FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: MV88Z

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 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 193
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2103340.651745
FMO2-HF: Nuclear repulsion 2028379.654357
FMO2-HF: Total energy -74960.997388
FMO2-MP2: Total energy -75181.882036


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.
-4.227-0.2620.051-1.959-2.0570.004
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 : 0.018 / q_NPA : 0.005
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].
3A4TYR00.026-0.0063.647-2.3861.026-0.016-1.816-1.5800.004
4A5VAL0-0.020-0.0126.2380.4160.4160.0000.0000.0000.000
5A6GLY0-0.0090.0037.4170.0870.0870.0000.0000.0000.000
6A7LYS10.8640.9282.930-0.0130.5400.067-0.143-0.4770.000
7A8GLU-1-0.919-0.9548.625-0.529-0.5290.0000.0000.0000.000
8A9ALA0-0.017-0.0109.247-0.215-0.2150.0000.0000.0000.000
9A10PRO00.0140.0178.5540.0900.0900.0000.0000.0000.000
10A11PHE00.0150.00111.1490.1030.1030.0000.0000.0000.000
11A12PHE00.0340.01514.452-0.019-0.0190.0000.0000.0000.000
12A13LYS10.9430.96317.0580.2650.2650.0000.0000.0000.000
13A14ALA00.0010.00920.703-0.005-0.0050.0000.0000.0000.000
14A15GLU-1-0.836-0.90422.866-0.158-0.1580.0000.0000.0000.000
15A16ALA0-0.010-0.01225.885-0.012-0.0120.0000.0000.0000.000
16A17VAL0-0.064-0.02627.9590.0140.0140.0000.0000.0000.000
17A18PHE00.0590.03729.148-0.008-0.0080.0000.0000.0000.000
18A19GLY00.0640.02832.3060.0050.0050.0000.0000.0000.000
19A20ASP-1-0.895-0.93434.538-0.106-0.1060.0000.0000.0000.000
20A21ASN0-0.088-0.05935.6760.0020.0020.0000.0000.0000.000
21A22SER0-0.022-0.00535.9850.0000.0000.0000.0000.0000.000
22A23PHE0-0.041-0.04232.543-0.006-0.0060.0000.0000.0000.000
23A24GLY00.015-0.00331.0120.0070.0070.0000.0000.0000.000
24A25GLU-1-0.969-0.98025.701-0.197-0.1970.0000.0000.0000.000
25A26VAL0-0.0120.00822.9650.0080.0080.0000.0000.0000.000
26A27ASN0-0.027-0.02621.022-0.026-0.0260.0000.0000.0000.000
27A28LEU00.0270.02015.3720.0270.0270.0000.0000.0000.000
28A29THR00.0700.02319.5810.0040.0040.0000.0000.0000.000
29A30GLN0-0.039-0.00520.9570.0150.0150.0000.0000.0000.000
30A31PHE0-0.003-0.01821.8500.0220.0220.0000.0000.0000.000
31A32ILE00.0100.03117.7170.0100.0100.0000.0000.0000.000
32A33GLY0-0.005-0.00821.4420.0180.0180.0000.0000.0000.000
33A34LYS10.8490.92923.8090.1650.1650.0000.0000.0000.000
34A35LYS10.8890.93624.4480.1770.1770.0000.0000.0000.000
35A36TYR0-0.032-0.02620.756-0.015-0.0150.0000.0000.0000.000
36A37VAL0-0.0010.00919.4310.0150.0150.0000.0000.0000.000
37A38LEU0-0.0010.00819.479-0.026-0.0260.0000.0000.0000.000
38A39LEU00.0070.00616.4200.0240.0240.0000.0000.0000.000
39A40TYR0-0.055-0.05618.689-0.021-0.0210.0000.0000.0000.000
40A41PHE00.0050.00615.3980.0170.0170.0000.0000.0000.000
41A42TYR0-0.064-0.05319.8130.0200.0200.0000.0000.0000.000
42A43PRO00.004-0.00121.929-0.002-0.0020.0000.0000.0000.000
43A44LEU00.009-0.01522.877-0.001-0.0010.0000.0000.0000.000
44A45ASP-1-0.709-0.83426.309-0.159-0.1590.0000.0000.0000.000
45A46PHE0-0.041-0.02229.4490.0050.0050.0000.0000.0000.000
46A47THR0-0.017-0.01028.4260.0040.0040.0000.0000.0000.000
47A48PHE00.001-0.01929.9350.0040.0040.0000.0000.0000.000
48A49VAL00.0240.02426.7850.0020.0020.0000.0000.0000.000
49A50CYS0-0.0350.03626.528-0.005-0.0050.0000.0000.0000.000
50A51PRO00.0540.04427.999-0.005-0.0050.0000.0000.0000.000
51A52SER0-0.068-0.05530.3190.0030.0030.0000.0000.0000.000
52A53GLU-1-0.740-0.88625.084-0.183-0.1830.0000.0000.0000.000
53A54ILE00.0130.01427.5370.0000.0000.0000.0000.0000.000
54A55ILE0-0.014-0.01429.4380.0030.0030.0000.0000.0000.000
55A56ALA0-0.045-0.02030.4980.0050.0050.0000.0000.0000.000
56A57LEU00.007-0.00225.4890.0030.0030.0000.0000.0000.000
57A58ASP-1-0.801-0.89429.844-0.124-0.1240.0000.0000.0000.000
58A59LYS10.9230.95932.4940.0940.0940.0000.0000.0000.000
59A60ALA00.0050.01831.0710.0060.0060.0000.0000.0000.000
60A61LEU00.013-0.00830.396-0.004-0.0040.0000.0000.0000.000
61A62ASP-1-0.868-0.93831.997-0.100-0.1000.0000.0000.0000.000
62A63ALA0-0.0160.00331.4450.0020.0020.0000.0000.0000.000
63A64PHE0-0.0130.00525.628-0.004-0.0040.0000.0000.0000.000
64A65HIS00.0090.00128.963-0.009-0.0090.0000.0000.0000.000
65A66GLU-1-0.970-0.97431.543-0.086-0.0860.0000.0000.0000.000
66A67ARG10.7730.87526.9260.1150.1150.0000.0000.0000.000
67A68ASN00.0000.00526.957-0.007-0.0070.0000.0000.0000.000
68A69VAL0-0.011-0.01123.953-0.012-0.0120.0000.0000.0000.000
69A70GLU-1-0.959-0.99224.555-0.166-0.1660.0000.0000.0000.000
70A71LEU0-0.0200.00224.048-0.024-0.0240.0000.0000.0000.000
71A72LEU0-0.005-0.01321.5010.0100.0100.0000.0000.0000.000
72A73GLY00.0580.03722.594-0.022-0.0220.0000.0000.0000.000
73A74CYS0-0.075-0.02219.0600.0080.0080.0000.0000.0000.000
74A75SER00.0370.01521.604-0.008-0.0080.0000.0000.0000.000
75A76VAL00.0560.02120.291-0.004-0.0040.0000.0000.0000.000
76A77ASP-1-0.805-0.87422.770-0.163-0.1630.0000.0000.0000.000
77A78SER00.0440.02526.205-0.009-0.0090.0000.0000.0000.000
78A79LYS10.9240.94828.5650.1500.1500.0000.0000.0000.000
79A80TYR00.001-0.01730.1130.0050.0050.0000.0000.0000.000
80A81THR0-0.0020.00430.3990.0100.0100.0000.0000.0000.000
81A82HIS10.8270.89226.0330.1950.1950.0000.0000.0000.000
82A83LEU0-0.0060.00831.5740.0070.0070.0000.0000.0000.000
83A84ALA00.0040.00035.0060.0070.0070.0000.0000.0000.000
84A85TRP00.0240.02728.9370.0050.0050.0000.0000.0000.000
85A86LYS10.8950.95233.3600.1310.1310.0000.0000.0000.000
86A87LYS10.8920.95436.2610.0920.0920.0000.0000.0000.000
87A88THR0-0.039-0.01937.7860.0070.0070.0000.0000.0000.000
88A89PRO00.010-0.00239.000-0.003-0.0030.0000.0000.0000.000
89A90LEU00.0770.02937.6030.0000.0000.0000.0000.0000.000
90A91ALA0-0.027-0.00539.7790.0000.0000.0000.0000.0000.000
91A92LYS10.8780.93541.3820.0690.0690.0000.0000.0000.000
92A93GLY00.0360.03137.409-0.001-0.0010.0000.0000.0000.000
93A94GLY0-0.016-0.00735.710-0.006-0.0060.0000.0000.0000.000
94A95ILE00.0020.00331.5140.0020.0020.0000.0000.0000.000
95A96GLY0-0.0080.00735.1280.0010.0010.0000.0000.0000.000
96A97ASN0-0.008-0.02336.456-0.009-0.0090.0000.0000.0000.000
97A98ILE0-0.023-0.00330.9310.0030.0030.0000.0000.0000.000
98A99LYS10.9680.96134.5750.1000.1000.0000.0000.0000.000
99A100HIS0-0.0440.01427.678-0.010-0.0100.0000.0000.0000.000
100A101THR00.0060.00426.9670.0080.0080.0000.0000.0000.000
101A102LEU0-0.020-0.00426.578-0.011-0.0110.0000.0000.0000.000
102A103LEU00.041-0.00521.1010.0120.0120.0000.0000.0000.000
103A104SER0-0.058-0.02924.5900.0060.0060.0000.0000.0000.000
104A105ASP-1-0.711-0.87018.137-0.418-0.4180.0000.0000.0000.000
105A106ILE0-0.003-0.00321.460-0.004-0.0040.0000.0000.0000.000
106A107THR0-0.027-0.01019.6800.0000.0000.0000.0000.0000.000
107A108LYS10.8220.91217.8440.2370.2370.0000.0000.0000.000
108A109SER0-0.014-0.01515.379-0.048-0.0480.0000.0000.0000.000
109A110ILE00.0800.04213.944-0.086-0.0860.0000.0000.0000.000
110A111SER0-0.024-0.04613.763-0.083-0.0830.0000.0000.0000.000
111A112LYS10.8870.94512.1570.3080.3080.0000.0000.0000.000
112A113ASP-1-0.895-0.9359.664-1.008-1.0080.0000.0000.0000.000
113A114TYR0-0.055-0.0348.781-0.307-0.3070.0000.0000.0000.000
114A115ASN0-0.059-0.0246.347-0.482-0.4820.0000.0000.0000.000
115A116VAL00.0280.0159.4620.1160.1160.0000.0000.0000.000
116A117LEU0-0.052-0.02112.9140.1080.1080.0000.0000.0000.000
117A118PHE0-0.0050.00014.242-0.008-0.0080.0000.0000.0000.000
118A119ASP-1-0.845-0.93116.872-0.134-0.1340.0000.0000.0000.000
119A120ASP-1-0.952-0.96416.717-0.227-0.2270.0000.0000.0000.000
120A121SER0-0.096-0.05118.3230.0190.0190.0000.0000.0000.000
121A122VAL0-0.006-0.00920.013-0.002-0.0020.0000.0000.0000.000
122A123SER00.0330.02517.181-0.005-0.0050.0000.0000.0000.000
123A124LEU00.003-0.00714.4720.0470.0470.0000.0000.0000.000
124A125ARG10.7940.86117.9280.1570.1570.0000.0000.0000.000
125A126ALA00.0200.01615.3850.0030.0030.0000.0000.0000.000
126A127PHE0-0.023-0.01017.2790.0280.0280.0000.0000.0000.000
127A128VAL00.0380.01913.477-0.048-0.0480.0000.0000.0000.000
128A129LEU0-0.0210.00115.8950.0410.0410.0000.0000.0000.000
129A130ILE0-0.009-0.00414.824-0.036-0.0360.0000.0000.0000.000
130A131ASP-1-0.750-0.87516.496-0.242-0.2420.0000.0000.0000.000
131A132MET00.002-0.00618.548-0.013-0.0130.0000.0000.0000.000
132A133ASN0-0.0040.00117.5840.0170.0170.0000.0000.0000.000
133A134GLY0-0.0100.00116.135-0.009-0.0090.0000.0000.0000.000
134A135ILE0-0.017-0.00911.583-0.077-0.0770.0000.0000.0000.000
135A136VAL0-0.025-0.00410.4640.0490.0490.0000.0000.0000.000
136A137GLN0-0.011-0.01011.7500.0140.0140.0000.0000.0000.000
137A138HIS0-0.024-0.01814.1790.0170.0170.0000.0000.0000.000
138A139LEU00.0210.0149.944-0.049-0.0490.0000.0000.0000.000
139A140LEU0-0.050-0.00613.8730.0610.0610.0000.0000.0000.000
140A141VAL00.0340.01512.739-0.022-0.0220.0000.0000.0000.000
141A142ASN0-0.0140.00316.0660.0370.0370.0000.0000.0000.000
142A143ASN00.0650.01618.960-0.035-0.0350.0000.0000.0000.000
143A144LEU00.0700.01420.4170.0050.0050.0000.0000.0000.000
144A145ALA0-0.0440.00322.9770.0030.0030.0000.0000.0000.000
145A146ILE0-0.029-0.00623.2450.0110.0110.0000.0000.0000.000
146A147GLY00.0350.01823.960-0.018-0.0180.0000.0000.0000.000
147A148ARG10.7850.88720.2780.2610.2610.0000.0000.0000.000
148A149SER00.0070.00124.7480.0090.0090.0000.0000.0000.000
149A150VAL00.0560.01325.411-0.013-0.0130.0000.0000.0000.000
150A151ASP-1-0.877-0.94727.412-0.098-0.0980.0000.0000.0000.000
151A152GLU-1-0.868-0.92922.751-0.119-0.1190.0000.0000.0000.000
152A153ILE00.001-0.00521.060-0.004-0.0040.0000.0000.0000.000
153A154LEU00.0140.00923.429-0.006-0.0060.0000.0000.0000.000
154A155ARG10.8610.95222.5550.1050.1050.0000.0000.0000.000
155A156ILE0-0.045-0.02019.1510.0060.0060.0000.0000.0000.000
156A157ILE0-0.009-0.01121.803-0.002-0.0020.0000.0000.0000.000
157A158ASP-1-0.861-0.92623.158-0.101-0.1010.0000.0000.0000.000
158A159ALA0-0.049-0.04122.3150.0090.0090.0000.0000.0000.000
159A160ILE00.002-0.00217.9850.0080.0080.0000.0000.0000.000
160A161GLN0-0.013-0.02021.2650.0170.0170.0000.0000.0000.000
161A162HIS0-0.075-0.03324.2680.0060.0060.0000.0000.0000.000
162A163HIS0-0.044-0.03819.6420.0040.0040.0000.0000.0000.000
163A164GLU-1-0.826-0.88820.730-0.157-0.1570.0000.0000.0000.000
164A165LYS10.8760.95823.2750.0820.0820.0000.0000.0000.000
165A166TYR0-0.047-0.03326.6760.0050.0050.0000.0000.0000.000
166A167GLY00.0110.02823.8720.0070.0070.0000.0000.0000.000
167A168ASP-1-0.890-0.93924.175-0.024-0.0240.0000.0000.0000.000
168A169VAL0-0.013-0.00620.822-0.011-0.0110.0000.0000.0000.000
169A170CYS0-0.003-0.00622.5110.0030.0030.0000.0000.0000.000
170A171PRO0-0.0160.02022.8430.0000.0000.0000.0000.0000.000
171A172ALA00.030-0.00224.273-0.011-0.0110.0000.0000.0000.000
172A173ASN0-0.023-0.02225.212-0.004-0.0040.0000.0000.0000.000
173A174TRP0-0.053-0.01725.872-0.001-0.0010.0000.0000.0000.000
174A175GLN00.1010.03327.297-0.014-0.0140.0000.0000.0000.000
175A176LYS10.9781.03528.9460.0940.0940.0000.0000.0000.000
176A177GLY00.016-0.00431.800-0.001-0.0010.0000.0000.0000.000
177A178LYS10.8690.91830.1580.0430.0430.0000.0000.0000.000
178A179VAL00.0190.01831.710-0.003-0.0030.0000.0000.0000.000
179A180SER0-0.059-0.04827.649-0.001-0.0010.0000.0000.0000.000
180A181MET00.0270.01426.1500.0070.0070.0000.0000.0000.000
181A182LYS11.0401.04526.3340.0010.0010.0000.0000.0000.000
182A183PRO00.0160.01422.6380.0070.0070.0000.0000.0000.000
183A184SER0-0.022-0.02024.5220.0060.0060.0000.0000.0000.000
184A185GLU-1-0.899-0.97426.8820.0460.0460.0000.0000.0000.000
185A186GLU-1-0.926-0.94728.7680.0130.0130.0000.0000.0000.000
186A187GLY0-0.018-0.02329.678-0.001-0.0010.0000.0000.0000.000
187A188VAL00.030-0.01626.595-0.005-0.0050.0000.0000.0000.000
188A189ALA0-0.0460.03428.610-0.004-0.0040.0000.0000.0000.000
189A190GLN00.0110.00031.688-0.003-0.0030.0000.0000.0000.000
190A191TYR00.014-0.01529.333-0.005-0.0050.0000.0000.0000.000
191A192LEU0-0.088-0.06028.060-0.002-0.0020.0000.0000.0000.000
192A193SER0-0.006-0.01432.0620.0020.0020.0000.0000.0000.000
193A194THR0-0.0710.00733.915-0.001-0.0010.0000.0000.0000.000