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: 72R8K

Calculation Name: 4ALN-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ALN

Chain ID: F

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 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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2357358.666414
FMO2-HF: Nuclear repulsion 2278381.273018
FMO2-HF: Total energy -78977.393396
FMO2-MP2: Total energy -79211.104833


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(F:3:ASN)


Summations of interaction energy for fragment #1(F: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.
-28.381-23.73815.586-9.863-10.362-0.065
Interaction energy analysis for fragmet #1(F:3:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.044 / q_NPA : -0.024
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].
3F5GLU-1-0.814-0.8981.846-17.029-17.61612.482-6.712-5.182-0.048
4F6ASN0-0.107-0.0615.0601.2071.271-0.001-0.004-0.0590.000
5F7LYS10.8680.9446.4032.2282.2280.0000.0000.0000.000
6F8THR0-0.017-0.0109.121-0.103-0.1030.0000.0000.0000.000
7F9TYR0-0.017-0.0146.568-0.079-0.0790.0000.0000.0000.000
8F10VAL00.0240.01511.8540.0490.0490.0000.0000.0000.000
9F11ILE0-0.045-0.01811.528-0.019-0.0190.0000.0000.0000.000
10F12MET00.0120.01115.4560.0900.0900.0000.0000.0000.000
11F13GLY00.0620.02518.379-0.008-0.0080.0000.0000.0000.000
12F14ILE0-0.097-0.04316.1700.0310.0310.0000.0000.0000.000
13F15ALA0-0.022-0.01520.3930.0350.0350.0000.0000.0000.000
14F16ASN0-0.027-0.03322.7420.0310.0310.0000.0000.0000.000
15F17LYS10.8880.92320.9560.3870.3870.0000.0000.0000.000
16F18ARG10.9230.96820.7220.3040.3040.0000.0000.0000.000
17F19SER00.0350.03320.1800.0220.0220.0000.0000.0000.000
18F20ILE00.0890.03216.011-0.055-0.0550.0000.0000.0000.000
19F21ALA00.0550.03315.237-0.086-0.0860.0000.0000.0000.000
20F22PHE00.0160.00114.617-0.123-0.1230.0000.0000.0000.000
21F23GLY0-0.044-0.02014.173-0.067-0.0670.0000.0000.0000.000
22F24VAL00.0360.01210.007-0.146-0.1460.0000.0000.0000.000
23F25ALA00.0020.0039.838-0.358-0.3580.0000.0000.0000.000
24F26LYS10.9170.96910.7160.5570.5570.0000.0000.0000.000
25F27VAL0-0.0050.0046.239-0.067-0.0670.0000.0000.0000.000
26F28LEU00.0270.0075.440-0.768-0.7680.0000.0000.0000.000
27F29ASP-1-0.798-0.8716.628-2.573-2.5730.0000.0000.0000.000
28F30GLN0-0.058-0.0247.378-0.257-0.2570.0000.0000.0000.000
29F31LEU0-0.032-0.0162.275-0.9500.3542.360-1.027-2.6370.001
30F32GLY00.0300.0112.604-7.647-5.4010.589-1.624-1.211-0.019
31F33ALA0-0.0010.0185.0680.5270.562-0.001-0.003-0.0310.000
32F34LYS10.9220.9767.4931.9211.9210.0000.0000.0000.000
33F35LEU0-0.049-0.0329.549-0.002-0.0020.0000.0000.0000.000
34F36VAL00.0210.01113.2970.1890.1890.0000.0000.0000.000
35F37PHE0-0.008-0.00914.569-0.024-0.0240.0000.0000.0000.000
36F38THR00.0380.01718.5190.0690.0690.0000.0000.0000.000
37F39TYR0-0.051-0.03721.477-0.006-0.0060.0000.0000.0000.000
38F40ARG10.9150.93724.2770.3470.3470.0000.0000.0000.000
39F41LYS10.9390.95927.5270.3060.3060.0000.0000.0000.000
40F42GLU-1-0.720-0.83129.259-0.398-0.3980.0000.0000.0000.000
41F43ARG10.8890.93430.2990.2570.2570.0000.0000.0000.000
42F44SER0-0.049-0.04226.243-0.006-0.0060.0000.0000.0000.000
43F45ARG10.8780.95625.7070.4660.4660.0000.0000.0000.000
44F46LYS10.9780.98325.6590.3100.3100.0000.0000.0000.000
45F47GLU-1-0.778-0.86124.124-0.456-0.4560.0000.0000.0000.000
46F48LEU00.0290.00219.192-0.022-0.0220.0000.0000.0000.000
47F49GLU-1-0.817-0.90821.470-0.537-0.5370.0000.0000.0000.000
48F50LYS10.7630.85422.4160.4080.4080.0000.0000.0000.000
49F51LEU0-0.089-0.03919.2670.0070.0070.0000.0000.0000.000
50F52LEU00.0260.01217.174-0.060-0.0600.0000.0000.0000.000
51F53GLU-1-0.808-0.87217.763-0.504-0.5040.0000.0000.0000.000
52F54GLN0-0.106-0.04917.9210.0380.0380.0000.0000.0000.000
53F55LEU0-0.071-0.02713.229-0.029-0.0290.0000.0000.0000.000
54F56ASN0-0.057-0.03910.9360.3050.3050.0000.0000.0000.000
55F57GLN0-0.024-0.03910.5600.0260.0260.0000.0000.0000.000
56F58PRO0-0.0160.01312.8310.1520.1520.0000.0000.0000.000
57F59GLU-1-0.823-0.92015.773-0.820-0.8200.0000.0000.0000.000
58F60ALA0-0.0090.00218.035-0.078-0.0780.0000.0000.0000.000
59F61HIS10.8480.91916.9780.9980.9980.0000.0000.0000.000
60F62LEU0-0.039-0.00819.815-0.043-0.0430.0000.0000.0000.000
61F63TYR0-0.014-0.04520.9820.0290.0290.0000.0000.0000.000
62F64GLN0-0.058-0.03324.186-0.009-0.0090.0000.0000.0000.000
63F65ILE00.0410.01423.0310.0020.0020.0000.0000.0000.000
64F66ASP-1-0.861-0.91926.052-0.335-0.3350.0000.0000.0000.000
65F67VAL0-0.004-0.01723.8200.0110.0110.0000.0000.0000.000
66F68GLN0-0.089-0.02327.1760.0270.0270.0000.0000.0000.000
67F69SER0-0.056-0.03930.1570.0280.0280.0000.0000.0000.000
68F70ASP-1-0.776-0.90430.327-0.270-0.2700.0000.0000.0000.000
69F71GLU-1-0.950-0.96830.405-0.259-0.2590.0000.0000.0000.000
70F72GLU-1-0.811-0.88729.019-0.339-0.3390.0000.0000.0000.000
71F73VAL0-0.027-0.01624.723-0.035-0.0350.0000.0000.0000.000
72F74ILE00.0180.01525.947-0.029-0.0290.0000.0000.0000.000
73F75ASN0-0.058-0.04227.391-0.016-0.0160.0000.0000.0000.000
74F76GLY00.0100.00625.549-0.015-0.0150.0000.0000.0000.000
75F77PHE00.004-0.01118.915-0.052-0.0520.0000.0000.0000.000
76F78GLU-1-0.800-0.87023.414-0.383-0.3830.0000.0000.0000.000
77F79GLN0-0.048-0.03725.7510.0260.0260.0000.0000.0000.000
78F80ILE0-0.025-0.00319.082-0.032-0.0320.0000.0000.0000.000
79F81GLY00.0490.01621.327-0.049-0.0490.0000.0000.0000.000
80F82LYS10.7150.83622.8690.3580.3580.0000.0000.0000.000
81F83ASP-1-0.836-0.89122.811-0.528-0.5280.0000.0000.0000.000
82F84VAL0-0.114-0.05716.838-0.066-0.0660.0000.0000.0000.000
83F85GLY0-0.0060.00818.126-0.078-0.0780.0000.0000.0000.000
84F86ASN0-0.003-0.01217.6740.0130.0130.0000.0000.0000.000
85F87ILE0-0.049-0.03314.542-0.128-0.1280.0000.0000.0000.000
86F88ASP-1-0.756-0.8549.997-1.515-1.5150.0000.0000.0000.000
87F89GLY00.033-0.02311.8000.1110.1110.0000.0000.0000.000
88F90VAL0-0.028-0.00612.715-0.056-0.0560.0000.0000.0000.000
89F91TYR00.0210.00012.4480.0460.0460.0000.0000.0000.000
90F92HIS00.0370.00014.4180.0010.0010.0000.0000.0000.000
91F93SER0-0.018-0.01017.4420.0840.0840.0000.0000.0000.000
92F94ILE0-0.074-0.03619.1730.0350.0350.0000.0000.0000.000
93F109THR00.0350.01239.665-0.003-0.0030.0000.0000.0000.000
94F110SER0-0.055-0.05842.5980.0020.0020.0000.0000.0000.000
95F111ARG10.9900.99441.3450.0990.0990.0000.0000.0000.000
96F112GLU-1-0.803-0.88940.331-0.127-0.1270.0000.0000.0000.000
97F113GLY00.0160.01538.231-0.010-0.0100.0000.0000.0000.000
98F114PHE0-0.007-0.01036.588-0.011-0.0110.0000.0000.0000.000
99F115LEU00.009-0.00935.615-0.007-0.0070.0000.0000.0000.000
100F116LEU00.0320.03234.010-0.009-0.0090.0000.0000.0000.000
101F117ALA0-0.011-0.00432.193-0.017-0.0170.0000.0000.0000.000
102F118GLN0-0.002-0.00130.832-0.023-0.0230.0000.0000.0000.000
103F119ASP-1-0.851-0.93330.354-0.261-0.2610.0000.0000.0000.000
104F120ILE00.0320.01527.943-0.021-0.0210.0000.0000.0000.000
105F121SER0-0.090-0.04026.489-0.033-0.0330.0000.0000.0000.000
106F122SER0-0.0020.00225.631-0.018-0.0180.0000.0000.0000.000
107F123TYR0-0.029-0.01026.314-0.011-0.0110.0000.0000.0000.000
108F124SER00.020-0.01725.447-0.019-0.0190.0000.0000.0000.000
109F125LEU0-0.0060.00619.479-0.031-0.0310.0000.0000.0000.000
110F126THR00.0100.00522.969-0.014-0.0140.0000.0000.0000.000
111F127ILE00.0030.01825.226-0.008-0.0080.0000.0000.0000.000
112F128VAL0-0.002-0.00820.155-0.016-0.0160.0000.0000.0000.000
113F129ALA00.005-0.00120.592-0.038-0.0380.0000.0000.0000.000
114F130HIS0-0.051-0.02321.5930.0160.0160.0000.0000.0000.000
115F131GLU-1-0.781-0.88524.005-0.319-0.3190.0000.0000.0000.000
116F132ALA0-0.004-0.00218.501-0.013-0.0130.0000.0000.0000.000
117F133LYS10.8670.93019.8950.1990.1990.0000.0000.0000.000
118F134LYS10.7470.86021.3800.3340.3340.0000.0000.0000.000
119F135LEU0-0.058-0.00419.1870.0070.0070.0000.0000.0000.000
120F136MET0-0.0230.00915.022-0.069-0.0690.0000.0000.0000.000
121F137PRO00.003-0.00618.4680.0570.0570.0000.0000.0000.000
122F138GLU-1-0.963-0.97417.288-0.319-0.3190.0000.0000.0000.000
123F139GLY00.0110.02016.0020.0800.0800.0000.0000.0000.000
124F140GLY0-0.001-0.01012.882-0.099-0.0990.0000.0000.0000.000
125F141SER0-0.115-0.05810.5050.1720.1720.0000.0000.0000.000
126F142ILE00.0260.01912.577-0.175-0.1750.0000.0000.0000.000
127F143VAL0-0.008-0.00611.1160.0830.0830.0000.0000.0000.000
128F144ALA00.0550.03414.495-0.052-0.0520.0000.0000.0000.000
129F145THR0-0.079-0.04116.346-0.056-0.0560.0000.0000.0000.000
130F146THR00.0150.01218.5890.0180.0180.0000.0000.0000.000
131F147TYR00.007-0.01021.3730.0020.0020.0000.0000.0000.000
132F148LEU00.0430.03820.544-0.009-0.0090.0000.0000.0000.000
133F149GLY0-0.020-0.02622.5470.0230.0230.0000.0000.0000.000
134F150GLY0-0.071-0.04125.587-0.022-0.0220.0000.0000.0000.000
135F151GLU-1-0.780-0.86728.177-0.151-0.1510.0000.0000.0000.000
136F152PHE0-0.068-0.06228.972-0.021-0.0210.0000.0000.0000.000
137F153ALA0-0.030-0.01031.2270.0070.0070.0000.0000.0000.000
138F154VAL0-0.0270.00632.6650.0030.0030.0000.0000.0000.000
139F155GLN00.0070.00135.4420.0170.0170.0000.0000.0000.000
140F156ASN0-0.016-0.02338.660-0.001-0.0010.0000.0000.0000.000
141F157TYR0-0.017-0.00539.233-0.001-0.0010.0000.0000.0000.000
142F158ASN00.0820.03932.347-0.012-0.0120.0000.0000.0000.000
143F159VAL00.0230.00634.990-0.001-0.0010.0000.0000.0000.000
144F160MET00.0160.00830.513-0.009-0.0090.0000.0000.0000.000
145F161GLY00.0300.02530.595-0.010-0.0100.0000.0000.0000.000
146F162VAL00.002-0.00330.777-0.001-0.0010.0000.0000.0000.000
147F163ALA00.0010.00430.5240.0010.0010.0000.0000.0000.000
148F164LYS10.8680.92926.0110.2540.2540.0000.0000.0000.000
149F165ALA00.0250.01626.607-0.005-0.0050.0000.0000.0000.000
150F166SER0-0.0170.00028.3640.0010.0010.0000.0000.0000.000
151F167LEU00.0080.01222.1350.0020.0020.0000.0000.0000.000
152F168GLU-1-0.834-0.91523.202-0.162-0.1620.0000.0000.0000.000
153F169ALA0-0.032-0.00724.2010.0100.0100.0000.0000.0000.000
154F170ASN0-0.030-0.02925.2950.0050.0050.0000.0000.0000.000
155F171VAL00.0330.01419.226-0.004-0.0040.0000.0000.0000.000
156F172LYS10.8650.94321.3570.1300.1300.0000.0000.0000.000
157F173TYR0-0.031-0.02323.1800.0190.0190.0000.0000.0000.000
158F174LEU00.0170.01221.7530.0060.0060.0000.0000.0000.000
159F175ALA0-0.0110.00219.676-0.003-0.0030.0000.0000.0000.000
160F176LEU0-0.091-0.04120.7380.0260.0260.0000.0000.0000.000
161F177ASP-1-0.951-0.99223.949-0.164-0.1640.0000.0000.0000.000
162F178LEU00.0140.00720.414-0.003-0.0030.0000.0000.0000.000
163F179GLY00.0190.02719.447-0.006-0.0060.0000.0000.0000.000
164F180PRO0-0.059-0.04420.3690.0230.0230.0000.0000.0000.000
165F181ASP-1-0.833-0.90220.689-0.190-0.1900.0000.0000.0000.000
166F182ASN0-0.053-0.03615.1110.0150.0150.0000.0000.0000.000
167F183ILE0-0.0140.00615.885-0.051-0.0510.0000.0000.0000.000
168F184ARG10.8390.9328.8280.3500.3500.0000.0000.0000.000
169F185VAL00.007-0.00315.338-0.105-0.1050.0000.0000.0000.000
170F186ASN0-0.012-0.01513.2510.1500.1500.0000.0000.0000.000
171F187ALA0-0.035-0.01916.069-0.066-0.0660.0000.0000.0000.000
172F188ILE00.0160.01912.3180.0000.0000.0000.0000.0000.000
173F189SER0-0.033-0.01616.858-0.017-0.0170.0000.0000.0000.000
174F190ALA00.0490.02418.8880.0160.0160.0000.0000.0000.000
175F191GLY0-0.042-0.02319.8550.0490.0490.0000.0000.0000.000
176F222ASP-1-0.753-0.87616.472-0.452-0.4520.0000.0000.0000.000
177F223GLN0-0.086-0.06016.413-0.021-0.0210.0000.0000.0000.000
178F224VAL0-0.012-0.01311.910-0.155-0.1550.0000.0000.0000.000
179F225GLU-1-0.866-0.91411.878-0.327-0.3270.0000.0000.0000.000
180F226VAL00.004-0.00312.539-0.039-0.0390.0000.0000.0000.000
181F227GLY00.0200.00510.638-0.109-0.1090.0000.0000.0000.000
182F228LYS10.8640.9177.731-0.167-0.1670.0000.0000.0000.000
183F229THR0-0.0030.0067.697-0.171-0.1710.0000.0000.0000.000
184F230ALA00.002-0.0079.3620.0140.0140.0000.0000.0000.000
185F231ALA00.0290.0134.315-0.125-0.116-0.001-0.004-0.0040.000
186F232TYR0-0.028-0.0064.928-0.923-0.862-0.001-0.002-0.0570.000
187F233LEU00.0080.0096.0230.2360.2360.0000.0000.0000.000
188F234LEU0-0.0220.0097.3620.2470.2470.0000.0000.0000.000
189F235SER0-0.0330.0032.909-0.2410.1990.095-0.171-0.3640.000
190F236ASP-1-0.864-0.9544.8521.6221.747-0.001-0.004-0.1190.000
191F237LEU0-0.032-0.0113.047-0.968-0.0220.065-0.312-0.6980.001
192F238SER0-0.031-0.0236.219-0.112-0.1120.0000.0000.0000.000
193F239SER00.0290.0159.069-0.253-0.2530.0000.0000.0000.000
194F240GLY0-0.025-0.00610.976-0.097-0.0970.0000.0000.0000.000
195F241VAL0-0.051-0.02112.300-0.039-0.0390.0000.0000.0000.000
196F242THR00.0580.02513.685-0.135-0.1350.0000.0000.0000.000
197F243GLY00.0090.00316.5130.0500.0500.0000.0000.0000.000
198F244GLU-1-0.901-0.94115.8220.0070.0070.0000.0000.0000.000
199F245ASN0-0.082-0.07917.326-0.116-0.1160.0000.0000.0000.000
200F246ILE00.0180.01612.3970.0420.0420.0000.0000.0000.000
201F247HIS00.0330.01616.571-0.081-0.0810.0000.0000.0000.000
202F248VAL0-0.062-0.02914.6810.0280.0280.0000.0000.0000.000
203F249ASP-1-0.732-0.84717.738-0.121-0.1210.0000.0000.0000.000
204F250SER0-0.068-0.04120.2540.0260.0260.0000.0000.0000.000
205F251GLY00.0140.00721.6970.0310.0310.0000.0000.0000.000
206F252PHE0-0.043-0.01523.0250.0130.0130.0000.0000.0000.000
207F253HIS0-0.051-0.05920.9550.0320.0320.0000.0000.0000.000
208F254ALA0-0.0180.00625.2430.0070.0070.0000.0000.0000.000
209F255ILE0-0.101-0.03627.0070.0090.0090.0000.0000.0000.000