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: VRGR1

Calculation Name: 3P5J-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3P5J

Chain ID: B

ChEMBL ID:

UniProt ID: Q9CWY8

Base Structure: X-ray

Registration Date: 2023-06-19

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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1811901.409185
FMO2-HF: Nuclear repulsion 1741042.956118
FMO2-HF: Total energy -70858.453067
FMO2-MP2: Total energy -71068.480248


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:11:ALA)


Summations of interaction energy for fragment #1(B:11: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.
1.4583.508-0.007-0.975-1.070.004
Interaction energy analysis for fragmet #1(B:11:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.059 / q_NPA : 0.031
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].
3B13ARG10.9480.9683.8820.6032.413-0.005-0.962-0.8440.004
4B14GLN0-0.010-0.0074.3520.5040.663-0.001-0.008-0.1510.000
5B15LEU0-0.049-0.0317.618-0.007-0.0070.0000.0000.0000.000
6B16VAL00.0500.03211.3340.0690.0690.0000.0000.0000.000
7B17PHE00.009-0.00613.709-0.002-0.0020.0000.0000.0000.000
8B18LEU00.0160.03117.0580.0270.0270.0000.0000.0000.000
9B19LEU0-0.002-0.01619.500-0.008-0.0080.0000.0000.0000.000
10B20PRO0-0.011-0.00122.3880.0130.0130.0000.0000.0000.000
11B21GLU-1-0.836-0.91825.578-0.062-0.0620.0000.0000.0000.000
12B22HIS00.0260.01226.8360.0050.0050.0000.0000.0000.000
13B23LEU0-0.069-0.03523.8250.0030.0030.0000.0000.0000.000
14B24LYS10.8860.95223.0040.0500.0500.0000.0000.0000.000
15B25ASP-1-0.822-0.88524.620-0.050-0.0500.0000.0000.0000.000
16B26ALA00.006-0.01728.019-0.006-0.0060.0000.0000.0000.000
17B27SER0-0.068-0.05129.3910.0000.0000.0000.0000.0000.000
18B28LYS10.8250.90627.3260.0910.0910.0000.0000.0000.000
19B29LYS10.8760.94733.2380.0550.0550.0000.0000.0000.000
20B30LYS11.0331.01932.8020.0510.0510.0000.0000.0000.000
21B31LYS10.8890.93730.5220.0690.0690.0000.0000.0000.000
22B32LYS10.9750.99425.6700.0610.0610.0000.0000.0000.000
23B33SER00.0230.02124.282-0.003-0.0030.0000.0000.0000.000
24B34SER0-0.012-0.02124.9780.0000.0000.0000.0000.0000.000
25B35LEU00.0240.02320.5530.0040.0040.0000.0000.0000.000
26B36LEU00.0210.00523.004-0.009-0.0090.0000.0000.0000.000
27B37PHE00.0040.00418.7950.0020.0020.0000.0000.0000.000
28B38VAL00.0160.00922.521-0.010-0.0100.0000.0000.0000.000
29B39LYS10.8920.93821.5240.3110.3110.0000.0000.0000.000
30B40LEU0-0.023-0.00325.6690.0160.0160.0000.0000.0000.000
31B41ALA00.0310.00328.662-0.011-0.0110.0000.0000.0000.000
32B42ASN0-0.015-0.00628.5880.0140.0140.0000.0000.0000.000
33B43PRO0-0.005-0.00531.2330.0060.0060.0000.0000.0000.000
34B44HIS0-0.048-0.00432.7110.0020.0020.0000.0000.0000.000
35B45SER00.018-0.00633.2240.0060.0060.0000.0000.0000.000
36B46GLY00.0310.01930.422-0.010-0.0100.0000.0000.0000.000
37B47GLU-1-0.913-0.95729.142-0.180-0.1800.0000.0000.0000.000
38B48GLY0-0.058-0.03927.6500.0040.0040.0000.0000.0000.000
39B49ALA00.0030.00824.843-0.010-0.0100.0000.0000.0000.000
40B50THR0-0.040-0.02320.4350.0000.0000.0000.0000.0000.000
41B51TYR00.0800.04723.5750.0100.0100.0000.0000.0000.000
42B52LEU0-0.0240.00621.731-0.008-0.0080.0000.0000.0000.000
43B53ILE00.008-0.01024.6360.0150.0150.0000.0000.0000.000
44B54ASP-1-0.780-0.88526.860-0.104-0.1040.0000.0000.0000.000
45B55MET00.0390.01628.2430.0060.0060.0000.0000.0000.000
46B56CYS0-0.126-0.05029.5210.0060.0060.0000.0000.0000.000
47B57LEU00.017-0.00831.2190.0060.0060.0000.0000.0000.000
48B58GLN0-0.085-0.02732.3140.0060.0060.0000.0000.0000.000
49B59GLN00.0590.02431.0590.0010.0010.0000.0000.0000.000
50B60LEU00.0160.01629.053-0.007-0.0070.0000.0000.0000.000
51B61PHE00.0310.01126.1130.0080.0080.0000.0000.0000.000
52B62GLU-1-0.787-0.86526.666-0.171-0.1710.0000.0000.0000.000
53B63ILE0-0.055-0.03519.983-0.005-0.0050.0000.0000.0000.000
54B64LYS10.8930.96123.1860.1590.1590.0000.0000.0000.000
55B65VAL0-0.020-0.03517.639-0.019-0.0190.0000.0000.0000.000
56B66PHE00.0070.02718.8250.0130.0130.0000.0000.0000.000
57B67LYS10.8090.86816.1340.3330.3330.0000.0000.0000.000
58B68GLU-1-0.798-0.88618.967-0.140-0.1400.0000.0000.0000.000
59B69LYS10.8960.94819.0070.1710.1710.0000.0000.0000.000
60B70HIS0-0.005-0.00617.606-0.005-0.0050.0000.0000.0000.000
61B71HIS00.0720.04316.2670.0250.0250.0000.0000.0000.000
62B72SER0-0.121-0.06411.099-0.056-0.0560.0000.0000.0000.000
63B73TRP00.005-0.01710.1080.0730.0730.0000.0000.0000.000
64B74PHE00.0620.0359.584-0.033-0.0330.0000.0000.0000.000
65B75ILE0-0.021-0.0067.978-0.025-0.0250.0000.0000.0000.000
66B76ASN00.000-0.0038.5100.0820.0820.0000.0000.0000.000
67B77GLN00.0140.0149.174-0.093-0.0930.0000.0000.0000.000
68B78SER0-0.012-0.0134.5430.1310.212-0.001-0.005-0.0750.000
69B79VAL00.0500.0285.891-0.154-0.1540.0000.0000.0000.000
70B80GLN0-0.0050.0085.386-0.730-0.7300.0000.0000.0000.000
71B81SER00.0280.0167.1750.2040.2040.0000.0000.0000.000
72B82GLY0-0.015-0.0079.904-0.081-0.0810.0000.0000.0000.000
73B83GLY00.1040.04612.2230.0770.0770.0000.0000.0000.000
74B84LEU0-0.051-0.01513.1370.0360.0360.0000.0000.0000.000
75B85LEU00.0290.02714.478-0.014-0.0140.0000.0000.0000.000
76B86HIS0-0.014-0.01314.2060.0350.0350.0000.0000.0000.000
77B87PHE00.0380.01018.3440.0230.0230.0000.0000.0000.000
78B88ALA0-0.0170.00121.781-0.008-0.0080.0000.0000.0000.000
79B89THR00.0460.01623.7180.0120.0120.0000.0000.0000.000
80B90PRO0-0.033-0.02627.303-0.005-0.0050.0000.0000.0000.000
81B91MET00.0050.01730.1930.0000.0000.0000.0000.0000.000
82B92ASP-1-0.781-0.88532.002-0.082-0.0820.0000.0000.0000.000
83B93PRO00.000-0.02734.689-0.003-0.0030.0000.0000.0000.000
84B94LEU00.0020.02336.043-0.002-0.0020.0000.0000.0000.000
85B95PHE00.0570.01535.5240.0020.0020.0000.0000.0000.000
86B96LEU00.009-0.00230.669-0.001-0.0010.0000.0000.0000.000
87B97LEU0-0.065-0.03635.321-0.001-0.0010.0000.0000.0000.000
88B98LEU00.0020.01638.5430.0050.0050.0000.0000.0000.000
89B99HIS00.0350.01335.1460.0070.0070.0000.0000.0000.000
90B100TYR00.0170.02139.3290.0000.0000.0000.0000.0000.000
91B101LEU0-0.018-0.00940.9790.0040.0040.0000.0000.0000.000
92B102LEU0-0.015-0.01440.6470.0030.0030.0000.0000.0000.000
93B103LYS10.9060.95038.6040.1090.1090.0000.0000.0000.000
94B104ALA00.0060.01944.7040.0030.0030.0000.0000.0000.000
95B105GLY00.0470.02447.8670.0030.0030.0000.0000.0000.000
96B106LYS10.9010.95549.4790.0660.0660.0000.0000.0000.000
97B123PRO00.006-0.01829.7520.0040.0040.0000.0000.0000.000
98B124ASP-1-0.815-0.90227.279-0.182-0.1820.0000.0000.0000.000
99B125CYS0-0.071-0.05630.9520.0060.0060.0000.0000.0000.000
100B126THR00.0220.01134.1470.0040.0040.0000.0000.0000.000
101B127LEU0-0.010-0.00829.4530.0080.0080.0000.0000.0000.000
102B128LEU0-0.0120.00432.1250.0030.0030.0000.0000.0000.000
103B129LEU00.0240.01333.5510.0030.0030.0000.0000.0000.000
104B130ARG10.9010.94634.5370.0950.0950.0000.0000.0000.000
105B131PHE00.0300.01331.924-0.001-0.0010.0000.0000.0000.000
106B132PRO00.0180.00537.5660.0030.0030.0000.0000.0000.000
107B133GLU-1-0.821-0.91739.977-0.057-0.0570.0000.0000.0000.000
108B134LEU00.0170.03840.535-0.001-0.0010.0000.0000.0000.000
109B135GLU-1-0.814-0.90242.028-0.053-0.0530.0000.0000.0000.000
110B136LYS10.8540.90945.0490.0540.0540.0000.0000.0000.000
111B137SER0-0.031-0.00240.9660.0020.0020.0000.0000.0000.000
112B138LEU00.0320.00042.456-0.001-0.0010.0000.0000.0000.000
113B139ARG10.8170.91045.1040.0510.0510.0000.0000.0000.000
114B140HIS00.006-0.00445.3380.0020.0020.0000.0000.0000.000
115B141VAL00.0140.02143.5830.0010.0010.0000.0000.0000.000
116B142THR0-0.041-0.01645.5130.0010.0010.0000.0000.0000.000
117B143GLU-1-0.795-0.88548.108-0.051-0.0510.0000.0000.0000.000
118B151LYS11.0161.01250.1770.0490.0490.0000.0000.0000.000
119B152TYR0-0.044-0.03450.173-0.002-0.0020.0000.0000.0000.000
120B153TYR00.0420.02446.9730.0000.0000.0000.0000.0000.000
121B154LYS10.8790.92749.9280.0540.0540.0000.0000.0000.000
122B155TYR00.0330.00445.7740.0010.0010.0000.0000.0000.000
123B156SER0-0.028-0.01649.4210.0040.0040.0000.0000.0000.000
124B157SER00.0870.03449.748-0.002-0.0020.0000.0000.0000.000
125B158GLU-1-0.776-0.87550.657-0.050-0.0500.0000.0000.0000.000
126B159LYS10.8410.91250.5100.0540.0540.0000.0000.0000.000
127B160THR00.000-0.00545.182-0.002-0.0020.0000.0000.0000.000
128B161LEU00.0290.03446.876-0.002-0.0020.0000.0000.0000.000
129B162LYS10.8340.90448.9260.0480.0480.0000.0000.0000.000
130B163TRP0-0.079-0.03940.0450.0010.0010.0000.0000.0000.000
131B164LEU00.0490.00041.977-0.001-0.0010.0000.0000.0000.000
132B165GLU-1-0.713-0.83144.620-0.056-0.0560.0000.0000.0000.000
133B166LYS10.9020.96645.5840.0600.0600.0000.0000.0000.000
134B167LYS10.8440.92838.9750.0820.0820.0000.0000.0000.000
135B168VAL00.0590.04942.232-0.001-0.0010.0000.0000.0000.000
136B169ASN0-0.051-0.04043.5710.0020.0020.0000.0000.0000.000
137B170GLN0-0.029-0.01741.221-0.001-0.0010.0000.0000.0000.000
138B171THR0-0.035-0.04238.2330.0000.0000.0000.0000.0000.000
139B172VAL00.0470.02340.377-0.001-0.0010.0000.0000.0000.000
140B173VAL0-0.038-0.01342.7830.0020.0020.0000.0000.0000.000
141B174ALA0-0.011-0.00637.6320.0010.0010.0000.0000.0000.000
142B175LEU00.0000.00737.4650.0000.0000.0000.0000.0000.000
143B176LYS10.8020.89139.6800.0510.0510.0000.0000.0000.000
144B177ALA0-0.040-0.00739.6690.0020.0020.0000.0000.0000.000
145B178ASN0-0.040-0.03935.2270.0040.0040.0000.0000.0000.000
146B179ASN0-0.0240.00036.571-0.001-0.0010.0000.0000.0000.000
147B180VAL0-0.011-0.00235.188-0.001-0.0010.0000.0000.0000.000
148B181ASN0-0.0280.00037.3440.0040.0040.0000.0000.0000.000
149B203GLU-1-0.812-0.89648.683-0.047-0.0470.0000.0000.0000.000
150B204ASP-1-0.890-0.95545.108-0.054-0.0540.0000.0000.0000.000
151B205TYR00.0730.02342.270-0.002-0.0020.0000.0000.0000.000
152B206VAL0-0.057-0.01844.061-0.003-0.0030.0000.0000.0000.000
153B207ARG10.8670.93744.8760.0510.0510.0000.0000.0000.000
154B208TYR00.0490.02735.685-0.004-0.0040.0000.0000.0000.000
155B209ALA00.015-0.01039.990-0.005-0.0050.0000.0000.0000.000
156B210HIS0-0.050-0.02440.849-0.002-0.0020.0000.0000.0000.000
157B211GLY00.0400.01339.543-0.003-0.0030.0000.0000.0000.000
158B212LEU0-0.0010.00834.739-0.005-0.0050.0000.0000.0000.000
159B213ILE0-0.042-0.02235.847-0.006-0.0060.0000.0000.0000.000
160B214SER00.0550.02937.366-0.003-0.0030.0000.0000.0000.000
161B215ASP-1-0.907-0.93632.567-0.129-0.1290.0000.0000.0000.000
162B216TYR0-0.151-0.10630.407-0.010-0.0100.0000.0000.0000.000
163B217ILE0-0.070-0.04035.1240.0010.0010.0000.0000.0000.000
164B218PRO00.0620.04038.2760.0020.0020.0000.0000.0000.000
165B219LYS10.7400.85939.8260.0770.0770.0000.0000.0000.000
166B220GLU-1-0.749-0.89340.898-0.079-0.0790.0000.0000.0000.000
167B221LEU0-0.0170.00040.4610.0020.0020.0000.0000.0000.000
168B222SER0-0.059-0.03244.1280.0040.0040.0000.0000.0000.000
169B223ASP-1-0.790-0.88244.930-0.069-0.0690.0000.0000.0000.000
170B224ASP-1-0.848-0.91345.935-0.070-0.0700.0000.0000.0000.000
171B225LEU0-0.020-0.00847.2210.0030.0030.0000.0000.0000.000
172B226SER00.000-0.02847.6730.0030.0030.0000.0000.0000.000
173B227LYS10.8290.93443.7330.0750.0750.0000.0000.0000.000
174B228PHE00.016-0.00648.4440.0020.0020.0000.0000.0000.000
175B229LEU0-0.014-0.01351.5360.0020.0020.0000.0000.0000.000
176B230LYS10.8280.91749.6710.0540.0540.0000.0000.0000.000
177B231LEU0-0.0290.00250.834-0.002-0.0020.0000.0000.0000.000