FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 17QMZ

Calculation Name: 5IF3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5IF3

Chain ID: A

ChEMBL ID:

UniProt ID: A4JKB1

Base Structure: X-ray

Registration Date: 2023-09-20

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 OptAll
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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2051161.85505
FMO2-HF: Nuclear repulsion 1974019.636914
FMO2-HF: Total energy -77142.218135
FMO2-MP2: Total energy -77368.559488


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:6:CYS)


Summations of interaction energy for fragment #1(A:6:CYS)
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.
-1.2360.015999999999999-0.004-0.54-0.7090.003
Interaction energy analysis for fragmet #1(A:6:CYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.024 / q_NPA : -0.027
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].
3A8PRO00.0570.0373.851-0.5770.675-0.004-0.540-0.7090.003
4A9ARG10.8770.9316.1350.3750.3750.0000.0000.0000.000
5A10VAL00.0070.0157.9040.2440.2440.0000.0000.0000.000
6A11ARG10.8160.8786.332-0.587-0.5870.0000.0000.0000.000
7A12ALA00.0030.00112.4790.0670.0670.0000.0000.0000.000
8A13ILE00.0130.02115.736-0.008-0.0080.0000.0000.0000.000
9A14VAL0-0.0050.00218.4870.0040.0040.0000.0000.0000.000
10A15THR00.0570.04021.311-0.004-0.0040.0000.0000.0000.000
11A16GLY00.010-0.00624.440-0.002-0.0020.0000.0000.0000.000
12A17HIS0-0.049-0.01620.7180.0140.0140.0000.0000.0000.000
13A18THR0-0.042-0.01323.257-0.017-0.0170.0000.0000.0000.000
14A19ARG10.9670.97425.4290.1110.1110.0000.0000.0000.000
15A20GLY00.0240.01528.1530.0030.0030.0000.0000.0000.000
16A21LEU00.0530.02727.188-0.012-0.0120.0000.0000.0000.000
17A22GLY00.0550.03024.979-0.012-0.0120.0000.0000.0000.000
18A23ALA0-0.031-0.00923.313-0.018-0.0180.0000.0000.0000.000
19A24SER00.0420.01522.778-0.019-0.0190.0000.0000.0000.000
20A25LEU0-0.029-0.00821.990-0.019-0.0190.0000.0000.0000.000
21A26ALA00.0100.00318.898-0.030-0.0300.0000.0000.0000.000
22A27GLU-1-0.822-0.92118.049-0.306-0.3060.0000.0000.0000.000
23A28GLN0-0.009-0.00818.766-0.028-0.0280.0000.0000.0000.000
24A29LEU0-0.044-0.02416.219-0.031-0.0310.0000.0000.0000.000
25A30LEU00.0200.01012.885-0.079-0.0790.0000.0000.0000.000
26A31GLN0-0.045-0.00914.227-0.086-0.0860.0000.0000.0000.000
27A32GLN0-0.081-0.03715.3650.0090.0090.0000.0000.0000.000
28A33ASP-1-0.846-0.9108.298-1.875-1.8750.0000.0000.0000.000
29A34ILE0-0.0390.00510.461-0.131-0.1310.0000.0000.0000.000
30A35ALA00.0450.0199.2230.0420.0420.0000.0000.0000.000
31A36VAL0-0.045-0.02911.3760.1510.1510.0000.0000.0000.000
32A37LEU00.0000.01414.665-0.005-0.0050.0000.0000.0000.000
33A38GLY00.0300.01016.1430.0160.0160.0000.0000.0000.000
34A39VAL0-0.007-0.00819.2620.0190.0190.0000.0000.0000.000
35A40SER00.005-0.02122.1230.0060.0060.0000.0000.0000.000
36A41ARG10.8550.92525.1680.0630.0630.0000.0000.0000.000
37A42SER0-0.0020.00125.9460.0070.0070.0000.0000.0000.000
38A43ARG10.8850.93019.5780.1530.1530.0000.0000.0000.000
39A44HIS0-0.014-0.02421.3140.0120.0120.0000.0000.0000.000
40A45PRO0-0.029-0.02022.650-0.014-0.0140.0000.0000.0000.000
41A46SER00.0020.00122.5590.0000.0000.0000.0000.0000.000
42A47LEU00.0160.02417.929-0.028-0.0280.0000.0000.0000.000
43A48ALA00.0480.01516.533-0.057-0.0570.0000.0000.0000.000
44A49ALA0-0.024-0.01716.099-0.065-0.0650.0000.0000.0000.000
45A50THR0-0.054-0.02217.498-0.008-0.0080.0000.0000.0000.000
46A51ALA0-0.030-0.00913.904-0.043-0.0430.0000.0000.0000.000
47A52GLY00.0540.03411.787-0.193-0.1930.0000.0000.0000.000
48A53ASP-1-0.899-0.9608.374-0.870-0.8700.0000.0000.0000.000
49A54ARG10.7260.8428.0721.3841.3840.0000.0000.0000.000
50A55LEU0-0.029-0.00310.1210.1460.1460.0000.0000.0000.000
51A56VAL00.0100.00211.6790.0210.0210.0000.0000.0000.000
52A57GLU-1-0.766-0.87914.309-0.215-0.2150.0000.0000.0000.000
53A58THR0-0.009-0.00618.0650.0280.0280.0000.0000.0000.000
54A59GLU-1-0.893-0.93720.178-0.104-0.1040.0000.0000.0000.000
55A60LEU00.029-0.00523.6820.0140.0140.0000.0000.0000.000
56A61ASP-1-0.779-0.84226.098-0.057-0.0570.0000.0000.0000.000
57A62LEU00.004-0.00725.2700.0080.0080.0000.0000.0000.000
58A63SER0-0.061-0.05329.2000.0040.0040.0000.0000.0000.000
59A64ASP-1-0.823-0.90431.637-0.010-0.0100.0000.0000.0000.000
60A65THR00.027-0.01231.2630.0020.0020.0000.0000.0000.000
61A66ALA00.0220.02731.7420.0060.0060.0000.0000.0000.000
62A67ALA00.0100.00328.9980.0060.0060.0000.0000.0000.000
63A68VAL0-0.032-0.02026.9150.0040.0040.0000.0000.0000.000
64A69ALA0-0.003-0.00326.7490.0080.0080.0000.0000.0000.000
65A70ALA00.0020.00227.4790.0110.0110.0000.0000.0000.000
66A71TRP0-0.006-0.01519.1010.0140.0140.0000.0000.0000.000
67A72LEU0-0.068-0.03622.5730.0130.0130.0000.0000.0000.000
68A73ALA0-0.0200.00123.2050.0170.0170.0000.0000.0000.000
69A74GLY00.0240.02722.4000.0130.0130.0000.0000.0000.000
70A75GLY0-0.004-0.01718.4490.0150.0150.0000.0000.0000.000
71A76ALA0-0.0090.00316.3870.0390.0390.0000.0000.0000.000
72A77LEU00.0590.02615.4630.0240.0240.0000.0000.0000.000
73A78ARG10.9440.95915.629-0.175-0.1750.0000.0000.0000.000
74A79SER00.001-0.00311.4190.0500.0500.0000.0000.0000.000
75A80PHE0-0.0200.00611.0420.1520.1520.0000.0000.0000.000
76A81VAL0-0.0060.00011.390-0.014-0.0140.0000.0000.0000.000
77A82ASP-1-0.856-0.91510.5090.9380.9380.0000.0000.0000.000
78A83GLY00.0380.0298.3870.2130.2130.0000.0000.0000.000
79A84ALA0-0.0070.0188.579-0.062-0.0620.0000.0000.0000.000
80A85SER0-0.046-0.02410.0360.0230.0230.0000.0000.0000.000
81A86LEU0-0.061-0.02612.1690.0070.0070.0000.0000.0000.000
82A87VAL00.0200.01913.389-0.048-0.0480.0000.0000.0000.000
83A88LEU0-0.003-0.00715.6180.0220.0220.0000.0000.0000.000
84A89LEU00.003-0.00318.385-0.001-0.0010.0000.0000.0000.000
85A90PHE00.0420.02319.3060.0080.0080.0000.0000.0000.000
86A91ASN0-0.003-0.01323.495-0.006-0.0060.0000.0000.0000.000
87A92ASN0-0.027-0.04825.7200.0040.0040.0000.0000.0000.000
88A93ALA0-0.046-0.01427.4420.0020.0020.0000.0000.0000.000
89A94GLY00.018-0.00829.2760.0070.0070.0000.0000.0000.000
90A95VAL0-0.071-0.02933.066-0.006-0.0060.0000.0000.0000.000
91A96VAL00.012-0.00136.4600.0030.0030.0000.0000.0000.000
92A97ASP-1-0.913-0.93739.621-0.050-0.0500.0000.0000.0000.000
93A98PRO0-0.028-0.01241.2260.0010.0010.0000.0000.0000.000
94A99ILE00.0150.00143.0740.0020.0020.0000.0000.0000.000
95A100GLY00.0300.01445.9520.0000.0000.0000.0000.0000.000
96A101PRO00.003-0.00449.5680.0010.0010.0000.0000.0000.000
97A102LEU00.0590.00850.0100.0000.0000.0000.0000.0000.000
98A103ALA0-0.018-0.00652.1160.0000.0000.0000.0000.0000.000
99A104ALA0-0.018-0.00151.6320.0000.0000.0000.0000.0000.000
100A105GLN0-0.084-0.04147.6420.0000.0000.0000.0000.0000.000
101A106ASP-1-0.764-0.88445.558-0.025-0.0250.0000.0000.0000.000
102A107PRO00.026-0.00145.936-0.001-0.0010.0000.0000.0000.000
103A108ALA0-0.0040.00943.4410.0010.0010.0000.0000.0000.000
104A109LEU0-0.015-0.01441.282-0.001-0.0010.0000.0000.0000.000
105A110VAL00.0030.00441.083-0.002-0.0020.0000.0000.0000.000
106A111ALA0-0.0080.00141.1720.0000.0000.0000.0000.0000.000
107A112ARG10.8700.91533.2490.0490.0490.0000.0000.0000.000
108A113ALA00.0400.01936.482-0.002-0.0020.0000.0000.0000.000
109A114VAL0-0.007-0.01236.780-0.001-0.0010.0000.0000.0000.000
110A115ALA0-0.014-0.00334.7870.0010.0010.0000.0000.0000.000
111A116LEU0-0.022-0.01330.5400.0000.0000.0000.0000.0000.000
112A117ASN0-0.039-0.03431.882-0.007-0.0070.0000.0000.0000.000
113A118VAL0-0.006-0.00333.692-0.001-0.0010.0000.0000.0000.000
114A119ALA00.0010.01532.5620.0030.0030.0000.0000.0000.000
115A120ALA00.0600.03128.5250.0050.0050.0000.0000.0000.000
116A121PRO00.0030.00527.8580.0040.0040.0000.0000.0000.000
117A122LEU00.0060.01827.8840.0030.0030.0000.0000.0000.000
118A123MET0-0.043-0.01228.3650.0060.0060.0000.0000.0000.000
119A124LEU0-0.004-0.00522.9020.0100.0100.0000.0000.0000.000
120A125SER0-0.037-0.04723.7840.0050.0050.0000.0000.0000.000
121A126ALA0-0.0240.00324.8820.0070.0070.0000.0000.0000.000
122A127ALA00.0400.00623.3730.0130.0130.0000.0000.0000.000
123A128LEU0-0.007-0.00518.0180.0200.0200.0000.0000.0000.000
124A129VAL00.005-0.00220.1400.0260.0260.0000.0000.0000.000
125A130GLN0-0.061-0.02522.1510.0070.0070.0000.0000.0000.000
126A131ALA0-0.030-0.00218.3670.0160.0160.0000.0000.0000.000
127A132ALA0-0.002-0.00416.4630.0500.0500.0000.0000.0000.000
128A133ALA00.0330.02915.877-0.028-0.0280.0000.0000.0000.000
129A134ALA0-0.0210.00316.916-0.019-0.0190.0000.0000.0000.000
130A135PRO00.002-0.02014.1230.0460.0460.0000.0000.0000.000
131A136THR0-0.040-0.02113.044-0.031-0.0310.0000.0000.0000.000
132A137GLU-1-0.708-0.82215.470-0.030-0.0300.0000.0000.0000.000
133A138CYS0-0.025-0.00417.0200.0010.0010.0000.0000.0000.000
134A139ARG10.8350.88819.6640.0640.0640.0000.0000.0000.000
135A140VAL00.0400.02521.503-0.017-0.0170.0000.0000.0000.000
136A141LEU0-0.019-0.01024.0500.0010.0010.0000.0000.0000.000
137A142HIS00.011-0.00425.993-0.014-0.0140.0000.0000.0000.000
138A143VAL00.0050.02027.495-0.002-0.0020.0000.0000.0000.000
139A144SER00.023-0.00230.1750.0050.0050.0000.0000.0000.000
140A145SER00.031-0.01433.856-0.006-0.0060.0000.0000.0000.000
141A146GLY00.0490.02736.9680.0030.0030.0000.0000.0000.000
142A147ALA00.020-0.00340.1250.0040.0040.0000.0000.0000.000
143A148ALA0-0.0140.00137.7750.0030.0030.0000.0000.0000.000
144A149ARG10.7680.85135.0850.0470.0470.0000.0000.0000.000
145A150ASN0-0.032-0.00542.3850.0030.0030.0000.0000.0000.000
146A151ALA00.0360.02044.722-0.001-0.0010.0000.0000.0000.000
147A152TYR00.0340.00243.325-0.001-0.0010.0000.0000.0000.000
148A153ALA00.0330.00948.0490.0010.0010.0000.0000.0000.000
149A154GLY00.0000.00749.080-0.002-0.0020.0000.0000.0000.000
150A155TRP00.0560.01840.311-0.002-0.0020.0000.0000.0000.000
151A156SER00.0080.01144.042-0.001-0.0010.0000.0000.0000.000
152A157VAL00.0830.04941.0860.0010.0010.0000.0000.0000.000
153A158TYR00.0350.03035.4110.0000.0000.0000.0000.0000.000
154A159CYS0-0.042-0.00739.726-0.001-0.0010.0000.0000.0000.000
155A160ALA00.0150.01341.0750.0000.0000.0000.0000.0000.000
156A161THR0-0.020-0.02837.2560.0000.0000.0000.0000.0000.000
157A162LYS10.9030.95132.1490.0620.0620.0000.0000.0000.000
158A163ALA00.0180.00736.6030.0000.0000.0000.0000.0000.000
159A164ALA0-0.031-0.00537.4670.0030.0030.0000.0000.0000.000
160A165LEU0-0.019-0.00331.4150.0030.0030.0000.0000.0000.000
161A166ASP-1-0.766-0.82833.759-0.037-0.0370.0000.0000.0000.000
162A167HIS00.0160.00835.798-0.001-0.0010.0000.0000.0000.000
163A168HIS00.0600.04529.527-0.002-0.0020.0000.0000.0000.000
164A169ALA00.007-0.00531.5870.0040.0040.0000.0000.0000.000
165A170ARG10.8370.90832.5310.0240.0240.0000.0000.0000.000
166A171ALA0-0.0030.01135.4490.0020.0020.0000.0000.0000.000
167A172VAL00.0480.01928.9930.0030.0030.0000.0000.0000.000
168A173ALA0-0.058-0.02931.2030.0040.0040.0000.0000.0000.000
169A174LEU0-0.049-0.02032.2310.0010.0010.0000.0000.0000.000
170A175ASP-1-0.892-0.92931.3800.0320.0320.0000.0000.0000.000
171A176ALA0-0.019-0.00731.1430.0000.0000.0000.0000.0000.000
172A177ASN0-0.069-0.04326.2450.0120.0120.0000.0000.0000.000
173A178ARG10.8220.89818.543-0.152-0.1520.0000.0000.0000.000
174A179ALA00.009-0.00720.6970.0030.0030.0000.0000.0000.000
175A180LEU0-0.0150.01021.485-0.006-0.0060.0000.0000.0000.000
176A181ARG10.8400.90922.1670.0050.0050.0000.0000.0000.000
177A182ILE00.0190.01324.673-0.005-0.0050.0000.0000.0000.000
178A183CYS0-0.033-0.00427.2930.0010.0010.0000.0000.0000.000
179A184SER00.020-0.01629.100-0.004-0.0040.0000.0000.0000.000
180A185VAL00.0170.00129.0290.0030.0030.0000.0000.0000.000
181A186ALA0-0.0120.00831.820-0.003-0.0030.0000.0000.0000.000
182A187PRO0-0.017-0.00430.635-0.001-0.0010.0000.0000.0000.000
183A188GLY00.0100.00632.438-0.006-0.0060.0000.0000.0000.000
184A189VAL0-0.020-0.00232.2730.0010.0010.0000.0000.0000.000
185A190VAL00.0020.00234.8650.0030.0030.0000.0000.0000.000
186A222SER0-0.034-0.01757.5310.0000.0000.0000.0000.0000.000
187A223THR0-0.031-0.04758.0000.0000.0000.0000.0000.0000.000
188A224PRO00.0370.00357.041-0.001-0.0010.0000.0000.0000.000
189A225ASP-1-0.846-0.92358.9430.0050.0050.0000.0000.0000.000
190A226GLU-1-0.887-0.92861.7470.0040.0040.0000.0000.0000.000
191A227ALA00.0200.01457.401-0.001-0.0010.0000.0000.0000.000
192A228ALA00.0250.00959.525-0.001-0.0010.0000.0000.0000.000
193A229ARG10.9260.97160.996-0.004-0.0040.0000.0000.0000.000
194A230HIS00.0310.02661.164-0.001-0.0010.0000.0000.0000.000
195A231LEU00.016-0.00156.232-0.001-0.0010.0000.0000.0000.000
196A232ILE0-0.005-0.00360.436-0.001-0.0010.0000.0000.0000.000
197A233ARG10.8690.93063.2380.0010.0010.0000.0000.0000.000
198A234TYR00.0150.01257.9510.0000.0000.0000.0000.0000.000
199A235ALA00.0170.00160.716-0.001-0.0010.0000.0000.0000.000
200A236LEU0-0.053-0.01762.298-0.001-0.0010.0000.0000.0000.000
201A237SER0-0.055-0.02364.4660.0000.0000.0000.0000.0000.000
202A238ASP-1-0.888-0.95865.745-0.008-0.0080.0000.0000.0000.000
203A239ALA0-0.026-0.01164.410-0.001-0.0010.0000.0000.0000.000
204A240PHE0-0.051-0.01557.9450.0000.0000.0000.0000.0000.000
205A241GLY0-0.017-0.00958.207-0.001-0.0010.0000.0000.0000.000
206A242ALA0-0.045-0.02158.908-0.001-0.0010.0000.0000.0000.000
207A243GLU-1-0.886-0.94256.427-0.016-0.0160.0000.0000.0000.000
208A244PRO0-0.073-0.02952.4010.0010.0010.0000.0000.0000.000
209A245THR0-0.052-0.03049.9230.0000.0000.0000.0000.0000.000
210A246ALA00.0180.00953.2220.0000.0000.0000.0000.0000.000
211A247ASP-1-0.794-0.88053.643-0.001-0.0010.0000.0000.0000.000
212A248VAL00.0310.00155.7030.0000.0000.0000.0000.0000.000
213A249ARG10.8040.87851.417-0.001-0.0010.0000.0000.0000.000
214A250ASN0-0.017-0.00355.9350.0010.0010.0000.0000.0000.000
215A251LEU0-0.0240.00459.912-0.001-0.0010.0000.0000.0000.000
216A252PRO0-0.023-0.00262.7060.0010.0010.0000.0000.0000.000