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: NNZNQ

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 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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2161617.520393
FMO2-HF: Nuclear repulsion 2088729.404728
FMO2-HF: Total energy -72888.115665
FMO2-MP2: Total energy -73106.621729


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.
-24.375-24.31714.967-8.331-6.694-0.066
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 : -0.010 / q_NPA : -0.018
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].
3A4TYR0-0.052-0.0592.759-6.821-3.0060.177-2.215-1.778-0.004
4A5HIS0-0.028-0.0085.4130.9590.9590.0000.0000.0000.000
5A6HIS0-0.050-0.0277.9710.0670.0670.0000.0000.0000.000
6A7HIS00.0250.0159.6740.0960.0960.0000.0000.0000.000
7A8HIS0-0.056-0.02711.4420.0910.0910.0000.0000.0000.000
8A9HIS0-0.023-0.02914.745-0.102-0.1020.0000.0000.0000.000
9A10HIS10.7550.85016.6690.6540.6540.0000.0000.0000.000
10A11LEU0-0.006-0.00219.617-0.019-0.0190.0000.0000.0000.000
11A12GLU-1-0.718-0.85217.086-0.534-0.5340.0000.0000.0000.000
12A13SER0-0.017-0.01521.0830.0260.0260.0000.0000.0000.000
13A14THR0-0.011-0.00821.8770.0200.0200.0000.0000.0000.000
14A15SER0-0.027-0.00123.5440.0340.0340.0000.0000.0000.000
15A16LEU00.032-0.00225.2610.0080.0080.0000.0000.0000.000
16A17TYR0-0.019-0.00926.6020.0190.0190.0000.0000.0000.000
17A18LYS10.8580.94123.5770.3860.3860.0000.0000.0000.000
18A19LYS10.9520.97028.0900.1660.1660.0000.0000.0000.000
19A20ALA0-0.003-0.00331.5850.0040.0040.0000.0000.0000.000
20A21GLY00.0160.01730.0920.0040.0040.0000.0000.0000.000
21A22LEU0-0.024-0.02031.1620.0010.0010.0000.0000.0000.000
22A23SER0-0.039-0.01926.0040.0090.0090.0000.0000.0000.000
23A24LYS10.9080.97026.3120.2360.2360.0000.0000.0000.000
24A25LYS10.7710.86025.0310.2770.2770.0000.0000.0000.000
25A26ILE00.0110.01020.5790.0200.0200.0000.0000.0000.000
26A27ALA00.0090.01421.984-0.042-0.0420.0000.0000.0000.000
27A28VAL00.004-0.00816.981-0.021-0.0210.0000.0000.0000.000
28A29LEU0-0.0070.02120.417-0.002-0.0020.0000.0000.0000.000
29A30ILE0-0.035-0.03014.544-0.026-0.0260.0000.0000.0000.000
30A31THR0-0.018-0.03817.8490.0530.0530.0000.0000.0000.000
31A32ASP-1-0.799-0.90715.948-0.905-0.9050.0000.0000.0000.000
32A33GLU-1-0.846-0.90413.397-0.606-0.6060.0000.0000.0000.000
33A34PHE0-0.0020.01910.2710.0560.0560.0000.0000.0000.000
34A35GLU-1-0.837-0.9118.263-2.090-2.0900.0000.0000.0000.000
35A36ASP-1-0.732-0.8656.233-3.195-3.1950.0000.0000.0000.000
36A37SER00.0460.0155.9910.3050.3050.0000.0000.0000.000
37A38GLU-1-0.799-0.9327.592-0.494-0.4940.0000.0000.0000.000
38A39PHE0-0.024-0.00510.3400.2450.2450.0000.0000.0000.000
39A40THR00.010-0.0126.6120.3350.3350.0000.0000.0000.000
40A41SER00.0060.0269.1620.2590.2590.0000.0000.0000.000
41A42PRO00.0270.01010.5740.1500.1500.0000.0000.0000.000
42A43ALA00.0200.01913.1060.1120.1120.0000.0000.0000.000
43A44ASP-1-0.785-0.86210.485-1.350-1.3500.0000.0000.0000.000
44A45GLU-1-0.906-0.93213.739-0.336-0.3360.0000.0000.0000.000
45A46PHE00.000-0.01716.0780.0790.0790.0000.0000.0000.000
46A47ARG10.8360.92313.7090.8780.8780.0000.0000.0000.000
47A48LYS10.8040.88513.1340.6750.6750.0000.0000.0000.000
48A49ALA0-0.036-0.00118.8750.0560.0560.0000.0000.0000.000
49A50GLY0-0.028-0.00721.6650.0360.0360.0000.0000.0000.000
50A51HIS00.0030.00121.8080.0250.0250.0000.0000.0000.000
51A52GLU-1-0.847-0.91721.453-0.471-0.4710.0000.0000.0000.000
52A53VAL00.010-0.00317.3160.0040.0040.0000.0000.0000.000
53A54ILE0-0.031-0.01420.485-0.002-0.0020.0000.0000.0000.000
54A55THR0-0.013-0.01517.0600.0340.0340.0000.0000.0000.000
55A56ILE0-0.024-0.01220.2390.0440.0440.0000.0000.0000.000
56A57GLU-1-0.718-0.84221.203-0.593-0.5930.0000.0000.0000.000
57A58LYS10.9120.94623.3290.4830.4830.0000.0000.0000.000
58A59GLN0-0.0140.00224.7050.0140.0140.0000.0000.0000.000
59A60ALA00.0260.02424.095-0.041-0.0410.0000.0000.0000.000
60A61GLY0-0.023-0.02223.1960.0270.0270.0000.0000.0000.000
61A62LYS10.7950.89720.0330.5930.5930.0000.0000.0000.000
62A63THR0-0.026-0.02115.794-0.026-0.0260.0000.0000.0000.000
63A64VAL0-0.0370.00015.5560.0480.0480.0000.0000.0000.000
64A65LYS10.9020.92912.2191.0121.0120.0000.0000.0000.000
65A66GLY00.0260.0229.5890.2030.2030.0000.0000.0000.000
66A67LYS10.8590.91610.3920.8030.8030.0000.0000.0000.000
67A68LYS10.8030.8844.7432.5372.596-0.001-0.002-0.0550.000
68A69GLY0-0.039-0.0146.913-0.107-0.1070.0000.0000.0000.000
69A70GLU-1-0.945-0.9551.782-18.854-22.67014.791-6.114-4.861-0.062
70A71ALA00.0350.0135.728-0.122-0.1220.0000.0000.0000.000
71A72SER0-0.052-0.0258.0720.6170.6170.0000.0000.0000.000
72A73VAL00.0410.02211.835-0.028-0.0280.0000.0000.0000.000
73A74THR0-0.007-0.00214.2930.0670.0670.0000.0000.0000.000
74A75ILE0-0.0080.01717.977-0.012-0.0120.0000.0000.0000.000
75A76ASP-1-0.773-0.85220.524-0.574-0.5740.0000.0000.0000.000
76A77LYS10.8180.89323.0700.3780.3780.0000.0000.0000.000
77A78SER0-0.0040.00024.969-0.036-0.0360.0000.0000.0000.000
78A79ILE00.015-0.01326.8430.0140.0140.0000.0000.0000.000
79A80ASP-1-0.877-0.92828.351-0.269-0.2690.0000.0000.0000.000
80A81GLU-1-0.857-0.89928.957-0.315-0.3150.0000.0000.0000.000
81A82VAL0-0.029-0.00827.536-0.003-0.0030.0000.0000.0000.000
82A83THR00.0060.00530.8410.0100.0100.0000.0000.0000.000
83A84PRO00.0650.01830.134-0.011-0.0110.0000.0000.0000.000
84A85ALA0-0.018-0.01731.173-0.002-0.0020.0000.0000.0000.000
85A86GLU-1-0.838-0.90929.623-0.293-0.2930.0000.0000.0000.000
86A87PHE00.0250.01426.136-0.012-0.0120.0000.0000.0000.000
87A88ASP-1-0.812-0.89527.217-0.248-0.2480.0000.0000.0000.000
88A89ALA0-0.023-0.02224.3180.0140.0140.0000.0000.0000.000
89A90LEU0-0.0220.00822.839-0.017-0.0170.0000.0000.0000.000
90A91LEU0-0.0060.00315.6050.0170.0170.0000.0000.0000.000
91A92LEU0-0.020-0.02719.501-0.015-0.0150.0000.0000.0000.000
92A93PRO00.0200.01214.1480.0250.0250.0000.0000.0000.000
93A94GLY00.0400.01414.7470.0730.0730.0000.0000.0000.000
94A95GLY0-0.016-0.01813.949-0.088-0.0880.0000.0000.0000.000
95A96HIS00.0580.01314.6070.0920.0920.0000.0000.0000.000
96A97SER00.0290.03616.5380.0540.0540.0000.0000.0000.000
97A98PRO00.014-0.00517.8090.0570.0570.0000.0000.0000.000
98A99ASP-1-0.947-0.96620.658-0.320-0.3200.0000.0000.0000.000
99A100TYR0-0.077-0.06518.4910.0600.0600.0000.0000.0000.000
100A101LEU0-0.022-0.00820.9900.0320.0320.0000.0000.0000.000
101A102ARG10.8550.92924.2360.3330.3330.0000.0000.0000.000
102A103GLY00.0050.01226.6090.0270.0270.0000.0000.0000.000
103A104ASP-1-0.811-0.88527.933-0.294-0.2940.0000.0000.0000.000
104A105ASN00.032-0.00729.632-0.013-0.0130.0000.0000.0000.000
105A106ARG10.8090.89129.6060.3060.3060.0000.0000.0000.000
106A107PHE00.0620.01824.017-0.004-0.0040.0000.0000.0000.000
107A108VAL0-0.0310.00528.011-0.003-0.0030.0000.0000.0000.000
108A109THR0-0.039-0.03929.8160.0130.0130.0000.0000.0000.000
109A110PHE00.0290.02626.6450.0060.0060.0000.0000.0000.000
110A111THR0-0.003-0.01826.683-0.006-0.0060.0000.0000.0000.000
111A112ARG10.8850.94428.5850.2150.2150.0000.0000.0000.000
112A113ASP-1-0.905-0.95832.063-0.200-0.2000.0000.0000.0000.000
113A114PHE0-0.038-0.00627.9190.0060.0060.0000.0000.0000.000
114A115VAL00.0060.02228.8610.0090.0090.0000.0000.0000.000
115A116ASN0-0.011-0.00731.1290.0130.0130.0000.0000.0000.000
116A117SER0-0.083-0.05032.2470.0110.0110.0000.0000.0000.000
117A118GLY0-0.009-0.00733.5230.0080.0080.0000.0000.0000.000
118A119LYS10.8020.91629.6020.2440.2440.0000.0000.0000.000
119A120PRO00.0200.00626.198-0.004-0.0040.0000.0000.0000.000
120A121VAL0-0.016-0.00324.128-0.018-0.0180.0000.0000.0000.000
121A122PHE00.0200.00519.9760.0190.0190.0000.0000.0000.000
122A123ALA0-0.002-0.00319.969-0.051-0.0510.0000.0000.0000.000
123A124ILE00.0000.00914.2670.0520.0520.0000.0000.0000.000
124A125CYS0-0.0050.00414.348-0.023-0.0230.0000.0000.0000.000
125A126HIS00.022-0.00616.5240.0790.0790.0000.0000.0000.000
126A127GLY00.0360.03318.4230.0290.0290.0000.0000.0000.000
127A128PRO00.001-0.02519.9450.0270.0270.0000.0000.0000.000
128A129GLN00.0250.01122.1380.0060.0060.0000.0000.0000.000
129A130LEU00.0150.01022.2220.0280.0280.0000.0000.0000.000
130A131LEU00.0150.00624.9000.0230.0230.0000.0000.0000.000
131A132ILE0-0.028-0.01226.7380.0220.0220.0000.0000.0000.000
132A133SER00.0090.01028.4020.0130.0130.0000.0000.0000.000
133A134ALA0-0.031-0.01329.6940.0130.0130.0000.0000.0000.000
134A135ASP-1-0.912-0.93731.504-0.154-0.1540.0000.0000.0000.000
135A136VAL0-0.012-0.00230.6000.0110.0110.0000.0000.0000.000
136A137ILE00.011-0.01128.608-0.001-0.0010.0000.0000.0000.000
137A138ARG10.8780.95332.1230.1560.1560.0000.0000.0000.000
138A139GLY0-0.019-0.02135.3300.0020.0020.0000.0000.0000.000
139A140ARG10.7180.84431.7910.1930.1930.0000.0000.0000.000
140A141LYS10.8380.91830.6700.1080.1080.0000.0000.0000.000
141A142LEU00.013-0.00625.865-0.013-0.0130.0000.0000.0000.000
142A143THR0-0.018-0.02321.9010.0150.0150.0000.0000.0000.000
143A144ALA00.0200.00221.296-0.025-0.0250.0000.0000.0000.000
144A145VAL00.0090.02017.0260.0420.0420.0000.0000.0000.000
145A146LYS10.9730.95719.8690.1160.1160.0000.0000.0000.000
146A147PRO0-0.024-0.01119.9280.0170.0170.0000.0000.0000.000
147A148ILE00.0630.04722.0730.0080.0080.0000.0000.0000.000
148A149ILE0-0.0360.00423.9560.0120.0120.0000.0000.0000.000
149A150ILE0-0.014-0.01726.3950.0090.0090.0000.0000.0000.000
150A151ASP-1-0.862-0.92927.134-0.209-0.2090.0000.0000.0000.000
151A152VAL0-0.016-0.01625.7700.0030.0030.0000.0000.0000.000
152A153LYS10.9290.97028.9760.1240.1240.0000.0000.0000.000
153A154ASN0-0.0100.00232.0340.0160.0160.0000.0000.0000.000
154A155ALA0-0.038-0.01231.4010.0060.0060.0000.0000.0000.000
155A156GLY0-0.004-0.01633.3950.0000.0000.0000.0000.0000.000
156A157ALA0-0.0110.02830.6690.0060.0060.0000.0000.0000.000
157A158GLU-1-0.816-0.88132.523-0.096-0.0960.0000.0000.0000.000
158A159PHE0-0.004-0.02924.876-0.003-0.0030.0000.0000.0000.000
159A160TYR0-0.035-0.02627.8670.0180.0180.0000.0000.0000.000
160A161ASP-1-0.900-0.92823.818-0.116-0.1160.0000.0000.0000.000
161A162GLN0-0.028-0.02524.2360.0290.0290.0000.0000.0000.000
162A163GLU-1-0.828-0.91819.635-0.115-0.1150.0000.0000.0000.000
163A164VAL0-0.0060.01519.897-0.046-0.0460.0000.0000.0000.000
164A165VAL0-0.089-0.02422.3120.0300.0300.0000.0000.0000.000
165A166VAL00.0390.01925.231-0.025-0.0250.0000.0000.0000.000
166A167ASP-1-0.774-0.87127.370-0.139-0.1390.0000.0000.0000.000
167A168LYS10.8180.89030.4110.1380.1380.0000.0000.0000.000
168A169ASP-1-0.812-0.88729.879-0.152-0.1520.0000.0000.0000.000
169A170GLN0-0.0120.00329.1940.0060.0060.0000.0000.0000.000
170A171LEU0-0.026-0.01026.614-0.023-0.0230.0000.0000.0000.000
171A172VAL00.0460.03621.5740.0210.0210.0000.0000.0000.000
172A173THR0-0.013-0.00321.502-0.026-0.0260.0000.0000.0000.000
173A174SER00.045-0.01517.7150.0260.0260.0000.0000.0000.000
174A175ARG10.7360.83018.6190.1030.1030.0000.0000.0000.000
175A176THR0-0.042-0.05313.888-0.034-0.0340.0000.0000.0000.000
176A177PRO00.0750.0309.4110.0540.0540.0000.0000.0000.000
177A178ASP-1-0.869-0.90911.546-0.042-0.0420.0000.0000.0000.000
178A179ASP-1-0.741-0.84313.196-0.134-0.1340.0000.0000.0000.000
179A180LEU0-0.024-0.01010.045-0.007-0.0070.0000.0000.0000.000
180A181PRO00.0020.00513.210-0.009-0.0090.0000.0000.0000.000
181A182ALA00.0100.01015.785-0.001-0.0010.0000.0000.0000.000
182A183PHE0-0.005-0.01515.755-0.007-0.0070.0000.0000.0000.000
183A184ASN00.019-0.01813.223-0.017-0.0170.0000.0000.0000.000
184A185ARG10.8010.91217.6810.1520.1520.0000.0000.0000.000
185A186GLU-1-0.781-0.89220.688-0.155-0.1550.0000.0000.0000.000
186A187ALA00.0140.01219.8250.0080.0080.0000.0000.0000.000
187A188LEU0-0.016-0.01818.8660.0090.0090.0000.0000.0000.000
188A189ARG10.7750.87822.4650.1780.1780.0000.0000.0000.000
189A190LEU0-0.050-0.02225.3870.0120.0120.0000.0000.0000.000
190A191LEU0-0.0220.01022.1850.0030.0030.0000.0000.0000.000
191A192GLY0-0.043-0.00526.2610.0060.0060.0000.0000.0000.000