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: YY2L2

Calculation Name: 2Z84-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2Z84

Chain ID: A

ChEMBL ID:

UniProt ID: Q9CZP0

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 210
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2372695.075884
FMO2-HF: Nuclear repulsion 2291487.756752
FMO2-HF: Total energy -81207.319133
FMO2-MP2: Total energy -81439.395132


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:7:SER)


Summations of interaction energy for fragment #1(A:7:SER)
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.
0.522.056-0.022-0.773-0.7410
Interaction energy analysis for fragmet #1(A:7:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / q_NPA : -0.018
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].
3A9LEU0-0.031-0.0083.8300.3861.922-0.022-0.773-0.7410.000
4A10GLU-1-0.944-0.9666.6040.2740.2740.0000.0000.0000.000
5A11LEU0-0.0020.0088.4210.0590.0590.0000.0000.0000.000
6A12LEU0-0.0020.00211.9330.0510.0510.0000.0000.0000.000
7A13LYS10.9750.99114.8030.1730.1730.0000.0000.0000.000
8A14ASP-1-0.809-0.87717.452-0.111-0.1110.0000.0000.0000.000
9A15VAL00.011-0.00319.1640.0180.0180.0000.0000.0000.000
10A16HIS00.1190.08321.7300.0000.0000.0000.0000.0000.000
11A17LEU0-0.042-0.01923.0590.0100.0100.0000.0000.0000.000
12A18GLY00.0140.00225.7720.0000.0000.0000.0000.0000.000
13A19LEU0-0.0160.00627.9830.0040.0040.0000.0000.0000.000
14A20PRO0-0.0140.01130.1670.0020.0020.0000.0000.0000.000
15A21VAL00.0130.00733.939-0.004-0.0040.0000.0000.0000.000
16A22PRO0-0.012-0.01435.6110.0020.0020.0000.0000.0000.000
17A23CYS0-0.052-0.01837.7410.0020.0020.0000.0000.0000.000
18A24HIS00.003-0.00940.8000.0010.0010.0000.0000.0000.000
19A25ASP-1-0.916-0.96443.373-0.031-0.0310.0000.0000.0000.000
20A26PRO0-0.072-0.02640.038-0.001-0.0010.0000.0000.0000.000
21A27ALA00.0460.03142.7610.0010.0010.0000.0000.0000.000
22A28ARG10.8090.88741.9680.0460.0460.0000.0000.0000.000
23A29LEU0-0.007-0.01434.946-0.002-0.0020.0000.0000.0000.000
24A30ALA0-0.0160.00235.7680.0020.0020.0000.0000.0000.000
25A31LEU00.014-0.00730.405-0.003-0.0030.0000.0000.0000.000
26A32LEU0-0.0090.01325.5370.0020.0020.0000.0000.0000.000
27A33SER00.0120.01728.0210.0000.0000.0000.0000.0000.000
28A34GLY00.0060.00524.284-0.008-0.0080.0000.0000.0000.000
29A35HIS10.7810.85419.6080.1250.1250.0000.0000.0000.000
30A36TYR00.022-0.01719.600-0.011-0.0110.0000.0000.0000.000
31A37LEU0-0.029-0.01713.1640.0170.0170.0000.0000.0000.000
32A38TYR0-0.026-0.05616.6490.0020.0020.0000.0000.0000.000
33A39TYR00.0470.01613.103-0.028-0.0280.0000.0000.0000.000
34A40HIS0-0.043-0.03615.2350.0270.0270.0000.0000.0000.000
35A41TYR00.000-0.00216.714-0.028-0.0280.0000.0000.0000.000
36A42GLY0-0.006-0.01015.5970.0060.0060.0000.0000.0000.000
37A43CYS0-0.094-0.01212.617-0.033-0.0330.0000.0000.0000.000
38A44ASP-1-0.822-0.91210.000-0.652-0.6520.0000.0000.0000.000
39A45GLY0-0.018-0.00510.569-0.096-0.0960.0000.0000.0000.000
40A46LEU0-0.055-0.01612.1540.0720.0720.0000.0000.0000.000
41A47ASP-1-0.800-0.89615.455-0.207-0.2070.0000.0000.0000.000
42A48ASP-1-0.731-0.86318.487-0.273-0.2730.0000.0000.0000.000
43A49ARG10.8500.90920.8210.2040.2040.0000.0000.0000.000
44A50GLY0-0.040-0.01622.9720.0080.0080.0000.0000.0000.000
45A51TRP0-0.018-0.00221.3840.0070.0070.0000.0000.0000.000
46A52GLY00.0300.00021.9320.0020.0020.0000.0000.0000.000
47A53CYM-1-0.802-0.84222.201-0.177-0.1770.0000.0000.0000.000
48A54GLY00.0640.03423.610-0.005-0.0050.0000.0000.0000.000
49A55TYR0-0.040-0.04220.644-0.006-0.0060.0000.0000.0000.000
50A56ARG10.7220.84714.8720.3850.3850.0000.0000.0000.000
51A57THR00.0180.00320.089-0.007-0.0070.0000.0000.0000.000
52A58LEU00.0330.01522.0320.0010.0010.0000.0000.0000.000
53A59GLN0-0.015-0.01715.2700.0160.0160.0000.0000.0000.000
54A60THR0-0.008-0.01118.655-0.015-0.0150.0000.0000.0000.000
55A61LEU0-0.055-0.00919.8930.0070.0070.0000.0000.0000.000
56A62CYS0-0.012-0.00419.0420.0120.0120.0000.0000.0000.000
57A63SER0-0.046-0.01716.867-0.002-0.0020.0000.0000.0000.000
58A64TRP0-0.0610.00818.3040.0040.0040.0000.0000.0000.000
59A65PRO00.0330.01021.544-0.002-0.0020.0000.0000.0000.000
60A66GLY00.039-0.00318.6090.0150.0150.0000.0000.0000.000
61A67GLY0-0.040-0.02217.3500.0090.0090.0000.0000.0000.000
62A68GLN0-0.053-0.03613.621-0.015-0.0150.0000.0000.0000.000
63A69SER00.0900.0289.8920.0070.0070.0000.0000.0000.000
64A70SER0-0.049-0.0189.972-0.015-0.0150.0000.0000.0000.000
65A71GLY00.0290.01911.201-0.020-0.0200.0000.0000.0000.000
66A72VAL0-0.040-0.00413.9680.0740.0740.0000.0000.0000.000
67A73PRO00.0030.01914.237-0.086-0.0860.0000.0000.0000.000
68A74GLY00.0640.02314.939-0.016-0.0160.0000.0000.0000.000
69A75LEU00.0500.01315.5810.0510.0510.0000.0000.0000.000
70A76PRO00.0040.00716.4430.0340.0340.0000.0000.0000.000
71A77ALA0-0.035-0.01617.2590.0330.0330.0000.0000.0000.000
72A78LEU00.0310.01319.1780.0290.0290.0000.0000.0000.000
73A79GLN00.003-0.00421.5770.0150.0150.0000.0000.0000.000
74A80GLY0-0.030-0.02022.3960.0190.0190.0000.0000.0000.000
75A81ALA00.0190.01923.2660.0160.0160.0000.0000.0000.000
76A82LEU00.0230.00224.9170.0140.0140.0000.0000.0000.000
77A83GLU-1-0.883-0.93727.049-0.122-0.1220.0000.0000.0000.000
78A84ALA0-0.062-0.02926.8950.0110.0110.0000.0000.0000.000
79A85MET0-0.052-0.01527.1840.0080.0080.0000.0000.0000.000
80A86GLY0-0.0100.01330.8580.0070.0070.0000.0000.0000.000
81A87ASP-1-0.892-0.94931.056-0.103-0.1030.0000.0000.0000.000
82A88LYS10.7960.90429.4420.1190.1190.0000.0000.0000.000
83A89PRO00.0140.01231.9560.0010.0010.0000.0000.0000.000
84A90PRO00.0460.00230.643-0.008-0.0080.0000.0000.0000.000
85A91GLY0-0.0110.00529.0210.0060.0060.0000.0000.0000.000
86A92PHE00.0080.01326.402-0.006-0.0060.0000.0000.0000.000
87A93ARG10.9560.97418.4540.2150.2150.0000.0000.0000.000
88A94GLY0-0.046-0.01922.8310.0080.0080.0000.0000.0000.000
89A95SER0-0.066-0.03223.8180.0070.0070.0000.0000.0000.000
90A96ARG10.9480.96523.9970.1420.1420.0000.0000.0000.000
91A97ASN0-0.0050.00126.2540.0130.0130.0000.0000.0000.000
92A98TRP00.0080.02126.711-0.016-0.0160.0000.0000.0000.000
93A99ILE0-0.049-0.01424.4920.0050.0050.0000.0000.0000.000
94A100GLY00.0680.01528.283-0.002-0.0020.0000.0000.0000.000
95A101CYS0-0.052-0.02029.275-0.007-0.0070.0000.0000.0000.000
96A102VAL00.0530.04330.941-0.002-0.0020.0000.0000.0000.000
97A103GLU-1-0.740-0.87228.306-0.125-0.1250.0000.0000.0000.000
98A104ALA00.0090.00126.501-0.008-0.0080.0000.0000.0000.000
99A105SER0-0.077-0.05027.096-0.004-0.0040.0000.0000.0000.000
100A106LEU00.0690.03929.402-0.001-0.0010.0000.0000.0000.000
101A107CYS0-0.051-0.02723.929-0.007-0.0070.0000.0000.0000.000
102A108LEU0-0.036-0.03323.930-0.012-0.0120.0000.0000.0000.000
103A109GLU-1-0.952-0.95725.508-0.106-0.1060.0000.0000.0000.000
104A110HIS0-0.029-0.01823.5390.0110.0110.0000.0000.0000.000
105A111PHE0-0.088-0.05819.813-0.008-0.0080.0000.0000.0000.000
106A112GLY00.0000.02021.707-0.013-0.0130.0000.0000.0000.000
107A113GLY0-0.022-0.00322.623-0.005-0.0050.0000.0000.0000.000
108A114PRO0-0.029-0.02222.9530.0190.0190.0000.0000.0000.000
109A115GLN00.0110.00726.026-0.001-0.0010.0000.0000.0000.000
110A116GLY00.0680.01929.552-0.001-0.0010.0000.0000.0000.000
111A117ARG10.9090.95830.5610.0780.0780.0000.0000.0000.000
112A118LEU00.0360.01532.995-0.001-0.0010.0000.0000.0000.000
113A119CYS0-0.084-0.03535.6810.0070.0070.0000.0000.0000.000
114A120HIS00.0260.01737.444-0.001-0.0010.0000.0000.0000.000
115A121LEU00.0200.01438.4890.0040.0040.0000.0000.0000.000
116A122PRO00.0440.02241.274-0.002-0.0020.0000.0000.0000.000
117A123ARG10.9200.98643.8030.0520.0520.0000.0000.0000.000
118A124GLY0-0.001-0.00845.8420.0020.0020.0000.0000.0000.000
119A125VAL00.0080.00345.824-0.001-0.0010.0000.0000.0000.000
120A126GLY00.0340.01443.398-0.001-0.0010.0000.0000.0000.000
121A127LEU00.0130.00437.529-0.003-0.0030.0000.0000.0000.000
122A128ARG10.6940.81841.7170.0610.0610.0000.0000.0000.000
123A129GLY00.0480.03444.7680.0010.0010.0000.0000.0000.000
124A130GLU-1-0.913-0.96540.130-0.063-0.0630.0000.0000.0000.000
125A131GLU-1-0.816-0.92740.507-0.057-0.0570.0000.0000.0000.000
126A132GLU-1-0.780-0.87740.750-0.048-0.0480.0000.0000.0000.000
127A133ARG10.8940.96337.8860.0690.0690.0000.0000.0000.000
128A134LEU0-0.005-0.00134.089-0.003-0.0030.0000.0000.0000.000
129A135TYR0-0.009-0.04036.573-0.003-0.0030.0000.0000.0000.000
130A136SER00.000-0.00137.8690.0000.0000.0000.0000.0000.000
131A137HIS0-0.069-0.02831.0490.0050.0050.0000.0000.0000.000
132A138PHE00.002-0.01030.145-0.002-0.0020.0000.0000.0000.000
133A139THR0-0.0050.00933.4470.0010.0010.0000.0000.0000.000
134A140THR0-0.099-0.05235.7230.0010.0010.0000.0000.0000.000
135A141GLY0-0.0050.00231.371-0.001-0.0010.0000.0000.0000.000
136A142GLY0-0.036-0.01730.173-0.006-0.0060.0000.0000.0000.000
137A143GLY00.0490.00827.4170.0000.0000.0000.0000.0000.000
138A144PRO0-0.0050.00123.9980.0080.0080.0000.0000.0000.000
139A145VAL0-0.0180.01127.256-0.002-0.0020.0000.0000.0000.000
140A146MET0-0.0150.00826.940-0.003-0.0030.0000.0000.0000.000
141A147VAL0-0.009-0.01428.7980.0110.0110.0000.0000.0000.000
142A148GLY00.013-0.00929.980-0.008-0.0080.0000.0000.0000.000
143A149GLY00.0520.02430.4730.0040.0040.0000.0000.0000.000
144A150ASP-1-0.879-0.96031.347-0.102-0.1020.0000.0000.0000.000
145A151ALA0-0.055-0.02734.6870.0030.0030.0000.0000.0000.000
146A152ASP-1-0.851-0.93233.150-0.096-0.0960.0000.0000.0000.000
147A153ALA0-0.039-0.00731.423-0.001-0.0010.0000.0000.0000.000
148A154GLN0-0.006-0.01128.425-0.006-0.0060.0000.0000.0000.000
149A155SER00.005-0.01726.1280.0080.0080.0000.0000.0000.000
150A156LYS10.8070.90526.9720.1010.1010.0000.0000.0000.000
151A157ALA0-0.0010.00725.125-0.002-0.0020.0000.0000.0000.000
152A158LEU0-0.002-0.00127.1630.0050.0050.0000.0000.0000.000
153A159LEU0-0.021-0.02624.865-0.004-0.0040.0000.0000.0000.000
154A160GLY00.0420.01128.9590.0030.0030.0000.0000.0000.000
155A161ILE0-0.035-0.01132.370-0.002-0.0020.0000.0000.0000.000
156A162CYS0-0.046-0.01036.0020.0020.0020.0000.0000.0000.000
157A163GLU-1-0.808-0.88138.759-0.047-0.0470.0000.0000.0000.000
158A164GLY00.0710.03742.1890.0010.0010.0000.0000.0000.000
159A165PRO00.007-0.00344.8210.0000.0000.0000.0000.0000.000
160A166GLY0-0.028-0.00348.3700.0010.0010.0000.0000.0000.000
161A167SER0-0.026-0.00846.0330.0000.0000.0000.0000.0000.000
162A168GLU-1-0.956-0.97943.707-0.043-0.0430.0000.0000.0000.000
163A169VAL00.0300.00639.312-0.001-0.0010.0000.0000.0000.000
164A170TYR0-0.039-0.03236.888-0.001-0.0010.0000.0000.0000.000
165A171VAL00.032-0.00133.8350.0000.0000.0000.0000.0000.000
166A172LEU0-0.035-0.00828.6130.0000.0000.0000.0000.0000.000
167A173ILE00.0020.00128.774-0.006-0.0060.0000.0000.0000.000
168A174LEU0-0.004-0.00221.4880.0000.0000.0000.0000.0000.000
169A175ASP-1-0.796-0.90625.237-0.144-0.1440.0000.0000.0000.000
170A176PRO00.0160.03121.380-0.007-0.0070.0000.0000.0000.000
171A177HIS10.8470.88021.0930.1310.1310.0000.0000.0000.000
172A178TYR00.0200.03617.9920.0120.0120.0000.0000.0000.000
173A179TRP00.0320.00617.776-0.027-0.0270.0000.0000.0000.000
174A180GLY00.0190.00516.8060.0260.0260.0000.0000.0000.000
175A181THR0-0.008-0.01911.876-0.030-0.0300.0000.0000.0000.000
176A182PRO0-0.0090.02114.6910.0360.0360.0000.0000.0000.000
177A183LYS10.9820.98215.3250.0720.0720.0000.0000.0000.000
178A184ASN00.011-0.00216.3520.0080.0080.0000.0000.0000.000
179A185ARG10.9440.95818.5320.0800.0800.0000.0000.0000.000
180A186CYS0-0.0050.00221.1410.0000.0000.0000.0000.0000.000
181A187GLU-1-0.893-0.94220.536-0.074-0.0740.0000.0000.0000.000
182A188LEU0-0.048-0.02519.070-0.003-0.0030.0000.0000.0000.000
183A189GLN0-0.074-0.05623.0970.0070.0070.0000.0000.0000.000
184A190ALA0-0.028-0.00826.2560.0030.0030.0000.0000.0000.000
185A191ALA0-0.030-0.01725.5550.0030.0030.0000.0000.0000.000
186A192GLY00.0030.01527.606-0.001-0.0010.0000.0000.0000.000
187A193TRP0-0.014-0.00123.252-0.007-0.0070.0000.0000.0000.000
188A194VAL0-0.030-0.01923.256-0.010-0.0100.0000.0000.0000.000
189A195GLY00.0320.01026.1620.0070.0070.0000.0000.0000.000
190A196TRP0-0.0040.01429.807-0.004-0.0040.0000.0000.0000.000
191A197GLN00.0320.01531.1140.0050.0050.0000.0000.0000.000
192A198LYS10.9730.99735.4270.0490.0490.0000.0000.0000.000
193A199VAL00.0860.05238.038-0.002-0.0020.0000.0000.0000.000
194A200LYS10.9090.95539.3210.0470.0470.0000.0000.0000.000
195A201SER0-0.111-0.07138.0520.0000.0000.0000.0000.0000.000
196A202VAL00.0430.03434.020-0.002-0.0020.0000.0000.0000.000
197A203PHE0-0.022-0.02134.709-0.003-0.0030.0000.0000.0000.000
198A204ASP-1-0.791-0.88838.932-0.055-0.0550.0000.0000.0000.000
199A205SER00.0030.00441.608-0.001-0.0010.0000.0000.0000.000
200A206ASN0-0.022-0.01844.5730.0030.0030.0000.0000.0000.000
201A207SER0-0.0070.00240.2270.0000.0000.0000.0000.0000.000
202A208PHE0-0.052-0.02540.9630.0030.0030.0000.0000.0000.000
203A209TYR00.0590.03835.554-0.001-0.0010.0000.0000.0000.000
204A210ASN0-0.0020.01034.5960.0070.0070.0000.0000.0000.000
205A211LEU00.030-0.00433.223-0.005-0.0050.0000.0000.0000.000
206A212CYS0-0.013-0.00429.3840.0030.0030.0000.0000.0000.000
207A213PHE0-0.008-0.00830.405-0.006-0.0060.0000.0000.0000.000
208A214THR00.0400.00926.2950.0000.0000.0000.0000.0000.000
209A215ARG10.8210.90629.3720.0860.0860.0000.0000.0000.000
210A216LEU00.0460.03724.683-0.003-0.0030.0000.0000.0000.000