Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: VQK31

Calculation Name: 1YZF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YZF

Chain ID: A

ChEMBL ID:

UniProt ID: Q839J6

Base Structure: X-ray

Registration Date: 2023-09-22

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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2191789.505049
FMO2-HF: Nuclear repulsion 2116985.797224
FMO2-HF: Total energy -74803.707825
FMO2-MP2: Total energy -75023.70498


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-13.331-7.47311.294-4.884-12.266-0.043
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.030 / q_NPA : -0.006
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].
3A3LYS10.8300.9043.130-1.9951.0790.092-1.708-1.458-0.004
4A4ILE0-0.011-0.0085.5180.1950.1950.0000.0000.0000.000
5A5VAL00.0160.0058.1480.3310.3310.0000.0000.0000.000
6A6LEU00.0060.00411.155-0.069-0.0690.0000.0000.0000.000
7A7PHE00.029-0.00513.9240.0410.0410.0000.0000.0000.000
8A8GLY00.0620.00916.992-0.024-0.0240.0000.0000.0000.000
9A9ASP-1-0.816-0.91720.3920.0150.0150.0000.0000.0000.000
10A10SER00.0650.01022.0770.0110.0110.0000.0000.0000.000
11A11ILE00.0080.02622.2460.0130.0130.0000.0000.0000.000
12A12THR0-0.0060.00717.0780.0040.0040.0000.0000.0000.000
13A13ALA0-0.0120.00618.1080.0300.0300.0000.0000.0000.000
14A14GLY00.0510.03619.2990.0280.0280.0000.0000.0000.000
15A15TYR0-0.068-0.05520.1740.0100.0100.0000.0000.0000.000
16A16LEU0-0.0120.00522.161-0.001-0.0010.0000.0000.0000.000
17A17ASP-1-0.879-0.93925.8380.0410.0410.0000.0000.0000.000
18A18GLU-1-0.962-0.95924.0030.0850.0850.0000.0000.0000.000
19A19ALA00.0150.00023.8220.0050.0050.0000.0000.0000.000
20A20VAL0-0.018-0.02619.5070.0020.0020.0000.0000.0000.000
21A21SER00.0040.00618.7930.0110.0110.0000.0000.0000.000
22A22PRO0-0.0010.00813.9560.0110.0110.0000.0000.0000.000
23A23VAL0-0.0050.00314.0290.0410.0410.0000.0000.0000.000
24A24LEU00.0520.03115.394-0.001-0.0010.0000.0000.0000.000
25A25VAL00.001-0.0079.570-0.007-0.0070.0000.0000.0000.000
26A26ASP-1-0.817-0.92010.5730.6660.6660.0000.0000.0000.000
27A27LEU0-0.057-0.00711.849-0.034-0.0340.0000.0000.0000.000
28A28VAL00.0400.0179.885-0.035-0.0350.0000.0000.0000.000
29A29LYS10.8210.9076.402-1.308-1.3080.0000.0000.0000.000
30A30ARG10.8620.9289.136-0.230-0.2300.0000.0000.0000.000
31A31ASP-1-0.793-0.89911.723-0.008-0.0080.0000.0000.0000.000
32A32ILE0-0.007-0.0078.128-0.064-0.0640.0000.0000.0000.000
33A33ALA0-0.014-0.0078.765-0.066-0.0660.0000.0000.0000.000
34A34ALA0-0.027-0.01010.472-0.021-0.0210.0000.0000.0000.000
35A35MET0-0.090-0.03113.212-0.003-0.0030.0000.0000.0000.000
36A36GLY0-0.0050.00612.611-0.011-0.0110.0000.0000.0000.000
37A37LEU0-0.032-0.0119.886-0.009-0.0090.0000.0000.0000.000
38A38GLU-1-0.800-0.8835.327-1.101-1.1010.0000.0000.0000.000
39A39GLU-1-0.871-0.9382.392-5.355-3.5322.877-1.483-3.216-0.012
40A40VAL0-0.020-0.0082.507-3.544-2.1143.448-1.640-3.237-0.019
41A41ALA00.0280.0062.2291.9302.1094.789-0.869-4.099-0.008
42A42VAL0-0.018-0.0053.704-1.114-1.7620.0880.816-0.2560.000
43A43ILE0-0.020-0.0117.1450.3380.3380.0000.0000.0000.000
44A44ASN0-0.008-0.0179.846-0.199-0.1990.0000.0000.0000.000
45A45ALA00.0230.02013.5720.0130.0130.0000.0000.0000.000
46A46GLY00.0190.00716.100-0.045-0.0450.0000.0000.0000.000
47A47MET0-0.018-0.00418.9490.0220.0220.0000.0000.0000.000
48A48PRO0-0.005-0.01622.214-0.013-0.0130.0000.0000.0000.000
49A49GLY00.0040.01125.196-0.003-0.0030.0000.0000.0000.000
50A50ASP-1-0.751-0.86423.6750.0060.0060.0000.0000.0000.000
51A51THR0-0.057-0.04826.580-0.004-0.0040.0000.0000.0000.000
52A52THR00.004-0.04025.6100.0000.0000.0000.0000.0000.000
53A53GLU-1-0.856-0.91526.558-0.022-0.0220.0000.0000.0000.000
54A54ASP-1-0.846-0.89127.224-0.001-0.0010.0000.0000.0000.000
55A55GLY00.0750.03823.2650.0030.0030.0000.0000.0000.000
56A56LEU0-0.031-0.02422.987-0.005-0.0050.0000.0000.0000.000
57A57LYS10.7370.86524.9390.0090.0090.0000.0000.0000.000
58A58ARG10.7340.84319.177-0.031-0.0310.0000.0000.0000.000
59A59LEU00.0390.03619.6120.0050.0050.0000.0000.0000.000
60A60ASN00.0460.00118.673-0.029-0.0290.0000.0000.0000.000
61A61LYS10.8390.90017.859-0.110-0.1100.0000.0000.0000.000
62A62GLU-1-0.845-0.90616.3070.1160.1160.0000.0000.0000.000
63A63VAL00.0170.02214.4460.0170.0170.0000.0000.0000.000
64A64LEU00.0030.01313.963-0.072-0.0720.0000.0000.0000.000
65A65ILE0-0.023-0.01814.241-0.065-0.0650.0000.0000.0000.000
66A66GLU-1-0.815-0.8989.4200.2860.2860.0000.0000.0000.000
67A67LYS10.8140.9189.2970.3480.3480.0000.0000.0000.000
68A68PRO00.0200.0139.050-0.308-0.3080.0000.0000.0000.000
69A69ASP-1-0.844-0.9116.695-2.849-2.8490.0000.0000.0000.000
70A70GLU-1-0.836-0.9389.781-0.685-0.6850.0000.0000.0000.000
71A71VAL0-0.014-0.01211.0400.0360.0360.0000.0000.0000.000
72A72VAL00.0110.01312.8640.0080.0080.0000.0000.0000.000
73A73ILE0-0.0140.00415.3180.0430.0430.0000.0000.0000.000
74A74PHE0-0.003-0.02118.754-0.003-0.0030.0000.0000.0000.000
75A75PHE00.0240.02320.7060.0170.0170.0000.0000.0000.000
76A76GLY00.033-0.00224.253-0.009-0.0090.0000.0000.0000.000
77A77ALA0-0.0040.01427.0220.0010.0010.0000.0000.0000.000
78A78ASN0-0.074-0.03727.6510.0050.0050.0000.0000.0000.000
79A79ASP-1-0.717-0.84528.553-0.027-0.0270.0000.0000.0000.000
80A80ALA00.0100.00431.543-0.001-0.0010.0000.0000.0000.000
81A81SER0-0.053-0.02833.5960.0020.0020.0000.0000.0000.000
82A82LEU0-0.022-0.02835.658-0.002-0.0020.0000.0000.0000.000
83A83ASP-1-0.921-0.94137.3420.0010.0010.0000.0000.0000.000
84A84ARG10.7590.85830.078-0.003-0.0030.0000.0000.0000.000
85A85ASN00.0160.00935.498-0.001-0.0010.0000.0000.0000.000
86A86ILE0-0.0140.01631.692-0.003-0.0030.0000.0000.0000.000
87A87THR00.032-0.00334.876-0.001-0.0010.0000.0000.0000.000
88A88VAL00.027-0.00135.052-0.003-0.0030.0000.0000.0000.000
89A89ALA0-0.021-0.00634.497-0.004-0.0040.0000.0000.0000.000
90A90THR00.0750.04632.822-0.004-0.0040.0000.0000.0000.000
91A91PHE00.0110.01327.554-0.004-0.0040.0000.0000.0000.000
92A92ARG10.8430.90429.4820.0610.0610.0000.0000.0000.000
93A93GLU-1-0.926-0.96129.684-0.059-0.0590.0000.0000.0000.000
94A94ASN00.0360.00627.682-0.008-0.0080.0000.0000.0000.000
95A95LEU00.0090.00124.284-0.009-0.0090.0000.0000.0000.000
96A96GLU-1-0.846-0.91025.032-0.130-0.1300.0000.0000.0000.000
97A97THR0-0.007-0.01026.135-0.012-0.0120.0000.0000.0000.000
98A98MET0-0.067-0.02621.661-0.011-0.0110.0000.0000.0000.000
99A99ILE0-0.023-0.01621.415-0.025-0.0250.0000.0000.0000.000
100A100HIS0-0.116-0.05422.151-0.023-0.0230.0000.0000.0000.000
101A101GLU-1-0.893-0.94221.996-0.138-0.1380.0000.0000.0000.000
102A102ILE0-0.048-0.01316.249-0.022-0.0220.0000.0000.0000.000
103A103GLY00.0390.03517.704-0.061-0.0610.0000.0000.0000.000
104A104SER00.0370.00318.457-0.019-0.0190.0000.0000.0000.000
105A105GLU-1-0.849-0.91116.270-0.379-0.3790.0000.0000.0000.000
106A106LYS10.8200.89713.5850.4210.4210.0000.0000.0000.000
107A107VAL0-0.0310.00214.693-0.013-0.0130.0000.0000.0000.000
108A108ILE00.0010.00113.7630.0010.0010.0000.0000.0000.000
109A109LEU0-0.0130.00417.5450.0210.0210.0000.0000.0000.000
110A110ILE0-0.020-0.00717.968-0.001-0.0010.0000.0000.0000.000
111A111THR0-0.064-0.03521.9550.0070.0070.0000.0000.0000.000
112A112PRO00.0350.00325.3150.0060.0060.0000.0000.0000.000
113A113PRO00.0140.02326.388-0.003-0.0030.0000.0000.0000.000
114A114TYR0-0.085-0.07827.992-0.002-0.0020.0000.0000.0000.000
115A115ALA00.0210.00730.6140.0040.0040.0000.0000.0000.000
116A116ASP-1-0.761-0.85433.200-0.004-0.0040.0000.0000.0000.000
117A117SER0-0.041-0.04636.7040.0010.0010.0000.0000.0000.000
118A118GLY0-0.039-0.00538.9830.0000.0000.0000.0000.0000.000
119A119ARG10.7750.86935.595-0.005-0.0050.0000.0000.0000.000
120A120ARG10.7350.85234.661-0.005-0.0050.0000.0000.0000.000
121A121PRO00.0420.02838.387-0.003-0.0030.0000.0000.0000.000
122A122GLU-1-0.774-0.82936.6520.0010.0010.0000.0000.0000.000
123A123ARG10.8460.89131.617-0.004-0.0040.0000.0000.0000.000
124A124PRO00.0450.02937.216-0.001-0.0010.0000.0000.0000.000
125A125GLN00.0590.04035.736-0.005-0.0050.0000.0000.0000.000
126A126THR0-0.039-0.02937.366-0.002-0.0020.0000.0000.0000.000
127A127ARG10.8860.94735.2940.0210.0210.0000.0000.0000.000
128A128ILE00.0280.01631.962-0.003-0.0030.0000.0000.0000.000
129A129LYS10.9310.96233.1000.0260.0260.0000.0000.0000.000
130A130GLU-1-0.897-0.94134.740-0.035-0.0350.0000.0000.0000.000
131A131LEU0-0.0010.00730.895-0.005-0.0050.0000.0000.0000.000
132A132VAL0-0.0120.00129.680-0.007-0.0070.0000.0000.0000.000
133A133LYS10.8750.93130.3090.0480.0480.0000.0000.0000.000
134A134VAL0-0.033-0.01730.215-0.006-0.0060.0000.0000.0000.000
135A135ALA00.0450.01826.341-0.007-0.0070.0000.0000.0000.000
136A136GLN0-0.059-0.04727.152-0.009-0.0090.0000.0000.0000.000
137A137GLU-1-0.811-0.87228.830-0.071-0.0710.0000.0000.0000.000
138A138VAL0-0.0050.00525.704-0.005-0.0050.0000.0000.0000.000
139A139GLY00.0240.00424.784-0.011-0.0110.0000.0000.0000.000
140A140ALA0-0.006-0.00825.620-0.012-0.0120.0000.0000.0000.000
141A141ALA0-0.035-0.01328.325-0.005-0.0050.0000.0000.0000.000
142A142HIS10.7830.86224.4580.1380.1380.0000.0000.0000.000
143A143ASN0-0.062-0.02124.322-0.012-0.0120.0000.0000.0000.000
144A144LEU0-0.0110.02220.396-0.016-0.0160.0000.0000.0000.000
145A145PRO0-0.016-0.01817.8330.0220.0220.0000.0000.0000.000
146A146VAL00.0170.01020.8190.0030.0030.0000.0000.0000.000
147A147ILE00.0150.01817.5280.0080.0080.0000.0000.0000.000
148A148ASP-1-0.790-0.88822.160-0.054-0.0540.0000.0000.0000.000
149A149LEU00.0330.01223.1090.0050.0050.0000.0000.0000.000
150A150TYR00.003-0.01025.4220.0060.0060.0000.0000.0000.000
151A151LYS10.9080.97229.1210.0570.0570.0000.0000.0000.000
152A152ALA0-0.033-0.01926.3790.0020.0020.0000.0000.0000.000
153A153MET00.0100.02027.3590.0030.0030.0000.0000.0000.000
154A154THR0-0.036-0.03829.6920.0020.0020.0000.0000.0000.000
155A155VAL0-0.086-0.03431.128-0.001-0.0010.0000.0000.0000.000
156A156TYR00.0070.01530.863-0.001-0.0010.0000.0000.0000.000
157A157PRO0-0.021-0.02832.9770.0020.0020.0000.0000.0000.000
158A158GLY00.0220.03234.6690.0010.0010.0000.0000.0000.000
159A159THR0-0.017-0.02132.3320.0020.0020.0000.0000.0000.000
160A160ASP-1-0.776-0.90432.147-0.002-0.0020.0000.0000.0000.000
161A161GLU-1-0.914-0.94032.2070.0080.0080.0000.0000.0000.000
162A162PHE0-0.0540.00027.7190.0030.0030.0000.0000.0000.000
163A163LEU0-0.069-0.01528.3380.0030.0030.0000.0000.0000.000
164A164GLN00.0310.00328.831-0.001-0.0010.0000.0000.0000.000
165A165ALA00.021-0.00731.604-0.004-0.0040.0000.0000.0000.000
166A166ASP-1-0.776-0.87032.2770.0190.0190.0000.0000.0000.000
167A167GLY00.0140.01834.172-0.003-0.0030.0000.0000.0000.000
168A168LEU0-0.048-0.04230.052-0.006-0.0060.0000.0000.0000.000
169A169HIS0-0.023-0.02526.4720.0020.0020.0000.0000.0000.000
170A170PHE00.011-0.00623.632-0.006-0.0060.0000.0000.0000.000
171A171SER00.029-0.01626.2320.0090.0090.0000.0000.0000.000
172A172GLN0-0.050-0.03823.5490.0040.0040.0000.0000.0000.000
173A173VAL00.0580.02423.8880.0010.0010.0000.0000.0000.000
174A174GLY00.0210.01725.176-0.008-0.0080.0000.0000.0000.000
175A175TYR0-0.044-0.03619.848-0.007-0.0070.0000.0000.0000.000
176A176GLU-1-0.884-0.93320.1260.0340.0340.0000.0000.0000.000
177A177LEU0-0.041-0.00720.639-0.011-0.0110.0000.0000.0000.000
178A178LEU0-0.010-0.00818.874-0.015-0.0150.0000.0000.0000.000
179A179GLY00.0360.00616.566-0.013-0.0130.0000.0000.0000.000
180A180ALA00.0120.00016.325-0.021-0.0210.0000.0000.0000.000
181A181LEU0-0.046-0.02618.132-0.027-0.0270.0000.0000.0000.000
182A182ILE00.0170.00313.168-0.031-0.0310.0000.0000.0000.000
183A183VAL0-0.019-0.01112.706-0.054-0.0540.0000.0000.0000.000
184A184ARG10.7680.85314.3900.1110.1110.0000.0000.0000.000
185A185GLU-1-0.808-0.87816.019-0.197-0.1970.0000.0000.0000.000
186A186ILE00.0370.0199.241-0.032-0.0320.0000.0000.0000.000
187A187LYS10.9130.96811.8220.0730.0730.0000.0000.0000.000
188A188GLY0-0.039-0.00912.856-0.012-0.0120.0000.0000.0000.000
189A189ARG10.7760.88511.2880.5810.5810.0000.0000.0000.000
190A190LEU0-0.038-0.0047.151-0.245-0.2450.0000.0000.0000.000
191A191LYS10.8140.8816.4731.0271.0270.0000.0000.0000.000
192A192PRO00.027-0.0039.809-0.034-0.0340.0000.0000.0000.000
193A193LYS10.8610.9425.7470.5960.5960.0000.0000.0000.000
194A194GLN0-0.043-0.02910.3260.0270.0270.0000.0000.0000.000
195A195ALA00.0050.01511.747-0.005-0.0050.0000.0000.0000.000