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: 53MGZ

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 OptH
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 -1664807.971104
FMO2-HF: Nuclear repulsion 1593590.454114
FMO2-HF: Total energy -71217.51699
FMO2-MP2: Total energy -71422.299435


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.
-1.8061.0650.247-1.527-1.5910.006
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 : 0.028 / q_NPA : 0.010
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-1GLY0-0.0220.0042.542-2.3870.3600.248-1.522-1.4740.006
4B0SER0-0.007-0.0084.2650.4400.564-0.001-0.005-0.1170.000
5B1MET00.0110.0197.348-0.122-0.1220.0000.0000.0000.000
6B2PHE0-0.009-0.01710.1960.0210.0210.0000.0000.0000.000
7B3GLY00.0240.00812.832-0.007-0.0070.0000.0000.0000.000
8B4CYS0-0.056-0.01415.5270.0160.0160.0000.0000.0000.000
9B5LEU00.0140.00118.2960.0060.0060.0000.0000.0000.000
10B6VAL00.0550.04121.2850.0020.0020.0000.0000.0000.000
11B7ALA0-0.011-0.01224.400-0.002-0.0020.0000.0000.0000.000
12B8GLY00.0090.00327.2170.0080.0080.0000.0000.0000.000
13B9ARG10.8010.90423.7090.0220.0220.0000.0000.0000.000
14B10LEU00.0150.00320.158-0.011-0.0110.0000.0000.0000.000
15B11VAL0-0.035-0.01816.2470.0070.0070.0000.0000.0000.000
16B12GLN00.0010.01016.0230.0000.0000.0000.0000.0000.000
17B13THR00.043-0.00411.3370.0060.0060.0000.0000.0000.000
18B14ALA0-0.034-0.0089.875-0.043-0.0430.0000.0000.0000.000
19B15ALA0-0.0070.00710.8320.0460.0460.0000.0000.0000.000
20B16GLN0-0.0040.00510.5520.0720.0720.0000.0000.0000.000
21B17GLN0-0.025-0.0118.4740.0490.0490.0000.0000.0000.000
22B18VAL0-0.027-0.01211.6150.0350.0350.0000.0000.0000.000
23B19ALA0-0.030-0.02613.6400.0030.0030.0000.0000.0000.000
24B20GLU-1-0.909-0.95610.2000.0310.0310.0000.0000.0000.000
25B21ASP-1-0.895-0.94211.400-0.067-0.0670.0000.0000.0000.000
26B22LYS10.8130.90513.694-0.029-0.0290.0000.0000.0000.000
27B23PHE00.0120.0009.2250.0220.0220.0000.0000.0000.000
28B24VAL00.0000.00514.244-0.020-0.0200.0000.0000.0000.000
29B25PHE0-0.019-0.01513.6350.0170.0170.0000.0000.0000.000
30B26ASP-1-0.812-0.89517.3490.0710.0710.0000.0000.0000.000
31B27LEU0-0.063-0.05420.017-0.009-0.0090.0000.0000.0000.000
32B28PRO00.011-0.00222.0020.0030.0030.0000.0000.0000.000
33B29ASP-1-0.788-0.87025.199-0.007-0.0070.0000.0000.0000.000
34B30TYR00.0460.00728.501-0.006-0.0060.0000.0000.0000.000
35B31GLU-1-0.905-0.95829.3660.0050.0050.0000.0000.0000.000
36B32SER0-0.085-0.05230.289-0.006-0.0060.0000.0000.0000.000
37B33ILE0-0.044-0.01025.866-0.007-0.0070.0000.0000.0000.000
38B34ASN00.0050.00429.5330.0030.0030.0000.0000.0000.000
39B35HIS00.030-0.00728.7810.0000.0000.0000.0000.0000.000
40B36VAL00.0390.02222.7920.0010.0010.0000.0000.0000.000
41B37VAL0-0.042-0.01722.360-0.003-0.0030.0000.0000.0000.000
42B38VAL00.0300.02118.544-0.003-0.0030.0000.0000.0000.000
43B39PHE0-0.016-0.02616.9230.0040.0040.0000.0000.0000.000
44B40MET0-0.0170.01415.2470.0040.0040.0000.0000.0000.000
45B41LEU0-0.044-0.02210.5630.0240.0240.0000.0000.0000.000
46B42GLY0-0.0100.00214.256-0.005-0.0050.0000.0000.0000.000
47B43THR0-0.036-0.0169.3550.0570.0570.0000.0000.0000.000
48B44ILE00.0140.0046.780-0.118-0.1180.0000.0000.0000.000
49B45PRO0-0.022-0.00211.3830.0950.0950.0000.0000.0000.000
50B46PHE00.008-0.01413.441-0.019-0.0190.0000.0000.0000.000
51B47PRO00.0380.01113.667-0.011-0.0110.0000.0000.0000.000
52B48GLU-1-0.895-0.95716.204-0.151-0.1510.0000.0000.0000.000
53B49GLY00.0110.00819.8130.0140.0140.0000.0000.0000.000
54B50MET0-0.0310.00417.7090.0240.0240.0000.0000.0000.000
55B51GLY0-0.019-0.02719.669-0.020-0.0200.0000.0000.0000.000
56B52GLY00.0170.00818.9060.0040.0040.0000.0000.0000.000
57B53SER0-0.017-0.01519.538-0.002-0.0020.0000.0000.0000.000
58B54VAL0-0.016-0.01020.5200.0030.0030.0000.0000.0000.000
59B55TYR00.015-0.00722.1130.0050.0050.0000.0000.0000.000
60B56PHE00.020-0.00423.063-0.002-0.0020.0000.0000.0000.000
61B57SER00.0070.01024.8460.0010.0010.0000.0000.0000.000
62B58TYR0-0.009-0.01426.7090.0000.0000.0000.0000.0000.000
63B59PRO00.0390.02229.2510.0010.0010.0000.0000.0000.000
64B60ASP-1-0.765-0.85731.9080.0040.0040.0000.0000.0000.000
65B61SER0-0.101-0.06335.2370.0040.0040.0000.0000.0000.000
66B62ASN0-0.047-0.04836.4120.0030.0030.0000.0000.0000.000
67B63GLY0-0.0160.02134.2310.0030.0030.0000.0000.0000.000
68B64MET0-0.060-0.05432.1940.0040.0040.0000.0000.0000.000
69B65PRO00.0040.02427.777-0.004-0.0040.0000.0000.0000.000
70B66VAL00.0030.00929.8730.0010.0010.0000.0000.0000.000
71B67TRP00.010-0.01321.882-0.007-0.0070.0000.0000.0000.000
72B68GLN0-0.006-0.00928.0890.0020.0020.0000.0000.0000.000
73B69LEU0-0.0100.00925.800-0.002-0.0020.0000.0000.0000.000
74B70LEU0-0.016-0.01724.9440.0000.0000.0000.0000.0000.000
75B71GLY00.035-0.00226.074-0.001-0.0010.0000.0000.0000.000
76B72PHE00.0110.02223.609-0.001-0.0010.0000.0000.0000.000
77B73VAL0-0.027-0.00118.894-0.001-0.0010.0000.0000.0000.000
78B74THR00.0320.01020.661-0.003-0.0030.0000.0000.0000.000
79B75ASN00.0870.02317.970-0.023-0.0230.0000.0000.0000.000
80B76GLY0-0.0070.00820.509-0.006-0.0060.0000.0000.0000.000
81B77LYS10.8630.93623.4180.1340.1340.0000.0000.0000.000
82B78PRO00.0490.03319.4660.0120.0120.0000.0000.0000.000
83B79SER0-0.022-0.01519.941-0.008-0.0080.0000.0000.0000.000
84B80ALA0-0.004-0.00122.3320.0110.0110.0000.0000.0000.000
85B81ILE00.0010.00524.222-0.001-0.0010.0000.0000.0000.000
86B82PHE0-0.009-0.01123.8450.0040.0040.0000.0000.0000.000
87B83LYS10.8310.91928.3190.0390.0390.0000.0000.0000.000
88B84ILE00.0110.00827.1290.0010.0010.0000.0000.0000.000
89B85SER0-0.0070.01730.8200.0010.0010.0000.0000.0000.000
90B95HIS00.0330.02025.589-0.005-0.0050.0000.0000.0000.000
91B96PRO0-0.034-0.00721.4230.0080.0080.0000.0000.0000.000
92B97PHE00.0780.04017.9610.0070.0070.0000.0000.0000.000
93B107SER00.0200.00129.3590.0030.0030.0000.0000.0000.000
94B108VAL0-0.033-0.02023.570-0.004-0.0040.0000.0000.0000.000
95B109ALA00.0180.02725.6590.0010.0010.0000.0000.0000.000
96B110GLN0-0.048-0.03320.6310.0020.0020.0000.0000.0000.000
97B111ILE0-0.023-0.00319.185-0.009-0.0090.0000.0000.0000.000
98B112GLY00.0110.01418.7610.0090.0090.0000.0000.0000.000
99B113ILE0-0.048-0.02715.549-0.012-0.0120.0000.0000.0000.000
100B114SER0-0.009-0.00816.6400.0130.0130.0000.0000.0000.000
101B115VAL0-0.021-0.01214.067-0.017-0.0170.0000.0000.0000.000
102B116GLU-1-0.856-0.92017.407-0.042-0.0420.0000.0000.0000.000
103B117LEU00.0700.01620.777-0.018-0.0180.0000.0000.0000.000
104B118LEU0-0.010-0.02122.5560.0070.0070.0000.0000.0000.000
105B119ASP-1-0.905-0.94924.888-0.084-0.0840.0000.0000.0000.000
106B120SER0-0.072-0.04425.6760.0100.0100.0000.0000.0000.000
107B121MET0-0.0090.00723.0390.0010.0010.0000.0000.0000.000
108B122ALA0-0.051-0.01426.9160.0030.0030.0000.0000.0000.000
109B123GLN0-0.022-0.00730.1990.0050.0050.0000.0000.0000.000
110B124GLN0-0.0230.00026.2820.0000.0000.0000.0000.0000.000
111B125THR0-0.030-0.02630.997-0.002-0.0020.0000.0000.0000.000
112B126PRO0-0.0370.00129.0800.0040.0040.0000.0000.0000.000
113B127VAL00.0380.01630.9860.0000.0000.0000.0000.0000.000
114B128GLY00.0290.02929.9480.0020.0020.0000.0000.0000.000
115B129ASN00.018-0.00331.031-0.003-0.0030.0000.0000.0000.000
116B130ALA00.0450.03930.9110.0020.0020.0000.0000.0000.000
117B131ALA0-0.081-0.04231.8430.0010.0010.0000.0000.0000.000
118B132VAL0-0.033-0.02435.0640.0040.0040.0000.0000.0000.000
119B133SER00.013-0.00433.051-0.003-0.0030.0000.0000.0000.000
120B134SER00.0470.01632.980-0.002-0.0020.0000.0000.0000.000
121B135VAL0-0.0020.00035.3700.0010.0010.0000.0000.0000.000
122B136ASP-1-0.866-0.93537.301-0.027-0.0270.0000.0000.0000.000
123B137SER0-0.023-0.01539.0750.0020.0020.0000.0000.0000.000
124B138PHE0-0.0150.00038.4700.0010.0010.0000.0000.0000.000
125B139THR00.0200.00342.5780.0010.0010.0000.0000.0000.000
126B140GLN00.020-0.00241.0410.0010.0010.0000.0000.0000.000
127B141PHE0-0.0020.00744.8620.0020.0020.0000.0000.0000.000
128B142THR00.0070.00446.7880.0010.0010.0000.0000.0000.000
129B143GLN0-0.029-0.03546.8780.0020.0020.0000.0000.0000.000
130B144LYS10.9660.98847.5480.0140.0140.0000.0000.0000.000
131B145MET0-0.0140.01050.8650.0010.0010.0000.0000.0000.000
132B146LEU0-0.029-0.02752.5280.0010.0010.0000.0000.0000.000
133B147ASP-1-0.930-0.95153.804-0.010-0.0100.0000.0000.0000.000
134B148ASN0-0.039-0.01354.9650.0010.0010.0000.0000.0000.000
135B149PHE00.008-0.00156.7570.0010.0010.0000.0000.0000.000
136B150TYR0-0.002-0.00958.5000.0000.0000.0000.0000.0000.000
137B151ASN0-0.0010.00259.1720.0010.0010.0000.0000.0000.000
138B152PHE0-0.042-0.01061.0110.0010.0010.0000.0000.0000.000
139B153ALA00.001-0.01962.8050.0000.0000.0000.0000.0000.000
140B154SER0-0.037-0.01163.9200.0000.0000.0000.0000.0000.000
141B155SER0-0.001-0.00665.6310.0000.0000.0000.0000.0000.000
142B156PHE0-0.045-0.02067.5510.0000.0000.0000.0000.0000.000
143B157ALA0-0.0360.00367.5620.0000.0000.0000.0000.0000.000
144B158VAL00.0250.01969.6230.0010.0010.0000.0000.0000.000
145B159SER0-0.027-0.02072.196-0.001-0.0010.0000.0000.0000.000
146B160GLN00.048-0.01973.9980.0000.0000.0000.0000.0000.000
147B161ALA0-0.031-0.01376.5640.0000.0000.0000.0000.0000.000
148B162GLN0-0.020-0.00774.5100.0000.0000.0000.0000.0000.000
149B163MET0-0.0330.02073.9240.0000.0000.0000.0000.0000.000
150B164THR0-0.0010.00778.5830.0000.0000.0000.0000.0000.000
151B165PRO0-0.012-0.02680.8370.0000.0000.0000.0000.0000.000
152B166SER00.0590.02779.6830.0000.0000.0000.0000.0000.000
153B167PRO0-0.038-0.02979.7200.0000.0000.0000.0000.0000.000
154B168SER0-0.035-0.00679.2970.0000.0000.0000.0000.0000.000
155B169GLU-1-0.934-0.95174.983-0.011-0.0110.0000.0000.0000.000
156B170MET0-0.023-0.00871.4740.0000.0000.0000.0000.0000.000
157B171PHE00.0610.02770.7190.0000.0000.0000.0000.0000.000
158B172ILE0-0.019-0.01564.122-0.001-0.0010.0000.0000.0000.000
159B173PRO0-0.016-0.00565.3940.0010.0010.0000.0000.0000.000
160B174ALA00.1310.05264.217-0.001-0.0010.0000.0000.0000.000
161B175ASN0-0.021-0.01561.835-0.001-0.0010.0000.0000.0000.000
162B176VAL00.001-0.01060.486-0.001-0.0010.0000.0000.0000.000
163B177VAL00.0250.02356.769-0.001-0.0010.0000.0000.0000.000
164B178LEU00.0160.00856.166-0.001-0.0010.0000.0000.0000.000
165B179LYS11.0151.01255.4940.0190.0190.0000.0000.0000.000
166B180TRP00.0000.02650.553-0.001-0.0010.0000.0000.0000.000
167B181TYR00.0510.03048.351-0.002-0.0020.0000.0000.0000.000
168B182GLU-1-0.895-0.95050.762-0.024-0.0240.0000.0000.0000.000
169B183ASN0-0.102-0.08750.797-0.003-0.0030.0000.0000.0000.000
170B184PHE00.0080.00445.025-0.002-0.0020.0000.0000.0000.000
171B185GLN00.0310.00846.433-0.002-0.0020.0000.0000.0000.000
172B186ARG10.9460.98945.5790.0320.0320.0000.0000.0000.000
173B187ARG10.8940.94944.2990.0420.0420.0000.0000.0000.000
174B188LEU0-0.006-0.00741.588-0.003-0.0030.0000.0000.0000.000
175B189ALA00.0030.00541.375-0.003-0.0030.0000.0000.0000.000
176B190GLN0-0.075-0.02440.666-0.002-0.0020.0000.0000.0000.000
177B191ASN00.0250.00339.288-0.005-0.0050.0000.0000.0000.000
178B192PRO00.0940.05636.5170.0030.0030.0000.0000.0000.000
179B193LEU0-0.046-0.03435.9440.0020.0020.0000.0000.0000.000
180B194PHE0-0.058-0.03440.2430.0000.0000.0000.0000.0000.000
181B195TRP0-0.0140.00640.4260.0000.0000.0000.0000.0000.000
182B196LYS10.9380.98637.8950.0530.0530.0000.0000.0000.000