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: 6NQ5Z

Calculation Name: 3E57-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: 3E57

Chain ID: A

ChEMBL ID:
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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 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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2044227.646215
FMO2-HF: Nuclear repulsion 1972067.641853
FMO2-HF: Total energy -72160.004363
FMO2-MP2: Total energy -72374.1737


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.
94.92292.01137.447-16.948-17.5850.185
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 : -0.772 / q_NPA : -0.863
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].
3A6ILE0-0.012-0.0062.2700.3083.4442.192-2.114-3.2140.008
4A7LEU0-0.025-0.0064.482-5.566-5.453-0.001-0.025-0.0870.000
5A8VAL0-0.031-0.0168.1201.2251.2250.0000.0000.0000.000
6A9VAL00.0380.02510.838-1.395-1.3950.0000.0000.0000.000
7A10LYS10.8080.88114.644-13.609-13.6090.0000.0000.0000.000
8A11THR0-0.003-0.02517.312-0.098-0.0980.0000.0000.0000.000
9A12GLU-1-0.879-0.93418.86512.25712.2570.0000.0000.0000.000
10A13ASP-1-0.797-0.89920.09213.53213.5320.0000.0000.0000.000
11A14PHE00.005-0.00718.698-0.240-0.2400.0000.0000.0000.000
12A15LEU00.0100.01020.771-0.436-0.4360.0000.0000.0000.000
13A16LYS10.7950.89423.894-12.381-12.3810.0000.0000.0000.000
14A17GLU-1-0.850-0.87523.25911.53811.5380.0000.0000.0000.000
15A18PHE0-0.036-0.02820.840-0.193-0.1930.0000.0000.0000.000
16A19GLY00.0040.01325.303-0.248-0.2480.0000.0000.0000.000
17A20GLU-1-0.965-0.98425.09511.59811.5980.0000.0000.0000.000
18A21PHE0-0.023-0.02221.653-0.359-0.3590.0000.0000.0000.000
19A22GLU-1-0.790-0.85523.37614.39714.3970.0000.0000.0000.000
20A23GLY0-0.007-0.01423.136-0.567-0.5670.0000.0000.0000.000
21A24PHE0-0.003-0.02222.2320.6640.6640.0000.0000.0000.000
22A25MET0-0.0190.00823.743-0.867-0.8670.0000.0000.0000.000
23A26ARG10.9580.99124.384-10.772-10.7720.0000.0000.0000.000
24A27VAL0-0.0010.00323.164-0.369-0.3690.0000.0000.0000.000
25A28ASN0-0.036-0.03926.0990.2500.2500.0000.0000.0000.000
26A29PHE00.0390.01418.9450.3080.3080.0000.0000.0000.000
27A30GLU-1-0.905-0.94222.37512.07212.0720.0000.0000.0000.000
28A31ASP-1-0.806-0.90423.33411.87911.8790.0000.0000.0000.000
29A32PHE0-0.0020.00915.9720.2380.2380.0000.0000.0000.000
30A33LEU0-0.003-0.00617.9680.7700.7700.0000.0000.0000.000
31A34ASN0-0.032-0.03019.4610.6070.6070.0000.0000.0000.000
32A35PHE0-0.0020.00617.4180.1140.1140.0000.0000.0000.000
33A36LEU0-0.003-0.00614.0740.3920.3920.0000.0000.0000.000
34A37ASP-1-0.781-0.88316.33916.81016.8100.0000.0000.0000.000
35A38GLN0-0.084-0.02118.315-0.430-0.4300.0000.0000.0000.000
36A39TYR0-0.084-0.08118.232-0.646-0.6460.0000.0000.0000.000
37A40GLY0-0.0020.01414.1580.5880.5880.0000.0000.0000.000
38A41PHE0-0.064-0.03812.427-0.656-0.6560.0000.0000.0000.000
39A42PHE00.0540.0276.6061.3551.3550.0000.0000.0000.000
40A43ARG10.7530.8557.595-24.691-24.6910.0000.0000.0000.000
41A44GLU-1-0.804-0.8973.96731.52231.6460.000-0.085-0.0380.000
42A45ARG10.8100.8871.752-94.291-96.30413.476-5.499-5.9650.067
43A46ASP-1-0.924-0.9684.18633.11833.4950.000-0.064-0.3120.000
44A47GLU-1-0.908-0.9356.61219.40719.4070.0000.0000.0000.000
45A48ALA00.012-0.0057.766-1.503-1.5030.0000.0000.0000.000
46A49GLU-1-0.886-0.9326.92637.91437.9140.0000.0000.0000.000
47A50TYR0-0.077-0.0589.330-3.066-3.0660.0000.0000.0000.000
48A51ASP-1-0.784-0.85012.53016.75716.7570.0000.0000.0000.000
49A52GLU-1-0.773-0.87414.23016.80216.8020.0000.0000.0000.000
50A53THR0-0.070-0.03116.403-1.057-1.0570.0000.0000.0000.000
51A54THR0-0.112-0.05312.781-0.203-0.2030.0000.0000.0000.000
52A55LYS10.8290.92813.186-17.981-17.9810.0000.0000.0000.000
53A56GLN00.0500.0177.1254.7174.7170.0000.0000.0000.000
54A57VAL0-0.012-0.0109.914-1.744-1.7440.0000.0000.0000.000
55A58ILE0-0.046-0.0117.9203.1483.1480.0000.0000.0000.000
56A59PRO0-0.023-0.0049.990-3.210-3.2100.0000.0000.0000.000
57A60TYR0-0.004-0.01312.3170.7900.7900.0000.0000.0000.000
58A61VAL00.0240.01514.828-2.043-2.0430.0000.0000.0000.000
59A62VAL00.0110.01017.0320.1610.1610.0000.0000.0000.000
60A63ILE0-0.0030.00518.038-0.625-0.6250.0000.0000.0000.000
61A64MET0-0.030-0.02021.360-0.425-0.4250.0000.0000.0000.000
62A65ASP-1-0.844-0.91825.20711.70011.7000.0000.0000.0000.000
63A66GLY0-0.021-0.01127.706-0.271-0.2710.0000.0000.0000.000
64A67ASP-1-0.904-0.96730.7789.8069.8060.0000.0000.0000.000
65A68ARG10.7940.88528.938-10.252-10.2520.0000.0000.0000.000
66A69VAL00.0050.00323.9590.2080.2080.0000.0000.0000.000
67A70LEU0-0.019-0.00519.412-0.312-0.3120.0000.0000.0000.000
68A71ILE0-0.0110.00021.4280.2390.2390.0000.0000.0000.000
69A72THR0-0.017-0.00716.695-0.539-0.5390.0000.0000.0000.000
70A73LYS10.7990.88119.719-13.203-13.2030.0000.0000.0000.000
71A74ARG10.9370.99711.843-25.365-25.3650.0000.0000.0000.000
72A87TYR0-0.039-0.06521.400-0.311-0.3110.0000.0000.0000.000
73A88SER0-0.058-0.04016.692-0.279-0.2790.0000.0000.0000.000
74A89LEU0-0.003-0.02819.350-0.492-0.4920.0000.0000.0000.000
75A90GLY0-0.0090.00117.607-0.532-0.5320.0000.0000.0000.000
76A91ILE0-0.0060.02312.3910.3260.3260.0000.0000.0000.000
77A92GLY00.0570.01011.500-1.357-1.3570.0000.0000.0000.000
78A93GLY0-0.0100.0007.3881.2041.2040.0000.0000.0000.000
79A94HIS00.0240.0153.5722.2143.1580.036-0.372-0.6080.002
80A95VAL00.0170.0385.2652.4682.616-0.001-0.003-0.1430.000
81A96ARG10.7810.8551.724-108.559-114.33721.746-8.783-7.1850.108
82A97GLU-1-0.817-0.8915.00621.34521.383-0.001-0.003-0.0330.000
83A98GLY0-0.030-0.0136.801-3.058-3.0580.0000.0000.0000.000
84A99ASP-1-0.783-0.8457.79037.98737.9870.0000.0000.0000.000
85A100GLY0-0.025-0.02910.068-2.047-2.0470.0000.0000.0000.000
86A101ALA0-0.047-0.01312.6290.6530.6530.0000.0000.0000.000
87A102THR0-0.036-0.04215.337-0.423-0.4230.0000.0000.0000.000
88A103PRO00.0280.01112.8281.1291.1290.0000.0000.0000.000
89A104ARG10.8180.88213.589-13.378-13.3780.0000.0000.0000.000
90A105GLU-1-0.872-0.90015.31017.52717.5270.0000.0000.0000.000
91A106ALA00.0010.0049.9180.7310.7310.0000.0000.0000.000
92A107PHE00.031-0.00411.1101.7541.7540.0000.0000.0000.000
93A108LEU0-0.018-0.00712.5790.4630.4630.0000.0000.0000.000
94A109LYS10.8120.89611.822-22.939-22.9390.0000.0000.0000.000
95A110GLY00.0250.0079.1830.9110.9110.0000.0000.0000.000
96A111LEU0-0.011-0.0059.7711.5241.5240.0000.0000.0000.000
97A112GLU-1-0.863-0.90912.38121.07521.0750.0000.0000.0000.000
98A113ARG10.7030.7865.867-45.639-45.6390.0000.0000.0000.000
99A114GLU-1-0.865-0.9488.93426.21826.2180.0000.0000.0000.000
100A115VAL00.0270.0109.921-0.839-0.8390.0000.0000.0000.000
101A116ASN0-0.064-0.03913.103-1.694-1.6940.0000.0000.0000.000
102A117GLU-1-0.839-0.8906.71447.08447.0840.0000.0000.0000.000
103A118GLU-1-0.811-0.90411.17623.16623.1660.0000.0000.0000.000
104A119VAL0-0.026-0.01713.243-1.962-1.9620.0000.0000.0000.000
105A120ASP-1-0.887-0.92616.43016.83216.8320.0000.0000.0000.000
106A121VAL00.025-0.00218.506-0.843-0.8430.0000.0000.0000.000
107A122SER0-0.032-0.01121.2740.0250.0250.0000.0000.0000.000
108A123LEU0-0.022-0.00618.620-0.580-0.5800.0000.0000.0000.000
109A124ARG10.7810.88422.948-11.021-11.0210.0000.0000.0000.000
110A125GLU-1-0.853-0.92624.91610.97410.9740.0000.0000.0000.000
111A126LEU0-0.0050.00117.5260.1890.1890.0000.0000.0000.000
112A127GLU-1-0.849-0.89722.21311.75911.7590.0000.0000.0000.000
113A128PHE00.0110.01019.3860.1760.1760.0000.0000.0000.000
114A129LEU0-0.018-0.01522.185-0.796-0.7960.0000.0000.0000.000
115A130GLY0-0.007-0.03022.170-0.793-0.7930.0000.0000.0000.000
116A131LEU0-0.0090.01918.4980.8440.8440.0000.0000.0000.000
117A132ILE0-0.034-0.01818.056-0.931-0.9310.0000.0000.0000.000
118A133ASN00.0150.00517.9891.9161.9160.0000.0000.0000.000
119A134SER00.0450.01918.820-0.520-0.5200.0000.0000.0000.000
120A135SER0-0.016-0.03619.0480.7340.7340.0000.0000.0000.000
121A136THR0-0.035-0.02421.0350.0760.0760.0000.0000.0000.000
122A137THR0-0.032-0.01117.3970.1790.1790.0000.0000.0000.000
123A138GLU-1-0.781-0.88415.89116.16916.1690.0000.0000.0000.000
124A139VAL00.0300.01311.3380.3630.3630.0000.0000.0000.000
125A140SER0-0.054-0.03313.1830.8540.8540.0000.0000.0000.000
126A141ARG10.7250.83615.652-15.959-15.9590.0000.0000.0000.000
127A142VAL00.0080.02311.308-0.421-0.4210.0000.0000.0000.000
128A143HIS0-0.065-0.0328.4483.7933.7930.0000.0000.0000.000
129A144LEU00.0020.01112.620-2.188-2.1880.0000.0000.0000.000
130A145GLY00.0190.01613.5881.6171.6170.0000.0000.0000.000
131A146ALA0-0.021-0.01615.254-1.457-1.4570.0000.0000.0000.000
132A147LEU0-0.0130.00716.6110.7040.7040.0000.0000.0000.000
133A148PHE00.003-0.01816.063-0.810-0.8100.0000.0000.0000.000
134A149LEU00.0100.01520.0150.1460.1460.0000.0000.0000.000
135A150GLY00.0330.00020.731-0.162-0.1620.0000.0000.0000.000
136A151ARG10.8410.91221.669-11.615-11.6150.0000.0000.0000.000
137A152GLY00.030-0.00724.6060.1890.1890.0000.0000.0000.000
138A153LYS10.8960.97125.174-11.208-11.2080.0000.0000.0000.000
139A154PHE00.0390.01220.3480.5010.5010.0000.0000.0000.000
140A155PHE0-0.084-0.03922.880-0.897-0.8970.0000.0000.0000.000
141A156SER0-0.034-0.01521.453-0.261-0.2610.0000.0000.0000.000
142A157VAL00.0280.01818.1090.4950.4950.0000.0000.0000.000
143A158LYS10.7840.88014.824-20.635-20.6350.0000.0000.0000.000
144A159GLU-1-0.902-0.95413.42122.50122.5010.0000.0000.0000.000
145A160LYS10.8250.87617.230-14.284-14.2840.0000.0000.0000.000
146A161ASP-1-0.877-0.91418.72914.62514.6250.0000.0000.0000.000
147A162LEU0-0.033-0.00312.6610.3220.3220.0000.0000.0000.000
148A163PHE0-0.037-0.02512.6880.4170.4170.0000.0000.0000.000
149A164GLU-1-0.836-0.89818.64112.55412.5540.0000.0000.0000.000
150A165TRP0-0.019-0.03420.8240.6670.6670.0000.0000.0000.000
151A166GLU-1-0.830-0.86522.81811.56211.5620.0000.0000.0000.000
152A167LEU00.0140.00924.7130.4200.4200.0000.0000.0000.000
153A168ILE0-0.0100.02026.991-0.616-0.6160.0000.0000.0000.000
154A169LYS10.8280.90229.226-8.787-8.7870.0000.0000.0000.000
155A170LEU00.0720.02828.4690.0710.0710.0000.0000.0000.000
156A171GLU-1-0.853-0.91331.5728.8038.8030.0000.0000.0000.000
157A172GLU-1-0.838-0.92531.45310.07910.0790.0000.0000.0000.000
158A173LEU00.0110.01026.1670.1690.1690.0000.0000.0000.000
159A174GLU-1-0.888-0.93929.65210.08410.0840.0000.0000.0000.000
160A175LYS10.8390.91731.801-10.084-10.0840.0000.0000.0000.000
161A176PHE00.003-0.01227.346-0.056-0.0560.0000.0000.0000.000
162A177SER00.0060.00527.1200.3740.3740.0000.0000.0000.000
163A178GLY0-0.014-0.00827.7050.2230.2230.0000.0000.0000.000
164A179VAL0-0.047-0.03427.2990.0030.0030.0000.0000.0000.000
165A180MET0-0.0370.02123.3340.3820.3820.0000.0000.0000.000
166A181GLU-1-0.816-0.93621.68212.76412.7640.0000.0000.0000.000
167A182GLY00.0160.00320.0960.6570.6570.0000.0000.0000.000
168A183TRP00.0200.00413.524-0.440-0.4400.0000.0000.0000.000
169A184SER00.0310.03719.210-0.212-0.2120.0000.0000.0000.000
170A185LYS10.8580.95321.228-12.675-12.6750.0000.0000.0000.000
171A186ILE0-0.023-0.00121.110-0.536-0.5360.0000.0000.0000.000
172A187SER00.017-0.01220.608-0.340-0.3400.0000.0000.0000.000
173A188ALA00.0060.00023.250-0.398-0.3980.0000.0000.0000.000
174A189ALA00.0010.00526.164-0.454-0.4540.0000.0000.0000.000
175A190VAL0-0.018-0.00525.113-0.462-0.4620.0000.0000.0000.000
176A191LEU00.014-0.01023.660-0.364-0.3640.0000.0000.0000.000
177A192LEU0-0.022-0.00827.882-0.346-0.3460.0000.0000.0000.000
178A193ASN0-0.078-0.04230.972-0.439-0.4390.0000.0000.0000.000
179A194LEU0-0.041-0.00927.416-0.274-0.2740.0000.0000.0000.000
180A195PHE0-0.071-0.01528.766-0.274-0.2740.0000.0000.0000.000