Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 6NQJZ

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 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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2119964.952977
FMO2-HF: Nuclear repulsion 2045970.557548
FMO2-HF: Total energy -73994.395429
FMO2-MP2: Total energy -74213.144406


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.
-24.852-23.70817.887-9.819-9.214-0.058
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 : -0.069 / q_NPA : -0.030
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-1-0.802-0.8901.811-18.368-19.63516.154-8.527-6.361-0.055
4D6ASN0-0.116-0.0704.8400.9190.964-0.001-0.007-0.0370.000
5D7LYS10.8600.9466.1181.1981.1980.0000.0000.0000.000
6D8THR00.0340.0158.881-0.245-0.2450.0000.0000.0000.000
7D9TYR0-0.042-0.0247.4250.0560.0560.0000.0000.0000.000
8D10VAL00.0470.02912.863-0.010-0.0100.0000.0000.0000.000
9D11ILE0-0.048-0.03112.0860.0300.0300.0000.0000.0000.000
10D12MET0-0.014-0.00416.2550.0490.0490.0000.0000.0000.000
11D13GLY00.0550.02619.3980.0050.0050.0000.0000.0000.000
12D14ILE0-0.093-0.03716.7910.0130.0130.0000.0000.0000.000
13D15ALA0-0.047-0.02221.0230.0360.0360.0000.0000.0000.000
14D16ASN00.022-0.00523.4540.0080.0080.0000.0000.0000.000
15D17LYS11.0201.01021.0410.3380.3380.0000.0000.0000.000
16D18ARG10.9000.94920.5410.2860.2860.0000.0000.0000.000
17D19SER00.0450.04320.5870.0130.0130.0000.0000.0000.000
18D20ILE00.1030.04716.559-0.051-0.0510.0000.0000.0000.000
19D21ALA00.0710.04116.105-0.079-0.0790.0000.0000.0000.000
20D22PHE0-0.008-0.01215.282-0.093-0.0930.0000.0000.0000.000
21D23GLY0-0.041-0.01914.624-0.091-0.0910.0000.0000.0000.000
22D24VAL00.0170.00010.869-0.163-0.1630.0000.0000.0000.000
23D25ALA00.0250.01110.481-0.263-0.2630.0000.0000.0000.000
24D26LYS10.9460.97810.9270.5610.5610.0000.0000.0000.000
25D27VAL0-0.038-0.0076.419-0.120-0.1200.0000.0000.0000.000
26D28LEU00.0490.0156.128-0.695-0.6950.0000.0000.0000.000
27D29ASP-1-0.817-0.8777.217-2.063-2.0630.0000.0000.0000.000
28D30GLN0-0.044-0.0248.120-0.252-0.2520.0000.0000.0000.000
29D31LEU0-0.054-0.0242.217-1.816-0.5621.715-0.805-2.165-0.001
30D32GLY00.0080.0013.637-3.060-2.5270.010-0.373-0.170-0.002
31D33ALA00.0030.0205.9340.1100.1100.0000.0000.0000.000
32D34LYS10.8860.9507.7211.4231.4230.0000.0000.0000.000
33D35LEU0-0.055-0.03610.1670.1140.1140.0000.0000.0000.000
34D36VAL00.0330.02613.5250.1090.1090.0000.0000.0000.000
35D37PHE00.003-0.00214.892-0.006-0.0060.0000.0000.0000.000
36D38THR00.0640.02919.3190.0510.0510.0000.0000.0000.000
37D39TYR0-0.078-0.05522.340-0.016-0.0160.0000.0000.0000.000
38D40ARG10.9010.94025.0070.2630.2630.0000.0000.0000.000
39D41LYS10.9530.96528.2950.2300.2300.0000.0000.0000.000
40D42GLU-1-0.673-0.81029.745-0.314-0.3140.0000.0000.0000.000
41D43ARG10.8520.91430.9920.2070.2070.0000.0000.0000.000
42D44SER0-0.083-0.06726.846-0.003-0.0030.0000.0000.0000.000
43D45ARG10.9350.98926.3150.3660.3660.0000.0000.0000.000
44D46LYS10.9610.97126.3480.2660.2660.0000.0000.0000.000
45D47GLU-1-0.908-0.95824.653-0.412-0.4120.0000.0000.0000.000
46D48LEU00.0400.00220.219-0.024-0.0240.0000.0000.0000.000
47D49GLU-1-0.841-0.90121.972-0.443-0.4430.0000.0000.0000.000
48D50LYS10.8090.89623.1320.3680.3680.0000.0000.0000.000
49D51LEU0-0.053-0.02719.913-0.017-0.0170.0000.0000.0000.000
50D52LEU0-0.005-0.00817.731-0.050-0.0500.0000.0000.0000.000
51D53GLU-1-0.867-0.91118.561-0.476-0.4760.0000.0000.0000.000
52D54GLN0-0.111-0.06418.274-0.020-0.0200.0000.0000.0000.000
53D55LEU0-0.088-0.01613.638-0.033-0.0330.0000.0000.0000.000
54D56ASN0-0.048-0.02211.8430.2560.2560.0000.0000.0000.000
55D57GLN0-0.006-0.02411.186-0.048-0.0480.0000.0000.0000.000
56D58PRO0-0.031-0.00612.9580.1250.1250.0000.0000.0000.000
57D59GLU-1-0.840-0.91715.869-0.640-0.6400.0000.0000.0000.000
58D60ALA0-0.034-0.03117.663-0.071-0.0710.0000.0000.0000.000
59D61HIS00.0090.01217.2970.0920.0920.0000.0000.0000.000
60D62LEU0-0.066-0.03620.058-0.026-0.0260.0000.0000.0000.000
61D63TYR00.010-0.03721.3190.0180.0180.0000.0000.0000.000
62D64GLN0-0.110-0.05224.805-0.008-0.0080.0000.0000.0000.000
63D65ILE00.0390.01424.0030.0120.0120.0000.0000.0000.000
64D66ASP-1-0.837-0.91327.157-0.241-0.2410.0000.0000.0000.000
65D67VAL00.019-0.01125.0710.0140.0140.0000.0000.0000.000
66D68GLN0-0.103-0.02628.3860.0240.0240.0000.0000.0000.000
67D69SER0-0.066-0.04331.4490.0170.0170.0000.0000.0000.000
68D70ASP-1-0.832-0.92831.811-0.158-0.1580.0000.0000.0000.000
69D71GLU-1-0.952-0.97831.578-0.180-0.1800.0000.0000.0000.000
70D72GLU-1-0.803-0.88530.120-0.260-0.2600.0000.0000.0000.000
71D73VAL0-0.022-0.00325.978-0.023-0.0230.0000.0000.0000.000
72D74ILE00.0120.01427.348-0.017-0.0170.0000.0000.0000.000
73D75ASN0-0.043-0.03228.547-0.008-0.0080.0000.0000.0000.000
74D76GLY00.009-0.01026.607-0.014-0.0140.0000.0000.0000.000
75D77PHE00.002-0.01520.102-0.034-0.0340.0000.0000.0000.000
76D78GLU-1-0.765-0.85024.145-0.247-0.2470.0000.0000.0000.000
77D79GLN0-0.098-0.04225.8630.0160.0160.0000.0000.0000.000
78D80ILE00.0300.03019.825-0.024-0.0240.0000.0000.0000.000
79D81GLY00.0600.01721.609-0.032-0.0320.0000.0000.0000.000
80D82LYS10.7360.84922.5570.2280.2280.0000.0000.0000.000
81D83ASP-1-0.877-0.91422.875-0.389-0.3890.0000.0000.0000.000
82D84VAL0-0.119-0.05816.882-0.052-0.0520.0000.0000.0000.000
83D85GLY0-0.028-0.00718.257-0.038-0.0380.0000.0000.0000.000
84D86ASN0-0.040-0.03917.611-0.014-0.0140.0000.0000.0000.000
85D87ILE0-0.028-0.01215.135-0.101-0.1010.0000.0000.0000.000
86D88ASP-1-0.757-0.85710.998-0.748-0.7480.0000.0000.0000.000
87D89GLY00.044-0.01112.9030.1580.1580.0000.0000.0000.000
88D90VAL0-0.049-0.01713.919-0.116-0.1160.0000.0000.0000.000
89D91TYR00.014-0.00613.3020.0340.0340.0000.0000.0000.000
90D92HIS00.033-0.00915.374-0.031-0.0310.0000.0000.0000.000
91D93SER0-0.045-0.01718.2520.0400.0400.0000.0000.0000.000
92D94ILE0-0.003-0.00620.0360.0140.0140.0000.0000.0000.000
93D109THR00.010-0.00241.229-0.002-0.0020.0000.0000.0000.000
94D110SER0-0.038-0.04542.9020.0020.0020.0000.0000.0000.000
95D111ARG11.0011.00641.9820.0620.0620.0000.0000.0000.000
96D112GLU-1-0.829-0.91141.052-0.086-0.0860.0000.0000.0000.000
97D113GLY00.0140.00838.903-0.006-0.0060.0000.0000.0000.000
98D114PHE0-0.003-0.00537.220-0.007-0.0070.0000.0000.0000.000
99D115LEU00.011-0.01036.062-0.004-0.0040.0000.0000.0000.000
100D116LEU00.0580.05534.883-0.005-0.0050.0000.0000.0000.000
101D117ALA0-0.024-0.01332.958-0.010-0.0100.0000.0000.0000.000
102D118GLN0-0.035-0.02431.490-0.012-0.0120.0000.0000.0000.000
103D119ASP-1-0.877-0.93830.997-0.160-0.1600.0000.0000.0000.000
104D120ILE00.0390.01328.537-0.012-0.0120.0000.0000.0000.000
105D121SER0-0.068-0.01127.144-0.021-0.0210.0000.0000.0000.000
106D122SER0-0.028-0.01626.157-0.010-0.0100.0000.0000.0000.000
107D123TYR00.0170.00926.8980.0000.0000.0000.0000.0000.000
108D124SER00.030-0.02526.036-0.009-0.0090.0000.0000.0000.000
109D125LEU0-0.0230.00820.382-0.014-0.0140.0000.0000.0000.000
110D126THR00.0270.01424.092-0.005-0.0050.0000.0000.0000.000
111D127ILE0-0.0010.01625.9420.0010.0010.0000.0000.0000.000
112D128VAL00.0340.00721.228-0.008-0.0080.0000.0000.0000.000
113D129ALA0-0.023-0.00121.604-0.014-0.0140.0000.0000.0000.000
114D130HIS0-0.062-0.04022.6270.0160.0160.0000.0000.0000.000
115D131GLU-1-0.794-0.89425.222-0.176-0.1760.0000.0000.0000.000
116D132ALA00.0170.00419.640-0.010-0.0100.0000.0000.0000.000
117D133LYS10.8660.93821.0060.0410.0410.0000.0000.0000.000
118D134LYS10.7570.86722.1750.1900.1900.0000.0000.0000.000
119D135LEU0-0.065-0.01619.7840.0000.0000.0000.0000.0000.000
120D136MET0-0.0380.00416.776-0.039-0.0390.0000.0000.0000.000
121D137PRO00.0040.00019.1440.0530.0530.0000.0000.0000.000
122D138GLU-1-0.977-0.99017.135-0.054-0.0540.0000.0000.0000.000
123D139GLY00.0160.01316.6880.0830.0830.0000.0000.0000.000
124D140GLY00.008-0.01113.456-0.071-0.0710.0000.0000.0000.000
125D141SER0-0.125-0.06011.1790.0660.0660.0000.0000.0000.000
126D142ILE00.0430.01213.341-0.138-0.1380.0000.0000.0000.000
127D143VAL00.005-0.00611.9110.0450.0450.0000.0000.0000.000
128D144ALA0-0.0050.01915.326-0.054-0.0540.0000.0000.0000.000
129D145THR0-0.0170.00716.419-0.011-0.0110.0000.0000.0000.000
130D146THR0-0.030-0.01618.5900.0120.0120.0000.0000.0000.000
131D156ASN00.0070.00037.916-0.001-0.0010.0000.0000.0000.000
132D157TYR00.0270.00038.8580.0050.0050.0000.0000.0000.000
133D158ASN00.0260.00834.140-0.010-0.0100.0000.0000.0000.000
134D159VAL00.0750.04335.0930.0010.0010.0000.0000.0000.000
135D160MET00.0130.00231.109-0.003-0.0030.0000.0000.0000.000
136D161GLY00.0230.02030.882-0.006-0.0060.0000.0000.0000.000
137D162VAL0-0.013-0.00831.0330.0020.0020.0000.0000.0000.000
138D163ALA00.0020.00030.6870.0040.0040.0000.0000.0000.000
139D164LYS10.9000.95126.2210.1850.1850.0000.0000.0000.000
140D165ALA00.0260.02427.0780.0020.0020.0000.0000.0000.000
141D166SER0-0.019-0.00528.5390.0060.0060.0000.0000.0000.000
142D167LEU00.0250.01222.8600.0060.0060.0000.0000.0000.000
143D168GLU-1-0.842-0.92323.404-0.050-0.0500.0000.0000.0000.000
144D169ALA0-0.062-0.02924.4590.0140.0140.0000.0000.0000.000
145D170ASN00.018-0.00725.4080.0170.0170.0000.0000.0000.000
146D171VAL0-0.022-0.00319.8100.0070.0070.0000.0000.0000.000
147D172LYS10.9000.96322.4150.0300.0300.0000.0000.0000.000
148D173TYR0-0.001-0.01923.9590.0170.0170.0000.0000.0000.000
149D174LEU00.0230.03122.7290.0050.0050.0000.0000.0000.000
150D175ALA0-0.018-0.01020.2900.0080.0080.0000.0000.0000.000
151D176LEU0-0.096-0.04121.4020.0280.0280.0000.0000.0000.000
152D177ASP-1-0.962-1.00124.470-0.013-0.0130.0000.0000.0000.000
153D178LEU00.002-0.00221.261-0.002-0.0020.0000.0000.0000.000
154D179GLY00.0180.02620.7040.0160.0160.0000.0000.0000.000
155D180PRO0-0.058-0.04221.1890.0300.0300.0000.0000.0000.000
156D181ASP-1-0.873-0.91922.198-0.002-0.0020.0000.0000.0000.000
157D182ASN0-0.040-0.03015.6220.0260.0260.0000.0000.0000.000
158D183ILE00.0130.02716.935-0.007-0.0070.0000.0000.0000.000
159D184ARG10.8160.9339.800-0.400-0.4000.0000.0000.0000.000
160D185VAL00.0020.00915.955-0.077-0.0770.0000.0000.0000.000
161D186ASN00.0170.00513.9280.0750.0750.0000.0000.0000.000
162D187ALA0-0.017-0.01116.595-0.066-0.0660.0000.0000.0000.000
163D188ILE0-0.0080.00712.6500.0030.0030.0000.0000.0000.000
164D189SER0-0.033-0.02516.960-0.018-0.0180.0000.0000.0000.000
165D190ALA00.0140.00419.4890.0090.0090.0000.0000.0000.000
166D222ASP-1-0.785-0.90516.596-0.504-0.5040.0000.0000.0000.000
167D223GLN0-0.100-0.07516.385-0.029-0.0290.0000.0000.0000.000
168D224VAL0-0.007-0.00611.799-0.105-0.1050.0000.0000.0000.000
169D225GLU-1-0.842-0.90011.703-0.568-0.5680.0000.0000.0000.000
170D226VAL00.0270.01212.254-0.041-0.0410.0000.0000.0000.000
171D227GLY00.0650.02510.857-0.053-0.0530.0000.0000.0000.000
172D228LYS10.8620.9307.6190.3320.3320.0000.0000.0000.000
173D229THR0-0.0060.0047.460-0.180-0.1800.0000.0000.0000.000
174D230ALA0-0.009-0.0179.1870.1000.1000.0000.0000.0000.000
175D231ALA0-0.0010.0014.6450.0370.046-0.001-0.002-0.0060.000
176D232TYR0-0.007-0.0055.3720.1380.1380.0000.0000.0000.000
177D233LEU0-0.012-0.0036.2810.5470.5470.0000.0000.0000.000
178D234LEU0-0.0180.0077.9680.2330.2330.0000.0000.0000.000
179D235SER0-0.038-0.0084.0030.2460.3880.000-0.027-0.1150.000
180D236ASP-1-0.866-0.9505.8822.2302.2300.0000.0000.0000.000
181D237LEU0-0.005-0.0153.286-1.021-0.5930.010-0.078-0.3600.000
182D238SER0-0.072-0.0256.668-0.346-0.3460.0000.0000.0000.000
183D239SER00.0490.0239.625-0.368-0.3680.0000.0000.0000.000
184D240GLY0-0.029-0.00511.680-0.120-0.1200.0000.0000.0000.000
185D241VAL0-0.077-0.02813.144-0.090-0.0900.0000.0000.0000.000
186D242THR00.0520.01614.640-0.059-0.0590.0000.0000.0000.000
187D243GLY00.0220.00117.2950.0090.0090.0000.0000.0000.000
188D244GLU-1-0.937-0.95516.4070.1100.1100.0000.0000.0000.000
189D245ASN0-0.061-0.04917.759-0.078-0.0780.0000.0000.0000.000
190D246ILE00.0070.00512.9890.0280.0280.0000.0000.0000.000
191D247HIS00.0120.00717.021-0.070-0.0700.0000.0000.0000.000
192D248VAL0-0.0260.00014.2400.0110.0110.0000.0000.0000.000
193D249ASP-1-0.824-0.90417.342-0.133-0.1330.0000.0000.0000.000
194D250SER0-0.086-0.04119.5860.0170.0170.0000.0000.0000.000
195D251GLY0-0.079-0.04920.7450.0370.0370.0000.0000.0000.000