Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 496NN

Calculation Name: 1TUE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TUE

Chain ID: A

ChEMBL ID:

UniProt ID: P06789

Base Structure: X-ray

Registration Date: 2023-06-22

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 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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2521423.231639
FMO2-HF: Nuclear repulsion 2437376.443741
FMO2-HF: Total energy -84046.787898
FMO2-MP2: Total energy -84290.412546


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:425:SER)


Summations of interaction energy for fragment #1(A:425: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.
-51.155-43.88312.856-9.388-10.7390.023
Interaction energy analysis for fragmet #1(A:425:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.048 / q_NPA : 0.017
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].
3A427SER0-0.0240.0012.033-10.780-8.1574.982-3.794-3.8110.025
4A428ASN00.0720.0214.0073.3773.5770.003-0.068-0.1350.000
5A429MET00.0700.0315.4660.1600.1600.0000.0000.0000.000
6A430SER00.0070.0047.210-0.571-0.5710.0000.0000.0000.000
7A431GLN00.008-0.0046.3320.3250.3250.0000.0000.0000.000
8A432TRP00.0000.0032.412-7.825-4.8292.506-2.399-3.104-0.032
9A433ILE00.0450.0244.969-0.660-0.612-0.001-0.001-0.0450.000
10A434ARG10.9740.9948.370-0.647-0.6470.0000.0000.0000.000
11A435PHE00.0020.0065.801-0.086-0.0860.0000.0000.0000.000
12A436ARG10.8110.8956.7370.7360.7360.0000.0000.0000.000
13A437CYS0-0.007-0.0109.1390.0380.0380.0000.0000.0000.000
14A438SER0-0.020-0.01311.6040.0350.0350.0000.0000.0000.000
15A439LYS10.8640.94910.2670.9270.9270.0000.0000.0000.000
16A440ILE0-0.053-0.00812.698-0.001-0.0010.0000.0000.0000.000
17A441ASP-1-0.874-0.93015.530-0.227-0.2270.0000.0000.0000.000
18A442GLU-1-0.815-0.91019.264-0.079-0.0790.0000.0000.0000.000
19A443GLY00.004-0.00121.296-0.013-0.0130.0000.0000.0000.000
20A444GLY0-0.045-0.01321.759-0.002-0.0020.0000.0000.0000.000
21A445ASP-1-0.746-0.91522.7760.0460.0460.0000.0000.0000.000
22A446TRP0-0.056-0.01922.0050.0080.0080.0000.0000.0000.000
23A447ARG10.8970.94523.073-0.044-0.0440.0000.0000.0000.000
24A448PRO00.0640.03825.2160.0120.0120.0000.0000.0000.000
25A449ILE00.0200.02619.7220.0030.0030.0000.0000.0000.000
26A450VAL0-0.039-0.01923.9100.0140.0140.0000.0000.0000.000
27A451GLN0-0.020-0.02425.9990.0010.0010.0000.0000.0000.000
28A452PHE00.0180.02624.961-0.001-0.0010.0000.0000.0000.000
29A453LEU0-0.0030.00322.8450.0040.0040.0000.0000.0000.000
30A454ARG10.8600.91227.220-0.116-0.1160.0000.0000.0000.000
31A455TYR0-0.046-0.03130.667-0.002-0.0020.0000.0000.0000.000
32A456GLN0-0.038-0.02428.333-0.002-0.0020.0000.0000.0000.000
33A457GLN0-0.041-0.01931.0490.0080.0080.0000.0000.0000.000
34A458ILE0-0.0170.01126.0860.0150.0150.0000.0000.0000.000
35A459GLU-1-0.810-0.90329.4880.1410.1410.0000.0000.0000.000
36A460PHE00.007-0.00223.1630.0220.0220.0000.0000.0000.000
37A461ILE00.0140.00125.1700.0250.0250.0000.0000.0000.000
38A462THR00.0320.01225.3480.0290.0290.0000.0000.0000.000
39A463PHE00.0370.02019.9050.0360.0360.0000.0000.0000.000
40A464LEU0-0.009-0.00119.7680.0380.0380.0000.0000.0000.000
41A465GLY00.0210.01020.3540.0560.0560.0000.0000.0000.000
42A466ALA0-0.024-0.02321.0080.0560.0560.0000.0000.0000.000
43A467LEU00.0110.00715.1360.0620.0620.0000.0000.0000.000
44A468LYS10.8780.93916.055-0.454-0.4540.0000.0000.0000.000
45A469SER0-0.068-0.03716.2240.1130.1130.0000.0000.0000.000
46A470PHE00.0010.00813.7880.1300.1300.0000.0000.0000.000
47A471LEU00.002-0.00710.6040.1590.1590.0000.0000.0000.000
48A472LYS10.8020.89411.412-0.643-0.6430.0000.0000.0000.000
49A473GLY0-0.0020.02213.6490.1440.1440.0000.0000.0000.000
50A474THR0-0.085-0.04414.398-0.064-0.0640.0000.0000.0000.000
51A475PRO00.0620.03218.017-0.047-0.0470.0000.0000.0000.000
52A476LYS10.8650.93720.132-0.412-0.4120.0000.0000.0000.000
53A477LYS10.8750.92420.106-0.465-0.4650.0000.0000.0000.000
54A478ASN00.0090.01414.1180.1610.1610.0000.0000.0000.000
55A479CYS0-0.0100.00416.1310.0350.0350.0000.0000.0000.000
56A480LEU0-0.0180.00217.580-0.035-0.0350.0000.0000.0000.000
57A481VAL00.0050.00019.942-0.020-0.0200.0000.0000.0000.000
58A482PHE0-0.013-0.00119.8880.0030.0030.0000.0000.0000.000
59A483CYS00.020-0.00224.425-0.019-0.0190.0000.0000.0000.000
60A484GLY00.0370.02827.8180.0010.0010.0000.0000.0000.000
61A485PRO00.0830.03529.699-0.006-0.0060.0000.0000.0000.000
62A486ALA00.0350.02329.1550.0030.0030.0000.0000.0000.000
63A487ASN00.0180.00429.6190.0010.0010.0000.0000.0000.000
64A488THR00.0210.01929.273-0.002-0.0020.0000.0000.0000.000
65A489GLY00.0120.00927.3920.0020.0020.0000.0000.0000.000
66A490LYS10.7900.90025.099-0.057-0.0570.0000.0000.0000.000
67A491SER00.014-0.02222.4570.0210.0210.0000.0000.0000.000
68A492TYR0-0.0160.01021.389-0.007-0.0070.0000.0000.0000.000
69A493PHE00.0120.01021.189-0.010-0.0100.0000.0000.0000.000
70A494GLY00.0440.01518.9490.0090.0090.0000.0000.0000.000
71A495MET00.0420.01217.1220.0030.0030.0000.0000.0000.000
72A496SER0-0.046-0.02416.400-0.046-0.0460.0000.0000.0000.000
73A497PHE0-0.0060.00412.333-0.028-0.0280.0000.0000.0000.000
74A498ILE00.0250.00112.0460.0060.0060.0000.0000.0000.000
75A499HIS0-0.050-0.02411.531-0.162-0.1620.0000.0000.0000.000
76A500PHE00.0280.01111.438-0.145-0.1450.0000.0000.0000.000
77A501ILE0-0.051-0.0337.465-0.121-0.1210.0000.0000.0000.000
78A502GLN0-0.037-0.0197.270-0.600-0.6000.0000.0000.0000.000
79A503GLY0-0.0070.0087.233-0.257-0.2570.0000.0000.0000.000
80A504ALA00.0030.0078.845-0.215-0.2150.0000.0000.0000.000
81A505VAL00.001-0.00510.5910.1920.1920.0000.0000.0000.000
82A506ILE0-0.038-0.01213.035-0.058-0.0580.0000.0000.0000.000
83A507SER00.0450.00615.5350.0210.0210.0000.0000.0000.000
84A508PHE0-0.015-0.01319.1610.0010.0010.0000.0000.0000.000
85A509VAL00.0170.01321.435-0.019-0.0190.0000.0000.0000.000
86A510ASN00.0070.00123.6900.0290.0290.0000.0000.0000.000
87A511SER0-0.034-0.01823.751-0.013-0.0130.0000.0000.0000.000
88A512THR00.0250.01726.1400.0090.0090.0000.0000.0000.000
89A513SER00.0150.00622.4460.0090.0090.0000.0000.0000.000
90A514HIS10.8930.93917.702-0.200-0.2000.0000.0000.0000.000
91A515PHE00.023-0.00417.4300.0070.0070.0000.0000.0000.000
92A516TRP00.0380.02717.188-0.027-0.0270.0000.0000.0000.000
93A517LEU0-0.022-0.01814.165-0.010-0.0100.0000.0000.0000.000
94A518GLU-1-0.906-0.95112.558-0.284-0.2840.0000.0000.0000.000
95A519PRO00.0030.00510.736-0.061-0.0610.0000.0000.0000.000
96A520LEU0-0.023-0.0118.836-0.106-0.1060.0000.0000.0000.000
97A521THR0-0.025-0.0337.6700.5010.5010.0000.0000.0000.000
98A522ASP-1-0.934-0.9584.026-1.681-1.5670.000-0.027-0.0870.000
99A523THR0-0.0010.0163.409-2.873-1.9220.013-0.537-0.428-0.004
100A524LYS10.8190.8972.034-28.645-28.3055.353-2.562-3.1290.034
101A525VAL0-0.014-0.0156.183-0.039-0.0390.0000.0000.0000.000
102A526ALA00.0140.0169.679-0.318-0.3180.0000.0000.0000.000
103A527MET0-0.0120.00411.6680.0450.0450.0000.0000.0000.000
104A528LEU0-0.040-0.01015.177-0.065-0.0650.0000.0000.0000.000
105A529ASP-1-0.808-0.87618.2190.0310.0310.0000.0000.0000.000
106A530ASP-1-0.871-0.93121.0970.0250.0250.0000.0000.0000.000
107A531ALA00.0130.01222.874-0.009-0.0090.0000.0000.0000.000
108A532THR00.0480.02624.5480.0050.0050.0000.0000.0000.000
109A533THR00.0510.00927.5490.0160.0160.0000.0000.0000.000
110A534THR00.0090.00328.5650.0120.0120.0000.0000.0000.000
111A535CYS00.0060.02122.9910.0060.0060.0000.0000.0000.000
112A536TRP00.0400.01422.6720.0300.0300.0000.0000.0000.000
113A537THR00.0070.00526.5470.0150.0150.0000.0000.0000.000
114A538TYR0-0.024-0.02820.6560.0200.0200.0000.0000.0000.000
115A539PHE00.032-0.01118.3320.0140.0140.0000.0000.0000.000
116A540ASP-1-0.814-0.89923.6290.2160.2160.0000.0000.0000.000
117A541THR0-0.0250.00826.7070.0060.0060.0000.0000.0000.000
118A542TYR0-0.013-0.02223.0100.0060.0060.0000.0000.0000.000
119A543MET0-0.0310.01316.5520.0070.0070.0000.0000.0000.000
120A544ARG10.9090.95420.596-0.165-0.1650.0000.0000.0000.000
121A545ASN00.002-0.00918.7210.0020.0020.0000.0000.0000.000
122A546ALA00.0330.02216.4090.0690.0690.0000.0000.0000.000
123A547LEU0-0.019-0.00517.3930.0820.0820.0000.0000.0000.000
124A548ASP-1-0.795-0.87320.0870.4260.4260.0000.0000.0000.000
125A549GLY0-0.029-0.00116.3100.0310.0310.0000.0000.0000.000
126A550ASN0-0.038-0.02016.5740.0980.0980.0000.0000.0000.000
127A551PRO0-0.004-0.00714.2110.0300.0300.0000.0000.0000.000
128A552ILE00.0120.00213.512-0.107-0.1070.0000.0000.0000.000
129A553SER00.0360.01415.1660.0240.0240.0000.0000.0000.000
130A554ILE00.0010.00912.981-0.004-0.0040.0000.0000.0000.000
131A555ASP-1-0.766-0.86816.4800.0140.0140.0000.0000.0000.000
132A556ARG10.9100.94318.8410.0690.0690.0000.0000.0000.000
133A557LYS11.0141.02319.6100.1970.1970.0000.0000.0000.000
134A558HIS0-0.004-0.01721.2370.0190.0190.0000.0000.0000.000
135A559LYS10.8440.89022.316-0.049-0.0490.0000.0000.0000.000
136A560PRO0-0.0090.02519.6090.0000.0000.0000.0000.0000.000
137A561LEU0-0.022-0.01719.147-0.016-0.0160.0000.0000.0000.000
138A562ILE00.0390.02913.0320.0230.0230.0000.0000.0000.000
139A563GLN0-0.025-0.02414.9830.0290.0290.0000.0000.0000.000
140A564LEU00.0310.0248.554-0.001-0.0010.0000.0000.0000.000
141A565LYS10.9180.9679.860-1.593-1.5930.0000.0000.0000.000
142A566CYS0-0.025-0.0049.7260.0960.0960.0000.0000.0000.000
143A567PRO00.0170.0267.9200.1330.1330.0000.0000.0000.000
144A568PRO00.0490.02310.032-0.315-0.3150.0000.0000.0000.000
145A569ILE0-0.020-0.01512.104-0.057-0.0570.0000.0000.0000.000
146A570LEU00.0010.00114.732-0.017-0.0170.0000.0000.0000.000
147A571LEU0-0.019-0.01316.980-0.053-0.0530.0000.0000.0000.000
148A572THR0-0.020-0.02519.9920.0090.0090.0000.0000.0000.000
149A573THR00.028-0.00322.912-0.007-0.0070.0000.0000.0000.000
150A574ASN00.0310.00726.2470.0050.0050.0000.0000.0000.000
151A575ILE0-0.020-0.00628.988-0.006-0.0060.0000.0000.0000.000
152A576HIS00.0490.00228.9000.0130.0130.0000.0000.0000.000
153A577PRO0-0.027-0.01026.092-0.008-0.0080.0000.0000.0000.000
154A578ALA0-0.018-0.00829.1650.0090.0090.0000.0000.0000.000
155A579LYS10.8160.89131.142-0.134-0.1340.0000.0000.0000.000
156A580ASP-1-0.792-0.88834.5140.1080.1080.0000.0000.0000.000
157A581ASN0-0.048-0.02934.565-0.015-0.0150.0000.0000.0000.000
158A582ARG10.8320.91133.386-0.095-0.0950.0000.0000.0000.000
159A583TRP0-0.057-0.02329.201-0.004-0.0040.0000.0000.0000.000
160A584PRO00.0980.04030.2660.0180.0180.0000.0000.0000.000
161A585TYR0-0.090-0.06424.6660.0020.0020.0000.0000.0000.000
162A586LEU0-0.020-0.03024.0340.0300.0300.0000.0000.0000.000
163A587GLU-1-0.829-0.89926.3140.1930.1930.0000.0000.0000.000
164A588SER0-0.042-0.00628.5640.0130.0130.0000.0000.0000.000
165A589ARG10.7500.84823.309-0.306-0.3060.0000.0000.0000.000
166A590ILE00.0350.03322.0810.0410.0410.0000.0000.0000.000
167A591THR0-0.012-0.00322.512-0.013-0.0130.0000.0000.0000.000
168A592VAL00.0180.00623.6730.0090.0090.0000.0000.0000.000
169A593PHE0-0.026-0.00622.7140.0010.0010.0000.0000.0000.000
170A594GLU-1-0.796-0.89726.7110.1280.1280.0000.0000.0000.000
171A595PHE0-0.047-0.02324.0880.0020.0020.0000.0000.0000.000
172A596PRO00.0070.00730.079-0.009-0.0090.0000.0000.0000.000
173A597ASN0-0.019-0.00732.822-0.011-0.0110.0000.0000.0000.000
174A598ALA00.0240.01332.4940.0010.0010.0000.0000.0000.000
175A599PHE00.001-0.00826.8530.0050.0050.0000.0000.0000.000
176A600PRO0-0.0250.00830.962-0.005-0.0050.0000.0000.0000.000
177A601PHE00.016-0.00631.508-0.005-0.0050.0000.0000.0000.000
178A602ASP-1-0.793-0.90935.289-0.021-0.0210.0000.0000.0000.000
179A603LYS10.9120.95037.7260.0080.0080.0000.0000.0000.000
180A604ASN0-0.092-0.05038.471-0.001-0.0010.0000.0000.0000.000
181A605GLY00.0100.01737.425-0.005-0.0050.0000.0000.0000.000
182A606ASN0-0.0040.00933.628-0.012-0.0120.0000.0000.0000.000
183A607PRO00.0030.00829.4160.0100.0100.0000.0000.0000.000
184A608VAL0-0.024-0.01131.758-0.001-0.0010.0000.0000.0000.000
185A609TYR0-0.023-0.02127.4590.0050.0050.0000.0000.0000.000
186A610GLU-1-0.878-0.92625.295-0.090-0.0900.0000.0000.0000.000
187A611ILE0-0.048-0.03820.0670.0130.0130.0000.0000.0000.000
188A612ASN00.0570.02119.494-0.015-0.0150.0000.0000.0000.000
189A613ASP-1-0.727-0.86014.321-0.379-0.3790.0000.0000.0000.000
190A614LYS10.9120.95316.6010.1820.1820.0000.0000.0000.000
191A615ASN00.0370.01918.9420.0220.0220.0000.0000.0000.000
192A616TRP00.006-0.01415.2080.0760.0760.0000.0000.0000.000
193A617LYS10.7820.89415.1540.2070.2070.0000.0000.0000.000
194A618CYS0-0.0070.01616.1340.0490.0490.0000.0000.0000.000
195A619PHE0-0.007-0.02317.4870.0340.0340.0000.0000.0000.000
196A620PHE00.0140.00413.2580.0630.0630.0000.0000.0000.000
197A621GLU-1-0.863-0.93816.3010.0750.0750.0000.0000.0000.000
198A622ARG10.9080.96818.125-0.093-0.0930.0000.0000.0000.000
199A623THR0-0.080-0.05018.6190.0220.0220.0000.0000.0000.000
200A624TRP00.0400.03410.9450.0550.0550.0000.0000.0000.000
201A625SER00.0290.00117.1640.0660.0660.0000.0000.0000.000
202A626ARG10.9010.94019.560-0.220-0.2200.0000.0000.0000.000
203A627LEU00.0010.01315.4130.0060.0060.0000.0000.0000.000
204A628ASP-1-0.868-0.92516.2460.8020.8020.0000.0000.0000.000
205A629LEU00.0040.01711.3130.1440.1440.0000.0000.0000.000