Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 72NNK

Calculation Name: 2I81-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2I81

Chain ID: A

ChEMBL ID:

UniProt ID: A5K421

Base Structure: X-ray

Registration Date: 2023-06-22

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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2104755.580454
FMO2-HF: Nuclear repulsion 2029793.615742
FMO2-HF: Total energy -74961.964712
FMO2-MP2: Total energy -75182.939259


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:2:PRO)


Summations of interaction energy for fragment #1(A:2:PRO)
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.
-3.659-0.1040.21-1.713-2.0520.003
Interaction energy analysis for fragmet #1(A:2:PRO)
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].
3A4TYR00.034-0.0033.824-1.6411.251-0.019-1.509-1.3640.002
4A5VAL0-0.018-0.0086.1970.3940.3940.0000.0000.0000.000
5A6GLY0-0.0030.0077.4500.0940.0940.0000.0000.0000.000
6A7LYS10.8140.8952.712-0.0540.6090.229-0.204-0.6880.001
7A8GLU-1-0.922-0.9538.769-0.567-0.5670.0000.0000.0000.000
8A9ALA0-0.008-0.0088.889-0.216-0.2160.0000.0000.0000.000
9A10PRO00.0140.0188.5920.0860.0860.0000.0000.0000.000
10A11PHE00.0230.01611.1680.1140.1140.0000.0000.0000.000
11A12PHE00.0350.01714.706-0.015-0.0150.0000.0000.0000.000
12A13LYS10.8090.87617.4270.2550.2550.0000.0000.0000.000
13A14ALA0-0.0030.00921.139-0.003-0.0030.0000.0000.0000.000
14A15GLU-1-0.827-0.90023.357-0.141-0.1410.0000.0000.0000.000
15A16ALA0-0.012-0.01126.154-0.010-0.0100.0000.0000.0000.000
16A17VAL0-0.049-0.01928.2350.0130.0130.0000.0000.0000.000
17A18PHE00.0540.03129.105-0.007-0.0070.0000.0000.0000.000
18A19GLY00.0820.04132.5150.0050.0050.0000.0000.0000.000
19A20ASP-1-0.881-0.92234.643-0.099-0.0990.0000.0000.0000.000
20A21ASN0-0.115-0.07935.7460.0020.0020.0000.0000.0000.000
21A22SER0-0.029-0.02036.1090.0000.0000.0000.0000.0000.000
22A23PHE0-0.032-0.03832.710-0.006-0.0060.0000.0000.0000.000
23A24GLY00.0210.00731.3950.0060.0060.0000.0000.0000.000
24A25GLU-1-0.844-0.90725.778-0.209-0.2090.0000.0000.0000.000
25A26VAL0-0.0190.00523.1240.0080.0080.0000.0000.0000.000
26A27ASN0-0.010-0.01921.208-0.024-0.0240.0000.0000.0000.000
27A28LEU00.0270.02315.0370.0260.0260.0000.0000.0000.000
28A29THR00.0840.02419.3890.0050.0050.0000.0000.0000.000
29A30GLN0-0.0310.01420.6660.0150.0150.0000.0000.0000.000
30A31PHE00.0430.00521.4220.0240.0240.0000.0000.0000.000
31A32ILE00.0140.02917.4200.0120.0120.0000.0000.0000.000
32A33GLY0-0.009-0.00721.1570.0170.0170.0000.0000.0000.000
33A34LYS10.7790.89423.5680.1860.1860.0000.0000.0000.000
34A35LYS10.8630.92624.0900.1750.1750.0000.0000.0000.000
35A36TYR0-0.020-0.02820.910-0.017-0.0170.0000.0000.0000.000
36A37VAL0-0.0130.00319.0770.0140.0140.0000.0000.0000.000
37A38LEU00.0030.01019.338-0.025-0.0250.0000.0000.0000.000
38A39LEU00.0110.01016.3860.0240.0240.0000.0000.0000.000
39A40TYR0-0.060-0.05718.544-0.016-0.0160.0000.0000.0000.000
40A41PHE00.0210.01315.1800.0180.0180.0000.0000.0000.000
41A42TYR0-0.072-0.06619.7330.0200.0200.0000.0000.0000.000
42A43PRO00.0160.00321.934-0.003-0.0030.0000.0000.0000.000
43A44LEU00.015-0.00322.878-0.001-0.0010.0000.0000.0000.000
44A45ASP-1-0.729-0.83226.297-0.136-0.1360.0000.0000.0000.000
45A46PHE0-0.036-0.02229.4120.0050.0050.0000.0000.0000.000
46A47THR0-0.021-0.00728.5220.0050.0050.0000.0000.0000.000
47A48PHE00.007-0.01129.9310.0030.0030.0000.0000.0000.000
48A49VAL00.0200.02026.7400.0010.0010.0000.0000.0000.000
49A50CYS0-0.0220.04626.544-0.004-0.0040.0000.0000.0000.000
50A51PRO00.0570.04327.979-0.006-0.0060.0000.0000.0000.000
51A52SER0-0.061-0.04630.3770.0020.0020.0000.0000.0000.000
52A53GLU-1-0.728-0.86124.803-0.149-0.1490.0000.0000.0000.000
53A54ILE00.0140.01327.570-0.001-0.0010.0000.0000.0000.000
54A55ILE0-0.013-0.01529.3530.0020.0020.0000.0000.0000.000
55A56ALA0-0.042-0.01830.4270.0040.0040.0000.0000.0000.000
56A57LEU00.0130.00325.3990.0020.0020.0000.0000.0000.000
57A58ASP-1-0.784-0.87629.733-0.113-0.1130.0000.0000.0000.000
58A59LYS10.9060.95232.3630.0820.0820.0000.0000.0000.000
59A60ALA00.0060.01731.1210.0050.0050.0000.0000.0000.000
60A61LEU00.0200.00430.117-0.004-0.0040.0000.0000.0000.000
61A62ASP-1-0.892-0.95432.004-0.093-0.0930.0000.0000.0000.000
62A63ALA0-0.0070.01231.5450.0010.0010.0000.0000.0000.000
63A64PHE0-0.009-0.01226.010-0.004-0.0040.0000.0000.0000.000
64A65HIS00.003-0.00229.041-0.009-0.0090.0000.0000.0000.000
65A66GLU-1-0.901-0.93631.541-0.083-0.0830.0000.0000.0000.000
66A67ARG10.7600.87627.0960.1010.1010.0000.0000.0000.000
67A68ASN00.0020.00227.106-0.011-0.0110.0000.0000.0000.000
68A69VAL0-0.004-0.01023.956-0.012-0.0120.0000.0000.0000.000
69A70GLU-1-0.945-0.97623.918-0.160-0.1600.0000.0000.0000.000
70A71LEU0-0.036-0.01123.746-0.022-0.0220.0000.0000.0000.000
71A72LEU00.002-0.00621.4560.0090.0090.0000.0000.0000.000
72A73GLY00.0570.02822.448-0.019-0.0190.0000.0000.0000.000
73A74CYS0-0.054-0.01819.964-0.003-0.0030.0000.0000.0000.000
74A75SER00.015-0.01621.513-0.005-0.0050.0000.0000.0000.000
75A76VAL00.0370.01120.342-0.006-0.0060.0000.0000.0000.000
76A77ASP-1-0.815-0.86322.707-0.139-0.1390.0000.0000.0000.000
77A78SER00.0260.02326.105-0.009-0.0090.0000.0000.0000.000
78A79LYS10.9170.93628.4620.1410.1410.0000.0000.0000.000
79A80TYR00.017-0.01030.1280.0040.0040.0000.0000.0000.000
80A81THR0-0.0080.00930.2820.0070.0070.0000.0000.0000.000
81A82HIS10.8390.88625.8720.1740.1740.0000.0000.0000.000
82A83LEU0-0.0030.01131.4670.0060.0060.0000.0000.0000.000
83A84ALA00.001-0.00134.8830.0060.0060.0000.0000.0000.000
84A85TRP00.0220.01228.8790.0050.0050.0000.0000.0000.000
85A86LYS10.8470.93033.2480.1170.1170.0000.0000.0000.000
86A87LYS10.9000.95636.1530.0840.0840.0000.0000.0000.000
87A88THR0-0.036-0.00337.6730.0070.0070.0000.0000.0000.000
88A89PRO00.008-0.00338.926-0.002-0.0020.0000.0000.0000.000
89A90LEU00.0700.02737.4800.0010.0010.0000.0000.0000.000
90A91ALA0-0.028-0.00739.7480.0000.0000.0000.0000.0000.000
91A92LYS10.8820.93741.3550.0560.0560.0000.0000.0000.000
92A93GLY00.0370.03037.393-0.001-0.0010.0000.0000.0000.000
93A94GLY0-0.011-0.00335.681-0.005-0.0050.0000.0000.0000.000
94A95ILE00.0050.00531.3190.0020.0020.0000.0000.0000.000
95A96GLY0-0.0020.00935.0500.0010.0010.0000.0000.0000.000
96A97ASN0-0.009-0.01236.343-0.004-0.0040.0000.0000.0000.000
97A98ILE0-0.0180.00230.7270.0030.0030.0000.0000.0000.000
98A99LYS10.9540.94834.3960.0920.0920.0000.0000.0000.000
99A100HIS0-0.0370.00627.561-0.010-0.0100.0000.0000.0000.000
100A101THR00.0010.00327.2170.0080.0080.0000.0000.0000.000
101A102LEU0-0.0140.00426.512-0.010-0.0100.0000.0000.0000.000
102A103LEU00.040-0.00521.1600.0100.0100.0000.0000.0000.000
103A104SER0-0.058-0.03624.5440.0090.0090.0000.0000.0000.000
104A105ASP-1-0.723-0.86318.016-0.384-0.3840.0000.0000.0000.000
105A106ILE0-0.003-0.00621.3790.0000.0000.0000.0000.0000.000
106A107THR0-0.022-0.01219.9150.0110.0110.0000.0000.0000.000
107A108LYS10.8340.92517.9290.1960.1960.0000.0000.0000.000
108A109SER00.0000.00115.527-0.037-0.0370.0000.0000.0000.000
109A110ILE00.0600.02714.147-0.086-0.0860.0000.0000.0000.000
110A111SER0-0.022-0.05213.722-0.080-0.0800.0000.0000.0000.000
111A112LYS10.7950.89212.1140.2440.2440.0000.0000.0000.000
112A113ASP-1-0.896-0.9399.883-0.988-0.9880.0000.0000.0000.000
113A114TYR0-0.069-0.0548.865-0.321-0.3210.0000.0000.0000.000
114A115ASN0-0.089-0.0335.977-0.565-0.5650.0000.0000.0000.000
115A116VAL00.0410.0239.4440.1260.1260.0000.0000.0000.000
116A117LEU0-0.073-0.02312.9300.0930.0930.0000.0000.0000.000
117A118PHE0-0.0010.00214.3260.0100.0100.0000.0000.0000.000
118A119ASP-1-0.846-0.93516.969-0.067-0.0670.0000.0000.0000.000
119A120ASP-1-0.861-0.92116.993-0.197-0.1970.0000.0000.0000.000
120A121SER0-0.076-0.03618.3970.0080.0080.0000.0000.0000.000
121A122VAL00.0070.00020.073-0.007-0.0070.0000.0000.0000.000
122A123SER00.0490.03317.1720.0040.0040.0000.0000.0000.000
123A124LEU0-0.012-0.01114.4860.0410.0410.0000.0000.0000.000
124A125ARG10.7700.83717.9590.1130.1130.0000.0000.0000.000
125A126ALA00.0170.01615.2450.0060.0060.0000.0000.0000.000
126A127PHE00.002-0.00517.2490.0180.0180.0000.0000.0000.000
127A128VAL00.0440.01513.314-0.043-0.0430.0000.0000.0000.000
128A129LEU0-0.0200.00416.0300.0360.0360.0000.0000.0000.000
129A130ILE0-0.008-0.00314.663-0.035-0.0350.0000.0000.0000.000
130A131ASP-1-0.744-0.86316.550-0.241-0.2410.0000.0000.0000.000
131A132MET00.008-0.00118.535-0.015-0.0150.0000.0000.0000.000
132A133ASN0-0.021-0.00917.4270.0190.0190.0000.0000.0000.000
133A134GLY00.0000.00515.850-0.014-0.0140.0000.0000.0000.000
134A135ILE0-0.013-0.00511.769-0.081-0.0810.0000.0000.0000.000
135A136VAL0-0.024-0.00610.6560.0540.0540.0000.0000.0000.000
136A137GLN0-0.007-0.01611.8640.0140.0140.0000.0000.0000.000
137A138HIS0-0.027-0.02014.2630.0230.0230.0000.0000.0000.000
138A139LEU00.0130.01110.031-0.050-0.0500.0000.0000.0000.000
139A140LEU0-0.053-0.00813.8730.0630.0630.0000.0000.0000.000
140A141VAL00.0390.01712.791-0.024-0.0240.0000.0000.0000.000
141A142ASN0-0.028-0.00916.0350.0420.0420.0000.0000.0000.000
142A143ASN00.0480.01419.026-0.029-0.0290.0000.0000.0000.000
143A144LEU00.0780.01320.523-0.001-0.0010.0000.0000.0000.000
144A145ALA0-0.036-0.00323.061-0.001-0.0010.0000.0000.0000.000
145A146ILE0-0.022-0.00423.2130.0070.0070.0000.0000.0000.000
146A147GLY00.0400.02923.998-0.016-0.0160.0000.0000.0000.000
147A148ARG10.7580.86120.3520.2210.2210.0000.0000.0000.000
148A149SER00.0130.00924.7300.0050.0050.0000.0000.0000.000
149A150VAL00.0540.01125.401-0.012-0.0120.0000.0000.0000.000
150A151ASP-1-0.872-0.94727.474-0.084-0.0840.0000.0000.0000.000
151A152GLU-1-0.813-0.87222.724-0.093-0.0930.0000.0000.0000.000
152A153ILE0-0.017-0.01720.877-0.004-0.0040.0000.0000.0000.000
153A154LEU00.0220.02423.485-0.008-0.0080.0000.0000.0000.000
154A155ARG10.7980.88322.5400.0830.0830.0000.0000.0000.000
155A156ILE0-0.035-0.01519.2630.0040.0040.0000.0000.0000.000
156A157ILE00.007-0.00221.839-0.004-0.0040.0000.0000.0000.000
157A158ASP-1-0.822-0.90023.231-0.091-0.0910.0000.0000.0000.000
158A159ALA0-0.039-0.03122.3250.0070.0070.0000.0000.0000.000
159A160ILE0-0.005-0.00617.8770.0060.0060.0000.0000.0000.000
160A161GLN0-0.011-0.01321.3040.0150.0150.0000.0000.0000.000
161A162HIS0-0.085-0.04624.3370.0040.0040.0000.0000.0000.000
162A163HIS0-0.059-0.04519.4300.0020.0020.0000.0000.0000.000
163A164GLU-1-0.824-0.88721.174-0.156-0.1560.0000.0000.0000.000
164A165LYS10.8770.96123.3310.0820.0820.0000.0000.0000.000
165A166TYR0-0.041-0.03426.6870.0050.0050.0000.0000.0000.000
166A167GLY00.0120.02923.8610.0060.0060.0000.0000.0000.000
167A168ASP-1-0.861-0.92224.125-0.024-0.0240.0000.0000.0000.000
168A169VAL0-0.013-0.00420.837-0.010-0.0100.0000.0000.0000.000
169A170CYS0-0.014-0.00622.4310.0030.0030.0000.0000.0000.000
170A171PRO0-0.0170.01622.7380.0010.0010.0000.0000.0000.000
171A172ALA00.0330.00424.141-0.009-0.0090.0000.0000.0000.000
172A173ASN0-0.023-0.02725.076-0.003-0.0030.0000.0000.0000.000
173A174TRP0-0.034-0.01325.809-0.002-0.0020.0000.0000.0000.000
174A175GLN00.0880.03027.251-0.013-0.0130.0000.0000.0000.000
175A176LYS10.8930.98228.6040.0910.0910.0000.0000.0000.000
176A177GLY00.016-0.00631.7910.0000.0000.0000.0000.0000.000
177A178LYS10.8610.91829.6340.0320.0320.0000.0000.0000.000
178A179VAL00.0160.00931.652-0.003-0.0030.0000.0000.0000.000
179A180SER0-0.065-0.05127.5820.0000.0000.0000.0000.0000.000
180A181MET00.0200.01525.9230.0070.0070.0000.0000.0000.000
181A182LYS10.9570.99826.2360.0000.0000.0000.0000.0000.000
182A183PRO00.0010.01022.4500.0070.0070.0000.0000.0000.000
183A184SER00.001-0.01624.3920.0040.0040.0000.0000.0000.000
184A185GLU-1-0.901-0.96826.7240.0410.0410.0000.0000.0000.000
185A186GLU-1-0.861-0.90828.5730.0050.0050.0000.0000.0000.000
186A187GLY0-0.001-0.01629.510-0.001-0.0010.0000.0000.0000.000
187A188VAL00.035-0.01426.378-0.004-0.0040.0000.0000.0000.000
188A189ALA0-0.0470.03528.426-0.003-0.0030.0000.0000.0000.000
189A190GLN0-0.002-0.00531.488-0.002-0.0020.0000.0000.0000.000
190A191TYR00.024-0.01128.898-0.004-0.0040.0000.0000.0000.000
191A192LEU0-0.087-0.05527.987-0.002-0.0020.0000.0000.0000.000
192A193SER0-0.017-0.02031.8670.0030.0030.0000.0000.0000.000
193A194THR0-0.0550.01233.879-0.001-0.0010.0000.0000.0000.000