FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: Q531Y

Calculation Name: 1YAR-O-Xray549

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1YAR

Chain ID: O

ChEMBL ID:

UniProt ID: P25156

Base Structure: X-ray

Registration Date: 2025-10-11

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 228
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2388378.765298
FMO2-HF: Nuclear repulsion 2301156.568348
FMO2-HF: Total energy -87222.19695
FMO2-MP2: Total energy -87477.31712


3D Structure Molmil
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(O:4:LYS)


Summations of interaction energy for fragment #1(O:4:LYS)
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.
-90.801-87.2680.114-1.233-2.415-0.007
Interaction energy analysis for fragmet #1(O:4:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.881 / q_NPA : 1.923
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].
3O6ALA00.0870.0453.1842.7824.4720.018-0.643-1.066-0.002
4O7ALA00.0180.0122.9344.7186.0020.093-0.466-0.911-0.004
5O8LEU0-0.0220.0013.6355.3615.9200.003-0.124-0.438-0.001
6O9ILE00.0300.0135.8347.0437.0430.0000.0000.0000.000
7O10GLN0-0.059-0.0277.8253.7003.7000.0000.0000.0000.000
8O11ASN00.0370.0056.5334.2254.2250.0000.0000.0000.000
9O12LEU0-0.0040.0099.4984.1684.1680.0000.0000.0000.000
10O13ARG10.8710.92411.66247.00047.0000.0000.0000.0000.000
11O14ASP-1-0.843-0.92012.097-44.826-44.8260.0000.0000.0000.000
12O15SER0-0.102-0.05013.7022.5132.5130.0000.0000.0000.000
13O16TYR00.0330.02215.4592.7132.7130.0000.0000.0000.000
14O17THR00.0270.00917.672-0.463-0.4630.0000.0000.0000.000
15O18GLU-1-0.801-0.88819.561-23.358-23.3580.0000.0000.0000.000
16O19THR00.0570.02622.9130.6890.6890.0000.0000.0000.000
17O20SER0-0.0140.00721.0900.4350.4350.0000.0000.0000.000
18O21SER00.0230.00323.4240.2600.2600.0000.0000.0000.000
19O22PHE0-0.063-0.02025.6781.0101.0100.0000.0000.0000.000
20O23ALA00.0820.03627.3310.7960.7960.0000.0000.0000.000
21O24VAL0-0.043-0.01527.2820.6680.6680.0000.0000.0000.000
22O25ILE0-0.031-0.01829.8060.8240.8240.0000.0000.0000.000
23O26GLU-1-0.917-0.97331.170-19.178-19.1780.0000.0000.0000.000
24O27GLU-1-0.865-0.92232.724-16.693-16.6930.0000.0000.0000.000
25O28TRP0-0.071-0.07631.3690.4490.4490.0000.0000.0000.000
26O29ALA0-0.030-0.01735.6410.5180.5180.0000.0000.0000.000
27O30ALA0-0.0130.00337.8140.4870.4870.0000.0000.0000.000
28O31GLY00.0380.02738.5390.3550.3550.0000.0000.0000.000
29O32THR0-0.004-0.01436.1950.2370.2370.0000.0000.0000.000
30O33LEU0-0.019-0.01138.6020.3820.3820.0000.0000.0000.000
31O34GLN0-0.029-0.01341.3880.2450.2450.0000.0000.0000.000
32O35GLU-1-0.754-0.83540.836-13.966-13.9660.0000.0000.0000.000
33O36ILE0-0.030-0.01539.3650.3090.3090.0000.0000.0000.000
34O37GLU-1-0.860-0.92743.524-12.567-12.5670.0000.0000.0000.000
35O38GLY00.003-0.00846.1650.3650.3650.0000.0000.0000.000
36O39ILE0-0.041-0.01642.8390.2860.2860.0000.0000.0000.000
37O40ALA00.0060.00647.2350.2780.2780.0000.0000.0000.000
38O41LYS10.8160.89849.31012.78812.7880.0000.0000.0000.000
39O42ALA00.0510.02950.1080.2420.2420.0000.0000.0000.000
40O43ALA0-0.020-0.00350.1410.1860.1860.0000.0000.0000.000
41O44ALA00.0430.02452.1990.2240.2240.0000.0000.0000.000
42O45GLU-1-0.986-0.98355.122-11.074-11.0740.0000.0000.0000.000
43O46ALA00.0200.00154.4710.2350.2350.0000.0000.0000.000
44O47HIS0-0.0030.00356.0230.4130.4130.0000.0000.0000.000
45O48GLY00.0090.00157.6950.2130.2130.0000.0000.0000.000
46O49VAL0-0.022-0.01059.7660.2300.2300.0000.0000.0000.000
47O50ILE0-0.0120.01056.8510.2000.2000.0000.0000.0000.000
48O51ARG10.8600.92860.69110.41410.4140.0000.0000.0000.000
49O52ASN0-0.015-0.01363.3520.2020.2020.0000.0000.0000.000
50O53SER0-0.039-0.01063.9300.1560.1560.0000.0000.0000.000
51O54THR0-0.035-0.02166.0680.0240.0240.0000.0000.0000.000
52O55TYR0-0.052-0.06560.0050.0180.0180.0000.0000.0000.000
53O56GLY00.0180.00066.9610.1560.1560.0000.0000.0000.000
54O57ARG10.8900.94966.3519.1299.1290.0000.0000.0000.000
55O58ALA00.0500.03065.525-0.126-0.1260.0000.0000.0000.000
56O59GLN00.0170.01262.625-0.042-0.0420.0000.0000.0000.000
57O60ALA00.0090.00861.250-0.200-0.2000.0000.0000.0000.000
58O61GLU-1-0.875-0.93960.881-9.511-9.5110.0000.0000.0000.000
59O62LYS10.8470.92757.03510.78510.7850.0000.0000.0000.000
60O63SER00.0180.01755.0600.0130.0130.0000.0000.0000.000
61O64PRO0-0.039-0.01555.994-0.024-0.0240.0000.0000.0000.000
62O65GLU-1-0.835-0.93553.448-11.389-11.3890.0000.0000.0000.000
63O66GLN0-0.0040.00152.433-0.230-0.2300.0000.0000.0000.000
64O67LEU00.0130.00052.267-0.178-0.1780.0000.0000.0000.000
65O68LEU00.0170.01349.588-0.275-0.2750.0000.0000.0000.000
66O69GLY00.0120.01247.975-0.320-0.3200.0000.0000.0000.000
67O70VAL0-0.003-0.00447.290-0.310-0.3100.0000.0000.0000.000
68O71LEU0-0.022-0.01446.458-0.311-0.3110.0000.0000.0000.000
69O72GLN0-0.054-0.02841.180-0.142-0.1420.0000.0000.0000.000
70O73ARG10.8220.88042.44913.25513.2550.0000.0000.0000.000
71O74TYR00.0370.00942.067-0.345-0.3450.0000.0000.0000.000
72O75GLN00.0270.01839.508-0.121-0.1210.0000.0000.0000.000
73O76ASP-1-0.870-0.93338.019-15.879-15.8790.0000.0000.0000.000
74O77LEU0-0.043-0.01136.983-0.548-0.5480.0000.0000.0000.000
75O78CYS0-0.015-0.02836.536-0.471-0.4710.0000.0000.0000.000
76O79HIS00.0060.00531.049-0.607-0.6070.0000.0000.0000.000
77O80ASN00.0050.00632.403-1.062-1.0620.0000.0000.0000.000
78O81VAL00.0210.00531.665-0.652-0.6520.0000.0000.0000.000
79O82TYR00.011-0.00428.211-0.252-0.2520.0000.0000.0000.000
80O83CYS0-0.050-0.02527.849-0.848-0.8480.0000.0000.0000.000
81O84GLN00.0270.03326.861-0.695-0.6950.0000.0000.0000.000
82O85ALA00.0240.00827.741-0.592-0.5920.0000.0000.0000.000
83O86GLU-1-0.762-0.86824.562-23.929-23.9290.0000.0000.0000.000
84O87THR0-0.065-0.01023.014-1.561-1.5610.0000.0000.0000.000
85O88ILE00.003-0.00622.887-1.243-1.2430.0000.0000.0000.000
86O89ARG10.8160.91023.84622.23422.2340.0000.0000.0000.000
87O90THR0-0.013-0.01318.395-1.186-1.1860.0000.0000.0000.000
88O91VAL0-0.029-0.01619.242-1.891-1.8910.0000.0000.0000.000
89O92ILE0-0.0070.00619.948-1.139-1.1390.0000.0000.0000.000
90O93ALA00.0390.02020.003-0.986-0.9860.0000.0000.0000.000
91O94ILE0-0.058-0.01414.768-1.383-1.3830.0000.0000.0000.000
92O95ARG10.7720.87615.30330.95030.9500.0000.0000.0000.000
93O96ILE00.0230.04817.4950.9410.9410.0000.0000.0000.000
94O97PRO0-0.073-0.02416.152-2.309-2.3090.0000.0000.0000.000
95O98GLU-1-0.863-0.92915.000-33.955-33.9550.0000.0000.0000.000
96O99HIS0-0.022-0.01516.5130.6440.6440.0000.0000.0000.000
97O100LYS10.8630.92217.79230.73430.7340.0000.0000.0000.000
98O101GLU-1-0.861-0.90922.289-22.856-22.8560.0000.0000.0000.000
99O102GLU-1-0.945-0.97823.943-23.293-23.2930.0000.0000.0000.000
100O103ASP-1-0.866-0.94922.447-26.878-26.8780.0000.0000.0000.000
101O104ASN00.0280.00723.598-1.797-1.7970.0000.0000.0000.000
102O105LEU00.0020.00325.5770.3510.3510.0000.0000.0000.000
103O106GLY00.0290.01025.0110.4490.4490.0000.0000.0000.000
104O107VAL00.0230.01822.017-0.140-0.1400.0000.0000.0000.000
105O108ALA0-0.006-0.00224.5750.1860.1860.0000.0000.0000.000
106O109VAL0-0.0070.00127.4510.4310.4310.0000.0000.0000.000
107O110GLN0-0.024-0.03920.1570.3940.3940.0000.0000.0000.000
108O111HIS00.0410.01423.7370.4840.4840.0000.0000.0000.000
109O112ALA0-0.046-0.01227.5570.5800.5800.0000.0000.0000.000
110O113VAL00.010-0.00928.3350.5510.5510.0000.0000.0000.000
111O114LEU00.0090.01023.7780.2050.2050.0000.0000.0000.000
112O115LYS10.9610.99028.26418.03718.0370.0000.0000.0000.000
113O116ILE0-0.005-0.00631.6040.5030.5030.0000.0000.0000.000
114O117ILE00.0040.01627.8270.4470.4470.0000.0000.0000.000
115O118ASP-1-0.810-0.89628.629-21.450-21.4500.0000.0000.0000.000
116O119GLU-1-0.910-0.94231.386-15.892-15.8920.0000.0000.0000.000
117O120LEU00.0210.01232.7400.5380.5380.0000.0000.0000.000
118O121GLU00.001-0.04628.2720.2160.2160.0000.0000.0000.000
119O122ILE0-0.0350.00931.0180.4430.4430.0000.0000.0000.000
120O123LYS10.7980.88234.76116.63516.6350.0000.0000.0000.000
121O124THR0-0.033-0.01437.6870.5400.5400.0000.0000.0000.000
122O125LEU00.0150.00934.0910.3810.3810.0000.0000.0000.000
123O126GLY00.0140.01638.0010.2800.2800.0000.0000.0000.000
124O127SER00.006-0.03333.6740.1020.1020.0000.0000.0000.000
125O128GLY0-0.0130.01134.419-0.243-0.2430.0000.0000.0000.000
126O129GLU-1-0.860-0.91834.938-16.339-16.3390.0000.0000.0000.000
127O130LYS10.8530.90536.76716.29216.2920.0000.0000.0000.000
128O131SER00.0130.02337.583-0.385-0.3850.0000.0000.0000.000
129O132GLY00.0260.01138.9420.0160.0160.0000.0000.0000.000
130O133SER00.000-0.01539.6770.2050.2050.0000.0000.0000.000
131O134GLY0-0.028-0.00941.0950.2960.2960.0000.0000.0000.000
132O135GLY0-0.0080.00542.4530.1510.1510.0000.0000.0000.000
133O136ALA00.010-0.01641.689-0.445-0.4450.0000.0000.0000.000
134O137PRO0-0.032-0.00741.5430.2760.2760.0000.0000.0000.000
135O138THR0-0.0160.00541.4520.3110.3110.0000.0000.0000.000
136O139PRO0-0.013-0.01144.1600.1020.1020.0000.0000.0000.000
137O140ILE0-0.024-0.00745.1650.3080.3080.0000.0000.0000.000
138O141GLY00.0140.02341.423-0.220-0.2200.0000.0000.0000.000
139O142MET0-0.019-0.00534.3270.0010.0010.0000.0000.0000.000
140O143TYR0-0.069-0.04235.2650.0050.0050.0000.0000.0000.000
141O144ALA00.0690.03941.4250.3560.3560.0000.0000.0000.000
142O145LEU00.0540.02944.1270.3860.3860.0000.0000.0000.000
143O146ARG10.9510.97642.64014.07814.0780.0000.0000.0000.000
144O147GLU-1-0.894-0.94444.608-13.410-13.4100.0000.0000.0000.000
145O148TYR0-0.027-0.03347.1810.2470.2470.0000.0000.0000.000
146O149LEU00.0220.00947.4990.2660.2660.0000.0000.0000.000
147O150SER0-0.050-0.02547.7330.1710.1710.0000.0000.0000.000
148O151ALA0-0.021-0.00550.4290.2290.2290.0000.0000.0000.000
149O152ARG10.7360.81052.98811.07711.0770.0000.0000.0000.000
150O153SER00.0290.00152.5900.2180.2180.0000.0000.0000.000
151O154THR0-0.027-0.01453.8770.2110.2110.0000.0000.0000.000
152O155VAL0-0.041-0.02956.4710.2210.2210.0000.0000.0000.000
153O156GLU-1-0.817-0.89856.674-10.853-10.8530.0000.0000.0000.000
154O157ASP-1-0.776-0.90257.605-10.518-10.5180.0000.0000.0000.000
155O158LYS10.8470.96459.77510.50510.5050.0000.0000.0000.000
156O159LEU0-0.110-0.07663.1260.1470.1470.0000.0000.0000.000
157O160LEU0-0.056-0.01360.4630.2110.2110.0000.0000.0000.000
158O161GLY0-0.0100.01163.782-0.009-0.0090.0000.0000.0000.000
159O162SER0-0.001-0.02058.6750.0040.0040.0000.0000.0000.000
160O163VAL0-0.063-0.03456.4060.0920.0920.0000.0000.0000.000
161O164ASP-1-0.938-0.97057.930-10.639-10.6390.0000.0000.0000.000
162O165ALA0-0.008-0.00160.2360.1390.1390.0000.0000.0000.000
163O166GLU-1-0.775-0.90162.534-9.355-9.3550.0000.0000.0000.000
164O167SER0-0.035-0.00565.4090.0350.0350.0000.0000.0000.000
165O168GLY00.0340.01067.2090.1510.1510.0000.0000.0000.000
166O169LYS10.8890.92370.3538.3848.3840.0000.0000.0000.000
167O170THR00.0320.00772.818-0.008-0.0080.0000.0000.0000.000
168O171LYS10.8180.91065.8389.3249.3240.0000.0000.0000.000
169O172GLY00.0290.03169.109-0.105-0.1050.0000.0000.0000.000
170O173GLY00.0450.03368.308-0.030-0.0300.0000.0000.0000.000
171O174SER0-0.019-0.01067.2520.1790.1790.0000.0000.0000.000
172O175GLN0-0.019-0.01469.3040.0990.0990.0000.0000.0000.000
173O176SER-1-0.759-0.86167.997-9.201-9.2010.0000.0000.0000.000
174O177PRO0-0.030-0.02269.208-0.067-0.0670.0000.0000.0000.000
175O178SER0-0.055-0.03466.444-0.071-0.0710.0000.0000.0000.000
176O179LEU0-0.005-0.00662.336-0.147-0.1470.0000.0000.0000.000
177O180LEU0-0.0140.00163.737-0.136-0.1360.0000.0000.0000.000
178O181LEU0-0.024-0.01664.863-0.086-0.0860.0000.0000.0000.000
179O182GLU-1-0.922-0.96559.180-10.610-10.6100.0000.0000.0000.000
180O183LEU0-0.014-0.00259.370-0.198-0.1980.0000.0000.0000.000
181O184ARG10.8700.93359.7229.6939.6930.0000.0000.0000.000
182O185GLN0-0.073-0.05259.4400.0580.0580.0000.0000.0000.000
183O186ILE00.0100.00954.391-0.206-0.2060.0000.0000.0000.000
184O187ASP-1-0.697-0.78455.195-11.173-11.1730.0000.0000.0000.000
185O188ALA00.0060.00255.678-0.164-0.1640.0000.0000.0000.000
186O189ASP-1-0.823-0.90954.934-11.119-11.1190.0000.0000.0000.000
187O190PHE0-0.033-0.02448.600-0.266-0.2660.0000.0000.0000.000
188O191MET0-0.0580.00650.868-0.282-0.2820.0000.0000.0000.000
189O192LEU00.0580.03751.791-0.195-0.1950.0000.0000.0000.000
190O193LYS10.8890.93348.99312.35612.3560.0000.0000.0000.000
191O194VAL00.0340.02746.572-0.301-0.3010.0000.0000.0000.000
192O195GLU-1-0.867-0.92447.794-11.843-11.8430.0000.0000.0000.000
193O196LEU0-0.032-0.00749.309-0.165-0.1650.0000.0000.0000.000
194O197ALA00.005-0.00144.400-0.211-0.2110.0000.0000.0000.000
195O198THR0-0.014-0.02844.071-0.332-0.3320.0000.0000.0000.000
196O199THR0-0.011-0.00844.436-0.250-0.2500.0000.0000.0000.000
197O200HIS00.0080.01142.976-0.107-0.1070.0000.0000.0000.000
198O201LEU00.0380.01537.697-0.333-0.3330.0000.0000.0000.000
199O202SER0-0.051-0.03640.246-0.345-0.3450.0000.0000.0000.000
200O203THR0-0.037-0.01542.115-0.012-0.0120.0000.0000.0000.000
201O204MET00.000-0.01037.070-0.307-0.3070.0000.0000.0000.000
202O205VAL00.0260.01536.213-0.440-0.4400.0000.0000.0000.000
203O206ARG10.9470.97236.84114.11814.1180.0000.0000.0000.000
204O207ALA0-0.0130.00238.382-0.176-0.1760.0000.0000.0000.000
205O208VAL00.005-0.00231.896-0.346-0.3460.0000.0000.0000.000
206O209ILE00.0120.01933.503-0.538-0.5380.0000.0000.0000.000
207O210ASN0-0.015-0.00934.721-0.185-0.1850.0000.0000.0000.000
208O211ALA0-0.012-0.00333.414-0.232-0.2320.0000.0000.0000.000
209O212TYR00.008-0.02826.184-0.658-0.6580.0000.0000.0000.000
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