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: 43MZN

Calculation Name: 2IZW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2IZW

Chain ID: A

ChEMBL ID:

UniProt ID: Q9E962

Base Structure: X-ray

Registration Date: 2023-06-21

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 178
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1765560.930935
FMO2-HF: Nuclear repulsion 1697876.953311
FMO2-HF: Total energy -67683.977625
FMO2-MP2: Total energy -67883.122314


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:58:GLN)


Summations of interaction energy for fragment #1(A:58:GLN)
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.
-29.861-22.0440.898-4.003-4.71-0.034
Interaction energy analysis for fragmet #1(A:58:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / q_NPA : -0.016
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].
3A60GLY00.0210.0102.678-4.898-2.0300.552-1.476-1.943-0.008
4A61ASP-1-0.876-0.9292.965-28.769-23.9560.347-2.523-2.637-0.026
5A62ILE0-0.054-0.0285.3021.9662.102-0.001-0.004-0.1300.000
6A63THR0-0.024-0.0087.7600.5070.5070.0000.0000.0000.000
7A64PRO0-0.0370.00110.6450.1820.1820.0000.0000.0000.000
8A65ALA00.0210.00613.4360.1130.1130.0000.0000.0000.000
9A66LYS10.9200.95016.9690.3550.3550.0000.0000.0000.000
10A67ASN0-0.0150.00919.4370.0770.0770.0000.0000.0000.000
11A68SER0-0.011-0.00323.1160.0030.0030.0000.0000.0000.000
12A69GLY00.0260.01126.476-0.019-0.0190.0000.0000.0000.000
13A70SER00.010-0.01829.5100.0160.0160.0000.0000.0000.000
14A71LEU0-0.0330.00028.940-0.012-0.0120.0000.0000.0000.000
15A72VAL00.0800.03132.4370.0010.0010.0000.0000.0000.000
16A73ARG10.8840.94936.1000.2090.2090.0000.0000.0000.000
17A74VAL00.0320.01239.488-0.001-0.0010.0000.0000.0000.000
18A75THR0-0.019-0.02041.9500.0120.0120.0000.0000.0000.000
19A76SER0-0.081-0.04845.570-0.004-0.0040.0000.0000.0000.000
20A77SER00.0800.04548.611-0.003-0.0030.0000.0000.0000.000
21A78ALA00.0250.00250.5670.0050.0050.0000.0000.0000.000
22A79THR0-0.027-0.00653.7000.0080.0080.0000.0000.0000.000
23A80ALA00.0350.00654.071-0.004-0.0040.0000.0000.0000.000
24A81GLY0-0.024-0.01853.3700.0020.0020.0000.0000.0000.000
25A82THR0-0.038-0.01351.077-0.002-0.0020.0000.0000.0000.000
26A83GLU-1-0.874-0.96446.781-0.165-0.1650.0000.0000.0000.000
27A84VAL0-0.061-0.01244.398-0.001-0.0010.0000.0000.0000.000
28A85SER0-0.013-0.01442.204-0.004-0.0040.0000.0000.0000.000
29A86GLY00.030-0.00539.4940.0010.0010.0000.0000.0000.000
30A87THR0-0.046-0.02234.962-0.006-0.0060.0000.0000.0000.000
31A88VAL00.0130.01430.553-0.002-0.0020.0000.0000.0000.000
32A89LEU00.0340.01928.939-0.012-0.0120.0000.0000.0000.000
33A90PHE00.0070.00621.956-0.005-0.0050.0000.0000.0000.000
34A91ASN00.0490.00723.194-0.071-0.0710.0000.0000.0000.000
35A92VAL0-0.009-0.00218.8760.0380.0380.0000.0000.0000.000
36A93ARG10.8570.94322.0400.8150.8150.0000.0000.0000.000
37A94ASN00.0010.02125.0110.0540.0540.0000.0000.0000.000
38A95ALA00.030-0.00328.1200.0170.0170.0000.0000.0000.000
39A96THR0-0.017-0.00829.3590.0210.0210.0000.0000.0000.000
40A97GLU-1-0.846-0.92731.024-0.348-0.3480.0000.0000.0000.000
41A98LEU0-0.068-0.01825.4200.0070.0070.0000.0000.0000.000
42A99PRO00.0230.01826.301-0.052-0.0520.0000.0000.0000.000
43A100TRP00.012-0.00619.535-0.055-0.0550.0000.0000.0000.000
44A101LEU00.0180.00820.347-0.045-0.0450.0000.0000.0000.000
45A102SER00.0640.02821.542-0.085-0.0850.0000.0000.0000.000
46A103GLY0-0.055-0.01022.412-0.040-0.0400.0000.0000.0000.000
47A104GLN0-0.019-0.00516.861-0.056-0.0560.0000.0000.0000.000
48A105GLY00.0570.00518.117-0.123-0.1230.0000.0000.0000.000
49A106SER0-0.070-0.03019.254-0.084-0.0840.0000.0000.0000.000
50A107ARG10.9130.96415.9890.8730.8730.0000.0000.0000.000
51A108TYR0-0.0130.00210.817-0.018-0.0180.0000.0000.0000.000
52A109SER00.0440.02614.2100.2710.2710.0000.0000.0000.000
53A110LYS10.8940.95913.3732.4192.4190.0000.0000.0000.000
54A111TYR0-0.058-0.06914.349-0.143-0.1430.0000.0000.0000.000
55A112ARG10.9400.99110.0241.6801.6800.0000.0000.0000.000
56A113VAL0-0.0090.00216.018-0.043-0.0430.0000.0000.0000.000
57A114ARG10.9050.97812.4370.7060.7060.0000.0000.0000.000
58A115TYR00.002-0.02517.2140.0930.0930.0000.0000.0000.000
59A116ALA00.0320.01620.810-0.029-0.0290.0000.0000.0000.000
60A117HIS10.8010.88823.9360.3480.3480.0000.0000.0000.000
61A118PHE00.0620.02626.349-0.006-0.0060.0000.0000.0000.000
62A119THR0-0.011-0.01230.5600.0120.0120.0000.0000.0000.000
63A120TRP0-0.013-0.01133.920-0.017-0.0170.0000.0000.0000.000
64A121GLU-1-0.917-0.96036.794-0.155-0.1550.0000.0000.0000.000
65A122PRO0-0.043-0.00738.602-0.003-0.0030.0000.0000.0000.000
66A123ILE00.0020.01741.7210.0000.0000.0000.0000.0000.000
67A124VAL0-0.049-0.01044.5620.0070.0070.0000.0000.0000.000
68A125GLY00.0520.03247.5060.0010.0010.0000.0000.0000.000
69A126SER00.013-0.03549.628-0.003-0.0030.0000.0000.0000.000
70A127ASN0-0.027-0.01150.503-0.002-0.0020.0000.0000.0000.000
71A128THR0-0.046-0.00849.922-0.002-0.0020.0000.0000.0000.000
72A129ASN00.0510.02151.4880.0000.0000.0000.0000.0000.000
73A130GLY00.046-0.00549.726-0.003-0.0030.0000.0000.0000.000
74A131GLU-1-0.981-1.00446.024-0.135-0.1350.0000.0000.0000.000
75A132VAL00.0190.00841.078-0.006-0.0060.0000.0000.0000.000
76A133ALA00.0260.00340.2890.0050.0050.0000.0000.0000.000
77A134MET0-0.052-0.02533.398-0.006-0.0060.0000.0000.0000.000
78A135ALA00.0120.01734.6290.0110.0110.0000.0000.0000.000
79A136MET0-0.046-0.01426.684-0.013-0.0130.0000.0000.0000.000
80A137LEU0-0.0080.00831.5640.0140.0140.0000.0000.0000.000
81A138TYR0-0.032-0.04526.589-0.008-0.0080.0000.0000.0000.000
82A139ASP-1-0.769-0.89229.898-0.400-0.4000.0000.0000.0000.000
83A140VAL0-0.080-0.03329.7510.0170.0170.0000.0000.0000.000
84A141ALA0-0.051-0.01432.3430.0150.0150.0000.0000.0000.000
85A142ASP-1-0.892-0.93735.527-0.290-0.2900.0000.0000.0000.000
86A143VAL0-0.028-0.02036.413-0.005-0.0050.0000.0000.0000.000
87A144THR00.000-0.00538.7350.0100.0100.0000.0000.0000.000
88A145SER0-0.046-0.03541.9710.0010.0010.0000.0000.0000.000
89A146ILE00.0510.04538.5190.0050.0050.0000.0000.0000.000
90A147THR00.006-0.00242.5680.0050.0050.0000.0000.0000.000
91A148ILE00.0670.02643.432-0.008-0.0080.0000.0000.0000.000
92A149GLU-1-0.915-0.96243.459-0.142-0.1420.0000.0000.0000.000
93A150ARG10.8720.93742.8380.1800.1800.0000.0000.0000.000
94A151LEU0-0.042-0.00137.993-0.009-0.0090.0000.0000.0000.000
95A152MET0-0.038-0.02539.131-0.006-0.0060.0000.0000.0000.000
96A153GLN0-0.082-0.01640.918-0.001-0.0010.0000.0000.0000.000
97A154THR00.0230.02035.380-0.009-0.0090.0000.0000.0000.000
98A155ARG10.8940.91728.2230.3300.3300.0000.0000.0000.000
99A156GLY0-0.025-0.02632.711-0.013-0.0130.0000.0000.0000.000
100A157GLY00.0490.02833.5950.0000.0000.0000.0000.0000.000
101A158THR0-0.093-0.04035.2720.0110.0110.0000.0000.0000.000
102A159TRP00.0360.00537.727-0.007-0.0070.0000.0000.0000.000
103A160GLY0-0.0130.00041.0670.0040.0040.0000.0000.0000.000
104A161PRO00.0320.00943.791-0.005-0.0050.0000.0000.0000.000
105A162ILE00.0120.03544.622-0.003-0.0030.0000.0000.0000.000
106A163TRP00.0230.03844.476-0.005-0.0050.0000.0000.0000.000
107A164SER0-0.018-0.00742.7230.0060.0060.0000.0000.0000.000
108A165PRO00.0150.01139.024-0.009-0.0090.0000.0000.0000.000
109A166THR0-0.0190.00536.2550.0020.0020.0000.0000.0000.000
110A167ARG10.9780.99037.2490.1070.1070.0000.0000.0000.000
111A168LYS10.9020.97633.8160.2020.2020.0000.0000.0000.000
112A169ARG11.0090.98427.2700.2240.2240.0000.0000.0000.000
113A170LEU0-0.0010.03830.4500.0030.0030.0000.0000.0000.000
114A171SER0-0.040-0.03526.379-0.011-0.0110.0000.0000.0000.000
115A172TYR00.0560.02720.463-0.003-0.0030.0000.0000.0000.000
116A173ASP-1-0.796-0.86724.243-0.390-0.3900.0000.0000.0000.000
117A174PRO00.0070.00019.014-0.019-0.0190.0000.0000.0000.000
118A175GLU-1-0.930-0.96920.461-0.395-0.3950.0000.0000.0000.000
119A176HIS10.7940.87421.8690.3720.3720.0000.0000.0000.000
120A177ALA00.0110.03219.9130.0090.0090.0000.0000.0000.000
121A178SER0-0.016-0.00921.9690.0120.0120.0000.0000.0000.000
122A179LEU0-0.011-0.01019.229-0.002-0.0020.0000.0000.0000.000
123A180PRO0-0.048-0.00514.868-0.021-0.0210.0000.0000.0000.000
124A181TRP0-0.025-0.0289.795-0.134-0.1340.0000.0000.0000.000
125A182TYR00.0570.03516.0220.0600.0600.0000.0000.0000.000
126A183LEU00.005-0.01017.902-0.157-0.1570.0000.0000.0000.000
127A184SER0-0.017-0.01318.6830.1630.1630.0000.0000.0000.000
128A185GLY00.018-0.00220.412-0.009-0.0090.0000.0000.0000.000
129A186VAL0-0.011-0.01723.5280.0240.0240.0000.0000.0000.000
130A187SER0-0.0210.00526.9970.0490.0490.0000.0000.0000.000
131A188SER00.0270.01728.990-0.005-0.0050.0000.0000.0000.000
132A189GLY00.0300.00332.178-0.007-0.0070.0000.0000.0000.000
133A190ALA00.0460.02032.159-0.019-0.0190.0000.0000.0000.000
134A191ALA00.0300.01130.154-0.023-0.0230.0000.0000.0000.000
135A192ALA00.010-0.00227.991-0.035-0.0350.0000.0000.0000.000
136A193GLY00.0470.02927.168-0.045-0.0450.0000.0000.0000.000
137A194ASN00.0330.00227.131-0.030-0.0300.0000.0000.0000.000
138A195ILE0-0.017-0.00122.751-0.034-0.0340.0000.0000.0000.000
139A196GLN0-0.016-0.00422.500-0.097-0.0970.0000.0000.0000.000
140A197THR0-0.054-0.00223.237-0.035-0.0350.0000.0000.0000.000
141A198PRO0-0.0270.00321.7220.0320.0320.0000.0000.0000.000
142A199PHE0-0.012-0.01623.2670.0360.0360.0000.0000.0000.000
143A200GLN00.010-0.01427.163-0.043-0.0430.0000.0000.0000.000
144A201ILE0-0.051-0.01129.2170.0170.0170.0000.0000.0000.000
145A202ALA00.0400.03732.3620.0040.0040.0000.0000.0000.000
146A203TRP0-0.018-0.02135.9810.0110.0110.0000.0000.0000.000
147A204ALA00.0460.00938.547-0.001-0.0010.0000.0000.0000.000
148A205ALA0-0.027-0.01742.3220.0030.0030.0000.0000.0000.000
149A206GLN00.0620.05644.7750.0020.0020.0000.0000.0000.000
150A207SER00.0640.01348.4970.0030.0030.0000.0000.0000.000
151A208SER00.0210.02650.7410.0000.0000.0000.0000.0000.000
152A209LEU0-0.046-0.01850.9120.0040.0040.0000.0000.0000.000
153A210VAL00.0410.03852.993-0.004-0.0040.0000.0000.0000.000
154A211SER0-0.032-0.00750.5930.0000.0000.0000.0000.0000.000
155A212THR00.0410.02749.953-0.002-0.0020.0000.0000.0000.000
156A213THR0-0.020-0.03443.545-0.005-0.0050.0000.0000.0000.000
157A214LEU00.0030.00244.6900.0050.0050.0000.0000.0000.000
158A215GLY00.0720.00841.7170.0070.0070.0000.0000.0000.000
159A216ARG10.8710.93836.7370.2010.2010.0000.0000.0000.000
160A217ILE00.0540.04433.0660.0070.0070.0000.0000.0000.000
161A218MET0-0.047-0.01231.939-0.019-0.0190.0000.0000.0000.000
162A219ALA00.0410.01427.316-0.007-0.0070.0000.0000.0000.000
163A220GLU-1-0.932-0.96125.688-0.256-0.2560.0000.0000.0000.000
164A221TYR00.003-0.01420.688-0.016-0.0160.0000.0000.0000.000
165A222LEU0-0.014-0.00814.9410.0240.0240.0000.0000.0000.000
166A223VAL0-0.013-0.01416.4450.0100.0100.0000.0000.0000.000
167A224GLU-1-0.827-0.92210.931-1.410-1.4100.0000.0000.0000.000
168A225LEU00.009-0.00812.6690.0970.0970.0000.0000.0000.000
169A226THR00.011-0.0018.601-0.275-0.2750.0000.0000.0000.000
170A227ASP-1-0.847-0.9259.383-3.106-3.1060.0000.0000.0000.000
171A228PRO00.0210.0049.1530.5410.5410.0000.0000.0000.000
172A229VAL0-0.050-0.02912.285-0.017-0.0170.0000.0000.0000.000
173A230ASP-1-0.847-0.93315.555-0.657-0.6570.0000.0000.0000.000
174A231VAL0-0.018-0.03518.3980.0070.0070.0000.0000.0000.000
175A232THR0-0.0020.01221.0120.0330.0330.0000.0000.0000.000
176A233ILE0-0.043-0.00319.5060.0200.0200.0000.0000.0000.000
177A234ASN0-0.052-0.02519.1530.0440.0440.0000.0000.0000.000
178A235GLN0-0.0060.00321.2540.0300.0300.0000.0000.0000.000