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: VR471

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 OptHSide
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 -2373988.723504
FMO2-HF: Nuclear repulsion 2292780.832823
FMO2-HF: Total energy -81207.890681
FMO2-MP2: Total energy -81440.017502


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.
-0.8520.888-0.022-0.887-0.8310.001
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 : -0.029 / q_NPA : -0.026
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].
3A9LEU0-0.026-0.0063.8300.6302.370-0.022-0.887-0.8310.001
4A10GLU-1-0.895-0.9486.129-2.296-2.2960.0000.0000.0000.000
5A11LEU0-0.0060.0108.2050.2150.2150.0000.0000.0000.000
6A12LEU0-0.009-0.00111.900-0.061-0.0610.0000.0000.0000.000
7A13LYS10.9420.97514.8020.5710.5710.0000.0000.0000.000
8A14ASP-1-0.808-0.87917.020-0.284-0.2840.0000.0000.0000.000
9A15VAL00.0190.01118.8730.0110.0110.0000.0000.0000.000
10A16HIS00.1240.08521.4410.0090.0090.0000.0000.0000.000
11A17LEU0-0.041-0.01922.6520.0130.0130.0000.0000.0000.000
12A18GLY00.0230.00425.253-0.005-0.0050.0000.0000.0000.000
13A19LEU0-0.0220.00727.6220.0090.0090.0000.0000.0000.000
14A20PRO0-0.0130.00929.794-0.001-0.0010.0000.0000.0000.000
15A21VAL00.0220.00333.546-0.001-0.0010.0000.0000.0000.000
16A22PRO0-0.017-0.01335.3760.0030.0030.0000.0000.0000.000
17A23CYS0-0.070-0.02337.5410.0050.0050.0000.0000.0000.000
18A24HIS00.014-0.00540.448-0.004-0.0040.0000.0000.0000.000
19A25ASP-1-0.915-0.96342.930-0.061-0.0610.0000.0000.0000.000
20A26PRO0-0.069-0.02139.7050.0020.0020.0000.0000.0000.000
21A27ALA00.0430.02442.406-0.001-0.0010.0000.0000.0000.000
22A28ARG10.7730.85341.6820.0650.0650.0000.0000.0000.000
23A29LEU0-0.002-0.01134.6590.0000.0000.0000.0000.0000.000
24A30ALA0-0.0030.00435.496-0.001-0.0010.0000.0000.0000.000
25A31LEU00.010-0.00629.5360.0010.0010.0000.0000.0000.000
26A32LEU0-0.0220.01125.5240.0000.0000.0000.0000.0000.000
27A33SER00.0010.01127.866-0.007-0.0070.0000.0000.0000.000
28A34GLY00.0150.00424.108-0.003-0.0030.0000.0000.0000.000
29A35HIS10.7880.86219.5200.3010.3010.0000.0000.0000.000
30A36TYR00.017-0.01919.438-0.001-0.0010.0000.0000.0000.000
31A37LEU0-0.020-0.01113.036-0.013-0.0130.0000.0000.0000.000
32A38TYR0-0.019-0.03816.6320.0370.0370.0000.0000.0000.000
33A39TYR00.0480.01813.311-0.037-0.0370.0000.0000.0000.000
34A40HIS0-0.044-0.03615.811-0.009-0.0090.0000.0000.0000.000
35A41TYR00.002-0.00917.5770.0120.0120.0000.0000.0000.000
36A42GLY0-0.007-0.00916.5660.0010.0010.0000.0000.0000.000
37A43CYS0-0.096-0.01313.5020.0400.0400.0000.0000.0000.000
38A44ASP-1-0.815-0.90210.906-0.032-0.0320.0000.0000.0000.000
39A45GLY0-0.019-0.00311.3850.0880.0880.0000.0000.0000.000
40A46LEU0-0.060-0.01813.1520.0040.0040.0000.0000.0000.000
41A47ASP-1-0.780-0.86916.2530.0510.0510.0000.0000.0000.000
42A48ASP-1-0.731-0.86319.483-0.014-0.0140.0000.0000.0000.000
43A49ARG10.8450.89421.771-0.081-0.0810.0000.0000.0000.000
44A50GLY0-0.031-0.01123.9460.0060.0060.0000.0000.0000.000
45A51TRP0-0.025-0.00421.877-0.005-0.0050.0000.0000.0000.000
46A52GLY00.0370.00922.764-0.006-0.0060.0000.0000.0000.000
47A53CYM-1-0.780-0.78922.989-0.063-0.0630.0000.0000.0000.000
48A54GLY00.0700.04724.356-0.014-0.0140.0000.0000.0000.000
49A55TYR0-0.029-0.03921.069-0.013-0.0130.0000.0000.0000.000
50A56ARG10.7160.83415.6580.0270.0270.0000.0000.0000.000
51A57THR00.006-0.01420.623-0.026-0.0260.0000.0000.0000.000
52A58LEU00.0360.01921.996-0.016-0.0160.0000.0000.0000.000
53A59GLN0-0.016-0.01115.5950.0010.0010.0000.0000.0000.000
54A60THR0-0.005-0.01818.722-0.030-0.0300.0000.0000.0000.000
55A61LEU0-0.059-0.01020.162-0.021-0.0210.0000.0000.0000.000
56A62CYS0-0.018-0.01019.0280.0000.0000.0000.0000.0000.000
57A63SER0-0.045-0.01816.843-0.028-0.0280.0000.0000.0000.000
58A64TRP0-0.0560.00718.304-0.033-0.0330.0000.0000.0000.000
59A65PRO00.0270.01521.3370.0050.0050.0000.0000.0000.000
60A66GLY00.0480.00418.3880.0020.0020.0000.0000.0000.000
61A67GLY0-0.029-0.01917.171-0.032-0.0320.0000.0000.0000.000
62A68GLN0-0.048-0.03413.416-0.036-0.0360.0000.0000.0000.000
63A69SER00.1050.0379.8730.0400.0400.0000.0000.0000.000
64A70SER0-0.051-0.01910.2620.0650.0650.0000.0000.0000.000
65A71GLY00.0270.01711.3540.0300.0300.0000.0000.0000.000
66A72VAL0-0.045-0.00614.0110.0850.0850.0000.0000.0000.000
67A73PRO00.0010.02114.237-0.028-0.0280.0000.0000.0000.000
68A74GLY00.0780.02814.9390.0030.0030.0000.0000.0000.000
69A75LEU00.0520.01415.5810.0100.0100.0000.0000.0000.000
70A76PRO00.0100.00616.4640.0010.0010.0000.0000.0000.000
71A77ALA0-0.035-0.01517.2650.0050.0050.0000.0000.0000.000
72A78LEU00.0270.01519.0540.0030.0030.0000.0000.0000.000
73A79GLN0-0.001-0.00721.5810.0130.0130.0000.0000.0000.000
74A80GLY0-0.030-0.02122.3990.0060.0060.0000.0000.0000.000
75A81ALA00.0110.01723.2740.0040.0040.0000.0000.0000.000
76A82LEU00.0170.00224.9270.0040.0040.0000.0000.0000.000
77A83GLU-1-0.865-0.94126.5260.0040.0040.0000.0000.0000.000
78A84ALA0-0.063-0.03126.8720.0030.0030.0000.0000.0000.000
79A85MET0-0.053-0.01227.297-0.002-0.0020.0000.0000.0000.000
80A86GLY0-0.0170.00930.8700.0010.0010.0000.0000.0000.000
81A87ASP-1-0.883-0.94330.955-0.047-0.0470.0000.0000.0000.000
82A88LYS10.7750.87129.4490.0340.0340.0000.0000.0000.000
83A89PRO00.0080.01331.9590.0000.0000.0000.0000.0000.000
84A90PRO00.041-0.00530.6330.0000.0000.0000.0000.0000.000
85A91GLY0-0.0140.00529.0170.0020.0020.0000.0000.0000.000
86A92PHE00.0090.01126.4830.0030.0030.0000.0000.0000.000
87A93ARG10.9490.98618.7920.0090.0090.0000.0000.0000.000
88A94GLY0-0.039-0.01722.8200.0100.0100.0000.0000.0000.000
89A95SER0-0.068-0.03523.8080.0070.0070.0000.0000.0000.000
90A96ARG10.9480.96524.409-0.059-0.0590.0000.0000.0000.000
91A97ASN0-0.0090.00026.690-0.003-0.0030.0000.0000.0000.000
92A98TRP00.0180.02527.088-0.004-0.0040.0000.0000.0000.000
93A99ILE0-0.037-0.01024.6220.0000.0000.0000.0000.0000.000
94A100GLY00.0620.01528.693-0.001-0.0010.0000.0000.0000.000
95A101CYS0-0.045-0.01629.544-0.006-0.0060.0000.0000.0000.000
96A102VAL00.0450.03631.029-0.005-0.0050.0000.0000.0000.000
97A103GLU-1-0.712-0.84228.237-0.051-0.0510.0000.0000.0000.000
98A104ALA00.0100.00426.522-0.007-0.0070.0000.0000.0000.000
99A105SER0-0.065-0.04927.096-0.009-0.0090.0000.0000.0000.000
100A106LEU00.0660.04029.402-0.006-0.0060.0000.0000.0000.000
101A107CYS0-0.059-0.03323.959-0.002-0.0020.0000.0000.0000.000
102A108LEU0-0.034-0.02923.945-0.013-0.0130.0000.0000.0000.000
103A109GLU-1-0.960-0.96325.620-0.094-0.0940.0000.0000.0000.000
104A110HIS0-0.026-0.01823.2050.0070.0070.0000.0000.0000.000
105A111PHE0-0.089-0.06119.846-0.001-0.0010.0000.0000.0000.000
106A112GLY00.0030.02221.809-0.023-0.0230.0000.0000.0000.000
107A113GLY0-0.023-0.00322.770-0.018-0.0180.0000.0000.0000.000
108A114PRO0-0.044-0.02223.2380.0160.0160.0000.0000.0000.000
109A115GLN00.0190.00626.1890.0120.0120.0000.0000.0000.000
110A116GLY00.0740.02129.687-0.004-0.0040.0000.0000.0000.000
111A117ARG10.9170.96230.5610.0810.0810.0000.0000.0000.000
112A118LEU00.0430.01533.014-0.002-0.0020.0000.0000.0000.000
113A119CYS0-0.061-0.02535.6810.0030.0030.0000.0000.0000.000
114A120HIS0-0.014-0.00537.6820.0010.0010.0000.0000.0000.000
115A121LEU0-0.0010.00638.7030.0000.0000.0000.0000.0000.000
116A122PRO00.0470.02641.6920.0020.0020.0000.0000.0000.000
117A123ARG10.9140.96644.3230.0260.0260.0000.0000.0000.000
118A124GLY0-0.007-0.01346.4060.0000.0000.0000.0000.0000.000
119A125VAL00.002-0.00246.2500.0000.0000.0000.0000.0000.000
120A126GLY00.0290.01443.659-0.001-0.0010.0000.0000.0000.000
121A127LEU00.013-0.00537.7540.0000.0000.0000.0000.0000.000
122A128ARG10.6840.81941.9730.0440.0440.0000.0000.0000.000
123A129GLY00.0420.02945.0660.0010.0010.0000.0000.0000.000
124A130GLU-1-0.801-0.87740.288-0.063-0.0630.0000.0000.0000.000
125A131GLU-1-0.817-0.91440.595-0.060-0.0600.0000.0000.0000.000
126A132GLU-1-0.749-0.84440.718-0.068-0.0680.0000.0000.0000.000
127A133ARG10.8020.88638.5240.0640.0640.0000.0000.0000.000
128A134LEU0-0.003-0.00234.102-0.006-0.0060.0000.0000.0000.000
129A135TYR00.007-0.04136.459-0.009-0.0090.0000.0000.0000.000
130A136SER0-0.0060.00337.702-0.005-0.0050.0000.0000.0000.000
131A137HIS0-0.057-0.00831.0730.0010.0010.0000.0000.0000.000
132A138PHE0-0.001-0.01130.145-0.006-0.0060.0000.0000.0000.000
133A139THR0-0.020-0.01733.274-0.006-0.0060.0000.0000.0000.000
134A140THR0-0.100-0.06035.525-0.002-0.0020.0000.0000.0000.000
135A141GLY00.0110.00731.178-0.001-0.0010.0000.0000.0000.000
136A142GLY0-0.046-0.02229.968-0.008-0.0080.0000.0000.0000.000
137A143GLY00.0370.00427.291-0.006-0.0060.0000.0000.0000.000
138A144PRO0-0.005-0.00524.0070.0140.0140.0000.0000.0000.000
139A145VAL0-0.0220.01227.3010.0010.0010.0000.0000.0000.000
140A146MET0-0.0180.00927.262-0.001-0.0010.0000.0000.0000.000
141A147VAL0-0.004-0.01129.1540.0060.0060.0000.0000.0000.000
142A148GLY00.021-0.00630.577-0.001-0.0010.0000.0000.0000.000
143A149GLY00.0520.02431.2750.0000.0000.0000.0000.0000.000
144A150ASP-1-0.864-0.94632.129-0.041-0.0410.0000.0000.0000.000
145A151ALA0-0.058-0.03635.432-0.001-0.0010.0000.0000.0000.000
146A152ASP-1-0.796-0.88534.057-0.045-0.0450.0000.0000.0000.000
147A153ALA0-0.041-0.00232.3690.0010.0010.0000.0000.0000.000
148A154GLN0-0.039-0.03929.3740.0020.0020.0000.0000.0000.000
149A155SER0-0.022-0.05026.833-0.003-0.0030.0000.0000.0000.000
150A156LYS10.7950.87027.4560.0580.0580.0000.0000.0000.000
151A157ALA0-0.0140.00425.430-0.002-0.0020.0000.0000.0000.000
152A158LEU0-0.015-0.00327.4640.0020.0020.0000.0000.0000.000
153A159LEU0-0.013-0.02224.799-0.008-0.0080.0000.0000.0000.000
154A160GLY00.0490.01128.896-0.007-0.0070.0000.0000.0000.000
155A161ILE0-0.035-0.01232.2220.0040.0040.0000.0000.0000.000
156A162CYS0-0.0170.00035.883-0.003-0.0030.0000.0000.0000.000
157A163GLU-1-0.814-0.85038.564-0.059-0.0590.0000.0000.0000.000
158A164GLY00.0870.04642.026-0.002-0.0020.0000.0000.0000.000
159A165PRO00.0200.00044.6240.0010.0010.0000.0000.0000.000
160A166GLY0-0.033-0.00648.2670.0010.0010.0000.0000.0000.000
161A167SER0-0.027-0.02845.9000.0020.0020.0000.0000.0000.000
162A168GLU-1-0.910-0.94043.623-0.054-0.0540.0000.0000.0000.000
163A169VAL00.0360.00939.331-0.003-0.0030.0000.0000.0000.000
164A170TYR0-0.074-0.07037.0220.0030.0030.0000.0000.0000.000
165A171VAL00.0310.00233.996-0.003-0.0030.0000.0000.0000.000
166A172LEU0-0.029-0.00328.2520.0010.0010.0000.0000.0000.000
167A173ILE00.002-0.00229.123-0.005-0.0050.0000.0000.0000.000
168A174LEU00.0000.00221.726-0.005-0.0050.0000.0000.0000.000
169A175ASP-1-0.769-0.88125.533-0.062-0.0620.0000.0000.0000.000
170A176PRO00.0090.02321.940-0.004-0.0040.0000.0000.0000.000
171A177HIS10.8010.83721.8240.0520.0520.0000.0000.0000.000
172A178TYR00.0210.03418.5720.0070.0070.0000.0000.0000.000
173A179TRP00.0320.00418.8200.0040.0040.0000.0000.0000.000
174A180GLY00.0120.00217.6200.0000.0000.0000.0000.0000.000
175A181THR0-0.006-0.01712.2690.0120.0120.0000.0000.0000.000
176A182PRO0-0.0170.01715.075-0.008-0.0080.0000.0000.0000.000
177A183LYS10.8690.91415.3500.0490.0490.0000.0000.0000.000
178A184ASN00.000-0.01016.014-0.033-0.0330.0000.0000.0000.000
179A185ARG10.9120.93818.2110.2760.2760.0000.0000.0000.000
180A186CYS00.0010.01020.8440.0110.0110.0000.0000.0000.000
181A187GLU-1-0.788-0.88020.327-0.076-0.0760.0000.0000.0000.000
182A188LEU0-0.027-0.01319.0200.0110.0110.0000.0000.0000.000
183A189GLN0-0.074-0.05823.1350.0170.0170.0000.0000.0000.000
184A190ALA0-0.041-0.01526.1530.0090.0090.0000.0000.0000.000
185A191ALA0-0.028-0.01725.7250.0080.0080.0000.0000.0000.000
186A192GLY00.0070.01827.7280.0070.0070.0000.0000.0000.000
187A193TRP0-0.017-0.00423.5760.0010.0010.0000.0000.0000.000
188A194VAL0-0.001-0.01223.224-0.009-0.0090.0000.0000.0000.000
189A195GLY00.0220.00826.2400.0020.0020.0000.0000.0000.000
190A196TRP0-0.0120.01129.8190.0010.0010.0000.0000.0000.000
191A197GLN00.0140.00731.2870.0080.0080.0000.0000.0000.000
192A198LYS10.9340.97835.5630.0510.0510.0000.0000.0000.000
193A199VAL00.0700.03638.3020.0010.0010.0000.0000.0000.000
194A200LYS10.9170.95839.5420.0390.0390.0000.0000.0000.000
195A201SER0-0.045-0.03437.7010.0030.0030.0000.0000.0000.000
196A202VAL0-0.0120.01534.3400.0010.0010.0000.0000.0000.000
197A203PHE00.000-0.00735.0280.0000.0000.0000.0000.0000.000
198A204ASP-1-0.747-0.85339.380-0.031-0.0310.0000.0000.0000.000
199A205SER0-0.0090.01042.1410.0000.0000.0000.0000.0000.000
200A206ASN0-0.054-0.03745.1570.0010.0010.0000.0000.0000.000
201A207SER00.0190.00740.8880.0030.0030.0000.0000.0000.000
202A208PHE0-0.055-0.03041.552-0.001-0.0010.0000.0000.0000.000
203A209TYR00.0390.02636.2010.0000.0000.0000.0000.0000.000
204A210ASN0-0.0250.00334.9020.0010.0010.0000.0000.0000.000
205A211LEU00.026-0.00533.556-0.003-0.0030.0000.0000.0000.000
206A212CYS0-0.023-0.00829.9250.0020.0020.0000.0000.0000.000
207A213PHE00.006-0.00430.508-0.008-0.0080.0000.0000.0000.000
208A214THR00.0450.00826.284-0.002-0.0020.0000.0000.0000.000
209A215ARG10.8170.90629.3720.1100.1100.0000.0000.0000.000
210A216LEU00.0490.03724.786-0.003-0.0030.0000.0000.0000.000