FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: 3J7QL

Calculation Name: 5LP5-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5LP5

Chain ID: F

ChEMBL ID:

UniProt ID: O26085

Base Structure: X-ray

Registration Date: 2023-09-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 156
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1445017.08907
FMO2-HF: Nuclear repulsion 1385691.435167
FMO2-HF: Total energy -59325.653903
FMO2-MP2: Total energy -59499.902065


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:92:LYS)


Summations of interaction energy for fragment #1(F:92: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.
-45.813-42.108-0.034-1.822-1.8480.003
Interaction energy analysis for fragmet #1(F:92:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.981 / q_NPA : 0.979
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].
3F94THR0-0.0240.0053.791-6.345-3.119-0.035-1.759-1.4320.003
4F95TYR00.0340.0216.1982.8812.8810.0000.0000.0000.000
5F96THR0-0.0060.0019.886-0.512-0.5120.0000.0000.0000.000
6F97PRO0-0.0140.00912.4110.7280.7280.0000.0000.0000.000
7F98THR0-0.010-0.02216.0780.2920.2920.0000.0000.0000.000
8F99PHE0-0.0150.00118.9240.2640.2640.0000.0000.0000.000
9F100MET00.0360.04022.3530.2080.2080.0000.0000.0000.000
10F101THR0-0.047-0.02924.9290.3510.3510.0000.0000.0000.000
11F102SER0-0.011-0.01427.7890.4280.4280.0000.0000.0000.000
12F103PHE00.0230.01028.729-0.341-0.3410.0000.0000.0000.000
13F104ILE0-0.058-0.01926.5100.1830.1830.0000.0000.0000.000
14F105SER0-0.024-0.01830.9160.3170.3170.0000.0000.0000.000
15F106LEU0-0.015-0.02033.661-0.013-0.0130.0000.0000.0000.000
16F107GLU-1-0.954-0.97236.214-7.622-7.6220.0000.0000.0000.000
17F108ASP-1-0.891-0.92831.826-9.219-9.2190.0000.0000.0000.000
18F109THR0-0.035-0.03031.5920.0280.0280.0000.0000.0000.000
19F110HIS00.026-0.00228.660-0.556-0.5560.0000.0000.0000.000
20F111SER00.023-0.00226.864-0.415-0.4150.0000.0000.0000.000
21F112VAL0-0.036-0.01624.0320.3580.3580.0000.0000.0000.000
22F113SER00.0260.02124.987-0.406-0.4060.0000.0000.0000.000
23F114LEU0-0.021-0.01319.3240.1320.1320.0000.0000.0000.000
24F115ASN0-0.032-0.00520.7830.6470.6470.0000.0000.0000.000
25F116PRO00.0210.00420.101-0.671-0.6710.0000.0000.0000.000
26F117ILE00.0140.00713.859-0.085-0.0850.0000.0000.0000.000
27F118VAL0-0.044-0.02515.9090.1810.1810.0000.0000.0000.000
28F119ASN0-0.023-0.02814.407-1.337-1.3370.0000.0000.0000.000
29F120LEU00.0370.05412.456-1.299-1.2990.0000.0000.0000.000
30F121GLU-1-0.867-0.93810.813-22.472-22.4720.0000.0000.0000.000
31F122GLU-1-0.865-0.93715.123-12.554-12.5540.0000.0000.0000.000
32F123ASN0-0.071-0.05217.984-0.045-0.0450.0000.0000.0000.000
33F124LYS10.8520.9398.50026.20726.2070.0000.0000.0000.000
34F125ILE0-0.006-0.01114.9080.3500.3500.0000.0000.0000.000
35F126TYR00.0380.02410.695-0.726-0.7260.0000.0000.0000.000
36F127GLY00.0570.03412.7341.3871.3870.0000.0000.0000.000
37F128LEU0-0.056-0.02314.304-0.626-0.6260.0000.0000.0000.000
38F129VAL00.0530.01813.7850.4910.4910.0000.0000.0000.000
39F130SER0-0.001-0.01616.8130.1410.1410.0000.0000.0000.000
40F131HIS0-0.0300.00119.069-0.654-0.6540.0000.0000.0000.000
41F132ASN0-0.030-0.02616.432-0.386-0.3860.0000.0000.0000.000
42F133GLN00.0280.02118.0690.3540.3540.0000.0000.0000.000
43F134ALA00.0560.03416.814-0.433-0.4330.0000.0000.0000.000
44F135ILE0-0.039-0.02618.3360.7570.7570.0000.0000.0000.000
45F136GLY00.0440.01519.2550.7930.7930.0000.0000.0000.000
46F137ILE0-0.0010.01216.921-0.924-0.9240.0000.0000.0000.000
47F138ALA0-0.013-0.01716.9170.7520.7520.0000.0000.0000.000
48F139VAL00.0010.01417.235-0.723-0.7230.0000.0000.0000.000
49F140LEU00.0090.02018.0570.5890.5890.0000.0000.0000.000
50F141GLU-1-0.794-0.89019.820-11.946-11.9460.0000.0000.0000.000
51F142LYS10.9280.95223.24710.81310.8130.0000.0000.0000.000
52F143GLY0-0.0060.00023.2250.3420.3420.0000.0000.0000.000
53F144ARG10.9170.96624.01410.29110.2910.0000.0000.0000.000
54F145LEU00.0120.01317.378-0.226-0.2260.0000.0000.0000.000
55F146ASN0-0.029-0.01621.3560.4860.4860.0000.0000.0000.000
56F147GLY00.0450.01721.277-0.610-0.6100.0000.0000.0000.000
57F148PHE0-0.044-0.02721.9180.7400.7400.0000.0000.0000.000
58F149LEU0-0.002-0.01022.384-0.481-0.4810.0000.0000.0000.000
59F150ASN00.048-0.00921.967-0.110-0.1100.0000.0000.0000.000
60F151ALA00.0080.01424.3120.0780.0780.0000.0000.0000.000
61F152HIS0-0.0080.01025.7450.2380.2380.0000.0000.0000.000
62F153LYS10.9730.98226.3929.0199.0190.0000.0000.0000.000
63F154ARG10.8060.87723.28811.75511.7550.0000.0000.0000.000
64F155CYS0-0.086-0.00521.726-0.743-0.7430.0000.0000.0000.000
65F156ALA00.0460.03220.6300.3700.3700.0000.0000.0000.000
66F157TYR0-0.026-0.03415.842-0.718-0.7180.0000.0000.0000.000
67F158SER0-0.0190.01414.6410.5770.5770.0000.0000.0000.000
68F159VAL0-0.015-0.00415.421-0.844-0.8440.0000.0000.0000.000
69F160MET0-0.057-0.01414.1010.1360.1360.0000.0000.0000.000
70F161ILE00.001-0.00518.492-0.035-0.0350.0000.0000.0000.000
71F162GLY00.0640.03621.7980.1190.1190.0000.0000.0000.000
72F163GLN0-0.041-0.02621.011-0.661-0.6610.0000.0000.0000.000
73F164ASN0-0.018-0.01520.937-0.514-0.5140.0000.0000.0000.000
74F165GLN0-0.058-0.02914.982-0.435-0.4350.0000.0000.0000.000
75F166VAL00.0350.02319.299-0.214-0.2140.0000.0000.0000.000
76F167LEU0-0.0020.00016.285-0.244-0.2440.0000.0000.0000.000
77F168GLY00.0450.02719.8630.6230.6230.0000.0000.0000.000
78F169PHE0-0.066-0.04217.577-0.833-0.8330.0000.0000.0000.000
79F170ILE0-0.028-0.00420.2430.5250.5250.0000.0000.0000.000
80F171GLY00.0480.01522.304-0.126-0.1260.0000.0000.0000.000
81F172THR0-0.050-0.02225.5730.1070.1070.0000.0000.0000.000
82F173ASN00.0580.00629.0940.1360.1360.0000.0000.0000.000
83F174PHE00.016-0.00732.6290.0060.0060.0000.0000.0000.000
84F175LYS10.7990.90635.5688.2008.2000.0000.0000.0000.000
85F176GLN0-0.047-0.02132.7240.0020.0020.0000.0000.0000.000
86F177GLU-1-0.780-0.84931.887-8.405-8.4050.0000.0000.0000.000
87F178LEU0-0.020-0.01723.882-0.098-0.0980.0000.0000.0000.000
88F179VAL0-0.018-0.01527.0180.1300.1300.0000.0000.0000.000
89F180VAL0-0.035-0.00722.610-0.434-0.4340.0000.0000.0000.000
90F181ASP-1-0.792-0.90724.667-9.351-9.3510.0000.0000.0000.000
91F182PHE0-0.057-0.04924.171-0.462-0.4620.0000.0000.0000.000
92F183ILE00.0020.01924.586-0.277-0.2770.0000.0000.0000.000
93F184VAL00.0270.00225.6220.3750.3750.0000.0000.0000.000
94F185PRO00.0740.02828.014-0.062-0.0620.0000.0000.0000.000
95F186SER0-0.048-0.03430.4670.0830.0830.0000.0000.0000.000
96F187ALA0-0.0240.00126.7650.0080.0080.0000.0000.0000.000
97F188GLU-1-0.946-0.97228.334-8.867-8.8670.0000.0000.0000.000
98F189ILE0-0.025-0.01325.613-0.312-0.3120.0000.0000.0000.000
99F190ASN0-0.014-0.01728.4550.6000.6000.0000.0000.0000.000
100F191ILE0-0.010-0.01329.355-0.256-0.2560.0000.0000.0000.000
101F192GLY0-0.036-0.01829.7070.1200.1200.0000.0000.0000.000
102F193ASP-1-0.855-0.91525.175-10.757-10.7570.0000.0000.0000.000
103F194GLN00.013-0.01021.6940.1530.1530.0000.0000.0000.000
104F195VAL00.0080.00620.510-0.090-0.0900.0000.0000.0000.000
105F196LEU0-0.015-0.00716.090-0.171-0.1710.0000.0000.0000.000
106F197THR00.0280.00312.2540.5240.5240.0000.0000.0000.000
107F198SER00.028-0.02113.598-0.932-0.9320.0000.0000.0000.000
108F199GLY0-0.035-0.0169.519-0.593-0.5930.0000.0000.0000.000
109F200LEU0-0.044-0.0288.645-1.536-1.5360.0000.0000.0000.000
110F201ASP-1-0.772-0.89810.946-18.742-18.7420.0000.0000.0000.000
111F202GLY0-0.0210.0028.3940.2560.2560.0000.0000.0000.000
112F203ILE0-0.077-0.0149.454-0.289-0.2890.0000.0000.0000.000
113F204PHE0-0.004-0.00210.453-0.776-0.7760.0000.0000.0000.000
114F205GLY00.0560.0177.468-1.144-1.1440.0000.0000.0000.000
115F206ALA0-0.011-0.0088.1591.9041.9040.0000.0000.0000.000
116F207GLY0-0.012-0.00710.457-0.808-0.8080.0000.0000.0000.000
117F208VAL0-0.023-0.00212.1380.5400.5400.0000.0000.0000.000
118F209PHE0-0.0130.00614.7910.4270.4270.0000.0000.0000.000
119F210VAL00.005-0.00318.102-0.175-0.1750.0000.0000.0000.000
120F211GLY00.028-0.00120.4850.4000.4000.0000.0000.0000.000
121F212GLU-1-0.854-0.90223.623-10.236-10.2360.0000.0000.0000.000
122F213VAL00.0200.01626.1100.2240.2240.0000.0000.0000.000
123F214SER0-0.072-0.04628.2970.2720.2720.0000.0000.0000.000
124F215SER0-0.011-0.01731.7010.3190.3190.0000.0000.0000.000
125F216ILE00.013-0.00930.504-0.280-0.2800.0000.0000.0000.000
126F217GLU-1-0.905-0.91532.781-8.045-8.0450.0000.0000.0000.000
127F218ASP-1-0.864-0.95233.303-8.350-8.3500.0000.0000.0000.000
128F219HIS0-0.047-0.03733.4190.3420.3420.0000.0000.0000.000
129F220TYR0-0.042-0.00335.9660.1010.1010.0000.0000.0000.000
130F221THR0-0.042-0.04333.924-0.107-0.1070.0000.0000.0000.000
131F222TYR0-0.040-0.01429.536-0.160-0.1600.0000.0000.0000.000
132F223LYS10.8420.95429.2579.1359.1350.0000.0000.0000.000
133F224SER0-0.0010.00328.692-0.297-0.2970.0000.0000.0000.000
134F225ALA00.014-0.00426.8450.2150.2150.0000.0000.0000.000
135F226VAL00.0340.03727.960-0.313-0.3130.0000.0000.0000.000
136F227LEU0-0.0060.01023.8240.0100.0100.0000.0000.0000.000
137F228LYS10.8320.90928.2019.8079.8070.0000.0000.0000.000
138F229ASN0-0.030-0.03727.483-0.085-0.0850.0000.0000.0000.000
139F230ALA00.0700.05524.667-0.367-0.3670.0000.0000.0000.000
140F231PHE0-0.034-0.01423.6620.3690.3690.0000.0000.0000.000
141F232LEU00.0420.02925.625-0.007-0.0070.0000.0000.0000.000
142F233SER0-0.015-0.01626.485-0.097-0.0970.0000.0000.0000.000
143F234GLY00.0320.03328.5860.2730.2730.0000.0000.0000.000
144F235ALA00.0410.00930.995-0.133-0.1330.0000.0000.0000.000
145F236LYS10.9170.96929.4599.9099.9090.0000.0000.0000.000
146F237LEU00.0350.02328.254-0.266-0.2660.0000.0000.0000.000
147F238LEU0-0.061-0.04024.0140.0760.0760.0000.0000.0000.000
148F239ARG10.9390.95224.73410.39210.3920.0000.0000.0000.000
149F240HIS00.0090.00221.189-0.442-0.4420.0000.0000.0000.000
150F241VAL00.0190.02318.233-0.130-0.1300.0000.0000.0000.000
151F242PHE0-0.006-0.01013.740-0.263-0.2630.0000.0000.0000.000
152F243LEU0-0.008-0.01012.8610.3800.3800.0000.0000.0000.000
153F244SER0-0.043-0.03310.139-1.989-1.9890.0000.0000.0000.000
154F245ASP-1-0.833-0.9307.377-29.041-29.0410.0000.0000.0000.000
155F246VAL00.0250.0274.625-5.136-5.045-0.001-0.019-0.0700.000
156F247LYS10.9020.9533.75030.84631.2340.002-0.044-0.3460.000