FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

tag_button

FMODB ID: 2J1ZR

Calculation Name: 4ALN-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ALN

Chain ID: D

ChEMBL ID:

UniProt ID: A0A0H3

Base Structure: X-ray

Registration Date: 2023-09-20

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 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 195
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2118346.606425
FMO2-HF: Nuclear repulsion 2044354.051345
FMO2-HF: Total energy -73992.55508
FMO2-MP2: Total energy -74211.427687


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(D:3:ASN)


Summations of interaction energy for fragment #1(D:3:ASN)
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.
-16.8-39.01549.318-16.356-10.746-0.069
Interaction energy analysis for fragmet #1(D:3:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.050 / q_NPA : -0.015
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].
3D5GLU-1-0.812-0.8981.733-11.192-35.16948.181-15.520-8.683-0.068
4D6ASN0-0.095-0.0604.8800.5130.560-0.001-0.004-0.0420.000
5D7LYS10.8970.9836.3752.6802.6800.0000.0000.0000.000
6D8THR00.014-0.0088.816-0.097-0.0970.0000.0000.0000.000
7D9TYR0-0.032-0.0156.939-0.095-0.0950.0000.0000.0000.000
8D10VAL00.0540.03012.4560.0550.0550.0000.0000.0000.000
9D11ILE0-0.058-0.03912.0250.0120.0120.0000.0000.0000.000
10D12MET00.0050.00216.3610.0770.0770.0000.0000.0000.000
11D13GLY00.0490.02519.6820.0010.0010.0000.0000.0000.000
12D14ILE0-0.076-0.03417.3810.0240.0240.0000.0000.0000.000
13D15ALA0-0.041-0.01921.4270.0380.0380.0000.0000.0000.000
14D16ASN00.0460.01523.8850.0080.0080.0000.0000.0000.000
15D17LYS11.0251.00521.5310.3270.3270.0000.0000.0000.000
16D18ARG10.8730.93421.0000.3210.3210.0000.0000.0000.000
17D19SER00.0520.03221.0080.0140.0140.0000.0000.0000.000
18D20ILE00.1000.04916.857-0.042-0.0420.0000.0000.0000.000
19D21ALA00.0780.04316.446-0.080-0.0800.0000.0000.0000.000
20D22PHE0-0.016-0.01115.675-0.097-0.0970.0000.0000.0000.000
21D23GLY0-0.033-0.01715.033-0.073-0.0730.0000.0000.0000.000
22D24VAL00.018-0.00811.267-0.135-0.1350.0000.0000.0000.000
23D25ALA00.0200.01010.900-0.283-0.2830.0000.0000.0000.000
24D26LYS10.9530.98211.2340.5060.5060.0000.0000.0000.000
25D27VAL0-0.038-0.0056.831-0.048-0.0480.0000.0000.0000.000
26D28LEU00.0450.0126.790-0.560-0.5600.0000.0000.0000.000
27D29ASP-1-0.857-0.9187.275-1.997-1.9970.0000.0000.0000.000
28D30GLN0-0.027-0.0158.214-0.280-0.2800.0000.0000.0000.000
29D31LEU0-0.065-0.0282.508-1.191-0.0381.134-0.581-1.7060.000
30D32GLY00.001-0.0043.643-2.911-2.5520.006-0.230-0.135-0.001
31D33ALA00.0000.0145.946-0.059-0.0590.0000.0000.0000.000
32D34LYS10.9300.9767.7371.8351.8350.0000.0000.0000.000
33D35LEU0-0.043-0.02410.5490.0530.0530.0000.0000.0000.000
34D36VAL00.0590.03713.3810.1460.1460.0000.0000.0000.000
35D37PHE0-0.023-0.01014.970-0.014-0.0140.0000.0000.0000.000
36D38THR00.0780.03219.1120.0510.0510.0000.0000.0000.000
37D39TYR0-0.067-0.01822.246-0.008-0.0080.0000.0000.0000.000
38D40ARG11.0191.01425.0860.3480.3480.0000.0000.0000.000
39D41LYS10.9290.94828.4710.2900.2900.0000.0000.0000.000
40D42GLU-1-0.700-0.85329.832-0.362-0.3620.0000.0000.0000.000
41D43ARG10.8500.91130.9480.2460.2460.0000.0000.0000.000
42D44SER0-0.079-0.04827.222-0.003-0.0030.0000.0000.0000.000
43D45ARG11.0171.03126.5070.4280.4280.0000.0000.0000.000
44D46LYS10.9710.97126.3430.2860.2860.0000.0000.0000.000
45D47GLU-1-0.937-0.97124.945-0.415-0.4150.0000.0000.0000.000
46D48LEU00.0430.00320.564-0.016-0.0160.0000.0000.0000.000
47D49GLU-1-0.910-0.94122.037-0.473-0.4730.0000.0000.0000.000
48D50LYS10.9050.94923.2920.3400.3400.0000.0000.0000.000
49D51LEU0-0.058-0.03220.284-0.007-0.0070.0000.0000.0000.000
50D52LEU0-0.003-0.00718.086-0.037-0.0370.0000.0000.0000.000
51D53GLU-1-0.954-0.95818.587-0.477-0.4770.0000.0000.0000.000
52D54GLN0-0.134-0.06918.532-0.006-0.0060.0000.0000.0000.000
53D55LEU0-0.081-0.02214.151-0.024-0.0240.0000.0000.0000.000
54D56ASN0-0.0150.00811.5910.2940.2940.0000.0000.0000.000
55D57GLN0-0.029-0.02811.383-0.104-0.1040.0000.0000.0000.000
56D58PRO0-0.024-0.00813.0230.1270.1270.0000.0000.0000.000
57D59GLU-1-0.924-0.96215.890-0.632-0.6320.0000.0000.0000.000
58D60ALA0-0.040-0.02417.686-0.082-0.0820.0000.0000.0000.000
59D61HIS00.0580.03917.0520.0990.0990.0000.0000.0000.000
60D62LEU0-0.066-0.03519.934-0.033-0.0330.0000.0000.0000.000
61D63TYR0-0.002-0.03820.9710.0200.0200.0000.0000.0000.000
62D64GLN0-0.050-0.02324.581-0.013-0.0130.0000.0000.0000.000
63D65ILE00.0520.02123.7730.0080.0080.0000.0000.0000.000
64D66ASP-1-0.943-0.97027.239-0.324-0.3240.0000.0000.0000.000
65D67VAL0-0.002-0.01825.3920.0130.0130.0000.0000.0000.000
66D68GLN0-0.098-0.03128.5920.0290.0290.0000.0000.0000.000
67D69SER0-0.052-0.06331.6310.0220.0220.0000.0000.0000.000
68D70ASP-1-0.860-0.89631.802-0.265-0.2650.0000.0000.0000.000
69D71GLU-1-0.961-0.98231.398-0.267-0.2670.0000.0000.0000.000
70D72GLU-1-0.860-0.93830.065-0.345-0.3450.0000.0000.0000.000
71D73VAL0-0.031-0.01125.924-0.030-0.0300.0000.0000.0000.000
72D74ILE00.0030.00926.992-0.026-0.0260.0000.0000.0000.000
73D75ASN00.0130.00228.098-0.013-0.0130.0000.0000.0000.000
74D76GLY0-0.010-0.01826.221-0.018-0.0180.0000.0000.0000.000
75D77PHE0-0.006-0.01920.001-0.045-0.0450.0000.0000.0000.000
76D78GLU-1-0.847-0.91723.733-0.360-0.3600.0000.0000.0000.000
77D79GLN0-0.085-0.02625.5570.0160.0160.0000.0000.0000.000
78D80ILE00.0130.03019.610-0.023-0.0230.0000.0000.0000.000
79D81GLY00.0490.01821.523-0.041-0.0410.0000.0000.0000.000
80D82LYS10.8270.91422.5970.3300.3300.0000.0000.0000.000
81D83ASP-1-0.872-0.92422.687-0.498-0.4980.0000.0000.0000.000
82D84VAL0-0.112-0.05216.907-0.048-0.0480.0000.0000.0000.000
83D85GLY0-0.050-0.02218.298-0.054-0.0540.0000.0000.0000.000
84D86ASN0-0.044-0.04817.626-0.002-0.0020.0000.0000.0000.000
85D87ILE0-0.0080.00114.814-0.104-0.1040.0000.0000.0000.000
86D88ASP-1-0.767-0.87410.895-1.584-1.5840.0000.0000.0000.000
87D89GLY00.024-0.09612.8260.0900.0900.0000.0000.0000.000
88D90VAL0-0.005-0.01613.892-0.075-0.0750.0000.0000.0000.000
89D91TYR00.014-0.00713.5570.0430.0430.0000.0000.0000.000
90D92HIS00.032-0.00715.5370.0000.0000.0000.0000.0000.000
91D93SER0-0.042-0.01318.5490.0500.0500.0000.0000.0000.000
92D94ILE0-0.003-0.01220.2400.0280.0280.0000.0000.0000.000
93D109THR00.0110.00541.363-0.002-0.0020.0000.0000.0000.000
94D110SER00.0090.00643.0600.0020.0020.0000.0000.0000.000
95D111ARG11.0241.00842.2520.1120.1120.0000.0000.0000.000
96D112GLU-1-0.882-0.95541.332-0.140-0.1400.0000.0000.0000.000
97D113GLY0-0.001-0.00239.065-0.009-0.0090.0000.0000.0000.000
98D114PHE0-0.007-0.00837.440-0.012-0.0120.0000.0000.0000.000
99D115LEU00.019-0.00736.364-0.009-0.0090.0000.0000.0000.000
100D116LEU00.0640.05735.085-0.009-0.0090.0000.0000.0000.000
101D117ALA0-0.029-0.01633.161-0.015-0.0150.0000.0000.0000.000
102D118GLN0-0.040-0.03431.747-0.022-0.0220.0000.0000.0000.000
103D119ASP-1-0.874-0.93231.332-0.261-0.2610.0000.0000.0000.000
104D120ILE00.0200.01028.580-0.019-0.0190.0000.0000.0000.000
105D121SER0-0.105-0.03527.374-0.029-0.0290.0000.0000.0000.000
106D122SER0-0.025-0.02226.476-0.024-0.0240.0000.0000.0000.000
107D123TYR00.0420.02027.310-0.011-0.0110.0000.0000.0000.000
108D124SER00.015-0.03226.299-0.017-0.0170.0000.0000.0000.000
109D125LEU0-0.0110.01121.107-0.024-0.0240.0000.0000.0000.000
110D126THR00.0530.03424.480-0.015-0.0150.0000.0000.0000.000
111D127ILE0-0.0100.00926.383-0.006-0.0060.0000.0000.0000.000
112D128VAL00.0370.01421.441-0.013-0.0130.0000.0000.0000.000
113D129ALA0-0.027-0.00521.997-0.028-0.0280.0000.0000.0000.000
114D130HIS0-0.060-0.03023.0500.0060.0060.0000.0000.0000.000
115D131GLU-1-0.871-0.95525.176-0.337-0.3370.0000.0000.0000.000
116D132ALA00.011-0.00619.535-0.013-0.0130.0000.0000.0000.000
117D133LYS10.9370.98120.7600.2450.2450.0000.0000.0000.000
118D134LYS10.8420.92422.2020.3330.3330.0000.0000.0000.000
119D135LEU0-0.080-0.02619.4480.0100.0100.0000.0000.0000.000
120D136MET0-0.0530.08615.478-0.067-0.0670.0000.0000.0000.000
121D137PRO00.0050.00518.9400.0570.0570.0000.0000.0000.000
122D138GLU-1-0.979-0.99217.087-0.347-0.3470.0000.0000.0000.000
123D139GLY00.0220.01216.8450.0390.0390.0000.0000.0000.000
124D140GLY00.001-0.01213.820-0.105-0.1050.0000.0000.0000.000
125D141SER0-0.119-0.05511.9560.1480.1480.0000.0000.0000.000
126D142ILE00.0410.01313.968-0.117-0.1170.0000.0000.0000.000
127D143VAL00.002-0.00912.4540.0500.0500.0000.0000.0000.000
128D144ALA0-0.0020.01715.764-0.023-0.0230.0000.0000.0000.000
129D145THR0-0.0140.01416.569-0.012-0.0120.0000.0000.0000.000
130D146THR0-0.036-0.00918.8310.0320.0320.0000.0000.0000.000
131D156ASN0-0.021-0.03238.231-0.005-0.0050.0000.0000.0000.000
132D157TYR00.0580.03139.6400.0030.0030.0000.0000.0000.000
133D158ASN00.0230.01134.321-0.009-0.0090.0000.0000.0000.000
134D159VAL00.0760.04535.430-0.003-0.0030.0000.0000.0000.000
135D160MET00.0230.00131.308-0.007-0.0070.0000.0000.0000.000
136D161GLY00.0140.01631.207-0.012-0.0120.0000.0000.0000.000
137D162VAL0-0.015-0.01031.472-0.004-0.0040.0000.0000.0000.000
138D163ALA00.003-0.00330.954-0.001-0.0010.0000.0000.0000.000
139D164LYS10.9210.96426.4300.2830.2830.0000.0000.0000.000
140D165ALA00.0510.03427.589-0.007-0.0070.0000.0000.0000.000
141D166SER0-0.0240.00029.139-0.004-0.0040.0000.0000.0000.000
142D167LEU00.0220.01323.0710.0000.0000.0000.0000.0000.000
143D168GLU-1-0.917-0.96024.284-0.224-0.2240.0000.0000.0000.000
144D169ALA0-0.060-0.02925.1580.0030.0030.0000.0000.0000.000
145D170ASN00.017-0.01125.8630.0110.0110.0000.0000.0000.000
146D171VAL0-0.027-0.00720.332-0.002-0.0020.0000.0000.0000.000
147D172LYS10.9520.98623.1770.1640.1640.0000.0000.0000.000
148D173TYR0-0.006-0.02424.7260.0140.0140.0000.0000.0000.000
149D174LEU00.0220.03223.5150.0050.0050.0000.0000.0000.000
150D175ALA0-0.021-0.01421.022-0.003-0.0030.0000.0000.0000.000
151D176LEU0-0.105-0.04922.2130.0190.0190.0000.0000.0000.000
152D177ASP-1-0.955-0.99625.208-0.193-0.1930.0000.0000.0000.000
153D178LEU0-0.004-0.00221.651-0.001-0.0010.0000.0000.0000.000
154D179GLY00.0170.02421.404-0.009-0.0090.0000.0000.0000.000
155D180PRO0-0.061-0.04121.8600.0100.0100.0000.0000.0000.000
156D181ASP-1-0.923-0.94423.014-0.223-0.2230.0000.0000.0000.000
157D182ASN0-0.048-0.03116.294-0.005-0.0050.0000.0000.0000.000
158D183ILE0-0.0060.01817.698-0.071-0.0710.0000.0000.0000.000
159D184ARG10.8260.94110.5930.5260.5260.0000.0000.0000.000
160D185VAL00.0130.02216.676-0.091-0.0910.0000.0000.0000.000
161D186ASN00.0360.01414.9210.1310.1310.0000.0000.0000.000
162D187ALA0-0.021-0.01217.287-0.062-0.0620.0000.0000.0000.000
163D188ILE0-0.0160.00612.931-0.007-0.0070.0000.0000.0000.000
164D189SER00.005-0.02217.396-0.001-0.0010.0000.0000.0000.000
165D190ALA00.0030.00519.6750.0180.0180.0000.0000.0000.000
166D222ASP-1-0.803-0.92016.995-0.459-0.4590.0000.0000.0000.000
167D223GLN0-0.075-0.05016.609-0.046-0.0460.0000.0000.0000.000
168D224VAL0-0.0030.00511.918-0.121-0.1210.0000.0000.0000.000
169D225GLU-1-0.946-0.96911.947-0.523-0.5230.0000.0000.0000.000
170D226VAL00.0230.01512.343-0.084-0.0840.0000.0000.0000.000
171D227GLY00.0590.02311.109-0.117-0.1170.0000.0000.0000.000
172D228LYS10.9630.9867.7850.2420.2420.0000.0000.0000.000
173D229THR00.0120.0187.663-0.316-0.3160.0000.0000.0000.000
174D230ALA0-0.013-0.0199.6820.0110.0110.0000.0000.0000.000
175D231ALA0-0.002-0.0034.872-0.072-0.0720.0000.0000.0000.000
176D232TYR0-0.0020.0086.012-0.077-0.0770.0000.0000.0000.000
177D233LEU0-0.0230.0206.9570.3470.3470.0000.0000.0000.000
178D234LEU0-0.0160.0058.2570.2060.2060.0000.0000.0000.000
179D235SER0-0.044-0.0244.7160.0860.104-0.001-0.007-0.0100.000
180D236ASP-1-0.896-0.9676.6981.2571.2570.0000.0000.0000.000
181D237LEU00.017-0.0064.009-0.0460.139-0.001-0.014-0.1700.000
182D238SER0-0.062-0.0446.7960.1000.1000.0000.0000.0000.000
183D239SER00.0120.00310.013-0.135-0.1350.0000.0000.0000.000
184D240GLY0-0.0100.00112.014-0.025-0.0250.0000.0000.0000.000
185D241VAL0-0.088-0.03313.401-0.009-0.0090.0000.0000.0000.000
186D242THR00.0510.00615.243-0.112-0.1120.0000.0000.0000.000
187D243GLY00.0180.00117.9220.0420.0420.0000.0000.0000.000
188D244GLU-1-0.977-0.97216.982-0.087-0.0870.0000.0000.0000.000
189D245ASN0-0.015-0.02618.456-0.095-0.0950.0000.0000.0000.000
190D246ILE00.0180.01013.4790.0390.0390.0000.0000.0000.000
191D247HIS0-0.006-0.00317.541-0.057-0.0570.0000.0000.0000.000
192D248VAL0-0.037-0.00914.6010.0100.0100.0000.0000.0000.000
193D249ASP-1-0.862-0.95117.647-0.224-0.2240.0000.0000.0000.000
194D250SER0-0.080-0.03819.7960.0310.0310.0000.0000.0000.000
195D251GLY0-0.0390.00421.1440.0430.0430.0000.0000.0000.000