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: QVNMY

Calculation Name: 2I9I-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2I9I

Chain ID: A

ChEMBL ID:

UniProt ID: O25234

Base Structure: X-ray

Registration Date: 2023-09-22

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 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2608224.330758
FMO2-HF: Nuclear repulsion 2518672.207454
FMO2-HF: Total energy -89552.123304
FMO2-MP2: Total energy -89815.340932


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:51:GLU)


Summations of interaction energy for fragment #1(A:51: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.
-173.848-173.47438.427-20.016-18.7830.169
Interaction energy analysis for fragmet #1(A:51:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.747 / q_NPA : -0.855
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].
3A53MET0-0.044-0.0103.5181.1123.996-0.008-1.173-1.7030.006
4A54LYS10.9780.9865.953-25.034-25.0340.0000.0000.0000.000
5A55THR00.015-0.0099.6071.5861.5860.0000.0000.0000.000
6A56SER0-0.027-0.00512.138-1.114-1.1140.0000.0000.0000.000
7A57SER00.0460.03015.6950.0600.0600.0000.0000.0000.000
8A58GLU-1-0.953-0.97918.89014.00414.0040.0000.0000.0000.000
9A59HIS0-0.051-0.04516.056-1.216-1.2160.0000.0000.0000.000
10A60VAL0-0.0040.01316.2810.9270.9270.0000.0000.0000.000
11A61THR0-0.063-0.05310.8770.0930.0930.0000.0000.0000.000
12A62PRO00.0050.00014.1620.0050.0050.0000.0000.0000.000
13A63LEU0-0.028-0.01113.6471.5201.5200.0000.0000.0000.000
14A64ASP-1-0.946-0.97412.37021.18521.1850.0000.0000.0000.000
15A65PHE0-0.056-0.02612.4521.3091.3090.0000.0000.0000.000
16A66ASN00.0400.00313.860-2.334-2.3340.0000.0000.0000.000
17A67TYR0-0.0040.0059.9361.4281.4280.0000.0000.0000.000
18A68PRO0-0.013-0.00714.008-1.467-1.4670.0000.0000.0000.000
19A69ILE00.0140.01816.0190.7360.7360.0000.0000.0000.000
20A70HIS0-0.0020.00017.589-1.424-1.4240.0000.0000.0000.000
21A71ILE0-0.014-0.00620.7070.0040.0040.0000.0000.0000.000
22A72VAL00.000-0.00323.565-0.233-0.2330.0000.0000.0000.000
23A73GLN0-0.077-0.04527.2570.2560.2560.0000.0000.0000.000
24A74ALA00.0310.02829.517-0.356-0.3560.0000.0000.0000.000
25A75PRO0-0.005-0.01031.273-0.083-0.0830.0000.0000.0000.000
26A76GLN00.0170.00733.1300.0940.0940.0000.0000.0000.000
27A77ASN00.0390.01631.729-0.402-0.4020.0000.0000.0000.000
28A78HIS0-0.015-0.01135.869-0.024-0.0240.0000.0000.0000.000
29A79HIS10.8190.90633.863-9.153-9.1530.0000.0000.0000.000
30A80VAL0-0.013-0.00233.5440.1440.1440.0000.0000.0000.000
31A81VAL00.0190.01028.053-0.116-0.1160.0000.0000.0000.000
32A82GLY00.0230.01330.372-0.122-0.1220.0000.0000.0000.000
33A83ILE0-0.014-0.01024.2190.3420.3420.0000.0000.0000.000
34A84LEU0-0.020-0.00826.657-0.388-0.3880.0000.0000.0000.000
35A85THR0-0.014-0.00525.4950.4910.4910.0000.0000.0000.000
36A86PRO0-0.0120.00321.096-0.097-0.0970.0000.0000.0000.000
37A87ARG10.9250.95923.004-12.006-12.0060.0000.0000.0000.000
38A88ILE0-0.0040.00316.9050.2090.2090.0000.0000.0000.000
39A89GLN0-0.028-0.00120.228-0.579-0.5790.0000.0000.0000.000
40A90VAL00.0080.00017.2860.8330.8330.0000.0000.0000.000
41A91SER00.025-0.00716.635-0.597-0.5970.0000.0000.0000.000
42A92ASP-1-0.843-0.93618.90813.00513.0050.0000.0000.0000.000
43A93ASN0-0.040-0.03215.607-0.045-0.0450.0000.0000.0000.000
44A94LEU0-0.006-0.01613.5850.6120.6120.0000.0000.0000.000
45A95LYS10.8920.94617.746-12.621-12.6210.0000.0000.0000.000
46A96PRO0-0.0050.00820.037-0.260-0.2600.0000.0000.0000.000
47A97TYR0-0.010-0.00316.8670.1510.1510.0000.0000.0000.000
48A98ILE0-0.023-0.00417.5060.5910.5910.0000.0000.0000.000
49A99ASP-1-0.831-0.91519.35113.53213.5320.0000.0000.0000.000
50A100LYS10.9690.99317.486-17.361-17.3610.0000.0000.0000.000
51A101PHE0-0.056-0.02411.9540.3210.3210.0000.0000.0000.000
52A102GLN00.048-0.00917.2950.7250.7250.0000.0000.0000.000
53A103ASP-1-0.867-0.92919.76513.47113.4710.0000.0000.0000.000
54A104ALA0-0.053-0.02317.597-0.382-0.3820.0000.0000.0000.000
55A105LEU00.0170.00514.2700.0420.0420.0000.0000.0000.000
56A106ILE0-0.0130.00018.069-0.275-0.2750.0000.0000.0000.000
57A107ASN00.0220.02921.670-0.949-0.9490.0000.0000.0000.000
58A108GLN00.0550.03116.4790.7100.7100.0000.0000.0000.000
59A109ILE00.0410.01817.886-0.266-0.2660.0000.0000.0000.000
60A110GLN0-0.0060.00120.819-0.280-0.2800.0000.0000.0000.000
61A111THR0-0.021-0.02421.821-0.308-0.3080.0000.0000.0000.000
62A112ILE0-0.0140.00318.104-0.290-0.2900.0000.0000.0000.000
63A113PHE0-0.002-0.01122.750-0.434-0.4340.0000.0000.0000.000
64A114GLU-1-0.836-0.91025.88811.06811.0680.0000.0000.0000.000
65A115LYS10.9270.97624.493-12.603-12.6030.0000.0000.0000.000
66A116ARG10.8640.92621.239-14.353-14.3530.0000.0000.0000.000
67A117GLY0-0.020-0.00227.717-0.287-0.2870.0000.0000.0000.000
68A118TYR0-0.092-0.07428.566-0.326-0.3260.0000.0000.0000.000
69A119GLN00.001-0.00930.8860.1180.1180.0000.0000.0000.000
70A120VAL00.0080.00127.4150.1190.1190.0000.0000.0000.000
71A121LEU0-0.032-0.00730.608-0.215-0.2150.0000.0000.0000.000
72A122ARG10.8710.90925.426-12.027-12.0270.0000.0000.0000.000
73A123PHE00.0130.00430.074-0.385-0.3850.0000.0000.0000.000
74A124GLN00.0130.01330.0320.3180.3180.0000.0000.0000.000
75A125ASP-1-0.848-0.95030.1379.9549.9540.0000.0000.0000.000
76A126GLU-1-0.862-0.95931.5789.1459.1450.0000.0000.0000.000
77A127LYS10.9080.95233.106-8.885-8.8850.0000.0000.0000.000
78A128ALA0-0.0160.01334.570-0.274-0.2740.0000.0000.0000.000
79A129LEU0-0.0370.00632.908-0.122-0.1220.0000.0000.0000.000
80A130ASN00.0190.01837.081-0.208-0.2080.0000.0000.0000.000
81A131ALA00.033-0.01340.3140.0940.0940.0000.0000.0000.000
82A132GLN00.0270.01542.303-0.049-0.0490.0000.0000.0000.000
83A133ASP-1-0.807-0.90537.6028.3658.3650.0000.0000.0000.000
84A134LYS10.8580.93936.214-8.661-8.6610.0000.0000.0000.000
85A135ARG10.8970.94038.371-7.160-7.1600.0000.0000.0000.000
86A136LYS10.9150.96539.057-7.927-7.9270.0000.0000.0000.000
87A137ILE0-0.037-0.00433.2110.0860.0860.0000.0000.0000.000
88A138PHE0-0.032-0.01830.891-0.119-0.1190.0000.0000.0000.000
89A139SER00.017-0.02429.706-0.010-0.0100.0000.0000.0000.000
90A140VAL0-0.029-0.00228.6420.0030.0030.0000.0000.0000.000
91A141LEU0-0.027-0.00421.2920.1910.1910.0000.0000.0000.000
92A142ASP-1-0.879-0.94324.76212.13212.1320.0000.0000.0000.000
93A143LEU00.003-0.00117.2430.4970.4970.0000.0000.0000.000
94A144LYS10.9160.95320.592-12.805-12.8050.0000.0000.0000.000
95A145GLY00.0310.00617.6630.8850.8850.0000.0000.0000.000
96A146TRP0-0.0380.01216.462-0.989-0.9890.0000.0000.0000.000
97A147VAL00.025-0.00112.7301.0861.0860.0000.0000.0000.000
98A148GLY00.0490.01713.253-1.102-1.1020.0000.0000.0000.000
99A149ILE0-0.023-0.02210.7322.0832.0830.0000.0000.0000.000
100A150LEU0-0.045-0.01112.232-1.319-1.3190.0000.0000.0000.000
101A151GLU-1-0.778-0.87612.75117.28617.2860.0000.0000.0000.000
102A152ASP-1-0.884-0.94714.99014.31514.3150.0000.0000.0000.000
103A153LEU0-0.035-0.01810.964-0.815-0.8150.0000.0000.0000.000
104A154LYS10.9720.98913.806-12.673-12.6730.0000.0000.0000.000
105A155MET0-0.067-0.0278.8950.1810.1810.0000.0000.0000.000
106A156ASN00.0610.03513.3280.3950.3950.0000.0000.0000.000
107A157LEU0-0.011-0.02710.2651.0641.0640.0000.0000.0000.000
108A158LYS10.8460.92010.775-16.946-16.9460.0000.0000.0000.000
109A159ASP-1-0.828-0.88913.28317.04517.0450.0000.0000.0000.000
110A160PRO0-0.004-0.00614.545-0.742-0.7420.0000.0000.0000.000
111A161ASN0-0.017-0.01217.205-1.369-1.3690.0000.0000.0000.000
112A162ASN0-0.122-0.06716.484-1.172-1.1720.0000.0000.0000.000
113A163PRO00.0620.03417.6540.4950.4950.0000.0000.0000.000
114A164ASN0-0.023-0.01319.4530.0620.0620.0000.0000.0000.000
115A165LEU0-0.012-0.00515.584-0.204-0.2040.0000.0000.0000.000
116A166ASP-1-0.770-0.87515.44914.40014.4000.0000.0000.0000.000
117A167THR0-0.064-0.04810.7360.5110.5110.0000.0000.0000.000
118A168LEU00.0000.02214.088-0.436-0.4360.0000.0000.0000.000
119A169VAL0-0.050-0.0429.0430.9520.9520.0000.0000.0000.000
120A170ASP-1-0.779-0.88010.60018.63418.6340.0000.0000.0000.000
121A171GLN0-0.080-0.0555.6632.1732.1730.0000.0000.0000.000
122A172SER0-0.009-0.0246.940-1.113-1.1130.0000.0000.0000.000
123A173SER0-0.026-0.0168.826-0.124-0.1240.0000.0000.0000.000
124A174GLY00.0600.03010.908-0.382-0.3820.0000.0000.0000.000
125A175SER00.0200.01111.5821.4241.4240.0000.0000.0000.000
126A176VAL0-0.020-0.00413.557-1.218-1.2180.0000.0000.0000.000
127A177TRP0-0.017-0.01815.7660.3940.3940.0000.0000.0000.000
128A178PHE00.025-0.00315.095-0.489-0.4890.0000.0000.0000.000
129A179ASN0-0.029-0.02020.233-0.519-0.5190.0000.0000.0000.000
130A180PHE00.0070.00523.672-0.108-0.1080.0000.0000.0000.000
131A181TYR0-0.0010.00325.975-0.106-0.1060.0000.0000.0000.000
132A182GLU-1-0.666-0.82129.5768.8188.8180.0000.0000.0000.000
133A183PRO0-0.036-0.01933.151-0.077-0.0770.0000.0000.0000.000
134A184GLU-1-0.902-0.96034.7577.7707.7700.0000.0000.0000.000
135A185SER0-0.060-0.05236.381-0.077-0.0770.0000.0000.0000.000
136A186ASN0-0.036-0.01433.4740.1230.1230.0000.0000.0000.000
137A187ARG10.9350.98032.288-9.293-9.2930.0000.0000.0000.000
138A188VAL00.0410.01026.5680.1040.1040.0000.0000.0000.000
139A189VAL0-0.071-0.02327.651-0.109-0.1090.0000.0000.0000.000
140A190HIS0-0.037-0.05120.263-0.615-0.6150.0000.0000.0000.000
141A191ASP-1-0.912-0.94522.31613.48413.4840.0000.0000.0000.000
142A192PHE00.000-0.00416.0880.4210.4210.0000.0000.0000.000
143A193ALA00.0380.01916.115-0.271-0.2710.0000.0000.0000.000
144A194VAL0-0.072-0.0439.7110.8500.8500.0000.0000.0000.000
145A195GLU-1-0.874-0.9329.54321.35221.3520.0000.0000.0000.000
146A196VAL00.001-0.0117.7643.5763.5760.0000.0000.0000.000
147A197GLY00.0140.0277.8601.2601.2600.0000.0000.0000.000
148A198THR0-0.0110.0003.499-3.648-2.9990.006-0.204-0.4510.000
149A199PHE0-0.049-0.0211.958-5.696-5.55211.836-5.343-6.638-0.001
150A200GLN00.0290.0173.738-5.241-4.4700.002-0.197-0.5750.000
151A201ALA00.0020.0035.0494.0203.998-0.001-0.0110.0350.000
152A202MET0-0.018-0.0167.650-2.381-2.3810.0000.0000.0000.000
153A203THR00.0180.02810.605-0.126-0.1260.0000.0000.0000.000
154A204TYR0-0.004-0.02613.683-0.710-0.7100.0000.0000.0000.000
155A205THR0-0.042-0.02213.3100.4680.4680.0000.0000.0000.000
156A206TYR0-0.0010.00616.034-0.509-0.5090.0000.0000.0000.000
157A207LYS10.9690.98118.736-11.840-11.8400.0000.0000.0000.000
158A208HIS00.0100.01020.530-0.878-0.8780.0000.0000.0000.000
159A209ASN00.0320.01823.9210.3080.3080.0000.0000.0000.000
160A210ASN00.004-0.01226.9860.3240.3240.0000.0000.0000.000
161A211SER0-0.012-0.00528.203-0.024-0.0240.0000.0000.0000.000
162A212GLY00.0070.02527.516-0.181-0.1810.0000.0000.0000.000
163A213GLY0-0.022-0.01828.604-0.100-0.1000.0000.0000.0000.000
164A214LEU00.0130.00527.9970.3220.3220.0000.0000.0000.000
165A215ASN0-0.054-0.03525.301-0.091-0.0910.0000.0000.0000.000
166A216SER00.0370.01127.6310.1790.1790.0000.0000.0000.000
167A217SER00.0160.03621.9780.3460.3460.0000.0000.0000.000
168A218ASN0-0.028-0.02622.5410.2510.2510.0000.0000.0000.000
169A219SER00.0070.02423.598-0.179-0.1790.0000.0000.0000.000
170A220ILE0-0.021-0.02019.6350.2620.2620.0000.0000.0000.000
171A221ILE00.0020.00623.164-0.248-0.2480.0000.0000.0000.000
172A222HIS00.0880.03719.4520.5710.5710.0000.0000.0000.000
173A223GLU-1-0.889-0.93622.93311.12111.1210.0000.0000.0000.000
174A224TYR0-0.052-0.02323.779-0.218-0.2180.0000.0000.0000.000
175A225LEU0-0.045-0.02018.3780.4440.4440.0000.0000.0000.000
176A226GLU-1-0.922-0.94918.84712.93812.9380.0000.0000.0000.000
177A227LYS10.9280.96319.044-13.697-13.6970.0000.0000.0000.000
178A228ASN00.0210.00615.191-0.041-0.0410.0000.0000.0000.000
179A229LYS10.9410.95114.121-13.045-13.0450.0000.0000.0000.000
180A230GLU-1-0.919-0.94914.76416.51616.5160.0000.0000.0000.000
181A231ASP-1-0.773-0.89212.98924.26424.2640.0000.0000.0000.000
182A232ALA0-0.011-0.01110.2052.4392.4390.0000.0000.0000.000
183A233ILE00.0220.0259.8832.8752.8750.0000.0000.0000.000
184A234HIS10.8640.93011.441-17.968-17.9680.0000.0000.0000.000
185A235LYS10.8920.9357.579-29.418-29.4180.0000.0000.0000.000
186A236ILE00.0060.0036.4266.2396.2390.0000.0000.0000.000
187A237LEU00.0310.0157.7042.8792.8790.0000.0000.0000.000
188A238ASN00.006-0.0028.539-1.114-1.1140.0000.0000.0000.000
189A239ARG10.7710.8591.743-136.384-140.64326.594-13.075-9.2610.164
190A240MET0-0.0050.0015.7220.6570.694-0.0010.000-0.0350.000
191A241TYR0-0.006-0.0208.353-1.732-1.7320.0000.0000.0000.000
192A242ALA0-0.0030.0006.893-1.673-1.6730.0000.0000.0000.000
193A243VAL0-0.042-0.0194.465-1.668-1.498-0.001-0.013-0.1550.000
194A244VAL00.0290.0257.539-3.417-3.4170.0000.0000.0000.000
195A245MET0-0.0130.00111.202-2.649-2.6490.0000.0000.0000.000
196A246LYS10.9580.9887.848-37.007-37.0070.0000.0000.0000.000
197A247LYS10.9170.97211.073-24.127-24.1270.0000.0000.0000.000
198A248ALA00.0170.00512.713-1.722-1.7220.0000.0000.0000.000
199A249VAL0-0.017-0.01614.803-1.393-1.3930.0000.0000.0000.000
200A250THR0-0.094-0.04413.652-0.823-0.8230.0000.0000.0000.000
201A251GLU-1-0.841-0.91416.14216.67516.6750.0000.0000.0000.000
202A252LEU0-0.0290.01318.538-1.168-1.1680.0000.0000.0000.000
203A253THR00.0170.01020.582-0.400-0.4000.0000.0000.0000.000
204A254LYS10.9430.96922.909-10.795-10.7950.0000.0000.0000.000
205A255GLU-1-0.905-0.96625.59711.94311.9430.0000.0000.0000.000
206A256ASN0-0.053-0.01921.580-0.880-0.8800.0000.0000.0000.000
207A257ILE0-0.018-0.00524.306-0.287-0.2870.0000.0000.0000.000
208A258ASP-1-0.790-0.88927.0369.9169.9160.0000.0000.0000.000
209A259LYS10.8450.95525.060-12.756-12.7560.0000.0000.0000.000
210A260TYR00.001-0.00730.313-0.257-0.2570.0000.0000.0000.000
211A261ARG10.9880.99233.486-9.133-9.1330.0000.0000.0000.000
212A262GLU-1-0.869-0.88734.9877.6047.6040.0000.0000.0000.000
213A263ALA00.0300.00837.360-0.204-0.2040.0000.0000.0000.000
214A264ILE00.0040.00633.275-0.183-0.1830.0000.0000.0000.000
215A265ASP-1-0.811-0.89837.7338.4828.4820.0000.0000.0000.000
216A266ARG10.7860.85539.860-7.842-7.8420.0000.0000.0000.000
217A267MET0-0.076-0.03038.057-0.214-0.2140.0000.0000.0000.000
218A268LYS10.8140.92436.651-8.732-8.7320.0000.0000.0000.000
219A269GLY0-0.0370.00042.269-0.125-0.1250.0000.0000.0000.000
220A270PHE0-0.055-0.01639.366-0.107-0.1070.0000.0000.0000.000
221A271LYS10.9540.97142.809-6.691-6.6910.0000.0000.0000.000