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

tag_button

FMODB ID: GNKM1

Calculation Name: 5JR9-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5JR9

Chain ID: B

ChEMBL ID:

UniProt ID: Q74ML9

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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2085237.863398
FMO2-HF: Nuclear repulsion 2008915.352596
FMO2-HF: Total energy -76322.510801
FMO2-MP2: Total energy -76548.263666


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:-1:GLY)


Summations of interaction energy for fragment #1(B:-1:GLY)
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.
0.6232.31-0.017-0.863-0.8090.004
Interaction energy analysis for fragmet #1(B:-1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.038 / q_NPA : 0.022
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].
3B1MET00.0290.0043.7890.5552.242-0.017-0.863-0.8090.004
4B2LEU0-0.0120.0086.3160.5220.5220.0000.0000.0000.000
5B3PRO00.0230.0059.529-0.125-0.1250.0000.0000.0000.000
6B4ASN0-0.013-0.00911.031-0.003-0.0030.0000.0000.0000.000
7B5LEU00.0670.0438.9040.0570.0570.0000.0000.0000.000
8B6ASP-1-0.877-0.94512.238-0.824-0.8240.0000.0000.0000.000
9B7ASN0-0.042-0.02614.9990.0950.0950.0000.0000.0000.000
10B8LEU00.0000.00414.0060.0510.0510.0000.0000.0000.000
11B9LYS10.8850.93815.7030.6190.6190.0000.0000.0000.000
12B10GLU-1-0.888-0.94417.394-0.378-0.3780.0000.0000.0000.000
13B11GLU-1-0.912-0.95820.155-0.277-0.2770.0000.0000.0000.000
14B12TYR0-0.090-0.06019.4380.0200.0200.0000.0000.0000.000
15B13GLN0-0.014-0.01820.7520.0430.0430.0000.0000.0000.000
16B14LYS10.9951.01323.2290.2600.2600.0000.0000.0000.000
17B15LEU0-0.018-0.01123.6380.0280.0280.0000.0000.0000.000
18B16GLU-1-0.800-0.86824.878-0.269-0.2690.0000.0000.0000.000
19B17GLU-1-0.871-0.92126.925-0.205-0.2050.0000.0000.0000.000
20B18LYS10.8150.87529.2160.2130.2130.0000.0000.0000.000
21B19LYS10.8400.92828.1990.2520.2520.0000.0000.0000.000
22B20GLN0-0.018-0.01631.2470.0080.0080.0000.0000.0000.000
23B21GLU-1-0.811-0.89233.080-0.151-0.1510.0000.0000.0000.000
24B22ILE0-0.035-0.00533.5580.0140.0140.0000.0000.0000.000
25B23VAL00.0020.00134.7060.0110.0110.0000.0000.0000.000
26B24ASP-1-0.789-0.87537.160-0.133-0.1330.0000.0000.0000.000
27B25ARG10.7990.86036.4640.1490.1490.0000.0000.0000.000
28B26SER0-0.012-0.01039.7920.0090.0090.0000.0000.0000.000
29B27ILE0-0.0060.01240.1820.0070.0070.0000.0000.0000.000
30B28ARG10.8260.88540.6490.1270.1270.0000.0000.0000.000
31B29MET0-0.028-0.00744.3450.0040.0040.0000.0000.0000.000
32B30SER0-0.025-0.02046.1590.0060.0060.0000.0000.0000.000
33B31LYS10.8930.94247.8530.0820.0820.0000.0000.0000.000
34B32LEU0-0.040-0.02648.6870.0040.0040.0000.0000.0000.000
35B33SER00.0340.01349.8460.0040.0040.0000.0000.0000.000
36B34LYS10.8920.93849.5350.0840.0840.0000.0000.0000.000
37B35SER0-0.046-0.00853.9150.0020.0020.0000.0000.0000.000
38B36LEU0-0.0120.00555.1470.0030.0030.0000.0000.0000.000
39B37ILE00.0500.02554.8550.0030.0030.0000.0000.0000.000
40B38TYR0-0.006-0.00758.1490.0030.0030.0000.0000.0000.000
41B39SER0-0.031-0.04059.3620.0020.0020.0000.0000.0000.000
42B40MET00.0030.00660.6910.0020.0020.0000.0000.0000.000
43B41ILE0-0.0330.00461.3030.0020.0020.0000.0000.0000.000
44B42ARG10.7470.84664.5660.0490.0490.0000.0000.0000.000
45B43GLU-1-0.817-0.88465.852-0.041-0.0410.0000.0000.0000.000
46B44ASP-1-0.827-0.88464.342-0.049-0.0490.0000.0000.0000.000
47B45TYR00.000-0.03763.859-0.002-0.0020.0000.0000.0000.000
48B46LYS10.9190.98263.3230.0430.0430.0000.0000.0000.000
49B47SER0-0.041-0.05160.342-0.002-0.0020.0000.0000.0000.000
50B48ALA00.0310.02659.241-0.003-0.0030.0000.0000.0000.000
51B49ASP-1-0.746-0.86458.573-0.055-0.0550.0000.0000.0000.000
52B50LYS10.8440.92553.7570.0680.0680.0000.0000.0000.000
53B51TYR0-0.031-0.03454.565-0.004-0.0040.0000.0000.0000.000
54B52LYS10.9390.98853.6540.0550.0550.0000.0000.0000.000
55B53GLU-1-0.953-0.95253.706-0.067-0.0670.0000.0000.0000.000
56B54GLU-1-0.849-0.92249.719-0.082-0.0820.0000.0000.0000.000
57B55LEU0-0.0050.00548.647-0.004-0.0040.0000.0000.0000.000
58B56THR0-0.007-0.03148.798-0.003-0.0030.0000.0000.0000.000
59B57ASN0-0.018-0.00248.072-0.002-0.0020.0000.0000.0000.000
60B58LEU0-0.0070.00343.957-0.005-0.0050.0000.0000.0000.000
61B59ALA00.0190.01044.073-0.005-0.0050.0000.0000.0000.000
62B60LYS10.9080.95644.5740.0730.0730.0000.0000.0000.000
63B61THR00.0280.01240.266-0.003-0.0030.0000.0000.0000.000
64B62GLN00.0310.01039.397-0.009-0.0090.0000.0000.0000.000
65B63ILE0-0.043-0.02139.884-0.005-0.0050.0000.0000.0000.000
66B64GLU-1-0.902-0.94239.156-0.117-0.1170.0000.0000.0000.000
67B65GLU-1-0.801-0.89935.466-0.160-0.1600.0000.0000.0000.000
68B66LEU0-0.030-0.01735.246-0.009-0.0090.0000.0000.0000.000
69B67LYS10.8940.96335.9870.0960.0960.0000.0000.0000.000
70B68LYS10.7670.88332.9310.1360.1360.0000.0000.0000.000
71B69TYR00.0040.00029.026-0.014-0.0140.0000.0000.0000.000
72B70PRO00.0540.03131.0130.0010.0010.0000.0000.0000.000
73B71MET0-0.031-0.00226.7260.0110.0110.0000.0000.0000.000
74B72PHE00.021-0.00327.357-0.002-0.0020.0000.0000.0000.000
75B73TYR0-0.010-0.02833.0850.0070.0070.0000.0000.0000.000
76B74SER0-0.005-0.01134.7040.0040.0040.0000.0000.0000.000
77B75ASN0-0.022-0.01433.330-0.002-0.0020.0000.0000.0000.000
78B76GLY00.0510.02236.7980.0020.0020.0000.0000.0000.000
79B77PHE0-0.043-0.00539.4210.0060.0060.0000.0000.0000.000
80B78ILE00.0530.01541.7470.0050.0050.0000.0000.0000.000
81B79GLY00.0590.03343.0370.0040.0040.0000.0000.0000.000
82B80LEU0-0.016-0.01342.2310.0050.0050.0000.0000.0000.000
83B81GLN0-0.020-0.01845.6690.0010.0010.0000.0000.0000.000
84B82GLU-1-0.733-0.83247.633-0.081-0.0810.0000.0000.0000.000
85B83TYR0-0.049-0.04148.1410.0040.0040.0000.0000.0000.000
86B84VAL0-0.041-0.02249.3390.0030.0030.0000.0000.0000.000
87B85GLU-1-0.926-0.95451.733-0.064-0.0640.0000.0000.0000.000
88B86ALA00.0170.00053.2830.0030.0030.0000.0000.0000.000
89B87LEU0-0.031-0.02652.8980.0030.0030.0000.0000.0000.000
90B88ALA00.0090.00655.7360.0030.0030.0000.0000.0000.000
91B89LEU00.0050.01057.6190.0030.0030.0000.0000.0000.000
92B90TYR0-0.079-0.09158.6830.0030.0030.0000.0000.0000.000
93B91TYR00.018-0.00357.3950.0000.0000.0000.0000.0000.000
94B92TYR0-0.045-0.03061.6640.0020.0020.0000.0000.0000.000
95B93ILE0-0.035-0.02863.3000.0020.0020.0000.0000.0000.000
96B94LYS10.8420.93963.3030.0500.0500.0000.0000.0000.000
97B95GLU-1-0.906-0.96563.954-0.046-0.0460.0000.0000.0000.000
98B96ASN0-0.087-0.03166.6310.0010.0010.0000.0000.0000.000
99B97ARG10.8060.88660.4780.0490.0490.0000.0000.0000.000
100B98ILE00.0210.00258.581-0.001-0.0010.0000.0000.0000.000
101B99PRO0-0.0260.02056.5080.0010.0010.0000.0000.0000.000
102B100SER00.045-0.00255.852-0.001-0.0010.0000.0000.0000.000
103B101LYS10.9060.92650.4050.0560.0560.0000.0000.0000.000
104B102GLU-1-0.831-0.88951.465-0.059-0.0590.0000.0000.0000.000
105B103GLU-1-0.818-0.87452.623-0.053-0.0530.0000.0000.0000.000
106B104LEU0-0.0100.00451.415-0.002-0.0020.0000.0000.0000.000
107B105GLY00.0010.01348.941-0.004-0.0040.0000.0000.0000.000
108B106VAL0-0.042-0.01346.549-0.004-0.0040.0000.0000.0000.000
109B107ASP-1-0.769-0.86943.546-0.084-0.0840.0000.0000.0000.000
110B108THR00.041-0.02446.4370.0010.0010.0000.0000.0000.000
111B109TRP00.0010.02143.7380.0050.0050.0000.0000.0000.000
112B110VAL00.012-0.00944.2860.0010.0010.0000.0000.0000.000
113B111TYR0-0.061-0.04146.7790.0010.0010.0000.0000.0000.000
114B112LEU00.0320.01450.1250.0020.0020.0000.0000.0000.000
115B113PHE0-0.006-0.00646.3900.0010.0010.0000.0000.0000.000
116B114GLY00.0490.02849.8460.0000.0000.0000.0000.0000.000
117B115ILE0-0.003-0.00851.4630.0020.0020.0000.0000.0000.000
118B116GLY0-0.028-0.01753.4770.0020.0020.0000.0000.0000.000
119B117ASP-1-0.792-0.88051.465-0.068-0.0680.0000.0000.0000.000
120B118ILE00.0100.00755.0540.0010.0010.0000.0000.0000.000
121B119ALA00.0150.01057.9460.0010.0010.0000.0000.0000.000
122B120GLY00.0170.01259.0930.0020.0020.0000.0000.0000.000
123B121GLU-1-0.827-0.93957.977-0.056-0.0560.0000.0000.0000.000
124B122ILE0-0.0080.01260.7870.0020.0020.0000.0000.0000.000
125B123LEU0-0.0100.01163.4400.0020.0020.0000.0000.0000.000
126B124ARG10.8570.94561.6940.0520.0520.0000.0000.0000.000
127B125LYS10.8160.88964.6350.0440.0440.0000.0000.0000.000
128B126SER00.008-0.02166.4140.0020.0020.0000.0000.0000.000
129B127SER0-0.040-0.03067.5310.0020.0020.0000.0000.0000.000
130B128GLU-1-0.785-0.87066.665-0.045-0.0450.0000.0000.0000.000
131B129GLU-1-0.798-0.88869.854-0.038-0.0380.0000.0000.0000.000
132B130LEU00.0210.02572.3780.0010.0010.0000.0000.0000.000
133B131ILE0-0.036-0.01571.4310.0010.0010.0000.0000.0000.000
134B132LYS10.7820.88572.0740.0390.0390.0000.0000.0000.000
135B133GLY0-0.025-0.00676.4730.0010.0010.0000.0000.0000.000
136B134ASN0-0.029-0.00974.8460.0020.0020.0000.0000.0000.000
137B135ILE00.0320.01075.783-0.001-0.0010.0000.0000.0000.000
138B136GLU-1-0.779-0.88876.367-0.030-0.0300.0000.0000.0000.000
139B137TYR00.0340.02167.886-0.001-0.0010.0000.0000.0000.000
140B138ALA00.0530.01871.628-0.001-0.0010.0000.0000.0000.000
141B139LYS10.8160.89072.1920.0290.0290.0000.0000.0000.000
142B140LYS10.8310.90970.3290.0370.0370.0000.0000.0000.000
143B141ALA00.0670.03768.1650.0000.0000.0000.0000.0000.000
144B142LYS10.8020.87968.4000.0320.0320.0000.0000.0000.000
145B143GLN0-0.017-0.00469.5450.0000.0000.0000.0000.0000.000
146B144ASP-1-0.757-0.83266.725-0.039-0.0390.0000.0000.0000.000
147B145LEU0-0.005-0.01663.116-0.001-0.0010.0000.0000.0000.000
148B146GLU-1-0.791-0.87464.986-0.034-0.0340.0000.0000.0000.000
149B147SER0-0.016-0.00666.4430.0000.0000.0000.0000.0000.000
150B148LEU00.0410.03259.319-0.001-0.0010.0000.0000.0000.000
151B149TYR0-0.030-0.02261.740-0.001-0.0010.0000.0000.0000.000
152B150LEU0-0.016-0.02062.2970.0000.0000.0000.0000.0000.000
153B151ASP-1-0.896-0.94460.981-0.041-0.0410.0000.0000.0000.000
154B152LEU0-0.077-0.05456.186-0.001-0.0010.0000.0000.0000.000
155B153LEU0-0.027-0.01558.257-0.001-0.0010.0000.0000.0000.000
156B154TYR0-0.037-0.01359.9770.0000.0000.0000.0000.0000.000
157B155ILE0-0.041-0.01254.3840.0000.0000.0000.0000.0000.000
158B156GLU-1-0.908-0.93755.808-0.040-0.0400.0000.0000.0000.000
159B157LEU0-0.003-0.00152.616-0.002-0.0020.0000.0000.0000.000
160B158LYS10.8710.91949.9560.0450.0450.0000.0000.0000.000
161B159ASN00.0060.00645.9380.0000.0000.0000.0000.0000.000
162B160PHE00.0370.01447.9890.0020.0020.0000.0000.0000.000
163B161ASP-1-0.795-0.89846.310-0.073-0.0730.0000.0000.0000.000
164B162LEU00.0080.00949.2990.0010.0010.0000.0000.0000.000
165B163ARG10.9540.97451.7520.0510.0510.0000.0000.0000.000
166B164ARG10.8530.92748.5650.0680.0680.0000.0000.0000.000
167B165LYS10.7470.85349.7200.0710.0710.0000.0000.0000.000
168B166LEU00.0160.02255.2240.0010.0010.0000.0000.0000.000
169B167ASP-1-0.878-0.94457.726-0.044-0.0440.0000.0000.0000.000
170B168TYR0-0.050-0.01356.9680.0020.0020.0000.0000.0000.000
171B169VAL00.0310.01258.9400.0010.0010.0000.0000.0000.000
172B170SER00.0280.02561.2920.0020.0020.0000.0000.0000.000
173B171ASN0-0.069-0.04661.3130.0020.0020.0000.0000.0000.000
174B172ILE0-0.0170.00260.4070.0010.0010.0000.0000.0000.000
175B173ILE00.0000.00564.4200.0010.0010.0000.0000.0000.000
176B174ASN0-0.044-0.03966.7870.0020.0020.0000.0000.0000.000
177B175LYS10.8150.90366.7140.0400.0400.0000.0000.0000.000
178B176LEU00.0250.00967.8080.0010.0010.0000.0000.0000.000
179B177ILE0-0.015-0.00270.2920.0010.0010.0000.0000.0000.000
180B178GLU-1-0.825-0.88370.816-0.036-0.0360.0000.0000.0000.000
181B179PHE0-0.017-0.03168.6370.0010.0010.0000.0000.0000.000
182B180ILE0-0.003-0.01173.4890.0010.0010.0000.0000.0000.000
183B181ILE0-0.0380.00576.2420.0010.0010.0000.0000.0000.000
184B182TRP0-0.026-0.01576.8840.0010.0010.0000.0000.0000.000
185B183LYS10.8630.93676.6520.0340.0340.0000.0000.0000.000
186B184SER0-0.059-0.02879.7110.0010.0010.0000.0000.0000.000