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

tag_button

FMODB ID: 72R4K

Calculation Name: 3E57-A-Xray372

Preferred Name:
Warning: Undefined array key "pref_name" in /home/FMODBwui_src/fmodbwui/detail.php on line 446

Target Type:
Warning: Undefined array key "target_type" in /home/FMODBwui_src/fmodbwui/detail.php on line 447

Ligand Name:
Warning: Undefined variable $Ligand in /home/FMODBwui_src/fmodbwui/detail.php on line 448

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 448

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 448

ligand 3-letter code:
Warning: Undefined variable $Ligand in /home/FMODBwui_src/fmodbwui/detail.php on line 449

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 449

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 449

PDB ID: 3E57

Chain ID: A

ChEMBL ID:
Warning: Undefined array key "chembl_id" in /home/FMODBwui_src/fmodbwui/detail.php on line 452

Warning: Undefined array key "chembl_id" in /home/FMODBwui_src/fmodbwui/detail.php on line 452

UniProt ID: Q9X1A2

Base Structure: X-ray

Registration Date: 2023-09-20

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 OptH
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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2036497.305993
FMO2-HF: Nuclear repulsion 1964338.982289
FMO2-HF: Total energy -72158.323703
FMO2-MP2: Total energy -72372.274527


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:4:GLU)


Summations of interaction energy for fragment #1(A:4:GLU)
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.
111.102124.53510.928-11.076-13.2830.085
Interaction energy analysis for fragmet #1(A:4:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.856 / q_NPA : -0.932
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].
3A6ILE0-0.003-0.0112.1812.1774.5901.676-1.529-2.5590.004
4A7LEU0-0.030-0.0124.595-5.025-4.936-0.001-0.018-0.0690.000
5A8VAL0-0.031-0.0178.2840.7000.7000.0000.0000.0000.000
6A9VAL00.0410.02210.822-1.232-1.2320.0000.0000.0000.000
7A10LYS10.9540.98014.607-13.682-13.6820.0000.0000.0000.000
8A11THR00.0270.00317.155-0.104-0.1040.0000.0000.0000.000
9A12GLU-1-0.960-0.98318.89711.89611.8960.0000.0000.0000.000
10A13ASP-1-0.863-0.93919.51213.63313.6330.0000.0000.0000.000
11A14PHE0-0.018-0.01918.644-0.280-0.2800.0000.0000.0000.000
12A15LEU0-0.016-0.01220.667-0.444-0.4440.0000.0000.0000.000
13A16LYS10.9010.96523.905-11.563-11.5630.0000.0000.0000.000
14A17GLU-1-0.956-0.97923.01911.47611.4760.0000.0000.0000.000
15A18PHE0-0.031-0.02920.953-0.254-0.2540.0000.0000.0000.000
16A19GLY00.0110.01925.342-0.285-0.2850.0000.0000.0000.000
17A20GLU-1-0.980-0.99025.50311.25711.2570.0000.0000.0000.000
18A21PHE0-0.035-0.03222.347-0.324-0.3240.0000.0000.0000.000
19A22GLU-1-0.793-0.87024.74513.77013.7700.0000.0000.0000.000
20A23GLY0-0.019-0.01924.077-0.514-0.5140.0000.0000.0000.000
21A24PHE0-0.018-0.01722.9060.5680.5680.0000.0000.0000.000
22A25MET0-0.0310.00224.261-0.803-0.8030.0000.0000.0000.000
23A26ARG10.9620.99224.762-10.300-10.3000.0000.0000.0000.000
24A27VAL00.0220.01522.909-0.289-0.2890.0000.0000.0000.000
25A28ASN0-0.001-0.00125.7640.3110.3110.0000.0000.0000.000
26A29PHE00.0640.01818.8510.2260.2260.0000.0000.0000.000
27A30GLU-1-0.945-0.96922.60611.61711.6170.0000.0000.0000.000
28A31ASP-1-0.867-0.94723.73811.65011.6500.0000.0000.0000.000
29A32PHE0-0.033-0.01215.9610.2590.2590.0000.0000.0000.000
30A33LEU0-0.015-0.01518.2120.6770.6770.0000.0000.0000.000
31A34ASN0-0.009-0.01519.4730.5840.5840.0000.0000.0000.000
32A35PHE00.0150.02117.5530.2420.2420.0000.0000.0000.000
33A36LEU0-0.005-0.00414.3250.4520.4520.0000.0000.0000.000
34A37ASP-1-0.828-0.92516.37716.59716.5970.0000.0000.0000.000
35A38GLN0-0.095-0.02818.374-0.153-0.1530.0000.0000.0000.000
36A39TYR0-0.043-0.04018.210-0.473-0.4730.0000.0000.0000.000
37A40GLY0-0.0160.01114.2010.4980.4980.0000.0000.0000.000
38A41PHE0-0.072-0.04112.165-0.593-0.5930.0000.0000.0000.000
39A42PHE00.0360.0226.6421.2371.2370.0000.0000.0000.000
40A43ARG10.8230.8967.311-24.740-24.7400.0000.0000.0000.000
41A44GLU-1-0.859-0.9342.64229.75032.2800.481-1.636-1.374-0.020
42A45ARG10.9020.9522.023-99.856-96.7478.000-5.196-5.9130.069
43A46ASP-1-0.891-0.9444.74135.18635.485-0.001-0.011-0.2880.000
44A47GLU-1-1.027-1.0146.95119.53419.5340.0000.0000.0000.000
45A48ALA0-0.055-0.0387.860-1.891-1.8910.0000.0000.0000.000
46A49GLU-1-0.990-0.9818.27131.76731.7670.0000.0000.0000.000
47A50TYR00.006-0.00710.112-1.533-1.5330.0000.0000.0000.000
48A51ASP-1-0.783-0.85312.96116.48716.4870.0000.0000.0000.000
49A52GLU-1-0.857-0.94214.54016.46016.4600.0000.0000.0000.000
50A53THR0-0.076-0.04716.407-1.055-1.0550.0000.0000.0000.000
51A54THR0-0.111-0.04512.651-0.018-0.0180.0000.0000.0000.000
52A55LYS10.8850.96313.675-17.447-17.4470.0000.0000.0000.000
53A56GLN00.0690.0268.1035.1245.1240.0000.0000.0000.000
54A57VAL0-0.004-0.00610.081-1.615-1.6150.0000.0000.0000.000
55A58ILE0-0.052-0.0148.8302.7442.7440.0000.0000.0000.000
56A59PRO0-0.0130.0039.943-2.918-2.9180.0000.0000.0000.000
57A60TYR00.0250.00912.2620.7540.7540.0000.0000.0000.000
58A61VAL00.0250.00414.865-1.772-1.7720.0000.0000.0000.000
59A62VAL00.0170.01817.1560.1610.1610.0000.0000.0000.000
60A63ILE00.0110.01318.562-0.451-0.4510.0000.0000.0000.000
61A64MET0-0.024-0.02321.779-0.460-0.4600.0000.0000.0000.000
62A65ASP-1-0.852-0.91725.58811.43411.4340.0000.0000.0000.000
63A66GLY0-0.022-0.01927.748-0.311-0.3110.0000.0000.0000.000
64A67ASP-1-0.957-0.98230.6099.5689.5680.0000.0000.0000.000
65A68ARG10.8620.91929.162-10.090-10.0900.0000.0000.0000.000
66A69VAL00.0010.00024.1100.2580.2580.0000.0000.0000.000
67A70LEU0-0.030-0.00919.875-0.321-0.3210.0000.0000.0000.000
68A71ILE0-0.024-0.00821.8510.3720.3720.0000.0000.0000.000
69A72THR00.0170.00817.503-0.468-0.4680.0000.0000.0000.000
70A73LYS10.9460.97420.553-12.874-12.8740.0000.0000.0000.000
71A74ARG11.0081.02011.768-24.542-24.5420.0000.0000.0000.000
72A87TYR0-0.036-0.04122.021-0.160-0.1600.0000.0000.0000.000
73A88SER0-0.037-0.00717.058-0.062-0.0620.0000.0000.0000.000
74A89LEU0-0.005-0.01619.775-0.309-0.3090.0000.0000.0000.000
75A90GLY0-0.019-0.01417.542-0.501-0.5010.0000.0000.0000.000
76A91ILE0-0.034-0.00812.8000.0690.0690.0000.0000.0000.000
77A92GLY00.0520.02211.674-0.736-0.7360.0000.0000.0000.000
78A93GLY00.0030.0017.6681.6541.6540.0000.0000.0000.000
79A94HIS0-0.014-0.0243.8313.0083.3940.004-0.153-0.2370.001
80A95VAL00.0000.0205.9270.8860.8860.0000.0000.0000.000
81A96ARG10.9120.9502.545-76.826-72.2190.769-2.533-2.8430.031
82A97GLU-1-0.810-0.9155.25722.46222.4620.0000.0000.0000.000
83A98GLY0-0.051-0.0276.394-3.044-3.0440.0000.0000.0000.000
84A99ASP-1-0.806-0.8857.75436.58536.5850.0000.0000.0000.000
85A100GLY0-0.010-0.0249.674-2.149-2.1490.0000.0000.0000.000
86A101ALA0-0.0330.00212.4130.6220.6220.0000.0000.0000.000
87A102THR00.0020.00515.003-0.271-0.2710.0000.0000.0000.000
88A103PRO00.0540.02112.7351.1791.1790.0000.0000.0000.000
89A104ARG10.9130.96313.681-13.283-13.2830.0000.0000.0000.000
90A105GLU-1-0.950-0.98015.82316.77016.7700.0000.0000.0000.000
91A106ALA0-0.0070.00610.0810.5960.5960.0000.0000.0000.000
92A107PHE00.008-0.00711.2821.7541.7540.0000.0000.0000.000
93A108LEU0-0.013-0.01112.7500.4330.4330.0000.0000.0000.000
94A109LYS10.9771.00711.480-23.684-23.6840.0000.0000.0000.000
95A110GLY0-0.005-0.0139.4030.9450.9450.0000.0000.0000.000
96A111LEU0-0.008-0.00210.0280.9210.9210.0000.0000.0000.000
97A112GLU-1-0.980-0.98612.71718.93118.9310.0000.0000.0000.000
98A113ARG10.6850.8155.951-42.931-42.9310.0000.0000.0000.000
99A114GLU-1-0.870-0.9389.06027.08427.0840.0000.0000.0000.000
100A115VAL00.0480.0299.969-0.725-0.7250.0000.0000.0000.000
101A116ASN0-0.040-0.02913.580-1.272-1.2720.0000.0000.0000.000
102A117GLU-1-0.922-0.9557.61941.04541.0450.0000.0000.0000.000
103A118GLU-1-0.900-0.93811.96721.51621.5160.0000.0000.0000.000
104A119VAL0-0.038-0.03113.933-1.766-1.7660.0000.0000.0000.000
105A120ASP-1-0.961-0.98217.26615.26315.2630.0000.0000.0000.000
106A121VAL00.0300.00418.911-0.909-0.9090.0000.0000.0000.000
107A122SER0-0.051-0.01921.2880.2490.2490.0000.0000.0000.000
108A123LEU00.009-0.00118.767-0.565-0.5650.0000.0000.0000.000
109A124ARG10.8990.94623.219-10.607-10.6070.0000.0000.0000.000
110A125GLU-1-0.952-0.98325.03710.68010.6800.0000.0000.0000.000
111A126LEU00.0020.01417.8900.1210.1210.0000.0000.0000.000
112A127GLU-1-0.964-0.97022.42411.26611.2660.0000.0000.0000.000
113A128PHE0-0.024-0.01219.3140.3050.3050.0000.0000.0000.000
114A129LEU0-0.005-0.01622.040-0.692-0.6920.0000.0000.0000.000
115A130GLY00.000-0.02822.002-0.759-0.7590.0000.0000.0000.000
116A131LEU0-0.0170.01018.8120.8380.8380.0000.0000.0000.000
117A132ILE0-0.025-0.01618.486-0.921-0.9210.0000.0000.0000.000
118A133ASN00.0290.01518.7211.8391.8390.0000.0000.0000.000
119A134SER00.0210.01119.874-0.579-0.5790.0000.0000.0000.000
120A135SER0-0.031-0.05020.2750.7130.7130.0000.0000.0000.000
121A136THR0-0.025-0.01622.2230.0700.0700.0000.0000.0000.000
122A137THR0-0.027-0.01018.4220.1190.1190.0000.0000.0000.000
123A138GLU-1-0.893-0.96116.89816.36116.3610.0000.0000.0000.000
124A139VAL00.0610.03312.7740.2830.2830.0000.0000.0000.000
125A140SER0-0.056-0.02814.5540.5700.5700.0000.0000.0000.000
126A141ARG10.8530.92816.973-15.112-15.1120.0000.0000.0000.000
127A142VAL00.0260.04412.379-0.465-0.4650.0000.0000.0000.000
128A143HIS0-0.078-0.0339.9482.7762.7760.0000.0000.0000.000
129A144LEU0-0.011-0.00413.620-1.845-1.8450.0000.0000.0000.000
130A145GLY00.0100.00714.1271.5121.5120.0000.0000.0000.000
131A146ALA0-0.017-0.00615.179-1.440-1.4400.0000.0000.0000.000
132A147LEU0-0.0080.00016.5310.7220.7220.0000.0000.0000.000
133A148PHE00.0160.00016.349-0.807-0.8070.0000.0000.0000.000
134A149LEU00.0040.00820.0970.1910.1910.0000.0000.0000.000
135A150GLY00.0350.00021.093-0.142-0.1420.0000.0000.0000.000
136A151ARG10.9250.97822.021-11.260-11.2600.0000.0000.0000.000
137A152GLY00.024-0.01424.7390.0880.0880.0000.0000.0000.000
138A153LYS10.8830.97825.590-10.929-10.9290.0000.0000.0000.000
139A154PHE00.0530.01820.9470.4790.4790.0000.0000.0000.000
140A155PHE0-0.094-0.04923.477-0.908-0.9080.0000.0000.0000.000
141A156SER0-0.012-0.01322.645-0.295-0.2950.0000.0000.0000.000
142A157VAL00.0400.03318.7180.4510.4510.0000.0000.0000.000
143A158LYS10.8670.94915.577-19.813-19.8130.0000.0000.0000.000
144A159GLU-1-0.906-0.95914.25921.68021.6800.0000.0000.0000.000
145A160LYS10.9340.94717.615-13.483-13.4830.0000.0000.0000.000
146A161ASP-1-0.972-0.98618.82715.53415.5340.0000.0000.0000.000
147A162LEU0-0.0610.00712.9970.3910.3910.0000.0000.0000.000
148A163PHE00.007-0.01712.8170.0420.0420.0000.0000.0000.000
149A164GLU-1-0.952-0.96118.77512.64712.6470.0000.0000.0000.000
150A165TRP0-0.017-0.03321.4040.4890.4890.0000.0000.0000.000
151A166GLU-1-0.919-0.95523.31110.93910.9390.0000.0000.0000.000
152A167LEU00.0080.00625.2600.3680.3680.0000.0000.0000.000
153A168ILE0-0.0100.00927.451-0.526-0.5260.0000.0000.0000.000
154A169LYS10.9400.97329.572-8.612-8.6120.0000.0000.0000.000
155A170LEU00.0760.03029.1050.0430.0430.0000.0000.0000.000
156A171GLU-1-0.960-0.98432.0248.6608.6600.0000.0000.0000.000
157A172GLU-1-0.877-0.93832.0609.7599.7590.0000.0000.0000.000
158A173LEU00.0000.00226.5030.1820.1820.0000.0000.0000.000
159A174GLU-1-0.920-0.95330.2359.6139.6130.0000.0000.0000.000
160A175LYS10.9300.96932.444-9.789-9.7890.0000.0000.0000.000
161A176PHE0-0.009-0.02027.5320.0210.0210.0000.0000.0000.000
162A177SER0-0.011-0.01127.3430.3160.3160.0000.0000.0000.000
163A178GLY0-0.017-0.00328.3680.1400.1400.0000.0000.0000.000
164A179VAL0-0.081-0.04226.978-0.071-0.0710.0000.0000.0000.000
165A180MET0-0.0610.00023.5110.4790.4790.0000.0000.0000.000
166A181GLU-1-0.890-0.95222.29212.40912.4090.0000.0000.0000.000
167A182GLY00.002-0.01420.4670.5940.5940.0000.0000.0000.000
168A183TRP00.0420.01714.039-0.617-0.6170.0000.0000.0000.000
169A184SER00.0490.04319.378-0.350-0.3500.0000.0000.0000.000
170A185LYS10.9961.00821.354-12.072-12.0720.0000.0000.0000.000
171A186ILE0-0.033-0.01021.800-0.572-0.5720.0000.0000.0000.000
172A187SER00.035-0.00220.831-0.336-0.3360.0000.0000.0000.000
173A188ALA00.0170.00923.375-0.365-0.3650.0000.0000.0000.000
174A189ALA0-0.022-0.00226.244-0.445-0.4450.0000.0000.0000.000
175A190VAL0-0.020-0.00825.127-0.453-0.4530.0000.0000.0000.000
176A191LEU00.019-0.00424.449-0.366-0.3660.0000.0000.0000.000
177A192LEU0-0.016-0.01227.878-0.336-0.3360.0000.0000.0000.000
178A193ASN0-0.046-0.01731.018-0.537-0.5370.0000.0000.0000.000
179A194LEU0-0.060-0.02027.566-0.270-0.2700.0000.0000.0000.000
180A195PHE0-0.058-0.01428.725-0.339-0.3390.0000.0000.0000.000