FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: G5Q11

Calculation Name: 4L11-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4L11

Chain ID: A

ChEMBL ID:

UniProt ID: Q7QJX3

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 OptH
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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2228929.575068
FMO2-HF: Nuclear repulsion 2148509.017633
FMO2-HF: Total energy -80420.557435
FMO2-MP2: Total energy -80652.618961


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:537:THR)


Summations of interaction energy for fragment #1(A:537:THR)
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.
-2.786-0.3510.018-0.911-1.5420.003
Interaction energy analysis for fragmet #1(A:537:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : -0.003
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].
3A539ARG10.9510.9523.147-1.6130.6610.020-0.896-1.3980.003
4A540TYR00.0840.0455.1920.1030.152-0.001-0.006-0.0420.000
5A541HIS00.0630.0187.323-0.043-0.0430.0000.0000.0000.000
6A542THR0-0.012-0.0055.783-0.104-0.1040.0000.0000.0000.000
7A543GLN0-0.055-0.0376.900-0.192-0.1920.0000.0000.0000.000
8A544MET00.0080.0089.952-0.067-0.0670.0000.0000.0000.000
9A545LEU0-0.018-0.03112.410-0.063-0.0630.0000.0000.0000.000
10A546ARG11.0181.0275.647-0.772-0.7720.0000.0000.0000.000
11A547VAL00.0310.01913.326-0.055-0.0550.0000.0000.0000.000
12A548ARG10.8160.90215.070-0.295-0.2950.0000.0000.0000.000
13A549GLU-1-0.903-0.95414.2030.2600.2600.0000.0000.0000.000
14A550PHE00.0540.02716.224-0.026-0.0260.0000.0000.0000.000
15A551ILE00.0270.00019.115-0.020-0.0200.0000.0000.0000.000
16A552ARG10.8460.96420.612-0.119-0.1190.0000.0000.0000.000
17A553PHE0-0.007-0.01918.069-0.016-0.0160.0000.0000.0000.000
18A554HIS10.8140.92221.050-0.102-0.1020.0000.0000.0000.000
19A555GLN00.0530.03024.8290.0020.0020.0000.0000.0000.000
20A556ILE00.0350.03022.954-0.005-0.0050.0000.0000.0000.000
21A557PRO00.0240.01826.8980.0020.0020.0000.0000.0000.000
22A558ASN00.054-0.00327.6430.0120.0120.0000.0000.0000.000
23A559PRO00.0390.02028.1320.0060.0060.0000.0000.0000.000
24A560LEU00.0360.03425.1670.0020.0020.0000.0000.0000.000
25A561ARG10.8830.96123.556-0.112-0.1120.0000.0000.0000.000
26A562GLN0-0.019-0.02923.3990.0030.0030.0000.0000.0000.000
27A563ARG10.7730.85224.196-0.102-0.1020.0000.0000.0000.000
28A564LEU00.0090.00720.4110.0080.0080.0000.0000.0000.000
29A565GLU-1-0.853-0.92819.3990.1740.1740.0000.0000.0000.000
30A566GLU-1-0.826-0.88519.6250.1360.1360.0000.0000.0000.000
31A567TYR0-0.022-0.01017.5530.0000.0000.0000.0000.0000.000
32A568PHE0-0.019-0.01111.4730.0210.0210.0000.0000.0000.000
33A569GLN0-0.057-0.01715.5520.0350.0350.0000.0000.0000.000
34A570HIS0-0.055-0.02616.4620.0280.0280.0000.0000.0000.000
35A571ALA00.0200.00416.532-0.010-0.0100.0000.0000.0000.000
36A572TRP00.0110.0158.323-0.041-0.0410.0000.0000.0000.000
37A573THR00.0070.0159.550-0.037-0.0370.0000.0000.0000.000
38A574TYR00.0180.0104.591-0.298-0.186-0.001-0.009-0.1020.000
39A575THR00.0360.0175.2410.7680.7680.0000.0000.0000.000
40A576ASN00.011-0.0046.189-0.083-0.0830.0000.0000.0000.000
41A577GLY00.0760.0045.783-0.009-0.0090.0000.0000.0000.000
42A578ILE0-0.1150.0026.800-0.083-0.0830.0000.0000.0000.000
43A579ASP-1-0.917-0.9387.443-0.019-0.0190.0000.0000.0000.000
44A580MET00.0370.0099.4710.0330.0330.0000.0000.0000.000
45A581ASN00.060-0.02613.1540.0250.0250.0000.0000.0000.000
46A582SER00.0290.00711.149-0.016-0.0160.0000.0000.0000.000
47A583VAL00.002-0.02110.733-0.027-0.0270.0000.0000.0000.000
48A584LEU0-0.0620.02013.524-0.008-0.0080.0000.0000.0000.000
49A585LYS10.9920.98615.624-0.080-0.0800.0000.0000.0000.000
50A586GLY0-0.072-0.03316.002-0.009-0.0090.0000.0000.0000.000
51A587PHE0-0.0220.00615.6250.0150.0150.0000.0000.0000.000
52A588PRO00.0110.03119.547-0.013-0.0130.0000.0000.0000.000
53A589GLU-1-0.866-0.94323.1050.0710.0710.0000.0000.0000.000
54A590CYS0-0.039-0.05125.829-0.002-0.0020.0000.0000.0000.000
55A591LEU00.0170.01122.429-0.003-0.0030.0000.0000.0000.000
56A592GLN00.038-0.00122.0650.0080.0080.0000.0000.0000.000
57A593ALA00.0420.02923.826-0.007-0.0070.0000.0000.0000.000
58A594ASP-1-0.850-0.93527.3870.0720.0720.0000.0000.0000.000
59A595ILE0-0.061-0.01721.535-0.002-0.0020.0000.0000.0000.000
60A596CYS0-0.0120.00925.394-0.006-0.0060.0000.0000.0000.000
61A597LEU00.0280.03327.120-0.005-0.0050.0000.0000.0000.000
62A598HIS0-0.073-0.05227.050-0.007-0.0070.0000.0000.0000.000
63A599LEU0-0.040-0.04123.456-0.001-0.0010.0000.0000.0000.000
64A600ASN00.024-0.00528.119-0.005-0.0050.0000.0000.0000.000
65A601ARG10.9030.96231.187-0.053-0.0530.0000.0000.0000.000
66A602ASN0-0.105-0.03229.0710.0010.0010.0000.0000.0000.000
67A603LEU00.0740.04532.321-0.002-0.0020.0000.0000.0000.000
68A604LEU0-0.024-0.01934.026-0.002-0.0020.0000.0000.0000.000
69A605ASN0-0.055-0.03936.115-0.003-0.0030.0000.0000.0000.000
70A606ASN0-0.090-0.03935.661-0.001-0.0010.0000.0000.0000.000
71A607CYS0-0.0040.02737.269-0.002-0.0020.0000.0000.0000.000
72A608SER00.0380.00939.0530.0000.0000.0000.0000.0000.000
73A609ALA00.0220.00940.925-0.001-0.0010.0000.0000.0000.000
74A610PHE0-0.032-0.04137.5160.0000.0000.0000.0000.0000.000
75A611GLU-1-0.864-0.91342.1640.0230.0230.0000.0000.0000.000
76A612ALA0-0.027-0.02344.807-0.001-0.0010.0000.0000.0000.000
77A613ALA0-0.0300.00743.1400.0000.0000.0000.0000.0000.000
78A614SER00.0510.03045.1740.0020.0020.0000.0000.0000.000
79A615PRO00.0310.00843.2920.0010.0010.0000.0000.0000.000
80A616GLY0-0.066-0.03742.4600.0020.0020.0000.0000.0000.000
81A617CYS00.0450.03842.4890.0010.0010.0000.0000.0000.000
82A618LEU00.0380.00939.7930.0010.0010.0000.0000.0000.000
83A619ARG10.9040.95138.267-0.030-0.0300.0000.0000.0000.000
84A620ALA00.0400.02537.4950.0020.0020.0000.0000.0000.000
85A621LEU00.0490.03037.3170.0010.0010.0000.0000.0000.000
86A622SER0-0.106-0.06134.1560.0020.0020.0000.0000.0000.000
87A623LEU0-0.057-0.03432.8670.0040.0040.0000.0000.0000.000
88A624LYS10.7350.88632.604-0.019-0.0190.0000.0000.0000.000
89A625PHE0-0.0450.00031.466-0.002-0.0020.0000.0000.0000.000
90A626LYS10.8950.95626.915-0.017-0.0170.0000.0000.0000.000
91A627THR00.0380.01123.7460.0000.0000.0000.0000.0000.000
92A628THR0-0.099-0.06522.044-0.001-0.0010.0000.0000.0000.000
93A629HIS0-0.004-0.00318.6380.0140.0140.0000.0000.0000.000
94A630ALA00.0380.01619.698-0.005-0.0050.0000.0000.0000.000
95A631PRO00.0170.01016.7800.0150.0150.0000.0000.0000.000
96A632PRO0-0.0320.00217.827-0.003-0.0030.0000.0000.0000.000
97A633GLY0-0.055-0.03019.321-0.017-0.0170.0000.0000.0000.000
98A634ASP-1-0.896-0.98420.325-0.071-0.0710.0000.0000.0000.000
99A635ILE0-0.0190.00122.6720.0090.0090.0000.0000.0000.000
100A636LEU0-0.041-0.00725.3880.0010.0010.0000.0000.0000.000
101A637VAL0-0.016-0.00227.3830.0020.0020.0000.0000.0000.000
102A638HIS0-0.009-0.00327.685-0.004-0.0040.0000.0000.0000.000
103A639LYS11.0031.00532.4560.0260.0260.0000.0000.0000.000
104A640GLY0-0.017-0.00336.0700.0030.0030.0000.0000.0000.000
105A641ASP-1-0.826-0.92631.753-0.027-0.0270.0000.0000.0000.000
106A642VAL0-0.0120.00335.4260.0020.0020.0000.0000.0000.000
107A643LEU0-0.0190.01335.5810.0000.0000.0000.0000.0000.000
108A644THR0-0.041-0.01532.3750.0030.0030.0000.0000.0000.000
109A645TYR00.020-0.00630.3920.0040.0040.0000.0000.0000.000
110A646LEU00.0070.03033.748-0.002-0.0020.0000.0000.0000.000
111A647TYR0-0.019-0.03428.1080.0030.0030.0000.0000.0000.000
112A648PHE00.0670.03031.801-0.001-0.0010.0000.0000.0000.000
113A649ILE0-0.0250.00128.9670.0030.0030.0000.0000.0000.000
114A650ALA00.0260.01827.7410.0020.0020.0000.0000.0000.000
115A651ARG10.8440.90024.766-0.058-0.0580.0000.0000.0000.000
116A652GLY00.0320.00725.787-0.002-0.0020.0000.0000.0000.000
117A653SER00.006-0.01126.3060.0010.0010.0000.0000.0000.000
118A654ILE00.0190.00826.956-0.004-0.0040.0000.0000.0000.000
119A655GLU-1-0.845-0.93429.122-0.037-0.0370.0000.0000.0000.000
120A656ILE0-0.017-0.00930.775-0.002-0.0020.0000.0000.0000.000
121A657LEU0-0.064-0.02730.4050.0000.0000.0000.0000.0000.000
122A658LYS10.9010.94134.4480.0190.0190.0000.0000.0000.000
123A659ASP-1-0.913-0.93935.807-0.030-0.0300.0000.0000.0000.000
124A660ASP-1-0.940-0.98435.117-0.030-0.0300.0000.0000.0000.000
125A661VAL0-0.018-0.00833.4490.0020.0020.0000.0000.0000.000
126A662VAL00.0130.00735.6180.0020.0020.0000.0000.0000.000
127A663MET0-0.032-0.01136.2170.0020.0020.0000.0000.0000.000
128A664ALA0-0.019-0.00433.067-0.002-0.0020.0000.0000.0000.000
129A665ILE00.0030.00632.6140.0020.0020.0000.0000.0000.000
130A666LEU00.006-0.03030.990-0.001-0.0010.0000.0000.0000.000
131A667GLY00.0330.01730.5090.0000.0000.0000.0000.0000.000
132A668LYS10.7360.85131.417-0.010-0.0100.0000.0000.0000.000
133A669ASP-1-0.905-0.94633.5440.0250.0250.0000.0000.0000.000
134A670ASP-1-0.828-0.89433.9850.0060.0060.0000.0000.0000.000
135A671ILE00.017-0.00134.2250.0010.0010.0000.0000.0000.000
136A672PHE00.0150.00230.124-0.002-0.0020.0000.0000.0000.000
137A673GLY00.0220.00035.2960.0010.0010.0000.0000.0000.000
138A674GLU-1-0.716-0.87237.350-0.004-0.0040.0000.0000.0000.000
139A675ASN00.1020.03640.0080.0020.0020.0000.0000.0000.000
140A676PRO0-0.032-0.02640.064-0.001-0.0010.0000.0000.0000.000
141A677CYS0-0.0080.00542.9990.0000.0000.0000.0000.0000.000
142A678ILE0-0.0030.00745.9300.0000.0000.0000.0000.0000.000
143A679HIS0-0.028-0.00644.754-0.001-0.0010.0000.0000.0000.000
144A680SER00.0190.01447.2450.0000.0000.0000.0000.0000.000
145A681THR0-0.0020.01347.2780.0000.0000.0000.0000.0000.000
146A682LEU0-0.026-0.01439.4160.0010.0010.0000.0000.0000.000
147A683GLY00.0210.00642.321-0.001-0.0010.0000.0000.0000.000
148A684LYS10.8620.90439.4370.0170.0170.0000.0000.0000.000
149A685SER0-0.015-0.01735.2820.0020.0020.0000.0000.0000.000
150A686ASN00.1230.08337.994-0.001-0.0010.0000.0000.0000.000
151A687SER0-0.090-0.07236.163-0.001-0.0010.0000.0000.0000.000
152A688ASN00.0150.01730.5330.0020.0020.0000.0000.0000.000
153A689VAL00.0350.02129.0460.0020.0020.0000.0000.0000.000
154A690LYS10.8700.95024.6020.0470.0470.0000.0000.0000.000
155A691ALA00.0140.01822.8120.0070.0070.0000.0000.0000.000
156A692LEU0-0.007-0.00123.760-0.010-0.0100.0000.0000.0000.000
157A693THR00.000-0.01522.316-0.005-0.0050.0000.0000.0000.000
158A694TYR0-0.0060.00114.214-0.003-0.0030.0000.0000.0000.000
159A695CYS0-0.063-0.02220.9570.0050.0050.0000.0000.0000.000
160A696ASP-1-0.843-0.88322.8220.0610.0610.0000.0000.0000.000
161A697LEU0-0.017-0.01624.921-0.004-0.0040.0000.0000.0000.000
162A698HIS00.0590.03826.8430.0040.0040.0000.0000.0000.000
163A699LYS10.9060.96426.111-0.010-0.0100.0000.0000.0000.000
164A700ILE00.0390.01930.7670.0030.0030.0000.0000.0000.000
165A701HIS0-0.010-0.00432.747-0.002-0.0020.0000.0000.0000.000
166A702ARG11.0040.99634.663-0.001-0.0010.0000.0000.0000.000
167A703ASP-1-0.838-0.92537.8410.0060.0060.0000.0000.0000.000
168A704ASP-1-0.839-0.91534.4520.0210.0210.0000.0000.0000.000
169A705LEU0-0.033-0.01838.0010.0010.0010.0000.0000.0000.000
170A706LEU0-0.015-0.02839.7900.0000.0000.0000.0000.0000.000
171A707ASP-1-0.788-0.88640.4120.0150.0150.0000.0000.0000.000
172A708VAL0-0.078-0.05239.5870.0010.0010.0000.0000.0000.000
173A709LEU0-0.004-0.01042.5700.0000.0000.0000.0000.0000.000
174A710ASP-1-0.896-0.92645.5290.0110.0110.0000.0000.0000.000
175A711LEU0-0.132-0.06443.2790.0000.0000.0000.0000.0000.000
176A712PHE0-0.076-0.04243.6300.0010.0010.0000.0000.0000.000
177A713PRO00.0560.03947.8230.0000.0000.0000.0000.0000.000
178A714GLU-1-0.936-0.99149.4830.0160.0160.0000.0000.0000.000
179A715PHE0-0.028-0.02042.9090.0000.0000.0000.0000.0000.000
180A716TYR0-0.007-0.01947.8220.0000.0000.0000.0000.0000.000
181A717ASP-1-0.874-0.93549.0720.0090.0090.0000.0000.0000.000
182A718SER00.0270.00047.6080.0000.0000.0000.0000.0000.000
183A719PHE00.0050.01940.9460.0000.0000.0000.0000.0000.000
184A720VAL0-0.047-0.02945.670-0.001-0.0010.0000.0000.0000.000
185A721ASN0-0.104-0.05047.6860.0000.0000.0000.0000.0000.000
186A722SER00.0110.01145.7230.0000.0000.0000.0000.0000.000
187A723LEU0-0.073-0.02839.8890.0010.0010.0000.0000.0000.000
188A724GLU-1-0.940-0.96542.2620.0070.0070.0000.0000.0000.000
189A725ILE0-0.063-0.03539.3270.0000.0000.0000.0000.0000.000
190A726THR0-0.0070.01237.7200.0000.0000.0000.0000.0000.000
191A727TYR00.008-0.00737.068-0.002-0.0020.0000.0000.0000.000
192A728ASN00.045-0.00138.6270.0010.0010.0000.0000.0000.000
193A729MET0-0.054-0.02234.159-0.002-0.0020.0000.0000.0000.000
194A730ARG10.8290.92639.4760.0030.0030.0000.0000.0000.000
195A731ASP-1-0.923-0.97541.898-0.016-0.0160.0000.0000.0000.000
196A732GLU-1-1.007-0.99843.436-0.004-0.0040.0000.0000.0000.000
197A733GLU-1-1.049-1.00744.628-0.016-0.0160.0000.0000.0000.000