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: 82Z1Y

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 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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2094800.882525
FMO2-HF: Nuclear repulsion 2018478.164939
FMO2-HF: Total energy -76322.717586
FMO2-MP2: Total energy -76548.587264


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.
0.5462.247-0.012-0.929-0.760.003
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 : 0.051 / q_NPA : 0.026
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].
3B1MET00.0280.0103.8630.3272.028-0.012-0.929-0.7600.003
4B2LEU0-0.0110.0036.7200.5300.5300.0000.0000.0000.000
5B3PRO00.0350.0099.486-0.098-0.0980.0000.0000.0000.000
6B4ASN0-0.028-0.02111.167-0.018-0.0180.0000.0000.0000.000
7B5LEU00.0270.0328.8470.0510.0510.0000.0000.0000.000
8B6ASP-1-0.801-0.89712.237-0.728-0.7280.0000.0000.0000.000
9B7ASN0-0.011-0.00114.7370.0710.0710.0000.0000.0000.000
10B8LEU00.0130.00514.0880.0480.0480.0000.0000.0000.000
11B9LYS10.8040.88315.3430.6290.6290.0000.0000.0000.000
12B10GLU-1-0.860-0.92117.513-0.380-0.3800.0000.0000.0000.000
13B11GLU-1-0.865-0.93520.288-0.247-0.2470.0000.0000.0000.000
14B12TYR0-0.071-0.04519.5720.0170.0170.0000.0000.0000.000
15B13GLN0-0.014-0.01020.9860.0440.0440.0000.0000.0000.000
16B14LYS10.9100.95223.4470.2720.2720.0000.0000.0000.000
17B15LEU0-0.025-0.01523.7380.0270.0270.0000.0000.0000.000
18B16GLU-1-0.794-0.86625.057-0.282-0.2820.0000.0000.0000.000
19B17GLU-1-0.872-0.91927.110-0.195-0.1950.0000.0000.0000.000
20B18LYS10.8070.87629.4320.2050.2050.0000.0000.0000.000
21B19LYS10.8330.91827.9050.2680.2680.0000.0000.0000.000
22B20GLN0-0.024-0.01831.4230.0060.0060.0000.0000.0000.000
23B21GLU-1-0.808-0.88733.299-0.145-0.1450.0000.0000.0000.000
24B22ILE0-0.038-0.00433.6210.0130.0130.0000.0000.0000.000
25B23VAL00.0250.01735.2500.0110.0110.0000.0000.0000.000
26B24ASP-1-0.779-0.87337.404-0.134-0.1340.0000.0000.0000.000
27B25ARG10.7690.85736.0520.1510.1510.0000.0000.0000.000
28B26SER00.003-0.01740.1020.0090.0090.0000.0000.0000.000
29B27ILE0-0.0070.00840.2250.0070.0070.0000.0000.0000.000
30B28ARG10.8050.87540.7170.1270.1270.0000.0000.0000.000
31B29MET0-0.0190.00244.2260.0040.0040.0000.0000.0000.000
32B30SER0-0.020-0.01546.2480.0060.0060.0000.0000.0000.000
33B31LYS10.8980.93947.8210.0830.0830.0000.0000.0000.000
34B32LEU0-0.075-0.04348.6880.0050.0050.0000.0000.0000.000
35B33SER00.0220.00449.9340.0040.0040.0000.0000.0000.000
36B34LYS10.8830.92649.6760.0880.0880.0000.0000.0000.000
37B35SER0-0.046-0.00753.9820.0020.0020.0000.0000.0000.000
38B36LEU0-0.0050.02255.0800.0030.0030.0000.0000.0000.000
39B37ILE00.0520.03154.9160.0030.0030.0000.0000.0000.000
40B38TYR00.0180.00958.3840.0040.0040.0000.0000.0000.000
41B39SER0-0.036-0.04559.2880.0020.0020.0000.0000.0000.000
42B40MET00.0000.00660.6000.0020.0020.0000.0000.0000.000
43B41ILE0-0.024-0.00461.3420.0020.0020.0000.0000.0000.000
44B42ARG10.7590.84664.5060.0500.0500.0000.0000.0000.000
45B43GLU-1-0.793-0.85365.699-0.042-0.0420.0000.0000.0000.000
46B44ASP-1-0.805-0.85964.376-0.048-0.0480.0000.0000.0000.000
47B45TYR0-0.013-0.05663.767-0.002-0.0020.0000.0000.0000.000
48B46LYS10.8610.93663.1300.0440.0440.0000.0000.0000.000
49B47SER0-0.043-0.04760.176-0.002-0.0020.0000.0000.0000.000
50B48ALA00.0320.02559.074-0.002-0.0020.0000.0000.0000.000
51B49ASP-1-0.723-0.84058.346-0.055-0.0550.0000.0000.0000.000
52B50LYS10.8580.92653.9350.0670.0670.0000.0000.0000.000
53B51TYR0-0.023-0.02754.580-0.004-0.0040.0000.0000.0000.000
54B52LYS10.9200.97553.5240.0550.0550.0000.0000.0000.000
55B53GLU-1-0.935-0.94653.462-0.066-0.0660.0000.0000.0000.000
56B54GLU-1-0.842-0.90849.865-0.081-0.0810.0000.0000.0000.000
57B55LEU0-0.0030.00348.683-0.004-0.0040.0000.0000.0000.000
58B56THR00.002-0.02348.639-0.003-0.0030.0000.0000.0000.000
59B57ASN0-0.043-0.01947.874-0.003-0.0030.0000.0000.0000.000
60B58LEU0-0.0150.00843.862-0.005-0.0050.0000.0000.0000.000
61B59ALA00.0350.01143.962-0.005-0.0050.0000.0000.0000.000
62B60LYS10.8620.91644.5310.0720.0720.0000.0000.0000.000
63B61THR00.0080.00040.392-0.002-0.0020.0000.0000.0000.000
64B62GLN00.007-0.01039.260-0.009-0.0090.0000.0000.0000.000
65B63ILE0-0.039-0.01839.960-0.005-0.0050.0000.0000.0000.000
66B64GLU-1-0.896-0.93638.909-0.114-0.1140.0000.0000.0000.000
67B65GLU-1-0.776-0.88935.292-0.161-0.1610.0000.0000.0000.000
68B66LEU0-0.009-0.00135.321-0.008-0.0080.0000.0000.0000.000
69B67LYS10.8760.94936.0410.0960.0960.0000.0000.0000.000
70B68LYS10.7750.89333.1420.1350.1350.0000.0000.0000.000
71B69TYR0-0.011-0.00928.973-0.016-0.0160.0000.0000.0000.000
72B70PRO00.0450.02531.555-0.001-0.0010.0000.0000.0000.000
73B71MET0-0.036-0.00627.0070.0100.0100.0000.0000.0000.000
74B72PHE00.0310.00727.615-0.003-0.0030.0000.0000.0000.000
75B73TYR0-0.011-0.03433.3750.0080.0080.0000.0000.0000.000
76B74SER00.002-0.00734.9310.0060.0060.0000.0000.0000.000
77B75ASN0-0.016-0.00633.658-0.002-0.0020.0000.0000.0000.000
78B76GLY00.0500.03137.0740.0030.0030.0000.0000.0000.000
79B77PHE0-0.037-0.01039.6550.0060.0060.0000.0000.0000.000
80B78ILE00.0560.01842.0320.0050.0050.0000.0000.0000.000
81B79GLY00.0400.02443.1380.0050.0050.0000.0000.0000.000
82B80LEU0-0.025-0.02242.4560.0050.0050.0000.0000.0000.000
83B81GLN0-0.020-0.01645.8740.0010.0010.0000.0000.0000.000
84B82GLU-1-0.718-0.83047.967-0.083-0.0830.0000.0000.0000.000
85B83TYR0-0.037-0.03548.2580.0040.0040.0000.0000.0000.000
86B84VAL0-0.036-0.01649.6080.0040.0040.0000.0000.0000.000
87B85GLU-1-0.924-0.96151.940-0.068-0.0680.0000.0000.0000.000
88B86ALA00.0170.00353.4790.0030.0030.0000.0000.0000.000
89B87LEU0-0.038-0.02652.8810.0030.0030.0000.0000.0000.000
90B88ALA00.0100.00555.8600.0030.0030.0000.0000.0000.000
91B89LEU00.0000.00757.7960.0030.0030.0000.0000.0000.000
92B90TYR0-0.062-0.08458.7630.0030.0030.0000.0000.0000.000
93B91TYR00.004-0.00757.1260.0010.0010.0000.0000.0000.000
94B92TYR0-0.040-0.03261.7560.0020.0020.0000.0000.0000.000
95B93ILE0-0.044-0.03063.5400.0020.0020.0000.0000.0000.000
96B94LYS10.8100.90563.0960.0510.0510.0000.0000.0000.000
97B95GLU-1-0.872-0.94563.514-0.047-0.0470.0000.0000.0000.000
98B96ASN0-0.062-0.02266.4840.0020.0020.0000.0000.0000.000
99B97ARG10.7690.86760.3470.0510.0510.0000.0000.0000.000
100B98ILE00.0330.01458.566-0.001-0.0010.0000.0000.0000.000
101B99PRO0-0.0240.01256.4100.0010.0010.0000.0000.0000.000
102B100SER00.027-0.01755.688-0.001-0.0010.0000.0000.0000.000
103B101LYS10.9190.93050.3130.0610.0610.0000.0000.0000.000
104B102GLU-1-0.827-0.87551.272-0.063-0.0630.0000.0000.0000.000
105B103GLU-1-0.796-0.86052.486-0.055-0.0550.0000.0000.0000.000
106B104LEU00.0130.01251.130-0.002-0.0020.0000.0000.0000.000
107B105GLY00.0110.03148.726-0.004-0.0040.0000.0000.0000.000
108B106VAL0-0.039-0.01846.451-0.004-0.0040.0000.0000.0000.000
109B107ASP-1-0.767-0.86543.722-0.089-0.0890.0000.0000.0000.000
110B108THR00.038-0.02146.5070.0010.0010.0000.0000.0000.000
111B109TRP00.0060.02244.1440.0050.0050.0000.0000.0000.000
112B110VAL00.017-0.00344.2750.0010.0010.0000.0000.0000.000
113B111TYR0-0.062-0.03946.9050.0010.0010.0000.0000.0000.000
114B112LEU00.0200.00250.4830.0020.0020.0000.0000.0000.000
115B113PHE0-0.011-0.01446.7480.0010.0010.0000.0000.0000.000
116B114GLY00.0520.03750.0660.0010.0010.0000.0000.0000.000
117B115ILE0-0.025-0.01951.6920.0020.0020.0000.0000.0000.000
118B116GLY00.0060.00953.8080.0030.0030.0000.0000.0000.000
119B117ASP-1-0.767-0.85851.764-0.073-0.0730.0000.0000.0000.000
120B118ILE00.0150.00155.3010.0020.0020.0000.0000.0000.000
121B119ALA00.0320.02358.0780.0020.0020.0000.0000.0000.000
122B120GLY00.0220.02259.3390.0020.0020.0000.0000.0000.000
123B121GLU-1-0.842-0.95358.120-0.058-0.0580.0000.0000.0000.000
124B122ILE00.0050.02261.0050.0020.0020.0000.0000.0000.000
125B123LEU00.0100.02563.7320.0020.0020.0000.0000.0000.000
126B124ARG10.8440.93761.6530.0550.0550.0000.0000.0000.000
127B125LYS10.7950.87864.7490.0460.0460.0000.0000.0000.000
128B126SER00.011-0.02466.5140.0020.0020.0000.0000.0000.000
129B127SER0-0.044-0.03167.8490.0020.0020.0000.0000.0000.000
130B128GLU-1-0.782-0.86466.634-0.047-0.0470.0000.0000.0000.000
131B129GLU-1-0.797-0.87969.840-0.040-0.0400.0000.0000.0000.000
132B130LEU00.0190.02272.4820.0010.0010.0000.0000.0000.000
133B131ILE0-0.043-0.02271.1590.0010.0010.0000.0000.0000.000
134B132LYS10.8010.89571.9970.0410.0410.0000.0000.0000.000
135B133GLY00.0000.01176.5670.0010.0010.0000.0000.0000.000
136B134ASN0-0.059-0.02574.4700.0020.0020.0000.0000.0000.000
137B135ILE00.0350.00075.479-0.001-0.0010.0000.0000.0000.000
138B136GLU-1-0.784-0.87976.273-0.032-0.0320.0000.0000.0000.000
139B137TYR00.0410.02567.778-0.001-0.0010.0000.0000.0000.000
140B138ALA00.0400.01771.587-0.001-0.0010.0000.0000.0000.000
141B139LYS10.8210.88672.2790.0310.0310.0000.0000.0000.000
142B140LYS10.8120.91670.0370.0400.0400.0000.0000.0000.000
143B141ALA00.0640.02568.0700.0000.0000.0000.0000.0000.000
144B142LYS10.7900.87668.3430.0350.0350.0000.0000.0000.000
145B143GLN0-0.004-0.00769.4330.0000.0000.0000.0000.0000.000
146B144ASP-1-0.766-0.82866.663-0.042-0.0420.0000.0000.0000.000
147B145LEU0-0.001-0.00963.045-0.001-0.0010.0000.0000.0000.000
148B146GLU-1-0.792-0.88665.070-0.038-0.0380.0000.0000.0000.000
149B147SER0-0.030-0.02066.7220.0000.0000.0000.0000.0000.000
150B148LEU00.0350.02259.314-0.001-0.0010.0000.0000.0000.000
151B149TYR0-0.031-0.02161.641-0.001-0.0010.0000.0000.0000.000
152B150LEU0-0.001-0.01062.5380.0000.0000.0000.0000.0000.000
153B151ASP-1-0.909-0.95061.158-0.045-0.0450.0000.0000.0000.000
154B152LEU0-0.050-0.04656.254-0.001-0.0010.0000.0000.0000.000
155B153LEU0-0.024-0.00958.293-0.001-0.0010.0000.0000.0000.000
156B154TYR0-0.030-0.00560.2710.0000.0000.0000.0000.0000.000
157B155ILE0-0.051-0.02054.8900.0000.0000.0000.0000.0000.000
158B156GLU-1-0.865-0.91355.885-0.048-0.0480.0000.0000.0000.000
159B157LEU0-0.0040.00952.943-0.002-0.0020.0000.0000.0000.000
160B158LYS10.8170.88150.4170.0520.0520.0000.0000.0000.000
161B159ASN0-0.017-0.02346.5500.0010.0010.0000.0000.0000.000
162B160PHE00.0320.01248.4250.0020.0020.0000.0000.0000.000
163B161ASP-1-0.777-0.87547.098-0.081-0.0810.0000.0000.0000.000
164B162LEU00.0320.01649.5240.0020.0020.0000.0000.0000.000
165B163ARG10.9410.98352.2730.0600.0600.0000.0000.0000.000
166B164ARG10.8470.91948.7620.0770.0770.0000.0000.0000.000
167B165LYS10.7500.85649.9430.0770.0770.0000.0000.0000.000
168B166LEU00.0240.02555.5560.0010.0010.0000.0000.0000.000
169B167ASP-1-0.882-0.95358.237-0.050-0.0500.0000.0000.0000.000
170B168TYR0-0.081-0.03157.3780.0020.0020.0000.0000.0000.000
171B169VAL00.0330.00959.2990.0010.0010.0000.0000.0000.000
172B170SER00.0030.01461.6960.0020.0020.0000.0000.0000.000
173B171ASN0-0.058-0.03962.0830.0020.0020.0000.0000.0000.000
174B172ILE0-0.0110.00760.7650.0010.0010.0000.0000.0000.000
175B173ILE0-0.0050.00864.8790.0010.0010.0000.0000.0000.000
176B174ASN0-0.045-0.03567.4410.0030.0030.0000.0000.0000.000
177B175LYS10.8050.89266.9300.0440.0440.0000.0000.0000.000
178B176LEU00.0220.00767.7460.0010.0010.0000.0000.0000.000
179B177ILE0-0.009-0.00270.5970.0010.0010.0000.0000.0000.000
180B178GLU-1-0.825-0.88671.295-0.040-0.0400.0000.0000.0000.000
181B179PHE0-0.012-0.02968.8420.0010.0010.0000.0000.0000.000
182B180ILE0-0.003-0.00673.6990.0010.0010.0000.0000.0000.000
183B181ILE0-0.0220.01276.3520.0010.0010.0000.0000.0000.000
184B182TRP0-0.012-0.01176.9250.0010.0010.0000.0000.0000.000
185B183LYS10.8310.92076.8040.0350.0350.0000.0000.0000.000
186B184SER0-0.065-0.02879.8360.0010.0010.0000.0000.0000.000