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: YYLR2

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 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 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1664865.76474
FMO2-HF: Nuclear repulsion 1593647.787237
FMO2-HF: Total energy -71217.977503
FMO2-MP2: Total energy -71422.775323


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.
-1.731.180.1-1.51-1.4980.006
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 : 0.022 / q_NPA : 0.005
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-1GLY0-0.0210.0012.738-2.3220.4680.101-1.504-1.3860.006
4B0SER0-0.004-0.0174.4390.4290.549-0.001-0.006-0.1120.000
5B1MET0-0.0100.0087.490-0.125-0.1250.0000.0000.0000.000
6B2PHE0-0.012-0.01710.3680.0180.0180.0000.0000.0000.000
7B3GLY00.0290.01212.956-0.005-0.0050.0000.0000.0000.000
8B4CYS0-0.059-0.01515.6510.0140.0140.0000.0000.0000.000
9B5LEU00.0160.00018.3970.0060.0060.0000.0000.0000.000
10B6VAL00.0560.04421.3790.0020.0020.0000.0000.0000.000
11B7ALA0-0.014-0.01224.478-0.002-0.0020.0000.0000.0000.000
12B8GLY00.0150.00527.3040.0070.0070.0000.0000.0000.000
13B9ARG10.7780.88023.8610.0200.0200.0000.0000.0000.000
14B10LEU00.0110.00520.291-0.010-0.0100.0000.0000.0000.000
15B11VAL0-0.030-0.01816.3810.0070.0070.0000.0000.0000.000
16B12GLN0-0.0080.00116.017-0.002-0.0020.0000.0000.0000.000
17B13THR00.044-0.00611.4270.0060.0060.0000.0000.0000.000
18B14ALA0-0.0300.0069.906-0.042-0.0420.0000.0000.0000.000
19B15ALA0-0.0100.00910.8840.0450.0450.0000.0000.0000.000
20B16GLN0-0.032-0.02210.5620.0690.0690.0000.0000.0000.000
21B17GLN0-0.036-0.0148.2200.0490.0490.0000.0000.0000.000
22B18VAL0-0.025-0.01411.6090.0330.0330.0000.0000.0000.000
23B19ALA0-0.026-0.01913.6650.0030.0030.0000.0000.0000.000
24B20GLU-1-0.906-0.95910.1890.0720.0720.0000.0000.0000.000
25B21ASP-1-0.903-0.94611.458-0.053-0.0530.0000.0000.0000.000
26B22LYS10.8260.91713.749-0.030-0.0300.0000.0000.0000.000
27B23PHE00.007-0.0029.2530.0170.0170.0000.0000.0000.000
28B24VAL00.0000.00314.280-0.021-0.0210.0000.0000.0000.000
29B25PHE0-0.012-0.01013.9760.0160.0160.0000.0000.0000.000
30B26ASP-1-0.783-0.87217.3880.0740.0740.0000.0000.0000.000
31B27LEU0-0.046-0.03420.025-0.008-0.0080.0000.0000.0000.000
32B28PRO00.018-0.00221.9820.0020.0020.0000.0000.0000.000
33B29ASP-1-0.801-0.86625.199-0.007-0.0070.0000.0000.0000.000
34B30TYR00.0740.02428.531-0.006-0.0060.0000.0000.0000.000
35B31GLU-1-0.895-0.94829.3920.0060.0060.0000.0000.0000.000
36B32SER0-0.095-0.06530.400-0.006-0.0060.0000.0000.0000.000
37B33ILE0-0.038-0.00825.838-0.007-0.0070.0000.0000.0000.000
38B34ASN0-0.0040.01629.5920.0010.0010.0000.0000.0000.000
39B35HIS00.030-0.00528.8310.0010.0010.0000.0000.0000.000
40B36VAL00.0410.02022.7570.0010.0010.0000.0000.0000.000
41B37VAL0-0.046-0.02222.604-0.003-0.0030.0000.0000.0000.000
42B38VAL00.0300.02118.708-0.003-0.0030.0000.0000.0000.000
43B39PHE0-0.014-0.02517.4550.0030.0030.0000.0000.0000.000
44B40MET0-0.0170.01415.4210.0040.0040.0000.0000.0000.000
45B41LEU0-0.046-0.02210.7890.0220.0220.0000.0000.0000.000
46B42GLY0-0.0120.00014.432-0.005-0.0050.0000.0000.0000.000
47B43THR0-0.037-0.0149.6950.0540.0540.0000.0000.0000.000
48B44ILE00.0120.0006.919-0.119-0.1190.0000.0000.0000.000
49B45PRO0-0.0170.00311.5930.0930.0930.0000.0000.0000.000
50B46PHE00.016-0.01413.581-0.019-0.0190.0000.0000.0000.000
51B47PRO00.0360.01013.765-0.010-0.0100.0000.0000.0000.000
52B48GLU-1-0.908-0.96216.337-0.152-0.1520.0000.0000.0000.000
53B49GLY00.0240.01419.9460.0140.0140.0000.0000.0000.000
54B50MET0-0.0390.00517.8100.0240.0240.0000.0000.0000.000
55B51GLY0-0.017-0.02719.789-0.020-0.0200.0000.0000.0000.000
56B52GLY00.0120.00419.0090.0040.0040.0000.0000.0000.000
57B53SER0-0.027-0.02919.641-0.002-0.0020.0000.0000.0000.000
58B54VAL0-0.020-0.01320.6800.0030.0030.0000.0000.0000.000
59B55TYR0-0.017-0.02322.1920.0080.0080.0000.0000.0000.000
60B56PHE00.017-0.00123.148-0.002-0.0020.0000.0000.0000.000
61B57SER00.0000.00924.7330.0020.0020.0000.0000.0000.000
62B58TYR0-0.020-0.03226.7500.0000.0000.0000.0000.0000.000
63B59PRO00.0290.01429.3710.0010.0010.0000.0000.0000.000
64B60ASP-1-0.761-0.85831.9230.0050.0050.0000.0000.0000.000
65B61SER0-0.096-0.06035.1430.0030.0030.0000.0000.0000.000
66B62ASN0-0.048-0.04636.2980.0030.0030.0000.0000.0000.000
67B63GLY0-0.0240.02234.2880.0030.0030.0000.0000.0000.000
68B64MET0-0.054-0.05532.1830.0040.0040.0000.0000.0000.000
69B65PRO0-0.0100.01827.760-0.003-0.0030.0000.0000.0000.000
70B66VAL00.0050.00529.8860.0010.0010.0000.0000.0000.000
71B67TRP00.021-0.00921.833-0.006-0.0060.0000.0000.0000.000
72B68GLN00.0130.02028.1520.0020.0020.0000.0000.0000.000
73B69LEU00.0010.01225.767-0.002-0.0020.0000.0000.0000.000
74B70LEU0-0.011-0.01525.1720.0000.0000.0000.0000.0000.000
75B71GLY00.037-0.00326.196-0.001-0.0010.0000.0000.0000.000
76B72PHE00.0270.02723.720-0.002-0.0020.0000.0000.0000.000
77B73VAL0-0.043-0.00919.098-0.001-0.0010.0000.0000.0000.000
78B74THR00.0340.01020.777-0.004-0.0040.0000.0000.0000.000
79B75ASN00.0780.02218.041-0.026-0.0260.0000.0000.0000.000
80B76GLY0-0.0020.01120.646-0.006-0.0060.0000.0000.0000.000
81B77LYS10.8540.92923.6210.1330.1330.0000.0000.0000.000
82B78PRO00.0480.03219.6000.0120.0120.0000.0000.0000.000
83B79SER0-0.008-0.00820.120-0.007-0.0070.0000.0000.0000.000
84B80ALA0-0.012-0.00722.5040.0100.0100.0000.0000.0000.000
85B81ILE00.0050.00724.366-0.001-0.0010.0000.0000.0000.000
86B82PHE0-0.003-0.01023.7730.0030.0030.0000.0000.0000.000
87B83LYS10.8270.91428.4420.0370.0370.0000.0000.0000.000
88B84ILE00.0080.00727.0190.0010.0010.0000.0000.0000.000
89B85SER00.0170.02330.9080.0010.0010.0000.0000.0000.000
90B95HIS00.0310.01925.425-0.006-0.0060.0000.0000.0000.000
91B96PRO0-0.053-0.02021.4610.0070.0070.0000.0000.0000.000
92B97PHE00.0650.03617.8860.0070.0070.0000.0000.0000.000
93B107SER00.0060.00029.5690.0010.0010.0000.0000.0000.000
94B108VAL0-0.029-0.02523.550-0.004-0.0040.0000.0000.0000.000
95B109ALA00.0290.03225.6840.0010.0010.0000.0000.0000.000
96B110GLN0-0.044-0.03220.9120.0000.0000.0000.0000.0000.000
97B111ILE0-0.022-0.00319.185-0.009-0.0090.0000.0000.0000.000
98B112GLY00.0160.01818.8300.0090.0090.0000.0000.0000.000
99B113ILE0-0.060-0.03315.786-0.013-0.0130.0000.0000.0000.000
100B114SER0-0.023-0.03816.7020.0140.0140.0000.0000.0000.000
101B115VAL0-0.015-0.01114.131-0.017-0.0170.0000.0000.0000.000
102B116GLU-1-0.745-0.84417.499-0.038-0.0380.0000.0000.0000.000
103B117LEU00.0820.02620.873-0.017-0.0170.0000.0000.0000.000
104B118LEU0-0.006-0.01822.6880.0070.0070.0000.0000.0000.000
105B119ASP-1-0.917-0.95625.005-0.084-0.0840.0000.0000.0000.000
106B120SER0-0.052-0.03725.7530.0100.0100.0000.0000.0000.000
107B121MET0-0.0280.00422.7770.0010.0010.0000.0000.0000.000
108B122ALA0-0.050-0.01327.0190.0030.0030.0000.0000.0000.000
109B123GLN0-0.045-0.01830.2960.0070.0070.0000.0000.0000.000
110B124GLN0-0.045-0.01325.6410.0000.0000.0000.0000.0000.000
111B125THR0-0.030-0.02631.086-0.002-0.0020.0000.0000.0000.000
112B126PRO0-0.0370.00229.1180.0040.0040.0000.0000.0000.000
113B127VAL00.0210.01031.0700.0000.0000.0000.0000.0000.000
114B128GLY00.0370.03330.0730.0020.0020.0000.0000.0000.000
115B129ASN00.022-0.00831.155-0.002-0.0020.0000.0000.0000.000
116B130ALA00.0460.04331.0420.0020.0020.0000.0000.0000.000
117B131ALA0-0.084-0.04431.9790.0010.0010.0000.0000.0000.000
118B132VAL0-0.030-0.02435.1860.0040.0040.0000.0000.0000.000
119B133SER00.015-0.00433.154-0.003-0.0030.0000.0000.0000.000
120B134SER00.0250.01033.086-0.002-0.0020.0000.0000.0000.000
121B135VAL0-0.015-0.00935.4990.0010.0010.0000.0000.0000.000
122B136ASP-1-0.843-0.93237.041-0.026-0.0260.0000.0000.0000.000
123B137SER0-0.016-0.01639.1830.0020.0020.0000.0000.0000.000
124B138PHE0-0.0140.00238.2750.0010.0010.0000.0000.0000.000
125B139THR00.018-0.00342.7010.0010.0010.0000.0000.0000.000
126B140GLN00.0280.01240.7580.0010.0010.0000.0000.0000.000
127B141PHE00.0040.01144.9700.0020.0020.0000.0000.0000.000
128B142THR00.004-0.00246.8960.0010.0010.0000.0000.0000.000
129B143GLN0-0.019-0.02447.0600.0020.0020.0000.0000.0000.000
130B144LYS10.8640.91848.5520.0130.0130.0000.0000.0000.000
131B145MET0-0.0110.01150.9720.0010.0010.0000.0000.0000.000
132B146LEU0-0.023-0.02352.6780.0010.0010.0000.0000.0000.000
133B147ASP-1-0.863-0.90353.748-0.010-0.0100.0000.0000.0000.000
134B148ASN0-0.031-0.01055.0730.0010.0010.0000.0000.0000.000
135B149PHE00.009-0.00156.8550.0010.0010.0000.0000.0000.000
136B150TYR0-0.004-0.00958.6060.0000.0000.0000.0000.0000.000
137B151ASN0-0.015-0.00459.3070.0010.0010.0000.0000.0000.000
138B152PHE0-0.028-0.00361.1070.0010.0010.0000.0000.0000.000
139B153ALA00.005-0.01662.9090.0000.0000.0000.0000.0000.000
140B154SER00.005-0.00263.9210.0000.0000.0000.0000.0000.000
141B155SER0-0.048-0.02365.7350.0000.0000.0000.0000.0000.000
142B156PHE0-0.041-0.01867.3960.0000.0000.0000.0000.0000.000
143B157ALA0-0.0350.00667.6560.0000.0000.0000.0000.0000.000
144B158VAL00.0100.00969.7370.0010.0010.0000.0000.0000.000
145B159SER0-0.036-0.04172.315-0.001-0.0010.0000.0000.0000.000
146B160GLN00.037-0.02574.0760.0000.0000.0000.0000.0000.000
147B161ALA0-0.021-0.00776.6550.0000.0000.0000.0000.0000.000
148B162GLN00.0060.02374.7870.0000.0000.0000.0000.0000.000
149B163MET0-0.0320.02073.8380.0000.0000.0000.0000.0000.000
150B164THR00.0240.02378.7050.0000.0000.0000.0000.0000.000
151B165PRO0-0.040-0.04480.9620.0000.0000.0000.0000.0000.000
152B166SER00.0140.00879.5950.0000.0000.0000.0000.0000.000
153B167PRO0-0.027-0.02479.8520.0000.0000.0000.0000.0000.000
154B168SER0-0.0020.00879.4330.0000.0000.0000.0000.0000.000
155B169GLU-1-0.945-0.95175.225-0.010-0.0100.0000.0000.0000.000
156B170MET0-0.010-0.00371.2750.0000.0000.0000.0000.0000.000
157B171PHE00.0520.02070.8430.0000.0000.0000.0000.0000.000
158B172ILE0-0.006-0.00864.266-0.001-0.0010.0000.0000.0000.000
159B173PRO0-0.013-0.00665.5630.0000.0000.0000.0000.0000.000
160B174ALA00.1300.05364.343-0.001-0.0010.0000.0000.0000.000
161B175ASN00.0120.00161.912-0.001-0.0010.0000.0000.0000.000
162B176VAL0-0.005-0.01160.582-0.001-0.0010.0000.0000.0000.000
163B177VAL00.0240.02257.071-0.001-0.0010.0000.0000.0000.000
164B178LEU00.0160.01256.298-0.001-0.0010.0000.0000.0000.000
165B179LYS10.9670.98955.5830.0170.0170.0000.0000.0000.000
166B180TRP00.0010.00950.598-0.001-0.0010.0000.0000.0000.000
167B181TYR00.0380.02748.544-0.001-0.0010.0000.0000.0000.000
168B182GLU-1-0.876-0.94850.874-0.023-0.0230.0000.0000.0000.000
169B183ASN0-0.077-0.05050.895-0.003-0.0030.0000.0000.0000.000
170B184PHE00.0200.01245.416-0.002-0.0020.0000.0000.0000.000
171B185GLN00.0290.00746.540-0.001-0.0010.0000.0000.0000.000
172B186ARG10.9120.95945.6770.0310.0310.0000.0000.0000.000
173B187ARG10.8930.93645.3010.0410.0410.0000.0000.0000.000
174B188LEU0-0.006-0.00541.824-0.003-0.0030.0000.0000.0000.000
175B189ALA0-0.0060.00241.476-0.002-0.0020.0000.0000.0000.000
176B190GLN0-0.056-0.00540.773-0.002-0.0020.0000.0000.0000.000
177B191ASN00.0270.00639.661-0.005-0.0050.0000.0000.0000.000
178B192PRO00.0950.05236.7310.0030.0030.0000.0000.0000.000
179B193LEU0-0.054-0.03336.0910.0020.0020.0000.0000.0000.000
180B194PHE0-0.047-0.02640.3970.0000.0000.0000.0000.0000.000
181B195TRP0-0.017-0.00140.3590.0000.0000.0000.0000.0000.000
182B196LYS10.9360.98837.8730.0500.0500.0000.0000.0000.000