Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 89G9Y

Calculation Name: 1OI4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1OI4

Chain ID: A

ChEMBL ID:

UniProt ID: P45470

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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2158910.467838
FMO2-HF: Nuclear repulsion 2086023.324264
FMO2-HF: Total energy -72887.143573
FMO2-MP2: Total energy -73105.618735


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:SER)


Summations of interaction energy for fragment #1(A:2:SER)
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.
-23.79-30.78924.77-10.539-7.233-0.069
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : -0.025
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].
3A4TYR0-0.037-0.0302.685-7.188-3.2470.252-2.300-1.894-0.006
4A5HIS0-0.027-0.0155.3280.9000.980-0.001-0.004-0.0750.000
5A6HIS0-0.038-0.0207.9150.0680.0680.0000.0000.0000.000
6A7HIS00.0030.0029.6660.1470.1470.0000.0000.0000.000
7A8HIS0-0.0050.00611.3620.1100.1100.0000.0000.0000.000
8A9HIS0-0.021-0.02214.758-0.110-0.1100.0000.0000.0000.000
9A10HIS10.8000.88116.6720.6460.6460.0000.0000.0000.000
10A11LEU00.0310.01219.551-0.018-0.0180.0000.0000.0000.000
11A12GLU-1-0.844-0.93417.847-0.418-0.4180.0000.0000.0000.000
12A13SER0-0.058-0.03321.0330.0300.0300.0000.0000.0000.000
13A14THR00.0300.01121.8040.0230.0230.0000.0000.0000.000
14A15SER0-0.0270.00023.5860.0320.0320.0000.0000.0000.000
15A16LEU00.036-0.00325.2200.0080.0080.0000.0000.0000.000
16A17TYR0-0.019-0.01126.9530.0110.0110.0000.0000.0000.000
17A18LYS10.8880.96523.8830.3530.3530.0000.0000.0000.000
18A19LYS10.9520.96828.0530.1580.1580.0000.0000.0000.000
19A20ALA0-0.003-0.00231.5280.0030.0030.0000.0000.0000.000
20A21GLY00.0170.01730.1120.0040.0040.0000.0000.0000.000
21A22LEU0-0.022-0.01931.1830.0010.0010.0000.0000.0000.000
22A23SER0-0.032-0.00426.0360.0090.0090.0000.0000.0000.000
23A24LYS10.9460.99426.2500.2320.2320.0000.0000.0000.000
24A25LYS10.8310.90525.0270.2780.2780.0000.0000.0000.000
25A26ILE00.0110.01320.4530.0200.0200.0000.0000.0000.000
26A27ALA00.0130.01221.970-0.041-0.0410.0000.0000.0000.000
27A28VAL00.006-0.00316.924-0.020-0.0200.0000.0000.0000.000
28A29LEU0-0.0090.01520.378-0.001-0.0010.0000.0000.0000.000
29A30ILE0-0.038-0.02615.158-0.027-0.0270.0000.0000.0000.000
30A31THR0-0.009-0.02417.7590.0450.0450.0000.0000.0000.000
31A32ASP-1-0.846-0.94515.906-0.889-0.8890.0000.0000.0000.000
32A33GLU-1-0.835-0.90113.506-0.605-0.6050.0000.0000.0000.000
33A34PHE0-0.0170.01510.0870.0440.0440.0000.0000.0000.000
34A35GLU-1-0.864-0.9238.631-1.883-1.8830.0000.0000.0000.000
35A36ASP-1-0.737-0.8756.149-3.303-3.3030.0000.0000.0000.000
36A37SER00.0630.0155.9550.3290.3290.0000.0000.0000.000
37A38GLU-1-0.780-0.9177.572-0.538-0.5380.0000.0000.0000.000
38A39PHE0-0.022-0.00310.3070.2450.2450.0000.0000.0000.000
39A40THR00.017-0.0076.5770.3560.3560.0000.0000.0000.000
40A41SER00.0090.0279.3090.2620.2620.0000.0000.0000.000
41A42PRO00.0230.00910.6120.1520.1520.0000.0000.0000.000
42A43ALA00.0160.01913.0570.1180.1180.0000.0000.0000.000
43A44ASP-1-0.864-0.92910.565-1.330-1.3300.0000.0000.0000.000
44A45GLU-1-0.953-0.98213.788-0.284-0.2840.0000.0000.0000.000
45A46PHE00.003-0.01316.1390.0790.0790.0000.0000.0000.000
46A47ARG10.9270.98014.9420.7480.7480.0000.0000.0000.000
47A48LYS10.8830.94212.8980.6500.6500.0000.0000.0000.000
48A49ALA0-0.0180.01218.8980.0530.0530.0000.0000.0000.000
49A50GLY0-0.030-0.00721.6900.0340.0340.0000.0000.0000.000
50A51HIS0-0.010-0.01321.7790.0240.0240.0000.0000.0000.000
51A52GLU-1-0.992-0.99921.483-0.439-0.4390.0000.0000.0000.000
52A53VAL00.0080.00117.2460.0040.0040.0000.0000.0000.000
53A54ILE0-0.023-0.01720.482-0.003-0.0030.0000.0000.0000.000
54A55THR0-0.004-0.01017.0100.0350.0350.0000.0000.0000.000
55A56ILE0-0.026-0.01220.1930.0440.0440.0000.0000.0000.000
56A57GLU-1-0.726-0.83820.727-0.575-0.5750.0000.0000.0000.000
57A58LYS10.9100.92823.2500.4590.4590.0000.0000.0000.000
58A59GLN0-0.013-0.00124.6180.0120.0120.0000.0000.0000.000
59A60ALA00.0340.02824.014-0.042-0.0420.0000.0000.0000.000
60A61GLY0-0.021-0.02123.1290.0260.0260.0000.0000.0000.000
61A62LYS10.8360.93319.9510.5700.5700.0000.0000.0000.000
62A63THR0-0.035-0.02215.731-0.057-0.0570.0000.0000.0000.000
63A64VAL0-0.0200.00515.1990.0460.0460.0000.0000.0000.000
64A65LYS10.9080.94312.2480.9420.9420.0000.0000.0000.000
65A66GLY00.0360.0319.4820.2000.2000.0000.0000.0000.000
66A67LYS10.9330.96410.4690.8910.8910.0000.0000.0000.000
67A68LYS10.8100.8884.7952.3622.415-0.001-0.002-0.0500.000
68A69GLY0-0.035-0.0106.967-0.094-0.0940.0000.0000.0000.000
69A70GLU-1-0.948-0.9521.662-18.070-29.14324.520-8.233-5.214-0.063
70A71ALA00.0390.0155.739-0.106-0.1060.0000.0000.0000.000
71A72SER0-0.056-0.0347.9870.6140.6140.0000.0000.0000.000
72A73VAL00.0370.02111.750-0.021-0.0210.0000.0000.0000.000
73A74THR00.0060.00814.2270.1160.1160.0000.0000.0000.000
74A75ILE0-0.0080.01017.915-0.016-0.0160.0000.0000.0000.000
75A76ASP-1-0.781-0.85520.459-0.556-0.5560.0000.0000.0000.000
76A77LYS10.9180.95423.0210.3900.3900.0000.0000.0000.000
77A78SER0-0.0050.00724.903-0.035-0.0350.0000.0000.0000.000
78A79ILE00.016-0.01726.9360.0130.0130.0000.0000.0000.000
79A80ASP-1-0.892-0.94428.283-0.260-0.2600.0000.0000.0000.000
80A81GLU-1-0.950-0.96629.035-0.307-0.3070.0000.0000.0000.000
81A82VAL0-0.0250.00227.589-0.004-0.0040.0000.0000.0000.000
82A83THR0-0.0020.00330.7940.0090.0090.0000.0000.0000.000
83A84PRO00.0690.01130.101-0.011-0.0110.0000.0000.0000.000
84A85ALA0-0.022-0.02331.150-0.002-0.0020.0000.0000.0000.000
85A86GLU-1-0.871-0.93629.622-0.288-0.2880.0000.0000.0000.000
86A87PHE0-0.0010.00226.070-0.013-0.0130.0000.0000.0000.000
87A88ASP-1-0.816-0.89427.357-0.246-0.2460.0000.0000.0000.000
88A89ALA0-0.019-0.01824.3450.0140.0140.0000.0000.0000.000
89A90LEU0-0.0160.01122.693-0.016-0.0160.0000.0000.0000.000
90A91LEU0-0.021-0.00315.5800.0160.0160.0000.0000.0000.000
91A92LEU0-0.026-0.03019.459-0.015-0.0150.0000.0000.0000.000
92A93PRO00.0170.00514.1340.0260.0260.0000.0000.0000.000
93A94GLY00.0450.00814.6930.0740.0740.0000.0000.0000.000
94A95GLY0-0.020-0.01614.007-0.087-0.0870.0000.0000.0000.000
95A96HIS0-0.002-0.02314.6620.0940.0940.0000.0000.0000.000
96A97SER00.0430.04116.4350.0510.0510.0000.0000.0000.000
97A98PRO00.001-0.01317.6920.0610.0610.0000.0000.0000.000
98A99ASP-1-0.955-0.97220.713-0.337-0.3370.0000.0000.0000.000
99A100TYR0-0.071-0.05918.5080.0620.0620.0000.0000.0000.000
100A101LEU0-0.027-0.01320.6660.0330.0330.0000.0000.0000.000
101A102ARG10.8430.92424.1440.3420.3420.0000.0000.0000.000
102A103GLY00.0060.01226.5210.0270.0270.0000.0000.0000.000
103A104ASP-1-0.812-0.89227.853-0.292-0.2920.0000.0000.0000.000
104A105ASN00.032-0.00829.547-0.010-0.0100.0000.0000.0000.000
105A106ARG10.8040.89529.4320.3060.3060.0000.0000.0000.000
106A107PHE00.0620.01824.352-0.004-0.0040.0000.0000.0000.000
107A108VAL0-0.0250.01127.937-0.003-0.0030.0000.0000.0000.000
108A109THR0-0.026-0.02029.7450.0130.0130.0000.0000.0000.000
109A110PHE00.0290.02526.3570.0070.0070.0000.0000.0000.000
110A111THR00.001-0.01626.670-0.006-0.0060.0000.0000.0000.000
111A112ARG10.9170.95928.5360.2170.2170.0000.0000.0000.000
112A113ASP-1-0.913-0.95832.015-0.202-0.2020.0000.0000.0000.000
113A114PHE0-0.033-0.00127.6320.0070.0070.0000.0000.0000.000
114A115VAL00.0030.04628.8840.0090.0090.0000.0000.0000.000
115A116ASN0-0.013-0.01231.1030.0140.0140.0000.0000.0000.000
116A117SER0-0.095-0.07632.1570.0110.0110.0000.0000.0000.000
117A118GLY0-0.014-0.01533.5130.0080.0080.0000.0000.0000.000
118A119LYS10.8030.91329.5700.2450.2450.0000.0000.0000.000
119A120PRO00.0050.00126.282-0.004-0.0040.0000.0000.0000.000
120A121VAL0-0.0030.00424.204-0.019-0.0190.0000.0000.0000.000
121A122PHE00.0110.00319.9900.0200.0200.0000.0000.0000.000
122A123ALA00.0080.00219.964-0.051-0.0510.0000.0000.0000.000
123A124ILE00.0100.00914.2480.0520.0520.0000.0000.0000.000
124A125CYS0-0.0210.00214.207-0.016-0.0160.0000.0000.0000.000
125A126HIS0-0.007-0.01916.7890.0770.0770.0000.0000.0000.000
126A127GLY00.0440.03518.3690.0310.0310.0000.0000.0000.000
127A128PRO00.000-0.02519.8910.0280.0280.0000.0000.0000.000
128A129GLN00.0250.01021.7780.0030.0030.0000.0000.0000.000
129A130LEU00.0260.01522.1910.0280.0280.0000.0000.0000.000
130A131LEU00.0080.00425.0130.0230.0230.0000.0000.0000.000
131A132ILE0-0.028-0.01126.9590.0220.0220.0000.0000.0000.000
132A133SER00.0030.00428.3360.0130.0130.0000.0000.0000.000
133A134ALA0-0.043-0.01729.6330.0130.0130.0000.0000.0000.000
134A135ASP-1-0.978-0.98531.444-0.159-0.1590.0000.0000.0000.000
135A136VAL0-0.0170.00030.5350.0110.0110.0000.0000.0000.000
136A137ILE00.000-0.01628.645-0.001-0.0010.0000.0000.0000.000
137A138ARG10.9591.00732.0890.1480.1480.0000.0000.0000.000
138A139GLY0-0.036-0.03035.2950.0030.0030.0000.0000.0000.000
139A140ARG10.7270.85131.8120.1940.1940.0000.0000.0000.000
140A141LYS10.9350.97330.6610.1100.1100.0000.0000.0000.000
141A142LEU00.004-0.01125.833-0.013-0.0130.0000.0000.0000.000
142A143THR0-0.008-0.01721.8370.0150.0150.0000.0000.0000.000
143A144ALA00.012-0.00421.253-0.025-0.0250.0000.0000.0000.000
144A145VAL00.0070.02017.3590.0410.0410.0000.0000.0000.000
145A146LYS10.9760.95519.6690.1530.1530.0000.0000.0000.000
146A147PRO0-0.030-0.01319.8550.0190.0190.0000.0000.0000.000
147A148ILE00.0680.04922.0560.0080.0080.0000.0000.0000.000
148A149ILE0-0.0390.00424.1290.0110.0110.0000.0000.0000.000
149A150ILE0-0.006-0.01426.4120.0100.0100.0000.0000.0000.000
150A151ASP-1-0.863-0.93427.090-0.212-0.2120.0000.0000.0000.000
151A152VAL0-0.002-0.00725.7830.0030.0030.0000.0000.0000.000
152A153LYS10.9330.96828.9590.1290.1290.0000.0000.0000.000
153A154ASN00.0020.00832.0590.0170.0170.0000.0000.0000.000
154A155ALA0-0.037-0.00931.3570.0060.0060.0000.0000.0000.000
155A156GLY0-0.025-0.03533.3430.0010.0010.0000.0000.0000.000
156A157ALA0-0.0030.03030.6540.0060.0060.0000.0000.0000.000
157A158GLU-1-0.856-0.91132.490-0.099-0.0990.0000.0000.0000.000
158A159PHE0-0.019-0.03624.878-0.004-0.0040.0000.0000.0000.000
159A160TYR0-0.064-0.04627.8630.0190.0190.0000.0000.0000.000
160A161ASP-1-0.909-0.93923.979-0.121-0.1210.0000.0000.0000.000
161A162GLN0-0.031-0.02724.2540.0290.0290.0000.0000.0000.000
162A163GLU-1-0.907-0.94919.642-0.105-0.1050.0000.0000.0000.000
163A164VAL0-0.025-0.00619.918-0.046-0.0460.0000.0000.0000.000
164A165VAL0-0.071-0.00522.3360.0310.0310.0000.0000.0000.000
165A166VAL00.0330.01225.241-0.025-0.0250.0000.0000.0000.000
166A167ASP-1-0.801-0.87527.389-0.141-0.1410.0000.0000.0000.000
167A168LYS10.8550.90630.4180.1410.1410.0000.0000.0000.000
168A169ASP-1-0.853-0.91629.978-0.149-0.1490.0000.0000.0000.000
169A170GLN00.0090.01229.1900.0060.0060.0000.0000.0000.000
170A171LEU0-0.042-0.01926.623-0.023-0.0230.0000.0000.0000.000
171A172VAL00.0390.03421.5300.0210.0210.0000.0000.0000.000
172A173THR0-0.0030.00721.499-0.026-0.0260.0000.0000.0000.000
173A174SER00.043-0.01417.8910.0250.0250.0000.0000.0000.000
174A175ARG10.7730.87218.6050.1140.1140.0000.0000.0000.000
175A176THR00.003-0.01313.962-0.026-0.0260.0000.0000.0000.000
176A177PRO00.0690.0239.3980.0620.0620.0000.0000.0000.000
177A178ASP-1-0.896-0.94011.5480.0420.0420.0000.0000.0000.000
178A179ASP-1-0.762-0.86913.228-0.155-0.1550.0000.0000.0000.000
179A180LEU0-0.030-0.0179.948-0.004-0.0040.0000.0000.0000.000
180A181PRO00.0060.00713.203-0.008-0.0080.0000.0000.0000.000
181A182ALA00.0150.01215.8530.0010.0010.0000.0000.0000.000
182A183PHE0-0.014-0.02216.002-0.006-0.0060.0000.0000.0000.000
183A184ASN00.033-0.01013.287-0.028-0.0280.0000.0000.0000.000
184A185ARG10.8820.95317.7290.1520.1520.0000.0000.0000.000
185A186GLU-1-0.814-0.90520.750-0.157-0.1570.0000.0000.0000.000
186A187ALA00.0210.01919.8830.0080.0080.0000.0000.0000.000
187A188LEU0-0.019-0.02118.9910.0110.0110.0000.0000.0000.000
188A189ARG10.8050.90222.5150.1830.1830.0000.0000.0000.000
189A190LEU0-0.050-0.02425.4260.0130.0130.0000.0000.0000.000
190A191LEU0-0.0210.00622.2520.0030.0030.0000.0000.0000.000
191A192GLY0-0.055-0.01926.2980.0070.0070.0000.0000.0000.000