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: VKK21

Calculation Name: 3IO0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3IO0

Chain ID: A

ChEMBL ID:

UniProt ID: A5N734

Base Structure: X-ray

Registration Date: 2023-09-27

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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2499783.745097
FMO2-HF: Nuclear repulsion 2416081.385781
FMO2-HF: Total energy -83702.359316
FMO2-MP2: Total energy -83944.419053


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:76:PRO)


Summations of interaction energy for fragment #1(A:76: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.
-0.5751.396-0.006-0.816-1.1480.002
Interaction energy analysis for fragmet #1(A:76:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : -0.006
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].
3A78MET0-0.032-0.0093.829-0.3641.522-0.005-0.811-1.0690.002
4A79THR00.002-0.0085.1880.2740.359-0.001-0.005-0.0790.000
5A80GLU-1-0.839-0.9267.642-0.913-0.9130.0000.0000.0000.000
6A81PHE0-0.031-0.0018.6260.1200.1200.0000.0000.0000.000
7A82VAL0-0.028-0.01510.4690.0660.0660.0000.0000.0000.000
8A83GLY00.0750.06212.9270.0680.0680.0000.0000.0000.000
9A84THR0-0.024-0.01014.633-0.068-0.0680.0000.0000.0000.000
10A85ALA0-0.025-0.00717.0030.0270.0270.0000.0000.0000.000
11A86GLY00.0330.02320.705-0.014-0.0140.0000.0000.0000.000
12A87GLY00.002-0.00823.443-0.009-0.0090.0000.0000.0000.000
13A88ASP-1-0.851-0.92419.818-0.230-0.2300.0000.0000.0000.000
14A89THR0-0.027-0.01920.423-0.026-0.0260.0000.0000.0000.000
15A90VAL0-0.024-0.02814.820-0.023-0.0230.0000.0000.0000.000
16A91GLY00.033-0.01016.1660.0550.0550.0000.0000.0000.000
17A92LEU0-0.053-0.03112.556-0.093-0.0930.0000.0000.0000.000
18A93VAL00.0260.01313.7830.0930.0930.0000.0000.0000.000
19A94ILE0-0.015-0.00313.610-0.079-0.0790.0000.0000.0000.000
20A95ALA00.0270.00514.5300.0590.0590.0000.0000.0000.000
21A96ASN00.017-0.00816.3100.0650.0650.0000.0000.0000.000
22A97VAL0-0.0110.01318.278-0.013-0.0130.0000.0000.0000.000
23A98ASP-1-0.791-0.89318.976-0.229-0.2290.0000.0000.0000.000
24A99SER00.0370.00220.5560.0130.0130.0000.0000.0000.000
25A100LEU0-0.037-0.02323.2370.0170.0170.0000.0000.0000.000
26A101LEU0-0.054-0.04119.9960.0080.0080.0000.0000.0000.000
27A102HIS0-0.081-0.04222.7830.0170.0170.0000.0000.0000.000
28A103LYS10.9480.97326.2240.1650.1650.0000.0000.0000.000
29A104HIS0-0.014-0.00125.9130.0130.0130.0000.0000.0000.000
30A105LEU00.0320.03722.257-0.002-0.0020.0000.0000.0000.000
31A106GLY00.0340.00626.8400.0090.0090.0000.0000.0000.000
32A107LEU0-0.077-0.02322.9740.0060.0060.0000.0000.0000.000
33A108ASP-1-0.753-0.87027.373-0.135-0.1350.0000.0000.0000.000
34A109ASN00.0330.00726.297-0.021-0.0210.0000.0000.0000.000
35A110THR0-0.104-0.05726.554-0.002-0.0020.0000.0000.0000.000
36A111CYS0-0.023-0.01025.900-0.005-0.0050.0000.0000.0000.000
37A112ARG10.8880.93322.0230.1910.1910.0000.0000.0000.000
38A113SER0-0.0420.00119.208-0.029-0.0290.0000.0000.0000.000
39A114ILE00.019-0.01118.5060.0230.0230.0000.0000.0000.000
40A115GLY00.0240.01318.319-0.039-0.0390.0000.0000.0000.000
41A116ILE0-0.055-0.02817.0990.0280.0280.0000.0000.0000.000
42A117ILE00.0290.01919.039-0.021-0.0210.0000.0000.0000.000
43A118SER0-0.0150.00219.3670.0330.0330.0000.0000.0000.000
44A119ALA00.0440.01520.650-0.020-0.0200.0000.0000.0000.000
45A120ARG10.8130.89021.5230.2450.2450.0000.0000.0000.000
46A121VAL0-0.012-0.02224.2340.0150.0150.0000.0000.0000.000
47A122GLY00.0360.03727.015-0.003-0.0030.0000.0000.0000.000
48A123ALA00.034-0.00128.453-0.011-0.0110.0000.0000.0000.000
49A124PRO00.0090.00530.220-0.004-0.0040.0000.0000.0000.000
50A125ALA00.0230.02329.5470.0000.0000.0000.0000.0000.000
51A126GLN00.0220.00125.1170.0120.0120.0000.0000.0000.000
52A127MET0-0.0070.00427.623-0.003-0.0030.0000.0000.0000.000
53A128MET0-0.028-0.00729.9800.0030.0030.0000.0000.0000.000
54A129ALA0-0.034-0.01026.2380.0040.0040.0000.0000.0000.000
55A130ALA00.0450.00926.198-0.002-0.0020.0000.0000.0000.000
56A131ASP-1-0.746-0.86027.196-0.109-0.1090.0000.0000.0000.000
57A132GLU-1-0.881-0.92928.818-0.102-0.1020.0000.0000.0000.000
58A133ALA00.0010.00124.9980.0050.0050.0000.0000.0000.000
59A134VAL0-0.0060.01227.0400.0010.0010.0000.0000.0000.000
60A135LYS10.7800.89028.8780.1100.1100.0000.0000.0000.000
61A136GLY0-0.056-0.00928.7120.0090.0090.0000.0000.0000.000
62A137THR0-0.074-0.05524.230-0.005-0.0050.0000.0000.0000.000
63A138ASN0-0.042-0.01426.7190.0110.0110.0000.0000.0000.000
64A139THR0-0.038-0.02423.929-0.010-0.0100.0000.0000.0000.000
65A140GLU-1-0.883-0.93627.112-0.123-0.1230.0000.0000.0000.000
66A141VAL0-0.011-0.01127.337-0.017-0.0170.0000.0000.0000.000
67A142ALA0-0.053-0.01925.7400.0090.0090.0000.0000.0000.000
68A143THR0-0.087-0.09225.8260.0160.0160.0000.0000.0000.000
69A144ILE00.0040.00827.145-0.012-0.0120.0000.0000.0000.000
70A145GLU-1-0.882-0.90427.732-0.186-0.1860.0000.0000.0000.000
71A146LEU00.017-0.00528.415-0.010-0.0100.0000.0000.0000.000
72A147PRO00.0500.06826.6410.0110.0110.0000.0000.0000.000
73A148ARG10.8560.91729.9590.1220.1220.0000.0000.0000.000
74A149ASP-1-0.731-0.87325.428-0.209-0.2090.0000.0000.0000.000
75A150THR0-0.1030.01727.7730.0130.0130.0000.0000.0000.000
76A151LYS10.8710.94522.7060.1970.1970.0000.0000.0000.000
77A152GLY0-0.039-0.02328.416-0.002-0.0020.0000.0000.0000.000
78A153GLY0-0.055-0.00531.1490.0050.0050.0000.0000.0000.000
79A154ALA00.0590.01132.923-0.002-0.0020.0000.0000.0000.000
80A155GLY00.1090.01533.5430.0040.0040.0000.0000.0000.000
81A156HIS0-0.027-0.01231.205-0.002-0.0020.0000.0000.0000.000
82A157GLY0-0.007-0.00227.4490.0050.0050.0000.0000.0000.000
83A158ILE0-0.005-0.01625.1190.0100.0100.0000.0000.0000.000
84A159PHE00.0120.00520.606-0.030-0.0300.0000.0000.0000.000
85A160ILE00.0260.01623.8550.0200.0200.0000.0000.0000.000
86A161VAL0-0.0050.00421.974-0.027-0.0270.0000.0000.0000.000
87A162LEU00.0110.00422.9670.0240.0240.0000.0000.0000.000
88A163LYS10.8830.93722.9140.1310.1310.0000.0000.0000.000
89A164ALA00.0480.02022.6700.0160.0160.0000.0000.0000.000
90A165ALA00.0490.02623.743-0.013-0.0130.0000.0000.0000.000
91A166ASP-1-0.847-0.88520.795-0.192-0.1920.0000.0000.0000.000
92A167VAL00.0590.01815.478-0.008-0.0080.0000.0000.0000.000
93A168SER0-0.088-0.05517.980-0.017-0.0170.0000.0000.0000.000
94A169ASP-1-0.832-0.91618.929-0.148-0.1480.0000.0000.0000.000
95A170ALA00.0050.00119.4540.0030.0030.0000.0000.0000.000
96A171ARG10.8360.90210.9710.5620.5620.0000.0000.0000.000
97A172ARG10.9580.98817.7840.1360.1360.0000.0000.0000.000
98A173ALA00.0140.00620.4710.0100.0100.0000.0000.0000.000
99A174VAL0-0.0010.00617.1370.0100.0100.0000.0000.0000.000
100A175GLU-1-0.865-0.94615.404-0.315-0.3150.0000.0000.0000.000
101A176ILE0-0.063-0.02319.4780.0200.0200.0000.0000.0000.000
102A177ALA00.007-0.00122.4710.0120.0120.0000.0000.0000.000
103A178LEU00.0130.02216.8270.0130.0130.0000.0000.0000.000
104A179LYS10.9120.95821.3340.1350.1350.0000.0000.0000.000
105A180GLN0-0.023-0.00623.1010.0220.0220.0000.0000.0000.000
106A181THR00.0180.00323.8760.0110.0110.0000.0000.0000.000
107A182ASP-1-0.810-0.91223.504-0.153-0.1530.0000.0000.0000.000
108A183LYS10.7500.87226.6040.1180.1180.0000.0000.0000.000
109A184TYR0-0.007-0.03129.3590.0130.0130.0000.0000.0000.000
110A185LEU00.0360.03026.0380.0070.0070.0000.0000.0000.000
111A186GLY00.0320.01930.4220.0060.0060.0000.0000.0000.000
112A187ASN0-0.106-0.07632.8410.0140.0140.0000.0000.0000.000
113A188VAL00.001-0.00331.6520.0020.0020.0000.0000.0000.000
114A189TYR00.000-0.02034.5050.0030.0030.0000.0000.0000.000
115A190LEU00.0160.00330.962-0.002-0.0020.0000.0000.0000.000
116A191CYS0-0.049-0.03835.6760.0070.0070.0000.0000.0000.000
117A192ASP-1-0.839-0.91137.213-0.061-0.0610.0000.0000.0000.000
118A193ALA00.0050.00838.488-0.003-0.0030.0000.0000.0000.000
119A194GLY0-0.038-0.02838.208-0.001-0.0010.0000.0000.0000.000
120A195HIS0-0.068-0.02335.873-0.001-0.0010.0000.0000.0000.000
121A196LEU0-0.038-0.01337.8840.0030.0030.0000.0000.0000.000
122A197GLU-1-0.742-0.86533.429-0.118-0.1180.0000.0000.0000.000
123A198VAL0-0.041-0.02137.6520.0020.0020.0000.0000.0000.000
124A199GLN0-0.046-0.03233.2080.0040.0040.0000.0000.0000.000
125A200TYR00.0420.00137.2560.0040.0040.0000.0000.0000.000
126A201THR00.0220.01436.193-0.003-0.0030.0000.0000.0000.000
127A202ALA00.0150.00438.0440.0040.0040.0000.0000.0000.000
128A203ARG10.9280.97537.8910.0760.0760.0000.0000.0000.000
129A204ALA00.0200.02636.988-0.006-0.0060.0000.0000.0000.000
130A205SER0-0.043-0.04633.7160.0030.0030.0000.0000.0000.000
131A206LEU00.0820.02531.505-0.003-0.0030.0000.0000.0000.000
132A207ILE0-0.0130.01328.314-0.002-0.0020.0000.0000.0000.000
133A208PHE00.034-0.00332.4790.0000.0000.0000.0000.0000.000
134A209GLU-1-0.832-0.89235.845-0.091-0.0910.0000.0000.0000.000
135A210LYS10.9040.96231.1140.1480.1480.0000.0000.0000.000
136A211ALA0-0.057-0.02233.5440.0010.0010.0000.0000.0000.000
137A212PHE0-0.011-0.02835.3470.0020.0020.0000.0000.0000.000
138A213GLY00.0200.03438.8140.0050.0050.0000.0000.0000.000
139A214ALA0-0.056-0.03239.3200.0050.0050.0000.0000.0000.000
140A215PRO0-0.010-0.01741.228-0.001-0.0010.0000.0000.0000.000
141A216SER00.024-0.00439.5180.0010.0010.0000.0000.0000.000
142A217GLY0-0.060-0.02840.0470.0050.0050.0000.0000.0000.000
143A218GLN0-0.046-0.02441.3830.0060.0060.0000.0000.0000.000
144A219ALA00.0110.01441.579-0.004-0.0040.0000.0000.0000.000
145A220PHE0-0.016-0.02837.7690.0010.0010.0000.0000.0000.000
146A221GLY00.0220.00140.4390.0000.0000.0000.0000.0000.000
147A222ILE0-0.0250.00235.863-0.001-0.0010.0000.0000.0000.000
148A223MET0-0.020-0.00439.7390.0030.0030.0000.0000.0000.000
149A224HIS00.017-0.00235.2390.0020.0020.0000.0000.0000.000
150A225ALA00.008-0.00240.0110.0010.0010.0000.0000.0000.000
151A226ALA0-0.0240.02338.6370.0000.0000.0000.0000.0000.000
152A227PRO00.0700.01640.6270.0010.0010.0000.0000.0000.000
153A228ALA00.008-0.00542.6680.0020.0020.0000.0000.0000.000
154A229GLY0-0.029-0.00444.1080.0010.0010.0000.0000.0000.000
155A230VAL00.0370.00744.1860.0020.0020.0000.0000.0000.000
156A231GLY00.0430.02144.2160.0010.0010.0000.0000.0000.000
157A232MET00.0070.00744.806-0.001-0.0010.0000.0000.0000.000
158A233ILE00.0130.02248.4030.0010.0010.0000.0000.0000.000
159A234VAL0-0.0110.00543.7380.0020.0020.0000.0000.0000.000
160A235ALA00.0080.00046.4110.0010.0010.0000.0000.0000.000
161A236ASP-1-0.806-0.89147.663-0.044-0.0440.0000.0000.0000.000
162A237THR0-0.027-0.03650.1370.0010.0010.0000.0000.0000.000
163A238ALA00.0020.02147.6070.0020.0020.0000.0000.0000.000
164A239LEU0-0.025-0.00549.4930.0010.0010.0000.0000.0000.000
165A240LYS10.7870.88251.8900.0440.0440.0000.0000.0000.000
166A241THR0-0.086-0.04851.5620.0020.0020.0000.0000.0000.000
167A242ALA0-0.021-0.01451.5950.0020.0020.0000.0000.0000.000
168A243ASP-1-0.922-0.94253.698-0.044-0.0440.0000.0000.0000.000
169A244VAL0-0.036-0.01748.632-0.001-0.0010.0000.0000.0000.000
170A245LYS10.9540.97148.5230.0530.0530.0000.0000.0000.000
171A246LEU00.003-0.00246.654-0.002-0.0020.0000.0000.0000.000
172A247ILE0-0.070-0.03443.0290.0010.0010.0000.0000.0000.000
173A248THR00.0110.00040.836-0.003-0.0030.0000.0000.0000.000
174A249TYR00.0330.01543.9190.0010.0010.0000.0000.0000.000
175A250GLY00.0200.01641.913-0.001-0.0010.0000.0000.0000.000
176A251SER00.0190.00242.9650.0010.0010.0000.0000.0000.000
177A252PRO00.0440.01441.239-0.003-0.0030.0000.0000.0000.000
178A253THR0-0.011-0.03041.215-0.003-0.0030.0000.0000.0000.000
179A254ASN0-0.0310.00343.422-0.002-0.0020.0000.0000.0000.000
180A255GLY00.0340.02441.0070.0010.0010.0000.0000.0000.000
181A256VAL0-0.032-0.00239.776-0.004-0.0040.0000.0000.0000.000
182A257LEU0-0.0300.00037.344-0.005-0.0050.0000.0000.0000.000
183A258SER0-0.014-0.01633.2690.0050.0050.0000.0000.0000.000
184A259TYR0-0.059-0.04435.733-0.004-0.0040.0000.0000.0000.000
185A260THR0-0.060-0.02834.9310.0000.0000.0000.0000.0000.000
186A261ASN0-0.023-0.01937.5600.0070.0070.0000.0000.0000.000
187A262GLU-1-0.755-0.88436.117-0.103-0.1030.0000.0000.0000.000
188A263ILE0-0.073-0.03140.8980.0010.0010.0000.0000.0000.000
189A264LEU0-0.014-0.00937.8120.0000.0000.0000.0000.0000.000
190A265ILE00.001-0.00841.8600.0030.0030.0000.0000.0000.000
191A266THR0-0.0010.00039.655-0.002-0.0020.0000.0000.0000.000
192A267ILE00.0260.01942.7360.0030.0030.0000.0000.0000.000
193A268SER0-0.004-0.00143.602-0.002-0.0020.0000.0000.0000.000
194A269GLY00.0160.00645.6280.0030.0030.0000.0000.0000.000
195A270ASP-1-0.839-0.91046.877-0.049-0.0490.0000.0000.0000.000
196A271SER00.004-0.01045.1090.0000.0000.0000.0000.0000.000
197A272GLY00.0080.01046.415-0.001-0.0010.0000.0000.0000.000
198A273ALA00.0510.03049.2760.0000.0000.0000.0000.0000.000
199A274VAL00.0270.00543.7040.0000.0000.0000.0000.0000.000
200A275LEU0-0.018-0.01242.665-0.001-0.0010.0000.0000.0000.000
201A276GLN0-0.0260.00646.0320.0010.0010.0000.0000.0000.000
202A277SER00.009-0.02047.9200.0010.0010.0000.0000.0000.000
203A278LEU0-0.010-0.00642.0780.0000.0000.0000.0000.0000.000
204A279THR0-0.048-0.03444.958-0.001-0.0010.0000.0000.0000.000
205A280ALA0-0.0030.00946.4110.0010.0010.0000.0000.0000.000
206A281ALA00.0360.02845.6350.0010.0010.0000.0000.0000.000
207A282ARG10.9060.96239.9510.0600.0600.0000.0000.0000.000
208A283LYS10.9470.97244.5590.0370.0370.0000.0000.0000.000
209A284ALA00.002-0.00147.5120.0010.0010.0000.0000.0000.000
210A285GLY00.0560.01444.8670.0010.0010.0000.0000.0000.000
211A286LEU0-0.034-0.01441.5100.0010.0010.0000.0000.0000.000
212A287SER0-0.033-0.00445.2260.0020.0020.0000.0000.0000.000
213A288ILE00.0100.00947.7110.0020.0020.0000.0000.0000.000
214A289LEU00.0620.01041.1930.0010.0010.0000.0000.0000.000
215A290ARG10.8450.92342.4030.0450.0450.0000.0000.0000.000
216A291SER0-0.057-0.02647.3290.0020.0020.0000.0000.0000.000
217A292MET0-0.099-0.03945.2690.0010.0010.0000.0000.0000.000
218A293GLY0-0.010-0.00147.3590.0000.0000.0000.0000.0000.000
219A294GLN0-0.050-0.02141.482-0.003-0.0030.0000.0000.0000.000
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