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: 823QY

Calculation Name: 3WVZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WVZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q53FT3

Base Structure: X-ray

Registration Date: 2023-06-20

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 199
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1861657.045116
FMO2-HF: Nuclear repulsion 1784557.065949
FMO2-HF: Total energy -77099.979167
FMO2-MP2: Total energy -77321.294759


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:-3:ALA)


Summations of interaction energy for fragment #1(A:-3:ALA)
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.
-13.236-6.0492.351-4.728-4.81-0.017
Interaction energy analysis for fragmet #1(A:-3:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : 0.001
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].
3A-1GLY00.0130.0183.034-4.161-1.5580.063-1.414-1.2520.007
4A0SER00.0280.0134.6430.0870.170-0.001-0.011-0.0710.000
5A1MET0-0.0050.0217.526-0.312-0.3120.0000.0000.0000.000
6A2PHE0-0.012-0.0118.465-0.266-0.2660.0000.0000.0000.000
7A3GLY00.0290.00412.3670.0280.0280.0000.0000.0000.000
8A4CYS0-0.058-0.00715.605-0.033-0.0330.0000.0000.0000.000
9A5LEU00.0240.01318.507-0.011-0.0110.0000.0000.0000.000
10A6VAL00.0460.02322.171-0.003-0.0030.0000.0000.0000.000
11A7ALA00.010-0.00125.572-0.006-0.0060.0000.0000.0000.000
12A8GLY00.0150.00329.004-0.002-0.0020.0000.0000.0000.000
13A9ARG10.8130.91025.683-0.173-0.1730.0000.0000.0000.000
14A10LEU00.0140.00523.118-0.003-0.0030.0000.0000.0000.000
15A11VAL0-0.021-0.01118.2650.0090.0090.0000.0000.0000.000
16A12GLN0-0.029-0.01716.9220.0320.0320.0000.0000.0000.000
17A13THR00.017-0.01513.4210.0070.0070.0000.0000.0000.000
18A14ALA0-0.016-0.00211.7090.1350.1350.0000.0000.0000.000
19A15ALA00.0050.01410.456-0.061-0.0610.0000.0000.0000.000
20A16GLN00.0230.00310.4000.1480.1480.0000.0000.0000.000
21A17GLN0-0.042-0.0223.436-2.568-1.7640.028-0.462-0.3700.004
22A18VAL0-0.033-0.0158.528-0.168-0.1680.0000.0000.0000.000
23A19ALA00.0050.0097.600-0.300-0.3000.0000.0000.0000.000
24A20GLU-1-0.938-0.9782.390-5.959-3.3192.169-2.182-2.627-0.022
25A21ASP-1-0.823-0.8983.1511.0492.1060.092-0.659-0.490-0.006
26A22LYS10.8070.8915.705-0.846-0.8460.0000.0000.0000.000
27A23PHE0-0.005-0.0065.0950.0270.0270.0000.0000.0000.000
28A24VAL00.0160.00810.510-0.193-0.1930.0000.0000.0000.000
29A25PHE0-0.019-0.01113.4560.0620.0620.0000.0000.0000.000
30A26ASP-1-0.796-0.88916.6020.2880.2880.0000.0000.0000.000
31A27LEU0-0.064-0.03719.812-0.008-0.0080.0000.0000.0000.000
32A28PRO00.0330.01122.825-0.016-0.0160.0000.0000.0000.000
33A29ASP-1-0.831-0.89925.9930.1440.1440.0000.0000.0000.000
34A30TYR00.0250.02127.290-0.003-0.0030.0000.0000.0000.000
35A31GLU-1-0.802-0.89728.7480.1270.1270.0000.0000.0000.000
36A32SER0-0.114-0.06830.837-0.007-0.0070.0000.0000.0000.000
37A33ILE0-0.049-0.01826.2590.0000.0000.0000.0000.0000.000
38A34ASN00.0160.02630.306-0.005-0.0050.0000.0000.0000.000
39A35HIS0-0.003-0.01027.9780.0020.0020.0000.0000.0000.000
40A36VAL00.0080.00621.7580.0040.0040.0000.0000.0000.000
41A37VAL0-0.036-0.01021.917-0.012-0.0120.0000.0000.0000.000
42A38VAL00.0210.00416.6640.0210.0210.0000.0000.0000.000
43A39PHE0-0.015-0.02117.014-0.033-0.0330.0000.0000.0000.000
44A40MET00.0050.02912.0610.0550.0550.0000.0000.0000.000
45A41LEU0-0.071-0.03812.171-0.071-0.0710.0000.0000.0000.000
46A42GLY0-0.018-0.00814.661-0.041-0.0410.0000.0000.0000.000
47A43THR0-0.050-0.03210.541-0.059-0.0590.0000.0000.0000.000
48A44ILE00.0200.0096.410-0.124-0.1240.0000.0000.0000.000
49A45PRO0-0.013-0.01010.5180.1040.1040.0000.0000.0000.000
50A46PHE00.0350.0099.4150.0080.0080.0000.0000.0000.000
51A47PRO00.0230.0027.112-0.057-0.0570.0000.0000.0000.000
52A48GLU-1-0.917-0.9609.936-0.041-0.0410.0000.0000.0000.000
53A49GLY00.0260.01512.729-0.004-0.0040.0000.0000.0000.000
54A50MET0-0.056-0.0158.8440.0400.0400.0000.0000.0000.000
55A51GLY00.004-0.01212.764-0.022-0.0220.0000.0000.0000.000
56A52GLY00.0350.01112.0120.0550.0550.0000.0000.0000.000
57A53SER0-0.021-0.01913.180-0.049-0.0490.0000.0000.0000.000
58A54VAL0-0.032-0.01214.7700.0670.0670.0000.0000.0000.000
59A55TYR0-0.034-0.03915.363-0.068-0.0680.0000.0000.0000.000
60A56PHE00.008-0.00619.0210.0300.0300.0000.0000.0000.000
61A57SER00.0170.01820.772-0.027-0.0270.0000.0000.0000.000
62A58TYR0-0.002-0.03623.1860.0100.0100.0000.0000.0000.000
63A59PRO0-0.038-0.01026.662-0.001-0.0010.0000.0000.0000.000
64A60ASP-1-0.785-0.84729.8190.1000.1000.0000.0000.0000.000
65A61SER0-0.057-0.06131.946-0.004-0.0040.0000.0000.0000.000
66A62ASN0-0.076-0.05230.240-0.001-0.0010.0000.0000.0000.000
67A63GLY00.0250.02427.5530.0050.0050.0000.0000.0000.000
68A64MET0-0.045-0.02723.778-0.002-0.0020.0000.0000.0000.000
69A65PRO00.0240.00820.4000.0170.0170.0000.0000.0000.000
70A66VAL0-0.0050.01222.144-0.011-0.0110.0000.0000.0000.000
71A67TRP00.0360.00618.3600.0190.0190.0000.0000.0000.000
72A68GLN00.0480.02421.970-0.013-0.0130.0000.0000.0000.000
73A69LEU00.0090.00719.2300.0200.0200.0000.0000.0000.000
74A70LEU0-0.015-0.01621.186-0.024-0.0240.0000.0000.0000.000
75A71GLY0-0.002-0.01420.787-0.022-0.0220.0000.0000.0000.000
76A72PHE00.0170.01917.9280.0220.0220.0000.0000.0000.000
77A73VAL0-0.045-0.00614.555-0.019-0.0190.0000.0000.0000.000
78A74THR00.0530.01515.2200.0140.0140.0000.0000.0000.000
79A75ASN00.0600.01513.1680.0340.0340.0000.0000.0000.000
80A76GLY0-0.0040.01516.505-0.013-0.0130.0000.0000.0000.000
81A77LYS10.7950.88419.038-0.181-0.1810.0000.0000.0000.000
82A78PRO00.0760.04516.9170.0210.0210.0000.0000.0000.000
83A79SER00.0070.00217.3040.0360.0360.0000.0000.0000.000
84A80ALA0-0.001-0.00319.759-0.022-0.0220.0000.0000.0000.000
85A81ILE00.0000.00421.9680.0110.0110.0000.0000.0000.000
86A82PHE00.0010.00420.068-0.010-0.0100.0000.0000.0000.000
87A83LYS10.8520.93225.614-0.116-0.1160.0000.0000.0000.000
88A84ILE00.0230.00424.5610.0060.0060.0000.0000.0000.000
89A85SER0-0.008-0.01327.814-0.001-0.0010.0000.0000.0000.000
90A86GLY00.004-0.00831.589-0.002-0.0020.0000.0000.0000.000
91A87LEU0-0.044-0.00527.065-0.004-0.0040.0000.0000.0000.000
92A88LYS10.8320.89731.315-0.094-0.0940.0000.0000.0000.000
93A89SER00.0410.01030.2950.0060.0060.0000.0000.0000.000
94A90GLY0-0.0040.00929.517-0.008-0.0080.0000.0000.0000.000
95A91GLU-1-0.833-0.89529.8040.0890.0890.0000.0000.0000.000
96A92GLY00.0120.00326.5400.0090.0090.0000.0000.0000.000
97A93SER0-0.043-0.01822.212-0.006-0.0060.0000.0000.0000.000
98A94GLN00.0180.00922.8530.0110.0110.0000.0000.0000.000
99A95HIS0-0.0140.00218.5610.0280.0280.0000.0000.0000.000
100A96PRO00.0200.01814.205-0.025-0.0250.0000.0000.0000.000
101A97PHE00.0090.00012.6060.0170.0170.0000.0000.0000.000
102A98GLY0-0.023-0.00715.683-0.024-0.0240.0000.0000.0000.000
103A99ALA0-0.008-0.00614.137-0.018-0.0180.0000.0000.0000.000
104A100MET00.001-0.01815.863-0.011-0.0110.0000.0000.0000.000
105A101ASN0-0.032-0.01314.9120.0010.0010.0000.0000.0000.000
106A102ILE00.0180.02315.6550.0260.0260.0000.0000.0000.000
107A103VAL0-0.016-0.00318.272-0.035-0.0350.0000.0000.0000.000
108A104ARG10.8860.95221.234-0.195-0.1950.0000.0000.0000.000
109A105THR0-0.022-0.01423.867-0.016-0.0160.0000.0000.0000.000
110A106PRO00.027-0.00727.1870.0090.0090.0000.0000.0000.000
111A107SER00.012-0.01129.1390.0040.0040.0000.0000.0000.000
112A108VAL0-0.035-0.00523.1480.0010.0010.0000.0000.0000.000
113A109ALA0-0.0060.02924.5350.0040.0040.0000.0000.0000.000
114A110GLN0-0.046-0.04119.059-0.003-0.0030.0000.0000.0000.000
115A111ILE0-0.025-0.00416.702-0.026-0.0260.0000.0000.0000.000
116A112GLY00.0230.01615.0440.0510.0510.0000.0000.0000.000
117A113ILE0-0.028-0.02511.460-0.085-0.0850.0000.0000.0000.000
118A114SER0-0.040-0.05710.4920.1690.1690.0000.0000.0000.000
119A115VAL0-0.018-0.0126.830-0.092-0.0920.0000.0000.0000.000
120A116GLU-1-0.732-0.8199.7540.2990.2990.0000.0000.0000.000
121A117LEU00.0210.00712.596-0.014-0.0140.0000.0000.0000.000
122A118LEU0-0.001-0.01814.6110.0150.0150.0000.0000.0000.000
123A119ASP-1-0.882-0.93717.3400.0360.0360.0000.0000.0000.000
124A120SER0-0.002-0.00716.892-0.009-0.0090.0000.0000.0000.000
125A121MET0-0.060-0.00815.7800.0050.0050.0000.0000.0000.000
126A122ALA0-0.044-0.01819.0410.0000.0000.0000.0000.0000.000
127A123GLN0-0.046-0.02321.856-0.013-0.0130.0000.0000.0000.000
128A124GLN0-0.0290.00418.0060.0120.0120.0000.0000.0000.000
129A125THR0-0.039-0.03722.856-0.012-0.0120.0000.0000.0000.000
130A126PRO0-0.026-0.00922.9830.0040.0040.0000.0000.0000.000
131A127VAL0-0.0050.01325.024-0.013-0.0130.0000.0000.0000.000
132A128GLY00.0100.00527.7810.0000.0000.0000.0000.0000.000
133A129ASN0-0.072-0.05630.6030.0010.0010.0000.0000.0000.000
134A130ALA00.0600.05525.6390.0010.0010.0000.0000.0000.000
135A131ALA00.0510.02726.8680.0060.0060.0000.0000.0000.000
136A132VAL0-0.054-0.03927.781-0.008-0.0080.0000.0000.0000.000
137A133SER00.0250.00429.831-0.001-0.0010.0000.0000.0000.000
138A134SER0-0.0130.00232.535-0.001-0.0010.0000.0000.0000.000
139A135VAL00.0510.00635.184-0.001-0.0010.0000.0000.0000.000
140A136ASP-1-0.836-0.89436.7170.0620.0620.0000.0000.0000.000
141A137SER00.0060.00336.6310.0010.0010.0000.0000.0000.000
142A138PHE0-0.016-0.01438.557-0.002-0.0020.0000.0000.0000.000
143A139THR00.0160.00441.018-0.004-0.0040.0000.0000.0000.000
144A140GLN00.0090.00438.410-0.003-0.0030.0000.0000.0000.000
145A141PHE0-0.012-0.00542.482-0.002-0.0020.0000.0000.0000.000
146A142THR0-0.002-0.02244.393-0.003-0.0030.0000.0000.0000.000
147A143GLN00.0020.00244.2750.0000.0000.0000.0000.0000.000
148A144LYS10.9650.98642.649-0.061-0.0610.0000.0000.0000.000
149A145MET0-0.024-0.00547.353-0.002-0.0020.0000.0000.0000.000
150A146LEU0-0.0070.01350.184-0.002-0.0020.0000.0000.0000.000
151A147ASP-1-0.792-0.87949.9930.0400.0400.0000.0000.0000.000
152A148ASN0-0.066-0.01751.052-0.002-0.0020.0000.0000.0000.000
153A149PHE00.0380.02153.016-0.001-0.0010.0000.0000.0000.000
154A150TYR00.0390.02055.794-0.002-0.0020.0000.0000.0000.000
155A151ASN0-0.048-0.03554.658-0.002-0.0020.0000.0000.0000.000
156A152PHE00.0120.01256.931-0.001-0.0010.0000.0000.0000.000
157A153ALA00.0110.00958.623-0.001-0.0010.0000.0000.0000.000
158A154SER0-0.048-0.04460.474-0.001-0.0010.0000.0000.0000.000
159A155SER0-0.104-0.05560.680-0.001-0.0010.0000.0000.0000.000
160A156PHE00.0010.00561.806-0.001-0.0010.0000.0000.0000.000
161A157ALA0-0.048-0.01465.649-0.001-0.0010.0000.0000.0000.000
162A158VAL00.0010.00467.4990.0000.0000.0000.0000.0000.000
163A159SER0-0.027-0.03571.176-0.001-0.0010.0000.0000.0000.000
164A160GLN00.059-0.01174.3880.0000.0000.0000.0000.0000.000
165A161ALA0-0.034-0.00877.8070.0000.0000.0000.0000.0000.000
166A162GLN0-0.0040.01672.2030.0000.0000.0000.0000.0000.000
167A163MET0-0.0310.01173.7870.0000.0000.0000.0000.0000.000
168A164THR00.0310.02375.5590.0000.0000.0000.0000.0000.000
169A165PRO0-0.048-0.04077.5430.0000.0000.0000.0000.0000.000
170A166SER0-0.012-0.03575.5610.0000.0000.0000.0000.0000.000
171A167PRO0-0.037-0.02178.2880.0000.0000.0000.0000.0000.000
172A168SER0-0.006-0.00676.8220.0000.0000.0000.0000.0000.000
173A169GLU-1-0.891-0.88771.9710.0230.0230.0000.0000.0000.000
174A170MET0-0.034-0.02572.422-0.001-0.0010.0000.0000.0000.000
175A171PHE00.0390.02170.9450.0010.0010.0000.0000.0000.000
176A172ILE0-0.004-0.00566.622-0.001-0.0010.0000.0000.0000.000
177A173PRO00.0140.00769.3310.0000.0000.0000.0000.0000.000
178A174ALA00.0970.04166.5660.0000.0000.0000.0000.0000.000
179A175ASN00.0280.00665.7190.0010.0010.0000.0000.0000.000
180A176VAL0-0.0070.00166.1390.0000.0000.0000.0000.0000.000
181A177VAL00.0250.01462.0980.0000.0000.0000.0000.0000.000
182A178LEU00.0150.01960.5980.0010.0010.0000.0000.0000.000
183A179LYS10.8360.88861.226-0.024-0.0240.0000.0000.0000.000
184A180TRP0-0.0130.00056.7940.0000.0000.0000.0000.0000.000
185A181TYR0-0.033-0.04153.5500.0000.0000.0000.0000.0000.000
186A182GLU-1-0.776-0.87356.7550.0270.0270.0000.0000.0000.000
187A183ASN0-0.056-0.03456.8680.0000.0000.0000.0000.0000.000
188A184PHE00.0000.00952.4290.0000.0000.0000.0000.0000.000
189A185GLN0-0.009-0.00852.5210.0000.0000.0000.0000.0000.000
190A186ARG10.9000.94852.030-0.025-0.0250.0000.0000.0000.000
191A187ARG10.9310.96452.759-0.028-0.0280.0000.0000.0000.000
192A188LEU0-0.015-0.00548.2840.0000.0000.0000.0000.0000.000
193A189ALA0-0.011-0.00548.1050.0020.0020.0000.0000.0000.000
194A190GLN0-0.061-0.02548.1180.0000.0000.0000.0000.0000.000
195A191ASN00.015-0.00248.4080.0010.0010.0000.0000.0000.000
196A192PRO00.0470.01844.527-0.001-0.0010.0000.0000.0000.000
197A193LEU0-0.0030.00644.2370.0010.0010.0000.0000.0000.000
198A194PHE0-0.053-0.02248.549-0.002-0.0020.0000.0000.0000.000
199A195TRP0-0.027-0.00247.113-0.001-0.0010.0000.0000.0000.000