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: R5328

Calculation Name: 2J92-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2J92

Chain ID: B

ChEMBL ID:

UniProt ID: P03306

Base Structure: X-ray

Registration Date: 2023-06-21

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 OptH
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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1941956.949293
FMO2-HF: Nuclear repulsion 1869852.19075
FMO2-HF: Total energy -72104.758542
FMO2-MP2: Total energy -72308.053829


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:7:ASP)


Summations of interaction energy for fragment #1(B:7:ASP)
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.
-239.146-231.3542.361-4.698-5.4540.05
Interaction energy analysis for fragmet #1(B:7:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.901 / q_NPA : -0.960
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].
3B9GLN00.0810.0253.559-8.210-5.6680.038-1.200-1.3800.006
4B10LYS11.0041.0212.258-77.581-72.9742.311-3.172-3.7450.042
5B11MET0-0.088-0.0433.941-14.816-14.1730.012-0.326-0.3290.002
6B12VAL00.0490.0216.075-5.507-5.5070.0000.0000.0000.000
7B13MET00.0390.0537.085-4.867-4.8670.0000.0000.0000.000
8B14GLY0-0.031-0.0068.117-3.240-3.2400.0000.0000.0000.000
9B15ASN0-0.072-0.08210.002-2.337-2.3370.0000.0000.0000.000
10B16THR0-0.059-0.03611.327-2.058-2.0580.0000.0000.0000.000
11B17LYS10.8510.94313.582-20.801-20.8010.0000.0000.0000.000
12B18PRO00.0130.03216.914-0.108-0.1080.0000.0000.0000.000
13B19VAL00.036-0.00219.703-0.325-0.3250.0000.0000.0000.000
14B20GLU-1-0.913-0.96922.98513.28313.2830.0000.0000.0000.000
15B21LEU00.0120.00926.432-0.105-0.1050.0000.0000.0000.000
16B22ILE0-0.040-0.02329.587-0.118-0.1180.0000.0000.0000.000
17B23LEU00.0270.01632.637-0.046-0.0460.0000.0000.0000.000
18B24ASP-1-0.914-0.95636.2997.7737.7730.0000.0000.0000.000
19B25GLY0-0.073-0.02935.758-0.025-0.0250.0000.0000.0000.000
20B26LYS10.9350.97333.553-9.316-9.3160.0000.0000.0000.000
21B27THR00.007-0.01128.650-0.043-0.0430.0000.0000.0000.000
22B28VAL0-0.016-0.00431.806-0.084-0.0840.0000.0000.0000.000
23B29ALA00.0110.00728.681-0.008-0.0080.0000.0000.0000.000
24B30ILE0-0.0120.00523.4850.1670.1670.0000.0000.0000.000
25B31CYS0-0.041-0.01822.172-0.260-0.2600.0000.0000.0000.000
26B32CYS0-0.0410.01516.9720.6620.6620.0000.0000.0000.000
27B33ALA00.0570.03818.019-0.647-0.6470.0000.0000.0000.000
28B34THR0-0.024-0.01213.2021.6921.6920.0000.0000.0000.000
29B35GLY00.0030.00915.156-0.929-0.9290.0000.0000.0000.000
30B36VAL0-0.002-0.01614.2081.8971.8970.0000.0000.0000.000
31B37PHE00.0620.00614.5180.6880.6880.0000.0000.0000.000
32B38GLY0-0.0050.01916.686-0.731-0.7310.0000.0000.0000.000
33B39THR00.007-0.01518.7500.8050.8050.0000.0000.0000.000
34B40ALA00.0320.02119.964-0.572-0.5720.0000.0000.0000.000
35B41TYR0-0.006-0.01717.6411.5451.5450.0000.0000.0000.000
36B42LEU0-0.033-0.00116.879-0.758-0.7580.0000.0000.0000.000
37B43VAL00.0150.00019.4940.7480.7480.0000.0000.0000.000
38B44PRO00.005-0.00622.052-0.206-0.2060.0000.0000.0000.000
39B45ARG10.9240.96224.445-10.735-10.7350.0000.0000.0000.000
40B46HIS00.001-0.00527.605-0.355-0.3550.0000.0000.0000.000
41B47LEU00.0690.03725.294-0.179-0.1790.0000.0000.0000.000
42B48PHE0-0.051-0.03125.207-0.080-0.0800.0000.0000.0000.000
43B49ALA0-0.023-0.00430.098-0.217-0.2170.0000.0000.0000.000
44B50GLU-1-0.985-0.98431.8199.2679.2670.0000.0000.0000.000
45B51GLN0-0.0030.00534.209-0.056-0.0560.0000.0000.0000.000
46B52TYR0-0.055-0.04832.0710.2240.2240.0000.0000.0000.000
47B53ASP-1-0.811-0.90035.0198.3398.3390.0000.0000.0000.000
48B54LYS10.8500.91432.380-8.981-8.9810.0000.0000.0000.000
49B55ILE00.0100.01726.3630.1190.1190.0000.0000.0000.000
50B56MET0-0.0330.00126.207-0.174-0.1740.0000.0000.0000.000
51B57LEU00.0230.00120.5930.4440.4440.0000.0000.0000.000
52B58ASP-1-0.951-1.00018.84217.02217.0220.0000.0000.0000.000
53B59GLY00.0150.02021.166-0.092-0.0920.0000.0000.0000.000
54B60ARG10.8500.92524.421-12.696-12.6960.0000.0000.0000.000
55B61ALA00.0280.00526.2220.0460.0460.0000.0000.0000.000
56B62MET0-0.081-0.03024.9490.0720.0720.0000.0000.0000.000
57B63THR00.0440.02129.995-0.207-0.2070.0000.0000.0000.000
58B64ASP-1-0.778-0.90031.7879.8859.8850.0000.0000.0000.000
59B65SER0-0.082-0.03633.322-0.007-0.0070.0000.0000.0000.000
60B66ASP-1-0.874-0.94329.88110.04910.0490.0000.0000.0000.000
61B67TYR0-0.020-0.02427.6420.5770.5770.0000.0000.0000.000
62B68ARG10.8800.95528.646-10.181-10.1810.0000.0000.0000.000
63B69VAL00.0330.01127.4670.5250.5250.0000.0000.0000.000
64B70PHE0-0.015-0.00926.623-0.420-0.4200.0000.0000.0000.000
65B71GLU-1-0.854-0.93827.05610.49410.4940.0000.0000.0000.000
66B72PHE0-0.088-0.04722.1500.0700.0700.0000.0000.0000.000
67B73GLU-1-0.915-0.95727.6349.4079.4070.0000.0000.0000.000
68B82LEU00.000-0.00430.9880.0630.0630.0000.0000.0000.000
69B83SER0-0.013-0.00724.4720.1510.1510.0000.0000.0000.000
70B84ASP-1-0.844-0.92825.79811.16911.1690.0000.0000.0000.000
71B85ALA0-0.075-0.02621.9680.2550.2550.0000.0000.0000.000
72B86ALA00.0270.00923.915-0.380-0.3800.0000.0000.0000.000
73B87LEU0-0.032-0.03120.5340.8220.8220.0000.0000.0000.000
74B88MET00.0300.03422.825-0.679-0.6790.0000.0000.0000.000
75B89VAL0-0.017-0.02523.2950.7650.7650.0000.0000.0000.000
76B90LEU00.0210.00522.771-0.524-0.5240.0000.0000.0000.000
77B91HIS0-0.0100.02925.9390.3490.3490.0000.0000.0000.000
78B92ARG10.9640.97126.480-10.015-10.0150.0000.0000.0000.000
79B93GLY00.0370.01123.515-0.016-0.0160.0000.0000.0000.000
80B94ASN0-0.0020.01217.579-0.311-0.3110.0000.0000.0000.000
81B95LYS10.9590.98916.389-16.299-16.2990.0000.0000.0000.000
82B96VAL00.0200.03214.5360.8290.8290.0000.0000.0000.000
83B97ARG10.9050.9467.895-30.060-30.0600.0000.0000.0000.000
84B98ASP-1-0.833-0.90412.32719.03819.0380.0000.0000.0000.000
85B99ILE0-0.092-0.0579.1221.9271.9270.0000.0000.0000.000
86B100THR00.0700.01910.9000.6230.6230.0000.0000.0000.000
87B101LYS10.8990.9438.046-25.614-25.6140.0000.0000.0000.000
88B102HIS0-0.023-0.0095.601-0.023-0.0230.0000.0000.0000.000
89B103PHE00.0380.04410.0030.8180.8180.0000.0000.0000.000
90B104ARG10.9420.96410.182-22.245-22.2450.0000.0000.0000.000
91B105ASP-1-0.809-0.90815.80714.27014.2700.0000.0000.0000.000
92B106THR00.000-0.00918.627-0.666-0.6660.0000.0000.0000.000
93B107ALA0-0.0210.00316.6050.7570.7570.0000.0000.0000.000
94B108ARG10.9690.98718.164-13.447-13.4470.0000.0000.0000.000
95B109MET0-0.0050.02816.7060.8030.8030.0000.0000.0000.000
96B110LYS10.8890.93617.524-16.754-16.7540.0000.0000.0000.000
97B111LYS10.9250.94820.116-11.544-11.5440.0000.0000.0000.000
98B112GLY00.0100.00421.148-0.143-0.1430.0000.0000.0000.000
99B113THR0-0.067-0.02415.9590.7660.7660.0000.0000.0000.000
100B114PRO00.0540.01912.986-0.209-0.2090.0000.0000.0000.000
101B115VAL0-0.045-0.01313.6010.8050.8050.0000.0000.0000.000
102B116VAL0-0.037-0.0288.6960.4360.4360.0000.0000.0000.000
103B117GLY00.0330.01711.999-0.022-0.0220.0000.0000.0000.000
104B118VAL0-0.066-0.0368.7581.1911.1910.0000.0000.0000.000
105B119VAL00.018-0.00811.684-1.457-1.4570.0000.0000.0000.000
106B120ASN0-0.035-0.05013.9000.6570.6570.0000.0000.0000.000
107B121ASN00.0290.01416.033-0.633-0.6330.0000.0000.0000.000
108B122ALA00.0600.01819.8350.3150.3150.0000.0000.0000.000
109B123ASP-1-0.913-0.94422.57712.92312.9230.0000.0000.0000.000
110B124VAL0-0.058-0.03518.193-0.065-0.0650.0000.0000.0000.000
111B125GLY00.0350.03918.4320.6120.6120.0000.0000.0000.000
112B126ARG10.8570.9089.789-26.727-26.7270.0000.0000.0000.000
113B127LEU00.0190.01514.0980.0950.0950.0000.0000.0000.000
114B128ILE00.004-0.0018.4750.9910.9910.0000.0000.0000.000
115B129PHE0-0.0020.01912.228-1.009-1.0090.0000.0000.0000.000
116B130SER0-0.009-0.01013.6471.0941.0940.0000.0000.0000.000
117B131GLY00.0380.00515.195-1.264-1.2640.0000.0000.0000.000
118B132GLU-1-0.947-0.95516.76915.49815.4980.0000.0000.0000.000
119B133ALA0-0.0190.00718.614-0.765-0.7650.0000.0000.0000.000
120B134LEU00.0160.00220.219-0.432-0.4320.0000.0000.0000.000
121B135THR0-0.011-0.01723.168-0.721-0.7210.0000.0000.0000.000
122B136TYR00.0150.02522.9170.7810.7810.0000.0000.0000.000
123B137LYS10.8290.90420.981-13.122-13.1220.0000.0000.0000.000
124B138ASP-1-0.899-0.95621.82912.72412.7240.0000.0000.0000.000
125B139ILE0-0.040-0.00218.996-0.322-0.3220.0000.0000.0000.000
126B140VAL00.0550.02022.0790.1580.1580.0000.0000.0000.000
127B148MET00.0340.00926.5410.3500.3500.0000.0000.0000.000
128B149PRO00.0060.00922.290-0.170-0.1700.0000.0000.0000.000
129B150GLY00.0370.03124.523-0.016-0.0160.0000.0000.0000.000
130B151LEU00.0550.02423.7880.4610.4610.0000.0000.0000.000
131B152PHE0-0.004-0.01916.819-0.193-0.1930.0000.0000.0000.000
132B153ALA00.0310.02021.5220.2850.2850.0000.0000.0000.000
133B154TYR0-0.005-0.04219.0710.4640.4640.0000.0000.0000.000
134B155LYS10.9290.99821.348-13.168-13.1680.0000.0000.0000.000
135B156ALA00.052-0.00519.2770.7390.7390.0000.0000.0000.000
136B157ALA0-0.043-0.00120.914-0.695-0.6950.0000.0000.0000.000
137B158THR0-0.026-0.01019.6930.5910.5910.0000.0000.0000.000
138B159ARG10.9480.97421.880-14.233-14.2330.0000.0000.0000.000
139B160ALA00.0790.03322.9460.5180.5180.0000.0000.0000.000
140B161GLY00.0660.03623.1680.1760.1760.0000.0000.0000.000
141B162TYR0-0.041-0.02418.9940.6870.6870.0000.0000.0000.000
142B163ALA00.0170.02018.9920.8490.8490.0000.0000.0000.000
143B164GLY00.0470.01719.497-0.067-0.0670.0000.0000.0000.000
144B165GLY00.0170.02415.5850.8510.8510.0000.0000.0000.000
145B166ALA0-0.014-0.00311.796-0.685-0.6850.0000.0000.0000.000
146B167VAL00.0280.01113.2440.7570.7570.0000.0000.0000.000
147B168LEU0-0.056-0.0377.3300.7490.7490.0000.0000.0000.000
148B169ALA00.0390.02111.271-1.140-1.1400.0000.0000.0000.000
149B170LYS10.9080.9489.467-24.971-24.9710.0000.0000.0000.000
150B171ASP-1-0.872-0.94312.72215.89915.8990.0000.0000.0000.000
151B172GLY0-0.003-0.00214.213-0.086-0.0860.0000.0000.0000.000
152B173ALA00.0270.00112.2040.2760.2760.0000.0000.0000.000
153B174ASP-1-0.912-0.9429.38426.21726.2170.0000.0000.0000.000
154B175THR0-0.044-0.0246.665-2.395-2.3950.0000.0000.0000.000
155B176PHE0-0.051-0.0378.1701.5041.5040.0000.0000.0000.000
156B177ILE00.011-0.0079.5840.5190.5190.0000.0000.0000.000
157B178VAL0-0.010-0.01112.070-1.451-1.4510.0000.0000.0000.000
158B179GLY00.0480.01215.400-1.264-1.2640.0000.0000.0000.000
159B180THR0-0.0280.00215.9221.0071.0070.0000.0000.0000.000
160B181HIS00.0330.03217.708-0.416-0.4160.0000.0000.0000.000
161B182SER00.0150.00319.5060.0470.0470.0000.0000.0000.000
162B183ALA00.0540.03123.199-0.535-0.5350.0000.0000.0000.000
163B184GLY0-0.003-0.01024.0600.5660.5660.0000.0000.0000.000
164B185GLY00.0190.02525.493-0.302-0.3020.0000.0000.0000.000
165B186ASN00.0420.01728.2870.1440.1440.0000.0000.0000.000
166B187GLY0-0.049-0.01126.1510.0290.0290.0000.0000.0000.000
167B188VAL0-0.014-0.02124.7220.4840.4840.0000.0000.0000.000
168B189GLY0-0.0020.00522.067-0.265-0.2650.0000.0000.0000.000
169B190TYR00.024-0.00622.836-0.045-0.0450.0000.0000.0000.000
170B191CYS0-0.0130.01317.6380.0960.0960.0000.0000.0000.000
171B192SER00.0340.01721.067-0.655-0.6550.0000.0000.0000.000
172B193CYS0-0.062-0.02919.6270.6590.6590.0000.0000.0000.000
173B194VAL00.006-0.00418.188-0.714-0.7140.0000.0000.0000.000
174B195SER00.0330.00817.8130.7450.7450.0000.0000.0000.000
175B196ARG10.9740.98614.428-17.463-17.4630.0000.0000.0000.000
176B197SER0-0.003-0.01017.604-0.477-0.4770.0000.0000.0000.000
177B198MET0-0.061-0.01321.203-0.349-0.3490.0000.0000.0000.000
178B199LEU00.0470.02416.264-0.321-0.3210.0000.0000.0000.000
179B200GLN0-0.026-0.01517.8620.4830.4830.0000.0000.0000.000
180B201LYS10.9370.96820.779-12.165-12.1650.0000.0000.0000.000
181B202MET00.0200.02422.652-0.431-0.4310.0000.0000.0000.000
182B203LYS10.8860.94020.075-13.922-13.9220.0000.0000.0000.000
183B204ALA0-0.057-0.03022.505-0.154-0.1540.0000.0000.0000.000
184B205HIS00.0100.01325.382-0.307-0.3070.0000.0000.0000.000
185B206VAL0-0.0420.00124.573-0.182-0.1820.0000.0000.0000.000