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: R5GQ8

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 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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2408436.673193
FMO2-HF: Nuclear repulsion 2326441.412627
FMO2-HF: Total energy -81995.260566
FMO2-MP2: Total energy -82235.626528


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.
1.5453.049-0.008-0.782-0.7140.004
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 : 0.041 / 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].
3A1MET0-0.0020.0003.8200.2981.802-0.008-0.782-0.7140.004
4A2TYR0-0.041-0.0356.1350.5710.5710.0000.0000.0000.000
5A3ARG10.7920.8719.0320.7840.7840.0000.0000.0000.000
6A4SER0-0.028-0.00512.3650.0450.0450.0000.0000.0000.000
7A5ARG10.8790.92915.7780.2500.2500.0000.0000.0000.000
8A6ASP-1-0.806-0.87318.439-0.550-0.5500.0000.0000.0000.000
9A7PHE0-0.052-0.02819.8100.0420.0420.0000.0000.0000.000
10A8TYR00.0500.02023.614-0.025-0.0250.0000.0000.0000.000
11A9VAL0-0.0030.00027.1040.0140.0140.0000.0000.0000.000
12A10ARG10.9550.98029.9940.1310.1310.0000.0000.0000.000
13A11VAL0-0.008-0.01631.3430.0060.0060.0000.0000.0000.000
14A12SER0-0.013-0.00434.3850.0020.0020.0000.0000.0000.000
15A13GLY00.0810.02338.0080.0010.0010.0000.0000.0000.000
16A14GLN0-0.019-0.00840.4920.0030.0030.0000.0000.0000.000
17A15ARG10.8340.91542.4130.0910.0910.0000.0000.0000.000
18A16ALA00.0210.01237.529-0.005-0.0050.0000.0000.0000.000
19A17LEU0-0.021-0.01238.2220.0060.0060.0000.0000.0000.000
20A18PHE00.0240.01633.638-0.005-0.0050.0000.0000.0000.000
21A19THR00.0220.00935.5150.0010.0010.0000.0000.0000.000
22A20ASN00.029-0.00233.841-0.016-0.0160.0000.0000.0000.000
23A21PRO0-0.031-0.00231.6270.0100.0100.0000.0000.0000.000
24A22ALA00.0720.00933.399-0.004-0.0040.0000.0000.0000.000
25A23THR0-0.0030.00435.9610.0000.0000.0000.0000.0000.000
26A24LYS10.8580.95438.5140.1140.1140.0000.0000.0000.000
27A25GLY00.0610.02841.208-0.002-0.0020.0000.0000.0000.000
28A26GLY0-0.030-0.00142.3060.0030.0030.0000.0000.0000.000
29A27SER0-0.015-0.02443.115-0.002-0.0020.0000.0000.0000.000
30A28GLU-1-0.869-0.92245.923-0.068-0.0680.0000.0000.0000.000
31A29ARG10.8600.92541.2870.0880.0880.0000.0000.0000.000
32A30SER00.0270.02642.1220.0010.0010.0000.0000.0000.000
33A31SER0-0.001-0.01538.567-0.005-0.0050.0000.0000.0000.000
34A32TYR00.0020.01033.9400.0010.0010.0000.0000.0000.000
35A33SER00.0320.01937.5740.0020.0020.0000.0000.0000.000
36A34VAL00.0190.01632.7190.0000.0000.0000.0000.0000.000
37A35PRO0-0.0110.00130.8090.0020.0020.0000.0000.0000.000
38A36THR00.0570.03629.438-0.010-0.0100.0000.0000.0000.000
39A37ARG10.9060.94518.4160.4610.4610.0000.0000.0000.000
40A38GLN00.0190.00924.906-0.008-0.0080.0000.0000.0000.000
41A39ALA00.0010.00726.9420.0020.0020.0000.0000.0000.000
42A40LEU00.0260.01026.5940.0040.0040.0000.0000.0000.000
43A41ASN0-0.019-0.02422.287-0.019-0.0190.0000.0000.0000.000
44A42GLY00.0080.01124.9650.0020.0020.0000.0000.0000.000
45A43ILE00.0130.02028.0070.0080.0080.0000.0000.0000.000
46A44VAL0-0.013-0.01323.2430.0070.0070.0000.0000.0000.000
47A45ASP-1-0.859-0.93023.050-0.286-0.2860.0000.0000.0000.000
48A46ALA0-0.075-0.02225.7090.0150.0150.0000.0000.0000.000
49A47ILE00.0110.01727.3340.0140.0140.0000.0000.0000.000
50A48TYR0-0.049-0.07022.5020.0300.0300.0000.0000.0000.000
51A49TYR00.0530.04021.087-0.006-0.0060.0000.0000.0000.000
52A50LYS10.8130.90621.1390.1810.1810.0000.0000.0000.000
53A51PRO00.0140.02120.565-0.025-0.0250.0000.0000.0000.000
54A52THR0-0.028-0.04616.309-0.013-0.0130.0000.0000.0000.000
55A53PHE0-0.0030.00415.707-0.048-0.0480.0000.0000.0000.000
56A54THR0-0.041-0.01615.4460.0700.0700.0000.0000.0000.000
57A55ASN0-0.019-0.03016.688-0.093-0.0930.0000.0000.0000.000
58A56ILE0-0.037-0.01614.9930.0130.0130.0000.0000.0000.000
59A57VAL00.0650.02718.516-0.009-0.0090.0000.0000.0000.000
60A58THR0-0.053-0.03518.470-0.017-0.0170.0000.0000.0000.000
61A59GLU-1-0.806-0.86821.314-0.329-0.3290.0000.0000.0000.000
62A60VAL0-0.020-0.00324.9260.0060.0060.0000.0000.0000.000
63A61LYS10.8600.94228.5170.2140.2140.0000.0000.0000.000
64A62VAL00.017-0.01631.7640.0060.0060.0000.0000.0000.000
65A63ILE0-0.0190.01234.6110.0030.0030.0000.0000.0000.000
66A64ASN00.0540.02237.5280.0020.0020.0000.0000.0000.000
67A65GLN00.0130.01240.263-0.004-0.0040.0000.0000.0000.000
68A66ILE0-0.022-0.01638.2070.0000.0000.0000.0000.0000.000
69A67GLN0-0.0100.00342.2620.0040.0040.0000.0000.0000.000
70A68THR00.002-0.01743.591-0.005-0.0050.0000.0000.0000.000
71A69GLU-1-0.875-0.92145.970-0.077-0.0770.0000.0000.0000.000
72A70LEU0-0.0250.00347.409-0.003-0.0030.0000.0000.0000.000
73A71GLN00.0200.00848.6350.0020.0020.0000.0000.0000.000
74A72GLY00.0070.00950.448-0.001-0.0010.0000.0000.0000.000
75A73VAL0-0.031-0.02049.6730.0010.0010.0000.0000.0000.000
76A74ARG10.9900.98852.8620.0490.0490.0000.0000.0000.000
77A85SER0-0.024-0.00950.2190.0010.0010.0000.0000.0000.000
78A86TYR00.0370.01849.9410.0010.0010.0000.0000.0000.000
79A87VAL0-0.006-0.00144.229-0.003-0.0030.0000.0000.0000.000
80A88SER0-0.044-0.01944.9380.0020.0020.0000.0000.0000.000
81A89TYR0-0.040-0.06942.474-0.004-0.0040.0000.0000.0000.000
82A90LEU00.0100.01338.2040.0020.0020.0000.0000.0000.000
83A91SER0-0.004-0.03042.2930.0030.0030.0000.0000.0000.000
84A92ASP-1-0.902-0.93543.373-0.109-0.1090.0000.0000.0000.000
85A93VAL00.0090.02038.016-0.004-0.0040.0000.0000.0000.000
86A94VAL00.024-0.00436.6100.0010.0010.0000.0000.0000.000
87A95TYR00.008-0.00632.243-0.002-0.0020.0000.0000.0000.000
88A96LEU00.0340.03031.2070.0010.0010.0000.0000.0000.000
89A97ILE0-0.055-0.02725.549-0.012-0.0120.0000.0000.0000.000
90A98LYS10.9420.98021.3780.4290.4290.0000.0000.0000.000
91A99PHE0-0.041-0.04121.198-0.017-0.0170.0000.0000.0000.000
92A100HIS00.0240.03314.176-0.006-0.0060.0000.0000.0000.000
93A101PHE00.0330.00615.8210.0260.0260.0000.0000.0000.000
94A102VAL00.0550.03411.211-0.074-0.0740.0000.0000.0000.000
95A103TRP00.032-0.0019.6790.1920.1920.0000.0000.0000.000
96A104ASN0-0.008-0.01311.846-0.130-0.1300.0000.0000.0000.000
97A105GLU-1-0.790-0.8758.416-0.366-0.3660.0000.0000.0000.000
98A106ASP-1-0.854-0.89911.831-0.193-0.1930.0000.0000.0000.000
99A107ARG10.7420.82614.8240.1490.1490.0000.0000.0000.000
100A108LYS10.9600.9659.7490.0440.0440.0000.0000.0000.000
101A109ASP-1-0.781-0.84814.585-0.014-0.0140.0000.0000.0000.000
102A110LEU0-0.053-0.01817.0740.0080.0080.0000.0000.0000.000
103A111ASN00.0490.01511.904-0.076-0.0760.0000.0000.0000.000
104A112SER00.0240.00914.908-0.025-0.0250.0000.0000.0000.000
105A113ASP-1-0.765-0.85417.519-0.157-0.1570.0000.0000.0000.000
106A114ARG10.8260.9239.8080.3000.3000.0000.0000.0000.000
107A115LEU0-0.008-0.00814.416-0.004-0.0040.0000.0000.0000.000
108A116PRO00.0710.02813.9990.0060.0060.0000.0000.0000.000
109A117ALA00.0580.03016.4410.0020.0020.0000.0000.0000.000
110A118LYS10.8840.93519.8280.1330.1330.0000.0000.0000.000
111A119HIS0-0.009-0.01217.7850.0080.0080.0000.0000.0000.000
112A120GLU-1-0.765-0.89217.239-0.452-0.4520.0000.0000.0000.000
113A121ALA00.0540.03621.0790.0150.0150.0000.0000.0000.000
114A122ILE0-0.089-0.04323.9010.0170.0170.0000.0000.0000.000
115A123MET00.0150.04521.8610.0250.0250.0000.0000.0000.000
116A124GLU-1-0.800-0.87724.594-0.226-0.2260.0000.0000.0000.000
117A125ARG10.8860.92926.5460.1560.1560.0000.0000.0000.000
118A126SER0-0.061-0.05027.6870.0160.0160.0000.0000.0000.000
119A127ILE00.0180.01725.7820.0090.0090.0000.0000.0000.000
120A128ARG10.8440.91929.9680.1680.1680.0000.0000.0000.000
121A129LYS10.8130.90632.7320.1340.1340.0000.0000.0000.000
122A130GLY00.0630.05033.6860.0080.0080.0000.0000.0000.000
123A131GLY0-0.039-0.01131.032-0.001-0.0010.0000.0000.0000.000
124A132ARG10.8350.91028.0870.1580.1580.0000.0000.0000.000
125A133ARG10.8960.95528.3960.1460.1460.0000.0000.0000.000
126A134ASP-1-0.867-0.92533.410-0.109-0.1090.0000.0000.0000.000
127A135VAL00.002-0.00232.174-0.009-0.0090.0000.0000.0000.000
128A136PHE0-0.017-0.00434.0570.0080.0080.0000.0000.0000.000
129A137LEU00.0040.00734.106-0.014-0.0140.0000.0000.0000.000
130A138GLY0-0.029-0.01834.1320.0060.0060.0000.0000.0000.000
131A139THR0-0.076-0.07135.1470.0020.0020.0000.0000.0000.000
132A140ARG10.9560.97235.8210.1020.1020.0000.0000.0000.000
133A141GLU-1-0.763-0.84139.439-0.096-0.0960.0000.0000.0000.000
134A142CYS0-0.066-0.00539.4580.0030.0030.0000.0000.0000.000
135A143LEU00.0010.00038.877-0.007-0.0070.0000.0000.0000.000
136A144GLY0-0.005-0.00636.7700.0000.0000.0000.0000.0000.000
137A145LEU0-0.0290.00237.6550.0030.0030.0000.0000.0000.000
138A146VAL0-0.028-0.02231.375-0.008-0.0080.0000.0000.0000.000
139A147ASP-1-0.823-0.91034.317-0.129-0.1290.0000.0000.0000.000
140A148ASP-1-0.844-0.93130.689-0.196-0.1960.0000.0000.0000.000
141A149ILE00.0050.02730.4420.0070.0070.0000.0000.0000.000
142A150SER00.0340.01329.419-0.016-0.0160.0000.0000.0000.000
143A151GLN0-0.057-0.05024.183-0.008-0.0080.0000.0000.0000.000
144A152GLU-1-0.897-0.95428.095-0.170-0.1700.0000.0000.0000.000
145A153GLU-1-0.869-0.91931.246-0.157-0.1570.0000.0000.0000.000
146A154TYR0-0.073-0.07426.9810.0070.0070.0000.0000.0000.000
147A155GLU-1-0.899-0.93626.546-0.283-0.2830.0000.0000.0000.000
148A156THR0-0.046-0.03530.9040.0090.0090.0000.0000.0000.000
149A157THR0-0.042-0.01034.2860.0140.0140.0000.0000.0000.000
150A158VAL0-0.020-0.01335.588-0.010-0.0100.0000.0000.0000.000
151A159SER0-0.029-0.03035.9230.0050.0050.0000.0000.0000.000
152A160TYR00.028-0.00837.9500.0040.0040.0000.0000.0000.000
153A161TYR0-0.003-0.00537.8380.0060.0060.0000.0000.0000.000
154A162ASN0-0.034-0.01537.370-0.013-0.0130.0000.0000.0000.000
155A163GLY00.0180.01238.0420.0080.0080.0000.0000.0000.000
156A164VAL0-0.0170.00139.0730.0050.0050.0000.0000.0000.000
157A165ASN0-0.027-0.03135.041-0.017-0.0170.0000.0000.0000.000
158A166ILE00.0170.01036.1730.0090.0090.0000.0000.0000.000
159A167ASP-1-0.822-0.90034.588-0.178-0.1780.0000.0000.0000.000
160A168LEU0-0.012-0.00933.8380.0090.0090.0000.0000.0000.000
161A169GLY00.0120.02235.0100.0060.0060.0000.0000.0000.000
162A170ILE0-0.043-0.03131.373-0.012-0.0120.0000.0000.0000.000
163A171MET0-0.028-0.01030.8900.0110.0110.0000.0000.0000.000
164A172PHE0-0.016-0.01728.437-0.014-0.0140.0000.0000.0000.000
165A173HIS0-0.0140.00221.4110.0120.0120.0000.0000.0000.000
166A174SER0-0.044-0.04823.179-0.016-0.0160.0000.0000.0000.000
167A175PHE00.0160.00225.3060.0090.0090.0000.0000.0000.000
168A176ALA00.0020.02821.075-0.026-0.0260.0000.0000.0000.000
169A177TYR0-0.007-0.01721.7630.0330.0330.0000.0000.0000.000
170A178PRO00.0300.02321.272-0.015-0.0150.0000.0000.0000.000
171A179LYS10.8600.90517.3700.3020.3020.0000.0000.0000.000
172A180ASP-1-0.769-0.86323.269-0.047-0.0470.0000.0000.0000.000
173A181LYS10.9550.97225.8290.0800.0800.0000.0000.0000.000
174A182LYS10.8080.87727.1030.0520.0520.0000.0000.0000.000
175A183THR00.0230.02428.5880.0000.0000.0000.0000.0000.000
176A184PRO0-0.050-0.01626.5750.0000.0000.0000.0000.0000.000
177A185LEU0-0.008-0.00722.7500.0130.0130.0000.0000.0000.000
178A186LYS10.9310.95722.0740.1640.1640.0000.0000.0000.000
179A187SER00.0060.01225.974-0.007-0.0070.0000.0000.0000.000
180A188TYR00.0200.01220.4620.0110.0110.0000.0000.0000.000
181A189PHE00.013-0.00226.0290.0020.0020.0000.0000.0000.000
182A190THR0-0.049-0.06325.533-0.017-0.0170.0000.0000.0000.000
183A191LYS10.9120.94628.2710.1780.1780.0000.0000.0000.000
184A192THR0-0.0050.00828.851-0.024-0.0240.0000.0000.0000.000
185A193VAL0-0.039-0.03030.0530.0140.0140.0000.0000.0000.000
186A194MET0-0.0060.03230.764-0.016-0.0160.0000.0000.0000.000
187A195LYS10.9600.96528.2310.2600.2600.0000.0000.0000.000
188A196ASN00.0080.01332.867-0.001-0.0010.0000.0000.0000.000
189A197GLY00.0600.02034.8960.0000.0000.0000.0000.0000.000
190A198VAL0-0.0180.00128.400-0.003-0.0030.0000.0000.0000.000
191A199ILE0-0.006-0.00427.6040.0050.0050.0000.0000.0000.000
192A200THR0-0.011-0.01522.843-0.003-0.0030.0000.0000.0000.000
193A201PHE0-0.058-0.04922.3860.0090.0090.0000.0000.0000.000
194A202LYS10.9290.99620.9080.2600.2600.0000.0000.0000.000
195A203ALA00.010-0.00616.5670.0120.0120.0000.0000.0000.000
196A204GLN00.001-0.04118.5930.0300.0300.0000.0000.0000.000
197A205SER0-0.027-0.01716.4440.0220.0220.0000.0000.0000.000
198A206GLU-1-0.871-0.91817.154-0.551-0.5510.0000.0000.0000.000
199A207CYS0-0.104-0.04320.3750.0320.0320.0000.0000.0000.000
200A208ASP-1-0.811-0.87423.771-0.227-0.2270.0000.0000.0000.000
201A209ILE00.0200.01926.9100.0140.0140.0000.0000.0000.000
202A210VAL00.0110.00323.242-0.014-0.0140.0000.0000.0000.000
203A211ASN0-0.033-0.00726.5600.0200.0200.0000.0000.0000.000
204A212THR00.0380.02026.950-0.010-0.0100.0000.0000.0000.000