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

tag_button

FMODB ID: YNNQ2

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 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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2498018.033134
FMO2-HF: Nuclear repulsion 2414316.932997
FMO2-HF: Total energy -83701.100137
FMO2-MP2: Total energy -83943.201499


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.
-0.3741.4280.001-0.745-1.0580.001
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 : 0.016 / q_NPA : -0.010
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].
3A78MET0-0.022-0.0073.740-0.2401.4910.002-0.741-0.9920.001
4A79THR00.0260.0135.2290.3420.413-0.001-0.004-0.0660.000
5A80GLU-1-0.861-0.9367.503-0.883-0.8830.0000.0000.0000.000
6A81PHE0-0.029-0.0028.4940.1210.1210.0000.0000.0000.000
7A82VAL0-0.045-0.02210.3050.0610.0610.0000.0000.0000.000
8A83GLY00.0850.06512.8470.0670.0670.0000.0000.0000.000
9A84THR0-0.042-0.01714.633-0.070-0.0700.0000.0000.0000.000
10A85ALA0-0.0010.00317.0030.0270.0270.0000.0000.0000.000
11A86GLY00.0430.03220.705-0.013-0.0130.0000.0000.0000.000
12A87GLY00.006-0.00723.451-0.010-0.0100.0000.0000.0000.000
13A88ASP-1-0.885-0.95519.850-0.218-0.2180.0000.0000.0000.000
14A89THR0-0.084-0.04620.418-0.032-0.0320.0000.0000.0000.000
15A90VAL00.025-0.00314.373-0.021-0.0210.0000.0000.0000.000
16A91GLY00.007-0.02316.0060.0530.0530.0000.0000.0000.000
17A92LEU0-0.052-0.03012.958-0.090-0.0900.0000.0000.0000.000
18A93VAL00.0240.01413.6700.0910.0910.0000.0000.0000.000
19A94ILE0-0.0040.00313.596-0.080-0.0800.0000.0000.0000.000
20A95ALA00.021-0.00614.4110.0580.0580.0000.0000.0000.000
21A96ASN0-0.014-0.03316.1810.0620.0620.0000.0000.0000.000
22A97VAL0-0.0030.01718.447-0.015-0.0150.0000.0000.0000.000
23A98ASP-1-0.811-0.90419.157-0.238-0.2380.0000.0000.0000.000
24A99SER00.042-0.00120.7060.0130.0130.0000.0000.0000.000
25A100LEU0-0.025-0.01323.3880.0170.0170.0000.0000.0000.000
26A101LEU0-0.041-0.03620.2540.0090.0090.0000.0000.0000.000
27A102HIS0-0.079-0.03422.9730.0160.0160.0000.0000.0000.000
28A103LYS10.9580.97626.4670.1630.1630.0000.0000.0000.000
29A104HIS0-0.030-0.00826.5300.0110.0110.0000.0000.0000.000
30A105LEU00.0300.03622.683-0.002-0.0020.0000.0000.0000.000
31A106GLY0-0.012-0.02127.1790.0090.0090.0000.0000.0000.000
32A107LEU0-0.076-0.02223.3400.0050.0050.0000.0000.0000.000
33A108ASP-1-0.757-0.87627.621-0.132-0.1320.0000.0000.0000.000
34A109ASN00.007-0.02226.453-0.020-0.0200.0000.0000.0000.000
35A110THR0-0.129-0.05626.577-0.003-0.0030.0000.0000.0000.000
36A111CYS0-0.002-0.00725.738-0.005-0.0050.0000.0000.0000.000
37A112ARG10.9600.99522.1820.1930.1930.0000.0000.0000.000
38A113SER0-0.042-0.00619.055-0.026-0.0260.0000.0000.0000.000
39A114ILE0-0.002-0.01318.7180.0240.0240.0000.0000.0000.000
40A115GLY00.0240.01118.180-0.038-0.0380.0000.0000.0000.000
41A116ILE0-0.051-0.02017.2990.0280.0280.0000.0000.0000.000
42A117ILE00.0270.01818.948-0.019-0.0190.0000.0000.0000.000
43A118SER0-0.0070.00219.6230.0320.0320.0000.0000.0000.000
44A119ALA00.0450.01420.631-0.018-0.0180.0000.0000.0000.000
45A120ARG10.7920.88621.4380.2340.2340.0000.0000.0000.000
46A121VAL0-0.015-0.02124.2270.0150.0150.0000.0000.0000.000
47A122GLY00.0410.03727.015-0.002-0.0020.0000.0000.0000.000
48A123ALA00.036-0.00228.439-0.011-0.0110.0000.0000.0000.000
49A124PRO00.0040.00330.204-0.004-0.0040.0000.0000.0000.000
50A125ALA00.0300.02329.5160.0000.0000.0000.0000.0000.000
51A126GLN00.0380.00824.6970.0130.0130.0000.0000.0000.000
52A127MET0-0.0180.00427.489-0.003-0.0030.0000.0000.0000.000
53A128MET0-0.050-0.01429.8310.0030.0030.0000.0000.0000.000
54A129ALA0-0.029-0.00726.1030.0040.0040.0000.0000.0000.000
55A130ALA00.0330.00526.009-0.002-0.0020.0000.0000.0000.000
56A131ASP-1-0.777-0.90027.078-0.107-0.1070.0000.0000.0000.000
57A132GLU-1-0.920-0.97328.728-0.095-0.0950.0000.0000.0000.000
58A133ALA0-0.0040.00024.9440.0050.0050.0000.0000.0000.000
59A134VAL0-0.0070.01726.9680.0010.0010.0000.0000.0000.000
60A135LYS10.8280.91928.7820.0990.0990.0000.0000.0000.000
61A136GLY0-0.046-0.00528.6860.0090.0090.0000.0000.0000.000
62A137THR0-0.073-0.04824.197-0.005-0.0050.0000.0000.0000.000
63A138ASN00.0010.01126.6560.0060.0060.0000.0000.0000.000
64A139THR0-0.023-0.02623.831-0.009-0.0090.0000.0000.0000.000
65A140GLU-1-0.907-0.94826.992-0.117-0.1170.0000.0000.0000.000
66A141VAL0-0.001-0.00327.164-0.017-0.0170.0000.0000.0000.000
67A142ALA0-0.088-0.03825.9990.0090.0090.0000.0000.0000.000
68A143THR0-0.075-0.05926.2220.0160.0160.0000.0000.0000.000
69A144ILE00.0130.00827.398-0.012-0.0120.0000.0000.0000.000
70A145GLU-1-0.901-0.93428.301-0.181-0.1810.0000.0000.0000.000
71A146LEU00.0310.00628.867-0.010-0.0100.0000.0000.0000.000
72A147PRO00.0750.11326.7020.0110.0110.0000.0000.0000.000
73A148ARG10.8610.93129.9960.1150.1150.0000.0000.0000.000
74A149ASP-1-0.738-0.87025.469-0.200-0.2000.0000.0000.0000.000
75A150THR0-0.074-0.01027.7750.0130.0130.0000.0000.0000.000
76A151LYS10.9050.98622.7150.1810.1810.0000.0000.0000.000
77A152GLY0-0.026-0.02528.419-0.002-0.0020.0000.0000.0000.000
78A153GLY0-0.076-0.00731.1510.0050.0050.0000.0000.0000.000
79A154ALA00.0830.00532.928-0.002-0.0020.0000.0000.0000.000
80A155GLY00.0770.02133.6100.0030.0030.0000.0000.0000.000
81A156HIS00.0100.01331.067-0.002-0.0020.0000.0000.0000.000
82A157GLY0-0.011-0.00827.4270.0050.0050.0000.0000.0000.000
83A158ILE00.002-0.01625.2930.0100.0100.0000.0000.0000.000
84A159PHE00.0080.00621.185-0.028-0.0280.0000.0000.0000.000
85A160ILE00.0280.01724.0870.0190.0190.0000.0000.0000.000
86A161VAL00.0060.00622.250-0.026-0.0260.0000.0000.0000.000
87A162LEU00.000-0.00622.9190.0240.0240.0000.0000.0000.000
88A163LYS10.9270.95922.8140.1300.1300.0000.0000.0000.000
89A164ALA00.0500.01922.6090.0170.0170.0000.0000.0000.000
90A165ALA00.0340.02523.584-0.013-0.0130.0000.0000.0000.000
91A166ASP-1-0.864-0.91420.657-0.185-0.1850.0000.0000.0000.000
92A167VAL00.0640.02315.541-0.010-0.0100.0000.0000.0000.000
93A168SER0-0.092-0.03717.940-0.016-0.0160.0000.0000.0000.000
94A169ASP-1-0.866-0.93418.887-0.145-0.1450.0000.0000.0000.000
95A170ALA00.0230.00419.2690.0030.0030.0000.0000.0000.000
96A171ARG10.8590.90110.7590.5520.5520.0000.0000.0000.000
97A172ARG10.9460.98117.7090.1270.1270.0000.0000.0000.000
98A173ALA00.0250.01220.4440.0100.0100.0000.0000.0000.000
99A174VAL00.0030.00317.0740.0100.0100.0000.0000.0000.000
100A175GLU-1-0.904-0.96115.831-0.274-0.2740.0000.0000.0000.000
101A176ILE0-0.081-0.02019.4490.0200.0200.0000.0000.0000.000
102A177ALA00.007-0.00522.3750.0120.0120.0000.0000.0000.000
103A178LEU00.0130.02016.7950.0130.0130.0000.0000.0000.000
104A179LYS10.9110.96121.2730.1190.1190.0000.0000.0000.000
105A180GLN0-0.018-0.00823.0960.0230.0230.0000.0000.0000.000
106A181THR00.0190.00023.8760.0090.0090.0000.0000.0000.000
107A182ASP-1-0.827-0.92823.415-0.138-0.1380.0000.0000.0000.000
108A183LYS10.8180.93226.6130.1030.1030.0000.0000.0000.000
109A184TYR0-0.036-0.03929.2240.0130.0130.0000.0000.0000.000
110A185LEU00.0530.03525.9860.0070.0070.0000.0000.0000.000
111A186GLY00.0210.01830.4220.0060.0060.0000.0000.0000.000
112A187ASN0-0.078-0.03232.8550.0140.0140.0000.0000.0000.000
113A188VAL0-0.017-0.00431.7890.0020.0020.0000.0000.0000.000
114A189TYR0-0.008-0.02734.5240.0030.0030.0000.0000.0000.000
115A190LEU00.0190.00030.924-0.002-0.0020.0000.0000.0000.000
116A191CYS0-0.039-0.02935.6970.0070.0070.0000.0000.0000.000
117A192ASP-1-0.906-0.94037.233-0.058-0.0580.0000.0000.0000.000
118A193ALA00.0240.01238.508-0.003-0.0030.0000.0000.0000.000
119A194GLY0-0.047-0.03338.216-0.001-0.0010.0000.0000.0000.000
120A195HIS0-0.068-0.03135.8820.0000.0000.0000.0000.0000.000
121A196LEU0-0.034-0.01437.8840.0030.0030.0000.0000.0000.000
122A197GLU-1-0.747-0.88733.366-0.110-0.1100.0000.0000.0000.000
123A198VAL0-0.045-0.02237.6550.0020.0020.0000.0000.0000.000
124A199GLN0-0.025-0.01633.1770.0040.0040.0000.0000.0000.000
125A200TYR00.0530.00437.1660.0040.0040.0000.0000.0000.000
126A201THR00.0110.01536.032-0.002-0.0020.0000.0000.0000.000
127A202ALA00.0280.00737.9630.0030.0030.0000.0000.0000.000
128A203ARG10.9210.97837.6630.0730.0730.0000.0000.0000.000
129A204ALA00.0400.03136.900-0.005-0.0050.0000.0000.0000.000
130A205SER0-0.055-0.03133.4290.0040.0040.0000.0000.0000.000
131A206LEU00.1010.03131.504-0.002-0.0020.0000.0000.0000.000
132A207ILE0-0.0050.01928.228-0.003-0.0030.0000.0000.0000.000
133A208PHE00.021-0.01532.3170.0000.0000.0000.0000.0000.000
134A209GLU-1-0.878-0.93135.682-0.086-0.0860.0000.0000.0000.000
135A210LYS10.9210.97031.6330.1410.1410.0000.0000.0000.000
136A211ALA0-0.053-0.02433.6160.0010.0010.0000.0000.0000.000
137A212PHE0-0.014-0.02635.4680.0020.0020.0000.0000.0000.000
138A213GLY00.0210.03238.8360.0050.0050.0000.0000.0000.000
139A214ALA0-0.055-0.03239.2040.0050.0050.0000.0000.0000.000
140A215PRO0-0.012-0.01941.067-0.001-0.0010.0000.0000.0000.000
141A216SER00.0320.02039.6010.0020.0020.0000.0000.0000.000
142A217GLY0-0.057-0.03439.9350.0050.0050.0000.0000.0000.000
143A218GLN0-0.052-0.01941.2850.0060.0060.0000.0000.0000.000
144A219ALA00.0130.01541.476-0.004-0.0040.0000.0000.0000.000
145A220PHE0-0.012-0.03137.8070.0010.0010.0000.0000.0000.000
146A221GLY00.017-0.00440.3320.0000.0000.0000.0000.0000.000
147A222ILE0-0.0270.00135.989-0.001-0.0010.0000.0000.0000.000
148A223MET0-0.0110.00139.6780.0030.0030.0000.0000.0000.000
149A224HIS00.006-0.00335.2420.0020.0020.0000.0000.0000.000
150A225ALA00.007-0.00240.0100.0010.0010.0000.0000.0000.000
151A226ALA0-0.0240.02338.674-0.001-0.0010.0000.0000.0000.000
152A227PRO00.0690.01740.6280.0010.0010.0000.0000.0000.000
153A228ALA00.013-0.00442.6690.0020.0020.0000.0000.0000.000
154A229GLY0-0.039-0.00544.1020.0010.0010.0000.0000.0000.000
155A230VAL00.0330.00344.1820.0020.0020.0000.0000.0000.000
156A231GLY00.0540.02044.1870.0010.0010.0000.0000.0000.000
157A232MET00.0010.00344.8010.0000.0000.0000.0000.0000.000
158A233ILE00.0030.01948.3960.0010.0010.0000.0000.0000.000
159A234VAL0-0.027-0.01243.8190.0020.0020.0000.0000.0000.000
160A235ALA00.014-0.00346.3450.0010.0010.0000.0000.0000.000
161A236ASP-1-0.843-0.93047.654-0.041-0.0410.0000.0000.0000.000
162A237THR0-0.037-0.02349.9410.0020.0020.0000.0000.0000.000
163A238ALA00.0190.01047.6170.0020.0020.0000.0000.0000.000
164A239LEU0-0.025-0.00749.2870.0010.0010.0000.0000.0000.000
165A240LYS10.8320.92651.7620.0400.0400.0000.0000.0000.000
166A241THR0-0.093-0.03851.5440.0020.0020.0000.0000.0000.000
167A242ALA0-0.032-0.01751.4960.0020.0020.0000.0000.0000.000
168A243ASP-1-0.925-0.94653.583-0.042-0.0420.0000.0000.0000.000
169A244VAL0-0.033-0.01148.505-0.001-0.0010.0000.0000.0000.000
170A245LYS10.9670.97348.3000.0520.0520.0000.0000.0000.000
171A246LEU00.008-0.00646.893-0.002-0.0020.0000.0000.0000.000
172A247ILE0-0.077-0.03443.0730.0010.0010.0000.0000.0000.000
173A248THR00.020-0.00340.942-0.003-0.0030.0000.0000.0000.000
174A249TYR00.0460.00844.0580.0010.0010.0000.0000.0000.000
175A250GLY00.0130.01242.080-0.002-0.0020.0000.0000.0000.000
176A251SER00.0300.01143.1260.0010.0010.0000.0000.0000.000
177A252PRO00.0360.00841.221-0.003-0.0030.0000.0000.0000.000
178A253THR00.009-0.02341.190-0.004-0.0040.0000.0000.0000.000
179A254ASN0-0.045-0.00243.472-0.003-0.0030.0000.0000.0000.000
180A255GLY00.0320.02241.3760.0010.0010.0000.0000.0000.000
181A256VAL0-0.0230.00240.032-0.004-0.0040.0000.0000.0000.000
182A257LEU0-0.044-0.00637.525-0.005-0.0050.0000.0000.0000.000
183A258SER0-0.051-0.06333.2480.0040.0040.0000.0000.0000.000
184A259TYR0-0.047-0.03735.708-0.004-0.0040.0000.0000.0000.000
185A260THR0-0.073-0.04534.8550.0000.0000.0000.0000.0000.000
186A261ASN0-0.028-0.02037.5440.0070.0070.0000.0000.0000.000
187A262GLU-1-0.768-0.88536.305-0.096-0.0960.0000.0000.0000.000
188A263ILE0-0.073-0.02040.8870.0010.0010.0000.0000.0000.000
189A264LEU0-0.009-0.01137.8960.0000.0000.0000.0000.0000.000
190A265ILE0-0.014-0.00441.8430.0030.0030.0000.0000.0000.000
191A266THR0-0.0030.01539.923-0.002-0.0020.0000.0000.0000.000
192A267ILE00.0080.00642.6970.0030.0030.0000.0000.0000.000
193A268SER00.0010.00643.468-0.002-0.0020.0000.0000.0000.000
194A269GLY00.0230.01145.4980.0030.0030.0000.0000.0000.000
195A270ASP-1-0.842-0.91046.780-0.046-0.0460.0000.0000.0000.000
196A271SER00.003-0.01245.1100.0000.0000.0000.0000.0000.000
197A272GLY00.0030.00846.348-0.001-0.0010.0000.0000.0000.000
198A273ALA00.0640.03849.2170.0000.0000.0000.0000.0000.000
199A274VAL00.0210.00643.6110.0000.0000.0000.0000.0000.000
200A275LEU0-0.013-0.01342.539-0.001-0.0010.0000.0000.0000.000
201A276GLN00.0080.03145.9590.0000.0000.0000.0000.0000.000
202A277SER00.008-0.01747.7670.0010.0010.0000.0000.0000.000
203A278LEU0-0.021-0.00641.9140.0000.0000.0000.0000.0000.000
204A279THR0-0.057-0.05044.958-0.001-0.0010.0000.0000.0000.000
205A280ALA0-0.0060.00646.4110.0010.0010.0000.0000.0000.000
206A281ALA00.0410.02745.5280.0010.0010.0000.0000.0000.000
207A282ARG10.9270.96340.9720.0520.0520.0000.0000.0000.000
208A283LYS10.9270.96444.5680.0340.0340.0000.0000.0000.000
209A284ALA00.004-0.00247.5260.0010.0010.0000.0000.0000.000
210A285GLY00.0590.02044.8760.0010.0010.0000.0000.0000.000
211A286LEU0-0.024-0.01341.6460.0010.0010.0000.0000.0000.000
212A287SER0-0.053-0.01345.2440.0020.0020.0000.0000.0000.000
213A288ILE00.0330.01447.6710.0020.0020.0000.0000.0000.000
214A289LEU00.0610.00841.8290.0010.0010.0000.0000.0000.000
215A290ARG10.9420.97843.9250.0390.0390.0000.0000.0000.000
216A291SER0-0.051-0.01847.3540.0020.0020.0000.0000.0000.000
217A292MET0-0.097-0.03645.3560.0000.0000.0000.0000.0000.000
218A293GLY0-0.007-0.00347.3830.0000.0000.0000.0000.0000.000
219A294GLN0-0.022-0.00141.814-0.003-0.0030.0000.0000.0000.000
220A295ASP-1-0.912-0.97141.501-0.034-0.0340.0000.0000.0000.000
221A296PRO0-0.064-0.01739.573-0.002-0.0020.0000.0000.0000.000
222A297VAL0-0.010-0.01035.8080.0030.0030.0000.0000.0000.000
223A298SER0-0.069-0.05834.901-0.004-0.0040.0000.0000.0000.000
224A299MET00.0470.01429.0750.0010.0010.0000.0000.0000.000
225A300SER0-0.097-0.00830.0110.0000.0000.0000.0000.0000.000
226A301LYS11.0020.98631.7660.0530.0530.0000.0000.0000.000
227A302PRO0-0.0160.02034.380-0.004-0.0040.0000.0000.0000.000
228A303THR00.008-0.01234.0160.0010.0010.0000.0000.0000.000
229A304PHE0-0.0340.00237.1250.0020.0020.0000.0000.0000.000