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: JQG49

Calculation Name: 3LAX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LAX

Chain ID: A

ChEMBL ID:

UniProt ID: A6L0Y5

Base Structure: X-ray

Registration Date: 2023-09-23

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 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 109
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -857185.381298
FMO2-HF: Nuclear repulsion 814350.081384
FMO2-HF: Total energy -42835.299915
FMO2-MP2: Total energy -42961.778938


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(A:324:SER)


Summations of interaction energy for fragment #1(A:324:SER)
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.
-46.516-37.71419.345-13.577-14.568-0.082
Interaction energy analysis for fragmet #1(A:324:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.045 / q_NPA : -0.025
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].
3A326ALA00.007-0.0042.177-5.061-2.4624.810-3.530-3.8790.029
4A327ASP-1-0.866-0.9421.954-34.007-32.61211.296-6.920-5.772-0.082
5A328ASP-1-0.933-0.9604.399-0.558-0.356-0.001-0.029-0.1720.000
6A329MET0-0.066-0.0267.3470.4070.4070.0000.0000.0000.000
7A330ILE00.0110.0199.6000.0970.0970.0000.0000.0000.000
8A331ILE00.000-0.00512.1220.0080.0080.0000.0000.0000.000
9A332LEU00.0170.00715.9060.0240.0240.0000.0000.0000.000
10A333LYN00.0020.00518.0700.0010.0010.0000.0000.0000.000
11A334GLY0-0.0100.00820.9330.0050.0050.0000.0000.0000.000
12A335VAL0-0.0170.00017.642-0.013-0.0130.0000.0000.0000.000
13A336ASN0-0.005-0.01915.4040.0280.0280.0000.0000.0000.000
14A337ILE0-0.009-0.00711.7320.0220.0220.0000.0000.0000.000
15A338PHE00.0500.0158.888-0.041-0.0410.0000.0000.0000.000
16A339PRO0-0.0010.0106.0870.1070.1070.0000.0000.0000.000
17A340ILE00.0620.0325.0140.4010.4010.0000.0000.0000.000
18A341GLN0-0.021-0.0226.814-0.006-0.0060.0000.0000.0000.000
19A342ILE0-0.008-0.0129.7650.0220.0220.0000.0000.0000.000
20A343GLU-1-0.868-0.9005.4111.9702.021-0.0010.000-0.0490.000
21A344THR0-0.025-0.0288.928-0.134-0.1340.0000.0000.0000.000
22A345ILE0-0.0060.00511.291-0.015-0.0150.0000.0000.0000.000
23A346LEU0-0.025-0.02011.010-0.022-0.0220.0000.0000.0000.000
24A347LEU00.004-0.0079.433-0.026-0.0260.0000.0000.0000.000
25A348GLN0-0.045-0.00813.508-0.044-0.0440.0000.0000.0000.000
26A349PHE0-0.0070.00816.750-0.018-0.0180.0000.0000.0000.000
27A350LYS10.8710.92618.173-0.032-0.0320.0000.0000.0000.000
28A351GLU-1-0.876-0.93620.3450.0530.0530.0000.0000.0000.000
29A352LEU0-0.035-0.01515.8920.0000.0000.0000.0000.0000.000
30A353GLY0-0.020-0.00915.160-0.023-0.0230.0000.0000.0000.000
31A354SER0-0.016-0.03310.056-0.015-0.0150.0000.0000.0000.000
32A355ASP-1-0.882-0.9119.2780.6180.6180.0000.0000.0000.000
33A356TYR0-0.022-0.0685.227-0.166-0.1660.0000.0000.0000.000
34A357LEU0-0.026-0.0178.3990.1120.1120.0000.0000.0000.000
35A358ILE00.0320.0258.089-0.125-0.1250.0000.0000.0000.000
36A359THR0-0.036-0.02710.577-0.023-0.0230.0000.0000.0000.000
37A360LEU0-0.0090.00612.465-0.008-0.0080.0000.0000.0000.000
38A361GLU-1-0.853-0.93515.3880.0660.0660.0000.0000.0000.000
39A362THR0-0.009-0.02718.771-0.002-0.0020.0000.0000.0000.000
40A363ALA00.0100.02722.2840.0030.0030.0000.0000.0000.000
41A364GLU-1-0.926-0.96024.7260.0050.0050.0000.0000.0000.000
42A365SER0-0.110-0.06227.684-0.003-0.0030.0000.0000.0000.000
43A366ASN0-0.051-0.02324.272-0.006-0.0060.0000.0000.0000.000
44A367ASP-1-0.790-0.91119.717-0.032-0.0320.0000.0000.0000.000
45A368GLU-1-0.963-0.96920.2740.0290.0290.0000.0000.0000.000
46A369MET0-0.001-0.00713.2290.0100.0100.0000.0000.0000.000
47A370THR0-0.020-0.00215.2520.0040.0040.0000.0000.0000.000
48A371VAL0-0.013-0.01312.4780.0270.0270.0000.0000.0000.000
49A372GLU-1-0.813-0.88313.4920.1320.1320.0000.0000.0000.000
50A373VAL00.0430.00512.6900.0750.0750.0000.0000.0000.000
51A374GLU-1-0.782-0.86713.8250.1780.1780.0000.0000.0000.000
52A375LEU00.0040.00715.8960.0020.0020.0000.0000.0000.000
53A376SER0-0.0020.00218.6450.0070.0070.0000.0000.0000.000
54A377GLN00.003-0.02619.8130.0030.0030.0000.0000.0000.000
55A378LEU0-0.046-0.02522.525-0.009-0.0090.0000.0000.0000.000
56A379PHE00.0160.01723.214-0.007-0.0070.0000.0000.0000.000
57A380THR0-0.016-0.02325.0190.0040.0040.0000.0000.0000.000
58A381ASP-1-0.920-0.94527.9070.0430.0430.0000.0000.0000.000
59A382ASP-1-0.802-0.87829.2890.0380.0380.0000.0000.0000.000
60A383TYR00.0400.00227.4110.0000.0000.0000.0000.0000.000
61A384GLY00.0380.02629.3640.0010.0010.0000.0000.0000.000
62A385ARG10.8540.89628.345-0.033-0.0330.0000.0000.0000.000
63A386LEU00.0390.03323.0610.0020.0020.0000.0000.0000.000
64A387GLN0-0.027-0.00125.0080.0030.0030.0000.0000.0000.000
65A388ALA0-0.036-0.01926.3020.0000.0000.0000.0000.0000.000
66A389LEU00.0280.02121.086-0.004-0.0040.0000.0000.0000.000
67A390THR00.018-0.01221.5840.0080.0080.0000.0000.0000.000
68A391ARG10.9090.96822.055-0.017-0.0170.0000.0000.0000.000
69A392GLU-1-0.795-0.86622.4660.0080.0080.0000.0000.0000.000
70A393ILE00.0210.01916.927-0.005-0.0050.0000.0000.0000.000
71A394THR0-0.057-0.05418.7570.0020.0020.0000.0000.0000.000
72A395ARG10.7950.88920.566-0.015-0.0150.0000.0000.0000.000
73A396GLN00.017-0.01518.951-0.005-0.0050.0000.0000.0000.000
74A397LEU00.0070.01313.900-0.009-0.0090.0000.0000.0000.000
75A398LYS10.8940.94917.133-0.008-0.0080.0000.0000.0000.000
76A399ASP-1-0.969-0.99319.836-0.035-0.0350.0000.0000.0000.000
77A400GLU-1-0.883-0.90814.754-0.183-0.1830.0000.0000.0000.000
78A401ILE0-0.036-0.02813.623-0.022-0.0220.0000.0000.0000.000
79A402LEU00.0020.01716.781-0.007-0.0070.0000.0000.0000.000
80A403VAL0-0.033-0.02117.3220.0090.0090.0000.0000.0000.000
81A404THR0-0.021-0.03019.7040.0050.0050.0000.0000.0000.000
82A405PRO00.0400.03916.372-0.001-0.0010.0000.0000.0000.000
83A406ARG10.9360.96218.428-0.070-0.0700.0000.0000.0000.000
84A407VAL00.0170.00717.3390.0180.0180.0000.0000.0000.000
85A408LYS10.7960.89117.549-0.138-0.1380.0000.0000.0000.000
86A409LEU00.0390.02817.4640.0240.0240.0000.0000.0000.000
87A410VAL0-0.022-0.00916.418-0.019-0.0190.0000.0000.0000.000
88A411PRO00.024-0.00318.9420.0070.0070.0000.0000.0000.000
89A412LYS10.9610.99217.500-0.124-0.1240.0000.0000.0000.000
90A413GLY0-0.074-0.04316.578-0.017-0.0170.0000.0000.0000.000
91A414ALA0-0.033-0.00616.966-0.002-0.0020.0000.0000.0000.000
92A415LEU0-0.0110.01011.859-0.005-0.0050.0000.0000.0000.000
93A416PRO0-0.018-0.02510.8610.0050.0050.0000.0000.0000.000
94A417LYS10.8600.9239.966-0.233-0.2330.0000.0000.0000.000
95A418SER0-0.050-0.01710.2770.0100.0100.0000.0000.0000.000
96A419GLU-1-0.810-0.9086.1980.5190.5190.0000.0000.0000.000
97A420GLY0-0.041-0.0117.597-0.002-0.0020.0000.0000.0000.000
98A421LYS10.8900.9263.151-2.712-2.0590.039-0.229-0.4630.001
99A422ALA00.0040.0122.392-2.624-0.6432.298-1.893-2.385-0.018
100A423VAL00.0100.0022.557-2.801-1.4250.876-0.867-1.385-0.012
101A424ARG10.8760.9363.240-1.786-1.2840.029-0.107-0.4240.000
102A425VAL0-0.026-0.0075.202-0.067-0.024-0.001-0.002-0.0390.000
103A426LYS10.8590.9357.793-0.322-0.3220.0000.0000.0000.000
104A427ASP-1-0.792-0.88810.932-0.054-0.0540.0000.0000.0000.000
105A428LEU0-0.049-0.02413.345-0.004-0.0040.0000.0000.0000.000
106A429ARG10.7390.85415.1310.0800.0800.0000.0000.0000.000
107A430LYS10.9070.94518.9450.0050.0050.0000.0000.0000.000
108A431THR00.0250.00817.9630.0000.0000.0000.0000.0000.000
109A432PHE0-0.0110.01320.346-0.003-0.0030.0000.0000.0000.000