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: K98R3

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 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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2520324.717462
FMO2-HF: Nuclear repulsion 2436278.821144
FMO2-HF: Total energy -84045.896318
FMO2-MP2: Total energy -84289.49965


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.
-36.92-30.3077.69-6.559-7.7450.039
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 : 0.052 / q_NPA : 0.018
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].
3A427SER0-0.0120.0061.969-14.053-11.2615.902-4.313-4.3810.038
4A428ASN00.0420.0104.1440.5860.7820.001-0.061-0.1360.000
5A429MET00.0730.0266.2230.9390.9390.0000.0000.0000.000
6A430SER00.0100.0057.748-0.164-0.1640.0000.0000.0000.000
7A431GLN00.000-0.0146.7060.3830.3830.0000.0000.0000.000
8A432TRP0-0.034-0.0133.406-1.3820.1720.205-0.624-1.135-0.002
9A433ILE00.0520.0246.095-0.972-0.9720.0000.0000.0000.000
10A434ARG10.9850.9939.689-1.447-1.4470.0000.0000.0000.000
11A435PHE00.0040.0046.559-0.436-0.4360.0000.0000.0000.000
12A436ARG10.8410.9117.612-0.625-0.6250.0000.0000.0000.000
13A437CYS0-0.015-0.01310.178-0.221-0.2210.0000.0000.0000.000
14A438SER0-0.0090.00811.622-0.130-0.1300.0000.0000.0000.000
15A439LYS10.8560.94210.0440.2480.2480.0000.0000.0000.000
16A440ILE0-0.046-0.00513.398-0.069-0.0690.0000.0000.0000.000
17A441ASP-1-0.892-0.94316.2300.0420.0420.0000.0000.0000.000
18A442GLU-1-0.880-0.94619.9890.2780.2780.0000.0000.0000.000
19A443GLY00.001-0.00622.209-0.023-0.0230.0000.0000.0000.000
20A444GLY0-0.056-0.02322.787-0.014-0.0140.0000.0000.0000.000
21A445ASP-1-0.766-0.92323.8000.1850.1850.0000.0000.0000.000
22A446TRP0-0.049-0.01922.8910.0080.0080.0000.0000.0000.000
23A447ARG10.9060.95224.191-0.171-0.1710.0000.0000.0000.000
24A448PRO00.0580.04126.1280.0020.0020.0000.0000.0000.000
25A449ILE00.0240.02420.514-0.007-0.0070.0000.0000.0000.000
26A450VAL0-0.036-0.01824.7270.0010.0010.0000.0000.0000.000
27A451GLN0-0.022-0.02826.807-0.007-0.0070.0000.0000.0000.000
28A452PHE00.0190.02925.521-0.011-0.0110.0000.0000.0000.000
29A453LEU0-0.0010.00223.508-0.005-0.0050.0000.0000.0000.000
30A454ARG10.9520.97227.755-0.184-0.1840.0000.0000.0000.000
31A455TYR0-0.063-0.05231.249-0.010-0.0100.0000.0000.0000.000
32A456GLN0-0.037-0.02828.716-0.013-0.0130.0000.0000.0000.000
33A457GLN0-0.019-0.01031.4210.0070.0070.0000.0000.0000.000
34A458ILE0-0.0270.00726.3870.0110.0110.0000.0000.0000.000
35A459GLU-1-0.924-0.96529.8430.2030.2030.0000.0000.0000.000
36A460PHE00.008-0.01024.0030.0230.0230.0000.0000.0000.000
37A461ILE00.0160.00225.7160.0300.0300.0000.0000.0000.000
38A462THR00.0330.01325.7850.0300.0300.0000.0000.0000.000
39A463PHE00.0420.02320.0520.0320.0320.0000.0000.0000.000
40A464LEU0-0.013-0.00220.5410.0420.0420.0000.0000.0000.000
41A465GLY00.0100.00320.7740.0600.0600.0000.0000.0000.000
42A466ALA0-0.023-0.02221.1890.0430.0430.0000.0000.0000.000
43A467LEU00.0110.00715.5340.0450.0450.0000.0000.0000.000
44A468LYS10.9420.97816.281-0.479-0.4790.0000.0000.0000.000
45A469SER0-0.065-0.03716.3670.0960.0960.0000.0000.0000.000
46A470PHE00.0000.00713.7650.0920.0920.0000.0000.0000.000
47A471LEU0-0.001-0.00711.3740.1140.1140.0000.0000.0000.000
48A472LYS10.8610.94011.349-0.682-0.6820.0000.0000.0000.000
49A473GLY00.0050.02313.2780.0760.0760.0000.0000.0000.000
50A474THR0-0.081-0.03514.046-0.082-0.0820.0000.0000.0000.000
51A475PRO00.0690.03317.716-0.040-0.0400.0000.0000.0000.000
52A476LYS10.8660.93720.003-0.321-0.3210.0000.0000.0000.000
53A477LYS10.9050.94619.591-0.431-0.4310.0000.0000.0000.000
54A478ASN00.0240.02013.9170.1640.1640.0000.0000.0000.000
55A479CYS0-0.0080.00216.1110.0290.0290.0000.0000.0000.000
56A480LEU0-0.0090.00517.596-0.021-0.0210.0000.0000.0000.000
57A481VAL00.0060.00519.832-0.021-0.0210.0000.0000.0000.000
58A482PHE0-0.023-0.00420.1440.0100.0100.0000.0000.0000.000
59A483CYS00.016-0.00424.303-0.024-0.0240.0000.0000.0000.000
60A484GLY00.0700.04327.8060.0050.0050.0000.0000.0000.000
61A485PRO00.0760.04229.714-0.007-0.0070.0000.0000.0000.000
62A486ALA00.0150.00729.2100.0090.0090.0000.0000.0000.000
63A487ASN00.0260.00929.8700.0070.0070.0000.0000.0000.000
64A488THR00.0170.01629.4330.0040.0040.0000.0000.0000.000
65A489GLY00.0210.01627.6240.0090.0090.0000.0000.0000.000
66A490LYS10.8440.92725.153-0.071-0.0710.0000.0000.0000.000
67A491SER00.019-0.03622.6450.0290.0290.0000.0000.0000.000
68A492TYR00.0230.03021.6390.0050.0050.0000.0000.0000.000
69A493PHE00.0080.00921.3960.0110.0110.0000.0000.0000.000
70A494GLY00.0510.01019.1320.0330.0330.0000.0000.0000.000
71A495MET00.0480.01417.3840.0320.0320.0000.0000.0000.000
72A496SER0-0.040-0.02816.599-0.003-0.0030.0000.0000.0000.000
73A497PHE0-0.0110.00112.7310.0370.0370.0000.0000.0000.000
74A498ILE00.0230.00312.3440.0930.0930.0000.0000.0000.000
75A499HIS0-0.054-0.02811.722-0.100-0.1000.0000.0000.0000.000
76A500PHE00.0280.01512.196-0.014-0.0140.0000.0000.0000.000
77A501ILE0-0.041-0.0178.0830.0780.0780.0000.0000.0000.000
78A502GLN0-0.017-0.0127.1160.0130.0130.0000.0000.0000.000
79A503GLY0-0.0030.0057.466-0.223-0.2230.0000.0000.0000.000
80A504ALA0-0.0010.0088.879-0.213-0.2130.0000.0000.0000.000
81A505VAL00.005-0.00310.5990.1770.1770.0000.0000.0000.000
82A506ILE0-0.041-0.01313.059-0.083-0.0830.0000.0000.0000.000
83A507SER00.018-0.00515.5420.0520.0520.0000.0000.0000.000
84A508PHE00.0240.00219.166-0.009-0.0090.0000.0000.0000.000
85A509VAL00.0250.01921.441-0.011-0.0110.0000.0000.0000.000
86A510ASN00.0080.00023.6960.0190.0190.0000.0000.0000.000
87A511SER0-0.048-0.02023.793-0.015-0.0150.0000.0000.0000.000
88A512THR00.0220.01126.1460.0090.0090.0000.0000.0000.000
89A513SER00.0230.01022.3440.0020.0020.0000.0000.0000.000
90A514HIS10.9380.95517.718-0.015-0.0150.0000.0000.0000.000
91A515PHE00.017-0.00917.433-0.012-0.0120.0000.0000.0000.000
92A516TRP00.0290.02317.188-0.043-0.0430.0000.0000.0000.000
93A517LEU0-0.019-0.01914.119-0.002-0.0020.0000.0000.0000.000
94A518GLU-1-0.908-0.95112.562-0.679-0.6790.0000.0000.0000.000
95A519PRO0-0.0030.02810.735-0.121-0.1210.0000.0000.0000.000
96A520LEU0-0.017-0.0118.841-0.100-0.1000.0000.0000.0000.000
97A521THR0-0.029-0.0607.9540.3940.3940.0000.0000.0000.000
98A522ASP-1-0.913-0.9474.016-2.092-2.010-0.001-0.027-0.0550.000
99A523THR0-0.0080.0143.410-2.888-1.9210.013-0.553-0.427-0.004
100A524LYS10.8550.9272.307-13.725-12.7031.570-0.981-1.6110.007
101A525VAL0-0.019-0.0135.8790.0330.0330.0000.0000.0000.000
102A526ALA00.0190.0199.658-0.263-0.2630.0000.0000.0000.000
103A527MET0-0.0360.00611.6820.0790.0790.0000.0000.0000.000
104A528LEU0-0.034-0.00815.190-0.080-0.0800.0000.0000.0000.000
105A529ASP-1-0.817-0.88118.2310.0700.0700.0000.0000.0000.000
106A530ASP-1-0.942-0.96921.1090.0100.0100.0000.0000.0000.000
107A531ALA00.0060.00622.927-0.014-0.0140.0000.0000.0000.000
108A532THR00.0550.02924.5610.0090.0090.0000.0000.0000.000
109A533THR00.0490.00527.5610.0130.0130.0000.0000.0000.000
110A534THR0-0.003-0.00528.0700.0090.0090.0000.0000.0000.000
111A535CYS0-0.0220.01922.7530.0050.0050.0000.0000.0000.000
112A536TRP00.0690.01922.8320.0160.0160.0000.0000.0000.000
113A537THR00.0110.01526.5610.0110.0110.0000.0000.0000.000
114A538TYR0-0.028-0.02420.7340.0100.0100.0000.0000.0000.000
115A539PHE00.022-0.01618.5200.0060.0060.0000.0000.0000.000
116A540ASP-1-0.830-0.90923.6420.1410.1410.0000.0000.0000.000
117A541THR0-0.0190.00326.7210.0040.0040.0000.0000.0000.000
118A542TYR0-0.013-0.02222.9870.0010.0010.0000.0000.0000.000
119A543MET0-0.0410.00716.522-0.014-0.0140.0000.0000.0000.000
120A544ARG10.9420.97520.610-0.089-0.0890.0000.0000.0000.000
121A545ASN00.0310.01218.7900.0290.0290.0000.0000.0000.000
122A546ALA00.0220.01816.4850.0510.0510.0000.0000.0000.000
123A547LEU0-0.034-0.01717.4090.0710.0710.0000.0000.0000.000
124A548ASP-1-0.793-0.85720.1040.3150.3150.0000.0000.0000.000
125A549GLY0-0.030-0.00416.3080.0320.0320.0000.0000.0000.000
126A550ASN0-0.040-0.02216.5860.0820.0820.0000.0000.0000.000
127A551PRO0-0.026-0.01914.2350.0150.0150.0000.0000.0000.000
128A552ILE00.011-0.00213.276-0.053-0.0530.0000.0000.0000.000
129A553SER00.0120.00015.175-0.009-0.0090.0000.0000.0000.000
130A554ILE00.0010.00712.8850.0200.0200.0000.0000.0000.000
131A555ASP-1-0.789-0.88616.485-0.167-0.1670.0000.0000.0000.000
132A556ARG10.9080.94618.8460.2020.2020.0000.0000.0000.000
133A557LYS11.0201.02419.5240.3820.3820.0000.0000.0000.000
134A558HIS0-0.006-0.02121.0470.0060.0060.0000.0000.0000.000
135A559LYS10.9000.93522.2310.1090.1090.0000.0000.0000.000
136A560PRO0-0.050-0.01119.6980.0060.0060.0000.0000.0000.000
137A561LEU0-0.001-0.00119.151-0.025-0.0250.0000.0000.0000.000
138A562ILE00.0260.02313.1960.0220.0220.0000.0000.0000.000
139A563GLN0-0.011-0.02214.9910.0360.0360.0000.0000.0000.000
140A564LEU00.0150.0218.254-0.038-0.0380.0000.0000.0000.000
141A565LYS10.9250.9709.880-1.097-1.0970.0000.0000.0000.000
142A566CYS0-0.028-0.0069.7380.0190.0190.0000.0000.0000.000
143A567PRO00.0290.0347.9660.1650.1650.0000.0000.0000.000
144A568PRO00.0450.0209.772-0.245-0.2450.0000.0000.0000.000
145A569ILE0-0.010-0.00412.122-0.050-0.0500.0000.0000.0000.000
146A570LEU00.0010.00014.7500.0030.0030.0000.0000.0000.000
147A571LEU0-0.014-0.01216.997-0.058-0.0580.0000.0000.0000.000
148A572THR0-0.019-0.01720.0080.0190.0190.0000.0000.0000.000
149A573THR00.018-0.00322.927-0.016-0.0160.0000.0000.0000.000
150A574ASN00.0310.00426.2620.0160.0160.0000.0000.0000.000
151A575ILE0-0.0150.00329.001-0.007-0.0070.0000.0000.0000.000
152A576HIS00.0630.01228.9160.0070.0070.0000.0000.0000.000
153A577PRO0-0.021-0.00926.194-0.009-0.0090.0000.0000.0000.000
154A578ALA0-0.007-0.00729.1820.0040.0040.0000.0000.0000.000
155A579LYS10.9200.95431.161-0.133-0.1330.0000.0000.0000.000
156A580ASP-1-0.789-0.87134.5750.0860.0860.0000.0000.0000.000
157A581ASN0-0.031-0.01634.603-0.014-0.0140.0000.0000.0000.000
158A582ARG10.8280.89633.333-0.075-0.0750.0000.0000.0000.000
159A583TRP0-0.077-0.02729.208-0.005-0.0050.0000.0000.0000.000
160A584PRO00.0830.04230.2830.0160.0160.0000.0000.0000.000
161A585TYR0-0.109-0.08724.6930.0050.0050.0000.0000.0000.000
162A586LEU0-0.023-0.02724.0020.0240.0240.0000.0000.0000.000
163A587GLU-1-0.838-0.91526.3320.1630.1630.0000.0000.0000.000
164A588SER0-0.047-0.01228.5830.0140.0140.0000.0000.0000.000
165A589ARG10.7750.86023.222-0.222-0.2220.0000.0000.0000.000
166A590ILE00.0330.02922.0700.0300.0300.0000.0000.0000.000
167A591THR0-0.044-0.01922.346-0.003-0.0030.0000.0000.0000.000
168A592VAL00.005-0.00223.3820.0090.0090.0000.0000.0000.000
169A593PHE0-0.036-0.01222.8660.0060.0060.0000.0000.0000.000
170A594GLU-1-0.893-0.96126.6900.1290.1290.0000.0000.0000.000
171A595PHE0-0.055-0.02824.3720.0090.0090.0000.0000.0000.000
172A596PRO00.0040.00730.190-0.013-0.0130.0000.0000.0000.000
173A597ASN0-0.018-0.00833.073-0.016-0.0160.0000.0000.0000.000
174A598ALA00.0310.02032.7540.0040.0040.0000.0000.0000.000
175A599PHE0-0.0030.01027.4220.0080.0080.0000.0000.0000.000
176A600PRO0-0.0200.00931.509-0.009-0.0090.0000.0000.0000.000
177A601PHE00.0250.00232.0560.0020.0020.0000.0000.0000.000
178A602ASP-1-0.837-0.92635.6890.0430.0430.0000.0000.0000.000
179A603LYS10.9250.94138.209-0.047-0.0470.0000.0000.0000.000
180A604ASN0-0.052-0.02338.819-0.005-0.0050.0000.0000.0000.000
181A605GLY0-0.0020.01137.622-0.005-0.0050.0000.0000.0000.000
182A606ASN0-0.0090.00734.020-0.008-0.0080.0000.0000.0000.000
183A607PRO00.0000.00529.7330.0050.0050.0000.0000.0000.000
184A608VAL0-0.012-0.00432.1870.0030.0030.0000.0000.0000.000
185A609TYR0-0.023-0.02128.2490.0100.0100.0000.0000.0000.000
186A610GLU-1-0.891-0.93825.9210.0430.0430.0000.0000.0000.000
187A611ILE0-0.051-0.02720.7670.0250.0250.0000.0000.0000.000
188A612ASN00.0660.02319.9150.0040.0040.0000.0000.0000.000
189A613ASP-1-0.771-0.89415.2320.1090.1090.0000.0000.0000.000
190A614LYS10.9680.99417.350-0.033-0.0330.0000.0000.0000.000
191A615ASN00.0250.00919.7920.0330.0330.0000.0000.0000.000
192A616TRP00.001-0.01416.1780.0730.0730.0000.0000.0000.000
193A617LYS10.8200.91016.446-0.221-0.2210.0000.0000.0000.000
194A618CYS00.0060.02517.4030.0400.0400.0000.0000.0000.000
195A619PHE0-0.006-0.02518.3270.0060.0060.0000.0000.0000.000
196A620PHE00.003-0.00814.0950.0400.0400.0000.0000.0000.000
197A621GLU-1-0.883-0.94117.4640.4740.4740.0000.0000.0000.000
198A622ARG10.8980.95819.374-0.300-0.3000.0000.0000.0000.000
199A623THR0-0.082-0.05119.471-0.003-0.0030.0000.0000.0000.000
200A624TRP00.0380.03112.0480.0340.0340.0000.0000.0000.000
201A625SER00.027-0.00118.0900.0530.0530.0000.0000.0000.000
202A626ARG10.9300.96220.511-0.379-0.3790.0000.0000.0000.000
203A627LEU0-0.0140.00315.963-0.020-0.0200.0000.0000.0000.000
204A628ASP-1-0.994-1.01016.8010.8320.8320.0000.0000.0000.000
205A629LEU0-0.0110.01412.0930.1390.1390.0000.0000.0000.000