FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: QY1RY

Calculation Name: 3R8K-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3R8K

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y5Z4

Base Structure: X-ray

Registration Date: 2023-06-21

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 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. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1856096.61317
FMO2-HF: Nuclear repulsion 1785216.5968
FMO2-HF: Total energy -70880.01637
FMO2-MP2: Total energy -71088.377211


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:19:ALA)


Summations of interaction energy for fragment #1(A:19:ALA)
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.
-1.2961.07-0.009-1.159-1.1970.004
Interaction energy analysis for fragmet #1(A:19:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : 0.008
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].
3A21GLU-1-0.978-0.9783.814-2.0660.259-0.008-1.157-1.1600.004
4A22THR00.004-0.0065.3490.3640.405-0.001-0.002-0.0370.000
5A23PRO0-0.0090.0167.8680.0740.0740.0000.0000.0000.000
6A24GLY00.0260.00611.2340.0610.0610.0000.0000.0000.000
7A25TRP0-0.028-0.01312.3500.0180.0180.0000.0000.0000.000
8A26LYS10.9320.94815.0290.0620.0620.0000.0000.0000.000
9A27ALA00.0210.01117.778-0.010-0.0100.0000.0000.0000.000
10A28PRO00.0080.01719.9650.0040.0040.0000.0000.0000.000
11A29GLU-1-0.810-0.91623.5450.0120.0120.0000.0000.0000.000
12A30ASP-1-0.956-0.97726.537-0.017-0.0170.0000.0000.0000.000
13A31ALA0-0.056-0.02922.4950.0000.0000.0000.0000.0000.000
14A32GLY0-0.038-0.01324.5280.0090.0090.0000.0000.0000.000
15A33PRO0-0.0130.01624.9990.0000.0000.0000.0000.0000.000
16A34GLN00.0580.01020.0220.0260.0260.0000.0000.0000.000
17A35PRO00.0120.03021.357-0.003-0.0030.0000.0000.0000.000
18A36GLY00.011-0.00323.9630.0150.0150.0000.0000.0000.000
19A37SER0-0.074-0.03926.338-0.005-0.0050.0000.0000.0000.000
20A38TYR0-0.083-0.06528.025-0.006-0.0060.0000.0000.0000.000
21A39GLU-1-0.846-0.91029.7020.0570.0570.0000.0000.0000.000
22A40ILE00.004-0.00331.214-0.003-0.0030.0000.0000.0000.000
23A41ARG10.7450.86634.157-0.049-0.0490.0000.0000.0000.000
24A42HIS00.0200.01737.4000.0000.0000.0000.0000.0000.000
25A43TYR0-0.048-0.02040.2250.0020.0020.0000.0000.0000.000
26A44GLY00.0400.01643.499-0.002-0.0020.0000.0000.0000.000
27A45PRO0-0.0090.00546.4140.0010.0010.0000.0000.0000.000
28A46ALA0-0.040-0.03249.8410.0000.0000.0000.0000.0000.000
29A47LYS10.9000.95851.585-0.014-0.0140.0000.0000.0000.000
30A48TRP0-0.023-0.00147.4980.0020.0020.0000.0000.0000.000
31A49VAL0-0.0020.01154.229-0.001-0.0010.0000.0000.0000.000
32A50SER00.0490.00254.7080.0020.0020.0000.0000.0000.000
33A51THR0-0.0130.00356.703-0.001-0.0010.0000.0000.0000.000
34A52SER00.0360.01956.8910.0010.0010.0000.0000.0000.000
35A53VAL0-0.063-0.03257.2450.0000.0000.0000.0000.0000.000
36A54GLU-1-0.829-0.91557.7670.0210.0210.0000.0000.0000.000
37A55SER00.0120.02055.9260.0000.0000.0000.0000.0000.000
38A56MET00.0250.01554.1510.0000.0000.0000.0000.0000.000
39A57ASP-1-0.883-0.93353.0900.0380.0380.0000.0000.0000.000
40A58TRP00.027-0.00247.6560.0000.0000.0000.0000.0000.000
41A59ASP-1-0.806-0.93149.3840.0460.0460.0000.0000.0000.000
42A60SER0-0.0270.00351.935-0.001-0.0010.0000.0000.0000.000
43A61ALA00.0320.01354.087-0.001-0.0010.0000.0000.0000.000
44A62ILE00.0100.00350.424-0.001-0.0010.0000.0000.0000.000
45A63GLN0-0.007-0.00853.637-0.001-0.0010.0000.0000.0000.000
46A64THR0-0.029-0.01155.949-0.001-0.0010.0000.0000.0000.000
47A65GLY00.026-0.00156.890-0.001-0.0010.0000.0000.0000.000
48A66PHE00.012-0.00353.647-0.001-0.0010.0000.0000.0000.000
49A67THR0-0.039-0.01756.3220.0000.0000.0000.0000.0000.000
50A68LYS10.8870.93659.733-0.023-0.0230.0000.0000.0000.000
51A69LEU0-0.024-0.00355.418-0.001-0.0010.0000.0000.0000.000
52A70ASN00.0110.00358.346-0.001-0.0010.0000.0000.0000.000
53A71SER00.017-0.00159.448-0.001-0.0010.0000.0000.0000.000
54A72TYR0-0.017-0.02760.3010.0000.0000.0000.0000.0000.000
55A73ILE0-0.0170.00556.956-0.001-0.0010.0000.0000.0000.000
56A74GLN0-0.002-0.00160.6510.0000.0000.0000.0000.0000.000
57A75GLY0-0.042-0.04163.0590.0000.0000.0000.0000.0000.000
58A76LYS10.8400.95265.363-0.021-0.0210.0000.0000.0000.000
59A77ASN0-0.018-0.03564.885-0.001-0.0010.0000.0000.0000.000
60A78GLU-1-0.838-0.94166.9780.0130.0130.0000.0000.0000.000
61A79LYS10.8040.92265.368-0.014-0.0140.0000.0000.0000.000
62A80GLU-1-0.958-0.97868.8320.0170.0170.0000.0000.0000.000
63A81MET0-0.045-0.01163.1540.0000.0000.0000.0000.0000.000
64A82LYS10.8810.95562.556-0.022-0.0220.0000.0000.0000.000
65A83ILE0-0.027-0.01857.5210.0000.0000.0000.0000.0000.000
66A84LYS10.9520.97154.873-0.024-0.0240.0000.0000.0000.000
67A85MET00.0440.03352.3940.0000.0000.0000.0000.0000.000
68A86THR0-0.092-0.09050.2530.0010.0010.0000.0000.0000.000
69A87ALA0-0.0410.01645.9000.0000.0000.0000.0000.0000.000
70A88PRO0-0.040-0.01444.154-0.001-0.0010.0000.0000.0000.000
71A89VAL00.0670.01246.525-0.002-0.0020.0000.0000.0000.000
72A90THR00.027-0.00646.4230.0020.0020.0000.0000.0000.000
73A91SER0-0.082-0.03447.639-0.002-0.0020.0000.0000.0000.000
74A92TYR00.0630.02347.7230.0010.0010.0000.0000.0000.000
75A93VAL0-0.007-0.00448.034-0.001-0.0010.0000.0000.0000.000
76A94GLU-1-0.884-0.96148.9070.0200.0200.0000.0000.0000.000
77A95PRO0-0.057-0.03448.5370.0000.0000.0000.0000.0000.000
78A96GLY00.0910.04851.686-0.002-0.0020.0000.0000.0000.000
79A97SER0-0.081-0.05253.3440.0000.0000.0000.0000.0000.000
80A98GLY00.0230.00551.9310.0000.0000.0000.0000.0000.000
81A99PRO0-0.032-0.02048.7200.0000.0000.0000.0000.0000.000
82A100PHE0-0.010-0.00850.5080.0010.0010.0000.0000.0000.000
83A101SER0-0.045-0.00454.101-0.001-0.0010.0000.0000.0000.000
84A102GLU-1-0.907-0.95554.9080.0240.0240.0000.0000.0000.000
85A103SER0-0.065-0.02552.5700.0000.0000.0000.0000.0000.000
86A104THR00.0280.02354.6830.0000.0000.0000.0000.0000.000
87A105ILE0-0.071-0.02852.0330.0010.0010.0000.0000.0000.000
88A106THR0-0.012-0.02452.893-0.001-0.0010.0000.0000.0000.000
89A107ILE0-0.061-0.00452.3770.0010.0010.0000.0000.0000.000
90A108SER00.017-0.01951.262-0.002-0.0020.0000.0000.0000.000
91A109LEU0-0.021-0.00851.8840.0020.0020.0000.0000.0000.000
92A110TYR00.0540.02249.637-0.001-0.0010.0000.0000.0000.000
93A111ILE00.0000.03751.9170.0010.0010.0000.0000.0000.000
94A112PRO00.0020.00452.9120.0000.0000.0000.0000.0000.000
95A113SER00.0380.00851.767-0.001-0.0010.0000.0000.0000.000
96A114GLU-1-0.942-0.96653.6860.0190.0190.0000.0000.0000.000
97A115GLN00.004-0.01057.186-0.001-0.0010.0000.0000.0000.000
98A116GLN0-0.010-0.00353.269-0.002-0.0020.0000.0000.0000.000
99A117PHE0-0.037-0.02156.731-0.001-0.0010.0000.0000.0000.000
100A118ASP-1-0.875-0.94159.4260.0120.0120.0000.0000.0000.000
101A119PRO0-0.0100.00359.3530.0010.0010.0000.0000.0000.000
102A120PRO0-0.048-0.01961.817-0.001-0.0010.0000.0000.0000.000
103A121ARG11.0371.04563.816-0.012-0.0120.0000.0000.0000.000
104A122PRO0-0.022-0.00863.3170.0000.0000.0000.0000.0000.000
105A123LEU0-0.0060.00865.398-0.001-0.0010.0000.0000.0000.000
106A124GLU-1-0.910-0.96165.4590.0210.0210.0000.0000.0000.000
107A125SER0-0.014-0.01366.5980.0000.0000.0000.0000.0000.000
108A126ASP-1-0.800-0.88263.8080.0200.0200.0000.0000.0000.000
109A127VAL0-0.043-0.01260.7830.0010.0010.0000.0000.0000.000
110A128PHE0-0.013-0.01857.731-0.001-0.0010.0000.0000.0000.000
111A129ILE0-0.016-0.01658.3930.0010.0010.0000.0000.0000.000
112A130GLU-1-0.820-0.89952.4540.0210.0210.0000.0000.0000.000
113A131ASP-1-0.882-0.94955.4390.0140.0140.0000.0000.0000.000
114A132ARG10.7980.90648.135-0.025-0.0250.0000.0000.0000.000
115A133ALA00.0250.00749.911-0.001-0.0010.0000.0000.0000.000
116A134GLU-1-0.930-0.96946.0070.0100.0100.0000.0000.0000.000
117A135MET0-0.030-0.01743.5960.0000.0000.0000.0000.0000.000
118A136THR00.0140.01537.6450.0010.0010.0000.0000.0000.000
119A137VAL0-0.042-0.02038.8090.0000.0000.0000.0000.0000.000
120A138PHE00.008-0.01233.8270.0010.0010.0000.0000.0000.000
121A139VAL00.0220.00135.2640.0010.0010.0000.0000.0000.000
122A140ARG10.9470.97629.496-0.088-0.0880.0000.0000.0000.000
123A141SER0-0.010-0.00933.973-0.001-0.0010.0000.0000.0000.000
124A142PHE0-0.047-0.02834.1120.0050.0050.0000.0000.0000.000
125A143ASP-1-0.867-0.93633.4210.0990.0990.0000.0000.0000.000
126A144GLY0-0.021-0.02036.7640.0000.0000.0000.0000.0000.000
127A145PHE0-0.022-0.02540.321-0.003-0.0030.0000.0000.0000.000
128A146SER0-0.002-0.00943.2480.0020.0020.0000.0000.0000.000
129A147SER00.0120.01444.0870.0000.0000.0000.0000.0000.000
130A148ALA00.0480.02544.8510.0010.0010.0000.0000.0000.000
131A149GLN0-0.006-0.00143.5710.0020.0020.0000.0000.0000.000
132A150LYS10.8770.95736.798-0.081-0.0810.0000.0000.0000.000
133A151ASN00.002-0.01040.0280.0040.0040.0000.0000.0000.000
134A152GLN00.0240.01040.2970.0020.0020.0000.0000.0000.000
135A153GLU-1-0.907-0.94036.5270.0820.0820.0000.0000.0000.000
136A154GLN00.0720.02934.4330.0020.0020.0000.0000.0000.000
137A155LEU0-0.010-0.00735.9320.0000.0000.0000.0000.0000.000
138A156LEU00.0120.02137.123-0.002-0.0020.0000.0000.0000.000
139A157THR0-0.022-0.00831.1220.0030.0030.0000.0000.0000.000
140A158LEU0-0.023-0.02232.2460.0020.0020.0000.0000.0000.000
141A159ALA0-0.016-0.01133.584-0.003-0.0030.0000.0000.0000.000
142A160SER0-0.061-0.03031.806-0.002-0.0020.0000.0000.0000.000
143A161ILE00.0520.01827.561-0.003-0.0030.0000.0000.0000.000
144A162LEU0-0.042-0.00329.698-0.004-0.0040.0000.0000.0000.000
145A163ARG10.8820.94331.719-0.037-0.0370.0000.0000.0000.000
146A164GLU-1-0.970-0.97126.7060.0700.0700.0000.0000.0000.000
147A165ASP-1-0.926-0.97026.5280.0530.0530.0000.0000.0000.000
148A166GLY0-0.019-0.01528.150-0.006-0.0060.0000.0000.0000.000
149A167LYS10.8630.95330.049-0.023-0.0230.0000.0000.0000.000
150A168VAL0-0.001-0.00233.2330.0010.0010.0000.0000.0000.000
151A169PHE0-0.014-0.01936.092-0.001-0.0010.0000.0000.0000.000
152A170ASP-1-0.909-0.97539.2080.0180.0180.0000.0000.0000.000
153A171GLU-1-0.937-0.96940.0030.0250.0250.0000.0000.0000.000
154A172LYS10.9000.95942.719-0.015-0.0150.0000.0000.0000.000
155A173VAL00.0390.03546.0260.0020.0020.0000.0000.0000.000
156A174TYR0-0.023-0.01642.9240.0020.0020.0000.0000.0000.000
157A175TYR00.0480.02543.394-0.001-0.0010.0000.0000.0000.000
158A176THR0-0.032-0.01943.2130.0030.0030.0000.0000.0000.000
159A177ALA00.0060.00642.411-0.003-0.0030.0000.0000.0000.000
160A178GLY00.0250.01742.8460.0040.0040.0000.0000.0000.000
161A179TYR0-0.071-0.06540.919-0.004-0.0040.0000.0000.0000.000
162A180ASN0-0.073-0.02641.949-0.001-0.0010.0000.0000.0000.000
163A181SER00.0430.03345.6300.0010.0010.0000.0000.0000.000
164A182PRO00.0470.01147.1310.0010.0010.0000.0000.0000.000
165A183VAL00.0320.02149.7400.0000.0000.0000.0000.0000.000
166A184LYS10.9220.99144.831-0.055-0.0550.0000.0000.0000.000
167A185LEU0-0.035-0.03447.5880.0000.0000.0000.0000.0000.000
168A186LEU00.017-0.00942.8480.0000.0000.0000.0000.0000.000
169A187ASN0-0.067-0.04039.9900.0000.0000.0000.0000.0000.000
170A188ARG10.9280.96338.419-0.050-0.0500.0000.0000.0000.000
171A189ASN00.0100.02434.697-0.003-0.0030.0000.0000.0000.000
172A190ASN00.0410.02638.430-0.005-0.0050.0000.0000.0000.000
173A191GLU-1-0.740-0.85737.9230.0580.0580.0000.0000.0000.000
174A192VAL0-0.034-0.00137.909-0.003-0.0030.0000.0000.0000.000
175A193TRP0-0.010-0.02438.3660.0000.0000.0000.0000.0000.000
176A194LEU00.0390.03437.605-0.001-0.0010.0000.0000.0000.000
177A195ILE00.0220.02039.4160.0000.0000.0000.0000.0000.000
178A196GLN00.000-0.00236.2940.0000.0000.0000.0000.0000.000
179A197LYS10.9270.96539.856-0.012-0.0120.0000.0000.0000.000
180A198ASN0-0.0140.00341.311-0.001-0.0010.0000.0000.0000.000