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: 2JM4R

Calculation Name: 4X0R-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4X0R

Chain ID: B

ChEMBL ID:

UniProt ID: P20592

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 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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2540262.632938
FMO2-HF: Nuclear repulsion 2449785.324759
FMO2-HF: Total energy -90477.308178
FMO2-MP2: Total energy -90739.767794


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:3:GLU)


Summations of interaction energy for fragment #1(B:3:GLU)
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.
-63.197-57.3955.517-4.622-6.696-0.009
Interaction energy analysis for fragmet #1(B:3:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.906 / q_NPA : -0.957
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].
3B5ASP-1-0.844-0.9132.37229.87632.6583.983-2.758-4.005-0.025
4B6LYS10.9240.9752.347-66.529-63.6521.535-1.851-2.5620.016
5B7MET00.012-0.0164.862-3.122-2.979-0.001-0.013-0.1290.000
6B8PHE00.0480.0166.958-3.148-3.1480.0000.0000.0000.000
7B9PHE0-0.022-0.0028.807-1.422-1.4220.0000.0000.0000.000
8B10LEU00.009-0.00310.393-2.006-2.0060.0000.0000.0000.000
9B11ILE0-0.017-0.00411.135-1.576-1.5760.0000.0000.0000.000
10B12GLU-1-0.901-0.95913.03618.48518.4850.0000.0000.0000.000
11B13LYS10.9100.97214.826-17.929-17.9290.0000.0000.0000.000
12B14ILE00.0210.02416.871-1.040-1.0400.0000.0000.0000.000
13B15LYS10.9780.99417.185-16.922-16.9220.0000.0000.0000.000
14B16MET0-0.005-0.00118.340-0.795-0.7950.0000.0000.0000.000
15B17PHE0-0.005-0.00820.697-0.784-0.7840.0000.0000.0000.000
16B18ASN00.008-0.02022.219-0.827-0.8270.0000.0000.0000.000
17B19GLN0-0.0060.00522.607-0.560-0.5600.0000.0000.0000.000
18B20ASP-1-0.831-0.91824.95211.72711.7270.0000.0000.0000.000
19B21ILE0-0.057-0.02326.680-0.533-0.5330.0000.0000.0000.000
20B22GLU-1-0.754-0.86628.0059.6769.6760.0000.0000.0000.000
21B23LYS10.9730.99327.426-11.579-11.5790.0000.0000.0000.000
22B24LEU0-0.064-0.03531.240-0.416-0.4160.0000.0000.0000.000
23B25VAL0-0.064-0.01732.732-0.395-0.3950.0000.0000.0000.000
24B26GLU-1-0.900-0.95632.3359.4659.4650.0000.0000.0000.000
25B27GLY0-0.042-0.00935.510-0.190-0.1900.0000.0000.0000.000
26B28GLU-1-0.994-1.00232.9899.2379.2370.0000.0000.0000.000
27B29GLU-1-0.805-0.90432.1479.2099.2090.0000.0000.0000.000
28B30VAL0-0.071-0.05229.537-0.141-0.1410.0000.0000.0000.000
29B31VAL0-0.0160.00532.4860.1260.1260.0000.0000.0000.000
30B32ARG10.8490.88534.750-8.431-8.4310.0000.0000.0000.000
31B33GLU-1-0.883-0.93936.4797.8267.8260.0000.0000.0000.000
32B34ASN0-0.051-0.02739.585-0.255-0.2550.0000.0000.0000.000
33B35GLU-1-0.862-0.90735.0538.9378.9370.0000.0000.0000.000
34B36THR00.0110.00939.819-0.014-0.0140.0000.0000.0000.000
35B37ARG10.9050.95435.874-8.517-8.5170.0000.0000.0000.000
36B38LEU0-0.0070.00136.033-0.241-0.2410.0000.0000.0000.000
37B39TYR00.003-0.02038.256-0.336-0.3360.0000.0000.0000.000
38B40ASN0-0.022-0.01441.073-0.180-0.1800.0000.0000.0000.000
39B41LYS10.9280.97738.775-8.189-8.1890.0000.0000.0000.000
40B42ILE00.0420.02340.343-0.147-0.1470.0000.0000.0000.000
41B43ARG10.9390.97343.923-7.336-7.3360.0000.0000.0000.000
42B44GLU-1-0.927-0.96346.8576.1726.1720.0000.0000.0000.000
43B45ASP-1-0.882-0.94447.2146.4156.4150.0000.0000.0000.000
44B46PHE00.0370.00444.856-0.136-0.1360.0000.0000.0000.000
45B47LYS10.9100.95849.937-6.145-6.1450.0000.0000.0000.000
46B48ASN0-0.029-0.01052.270-0.171-0.1710.0000.0000.0000.000
47B49TRP00.0550.01752.331-0.151-0.1510.0000.0000.0000.000
48B50VAL00.006-0.00153.688-0.130-0.1300.0000.0000.0000.000
49B51GLY0-0.0060.00356.102-0.126-0.1260.0000.0000.0000.000
50B52ILE0-0.002-0.00756.209-0.145-0.1450.0000.0000.0000.000
51B53LEU00.0070.01056.600-0.126-0.1260.0000.0000.0000.000
52B54ALA0-0.0030.00259.795-0.117-0.1170.0000.0000.0000.000
53B55THR0-0.020-0.00362.164-0.142-0.1420.0000.0000.0000.000
54B56ASN0-0.010-0.02061.667-0.121-0.1210.0000.0000.0000.000
55B57THR00.0420.05062.719-0.077-0.0770.0000.0000.0000.000
56B58GLN0-0.0140.00965.439-0.029-0.0290.0000.0000.0000.000
57B59LYS10.9200.96367.124-4.821-4.8210.0000.0000.0000.000
58B60VAL00.0340.00767.428-0.074-0.0740.0000.0000.0000.000
59B61LYS10.9240.98668.465-4.671-4.6710.0000.0000.0000.000
60B62ASN00.0350.00471.239-0.075-0.0750.0000.0000.0000.000
61B63ILE0-0.0130.01172.304-0.058-0.0580.0000.0000.0000.000
62B64ILE00.000-0.01372.506-0.059-0.0590.0000.0000.0000.000
63B65HIS0-0.0050.00475.175-0.003-0.0030.0000.0000.0000.000
64B66GLU-1-0.901-0.95477.1853.9813.9810.0000.0000.0000.000
65B67GLU-1-0.953-0.97977.1673.9953.9950.0000.0000.0000.000
66B68VAL0-0.014-0.01277.896-0.055-0.0550.0000.0000.0000.000
67B69GLU-1-0.850-0.92580.6703.8383.8380.0000.0000.0000.000
68B70LYS10.8310.93581.217-4.010-4.0100.0000.0000.0000.000
69B71TYR0-0.037-0.04280.835-0.065-0.0650.0000.0000.0000.000
70B72GLU-1-0.935-0.96983.1313.8293.8290.0000.0000.0000.000
71B73LYS10.9490.96486.175-3.779-3.7790.0000.0000.0000.000
72B74GLN0-0.093-0.03687.294-0.024-0.0240.0000.0000.0000.000
73B75ALA0-0.062-0.02488.798-0.041-0.0410.0000.0000.0000.000
74B76ALA0-0.0240.00690.614-0.038-0.0380.0000.0000.0000.000
75B87LYS10.9630.96774.332-4.296-4.2960.0000.0000.0000.000
76B88THR0-0.0020.00175.0230.0620.0620.0000.0000.0000.000
77B89PHE00.0580.02374.0640.0370.0370.0000.0000.0000.000
78B90GLU-1-0.880-0.94471.1484.4744.4740.0000.0000.0000.000
79B91ILE0-0.022-0.00270.1650.0750.0750.0000.0000.0000.000
80B92ILE00.0300.01670.0710.0690.0690.0000.0000.0000.000
81B93VAL0-0.0100.00266.6820.0690.0690.0000.0000.0000.000
82B94HIS00.0330.01764.9260.0610.0610.0000.0000.0000.000
83B95GLN00.016-0.01165.0500.0530.0530.0000.0000.0000.000
84B96TYR0-0.088-0.08663.1970.0900.0900.0000.0000.0000.000
85B97ILE00.0070.01260.4720.0810.0810.0000.0000.0000.000
86B98GLN00.013-0.00959.8900.1020.1020.0000.0000.0000.000
87B99GLN0-0.072-0.02960.5340.0640.0640.0000.0000.0000.000
88B100LEU0-0.046-0.02458.0280.0450.0450.0000.0000.0000.000
89B101VAL00.0120.01054.9480.1060.1060.0000.0000.0000.000
90B102GLU-1-0.870-0.93154.7185.8485.8480.0000.0000.0000.000
91B103PRO0-0.044-0.02154.2290.1150.1150.0000.0000.0000.000
92B104ALA0-0.021-0.00352.6140.1180.1180.0000.0000.0000.000
93B105LEU00.0310.00649.8890.1580.1580.0000.0000.0000.000
94B106SER0-0.0170.00549.4130.1750.1750.0000.0000.0000.000
95B107MET00.0010.01648.3740.1190.1190.0000.0000.0000.000
96B108LEU0-0.014-0.01043.8960.1710.1710.0000.0000.0000.000
97B109GLN00.0270.01444.8310.2100.2100.0000.0000.0000.000
98B110LYS10.9570.98344.708-6.541-6.5410.0000.0000.0000.000
99B111ALA00.014-0.01143.0440.1630.1630.0000.0000.0000.000
100B112MET00.0050.00740.0110.2630.2630.0000.0000.0000.000
101B113GLU-1-0.955-0.97039.5827.2497.2490.0000.0000.0000.000
102B114ILE0-0.057-0.02639.4880.2180.2180.0000.0000.0000.000
103B115ILE0-0.017-0.01335.9180.2310.2310.0000.0000.0000.000
104B116GLN0-0.0010.01535.4050.1470.1470.0000.0000.0000.000
105B117GLN0-0.017-0.00634.4100.1400.1400.0000.0000.0000.000
106B118ALA0-0.032-0.01734.0130.2690.2690.0000.0000.0000.000
107B119PHE00.0530.00430.9360.3560.3560.0000.0000.0000.000
108B120ILE0-0.0190.00229.6260.4280.4280.0000.0000.0000.000
109B121ASN0-0.022-0.02629.4370.3730.3730.0000.0000.0000.000
110B122VAL00.0120.01926.0740.2770.2770.0000.0000.0000.000
111B123ALA00.0380.01925.1790.5330.5330.0000.0000.0000.000
112B124LYS10.9100.95924.660-9.457-9.4570.0000.0000.0000.000
113B125LYS10.9040.97324.433-11.940-11.9400.0000.0000.0000.000
114B126HIS0-0.127-0.06821.1280.9270.9270.0000.0000.0000.000
115B127PHE0-0.001-0.03219.0130.9290.9290.0000.0000.0000.000
116B128GLY00.0000.01521.596-0.036-0.0360.0000.0000.0000.000
117B129GLU-1-0.924-0.96119.06513.79513.7950.0000.0000.0000.000
118B130PHE0-0.051-0.01115.0550.2680.2680.0000.0000.0000.000
119B131PHE00.0560.01519.940-0.281-0.2810.0000.0000.0000.000
120B132ASN0-0.029-0.02619.601-0.857-0.8570.0000.0000.0000.000
121B133LEU00.0200.01417.452-0.313-0.3130.0000.0000.0000.000
122B134ASN00.0400.00820.933-0.420-0.4200.0000.0000.0000.000
123B135GLN00.0070.00724.019-0.294-0.2940.0000.0000.0000.000
124B136THR0-0.037-0.01522.682-0.287-0.2870.0000.0000.0000.000
125B137VAL00.0570.04822.617-0.345-0.3450.0000.0000.0000.000
126B138GLN00.019-0.01125.327-0.203-0.2030.0000.0000.0000.000
127B139SER0-0.080-0.04227.583-0.339-0.3390.0000.0000.0000.000
128B140THR00.019-0.00526.402-0.264-0.2640.0000.0000.0000.000
129B141ILE0-0.017-0.01228.167-0.256-0.2560.0000.0000.0000.000
130B142GLU-1-0.892-0.94930.7758.0738.0730.0000.0000.0000.000
131B143ASP-1-0.902-0.95331.6918.7938.7930.0000.0000.0000.000
132B144ILE0-0.018-0.01429.371-0.274-0.2740.0000.0000.0000.000
133B145LYS10.9370.99133.647-8.220-8.2200.0000.0000.0000.000
134B146VAL00.0010.00036.309-0.275-0.2750.0000.0000.0000.000
135B147LYS10.9040.95833.221-9.052-9.0520.0000.0000.0000.000
136B148HIS0-0.036-0.01535.317-0.042-0.0420.0000.0000.0000.000
137B149THR00.0490.00239.012-0.152-0.1520.0000.0000.0000.000
138B150ALA0-0.0010.01541.607-0.196-0.1960.0000.0000.0000.000
139B151LYS10.8520.93338.027-8.165-8.1650.0000.0000.0000.000
140B152ALA00.0190.01643.085-0.154-0.1540.0000.0000.0000.000
141B153GLU-1-0.884-0.93944.7796.2556.2550.0000.0000.0000.000
142B154ASN0-0.038-0.02945.939-0.258-0.2580.0000.0000.0000.000
143B155MET0-0.011-0.01246.453-0.157-0.1570.0000.0000.0000.000
144B156ILE00.0160.02248.190-0.143-0.1430.0000.0000.0000.000
145B157GLN00.0330.01250.932-0.235-0.2350.0000.0000.0000.000
146B158LEU0-0.085-0.03851.052-0.145-0.1450.0000.0000.0000.000
147B159GLN0-0.0050.00052.544-0.016-0.0160.0000.0000.0000.000
148B160PHE00.0560.01454.176-0.117-0.1170.0000.0000.0000.000
149B161ARG10.9320.97852.866-5.866-5.8660.0000.0000.0000.000
150B162MET0-0.004-0.01553.719-0.098-0.0980.0000.0000.0000.000
151B163GLU-1-0.774-0.87658.0575.3575.3570.0000.0000.0000.000
152B164GLN0-0.033-0.00560.259-0.167-0.1670.0000.0000.0000.000
153B165MET0-0.103-0.06761.154-0.126-0.1260.0000.0000.0000.000
154B166VAL0-0.020-0.01560.633-0.073-0.0730.0000.0000.0000.000
155B167PHE0-0.0250.01463.575-0.072-0.0720.0000.0000.0000.000
156B168LYS10.9390.98065.905-4.800-4.8000.0000.0000.0000.000
157B180SER00.0140.00482.1330.0200.0200.0000.0000.0000.000
158B181VAL0-0.037-0.02683.290-0.034-0.0340.0000.0000.0000.000
159B182SER0-0.0100.00080.7830.0550.0550.0000.0000.0000.000
160B183SER00.0450.01481.485-0.040-0.0400.0000.0000.0000.000
161B184PHE00.0540.02180.9490.0500.0500.0000.0000.0000.000
162B185THR00.0570.03780.1300.0630.0630.0000.0000.0000.000
163B186GLU-1-0.914-0.96877.4634.1524.1520.0000.0000.0000.000
164B187ILE0-0.023-0.00875.9050.0700.0700.0000.0000.0000.000
165B188GLY00.0420.01875.2340.0670.0670.0000.0000.0000.000
166B189ILE0-0.0100.00074.4970.0770.0770.0000.0000.0000.000
167B190HIS00.0220.01172.3920.1150.1150.0000.0000.0000.000
168B191LEU00.0000.00570.7550.0940.0940.0000.0000.0000.000
169B192ASN00.005-0.00969.7790.1060.1060.0000.0000.0000.000
170B193ALA0-0.024-0.00468.8530.0810.0810.0000.0000.0000.000
171B194TYR00.0710.02664.3600.1120.1120.0000.0000.0000.000
172B195PHE00.0280.00365.0680.1000.1000.0000.0000.0000.000
173B196LEU0-0.053-0.01264.2690.1000.1000.0000.0000.0000.000
174B197GLU-1-0.967-0.98762.4205.0885.0880.0000.0000.0000.000
175B198THR00.012-0.00260.5290.1320.1320.0000.0000.0000.000
176B199SER0-0.052-0.01759.5030.1210.1210.0000.0000.0000.000
177B200LYS10.9550.96258.468-5.083-5.0830.0000.0000.0000.000
178B201ARG10.8480.92555.784-5.266-5.2660.0000.0000.0000.000
179B202LEU00.0410.00754.8230.1460.1460.0000.0000.0000.000
180B203ALA0-0.022-0.00953.9460.1190.1190.0000.0000.0000.000
181B204ASN0-0.032-0.00751.1140.1580.1580.0000.0000.0000.000
182B205GLN00.0010.01050.0340.1390.1390.0000.0000.0000.000
183B206ILE00.004-0.01049.7370.1170.1170.0000.0000.0000.000
184B207PRO00.0470.01447.5940.1430.1430.0000.0000.0000.000
185B208PHE00.0010.00645.8130.1830.1830.0000.0000.0000.000
186B209ILE0-0.0090.01244.5560.2060.2060.0000.0000.0000.000
187B210ILE00.0300.02043.5890.1960.1960.0000.0000.0000.000
188B211GLN0-0.034-0.02141.4450.0310.0310.0000.0000.0000.000
189B212TYR0-0.030-0.01139.9420.2500.2500.0000.0000.0000.000
190B213PHE00.015-0.01139.1220.2040.2040.0000.0000.0000.000
191B214MET00.0020.01138.5060.1880.1880.0000.0000.0000.000
192B215LEU0-0.023-0.01736.2560.1830.1830.0000.0000.0000.000
193B216ARG10.8610.92332.584-8.985-8.9850.0000.0000.0000.000
194B217GLU-1-0.857-0.93934.3408.3058.3050.0000.0000.0000.000
195B218ASN0-0.050-0.01133.9630.3900.3900.0000.0000.0000.000
196B219GLY00.0530.01531.2350.2780.2780.0000.0000.0000.000
197B220ASP-1-0.854-0.92629.67210.02510.0250.0000.0000.0000.000
198B221SER0-0.071-0.05129.1930.3970.3970.0000.0000.0000.000
199B222LEU0-0.0030.00027.0590.3310.3310.0000.0000.0000.000
200B223GLN0-0.008-0.01325.2480.8950.8950.0000.0000.0000.000
201B224LYS10.9530.96424.257-9.846-9.8460.0000.0000.0000.000
202B225ALA0-0.011-0.00124.3960.3790.3790.0000.0000.0000.000
203B226MET0-0.027-0.00721.0600.3410.3410.0000.0000.0000.000
204B227MET0-0.010-0.01018.9530.8870.8870.0000.0000.0000.000
205B228GLN0-0.052-0.03019.6450.6590.6590.0000.0000.0000.000
206B229ILE00.0420.02617.3910.2110.2110.0000.0000.0000.000
207B230LEU0-0.033-0.00514.5450.6510.6510.0000.0000.0000.000
208B231GLN0-0.0290.04014.8281.3681.3680.0000.0000.0000.000
209B232GLU-1-0.892-0.94915.83414.31414.3140.0000.0000.0000.000
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211B234ASN0-0.038-0.00912.2970.6670.6670.0000.0000.0000.000
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