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: K93Y3

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 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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1856295.227371
FMO2-HF: Nuclear repulsion 1785413.796895
FMO2-HF: Total energy -70881.430476
FMO2-MP2: Total energy -71089.6904


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.
-1.231.072-0.012-1.138-1.1510.004
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 : 0.014 / q_NPA : 0.004
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-1-0.953-0.9653.814-2.0230.279-0.012-1.138-1.1510.004
4A22THR0-0.028-0.0205.5030.3910.3910.0000.0000.0000.000
5A23PRO0-0.0020.0128.0260.0780.0780.0000.0000.0000.000
6A24GLY00.0320.01311.3640.0620.0620.0000.0000.0000.000
7A25TRP0-0.033-0.01612.4520.0100.0100.0000.0000.0000.000
8A26LYS10.9350.95015.1060.0360.0360.0000.0000.0000.000
9A27ALA00.0200.01217.849-0.011-0.0110.0000.0000.0000.000
10A28PRO00.0070.01519.9540.0040.0040.0000.0000.0000.000
11A29GLU-1-0.787-0.87723.5340.0190.0190.0000.0000.0000.000
12A30ASP-1-0.944-0.97426.520-0.009-0.0090.0000.0000.0000.000
13A31ALA0-0.055-0.02622.4510.0000.0000.0000.0000.0000.000
14A32GLY0-0.032-0.01024.5250.0090.0090.0000.0000.0000.000
15A33PRO0-0.0040.01524.9790.0010.0010.0000.0000.0000.000
16A34GLN00.0400.01519.9790.0210.0210.0000.0000.0000.000
17A35PRO00.0280.01621.532-0.002-0.0020.0000.0000.0000.000
18A36GLY00.0090.00623.9250.0150.0150.0000.0000.0000.000
19A37SER0-0.057-0.03026.320-0.005-0.0050.0000.0000.0000.000
20A38TYR0-0.085-0.09527.979-0.006-0.0060.0000.0000.0000.000
21A39GLU-1-0.841-0.90129.6730.0600.0600.0000.0000.0000.000
22A40ILE00.0000.00031.144-0.003-0.0030.0000.0000.0000.000
23A41ARG10.7240.82534.138-0.052-0.0520.0000.0000.0000.000
24A42HIS00.0040.00337.3860.0000.0000.0000.0000.0000.000
25A43TYR0-0.040-0.00940.2150.0020.0020.0000.0000.0000.000
26A44GLY00.0500.02043.488-0.002-0.0020.0000.0000.0000.000
27A45PRO0-0.021-0.00246.4100.0010.0010.0000.0000.0000.000
28A46ALA0-0.037-0.02649.8320.0000.0000.0000.0000.0000.000
29A47LYS10.8770.94051.575-0.015-0.0150.0000.0000.0000.000
30A48TRP0-0.020-0.01847.0970.0020.0020.0000.0000.0000.000
31A49VAL0-0.0160.00654.208-0.001-0.0010.0000.0000.0000.000
32A50SER00.032-0.01954.3510.0020.0020.0000.0000.0000.000
33A51THR0-0.0210.00256.669-0.001-0.0010.0000.0000.0000.000
34A52SER00.0090.00156.8500.0010.0010.0000.0000.0000.000
35A53VAL0-0.039-0.02457.2670.0000.0000.0000.0000.0000.000
36A54GLU-1-0.799-0.87857.7670.0230.0230.0000.0000.0000.000
37A55SER00.0300.02155.5810.0000.0000.0000.0000.0000.000
38A56MET00.0190.01954.1890.0000.0000.0000.0000.0000.000
39A57ASP-1-0.917-0.94553.1180.0400.0400.0000.0000.0000.000
40A58TRP00.039-0.00347.4890.0000.0000.0000.0000.0000.000
41A59ASP-1-0.774-0.90749.3450.0470.0470.0000.0000.0000.000
42A60SER0-0.0260.00551.956-0.001-0.0010.0000.0000.0000.000
43A61ALA00.0400.01654.086-0.001-0.0010.0000.0000.0000.000
44A62ILE00.0040.00050.323-0.001-0.0010.0000.0000.0000.000
45A63GLN0-0.0020.00553.667-0.001-0.0010.0000.0000.0000.000
46A64THR0-0.030-0.01855.972-0.001-0.0010.0000.0000.0000.000
47A65GLY00.0360.00256.844-0.001-0.0010.0000.0000.0000.000
48A66PHE0-0.014-0.00954.140-0.001-0.0010.0000.0000.0000.000
49A67THR0-0.027-0.02156.2820.0000.0000.0000.0000.0000.000
50A68LYS10.8370.88759.692-0.024-0.0240.0000.0000.0000.000
51A69LEU0-0.0180.00055.494-0.001-0.0010.0000.0000.0000.000
52A70ASN00.008-0.00258.1380.0000.0000.0000.0000.0000.000
53A71SER00.008-0.01059.416-0.001-0.0010.0000.0000.0000.000
54A72TYR0-0.018-0.01359.8220.0000.0000.0000.0000.0000.000
55A73ILE00.0140.01556.524-0.001-0.0010.0000.0000.0000.000
56A74GLN0-0.014-0.00859.416-0.001-0.0010.0000.0000.0000.000
57A75GLY0-0.0030.00463.0360.0000.0000.0000.0000.0000.000
58A76LYS10.8540.93965.333-0.022-0.0220.0000.0000.0000.000
59A77ASN0-0.037-0.06264.286-0.001-0.0010.0000.0000.0000.000
60A78GLU-1-0.831-0.93766.9570.0140.0140.0000.0000.0000.000
61A79LYS10.7560.88764.864-0.015-0.0150.0000.0000.0000.000
62A80GLU-1-0.955-0.97568.7460.0170.0170.0000.0000.0000.000
63A81MET0-0.036-0.00962.4430.0000.0000.0000.0000.0000.000
64A82LYS10.8310.92362.528-0.023-0.0230.0000.0000.0000.000
65A83ILE0-0.034-0.02457.5470.0000.0000.0000.0000.0000.000
66A84LYS10.8480.90755.183-0.024-0.0240.0000.0000.0000.000
67A85MET00.0300.02552.4490.0000.0000.0000.0000.0000.000
68A86THR0-0.066-0.06450.3300.0010.0010.0000.0000.0000.000
69A87ALA0-0.0460.00545.9510.0000.0000.0000.0000.0000.000
70A88PRO0-0.033-0.01343.979-0.001-0.0010.0000.0000.0000.000
71A89VAL00.0620.01246.498-0.002-0.0020.0000.0000.0000.000
72A90THR00.0260.00645.9120.0020.0020.0000.0000.0000.000
73A91SER0-0.090-0.06447.605-0.002-0.0020.0000.0000.0000.000
74A92TYR0-0.009-0.02147.7150.0020.0020.0000.0000.0000.000
75A93VAL00.0010.00048.045-0.001-0.0010.0000.0000.0000.000
76A94GLU-1-0.835-0.91248.8550.0220.0220.0000.0000.0000.000
77A95PRO0-0.030-0.02048.517-0.001-0.0010.0000.0000.0000.000
78A96GLY00.0820.04551.708-0.002-0.0020.0000.0000.0000.000
79A97SER0-0.064-0.04253.3160.0000.0000.0000.0000.0000.000
80A98GLY00.010-0.00151.8920.0000.0000.0000.0000.0000.000
81A99PRO0-0.027-0.01748.6640.0000.0000.0000.0000.0000.000
82A100PHE0-0.013-0.00950.4320.0010.0010.0000.0000.0000.000
83A101SER0-0.054-0.01154.138-0.001-0.0010.0000.0000.0000.000
84A102GLU-1-0.915-0.95254.9490.0260.0260.0000.0000.0000.000
85A103SER0-0.067-0.03052.6970.0000.0000.0000.0000.0000.000
86A104THR00.022-0.01654.6880.0000.0000.0000.0000.0000.000
87A105ILE0-0.089-0.04151.9620.0010.0010.0000.0000.0000.000
88A106THR00.0300.00252.835-0.001-0.0010.0000.0000.0000.000
89A107ILE0-0.066-0.00652.3350.0010.0010.0000.0000.0000.000
90A108SER00.0400.00051.237-0.001-0.0010.0000.0000.0000.000
91A109LEU0-0.035-0.01051.8520.0020.0020.0000.0000.0000.000
92A110TYR00.0510.03049.502-0.001-0.0010.0000.0000.0000.000
93A111ILE00.0070.02851.8970.0010.0010.0000.0000.0000.000
94A112PRO00.0060.01252.8930.0000.0000.0000.0000.0000.000
95A113SER00.0680.02151.776-0.001-0.0010.0000.0000.0000.000
96A114GLU-1-0.842-0.91253.6850.0220.0220.0000.0000.0000.000
97A115GLN0-0.033-0.02457.189-0.002-0.0020.0000.0000.0000.000
98A116GLN00.0090.01553.307-0.001-0.0010.0000.0000.0000.000
99A117PHE0-0.034-0.01656.727-0.001-0.0010.0000.0000.0000.000
100A118ASP-1-0.833-0.91359.4260.0130.0130.0000.0000.0000.000
101A119PRO00.0030.01459.2690.0010.0010.0000.0000.0000.000
102A120PRO0-0.044-0.02161.806-0.001-0.0010.0000.0000.0000.000
103A121ARG11.0311.03663.799-0.013-0.0130.0000.0000.0000.000
104A122PRO0-0.018-0.01063.0060.0000.0000.0000.0000.0000.000
105A123LEU0-0.0140.01565.373-0.001-0.0010.0000.0000.0000.000
106A124GLU-1-0.875-0.91165.4580.0220.0220.0000.0000.0000.000
107A125SER00.019-0.00366.5650.0000.0000.0000.0000.0000.000
108A126ASP-1-0.834-0.88963.9220.0210.0210.0000.0000.0000.000
109A127VAL0-0.048-0.01460.6050.0010.0010.0000.0000.0000.000
110A128PHE00.003-0.00357.482-0.001-0.0010.0000.0000.0000.000
111A129ILE0-0.018-0.01858.5140.0010.0010.0000.0000.0000.000
112A130GLU-1-0.788-0.83952.2790.0230.0230.0000.0000.0000.000
113A131ASP-1-0.877-0.94955.4040.0160.0160.0000.0000.0000.000
114A132ARG10.7620.84948.164-0.027-0.0270.0000.0000.0000.000
115A133ALA00.0260.01049.965-0.001-0.0010.0000.0000.0000.000
116A134GLU-1-0.895-0.94945.8310.0130.0130.0000.0000.0000.000
117A135MET0-0.024-0.01243.7990.0000.0000.0000.0000.0000.000
118A136THR0-0.0010.00537.6020.0010.0010.0000.0000.0000.000
119A137VAL0-0.047-0.03039.0640.0000.0000.0000.0000.0000.000
120A138PHE00.005-0.00333.5950.0020.0020.0000.0000.0000.000
121A139VAL00.0070.00135.2240.0010.0010.0000.0000.0000.000
122A140ARG10.9080.95029.474-0.093-0.0930.0000.0000.0000.000
123A141SER0-0.020-0.01733.934-0.001-0.0010.0000.0000.0000.000
124A142PHE0-0.051-0.02234.1230.0050.0050.0000.0000.0000.000
125A143ASP-1-0.853-0.92633.5720.0990.0990.0000.0000.0000.000
126A144GLY00.010-0.01036.7700.0000.0000.0000.0000.0000.000
127A145PHE0-0.025-0.02740.323-0.003-0.0030.0000.0000.0000.000
128A146SER00.012-0.00143.2580.0020.0020.0000.0000.0000.000
129A147SER00.0390.01644.1920.0000.0000.0000.0000.0000.000
130A148ALA00.0000.00844.8720.0010.0010.0000.0000.0000.000
131A149GLN0-0.028-0.01543.7260.0020.0020.0000.0000.0000.000
132A150LYS10.8540.93936.468-0.084-0.0840.0000.0000.0000.000
133A151ASN0-0.025-0.02140.0480.0050.0050.0000.0000.0000.000
134A152GLN00.0210.01040.3280.0020.0020.0000.0000.0000.000
135A153GLU-1-0.803-0.87336.4990.0850.0850.0000.0000.0000.000
136A154GLN00.000-0.01934.0800.0030.0030.0000.0000.0000.000
137A155LEU00.0060.00335.9700.0010.0010.0000.0000.0000.000
138A156LEU00.0110.02137.122-0.002-0.0020.0000.0000.0000.000
139A157THR0-0.046-0.02631.2820.0030.0030.0000.0000.0000.000
140A158LEU0-0.017-0.02132.2910.0020.0020.0000.0000.0000.000
141A159ALA0-0.008-0.00633.573-0.003-0.0030.0000.0000.0000.000
142A160SER0-0.062-0.03231.814-0.002-0.0020.0000.0000.0000.000
143A161ILE00.0540.02127.503-0.003-0.0030.0000.0000.0000.000
144A162LEU0-0.0270.00429.689-0.004-0.0040.0000.0000.0000.000
145A163ARG10.8400.91031.722-0.040-0.0400.0000.0000.0000.000
146A164GLU-1-0.966-0.97526.6330.0790.0790.0000.0000.0000.000
147A165ASP-1-0.907-0.92226.2930.0590.0590.0000.0000.0000.000
148A166GLY0-0.027-0.02228.161-0.006-0.0060.0000.0000.0000.000
149A167LYS10.8110.90029.530-0.032-0.0320.0000.0000.0000.000
150A168VAL0-0.008-0.00833.2540.0010.0010.0000.0000.0000.000
151A169PHE0-0.013-0.01135.449-0.001-0.0010.0000.0000.0000.000
152A170ASP-1-0.858-0.96039.1910.0210.0210.0000.0000.0000.000
153A171GLU-1-0.915-0.94640.1370.0300.0300.0000.0000.0000.000
154A172LYS10.8930.95642.709-0.017-0.0170.0000.0000.0000.000
155A173VAL00.0160.02646.2400.0020.0020.0000.0000.0000.000
156A174TYR0-0.011-0.00842.9600.0020.0020.0000.0000.0000.000
157A175TYR00.0470.01743.351-0.001-0.0010.0000.0000.0000.000
158A176THR0-0.0210.00643.1680.0030.0030.0000.0000.0000.000
159A177ALA0-0.0050.00042.335-0.003-0.0030.0000.0000.0000.000
160A178GLY00.0350.02142.8080.0040.0040.0000.0000.0000.000
161A179TYR0-0.074-0.07541.034-0.003-0.0030.0000.0000.0000.000
162A180ASN0-0.087-0.03641.826-0.001-0.0010.0000.0000.0000.000
163A181SER00.0640.04745.5950.0010.0010.0000.0000.0000.000
164A182PRO00.0340.00447.1300.0010.0010.0000.0000.0000.000
165A183VAL00.0240.01249.7090.0000.0000.0000.0000.0000.000
166A184LYS10.8680.96144.562-0.057-0.0570.0000.0000.0000.000
167A185LEU0-0.037-0.02247.5830.0000.0000.0000.0000.0000.000
168A186LEU00.019-0.00943.2970.0000.0000.0000.0000.0000.000
169A187ASN0-0.029-0.02040.1780.0000.0000.0000.0000.0000.000
170A188ARG10.9110.96138.500-0.054-0.0540.0000.0000.0000.000
171A189ASN00.0040.02234.493-0.004-0.0040.0000.0000.0000.000
172A190ASN00.0210.01338.393-0.006-0.0060.0000.0000.0000.000
173A191GLU-1-0.677-0.80037.9510.0590.0590.0000.0000.0000.000
174A192VAL0-0.027-0.00338.033-0.003-0.0030.0000.0000.0000.000
175A193TRP0-0.013-0.04038.3240.0000.0000.0000.0000.0000.000
176A194LEU00.0350.03937.681-0.001-0.0010.0000.0000.0000.000
177A195ILE00.0290.02239.3790.0000.0000.0000.0000.0000.000
178A196GLN00.0000.00136.1840.0010.0010.0000.0000.0000.000
179A197LYS10.9250.96739.824-0.017-0.0170.0000.0000.0000.000
180A198ASN0-0.0030.00441.174-0.001-0.0010.0000.0000.0000.000