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

tag_button

FMODB ID: Z6LYN

Calculation Name: 1VHK-B-Xray372

Preferred Name:
Warning: Undefined array key "pref_name" in /home/FMODBwui_src/fmodbwui/detail.php on line 446

Target Type:
Warning: Undefined array key "target_type" in /home/FMODBwui_src/fmodbwui/detail.php on line 447

Ligand Name:
Warning: Undefined variable $Ligand in /home/FMODBwui_src/fmodbwui/detail.php on line 448

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 448

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 448

ligand 3-letter code:
Warning: Undefined variable $Ligand in /home/FMODBwui_src/fmodbwui/detail.php on line 449

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 449

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 449

PDB ID: 1VHK

Chain ID: B

ChEMBL ID:
Warning: Undefined array key "chembl_id" in /home/FMODBwui_src/fmodbwui/detail.php on line 452

Warning: Undefined array key "chembl_id" in /home/FMODBwui_src/fmodbwui/detail.php on line 452

UniProt ID: P54461

Base Structure: X-ray

Registration Date: 2023-06-22

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 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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2278060.014474
FMO2-HF: Nuclear repulsion 2197862.595151
FMO2-HF: Total energy -80197.419322
FMO2-MP2: Total energy -80429.859604


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:2:GLN)


Summations of interaction energy for fragment #1(B:2:GLN)
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.
-20.489-16.85911.343-6.327-8.6470.026
Interaction energy analysis for fragmet #1(B:2:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : 0.016
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].
3B4TYR0-0.049-0.0291.847-15.839-14.10010.456-5.672-6.5240.027
4B5PHE0-0.039-0.0136.083-0.518-0.5180.0000.0000.0000.000
5B6ILE0-0.065-0.0329.3930.3730.3730.0000.0000.0000.000
6B7GLU-1-0.867-0.95411.8840.1920.1920.0000.0000.0000.000
7B8LEU0-0.081-0.02814.957-0.043-0.0430.0000.0000.0000.000
8B9THR0-0.022-0.02216.049-0.055-0.0550.0000.0000.0000.000
9B10LYS10.8320.91217.7200.3190.3190.0000.0000.0000.000
10B40GLN0-0.0100.0036.0110.2300.2300.0000.0000.0000.000
11B41ILE0-0.032-0.0342.325-1.415-0.4910.886-0.438-1.372-0.001
12B42ILE0-0.002-0.0053.6060.2600.9790.004-0.189-0.5340.000
13B43CYS0-0.028-0.0035.3550.2500.262-0.001-0.009-0.0010.000
14B44CYS00.0060.0098.103-0.127-0.1270.0000.0000.0000.000
15B45SER0-0.026-0.01710.9980.2010.2010.0000.0000.0000.000
16B46GLN00.0820.04714.1700.0030.0030.0000.0000.0000.000
17B47ASP-1-0.841-0.88716.484-0.285-0.2850.0000.0000.0000.000
18B48GLY00.0250.02215.431-0.010-0.0100.0000.0000.0000.000
19B49PHE0-0.016-0.01315.483-0.072-0.0720.0000.0000.0000.000
20B50GLU-1-0.690-0.8139.428-2.019-2.0190.0000.0000.0000.000
21B51ALA00.005-0.01010.1440.1350.1350.0000.0000.0000.000
22B52LYS10.8670.9487.0641.2871.2870.0000.0000.0000.000
23B53CYS0-0.0260.0077.5620.4420.4420.0000.0000.0000.000
24B65CYS0-0.029-0.0319.5640.0070.0070.0000.0000.0000.000
25B66LEU00.0140.00711.6490.0310.0310.0000.0000.0000.000
26B67VAL00.0360.01011.800-0.139-0.1390.0000.0000.0000.000
27B68ILE0-0.041-0.01710.6660.0950.0950.0000.0000.0000.000
28B69GLU-1-0.869-0.94711.792-1.208-1.2080.0000.0000.0000.000
29B70TRP0-0.0110.00012.302-0.184-0.1840.0000.0000.0000.000
30B71THR00.032-0.0119.9560.1650.1650.0000.0000.0000.000
31B72ASN0-0.079-0.03913.3260.1290.1290.0000.0000.0000.000
32B73GLU-1-0.894-0.91611.264-1.461-1.4610.0000.0000.0000.000
33B74ASN0-0.027-0.02314.241-0.011-0.0110.0000.0000.0000.000
34B75ARG10.8230.89910.4071.6271.6270.0000.0000.0000.000
35B76GLU-1-0.770-0.84015.541-0.486-0.4860.0000.0000.0000.000
36B77LEU00.0280.03018.1590.0070.0070.0000.0000.0000.000
37B78PRO0-0.077-0.03421.3990.0280.0280.0000.0000.0000.000
38B79ILE0-0.037-0.01924.4140.0250.0250.0000.0000.0000.000
39B80LYS10.9280.96624.6880.1760.1760.0000.0000.0000.000
40B81VAL00.0270.01624.5130.0220.0220.0000.0000.0000.000
41B82TYR0-0.003-0.01224.7160.0060.0060.0000.0000.0000.000
42B83ILE00.0210.00424.2730.0020.0020.0000.0000.0000.000
43B84ALA00.0550.03627.0100.0210.0210.0000.0000.0000.000
44B85SER0-0.034-0.02028.093-0.008-0.0080.0000.0000.0000.000
45B86GLY00.0250.00630.2880.0130.0130.0000.0000.0000.000
46B87LEU0-0.015-0.01929.5010.0010.0010.0000.0000.0000.000
47B88PRO0-0.0050.01627.905-0.003-0.0030.0000.0000.0000.000
48B89LYS10.9000.93130.466-0.038-0.0380.0000.0000.0000.000
49B90GLY0-0.014-0.00528.550-0.003-0.0030.0000.0000.0000.000
50B91ASP-1-0.864-0.93423.0290.2090.2090.0000.0000.0000.000
51B92LYS10.7820.87823.488-0.030-0.0300.0000.0000.0000.000
52B93LEU00.0250.00624.199-0.019-0.0190.0000.0000.0000.000
53B94GLU-1-0.823-0.90219.8410.2970.2970.0000.0000.0000.000
54B95TRP0-0.003-0.00719.549-0.027-0.0270.0000.0000.0000.000
55B96ILE0-0.0020.00220.109-0.032-0.0320.0000.0000.0000.000
56B97ILE0-0.0150.00618.056-0.036-0.0360.0000.0000.0000.000
57B98GLN00.0250.03612.882-0.107-0.1070.0000.0000.0000.000
58B99LYS10.8490.89315.5230.0930.0930.0000.0000.0000.000
59B100GLY00.0330.01418.352-0.054-0.0540.0000.0000.0000.000
60B101THR0-0.066-0.03414.307-0.019-0.0190.0000.0000.0000.000
61B102GLU-1-0.855-0.90214.107-0.430-0.4300.0000.0000.0000.000
62B103LEU0-0.047-0.02615.470-0.064-0.0640.0000.0000.0000.000
63B104GLY00.0700.03217.8720.0140.0140.0000.0000.0000.000
64B105ALA0-0.057-0.02419.2710.0230.0230.0000.0000.0000.000
65B106HIS0-0.061-0.04319.7760.0090.0090.0000.0000.0000.000
66B107ALA0-0.010-0.01121.7190.0270.0270.0000.0000.0000.000
67B108PHE0-0.0130.00319.520-0.006-0.0060.0000.0000.0000.000
68B109ILE0-0.019-0.02824.7670.0210.0210.0000.0000.0000.000
69B110PRO00.0180.02426.782-0.010-0.0100.0000.0000.0000.000
70B111PHE00.010-0.00229.4110.0050.0050.0000.0000.0000.000
71B112GLN0-0.014-0.01833.1940.0060.0060.0000.0000.0000.000
72B113ALA00.0150.00935.903-0.007-0.0070.0000.0000.0000.000
73B114ALA0-0.0040.00537.5060.0070.0070.0000.0000.0000.000
74B115ARG10.8210.90038.8090.0020.0020.0000.0000.0000.000
75B116SER0-0.046-0.02834.322-0.001-0.0010.0000.0000.0000.000
76B117VAL0-0.031-0.01635.9430.0020.0020.0000.0000.0000.000
77B118VAL0-0.0240.00031.6780.0120.0120.0000.0000.0000.000
78B129ARG10.7810.88222.454-0.209-0.2090.0000.0000.0000.000
79B130GLU-1-0.761-0.89621.0770.3320.3320.0000.0000.0000.000
80B131ARG10.8030.89118.560-0.280-0.2800.0000.0000.0000.000
81B132TRP00.036-0.00518.2060.0340.0340.0000.0000.0000.000
82B133THR00.0680.04917.626-0.050-0.0500.0000.0000.0000.000
83B134LYS10.9430.97813.803-0.843-0.8430.0000.0000.0000.000
84B135ILE0-0.038-0.01813.8890.0880.0880.0000.0000.0000.000
85B136ALA00.0320.02214.286-0.041-0.0410.0000.0000.0000.000
86B137LYS10.9340.98110.178-1.179-1.1790.0000.0000.0000.000
87B138GLU-1-0.909-0.9588.6290.4230.4230.0000.0000.0000.000
88B139ALA00.0290.0139.503-0.183-0.1830.0000.0000.0000.000
89B140ALA0-0.0130.00011.269-0.231-0.2310.0000.0000.0000.000
90B141GLU-1-0.894-0.9646.3441.4061.4060.0000.0000.0000.000
91B142GLN00.000-0.0094.777-1.187-1.098-0.001-0.002-0.0860.000
92B143SER0-0.043-0.0357.579-0.346-0.3460.0000.0000.0000.000
93B144TYR0-0.088-0.0513.839-0.259-0.112-0.001-0.017-0.1300.000
94B145ARG10.8200.9059.2920.5060.5060.0000.0000.0000.000
95B146ASN0-0.065-0.05811.309-0.235-0.2350.0000.0000.0000.000
96B147GLU-1-0.841-0.92013.705-0.130-0.1300.0000.0000.0000.000
97B148VAL0-0.0160.00113.078-0.007-0.0070.0000.0000.0000.000
98B149PRO00.0290.03915.5200.0310.0310.0000.0000.0000.000
99B150ARG10.9810.98818.7440.0630.0630.0000.0000.0000.000
100B151VAL0-0.018-0.02120.802-0.030-0.0300.0000.0000.0000.000
101B152MET0-0.026-0.01823.4430.0280.0280.0000.0000.0000.000
102B153ASP-1-0.829-0.91126.9810.1580.1580.0000.0000.0000.000
103B154VAL0-0.0260.00429.375-0.015-0.0150.0000.0000.0000.000
104B155HIS0-0.027-0.00831.143-0.009-0.0090.0000.0000.0000.000
105B156SER00.015-0.01634.301-0.002-0.0020.0000.0000.0000.000
106B157PHE00.0580.00937.340-0.003-0.0030.0000.0000.0000.000
107B158GLN00.0280.00739.141-0.008-0.0080.0000.0000.0000.000
108B159GLN00.0640.05536.446-0.002-0.0020.0000.0000.0000.000
109B160LEU00.0050.00933.585-0.005-0.0050.0000.0000.0000.000
110B161LEU00.0320.00436.512-0.006-0.0060.0000.0000.0000.000
111B162GLN0-0.054-0.02639.271-0.003-0.0030.0000.0000.0000.000
112B163ARG10.8650.93631.743-0.008-0.0080.0000.0000.0000.000
113B164MET0-0.045-0.02035.596-0.004-0.0040.0000.0000.0000.000
114B165GLN0-0.029-0.01137.107-0.009-0.0090.0000.0000.0000.000
115B166ASP-1-0.911-0.95633.997-0.031-0.0310.0000.0000.0000.000
116B167PHE0-0.076-0.04030.056-0.008-0.0080.0000.0000.0000.000
117B168ASP-1-0.782-0.87833.092-0.114-0.1140.0000.0000.0000.000
118B169LYS10.8370.92434.2990.0760.0760.0000.0000.0000.000
119B170CYS00.0110.02334.168-0.001-0.0010.0000.0000.0000.000
120B171VAL0-0.006-0.00133.8130.0000.0000.0000.0000.0000.000
121B172VAL00.0160.00234.9360.0050.0050.0000.0000.0000.000
122B173ALA0-0.037-0.01833.624-0.004-0.0040.0000.0000.0000.000
123B174TYR0-0.093-0.08235.7830.0090.0090.0000.0000.0000.000
124B175GLU-1-0.895-0.96039.224-0.069-0.0690.0000.0000.0000.000
125B176GLU-1-0.813-0.88042.058-0.026-0.0260.0000.0000.0000.000
126B177SER0-0.037-0.01845.6530.0020.0020.0000.0000.0000.000
127B178SER0-0.025-0.02944.6360.0000.0000.0000.0000.0000.000
128B179LYS10.8690.96238.1730.0680.0680.0000.0000.0000.000
129B180GLN0-0.027-0.05041.085-0.008-0.0080.0000.0000.0000.000
130B181GLY0-0.010-0.00639.7380.0020.0020.0000.0000.0000.000
131B182GLU-1-0.908-0.94240.740-0.082-0.0820.0000.0000.0000.000
132B183ILE00.0160.01742.975-0.003-0.0030.0000.0000.0000.000
133B184SER0-0.0230.00638.1250.0030.0030.0000.0000.0000.000
134B185ALA00.0520.02239.897-0.007-0.0070.0000.0000.0000.000
135B186PHE00.011-0.01030.411-0.007-0.0070.0000.0000.0000.000
136B187SER00.008-0.00834.391-0.006-0.0060.0000.0000.0000.000
137B188ALA00.0250.01935.451-0.008-0.0080.0000.0000.0000.000
138B189ILE00.0340.01734.704-0.005-0.0050.0000.0000.0000.000
139B190VAL00.0070.00329.970-0.006-0.0060.0000.0000.0000.000
140B191SER0-0.053-0.02832.095-0.015-0.0150.0000.0000.0000.000
141B192SER0-0.063-0.04033.923-0.006-0.0060.0000.0000.0000.000
142B193LEU0-0.0300.01231.4760.0070.0070.0000.0000.0000.000
143B194PRO00.0090.00931.979-0.017-0.0170.0000.0000.0000.000
144B195LYS10.9680.98125.6010.3220.3220.0000.0000.0000.000
145B196GLY0-0.0120.00327.4040.0090.0090.0000.0000.0000.000
146B197SER0-0.044-0.02128.4110.0130.0130.0000.0000.0000.000
147B198SER0-0.042-0.02728.914-0.014-0.0140.0000.0000.0000.000
148B199LEU0-0.034-0.02129.2080.0070.0070.0000.0000.0000.000
149B200LEU0-0.0100.01929.290-0.003-0.0030.0000.0000.0000.000
150B201ILE00.000-0.00228.783-0.003-0.0030.0000.0000.0000.000
151B202VAL00.0110.00330.9710.0080.0080.0000.0000.0000.000
152B203PHE00.0340.00228.968-0.007-0.0070.0000.0000.0000.000
153B204GLY00.0380.02233.0660.0110.0110.0000.0000.0000.000
154B205PRO00.0280.03332.830-0.004-0.0040.0000.0000.0000.000
155B206GLU-1-0.816-0.91932.1210.0350.0350.0000.0000.0000.000
156B207GLY0-0.030-0.01834.9590.0040.0040.0000.0000.0000.000
157B208GLY0-0.014-0.00637.068-0.004-0.0040.0000.0000.0000.000
158B209LEU00.0050.01236.5520.0070.0070.0000.0000.0000.000
159B210THR0-0.051-0.02739.3920.0000.0000.0000.0000.0000.000
160B211GLU-1-0.782-0.89843.061-0.009-0.0090.0000.0000.0000.000
161B212ALA00.0470.01745.880-0.001-0.0010.0000.0000.0000.000
162B213GLU-1-0.863-0.93240.1220.0080.0080.0000.0000.0000.000
163B214VAL00.0280.00041.170-0.003-0.0030.0000.0000.0000.000
164B215GLU-1-0.923-0.93743.123-0.018-0.0180.0000.0000.0000.000
165B216ARG10.9780.98644.098-0.005-0.0050.0000.0000.0000.000
166B217LEU0-0.063-0.03438.289-0.001-0.0010.0000.0000.0000.000
167B218THR0-0.045-0.03641.866-0.006-0.0060.0000.0000.0000.000
168B219GLU-1-0.951-0.97644.170-0.016-0.0160.0000.0000.0000.000
169B220GLN0-0.071-0.03641.510-0.001-0.0010.0000.0000.0000.000
170B221ASP-1-0.863-0.93241.596-0.062-0.0620.0000.0000.0000.000
171B222GLY0-0.046-0.01939.148-0.008-0.0080.0000.0000.0000.000
172B223VAL0-0.012-0.02038.9960.0020.0020.0000.0000.0000.000
173B224THR00.0340.03138.838-0.002-0.0020.0000.0000.0000.000
174B225CYS0-0.079-0.02836.863-0.008-0.0080.0000.0000.0000.000
175B226GLY00.0710.04537.3060.0020.0020.0000.0000.0000.000
176B227LEU0-0.021-0.02131.549-0.008-0.0080.0000.0000.0000.000
177B228GLY00.0130.01934.507-0.005-0.0050.0000.0000.0000.000
178B229PRO00.0550.01636.7510.0070.0070.0000.0000.0000.000
179B230ARG10.9340.96533.5000.1200.1200.0000.0000.0000.000
180B231ILE0-0.011-0.01136.025-0.002-0.0020.0000.0000.0000.000
181B232LEU00.0140.01830.2190.0000.0000.0000.0000.0000.000
182B233ARG10.9410.97529.6140.0320.0320.0000.0000.0000.000
183B234THR0-0.005-0.00429.649-0.007-0.0070.0000.0000.0000.000
184B235GLU-1-0.741-0.88625.366-0.003-0.0030.0000.0000.0000.000
185B236THR0-0.044-0.03025.648-0.010-0.0100.0000.0000.0000.000
186B237ALA00.0000.00927.253-0.018-0.0180.0000.0000.0000.000
187B238PRO00.0700.02225.434-0.016-0.0160.0000.0000.0000.000
188B239LEU00.0220.01621.789-0.020-0.0200.0000.0000.0000.000
189B240TYR0-0.0220.00424.709-0.030-0.0300.0000.0000.0000.000
190B241ALA00.0070.00927.623-0.015-0.0150.0000.0000.0000.000
191B242LEU00.0260.01321.821-0.003-0.0030.0000.0000.0000.000
192B243SER00.010-0.00423.480-0.039-0.0390.0000.0000.0000.000
193B244ALA0-0.049-0.02424.494-0.015-0.0150.0000.0000.0000.000
194B245ILE0-0.020-0.01125.268-0.006-0.0060.0000.0000.0000.000
195B246SER00.010-0.01321.367-0.002-0.0020.0000.0000.0000.000
196B247TYR00.0190.00923.824-0.001-0.0010.0000.0000.0000.000
197B248GLN00.003-0.01726.115-0.007-0.0070.0000.0000.0000.000
198B249THR0-0.061-0.06125.753-0.006-0.0060.0000.0000.0000.000
199B250GLU-1-0.812-0.88720.676-0.476-0.4760.0000.0000.0000.000
200B251LEU0-0.069-0.02221.669-0.016-0.0160.0000.0000.0000.000
201B252LEU0-0.073-0.01625.2540.0120.0120.0000.0000.0000.000
202B253ARG10.8930.97325.6140.2500.2500.0000.0000.0000.000