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: Q1GKY

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 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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2408688.869267
FMO2-HF: Nuclear repulsion 2326692.726016
FMO2-HF: Total energy -81996.14325
FMO2-MP2: Total energy -82236.251945


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.
2.2863.57-0.005-0.646-0.6330.003
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 : 0.049 / q_NPA : 0.022
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].
3A1MET0-0.0050.0073.8610.6271.911-0.005-0.646-0.6330.003
4A2TYR0-0.063-0.0586.1170.6080.6080.0000.0000.0000.000
5A3ARG10.7720.8489.4160.7970.7970.0000.0000.0000.000
6A4SER0-0.0290.00512.6070.0340.0340.0000.0000.0000.000
7A5ARG10.8760.91816.0910.2760.2760.0000.0000.0000.000
8A6ASP-1-0.795-0.86318.575-0.562-0.5620.0000.0000.0000.000
9A7PHE0-0.054-0.03220.0360.0430.0430.0000.0000.0000.000
10A8TYR00.013-0.00223.470-0.019-0.0190.0000.0000.0000.000
11A9VAL00.0020.00126.8310.0080.0080.0000.0000.0000.000
12A10ARG10.9300.96529.9320.1410.1410.0000.0000.0000.000
13A11VAL0-0.012-0.01631.2570.0000.0000.0000.0000.0000.000
14A12SER0-0.0110.00334.3870.0050.0050.0000.0000.0000.000
15A13GLY00.0670.01837.9350.0000.0000.0000.0000.0000.000
16A14GLN0-0.019-0.01640.7130.0030.0030.0000.0000.0000.000
17A15ARG10.8120.88642.4150.0970.0970.0000.0000.0000.000
18A16ALA00.0190.00837.762-0.006-0.0060.0000.0000.0000.000
19A17LEU0-0.021-0.01638.2700.0070.0070.0000.0000.0000.000
20A18PHE00.0420.02533.424-0.006-0.0060.0000.0000.0000.000
21A19THR00.0050.00935.7530.0000.0000.0000.0000.0000.000
22A20ASN00.0630.02133.727-0.016-0.0160.0000.0000.0000.000
23A21PRO0-0.0330.00331.4860.0110.0110.0000.0000.0000.000
24A22ALA00.022-0.01733.9430.0000.0000.0000.0000.0000.000
25A23THR00.0190.01035.9060.0010.0010.0000.0000.0000.000
26A24LYS10.8490.93838.4170.1180.1180.0000.0000.0000.000
27A25GLY00.0590.02741.222-0.001-0.0010.0000.0000.0000.000
28A26GLY0-0.0240.00342.3180.0010.0010.0000.0000.0000.000
29A27SER0-0.026-0.02843.052-0.002-0.0020.0000.0000.0000.000
30A28GLU-1-0.865-0.92145.936-0.070-0.0700.0000.0000.0000.000
31A29ARG10.8320.91341.6340.0950.0950.0000.0000.0000.000
32A30SER00.0560.02841.7680.0020.0020.0000.0000.0000.000
33A31SER0-0.013-0.00738.196-0.005-0.0050.0000.0000.0000.000
34A32TYR0-0.0030.00533.8540.0030.0030.0000.0000.0000.000
35A33SER00.0130.00837.2680.0000.0000.0000.0000.0000.000
36A34VAL00.0230.01732.5350.0010.0010.0000.0000.0000.000
37A35PRO0-0.007-0.00330.8330.0020.0020.0000.0000.0000.000
38A36THR00.0260.02529.760-0.011-0.0110.0000.0000.0000.000
39A37ARG10.9080.94818.7590.4550.4550.0000.0000.0000.000
40A38GLN00.0220.00825.008-0.012-0.0120.0000.0000.0000.000
41A39ALA0-0.007-0.00226.9860.0000.0000.0000.0000.0000.000
42A40LEU00.0270.01826.7200.0020.0020.0000.0000.0000.000
43A41ASN0-0.004-0.00921.957-0.017-0.0170.0000.0000.0000.000
44A42GLY00.0290.02225.011-0.001-0.0010.0000.0000.0000.000
45A43ILE0-0.0030.00627.8680.0080.0080.0000.0000.0000.000
46A44VAL00.0140.00623.3230.0060.0060.0000.0000.0000.000
47A45ASP-1-0.872-0.93422.939-0.341-0.3410.0000.0000.0000.000
48A46ALA0-0.072-0.03025.5890.0130.0130.0000.0000.0000.000
49A47ILE00.0070.01227.3510.0120.0120.0000.0000.0000.000
50A48TYR0-0.062-0.08222.5870.0270.0270.0000.0000.0000.000
51A49TYR00.0580.04720.533-0.011-0.0110.0000.0000.0000.000
52A50LYS10.8400.91121.2420.2730.2730.0000.0000.0000.000
53A51PRO00.0130.02320.152-0.033-0.0330.0000.0000.0000.000
54A52THR0-0.025-0.03716.370-0.007-0.0070.0000.0000.0000.000
55A53PHE0-0.0180.00015.489-0.073-0.0730.0000.0000.0000.000
56A54THR0-0.076-0.04015.6470.0590.0590.0000.0000.0000.000
57A55ASN00.009-0.01316.688-0.096-0.0960.0000.0000.0000.000
58A56ILE0-0.036-0.01915.1090.0030.0030.0000.0000.0000.000
59A57VAL00.0590.02118.626-0.004-0.0040.0000.0000.0000.000
60A58THR0-0.022-0.00818.431-0.014-0.0140.0000.0000.0000.000
61A59GLU-1-0.813-0.86721.005-0.303-0.3030.0000.0000.0000.000
62A60VAL0-0.0220.00224.7190.0020.0020.0000.0000.0000.000
63A61LYS10.8400.92228.4080.2040.2040.0000.0000.0000.000
64A62VAL00.017-0.00131.6800.0040.0040.0000.0000.0000.000
65A63ILE0-0.0210.01934.4550.0030.0030.0000.0000.0000.000
66A64ASN00.0310.00837.5580.0030.0030.0000.0000.0000.000
67A65GLN00.0060.01740.117-0.003-0.0030.0000.0000.0000.000
68A66ILE0-0.014-0.01737.926-0.001-0.0010.0000.0000.0000.000
69A67GLN0-0.0030.00341.8370.0050.0050.0000.0000.0000.000
70A68THR0-0.010-0.01443.575-0.005-0.0050.0000.0000.0000.000
71A69GLU-1-0.811-0.86345.846-0.082-0.0820.0000.0000.0000.000
72A70LEU0-0.037-0.01047.560-0.003-0.0030.0000.0000.0000.000
73A71GLN00.0050.00548.2380.0020.0020.0000.0000.0000.000
74A72GLY00.0310.01450.576-0.001-0.0010.0000.0000.0000.000
75A73VAL0-0.048-0.02849.8670.0010.0010.0000.0000.0000.000
76A74ARG11.0011.00053.1130.0540.0540.0000.0000.0000.000
77A85SER00.0000.00050.3060.0010.0010.0000.0000.0000.000
78A86TYR00.0130.00849.9920.0010.0010.0000.0000.0000.000
79A87VAL0-0.006-0.00544.360-0.003-0.0030.0000.0000.0000.000
80A88SER0-0.027-0.00645.0320.0010.0010.0000.0000.0000.000
81A89TYR0-0.016-0.04742.526-0.004-0.0040.0000.0000.0000.000
82A90LEU0-0.009-0.01038.3020.0030.0030.0000.0000.0000.000
83A91SER0-0.061-0.07442.5050.0010.0010.0000.0000.0000.000
84A92ASP-1-0.845-0.91043.376-0.114-0.1140.0000.0000.0000.000
85A93VAL0-0.0010.02638.388-0.004-0.0040.0000.0000.0000.000
86A94VAL00.019-0.00837.107-0.002-0.0020.0000.0000.0000.000
87A95TYR00.001-0.01432.573-0.001-0.0010.0000.0000.0000.000
88A96LEU00.0420.03431.2510.0010.0010.0000.0000.0000.000
89A97ILE0-0.040-0.02025.668-0.008-0.0080.0000.0000.0000.000
90A98LYS10.9390.97421.5110.4030.4030.0000.0000.0000.000
91A99PHE0-0.041-0.03021.261-0.018-0.0180.0000.0000.0000.000
92A100HIS00.0470.03814.196-0.019-0.0190.0000.0000.0000.000
93A101PHE00.0100.00115.9420.0350.0350.0000.0000.0000.000
94A102VAL00.0510.03011.281-0.070-0.0700.0000.0000.0000.000
95A103TRP00.0410.00110.0490.2090.2090.0000.0000.0000.000
96A104ASN0-0.006-0.00811.731-0.122-0.1220.0000.0000.0000.000
97A105GLU-1-0.773-0.8788.218-0.769-0.7690.0000.0000.0000.000
98A106ASP-1-0.864-0.90011.611-0.319-0.3190.0000.0000.0000.000
99A107ARG10.7630.83714.6070.2630.2630.0000.0000.0000.000
100A108LYS10.9350.9629.3770.3930.3930.0000.0000.0000.000
101A109ASP-1-0.767-0.84514.140-0.144-0.1440.0000.0000.0000.000
102A110LEU0-0.037-0.01117.1500.0170.0170.0000.0000.0000.000
103A111ASN00.0390.00511.707-0.129-0.1290.0000.0000.0000.000
104A112SER00.0140.00914.807-0.024-0.0240.0000.0000.0000.000
105A113ASP-1-0.762-0.85117.714-0.243-0.2430.0000.0000.0000.000
106A114ARG10.7930.9129.5680.6280.6280.0000.0000.0000.000
107A115LEU00.011-0.00114.708-0.033-0.0330.0000.0000.0000.000
108A116PRO00.0480.01914.4970.0200.0200.0000.0000.0000.000
109A117ALA00.0700.02616.7810.0180.0180.0000.0000.0000.000
110A118LYS10.8800.94520.1030.2290.2290.0000.0000.0000.000
111A119HIS00.0130.00218.2850.0260.0260.0000.0000.0000.000
112A120GLU-1-0.748-0.85517.228-0.515-0.5150.0000.0000.0000.000
113A121ALA00.0930.05021.4520.0210.0210.0000.0000.0000.000
114A122ILE0-0.107-0.03924.1010.0290.0290.0000.0000.0000.000
115A123MET00.0110.03921.9410.0310.0310.0000.0000.0000.000
116A124GLU-1-0.808-0.88324.924-0.250-0.2500.0000.0000.0000.000
117A125ARG10.8860.92426.8250.2010.2010.0000.0000.0000.000
118A126SER0-0.058-0.04227.7700.0170.0170.0000.0000.0000.000
119A127ILE00.0130.00925.8640.0100.0100.0000.0000.0000.000
120A128ARG10.8300.90230.0750.1920.1920.0000.0000.0000.000
121A129LYS10.8270.91932.9620.1600.1600.0000.0000.0000.000
122A130GLY00.0570.04133.8950.0070.0070.0000.0000.0000.000
123A131GLY00.0000.01130.867-0.002-0.0020.0000.0000.0000.000
124A132ARG10.8240.89027.8500.2050.2050.0000.0000.0000.000
125A133ARG10.8890.95727.8320.1910.1910.0000.0000.0000.000
126A134ASP-1-0.769-0.87633.502-0.135-0.1350.0000.0000.0000.000
127A135VAL00.0140.00232.368-0.009-0.0090.0000.0000.0000.000
128A136PHE0-0.036-0.01833.9290.0090.0090.0000.0000.0000.000
129A137LEU0-0.0040.00534.033-0.014-0.0140.0000.0000.0000.000
130A138GLY0-0.006-0.00834.1550.0060.0060.0000.0000.0000.000
131A139THR0-0.082-0.07035.1770.0020.0020.0000.0000.0000.000
132A140ARG10.8640.93236.2460.1230.1230.0000.0000.0000.000
133A141GLU-1-0.723-0.83139.105-0.106-0.1060.0000.0000.0000.000
134A142CYS0-0.091-0.01339.2810.0040.0040.0000.0000.0000.000
135A143LEU00.0190.00438.768-0.008-0.0080.0000.0000.0000.000
136A144GLY0-0.008-0.00137.1890.0020.0020.0000.0000.0000.000
137A145LEU0-0.042-0.00437.6820.0020.0020.0000.0000.0000.000
138A146VAL0-0.025-0.02731.439-0.008-0.0080.0000.0000.0000.000
139A147ASP-1-0.815-0.90134.151-0.143-0.1430.0000.0000.0000.000
140A148ASP-1-0.838-0.91530.753-0.212-0.2120.0000.0000.0000.000
141A149ILE00.0210.02930.2120.0080.0080.0000.0000.0000.000
142A150SER00.0190.01429.636-0.019-0.0190.0000.0000.0000.000
143A151GLN0-0.026-0.03223.850-0.016-0.0160.0000.0000.0000.000
144A152GLU-1-0.902-0.94628.050-0.163-0.1630.0000.0000.0000.000
145A153GLU-1-0.858-0.91531.194-0.161-0.1610.0000.0000.0000.000
146A154TYR0-0.058-0.05926.8730.0050.0050.0000.0000.0000.000
147A155GLU-1-0.894-0.93926.364-0.265-0.2650.0000.0000.0000.000
148A156THR0-0.045-0.05330.6640.0100.0100.0000.0000.0000.000
149A157THR0-0.045-0.02434.2420.0130.0130.0000.0000.0000.000
150A158VAL0-0.0070.00135.350-0.009-0.0090.0000.0000.0000.000
151A159SER0-0.026-0.02436.0470.0050.0050.0000.0000.0000.000
152A160TYR00.016-0.01138.0570.0050.0050.0000.0000.0000.000
153A161TYR00.003-0.00337.6850.0050.0050.0000.0000.0000.000
154A162ASN0-0.027-0.01637.083-0.012-0.0120.0000.0000.0000.000
155A163GLY00.0080.00837.8720.0070.0070.0000.0000.0000.000
156A164VAL0-0.030-0.00438.7120.0060.0060.0000.0000.0000.000
157A165ASN0-0.007-0.02134.649-0.019-0.0190.0000.0000.0000.000
158A166ILE00.0100.00935.7730.0090.0090.0000.0000.0000.000
159A167ASP-1-0.820-0.89934.436-0.159-0.1590.0000.0000.0000.000
160A168LEU0-0.004-0.00733.5770.0080.0080.0000.0000.0000.000
161A169GLY00.0090.01634.9810.0030.0030.0000.0000.0000.000
162A170ILE0-0.036-0.02531.085-0.012-0.0120.0000.0000.0000.000
163A171MET0-0.0160.00430.5990.0080.0080.0000.0000.0000.000
164A172PHE0-0.010-0.00928.550-0.010-0.0100.0000.0000.0000.000
165A173HIS00.0000.00321.1670.0110.0110.0000.0000.0000.000
166A174SER0-0.042-0.04023.169-0.019-0.0190.0000.0000.0000.000
167A175PHE00.0240.00825.4420.0160.0160.0000.0000.0000.000
168A176ALA0-0.0180.01120.999-0.029-0.0290.0000.0000.0000.000
169A177TYR00.0360.00221.8740.0270.0270.0000.0000.0000.000
170A178PRO0-0.011-0.00521.231-0.023-0.0230.0000.0000.0000.000
171A179LYS10.8640.91816.7410.4050.4050.0000.0000.0000.000
172A180ASP-1-0.773-0.86622.630-0.098-0.0980.0000.0000.0000.000
173A181LYS10.9410.96025.5090.1120.1120.0000.0000.0000.000
174A182LYS10.8200.89627.0520.0980.0980.0000.0000.0000.000
175A183THR0-0.0070.00228.5570.0050.0050.0000.0000.0000.000
176A184PRO0-0.027-0.00226.442-0.004-0.0040.0000.0000.0000.000
177A185LEU0-0.024-0.01823.0170.0150.0150.0000.0000.0000.000
178A186LYS10.9320.96021.9140.1770.1770.0000.0000.0000.000
179A187SER00.0280.01325.798-0.010-0.0100.0000.0000.0000.000
180A188TYR0-0.0050.00520.2890.0170.0170.0000.0000.0000.000
181A189PHE00.001-0.01025.9260.0000.0000.0000.0000.0000.000
182A190THR0-0.044-0.05525.451-0.012-0.0120.0000.0000.0000.000
183A191LYS10.8670.91527.9400.1550.1550.0000.0000.0000.000
184A192THR0-0.0200.00328.446-0.022-0.0220.0000.0000.0000.000
185A193VAL0-0.012-0.01929.8540.0140.0140.0000.0000.0000.000
186A194MET0-0.0140.03530.624-0.014-0.0140.0000.0000.0000.000
187A195LYS10.9530.96028.0640.2280.2280.0000.0000.0000.000
188A196ASN00.0180.01932.583-0.002-0.0020.0000.0000.0000.000
189A197GLY00.0560.02334.8020.0000.0000.0000.0000.0000.000
190A198VAL0-0.016-0.00828.202-0.005-0.0050.0000.0000.0000.000
191A199ILE0-0.014-0.01927.5600.0110.0110.0000.0000.0000.000
192A200THR0-0.003-0.01822.407-0.006-0.0060.0000.0000.0000.000
193A201PHE0-0.062-0.04522.3560.0170.0170.0000.0000.0000.000
194A202LYS10.8760.95020.5000.2210.2210.0000.0000.0000.000
195A203ALA00.0060.00116.377-0.004-0.0040.0000.0000.0000.000
196A204GLN00.008-0.04018.2380.0340.0340.0000.0000.0000.000
197A205SER0-0.021-0.01816.0400.0240.0240.0000.0000.0000.000
198A206GLU-1-0.843-0.89917.152-0.479-0.4790.0000.0000.0000.000
199A207CYS0-0.094-0.02820.3120.0300.0300.0000.0000.0000.000
200A208ASP-1-0.772-0.86123.634-0.205-0.2050.0000.0000.0000.000
201A209ILE00.0070.01026.5260.0170.0170.0000.0000.0000.000
202A210VAL00.000-0.00222.938-0.016-0.0160.0000.0000.0000.000
203A211ASN0-0.0160.00726.2770.0220.0220.0000.0000.0000.000
204A212THR00.0170.00926.526-0.013-0.0130.0000.0000.0000.000