FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 8993Y

Calculation Name: 2ISB-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 2ISB

Chain ID: A

ChEMBL ID:
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UniProt ID: O29167

Base Structure: X-ray

Registration Date: 2023-09-21

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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2000650.890217
FMO2-HF: Nuclear repulsion 1927471.837985
FMO2-HF: Total energy -73179.052232
FMO2-MP2: Total energy -73387.446614


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:-3:HIS)


Summations of interaction energy for fragment #1(A:-3:HIS)
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.
-17.458-16.005-0.008-0.517-0.9290.001
Interaction energy analysis for fragmet #1(A:-3:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.961 / q_NPA : 0.963
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].
3A-1HIS00.0350.0263.859-0.6630.790-0.008-0.517-0.9290.001
4A0HIS00.0450.0115.9300.9540.9540.0000.0000.0000.000
5A1MET0-0.039-0.0278.2020.6510.6510.0000.0000.0000.000
6A2VAL0-0.0190.00412.0460.3270.3270.0000.0000.0000.000
7A3MET0-0.019-0.00114.765-0.776-0.7760.0000.0000.0000.000
8A4GLU-1-0.827-0.90217.380-12.225-12.2250.0000.0000.0000.000
9A5TYR0-0.029-0.04317.895-0.571-0.5710.0000.0000.0000.000
10A6GLU-1-0.764-0.85022.999-10.512-10.5120.0000.0000.0000.000
11A7LEU0-0.018-0.00424.487-0.028-0.0280.0000.0000.0000.000
12A8ARG10.8830.92827.60511.16011.1600.0000.0000.0000.000
13A9THR0-0.041-0.02930.605-0.208-0.2080.0000.0000.0000.000
14A10PRO00.024-0.00233.5550.1120.1120.0000.0000.0000.000
15A11LEU0-0.063-0.01729.246-0.252-0.2520.0000.0000.0000.000
16A12VAL00.0200.01026.3410.1120.1120.0000.0000.0000.000
17A13LYS10.9210.94926.97410.35410.3540.0000.0000.0000.000
18A14ASP-1-0.877-0.94522.712-12.869-12.8690.0000.0000.0000.000
19A15GLN0-0.063-0.04422.346-0.789-0.7890.0000.0000.0000.000
20A16ILE00.0050.00123.050-0.477-0.4770.0000.0000.0000.000
21A17LEU0-0.011-0.00722.505-0.308-0.3080.0000.0000.0000.000
22A18LYS10.8330.93417.70514.71214.7120.0000.0000.0000.000
23A19LEU0-0.089-0.01618.283-0.801-0.8010.0000.0000.0000.000
24A20LYS10.8840.93613.03919.80719.8070.0000.0000.0000.000
25A21VAL0-0.030-0.02417.8830.3590.3590.0000.0000.0000.000
26A22GLY0-0.015-0.00417.511-0.767-0.7670.0000.0000.0000.000
27A23ASP-1-0.785-0.86716.913-18.309-18.3090.0000.0000.0000.000
28A24VAL00.007-0.00119.3020.8500.8500.0000.0000.0000.000
29A25VAL0-0.029-0.02122.389-0.320-0.3200.0000.0000.0000.000
30A26TYR0-0.026-0.00625.3780.5240.5240.0000.0000.0000.000
31A27ILE0-0.008-0.00528.417-0.248-0.2480.0000.0000.0000.000
32A28THR0-0.048-0.04131.1880.2330.2330.0000.0000.0000.000
33A29GLY00.0400.03232.992-0.223-0.2230.0000.0000.0000.000
34A30GLU-1-0.896-0.94235.837-7.648-7.6480.0000.0000.0000.000
35A31ILE0-0.047-0.00635.107-0.295-0.2950.0000.0000.0000.000
36A32PHE00.0190.00938.0970.2290.2290.0000.0000.0000.000
37A33THR0-0.027-0.00639.423-0.185-0.1850.0000.0000.0000.000
38A34ALA00.0370.00940.9540.1350.1350.0000.0000.0000.000
39A35ARG10.8190.87241.0006.6286.6280.0000.0000.0000.000
40A36ASP-1-0.714-0.83043.022-7.059-7.0590.0000.0000.0000.000
41A37GLU-1-0.866-0.92545.211-6.194-6.1940.0000.0000.0000.000
42A38ALA0-0.0020.00745.0320.0330.0330.0000.0000.0000.000
43A39HIS0-0.059-0.04839.967-0.256-0.2560.0000.0000.0000.000
44A40ALA00.0150.00644.417-0.013-0.0130.0000.0000.0000.000
45A41ARG10.8730.91647.5476.0626.0620.0000.0000.0000.000
46A42ALA0-0.020-0.01644.7120.0340.0340.0000.0000.0000.000
47A43LEU0-0.010-0.00843.053-0.032-0.0320.0000.0000.0000.000
48A44GLU-1-0.792-0.88346.929-5.940-5.9400.0000.0000.0000.000
49A45TRP0-0.021-0.03349.3200.0770.0770.0000.0000.0000.000
50A46MET0-0.043-0.02742.317-0.038-0.0380.0000.0000.0000.000
51A47GLU-1-1.007-0.99547.994-6.359-6.3590.0000.0000.0000.000
52A48GLU-1-0.895-0.93849.891-5.650-5.6500.0000.0000.0000.000
53A49GLY0-0.047-0.01350.7510.0910.0910.0000.0000.0000.000
54A50LYS10.7260.86351.7835.9165.9160.0000.0000.0000.000
55A51GLU-1-0.937-0.97248.313-6.742-6.7420.0000.0000.0000.000
56A52LEU0-0.025-0.00144.3650.0770.0770.0000.0000.0000.000
57A53PRO0-0.020-0.00147.917-0.052-0.0520.0000.0000.0000.000
58A54PHE00.000-0.01442.609-0.060-0.0600.0000.0000.0000.000
59A55SER00.0310.00740.5620.0310.0310.0000.0000.0000.000
60A56PHE00.0710.01437.689-0.136-0.1360.0000.0000.0000.000
61A57ASP-1-0.824-0.90736.349-9.151-9.1510.0000.0000.0000.000
62A58LYS10.7990.88633.2919.3849.3840.0000.0000.0000.000
63A59GLY00.0570.04534.447-0.069-0.0690.0000.0000.0000.000
64A60VAL0-0.016-0.02431.941-0.292-0.2920.0000.0000.0000.000
65A61VAL00.0090.02634.6240.2140.2140.0000.0000.0000.000
66A62TYR0-0.049-0.06435.323-0.317-0.3170.0000.0000.0000.000
67A63HIS00.0580.03835.8620.1270.1270.0000.0000.0000.000
68A64CYS0-0.102-0.05038.323-0.033-0.0330.0000.0000.0000.000
69A65GLY00.0560.01840.6480.0930.0930.0000.0000.0000.000
70A66PRO0-0.056-0.00743.4580.0300.0300.0000.0000.0000.000
71A67LEU0-0.0030.01144.8960.1650.1650.0000.0000.0000.000
72A68VAL00.001-0.01647.044-0.133-0.1330.0000.0000.0000.000
73A69LYS10.9050.95549.4286.3896.3890.0000.0000.0000.000
74A70LYS10.9350.96752.1335.7565.7560.0000.0000.0000.000
75A71ASN0-0.071-0.03554.029-0.014-0.0140.0000.0000.0000.000
76A72ASP-1-0.772-0.85552.871-6.089-6.0890.0000.0000.0000.000
77A73GLU-1-0.797-0.89149.506-6.536-6.5360.0000.0000.0000.000
78A74TRP0-0.018-0.01450.0410.0720.0720.0000.0000.0000.000
79A75ARG10.7690.84748.2606.3676.3670.0000.0000.0000.000
80A76VAL00.0540.02143.4450.0980.0980.0000.0000.0000.000
81A77VAL0-0.061-0.02346.255-0.010-0.0100.0000.0000.0000.000
82A78SER0-0.035-0.02843.053-0.151-0.1510.0000.0000.0000.000
83A79ALA00.0630.03339.9450.1260.1260.0000.0000.0000.000
84A80GLY00.0390.04138.355-0.269-0.2690.0000.0000.0000.000
85A81PRO00.0320.04634.9740.1670.1670.0000.0000.0000.000
86A82THR00.0140.00337.6470.1880.1880.0000.0000.0000.000
87A83THR0-0.025-0.02936.866-0.216-0.2160.0000.0000.0000.000
88A84SER00.0480.01034.3900.1320.1320.0000.0000.0000.000
89A85ALA00.0150.01935.8440.0930.0930.0000.0000.0000.000
90A86ARG10.7640.83137.0917.3857.3850.0000.0000.0000.000
91A87MET00.0290.02838.5830.2120.2120.0000.0000.0000.000
92A88ASN00.0170.02135.696-0.243-0.2430.0000.0000.0000.000
93A89PRO00.002-0.00238.236-0.076-0.0760.0000.0000.0000.000
94A90PHE00.0400.02640.6590.0800.0800.0000.0000.0000.000
95A91THR0-0.017-0.02334.914-0.072-0.0720.0000.0000.0000.000
96A92PRO00.0360.01436.005-0.163-0.1630.0000.0000.0000.000
97A93LYS10.8530.92037.0397.2277.2270.0000.0000.0000.000
98A94ILE0-0.012-0.00137.5790.0440.0440.0000.0000.0000.000
99A95LEU0-0.009-0.01732.363-0.076-0.0760.0000.0000.0000.000
100A96GLU-1-0.828-0.88135.551-7.775-7.7750.0000.0000.0000.000
101A97LYS10.9190.96337.1947.7697.7690.0000.0000.0000.000
102A98VAL0-0.053-0.00534.0230.0270.0270.0000.0000.0000.000
103A99GLU-1-0.811-0.88832.283-9.947-9.9470.0000.0000.0000.000
104A100CYS0-0.053-0.03730.252-0.448-0.4480.0000.0000.0000.000
105A101MET00.0110.02931.0760.4100.4100.0000.0000.0000.000
106A102GLY00.0170.00830.340-0.461-0.4610.0000.0000.0000.000
107A103ILE00.0010.00730.6930.3610.3610.0000.0000.0000.000
108A104ILE00.0160.01630.878-0.355-0.3550.0000.0000.0000.000
109A105GLY00.0430.01432.2380.3730.3730.0000.0000.0000.000
110A106LYS10.8740.93432.4437.8737.8730.0000.0000.0000.000
111A107GLY0-0.006-0.01232.3200.2430.2430.0000.0000.0000.000
112A108GLY00.0350.03130.704-0.053-0.0530.0000.0000.0000.000
113A109MET0-0.061-0.02930.9640.2490.2490.0000.0000.0000.000
114A110SER00.0160.00631.462-0.254-0.2540.0000.0000.0000.000
115A111GLU-1-0.745-0.86827.908-10.852-10.8520.0000.0000.0000.000
116A112GLU-1-0.943-0.95930.824-8.307-8.3070.0000.0000.0000.000
117A113VAL00.013-0.00431.331-0.038-0.0380.0000.0000.0000.000
118A114VAL0-0.038-0.01726.065-0.241-0.2410.0000.0000.0000.000
119A115GLU-1-0.814-0.86727.974-11.005-11.0050.0000.0000.0000.000
120A116ALA00.0010.00529.706-0.101-0.1010.0000.0000.0000.000
121A117MET0-0.039-0.01127.958-0.059-0.0590.0000.0000.0000.000
122A118ARG10.7950.86623.60711.26011.2600.0000.0000.0000.000
123A119GLY0-0.018-0.01425.7260.2810.2810.0000.0000.0000.000
124A120LYS10.7640.86326.8389.4619.4610.0000.0000.0000.000
125A121ALA0-0.013-0.00228.1020.1130.1130.0000.0000.0000.000
126A122ALA00.0270.00325.328-0.440-0.4400.0000.0000.0000.000
127A123TYR0-0.004-0.02426.6100.4150.4150.0000.0000.0000.000
128A124PHE00.028-0.00325.493-0.507-0.5070.0000.0000.0000.000
129A125ALA00.0130.00726.9520.4610.4610.0000.0000.0000.000
130A126PHE00.014-0.00528.333-0.306-0.3060.0000.0000.0000.000
131A127THR0-0.055-0.05227.365-0.066-0.0660.0000.0000.0000.000
132A128GLY00.0520.04230.502-0.039-0.0390.0000.0000.0000.000
133A129GLY0-0.012-0.02133.1070.3080.3080.0000.0000.0000.000
134A130ALA0-0.014-0.02635.3020.0190.0190.0000.0000.0000.000
135A131GLY00.0300.01437.7650.1920.1920.0000.0000.0000.000
136A132ALA00.0000.00439.1230.0350.0350.0000.0000.0000.000
137A133LEU00.019-0.00237.6300.0330.0330.0000.0000.0000.000
138A134ALA00.0430.02636.034-0.039-0.0390.0000.0000.0000.000
139A135ALA00.0120.00637.514-0.059-0.0590.0000.0000.0000.000
140A136MET0-0.019-0.00539.2360.1520.1520.0000.0000.0000.000
141A137SER0-0.032-0.01534.3790.0240.0240.0000.0000.0000.000
142A138ILE0-0.067-0.03237.419-0.094-0.0940.0000.0000.0000.000
143A139LYS10.8180.92237.3898.5668.5660.0000.0000.0000.000
144A140LYS10.8710.91742.0856.9846.9840.0000.0000.0000.000
145A141VAL0-0.025-0.00143.968-0.146-0.1460.0000.0000.0000.000
146A142LYN00.0180.03343.4100.2380.2380.0000.0000.0000.000
147A143GLY00.0170.00646.5390.1530.1530.0000.0000.0000.000
148A144VAL0-0.042-0.01447.659-0.143-0.1430.0000.0000.0000.000
149A145VAL0-0.0150.00247.8480.1520.1520.0000.0000.0000.000
150A146TRP00.0370.00747.027-0.122-0.1220.0000.0000.0000.000
151A147GLU-1-0.836-0.93351.980-5.976-5.9760.0000.0000.0000.000
152A148ASP-1-0.874-0.90753.462-5.839-5.8390.0000.0000.0000.000
153A149LEU00.0170.01749.8000.0600.0600.0000.0000.0000.000
154A150GLY00.0240.01952.744-0.003-0.0030.0000.0000.0000.000
155A151MET0-0.031-0.01349.630-0.130-0.1300.0000.0000.0000.000
156A152PRO0-0.046-0.01847.406-0.132-0.1320.0000.0000.0000.000
157A153GLU-1-0.755-0.86546.440-6.809-6.8090.0000.0000.0000.000
158A154ALA0-0.0360.00547.292-0.084-0.0840.0000.0000.0000.000
159A155VAL00.0050.00644.073-0.172-0.1720.0000.0000.0000.000
160A156TRP0-0.011-0.03544.4430.1070.1070.0000.0000.0000.000
161A157LEU00.0120.00343.362-0.209-0.2090.0000.0000.0000.000
162A158LEU0-0.044-0.03640.6930.1530.1530.0000.0000.0000.000
163A159GLU-1-0.835-0.92538.467-8.545-8.5450.0000.0000.0000.000
164A160VAL0-0.042-0.02135.1880.0990.0990.0000.0000.0000.000
165A161GLU-1-0.827-0.91134.452-8.813-8.8130.0000.0000.0000.000
166A162ARG10.8050.86625.87911.67011.6700.0000.0000.0000.000
167A163PHE00.0100.01031.9360.0670.0670.0000.0000.0000.000
168A164GLY0-0.011-0.00730.316-0.321-0.3210.0000.0000.0000.000
169A165PRO00.0190.01427.2120.2880.2880.0000.0000.0000.000
170A166CYS0-0.0230.00427.4360.5730.5730.0000.0000.0000.000
171A167ILE0-0.0030.00722.031-0.477-0.4770.0000.0000.0000.000
172A168VAL0-0.0090.00421.3190.5670.5670.0000.0000.0000.000
173A169ALA00.014-0.00622.192-0.450-0.4500.0000.0000.0000.000
174A170ILE0-0.016-0.00824.4590.1500.1500.0000.0000.0000.000
175A171ASP-1-0.761-0.87519.745-14.479-14.4790.0000.0000.0000.000
176A172ALA00.0680.04423.3060.2980.2980.0000.0000.0000.000
177A173HIS0-0.027-0.00419.4940.3780.3780.0000.0000.0000.000
178A174GLY00.0150.03021.9370.0540.0540.0000.0000.0000.000
179A175ASN0-0.075-0.04418.3070.2990.2990.0000.0000.0000.000
180A176SER00.050-0.00621.9180.3600.3600.0000.0000.0000.000
181A177LEU0-0.013-0.00520.941-0.119-0.1190.0000.0000.0000.000
182A178TYR00.0240.02323.9710.1330.1330.0000.0000.0000.000
183A179ARG10.7600.86422.86012.10312.1030.0000.0000.0000.000
184A180ARG10.9230.96225.63710.54410.5440.0000.0000.0000.000