000.000
104A167GLU-1-0.933-0.98735.7050.0170.0170.0000.0000.0000.000
105A168GLY0-0.020-0.00333.6190.0050.0050.0000.0000.0000.000
106A169ARG10.9250.96226.7250.0010.0010.0000.0000.0000.000
107A170GLY00.0380.03529.2170.0020.0020.0000.0000.0000.000
108A171GLY0-0.024-0.00830.861-0.008-0.0080.0000.0000.0000.000
109A172LEU00.0340.01729.9060.0010.0010.0000.0000.0000.000
110A173ALA0-0.032-0.00928.8460.0000.0000.0000.0000.0000.000
111A174LEU00.0320.01530.817-0.007-0.0070.0000.0000.0000.000
112A175ALA0-0.025-0.01833.5880.0020.0020.0000.0000.0000.000
113A176LEU0-0.0110.00935.201-0.001-0.0010.0000.0000.0000.000
114A177VAL00.018-0.01136.2220.0000.0000.0000.0000.0000.000
115A178GLY00.0400.02939.4420.0000.0000.0000.0000.0000.000
116A179THR0-0.046-0.04540.629-0.001-0.0010.0000.0000.0000.000
117A180GLN00.030-0.02443.1710.0000.0000.0000.0000.0000.000
118A181ASP-1-0.631-0.73042.788-0.064-0.0640.0000.0000.0000.000
119A182ARG10.8800.94945.5540.0540.0540.0000.0000.0000.000
120A183ILE0-0.044-0.00648.5550.0030.0030.0000.0000.0000.000
121A184SER0-0.026-0.01351.112-0.001-0.0010.0000.0000.0000.000
122A185ALA00.002-0.01154.2280.0020.0020.0000.0000.0000.000
123A186SER00.006-0.00157.2820.0010.0010.0000.0000.0000.000
124A187SER0-0.057-0.03053.5070.0020.0020.0000.0000.0000.000
125A188PRO00.0340.02753.909-0.002-0.0020.0000.0000.0000.000
126A189ARG10.8120.85347.4450.0320.0320.0000.0000.0000.000
127A190VAL0-0.002-0.00352.2760.0020.0020.0000.0000.0000.000
128A191VAL0-0.0450.00348.2570.0020.0020.0000.0000.0000.000
129A192GLY00.0290.01850.029-0.002-0.0020.0000.0000.0000.000
130A193ASP-1-0.814-0.90847.114-0.021-0.0210.0000.0000.0000.000
131A194ALA0-0.007-0.01047.6010.0010.0010.0000.0000.0000.000
132A195ARG10.8650.88949.2230.0210.0210.0000.0000.0000.000
133A196ALA00.0180.02444.9800.0010.0010.0000.0000.0000.000
134A197ARG10.8950.92944.1220.0140.0140.0000.0000.0000.000
135A198ALA00.0010.01544.7490.0020.0020.0000.0000.0000.000
136A199LEU00.0940.05643.5310.0020.0020.0000.0000.0000.000
137A200CAF10.0640.15938.8260.0100.0100.0000.0000.0000.000
138A201ALA-1-0.159-0.22842.115-0.009-0.0090.0000.0000.0000.000
139A202ASP-1-0.915-0.92942.4230.0000.0000.0000.0000.0000.000
140A203MET0-0.091-0.04239.1170.0010.0010.0000.0000.0000.000
141A204LYS10.9100.94737.908-0.005-0.0050.0000.0000.0000.000
142A205ARG10.9610.97930.280-0.034-0.0340.0000.0000.0000.000
143A206CYS0-0.0060.02834.065-0.005-0.0050.0000.0000.0000.000
144A207SER0-0.0020.00034.6870.0060.0060.0000.0000.0000.000
145A208TYR0-0.011-0.04036.675-0.003-0.0030.0000.0000.0000.000
146A209TYR0-0.052-0.06333.4310.0000.0000.0000.0000.0000.000
147A210GLU-1-0.735-0.80139.203-0.034-0.0340.0000.0000.0000.000
148A211THR0-0.016-0.00437.204-0.002-0.0020.0000.0000.0000.000
149A212CAF1-0.203-0.14340.1000.0660.0660.0000.0000.0000.000
150A213ALA-1-0.083-0.10838.548-0.074-0.0740.0000.0000.0000.000
151A214THR00.0440.01839.300-0.007-0.0070.0000.0000.0000.000
152A215TYR00.0230.00340.625-0.005-0.0050.0000.0000.0000.000
153A216GLY00.0160.02236.836-0.003-0.0030.0000.0000.0000.000
154A217LEU0-0.025-0.00736.295-0.002-0.0020.0000.0000.0000.000
155A218ASN0-0.004-0.02935.7810.0010.0010.0000.0000.0000.000
156A219VAL00.0130.01932.9530.0020.0020.0000.0000.0000.000
157A220ASP-1-0.827-0.94128.900-0.138-0.1380.0000.0000.0000.000
158A221ARG10.8380.90529.8500.0470.0470.0000.0000.0000.000
159A222VAL00.0160.02631.1600.0050.0050.0000.0000.0000.000
160A223PHE00.0300.00327.8670.0060.0060.0000.0000.0000.000
161A224GLN0-0.024-0.00923.7060.0120.0120.0000.0000.0000.000
162A225GLU-1-0.738-0.82726.478-0.036-0.0360.0000.0000.0000.000
163A226VAL0-0.021-0.01128.0540.0130.0130.0000.0000.0000.000
164A227ALA00.0240.01423.2430.0100.0100.0000.0000.0000.000
165A228GLN00.000-0.01623.420-0.002-0.0020.0000.0000.0000.000
166A229LYS10.8170.90625.0290.0390.0390.0000.0000.0000.000
167A230VAL0-0.0100.00522.6740.0160.0160.0000.0000.0000.000
168A231VAL00.0060.00519.7530.0210.0210.0000.0000.0000.000
169A232THR0-0.059-0.04822.1230.0290.0290.0000.0000.0000.000
170A233LEU0-0.052-0.01624.7250.0160.0160.0000.0000.0000.000
171A234ARG10.8420.89318.7320.0190.0190.0000.0000.0000.000
172A235LYS10.9430.97820.000-0.068-0.0680.0000.0000.0000.000
173A236GLN0-0.010-0.01522.2710.0100.0100.0000.0000.0000.000
174A237GLN0-0.036-0.02524.4520.0030.0030.0000.0000.0000.000
175A238GLN0-0.052-0.00819.0860.0250.0250.0000.0000.0000.000
176A239LEU0-0.0060.01621.7230.0160.0160.0000.0000.0000.000