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: 9GJY2

Calculation Name: 3IEF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3IEF

Chain ID: A

ChEMBL ID:

UniProt ID: Q6G1R9

Base Structure: X-ray

Registration Date: 2023-06-20

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 -2432547.728486
FMO2-HF: Nuclear repulsion 2343971.222691
FMO2-HF: Total energy -88576.505795
FMO2-MP2: Total energy -88833.162489


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:LYS)


Summations of interaction energy for fragment #1(A:2:LYS)
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.
-119.302-111.727.98-5.408-10.154-0.053
Interaction energy analysis for fragmet #1(A:2:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.912 / q_NPA : 0.954
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].
3A4GLN0-0.004-0.0172.868-10.357-8.0090.080-0.827-1.601-0.001
4A5ALA0-0.0010.0244.8455.4585.560-0.001-0.009-0.0920.000
5A6ARG10.8490.9208.13929.14029.1400.0000.0000.0000.000
6A7VAL0-0.009-0.00810.7761.7701.7700.0000.0000.0000.000
7A8LEU00.0280.01413.8010.0380.0380.0000.0000.0000.000
8A9THR0-0.025-0.06016.6300.9150.9150.0000.0000.0000.000
9A10LEU00.0390.01419.1460.0030.0030.0000.0000.0000.000
10A11TYR0-0.058-0.02620.5650.5780.5780.0000.0000.0000.000
11A12PRO00.0500.02316.639-0.477-0.4770.0000.0000.0000.000
12A13GLU-1-0.841-0.94016.291-15.493-15.4930.0000.0000.0000.000
13A14MET0-0.112-0.03718.7160.1920.1920.0000.0000.0000.000
14A15PHE0-0.031-0.00513.183-0.461-0.4610.0000.0000.0000.000
15A16PRO00.0320.00011.2230.0060.0060.0000.0000.0000.000
16A17GLY00.0790.04313.2820.5140.5140.0000.0000.0000.000
17A18PHE0-0.003-0.00915.802-0.546-0.5460.0000.0000.0000.000
18A19LEU00.0090.01912.135-0.267-0.2670.0000.0000.0000.000
19A20GLY0-0.007-0.00511.930-1.892-1.8920.0000.0000.0000.000
20A21CYS0-0.063-0.03513.0290.4080.4080.0000.0000.0000.000
21A22SER00.0090.00514.423-0.869-0.8690.0000.0000.0000.000
22A23LEU00.033-0.01413.734-0.974-0.9740.0000.0000.0000.000
23A24ALA00.0550.04911.147-1.658-1.6580.0000.0000.0000.000
24A25GLY00.0940.0559.779-2.842-2.8420.0000.0000.0000.000
25A26GLN0-0.040-0.0179.589-1.254-1.2540.0000.0000.0000.000
26A27ALA0-0.003-0.0207.496-1.643-1.6430.0000.0000.0000.000
27A28LEU00.0060.0245.265-5.206-5.2060.0000.0000.0000.000
28A29LYS10.8770.9395.14017.63417.695-0.0010.000-0.0600.000
29A30GLN0-0.045-0.0236.752-0.479-0.4790.0000.0000.0000.000
30A31GLY0-0.0050.0082.705-2.968-2.4050.342-0.319-0.586-0.001
31A32ILE0-0.018-0.0152.401-8.998-8.7494.718-1.528-3.440-0.027
32A33TRP0-0.049-0.0372.785-4.081-1.1790.989-1.738-2.153-0.017
33A34SER0-0.010-0.0132.110-11.701-10.4471.842-0.970-2.125-0.007
34A35LEU0-0.027-0.0123.7064.5474.6500.011-0.017-0.0970.000
35A36GLU-1-0.879-0.9137.314-29.592-29.5920.0000.0000.0000.000
36A37THR0-0.052-0.0239.1871.4791.4790.0000.0000.0000.000
37A38VAL00.0490.02112.963-0.101-0.1010.0000.0000.0000.000
38A39GLN0-0.008-0.00815.7010.8870.8870.0000.0000.0000.000
39A40ILE00.0540.01819.2220.2650.2650.0000.0000.0000.000
40A41ARG10.9400.95021.66111.93611.9360.0000.0000.0000.000
41A42ASP-1-0.943-0.95820.286-14.643-14.6430.0000.0000.0000.000
42A43PHE0-0.031-0.02619.2300.1600.1600.0000.0000.0000.000
43A44ALA0-0.038-0.01624.8840.3630.3630.0000.0000.0000.000
44A45LEU0-0.0390.00128.2810.3600.3600.0000.0000.0000.000
45A46ASP-1-0.819-0.88429.231-9.903-9.9030.0000.0000.0000.000
46A47LYS10.8060.87731.7919.4509.4500.0000.0000.0000.000
47A48HIS0-0.003-0.00334.0220.1730.1730.0000.0000.0000.000
48A49HIS0-0.021-0.01728.787-0.101-0.1010.0000.0000.0000.000
49A50SER0-0.002-0.00930.9780.0000.0000.0000.0000.0000.000
50A51VAL00.0230.01426.005-0.103-0.1030.0000.0000.0000.000
51A52ASP-1-0.943-0.97328.819-10.047-10.0470.0000.0000.0000.000
52A53ASP-1-0.846-0.91731.367-8.511-8.5110.0000.0000.0000.000
53A54THR0-0.045-0.04634.9400.0050.0050.0000.0000.0000.000
54A55PRO0-0.0110.01537.391-0.048-0.0480.0000.0000.0000.000
55A56ALA00.000-0.01238.3150.2520.2520.0000.0000.0000.000
56A57GLY0-0.030-0.01740.499-0.003-0.0030.0000.0000.0000.000
57A58GLY0-0.0190.00342.5980.1190.1190.0000.0000.0000.000
58A59GLY00.028-0.00239.782-0.099-0.0990.0000.0000.0000.000
59A60ALA0-0.051-0.01938.2650.1260.1260.0000.0000.0000.000
60A61GLY00.0250.00735.8730.0580.0580.0000.0000.0000.000
61A62MET0-0.047-0.00633.5390.2300.2300.0000.0000.0000.000
62A63VAL0-0.0140.00131.913-0.132-0.1320.0000.0000.0000.000
63A64MET0-0.038-0.01124.072-0.071-0.0710.0000.0000.0000.000
64A65ARG00.0630.03029.3260.1090.1090.0000.0000.0000.000
65A66ALA00.019-0.01127.850-0.417-0.4170.0000.0000.0000.000
66A67ASP-1-0.869-0.93627.125-10.749-10.7490.0000.0000.0000.000
67A68VAL00.002-0.00325.049-0.411-0.4110.0000.0000.0000.000
68A69LEU00.003-0.00822.297-0.665-0.6650.0000.0000.0000.000
69A70ALA0-0.0010.00622.226-0.695-0.6950.0000.0000.0000.000
70A71ALA0-0.0050.01422.295-0.614-0.6140.0000.0000.0000.000
71A72ALA00.0340.01819.704-0.598-0.5980.0000.0000.0000.000
72A73LEU0-0.035-0.02817.369-1.179-1.1790.0000.0000.0000.000
73A74ASP-1-0.829-0.86317.742-14.647-14.6470.0000.0000.0000.000
74A75SER0-0.098-0.04217.699-0.373-0.3730.0000.0000.0000.000
75A76CYS0-0.038-0.02413.157-1.223-1.2230.0000.0000.0000.000
76A77PRO0-0.0090.01711.8081.1911.1910.0000.0000.0000.000
77A78ASN00.013-0.01713.333-0.208-0.2080.0000.0000.0000.000
78A79ASP-1-0.874-0.9339.780-27.048-27.0480.0000.0000.0000.000
79A80SER0-0.047-0.0389.891-1.931-1.9310.0000.0000.0000.000
80A81PRO00.0020.00811.9581.1851.1850.0000.0000.0000.000
81A82ARG10.9771.00514.33815.58215.5820.0000.0000.0000.000
82A83LEU0-0.008-0.00116.1510.7860.7860.0000.0000.0000.000
83A84LEU00.0210.01518.457-0.534-0.5340.0000.0000.0000.000
84A85MET0-0.075-0.03717.6410.4640.4640.0000.0000.0000.000
85A86SER00.013-0.00222.1490.4110.4110.0000.0000.0000.000
86A87PRO00.0310.00425.866-0.111-0.1110.0000.0000.0000.000
87A88ARG10.8320.92228.64510.17410.1740.0000.0000.0000.000
88A89GLY0-0.0140.01625.7060.0660.0660.0000.0000.0000.000
89A90ARG10.9000.96022.50012.73412.7340.0000.0000.0000.000
90A91LEU00.0220.00125.114-0.373-0.3730.0000.0000.0000.000
91A92LEU0-0.0270.00118.716-0.134-0.1340.0000.0000.0000.000
92A93ASN00.0120.00021.9790.0660.0660.0000.0000.0000.000
93A94GLN00.0660.02518.003-0.405-0.4050.0000.0000.0000.000
94A95ALA0-0.014-0.01819.021-0.608-0.6080.0000.0000.0000.000
95A96TYR0-0.089-0.08218.964-0.600-0.6000.0000.0000.0000.000
96A97ALA00.0600.02916.212-0.711-0.7110.0000.0000.0000.000
97A98ARG10.7970.84814.61412.17912.1790.0000.0000.0000.000
98A99SER0-0.108-0.04114.158-0.788-0.7880.0000.0000.0000.000
99A100LEU00.0930.04113.257-0.649-0.6490.0000.0000.0000.000
100A101ALA0-0.012-0.00110.337-1.528-1.5280.0000.0000.0000.000
101A102ARG10.8720.9419.37914.76814.7680.0000.0000.0000.000
102A103SER0-0.0080.0109.5150.6760.6760.0000.0000.0000.000
103A104SER0-0.018-0.0115.661-0.472-0.4720.0000.0000.0000.000
104A105GLY00.031-0.0015.815-6.112-6.1120.0000.0000.0000.000
105A106VAL0-0.022-0.0127.8443.1363.1360.0000.0000.0000.000
106A107THR00.0490.03110.513-1.793-1.7930.0000.0000.0000.000
107A108LEU0-0.055-0.02413.1291.4781.4780.0000.0000.0000.000
108A109VAL00.0740.03115.698-0.406-0.4060.0000.0000.0000.000
109A110CYS0-0.077-0.03618.0780.4180.4180.0000.0000.0000.000
110A111GLY00.0700.04120.8650.2340.2340.0000.0000.0000.000
111A112ARG10.8290.90123.57512.35112.3510.0000.0000.0000.000
112A113PHE00.011-0.00726.4100.2000.2000.0000.0000.0000.000
113A114GLU-1-0.945-0.96529.274-10.225-10.2250.0000.0000.0000.000
114A115GLY00.0650.03630.3840.3530.3530.0000.0000.0000.000
115A116VAL0-0.021-0.02425.863-0.256-0.2560.0000.0000.0000.000
116A117ASP-1-0.810-0.89729.147-9.433-9.4330.0000.0000.0000.000
117A118GLU-1-0.837-0.93029.195-10.222-10.2220.0000.0000.0000.000
118A119ARG10.8530.92429.7949.0779.0770.0000.0000.0000.000
119A120ILE0-0.055-0.01524.435-0.192-0.1920.0000.0000.0000.000
120A121ILE0-0.022-0.00625.109-0.563-0.5630.0000.0000.0000.000
121A122GLU-1-0.908-0.96125.529-9.947-9.9470.0000.0000.0000.000
122A123ALA0-0.041-0.01526.671-0.212-0.2120.0000.0000.0000.000
123A124ARG10.6920.78921.33312.72412.7240.0000.0000.0000.000
124A125GLU-1-0.964-0.97621.267-13.393-13.3930.0000.0000.0000.000
125A126LEU0-0.067-0.01719.987-0.650-0.6500.0000.0000.0000.000
126A127GLU-1-0.794-0.86620.468-12.777-12.7770.0000.0000.0000.000
127A128GLU-1-0.801-0.90121.399-11.555-11.5550.0000.0000.0000.000
128A129VAL0-0.059-0.03419.7840.1760.1760.0000.0000.0000.000
129A130SER00.0610.04422.942-0.225-0.2250.0000.0000.0000.000
130A131ILE0-0.030-0.03421.705-0.173-0.1730.0000.0000.0000.000
131A132GLY0-0.032-0.02924.4140.1300.1300.0000.0000.0000.000
132A133ASP-1-0.920-0.93328.218-9.632-9.6320.0000.0000.0000.000
133A134TYR0-0.066-0.04627.0060.2230.2230.0000.0000.0000.000
134A135ILE00.0330.02429.940-0.302-0.3020.0000.0000.0000.000
135A136LEU0-0.026-0.01224.849-0.012-0.0120.0000.0000.0000.000
136A137SER0-0.031-0.02826.3580.0860.0860.0000.0000.0000.000
137A138GLY00.0550.01624.9810.1750.1750.0000.0000.0000.000
138A139GLY00.0300.02522.296-0.041-0.0410.0000.0000.0000.000
139A140GLU-1-0.693-0.81819.227-14.635-14.6350.0000.0000.0000.000
140A141THR0-0.061-0.02519.276-0.481-0.4810.0000.0000.0000.000
141A142ALA00.0410.01420.862-0.207-0.2070.0000.0000.0000.000
142A143ALA00.0360.01116.078-0.398-0.3980.0000.0000.0000.000
143A144LEU0-0.0080.00515.127-0.993-0.9930.0000.0000.0000.000
144A145VAL00.0150.01716.362-0.647-0.6470.0000.0000.0000.000
145A146LEU00.0080.00715.470-0.129-0.1290.0000.0000.0000.000
146A147LEU0-0.004-0.01410.693-0.900-0.9000.0000.0000.0000.000
147A148ASP-1-0.955-0.98013.071-18.138-18.1380.0000.0000.0000.000
148A149ALA0-0.035-0.02114.908-0.051-0.0510.0000.0000.0000.000
149A150ILE0-0.008-0.0029.9600.2550.2550.0000.0000.0000.000
150A151VAL00.0430.0138.570-0.301-0.3010.0000.0000.0000.000
151A152ARG10.9010.9549.88915.31315.3130.0000.0000.0000.000
152A153LEU0-0.051-0.03411.8291.1521.1520.0000.0000.0000.000
153A154LEU0-0.0060.0255.498-0.012-0.0120.0000.0000.0000.000
154A155PRO00.0280.0396.9810.4460.4460.0000.0000.0000.000
155A156GLY0-0.101-0.0616.723-0.559-0.5590.0000.0000.0000.000
156A157VAL0-0.050-0.0337.7360.2770.2770.0000.0000.0000.000
157A158MET00.0780.05010.1600.7760.7760.0000.0000.0000.000
158A159GLY0-0.035-0.00713.6020.1910.1910.0000.0000.0000.000
159A160ASN00.010-0.04410.7071.9691.9690.0000.0000.0000.000
160A161GLU-1-0.904-0.94113.313-17.416-17.4160.0000.0000.0000.000
161A162ILE0-0.066-0.03415.4580.5450.5450.0000.0000.0000.000
162A163SER0-0.028-0.00116.9770.7730.7730.0000.0000.0000.000
163A164ALA0-0.017-0.00619.0500.1430.1430.0000.0000.0000.000
164A165LYS10.9630.96818.52512.74812.7480.0000.0000.0000.000
165A166CYS0-0.069-0.03820.465-0.030-0.0300.0000.0000.0000.000
166A167GLU-1-0.899-0.93021.286-12.393-12.3930.0000.0000.0000.000
167A168SER00.038-0.00324.8170.1620.1620.0000.0000.0000.000
168A169PHE00.022-0.00123.8880.3610.3610.0000.0000.0000.000
169A170GLU-1-0.753-0.83723.043-11.902-11.9020.0000.0000.0000.000
170A171ASN0-0.066-0.03527.7310.1470.1470.0000.0000.0000.000
171A172GLY00.0230.00830.6270.3030.3030.0000.0000.0000.000
172A173LEU0-0.050-0.03531.8600.3200.3200.0000.0000.0000.000
173A174LEU0-0.017-0.00331.381-0.316-0.3160.0000.0000.0000.000
174A175GLU-1-0.888-0.94228.368-9.867-9.8670.0000.0000.0000.000
175A176HIS0-0.050-0.02331.5700.1490.1490.0000.0000.0000.000
176A177PRO0-0.0070.00133.725-0.184-0.1840.0000.0000.0000.000
177A178GLN0-0.002-0.01030.0460.2330.2330.0000.0000.0000.000
178A179TYR00.0340.00035.0160.1540.1540.0000.0000.0000.000
179A180THR00.0090.00834.613-0.077-0.0770.0000.0000.0000.000
180A181ARG10.9560.99936.9108.1718.1710.0000.0000.0000.000
181A182PRO00.010-0.00838.478-0.162-0.1620.0000.0000.0000.000
182A183ALA00.027-0.00141.967-0.019-0.0190.0000.0000.0000.000
183A184VAL00.0070.00044.2330.0480.0480.0000.0000.0000.000
184A185PHE00.0000.00443.150-0.040-0.0400.0000.0000.0000.000
185A186GLU-1-0.900-0.94945.261-6.737-6.7370.0000.0000.0000.000
186A187GLY00.0140.00448.0920.0520.0520.0000.0000.0000.000
187A188ARG10.8740.93945.6006.6826.6820.0000.0000.0000.000
188A189GLY00.0440.02846.003-0.076-0.0760.0000.0000.0000.000
189A190ILE0-0.008-0.00240.340-0.097-0.0970.0000.0000.0000.000
190A191PRO0-0.0100.00041.7050.1420.1420.0000.0000.0000.000
191A192PRO00.0900.03643.469-0.118-0.1180.0000.0000.0000.000
192A193VAL00.0220.01942.277-0.036-0.0360.0000.0000.0000.000
193A194LEU0-0.022-0.00538.119-0.103-0.1030.0000.0000.0000.000
194A195THR0-0.040-0.02440.253-0.153-0.1530.0000.0000.0000.000
195A196SER0-0.062-0.03942.8120.0790.0790.0000.0000.0000.000
196A197GLY00.0280.02041.3720.0940.0940.0000.0000.0000.000
197A198HIS00.0170.01742.156-0.144-0.1440.0000.0000.0000.000
198A199HIS00.0760.02036.799-0.054-0.0540.0000.0000.0000.000
199A200LYS10.9490.98238.9697.2787.2780.0000.0000.0000.000
200A201ALA00.0310.01540.661-0.014-0.0140.0000.0000.0000.000
201A202ILE00.0080.00637.147-0.020-0.0200.0000.0000.0000.000
202A203ALA0-0.0050.00136.696-0.070-0.0700.0000.0000.0000.000
203A204ASN00.0270.01037.834-0.189-0.1890.0000.0000.0000.000
204A205TRP00.0640.03039.151-0.068-0.0680.0000.0000.0000.000
205A206ARG10.9500.96233.9658.4618.4610.0000.0000.0000.000
206A207GLN00.0330.03137.136-0.241-0.2410.0000.0000.0000.000
207A208GLN0-0.017-0.00538.1160.0020.0020.0000.0000.0000.000
208A209GLN0-0.055-0.02639.0520.0360.0360.0000.0000.0000.000
209A210ALA00.0480.02735.3770.0020.0020.0000.0000.0000.000
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