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

tag_button

FMODB ID: VR7Y1

Calculation Name: 3WVZ-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WVZ

Chain ID: B

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 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1665633.895865
FMO2-HF: Nuclear repulsion 1594415.739996
FMO2-HF: Total energy -71218.155869
FMO2-MP2: Total energy -71422.966932


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(B:-3:ALA)


Summations of interaction energy for fragment #1(B:-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.
-1.1751.6850.114-1.528-1.4460.003
Interaction energy analysis for fragmet #1(B:-3:ALA)
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 : 0.011
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].
3B-1GLY0-0.0070.0102.861-1.9130.8430.115-1.522-1.3490.003
4B0SER0-0.010-0.0264.5530.3000.404-0.001-0.006-0.0970.000
5B1MET00.0100.0327.710-0.122-0.1220.0000.0000.0000.000
6B2PHE0-0.012-0.01510.0620.0260.0260.0000.0000.0000.000
7B3GLY00.0250.00312.661-0.022-0.0220.0000.0000.0000.000
8B4CYS0-0.056-0.00715.4720.0200.0200.0000.0000.0000.000
9B5LEU00.0170.00618.502-0.003-0.0030.0000.0000.0000.000
10B6VAL00.0410.03021.4610.0040.0040.0000.0000.0000.000
11B7ALA0-0.026-0.01924.684-0.006-0.0060.0000.0000.0000.000
12B8GLY00.0140.00727.5640.0080.0080.0000.0000.0000.000
13B9ARG10.7800.87423.9700.0370.0370.0000.0000.0000.000
14B10LEU00.0170.00620.276-0.011-0.0110.0000.0000.0000.000
15B11VAL0-0.026-0.01516.1960.0100.0100.0000.0000.0000.000
16B12GLN00.0020.00015.844-0.009-0.0090.0000.0000.0000.000
17B13THR00.046-0.00811.2110.0050.0050.0000.0000.0000.000
18B14ALA0-0.0200.0139.872-0.039-0.0390.0000.0000.0000.000
19B15ALA0-0.0050.01010.9270.0490.0490.0000.0000.0000.000
20B16GLN0-0.043-0.02610.3920.0690.0690.0000.0000.0000.000
21B17GLN0-0.038-0.0138.3400.0630.0630.0000.0000.0000.000
22B18VAL0-0.051-0.03311.1870.0370.0370.0000.0000.0000.000
23B19ALA0-0.018-0.01013.7750.0050.0050.0000.0000.0000.000
24B20GLU-1-0.895-0.9509.8870.2640.2640.0000.0000.0000.000
25B21ASP-1-0.884-0.94211.4260.0120.0120.0000.0000.0000.000
26B22LYS10.7960.90713.480-0.088-0.0880.0000.0000.0000.000
27B23PHE00.0470.0148.4570.0240.0240.0000.0000.0000.000
28B24VAL0-0.015-0.00513.530-0.026-0.0260.0000.0000.0000.000
29B25PHE0-0.006-0.00213.8010.0100.0100.0000.0000.0000.000
30B26ASP-1-0.788-0.87117.1700.0690.0690.0000.0000.0000.000
31B27LEU0-0.046-0.02819.919-0.013-0.0130.0000.0000.0000.000
32B28PRO00.0420.01421.9600.0030.0030.0000.0000.0000.000
33B29ASP-1-0.802-0.85725.210-0.023-0.0230.0000.0000.0000.000
34B30TYR00.0490.01928.511-0.007-0.0070.0000.0000.0000.000
35B31GLU-1-0.842-0.92029.3270.0000.0000.0000.0000.0000.000
36B32SER0-0.066-0.04630.459-0.005-0.0050.0000.0000.0000.000
37B33ILE0-0.016-0.00825.814-0.008-0.0080.0000.0000.0000.000
38B34ASN0-0.0170.00029.4600.0020.0020.0000.0000.0000.000
39B35HIS0-0.014-0.02528.9270.0020.0020.0000.0000.0000.000
40B36VAL00.0130.00822.8850.0000.0000.0000.0000.0000.000
41B37VAL0-0.031-0.00322.3010.0000.0000.0000.0000.0000.000
42B38VAL00.0160.00318.595-0.002-0.0020.0000.0000.0000.000
43B39PHE0-0.020-0.02417.1100.0060.0060.0000.0000.0000.000
44B40MET0-0.0010.02814.9000.0110.0110.0000.0000.0000.000
45B41LEU0-0.064-0.03310.6270.0270.0270.0000.0000.0000.000
46B42GLY0-0.019-0.00814.200-0.028-0.0280.0000.0000.0000.000
47B43THR0-0.037-0.0249.5560.0560.0560.0000.0000.0000.000
48B44ILE00.0140.0066.578-0.111-0.1110.0000.0000.0000.000
49B45PRO0-0.0100.00211.2080.0970.0970.0000.0000.0000.000
50B46PHE00.028-0.01013.414-0.015-0.0150.0000.0000.0000.000
51B47PRO00.0240.00314.082-0.010-0.0100.0000.0000.0000.000
52B48GLU-1-0.907-0.95216.546-0.126-0.1260.0000.0000.0000.000
53B49GLY00.0310.01720.2380.0160.0160.0000.0000.0000.000
54B50MET0-0.056-0.00417.7720.0210.0210.0000.0000.0000.000
55B51GLY0-0.008-0.01919.445-0.022-0.0220.0000.0000.0000.000
56B52GLY00.0180.00118.3080.0070.0070.0000.0000.0000.000
57B53SER0-0.028-0.02418.988-0.008-0.0080.0000.0000.0000.000
58B54VAL0-0.026-0.01319.9740.0030.0030.0000.0000.0000.000
59B55TYR0-0.031-0.04121.5340.0070.0070.0000.0000.0000.000
60B56PHE00.005-0.00822.522-0.005-0.0050.0000.0000.0000.000
61B57SER0-0.0100.00524.2110.0020.0020.0000.0000.0000.000
62B58TYR0-0.009-0.03026.307-0.003-0.0030.0000.0000.0000.000
63B59PRO00.0120.01128.9370.0010.0010.0000.0000.0000.000
64B60ASP-1-0.781-0.86731.5360.0060.0060.0000.0000.0000.000
65B61SER0-0.088-0.05034.7150.0030.0030.0000.0000.0000.000
66B62ASN0-0.052-0.04736.1120.0040.0040.0000.0000.0000.000
67B63GLY0-0.0250.01634.2470.0040.0040.0000.0000.0000.000
68B64MET0-0.045-0.04131.8940.0040.0040.0000.0000.0000.000
69B65PRO0-0.016-0.00227.254-0.004-0.0040.0000.0000.0000.000
70B66VAL00.0240.02829.2590.0020.0020.0000.0000.0000.000
71B67TRP00.019-0.01521.489-0.005-0.0050.0000.0000.0000.000
72B68GLN00.0060.01127.5400.0020.0020.0000.0000.0000.000
73B69LEU00.0050.02025.176-0.002-0.0020.0000.0000.0000.000
74B70LEU0-0.010-0.01225.039-0.001-0.0010.0000.0000.0000.000
75B71GLY00.020-0.01225.559-0.002-0.0020.0000.0000.0000.000
76B72PHE00.0360.03023.163-0.001-0.0010.0000.0000.0000.000
77B73VAL0-0.039-0.00518.551-0.004-0.0040.0000.0000.0000.000
78B74THR00.0450.01420.1650.0000.0000.0000.0000.0000.000
79B75ASN00.0630.01617.758-0.030-0.0300.0000.0000.0000.000
80B76GLY00.0020.01620.253-0.009-0.0090.0000.0000.0000.000
81B77LYS10.8140.89622.7930.1440.1440.0000.0000.0000.000
82B78PRO00.0680.03919.1940.0120.0120.0000.0000.0000.000
83B79SER00.0020.00119.544-0.011-0.0110.0000.0000.0000.000
84B80ALA0-0.008-0.00422.0470.0130.0130.0000.0000.0000.000
85B81ILE00.0060.00024.123-0.004-0.0040.0000.0000.0000.000
86B82PHE00.0030.00223.5960.0040.0040.0000.0000.0000.000
87B83LYS10.8380.93428.4870.0390.0390.0000.0000.0000.000
88B84ILE00.0160.01027.0840.0010.0010.0000.0000.0000.000
89B85SER00.0110.02330.9280.0020.0020.0000.0000.0000.000
90B95HIS00.0320.02024.834-0.007-0.0070.0000.0000.0000.000
91B96PRO0-0.054-0.02421.0570.0090.0090.0000.0000.0000.000
92B97PHE00.0490.03117.3040.0100.0100.0000.0000.0000.000
93B107SER0-0.001-0.01130.1260.0020.0020.0000.0000.0000.000
94B108VAL0-0.053-0.03923.999-0.003-0.0030.0000.0000.0000.000
95B109ALA00.0280.02825.7710.0030.0030.0000.0000.0000.000
96B110GLN0-0.042-0.03420.6770.0010.0010.0000.0000.0000.000
97B111ILE0-0.015-0.00318.754-0.008-0.0080.0000.0000.0000.000
98B112GLY00.0160.01718.1960.0120.0120.0000.0000.0000.000
99B113ILE0-0.053-0.03015.260-0.014-0.0140.0000.0000.0000.000
100B114SER0-0.009-0.03116.0270.0200.0200.0000.0000.0000.000
101B115VAL0-0.023-0.01713.677-0.021-0.0210.0000.0000.0000.000
102B116GLU-1-0.716-0.81317.095-0.014-0.0140.0000.0000.0000.000
103B117LEU00.0700.01720.725-0.018-0.0180.0000.0000.0000.000
104B118LEU0-0.002-0.00922.5330.0060.0060.0000.0000.0000.000
105B119ASP-1-0.894-0.94624.959-0.067-0.0670.0000.0000.0000.000
106B120SER0-0.037-0.02525.7790.0100.0100.0000.0000.0000.000
107B121MET0-0.031-0.00622.3180.0010.0010.0000.0000.0000.000
108B122ALA0-0.049-0.02126.7520.0020.0020.0000.0000.0000.000
109B123GLN0-0.066-0.02730.0360.0050.0050.0000.0000.0000.000
110B124GLN0-0.057-0.02925.1730.0000.0000.0000.0000.0000.000
111B125THR0-0.041-0.03330.622-0.002-0.0020.0000.0000.0000.000
112B126PRO0-0.0250.00828.3110.0040.0040.0000.0000.0000.000
113B127VAL00.0150.00330.2700.0000.0000.0000.0000.0000.000
114B128GLY00.0260.02829.6270.0010.0010.0000.0000.0000.000
115B129ASN00.017-0.00930.692-0.004-0.0040.0000.0000.0000.000
116B130ALA00.0430.02830.9850.0020.0020.0000.0000.0000.000
117B131ALA0-0.069-0.03531.9150.0000.0000.0000.0000.0000.000
118B132VAL0-0.022-0.01634.9160.0030.0030.0000.0000.0000.000
119B133SER00.000-0.02332.804-0.004-0.0040.0000.0000.0000.000
120B134SER00.009-0.01632.8650.0000.0000.0000.0000.0000.000
121B135VAL0-0.012-0.00335.0290.0000.0000.0000.0000.0000.000
122B136ASP-1-0.831-0.89536.545-0.021-0.0210.0000.0000.0000.000
123B137SER0-0.018-0.02038.8690.0010.0010.0000.0000.0000.000
124B138PHE0-0.011-0.00237.8470.0010.0010.0000.0000.0000.000
125B139THR00.0140.00541.9140.0010.0010.0000.0000.0000.000
126B140GLN00.0260.01339.9760.0000.0000.0000.0000.0000.000
127B141PHE00.0130.01444.6800.0020.0020.0000.0000.0000.000
128B142THR00.0150.00146.6340.0010.0010.0000.0000.0000.000
129B143GLN0-0.026-0.02646.4650.0020.0020.0000.0000.0000.000
130B144LYS10.8720.90948.3250.0110.0110.0000.0000.0000.000
131B145MET0-0.0060.01650.6160.0010.0010.0000.0000.0000.000
132B146LEU0-0.034-0.02252.1590.0010.0010.0000.0000.0000.000
133B147ASP-1-0.856-0.89753.213-0.008-0.0080.0000.0000.0000.000
134B148ASN0-0.031-0.01054.5660.0000.0000.0000.0000.0000.000
135B149PHE00.0120.00556.4000.0010.0010.0000.0000.0000.000
136B150TYR00.008-0.00658.0960.0000.0000.0000.0000.0000.000
137B151ASN0-0.015-0.00858.7370.0010.0010.0000.0000.0000.000
138B152PHE0-0.0150.00560.5640.0010.0010.0000.0000.0000.000
139B153ALA00.016-0.01162.4770.0000.0000.0000.0000.0000.000
140B154SER0-0.043-0.02363.3530.0000.0000.0000.0000.0000.000
141B155SER0-0.027-0.01365.2560.0010.0010.0000.0000.0000.000
142B156PHE0-0.042-0.01866.8350.0000.0000.0000.0000.0000.000
143B157ALA0-0.0360.00167.1160.0000.0000.0000.0000.0000.000
144B158VAL0-0.0060.00169.1870.0010.0010.0000.0000.0000.000
145B159SER0-0.021-0.03471.977-0.001-0.0010.0000.0000.0000.000
146B160GLN00.040-0.02073.5170.0000.0000.0000.0000.0000.000
147B161ALA0-0.030-0.00476.2520.0000.0000.0000.0000.0000.000
148B162GLN00.0030.01974.1530.0000.0000.0000.0000.0000.000
149B163MET0-0.0430.01172.9240.0000.0000.0000.0000.0000.000
150B164THR00.0380.02677.8720.0000.0000.0000.0000.0000.000
151B165PRO0-0.039-0.04380.3810.0000.0000.0000.0000.0000.000
152B166SER00.007-0.00578.9850.0000.0000.0000.0000.0000.000
153B167PRO0-0.033-0.03579.3250.0000.0000.0000.0000.0000.000
154B168SER0-0.0100.00378.6330.0000.0000.0000.0000.0000.000
155B169GLU-1-0.913-0.91374.749-0.010-0.0100.0000.0000.0000.000
156B170MET0-0.019-0.01570.7940.0000.0000.0000.0000.0000.000
157B171PHE00.0520.02770.6590.0000.0000.0000.0000.0000.000
158B172ILE00.008-0.00564.102-0.001-0.0010.0000.0000.0000.000
159B173PRO0-0.018-0.01265.3820.0010.0010.0000.0000.0000.000
160B174ALA00.1070.04663.577-0.001-0.0010.0000.0000.0000.000
161B175ASN00.0300.01161.244-0.001-0.0010.0000.0000.0000.000
162B176VAL0-0.020-0.02159.972-0.001-0.0010.0000.0000.0000.000
163B177VAL00.0290.02356.487-0.001-0.0010.0000.0000.0000.000
164B178LEU00.0040.01455.631-0.001-0.0010.0000.0000.0000.000
165B179LYS10.9710.98954.8510.0160.0160.0000.0000.0000.000
166B180TRP00.0060.00950.180-0.002-0.0020.0000.0000.0000.000
167B181TYR00.0340.02447.802-0.002-0.0020.0000.0000.0000.000
168B182GLU-1-0.874-0.95050.199-0.020-0.0200.0000.0000.0000.000
169B183ASN0-0.041-0.03350.198-0.003-0.0030.0000.0000.0000.000
170B184PHE00.0220.02344.995-0.002-0.0020.0000.0000.0000.000
171B185GLN00.0160.00245.674-0.001-0.0010.0000.0000.0000.000
172B186ARG10.8840.94045.1960.0290.0290.0000.0000.0000.000
173B187ARG10.8790.93745.4700.0400.0400.0000.0000.0000.000
174B188LEU00.003-0.00841.173-0.003-0.0030.0000.0000.0000.000
175B189ALA00.0010.00340.965-0.003-0.0030.0000.0000.0000.000
176B190GLN0-0.0360.00340.591-0.002-0.0020.0000.0000.0000.000
177B191ASN00.0210.00439.124-0.004-0.0040.0000.0000.0000.000
178B192PRO00.0780.04136.0240.0030.0030.0000.0000.0000.000
179B193LEU0-0.039-0.02235.7330.0020.0020.0000.0000.0000.000
180B194PHE0-0.050-0.02739.996-0.001-0.0010.0000.0000.0000.000
181B195TRP0-0.0140.00639.9040.0000.0000.0000.0000.0000.000
182B196LYS10.9280.98037.8240.0530.0530.0000.0000.0000.000