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: R9M58

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 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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2287097.401975
FMO2-HF: Nuclear repulsion 2206899.078351
FMO2-HF: Total energy -80198.323624
FMO2-MP2: Total energy -80430.783486


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.
-20.751-19.26212.76-6.299-7.9490.028
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 : 0.029 / q_NPA : 0.025
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].
3B4TYR0-0.038-0.0211.793-15.705-15.97012.027-5.673-6.0890.029
4B5PHE0-0.023-0.0146.229-0.568-0.5680.0000.0000.0000.000
5B6ILE0-0.040-0.0209.3910.4320.4320.0000.0000.0000.000
6B7GLU-1-0.873-0.95811.9280.3800.3800.0000.0000.0000.000
7B8LEU0-0.043-0.00314.548-0.042-0.0420.0000.0000.0000.000
8B9THR0-0.043-0.03016.059-0.060-0.0600.0000.0000.0000.000
9B10LYS10.8130.90017.4490.3070.3070.0000.0000.0000.000
10B40GLN0-0.005-0.0026.5400.1550.1550.0000.0000.0000.000
11B41ILE0-0.035-0.0292.382-1.474-0.6570.733-0.352-1.198-0.001
12B42ILE00.0120.0063.8380.8571.4750.001-0.200-0.4190.000
13B43CYS0-0.049-0.0295.2800.4050.4050.0000.0000.0000.000
14B44CYS00.0050.0128.013-0.137-0.1370.0000.0000.0000.000
15B45SER0-0.023-0.01911.1280.2080.2080.0000.0000.0000.000
16B46GLN00.0430.01914.271-0.001-0.0010.0000.0000.0000.000
17B47ASP-1-0.815-0.86216.559-0.247-0.2470.0000.0000.0000.000
18B48GLY00.0440.03015.625-0.016-0.0160.0000.0000.0000.000
19B49PHE0-0.008-0.00915.808-0.093-0.0930.0000.0000.0000.000
20B50GLU-1-0.683-0.80110.098-1.900-1.9000.0000.0000.0000.000
21B51ALA00.006-0.00410.8130.1510.1510.0000.0000.0000.000
22B52LYS10.8290.9187.4991.2641.2640.0000.0000.0000.000
23B53CYS0-0.0050.0137.7570.3980.3980.0000.0000.0000.000
24B65CYS0-0.021-0.0239.4710.0290.0290.0000.0000.0000.000
25B66LEU00.0050.00411.754-0.011-0.0110.0000.0000.0000.000
26B67VAL00.0320.00412.078-0.121-0.1210.0000.0000.0000.000
27B68ILE0-0.047-0.02111.0980.0930.0930.0000.0000.0000.000
28B69GLU-1-0.827-0.90612.340-1.270-1.2700.0000.0000.0000.000
29B70TRP00.000-0.00213.070-0.143-0.1430.0000.0000.0000.000
30B71THR0-0.005-0.03310.4640.1470.1470.0000.0000.0000.000
31B72ASN0-0.080-0.04413.8410.1410.1410.0000.0000.0000.000
32B73GLU-1-0.864-0.89211.784-1.460-1.4600.0000.0000.0000.000
33B74ASN0-0.055-0.04314.8710.0190.0190.0000.0000.0000.000
34B75ARG10.8150.89110.8321.6011.6010.0000.0000.0000.000
35B76GLU-1-0.756-0.84515.422-0.498-0.4980.0000.0000.0000.000
36B77LEU00.0280.02618.2650.0110.0110.0000.0000.0000.000
37B78PRO0-0.072-0.03421.4670.0280.0280.0000.0000.0000.000
38B79ILE0-0.011-0.00124.6240.0260.0260.0000.0000.0000.000
39B80LYS10.9230.96024.7750.1650.1650.0000.0000.0000.000
40B81VAL00.0310.01324.3120.0260.0260.0000.0000.0000.000
41B82TYR00.0210.01024.6100.0090.0090.0000.0000.0000.000
42B83ILE00.0100.00624.0110.0030.0030.0000.0000.0000.000
43B84ALA00.0450.02126.8550.0220.0220.0000.0000.0000.000
44B85SER0-0.035-0.02427.928-0.009-0.0090.0000.0000.0000.000
45B86GLY00.0490.02330.0960.0150.0150.0000.0000.0000.000
46B87LEU0-0.013-0.02429.616-0.001-0.0010.0000.0000.0000.000
47B88PRO0-0.0170.00427.847-0.003-0.0030.0000.0000.0000.000
48B89LYS10.8940.92630.202-0.033-0.0330.0000.0000.0000.000
49B90GLY00.0150.00328.135-0.007-0.0070.0000.0000.0000.000
50B91ASP-1-0.825-0.91622.3960.2080.2080.0000.0000.0000.000
51B92LYS10.7830.88423.090-0.021-0.0210.0000.0000.0000.000
52B93LEU00.0270.01124.041-0.021-0.0210.0000.0000.0000.000
53B94GLU-1-0.801-0.90219.5060.2760.2760.0000.0000.0000.000
54B95TRP0-0.014-0.00719.212-0.028-0.0280.0000.0000.0000.000
55B96ILE00.0100.01120.003-0.039-0.0390.0000.0000.0000.000
56B97ILE0-0.0090.00817.916-0.031-0.0310.0000.0000.0000.000
57B98GLN0-0.019-0.00412.484-0.107-0.1070.0000.0000.0000.000
58B99LYS10.8480.89015.0230.1800.1800.0000.0000.0000.000
59B100GLY00.0310.00618.284-0.048-0.0480.0000.0000.0000.000
60B101THR0-0.051-0.03014.189-0.020-0.0200.0000.0000.0000.000
61B102GLU-1-0.847-0.90314.113-0.430-0.4300.0000.0000.0000.000
62B103LEU0-0.061-0.02415.316-0.067-0.0670.0000.0000.0000.000
63B104GLY00.0610.02517.8040.0160.0160.0000.0000.0000.000
64B105ALA0-0.036-0.01919.0150.0240.0240.0000.0000.0000.000
65B106HIS0-0.051-0.03519.5900.0110.0110.0000.0000.0000.000
66B107ALA0-0.035-0.02721.4770.0300.0300.0000.0000.0000.000
67B108PHE0-0.0020.00719.308-0.011-0.0110.0000.0000.0000.000
68B109ILE00.008-0.00624.6160.0240.0240.0000.0000.0000.000
69B110PRO00.0150.01726.437-0.011-0.0110.0000.0000.0000.000
70B111PHE00.014-0.00329.0610.0060.0060.0000.0000.0000.000
71B112GLN0-0.013-0.01432.8600.0030.0030.0000.0000.0000.000
72B113ALA00.0270.01635.628-0.006-0.0060.0000.0000.0000.000
73B114ALA0-0.056-0.03237.3990.0070.0070.0000.0000.0000.000
74B115ARG10.8260.90838.6510.0050.0050.0000.0000.0000.000
75B116SER0-0.030-0.01234.074-0.002-0.0020.0000.0000.0000.000
76B117VAL0-0.035-0.00536.2270.0050.0050.0000.0000.0000.000
77B118VAL0-0.028-0.00731.2930.0120.0120.0000.0000.0000.000
78B129ARG10.7820.85822.380-0.227-0.2270.0000.0000.0000.000
79B130GLU-1-0.748-0.85820.2850.3480.3480.0000.0000.0000.000
80B131ARG10.7340.85418.229-0.235-0.2350.0000.0000.0000.000
81B132TRP00.017-0.00117.6880.0240.0240.0000.0000.0000.000
82B133THR0-0.001-0.01317.708-0.041-0.0410.0000.0000.0000.000
83B134LYS10.9490.97813.321-0.933-0.9330.0000.0000.0000.000
84B135ILE0-0.021-0.00713.4880.0850.0850.0000.0000.0000.000
85B136ALA00.0420.02713.976-0.063-0.0630.0000.0000.0000.000
86B137LYS10.8730.94410.282-1.100-1.1000.0000.0000.0000.000
87B138GLU-1-0.870-0.9328.6470.1990.1990.0000.0000.0000.000
88B139ALA00.0330.0159.364-0.238-0.2380.0000.0000.0000.000
89B140ALA00.0130.03011.065-0.262-0.2620.0000.0000.0000.000
90B141GLU-1-0.885-0.9426.0531.4111.4110.0000.0000.0000.000
91B142GLN0-0.015-0.0185.005-1.647-1.567-0.001-0.001-0.0780.000
92B143SER0-0.075-0.0617.556-0.339-0.3390.0000.0000.0000.000
93B144TYR0-0.058-0.0433.921-0.880-0.6410.000-0.073-0.1650.000
94B145ARG10.7930.8929.1080.5120.5120.0000.0000.0000.000
95B146ASN0-0.042-0.04211.362-0.217-0.2170.0000.0000.0000.000
96B147GLU-1-0.838-0.91013.985-0.098-0.0980.0000.0000.0000.000
97B148VAL00.0050.00612.868-0.021-0.0210.0000.0000.0000.000
98B149PRO0-0.0100.01915.3610.0470.0470.0000.0000.0000.000
99B150ARG10.9430.96718.6950.0620.0620.0000.0000.0000.000
100B151VAL00.004-0.00220.336-0.033-0.0330.0000.0000.0000.000
101B152MET0-0.018-0.00822.9240.0310.0310.0000.0000.0000.000
102B153ASP-1-0.828-0.90626.5120.1750.1750.0000.0000.0000.000
103B154VAL0-0.036-0.01028.936-0.018-0.0180.0000.0000.0000.000
104B155HIS0-0.0080.01230.843-0.010-0.0100.0000.0000.0000.000
105B156SER00.017-0.02733.953-0.004-0.0040.0000.0000.0000.000
106B157PHE00.0530.01137.170-0.003-0.0030.0000.0000.0000.000
107B158GLN00.0160.01638.885-0.008-0.0080.0000.0000.0000.000
108B159GLN00.0740.05236.148-0.003-0.0030.0000.0000.0000.000
109B160LEU0-0.0010.00633.582-0.004-0.0040.0000.0000.0000.000
110B161LEU00.0280.01036.317-0.007-0.0070.0000.0000.0000.000
111B162GLN0-0.059-0.02638.888-0.002-0.0020.0000.0000.0000.000
112B163ARG10.8410.91731.539-0.016-0.0160.0000.0000.0000.000
113B164MET0-0.055-0.01935.514-0.005-0.0050.0000.0000.0000.000
114B165GLN0-0.023-0.01437.093-0.009-0.0090.0000.0000.0000.000
115B166ASP-1-0.887-0.93333.282-0.020-0.0200.0000.0000.0000.000
116B167PHE0-0.057-0.04030.056-0.007-0.0070.0000.0000.0000.000
117B168ASP-1-0.826-0.90432.842-0.114-0.1140.0000.0000.0000.000
118B169LYS10.7750.88334.3200.0740.0740.0000.0000.0000.000
119B170CYS00.0050.02334.115-0.002-0.0020.0000.0000.0000.000
120B171VAL00.0020.00033.836-0.002-0.0020.0000.0000.0000.000
121B172VAL00.0130.00534.8420.0050.0050.0000.0000.0000.000
122B173ALA0-0.009-0.00533.178-0.004-0.0040.0000.0000.0000.000
123B174TYR0-0.122-0.09935.3260.0070.0070.0000.0000.0000.000
124B175GLU-1-0.847-0.93538.913-0.074-0.0740.0000.0000.0000.000
125B176GLU-1-0.842-0.89841.938-0.030-0.0300.0000.0000.0000.000
126B177SER0-0.038-0.01745.6190.0020.0020.0000.0000.0000.000
127B178SER0-0.006-0.01244.3940.0000.0000.0000.0000.0000.000
128B179LYS10.8390.93338.3980.0750.0750.0000.0000.0000.000
129B180GLN0-0.046-0.06340.922-0.009-0.0090.0000.0000.0000.000
130B181GLY0-0.005-0.00339.1080.0030.0030.0000.0000.0000.000
131B182GLU-1-0.917-0.94040.180-0.091-0.0910.0000.0000.0000.000
132B183ILE00.0190.01642.357-0.002-0.0020.0000.0000.0000.000
133B184SER0-0.032-0.02537.6550.0030.0030.0000.0000.0000.000
134B185ALA00.0500.01739.383-0.007-0.0070.0000.0000.0000.000
135B186PHE00.0140.00529.959-0.007-0.0070.0000.0000.0000.000
136B187SER00.006-0.00134.231-0.007-0.0070.0000.0000.0000.000
137B188ALA00.0440.02335.046-0.010-0.0100.0000.0000.0000.000
138B189ILE00.0170.01534.379-0.005-0.0050.0000.0000.0000.000
139B190VAL00.005-0.00329.662-0.006-0.0060.0000.0000.0000.000
140B191SER0-0.028-0.01631.656-0.017-0.0170.0000.0000.0000.000
141B192SER0-0.067-0.04333.631-0.006-0.0060.0000.0000.0000.000
142B193LEU0-0.0110.01331.3870.0050.0050.0000.0000.0000.000
143B194PRO00.0060.00731.716-0.018-0.0180.0000.0000.0000.000
144B195LYS10.9790.99325.6940.3300.3300.0000.0000.0000.000
145B196GLY0-0.021-0.00127.2650.0100.0100.0000.0000.0000.000
146B197SER0-0.048-0.02328.2840.0160.0160.0000.0000.0000.000
147B198SER0-0.028-0.03428.853-0.017-0.0170.0000.0000.0000.000
148B199LEU0-0.012-0.00429.2610.0060.0060.0000.0000.0000.000
149B200LEU0-0.0150.01729.308-0.003-0.0030.0000.0000.0000.000
150B201ILE0-0.016-0.01228.517-0.005-0.0050.0000.0000.0000.000
151B202VAL00.0120.01430.5930.0080.0080.0000.0000.0000.000
152B203PHE00.0330.00328.550-0.007-0.0070.0000.0000.0000.000
153B204GLY00.0470.02032.7860.0110.0110.0000.0000.0000.000
154B205PRO00.0240.04932.638-0.005-0.0050.0000.0000.0000.000
155B206GLU-1-0.846-0.92732.1960.0260.0260.0000.0000.0000.000
156B207GLY00.0220.01534.6850.0060.0060.0000.0000.0000.000
157B208GLY0-0.0170.00236.554-0.003-0.0030.0000.0000.0000.000
158B209LEU00.003-0.00436.1720.0080.0080.0000.0000.0000.000
159B210THR0-0.056-0.04239.144-0.001-0.0010.0000.0000.0000.000
160B211GLU-1-0.751-0.86542.820-0.011-0.0110.0000.0000.0000.000
161B212ALA00.0870.04145.578-0.002-0.0020.0000.0000.0000.000
162B213GLU-1-0.880-0.91639.6690.0110.0110.0000.0000.0000.000
163B214VAL00.0450.00340.545-0.002-0.0020.0000.0000.0000.000
164B215GLU-1-0.929-0.93942.618-0.018-0.0180.0000.0000.0000.000
165B216ARG10.9310.95043.985-0.005-0.0050.0000.0000.0000.000
166B217LEU0-0.054-0.03838.021-0.001-0.0010.0000.0000.0000.000
167B218THR0-0.023-0.01841.474-0.006-0.0060.0000.0000.0000.000
168B219GLU-1-0.949-0.98043.936-0.015-0.0150.0000.0000.0000.000
169B220GLN0-0.076-0.04341.046-0.002-0.0020.0000.0000.0000.000
170B221ASP-1-0.827-0.90641.087-0.066-0.0660.0000.0000.0000.000
171B222GLY0-0.0010.00738.933-0.008-0.0080.0000.0000.0000.000
172B223VAL0-0.023-0.02638.8140.0020.0020.0000.0000.0000.000
173B224THR00.0250.01638.568-0.003-0.0030.0000.0000.0000.000
174B225CYS0-0.058-0.01536.839-0.009-0.0090.0000.0000.0000.000
175B226GLY00.0230.03037.2230.0000.0000.0000.0000.0000.000
176B227LEU00.0180.01331.454-0.008-0.0080.0000.0000.0000.000
177B228GLY00.0110.00934.365-0.014-0.0140.0000.0000.0000.000
178B229PRO00.0540.03236.8470.0080.0080.0000.0000.0000.000
179B230ARG10.9610.98833.1300.1390.1390.0000.0000.0000.000
180B231ILE00.0190.01136.032-0.001-0.0010.0000.0000.0000.000
181B232LEU0-0.018-0.00330.233-0.003-0.0030.0000.0000.0000.000
182B233ARG10.9550.98229.4180.0490.0490.0000.0000.0000.000
183B234THR00.001-0.01229.416-0.009-0.0090.0000.0000.0000.000
184B235GLU-1-0.776-0.91025.320-0.019-0.0190.0000.0000.0000.000
185B236THR0-0.062-0.03825.311-0.011-0.0110.0000.0000.0000.000
186B237ALA00.0170.00927.298-0.020-0.0200.0000.0000.0000.000
187B238PRO00.0490.02125.268-0.015-0.0150.0000.0000.0000.000
188B239LEU00.0300.02721.598-0.019-0.0190.0000.0000.0000.000
189B240TYR0-0.044-0.02224.446-0.035-0.0350.0000.0000.0000.000
190B241ALA00.0040.00027.148-0.014-0.0140.0000.0000.0000.000
191B242LEU00.0020.01221.6110.0000.0000.0000.0000.0000.000
192B243SER00.004-0.00723.234-0.036-0.0360.0000.0000.0000.000
193B244ALA0-0.035-0.02024.215-0.016-0.0160.0000.0000.0000.000
194B245ILE00.0060.00325.1630.0000.0000.0000.0000.0000.000
195B246SER00.0010.01121.371-0.006-0.0060.0000.0000.0000.000
196B247TYR0-0.003-0.01623.7000.0020.0020.0000.0000.0000.000
197B248GLN00.0280.00626.045-0.002-0.0020.0000.0000.0000.000
198B249THR0-0.042-0.06025.711-0.007-0.0070.0000.0000.0000.000
199B250GLU-1-0.841-0.90720.670-0.486-0.4860.0000.0000.0000.000
200B251LEU0-0.057-0.02721.421-0.010-0.0100.0000.0000.0000.000
201B252LEU0-0.056-0.00925.2240.0110.0110.0000.0000.0000.000
202B253ARG10.8100.93425.3500.2610.2610.0000.0000.0000.000