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: ZY57N

Calculation Name: 3VZH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VZH

Chain ID: A

ChEMBL ID:

UniProt ID: Q99YS3

Base Structure: X-ray

Registration Date: 2023-06-19

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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2407666.727388
FMO2-HF: Nuclear repulsion 2325672.644814
FMO2-HF: Total energy -81994.082574
FMO2-MP2: Total energy -82234.530506


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:-1:GLY)


Summations of interaction energy for fragment #1(A:-1:GLY)
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.
1.382.885-0.008-0.783-0.7140.004
Interaction energy analysis for fragmet #1(A:-1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.040 / q_NPA : 0.021
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].
3A1MET0-0.0020.0003.8200.3271.832-0.008-0.783-0.7140.004
4A2TYR0-0.014-0.0116.1320.5640.5640.0000.0000.0000.000
5A3ARG10.8240.8959.0290.8000.8000.0000.0000.0000.000
6A4SER0-0.043-0.01912.3630.0430.0430.0000.0000.0000.000
7A5ARG10.8860.90615.7760.2410.2410.0000.0000.0000.000
8A6ASP-1-0.859-0.90318.437-0.545-0.5450.0000.0000.0000.000
9A7PHE0-0.050-0.02719.8620.0430.0430.0000.0000.0000.000
10A8TYR00.0390.01423.651-0.021-0.0210.0000.0000.0000.000
11A9VAL00.0040.00227.1040.0140.0140.0000.0000.0000.000
12A10ARG11.0281.01829.9520.1320.1320.0000.0000.0000.000
13A11VAL0-0.015-0.01431.3710.0070.0070.0000.0000.0000.000
14A12SER0-0.038-0.02134.3440.0020.0020.0000.0000.0000.000
15A13GLY00.0940.02837.9660.0010.0010.0000.0000.0000.000
16A14GLN00.0290.02540.4530.0020.0020.0000.0000.0000.000
17A15ARG10.9270.97442.3630.0910.0910.0000.0000.0000.000
18A16ALA00.0370.01937.481-0.004-0.0040.0000.0000.0000.000
19A17LEU0-0.009-0.01238.1680.0050.0050.0000.0000.0000.000
20A18PHE0-0.0040.01033.680-0.005-0.0050.0000.0000.0000.000
21A19THR00.0340.01135.5150.0000.0000.0000.0000.0000.000
22A20ASN00.0280.00233.849-0.014-0.0140.0000.0000.0000.000
23A21PRO0-0.039-0.02131.7510.0100.0100.0000.0000.0000.000
24A22ALA00.0710.01533.369-0.003-0.0030.0000.0000.0000.000
25A23THR0-0.0080.00235.9310.0000.0000.0000.0000.0000.000
26A24LYS10.8650.96038.5240.1110.1110.0000.0000.0000.000
27A25GLY00.0610.02841.146-0.002-0.0020.0000.0000.0000.000
28A26GLY0-0.034-0.00642.3110.0030.0030.0000.0000.0000.000
29A27SER0-0.026-0.03143.120-0.002-0.0020.0000.0000.0000.000
30A28GLU-1-0.875-0.92046.069-0.067-0.0670.0000.0000.0000.000
31A29ARG10.8780.93540.1730.0870.0870.0000.0000.0000.000
32A30SER00.0120.02042.0240.0010.0010.0000.0000.0000.000
33A31SER00.004-0.00638.553-0.004-0.0040.0000.0000.0000.000
34A32TYR00.0030.01333.7330.0010.0010.0000.0000.0000.000
35A33SER00.0350.01837.5220.0020.0020.0000.0000.0000.000
36A34VAL00.0350.02132.7560.0000.0000.0000.0000.0000.000
37A35PRO0-0.014-0.00530.7390.0030.0030.0000.0000.0000.000
38A36THR00.0550.04029.365-0.010-0.0100.0000.0000.0000.000
39A37ARG10.9200.94818.5850.4470.4470.0000.0000.0000.000
40A38GLN00.0130.00724.577-0.004-0.0040.0000.0000.0000.000
41A39ALA00.0010.01026.9060.0030.0030.0000.0000.0000.000
42A40LEU00.0240.00726.4100.0040.0040.0000.0000.0000.000
43A41ASN0-0.023-0.02422.489-0.020-0.0200.0000.0000.0000.000
44A42GLY00.0060.00624.9330.0020.0020.0000.0000.0000.000
45A43ILE00.0180.02227.9830.0080.0080.0000.0000.0000.000
46A44VAL0-0.008-0.01123.1730.0070.0070.0000.0000.0000.000
47A45ASP-1-0.871-0.94423.196-0.268-0.2680.0000.0000.0000.000
48A46ALA0-0.084-0.02625.6930.0150.0150.0000.0000.0000.000
49A47ILE00.0070.01327.2530.0140.0140.0000.0000.0000.000
50A48TYR0-0.051-0.07522.4350.0320.0320.0000.0000.0000.000
51A49TYR00.0710.05321.955-0.023-0.0230.0000.0000.0000.000
52A50LYS10.8830.93321.1200.1570.1570.0000.0000.0000.000
53A51PRO00.0020.01920.576-0.024-0.0240.0000.0000.0000.000
54A52THR0-0.020-0.04816.205-0.009-0.0090.0000.0000.0000.000
55A53PHE0-0.021-0.00915.722-0.041-0.0410.0000.0000.0000.000
56A54THR0-0.030-0.00615.3460.0640.0640.0000.0000.0000.000
57A55ASN0-0.016-0.01816.667-0.093-0.0930.0000.0000.0000.000
58A56ILE0-0.031-0.01414.9580.0140.0140.0000.0000.0000.000
59A57VAL00.0610.02618.476-0.010-0.0100.0000.0000.0000.000
60A58THR0-0.069-0.04418.381-0.018-0.0180.0000.0000.0000.000
61A59GLU-1-0.815-0.88021.253-0.327-0.3270.0000.0000.0000.000
62A60VAL0-0.0160.00124.8620.0060.0060.0000.0000.0000.000
63A61LYS10.9040.97228.4570.2190.2190.0000.0000.0000.000
64A62VAL00.012-0.01731.7010.0060.0060.0000.0000.0000.000
65A63ILE0-0.0160.01434.6920.0030.0030.0000.0000.0000.000
66A64ASN00.0450.00937.4670.0030.0030.0000.0000.0000.000
67A65GLN0-0.001-0.00240.202-0.004-0.0040.0000.0000.0000.000
68A66ILE0-0.025-0.01938.3800.0000.0000.0000.0000.0000.000
69A67GLN0-0.0130.00642.2010.0030.0030.0000.0000.0000.000
70A68THR0-0.001-0.02343.564-0.004-0.0040.0000.0000.0000.000
71A69GLU-1-0.953-0.96745.917-0.075-0.0750.0000.0000.0000.000
72A70LEU0-0.0200.00247.364-0.003-0.0030.0000.0000.0000.000
73A71GLN00.0130.00348.7580.0010.0010.0000.0000.0000.000
74A72GLY00.0030.00550.411-0.001-0.0010.0000.0000.0000.000
75A73VAL0-0.035-0.01949.4980.0010.0010.0000.0000.0000.000
76A74ARG10.9890.98752.8320.0480.0480.0000.0000.0000.000
77A85SER0-0.010-0.00550.1840.0010.0010.0000.0000.0000.000
78A86TYR00.0300.01549.7790.0010.0010.0000.0000.0000.000
79A87VAL0-0.0040.00244.208-0.003-0.0030.0000.0000.0000.000
80A88SER0-0.048-0.02245.0170.0010.0010.0000.0000.0000.000
81A89TYR0-0.072-0.10442.367-0.004-0.0040.0000.0000.0000.000
82A90LEU00.0220.01238.0650.0020.0020.0000.0000.0000.000
83A91SER0-0.012-0.03342.2440.0030.0030.0000.0000.0000.000
84A92ASP-1-0.929-0.95643.322-0.108-0.1080.0000.0000.0000.000
85A93VAL00.0110.02937.989-0.005-0.0050.0000.0000.0000.000
86A94VAL00.027-0.00436.4450.0020.0020.0000.0000.0000.000
87A95TYR00.002-0.00932.147-0.003-0.0030.0000.0000.0000.000
88A96LEU00.0330.03231.2330.0020.0020.0000.0000.0000.000
89A97ILE0-0.051-0.02625.491-0.012-0.0120.0000.0000.0000.000
90A98LYS11.0051.02021.3280.4400.4400.0000.0000.0000.000
91A99PHE0-0.041-0.04221.146-0.017-0.0170.0000.0000.0000.000
92A100HIS00.0320.03614.157-0.014-0.0140.0000.0000.0000.000
93A101PHE00.0420.01215.7370.0240.0240.0000.0000.0000.000
94A102VAL00.0540.03711.188-0.072-0.0720.0000.0000.0000.000
95A103TRP00.0370.0009.5950.1870.1870.0000.0000.0000.000
96A104ASN00.0080.00211.849-0.126-0.1260.0000.0000.0000.000
97A105GLU-1-0.832-0.9218.524-0.353-0.3530.0000.0000.0000.000
98A106ASP-1-0.825-0.89111.857-0.151-0.1510.0000.0000.0000.000
99A107ARG10.7210.82814.8560.1300.1300.0000.0000.0000.000
100A108LYS10.9650.9749.656-0.115-0.1150.0000.0000.0000.000
101A109ASP-1-0.782-0.86014.6410.0160.0160.0000.0000.0000.000
102A110LEU0-0.053-0.01517.1210.0060.0060.0000.0000.0000.000
103A111ASN00.0400.01211.891-0.075-0.0750.0000.0000.0000.000
104A112SER0-0.002-0.00414.906-0.026-0.0260.0000.0000.0000.000
105A113ASP-1-0.754-0.85417.518-0.140-0.1400.0000.0000.0000.000
106A114ARG10.8410.9439.8260.2280.2280.0000.0000.0000.000
107A115LEU0-0.028-0.01414.414-0.005-0.0050.0000.0000.0000.000
108A116PRO00.0650.01913.6260.0030.0030.0000.0000.0000.000
109A117ALA00.0670.03916.4390.0010.0010.0000.0000.0000.000
110A118LYS10.8560.92619.8260.1220.1220.0000.0000.0000.000
111A119HIS0-0.013-0.00717.8220.0030.0030.0000.0000.0000.000
112A120GLU-1-0.819-0.90817.837-0.413-0.4130.0000.0000.0000.000
113A121ALA00.0460.03321.0770.0130.0130.0000.0000.0000.000
114A122ILE0-0.095-0.04724.0560.0170.0170.0000.0000.0000.000
115A123MET00.0080.04122.0470.0230.0230.0000.0000.0000.000
116A124GLU-1-0.800-0.87224.456-0.217-0.2170.0000.0000.0000.000
117A125ARG10.9140.95326.7830.1430.1430.0000.0000.0000.000
118A126SER0-0.086-0.06627.6710.0160.0160.0000.0000.0000.000
119A127ILE00.0180.02325.8430.0080.0080.0000.0000.0000.000
120A128ARG10.8750.94929.9650.1610.1610.0000.0000.0000.000
121A129LYS10.8670.93632.4100.1280.1280.0000.0000.0000.000
122A130GLY00.0750.05333.7210.0070.0070.0000.0000.0000.000
123A131GLY0-0.049-0.01731.030-0.002-0.0020.0000.0000.0000.000
124A132ARG10.8090.88628.4860.1490.1490.0000.0000.0000.000
125A133ARG10.8960.95528.8680.1340.1340.0000.0000.0000.000
126A134ASP-1-0.850-0.91433.403-0.104-0.1040.0000.0000.0000.000
127A135VAL0-0.009-0.00432.116-0.008-0.0080.0000.0000.0000.000
128A136PHE0-0.012-0.00534.0350.0070.0070.0000.0000.0000.000
129A137LEU00.0050.00634.077-0.013-0.0130.0000.0000.0000.000
130A138GLY0-0.031-0.02234.0990.0050.0050.0000.0000.0000.000
131A139THR0-0.064-0.04435.1140.0020.0020.0000.0000.0000.000
132A140ARG10.9650.97035.5050.0970.0970.0000.0000.0000.000
133A141GLU-1-0.779-0.83339.419-0.091-0.0910.0000.0000.0000.000
134A142CYS0-0.075-0.01239.2870.0040.0040.0000.0000.0000.000
135A143LEU00.0150.00638.848-0.007-0.0070.0000.0000.0000.000
136A144GLY0-0.011-0.01136.7420.0000.0000.0000.0000.0000.000
137A145LEU0-0.0270.00637.6230.0030.0030.0000.0000.0000.000
138A146VAL0-0.043-0.03131.419-0.009-0.0090.0000.0000.0000.000
139A147ASP-1-0.855-0.93334.244-0.122-0.1220.0000.0000.0000.000
140A148ASP-1-0.872-0.96530.506-0.198-0.1980.0000.0000.0000.000
141A149ILE0-0.0080.01630.3620.0070.0070.0000.0000.0000.000
142A150SER00.0400.01829.420-0.015-0.0150.0000.0000.0000.000
143A151GLN0-0.051-0.05224.808-0.003-0.0030.0000.0000.0000.000
144A152GLU-1-0.889-0.94628.095-0.170-0.1700.0000.0000.0000.000
145A153GLU-1-0.889-0.93831.246-0.153-0.1530.0000.0000.0000.000
146A154TYR0-0.090-0.07527.0180.0070.0070.0000.0000.0000.000
147A155GLU-1-0.910-0.94526.606-0.281-0.2810.0000.0000.0000.000
148A156THR0-0.057-0.03430.9040.0090.0090.0000.0000.0000.000
149A157THR0-0.048-0.01934.2900.0140.0140.0000.0000.0000.000
150A158VAL0-0.038-0.02335.588-0.009-0.0090.0000.0000.0000.000
151A159SER0-0.029-0.03435.9100.0050.0050.0000.0000.0000.000
152A160TYR00.0240.00137.8820.0030.0030.0000.0000.0000.000
153A161TYR00.0070.00137.8270.0050.0050.0000.0000.0000.000
154A162ASN0-0.017-0.01037.368-0.013-0.0130.0000.0000.0000.000
155A163GLY00.0080.00738.0580.0080.0080.0000.0000.0000.000
156A164VAL0-0.0150.00439.0370.0050.0050.0000.0000.0000.000
157A165ASN0-0.020-0.03134.963-0.013-0.0130.0000.0000.0000.000
158A166ILE00.0080.00336.0960.0090.0090.0000.0000.0000.000
159A167ASP-1-0.867-0.92934.684-0.177-0.1770.0000.0000.0000.000
160A168LEU0-0.017-0.01433.8730.0090.0090.0000.0000.0000.000
161A169GLY00.0210.02234.9730.0060.0060.0000.0000.0000.000
162A170ILE0-0.048-0.03231.296-0.012-0.0120.0000.0000.0000.000
163A171MET0-0.029-0.00830.8380.0100.0100.0000.0000.0000.000
164A172PHE0-0.016-0.02228.399-0.014-0.0140.0000.0000.0000.000
165A173HIS0-0.0050.02621.3000.0150.0150.0000.0000.0000.000
166A174SER0-0.059-0.08123.134-0.014-0.0140.0000.0000.0000.000
167A175PHE00.0280.01325.2790.0080.0080.0000.0000.0000.000
168A176ALA0-0.0140.02121.258-0.026-0.0260.0000.0000.0000.000
169A177TYR0-0.005-0.01221.7500.0310.0310.0000.0000.0000.000
170A178PRO00.0210.01621.271-0.014-0.0140.0000.0000.0000.000
171A179LYS10.8620.91317.6030.2770.2770.0000.0000.0000.000
172A180ASP-1-0.775-0.86723.369-0.036-0.0360.0000.0000.0000.000
173A181LYS10.9600.97525.8800.0720.0720.0000.0000.0000.000
174A182LYS10.8060.87626.9700.0420.0420.0000.0000.0000.000
175A183THR00.0230.02028.798-0.002-0.0020.0000.0000.0000.000
176A184PRO0-0.035-0.00726.5660.0010.0010.0000.0000.0000.000
177A185LEU0-0.008-0.01322.7810.0120.0120.0000.0000.0000.000
178A186LYS10.9640.98221.5580.1700.1700.0000.0000.0000.000
179A187SER00.0020.00525.951-0.008-0.0080.0000.0000.0000.000
180A188TYR00.0350.01820.7190.0040.0040.0000.0000.0000.000
181A189PHE00.0120.00025.9850.0020.0020.0000.0000.0000.000
182A190THR00.007-0.00325.375-0.014-0.0140.0000.0000.0000.000
183A191LYS10.9371.00028.2110.1810.1810.0000.0000.0000.000
184A192THR0-0.027-0.00828.782-0.025-0.0250.0000.0000.0000.000
185A193VAL0-0.025-0.01929.9820.0130.0130.0000.0000.0000.000
186A194MET0-0.0090.02730.690-0.016-0.0160.0000.0000.0000.000
187A195LYS10.9470.96128.6840.2570.2570.0000.0000.0000.000
188A196ASN00.0260.02432.797-0.001-0.0010.0000.0000.0000.000
189A197GLY00.0620.02234.8250.0000.0000.0000.0000.0000.000
190A198VAL0-0.0180.00428.293-0.002-0.0020.0000.0000.0000.000
191A199ILE0-0.007-0.00627.4510.0040.0040.0000.0000.0000.000
192A200THR0-0.010-0.00922.719-0.002-0.0020.0000.0000.0000.000
193A201PHE0-0.060-0.05022.3420.0070.0070.0000.0000.0000.000
194A202LYS11.0171.03320.8160.2700.2700.0000.0000.0000.000
195A203ALA00.0260.01516.5550.0150.0150.0000.0000.0000.000
196A204GLN0-0.011-0.04118.5320.0230.0230.0000.0000.0000.000
197A205SER0-0.027-0.01916.4750.0170.0170.0000.0000.0000.000
198A206GLU-1-0.915-0.95116.869-0.566-0.5660.0000.0000.0000.000
199A207CYS0-0.128-0.05420.3100.0280.0280.0000.0000.0000.000
200A208ASP-1-0.834-0.92623.711-0.216-0.2160.0000.0000.0000.000
201A209ILE0-0.0110.00126.8790.0150.0150.0000.0000.0000.000
202A210VAL00.0120.00223.375-0.014-0.0140.0000.0000.0000.000
203A211ASN0-0.042-0.01326.5190.0200.0200.0000.0000.0000.000
204A212THR00.0140.00427.111-0.007-0.0070.0000.0000.0000.000