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: YVYJ2

Calculation Name: 1TF1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TF1

Chain ID: A

ChEMBL ID:

UniProt ID: P0ACN4

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:


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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1921269.508172
FMO2-HF: Nuclear repulsion 1850390.232791
FMO2-HF: Total energy -70879.275381
FMO2-MP2: Total energy -71081.671745


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:1:GLY)


Summations of interaction energy for fragment #1(A:1:GLY)
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.
0.2653.6030.093-1.332-2.0990
Interaction energy analysis for fragmet #1(A:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / q_NPA : -0.001
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].
3A3GLU-1-0.811-0.9033.167-0.6391.2820.034-0.758-1.1970.002
4A4ASN0-0.050-0.0292.9850.0161.0230.031-0.376-0.662-0.001
5A5LEU00.0740.0204.584-0.123-0.097-0.001-0.012-0.0130.000
6A6TYR0-0.012-0.0097.5160.2020.2020.0000.0000.0000.000
7A7PHE0-0.0410.0103.404-0.636-0.2520.029-0.186-0.227-0.001
8A8GLN0-0.014-0.0305.9060.4300.4300.0000.0000.0000.000
9A9GLY00.0580.0337.1760.2210.2210.0000.0000.0000.000
10A10HIS00.0180.0007.5980.2540.2540.0000.0000.0000.000
11A11MET0-0.038-0.01510.3190.2100.2100.0000.0000.0000.000
12A12ASP-1-0.825-0.90011.600-0.427-0.4270.0000.0000.0000.000
13A13VAL00.0110.01713.1120.0890.0890.0000.0000.0000.000
14A14LEU0-0.031-0.03014.6380.0700.0700.0000.0000.0000.000
15A15SER0-0.118-0.05616.1920.0560.0560.0000.0000.0000.000
16A16VAL00.0140.01017.8540.0370.0370.0000.0000.0000.000
17A17ALA00.0370.01619.3210.0310.0310.0000.0000.0000.000
18A18GLY00.0170.01321.0370.0210.0210.0000.0000.0000.000
19A19PRO0-0.047-0.05123.5820.0140.0140.0000.0000.0000.000
20A20PHE00.0550.03123.3150.0140.0140.0000.0000.0000.000
21A21MET00.0320.02922.0950.0050.0050.0000.0000.0000.000
22A22ARG10.9090.95225.7140.1410.1410.0000.0000.0000.000
23A23ARG10.9680.99128.8800.0780.0780.0000.0000.0000.000
24A24LEU00.0640.03926.0960.0070.0070.0000.0000.0000.000
25A25MET0-0.0110.03329.1050.0120.0120.0000.0000.0000.000
26A26LEU0-0.073-0.04630.7150.0070.0070.0000.0000.0000.000
27A27LEU0-0.045-0.02432.9580.0050.0050.0000.0000.0000.000
28A28SER0-0.010-0.00231.3510.0050.0050.0000.0000.0000.000
29A29GLY0-0.0160.00033.8550.0050.0050.0000.0000.0000.000
30A30GLU-1-0.777-0.88631.307-0.057-0.0570.0000.0000.0000.000
31A31THR0-0.032-0.02826.563-0.004-0.0040.0000.0000.0000.000
32A32VAL00.0030.01724.0690.0040.0040.0000.0000.0000.000
33A33ASN0-0.017-0.02121.609-0.022-0.0220.0000.0000.0000.000
34A34VAL00.0520.02216.4260.0130.0130.0000.0000.0000.000
35A35ALA0-0.016-0.00616.384-0.021-0.0210.0000.0000.0000.000
36A36ILE00.0210.01710.2760.0100.0100.0000.0000.0000.000
37A37ARG10.9010.94811.419-0.257-0.2570.0000.0000.0000.000
38A38ASN0-0.025-0.0047.715-0.035-0.0350.0000.0000.0000.000
39A39GLY00.0190.0069.763-0.010-0.0100.0000.0000.0000.000
40A40ASN0-0.024-0.00911.6460.0050.0050.0000.0000.0000.000
41A41GLU-1-0.834-0.89113.893-0.038-0.0380.0000.0000.0000.000
42A42ALA00.0150.00814.276-0.021-0.0210.0000.0000.0000.000
43A43VAL0-0.023-0.00113.0140.0060.0060.0000.0000.0000.000
44A44LEU0-0.0010.00015.547-0.035-0.0350.0000.0000.0000.000
45A45ILE00.0110.00012.755-0.015-0.0150.0000.0000.0000.000
46A46GLY00.0270.01616.323-0.014-0.0140.0000.0000.0000.000
47A47GLN0-0.079-0.06519.2580.0200.0200.0000.0000.0000.000
48A48LEU0-0.047-0.01122.956-0.003-0.0030.0000.0000.0000.000
49A49GLU-1-0.792-0.88826.363-0.103-0.1030.0000.0000.0000.000
50A50CYS0-0.0420.00329.2880.0020.0020.0000.0000.0000.000
51A51LYS10.9620.95432.5080.0790.0790.0000.0000.0000.000
52A52SER0-0.0160.00535.6730.0040.0040.0000.0000.0000.000
53A53MET00.0250.00336.001-0.003-0.0030.0000.0000.0000.000
54A54VAL00.0120.03636.751-0.001-0.0010.0000.0000.0000.000
55A55ARG10.8210.87131.2620.0880.0880.0000.0000.0000.000
56A56MET00.0310.06324.3250.0000.0000.0000.0000.0000.000
57A57CYS0-0.011-0.02127.909-0.002-0.0020.0000.0000.0000.000
58A58ALA00.0370.03224.1620.0010.0010.0000.0000.0000.000
59A59PRO00.0500.03922.739-0.007-0.0070.0000.0000.0000.000
60A60LEU00.0220.02418.699-0.001-0.0010.0000.0000.0000.000
61A61GLY0-0.022-0.01916.4360.0030.0030.0000.0000.0000.000
62A62SER0-0.062-0.05617.4840.0200.0200.0000.0000.0000.000
63A63ARG10.8050.87311.9240.1200.1200.0000.0000.0000.000
64A64LEU00.000-0.00818.2790.0160.0160.0000.0000.0000.000
65A65PRO00.0390.03918.9350.0080.0080.0000.0000.0000.000
66A66LEU00.028-0.01415.845-0.013-0.0130.0000.0000.0000.000
67A67HIS0-0.025-0.01519.9660.0000.0000.0000.0000.0000.000
68A68ALA00.0110.00623.473-0.001-0.0010.0000.0000.0000.000
69A69SER00.0080.02322.061-0.012-0.0120.0000.0000.0000.000
70A70GLY00.010-0.00723.7500.0050.0050.0000.0000.0000.000
71A71ALA0-0.003-0.02119.9860.0020.0020.0000.0000.0000.000
72A72GLY00.007-0.00319.011-0.005-0.0050.0000.0000.0000.000
73A73LYS10.8420.90519.6220.0160.0160.0000.0000.0000.000
74A74ALA0-0.030-0.01320.7170.0110.0110.0000.0000.0000.000
75A75LEU0-0.050-0.02514.503-0.003-0.0030.0000.0000.0000.000
76A76LEU0-0.013-0.00516.7810.0290.0290.0000.0000.0000.000
77A77TYR00.0520.02719.1730.0100.0100.0000.0000.0000.000
78A78PRO0-0.055-0.03017.8640.0080.0080.0000.0000.0000.000
79A79LEU0-0.058-0.00914.7030.0190.0190.0000.0000.0000.000
80A80ALA0-0.0050.00218.337-0.014-0.0140.0000.0000.0000.000
81A81GLU-1-0.851-0.94720.0220.1140.1140.0000.0000.0000.000
82A82GLU-1-0.906-0.95420.1570.1790.1790.0000.0000.0000.000
83A83GLU-1-0.876-0.93614.0130.4380.4380.0000.0000.0000.000
84A84LEU0-0.016-0.02317.8950.0080.0080.0000.0000.0000.000
85A85MET0-0.006-0.00320.111-0.009-0.0090.0000.0000.0000.000
86A86SER0-0.0070.00017.1780.0060.0060.0000.0000.0000.000
87A87ILE0-0.057-0.02615.4890.0080.0080.0000.0000.0000.000
88A88ILE00.0030.00218.067-0.012-0.0120.0000.0000.0000.000
89A89LEU0-0.0450.00120.956-0.013-0.0130.0000.0000.0000.000
90A90GLN0-0.078-0.05115.7280.0230.0230.0000.0000.0000.000
91A91THR0-0.049-0.03418.060-0.009-0.0090.0000.0000.0000.000
92A92GLY0-0.0180.01220.506-0.018-0.0180.0000.0000.0000.000
93A93LEU0-0.019-0.01023.502-0.001-0.0010.0000.0000.0000.000
94A94GLN00.0190.01325.275-0.001-0.0010.0000.0000.0000.000
95A95GLN00.0100.01127.0230.0000.0000.0000.0000.0000.000
96A96PHE0-0.060-0.04224.035-0.003-0.0030.0000.0000.0000.000
97A97THR0-0.023-0.03229.895-0.003-0.0030.0000.0000.0000.000
98A98PRO0-0.037-0.03833.1740.0040.0040.0000.0000.0000.000
99A99THR00.0040.00734.5750.0020.0020.0000.0000.0000.000
100A100THR0-0.016-0.00128.4680.0000.0000.0000.0000.0000.000
101A101LEU00.0040.00528.5210.0040.0040.0000.0000.0000.000
102A102VAL0-0.008-0.01828.6900.0020.0020.0000.0000.0000.000
103A103ASP-1-0.878-0.93130.3120.0460.0460.0000.0000.0000.000
104A104MET00.034-0.00123.876-0.004-0.0040.0000.0000.0000.000
105A105PRO00.006-0.00728.844-0.001-0.0010.0000.0000.0000.000
106A106THR00.0180.00931.313-0.002-0.0020.0000.0000.0000.000
107A107LEU00.0170.02224.113-0.005-0.0050.0000.0000.0000.000
108A108LEU00.0310.01824.975-0.004-0.0040.0000.0000.0000.000
109A109LYS10.9470.98027.762-0.039-0.0390.0000.0000.0000.000
110A110ASP-1-0.891-0.94828.3720.0040.0040.0000.0000.0000.000
111A111LEU0-0.023-0.02522.744-0.006-0.0060.0000.0000.0000.000
112A112GLU-1-0.938-0.97426.2600.0480.0480.0000.0000.0000.000
113A113GLN0-0.039-0.01028.223-0.008-0.0080.0000.0000.0000.000
114A114ALA00.0040.00025.920-0.005-0.0050.0000.0000.0000.000
115A115ARG10.9020.95422.147-0.066-0.0660.0000.0000.0000.000
116A116GLU-1-1.001-0.98326.2080.0090.0090.0000.0000.0000.000
117A117LEU0-0.025-0.01529.773-0.004-0.0040.0000.0000.0000.000
118A118GLY0-0.016-0.00726.119-0.006-0.0060.0000.0000.0000.000
119A119TYR0-0.021-0.00325.887-0.011-0.0110.0000.0000.0000.000
120A120THR00.0100.01924.2950.0080.0080.0000.0000.0000.000
121A121VAL00.014-0.01927.170-0.009-0.0090.0000.0000.0000.000
122A122ASP-1-0.829-0.88527.301-0.027-0.0270.0000.0000.0000.000
123A123LYS10.9520.96229.3510.0030.0030.0000.0000.0000.000
124A124GLU-1-0.831-0.89632.338-0.017-0.0170.0000.0000.0000.000
125A125GLU-1-0.792-0.85529.2290.0010.0010.0000.0000.0000.000
126A126HIS00.0010.01524.745-0.004-0.0040.0000.0000.0000.000
127A127VAL0-0.007-0.01928.0280.0000.0000.0000.0000.0000.000
128A128VAL00.0210.00030.6640.0000.0000.0000.0000.0000.000
129A129GLY0-0.021-0.01534.444-0.003-0.0030.0000.0000.0000.000
130A130LEU0-0.100-0.03027.833-0.006-0.0060.0000.0000.0000.000
131A131ASN00.0650.02231.6670.0060.0060.0000.0000.0000.000
132A132CYS0-0.100-0.05626.380-0.012-0.0120.0000.0000.0000.000
133A133ILE00.0020.01928.0030.0080.0080.0000.0000.0000.000
134A134ALA0-0.045-0.03122.759-0.012-0.0120.0000.0000.0000.000
135A135SER0-0.008-0.01923.1010.0110.0110.0000.0000.0000.000
136A136ALA00.0100.01218.698-0.019-0.0190.0000.0000.0000.000
137A137ILE0-0.031-0.01416.4600.0030.0030.0000.0000.0000.000
138A138TYR00.012-0.01116.076-0.009-0.0090.0000.0000.0000.000
139A139ASP-1-0.822-0.90812.164-0.085-0.0850.0000.0000.0000.000
140A140ASP-1-0.880-0.96115.122-0.062-0.0620.0000.0000.0000.000
141A141VAL0-0.138-0.05613.5020.0230.0230.0000.0000.0000.000
142A142GLY0-0.0140.00316.6560.0220.0220.0000.0000.0000.000
143A143SER0-0.089-0.03412.5820.0170.0170.0000.0000.0000.000
144A144VAL00.0070.00014.242-0.041-0.0410.0000.0000.0000.000
145A145VAL0-0.044-0.03110.8570.0060.0060.0000.0000.0000.000
146A146ALA0-0.022-0.01812.126-0.095-0.0950.0000.0000.0000.000
147A147ALA00.0100.02714.8110.0500.0500.0000.0000.0000.000
148A148ILE0-0.008-0.00218.446-0.028-0.0280.0000.0000.0000.000
149A149SER0-0.019-0.01621.3480.0200.0200.0000.0000.0000.000
150A150ILE00.0210.01924.356-0.011-0.0110.0000.0000.0000.000
151A151SER00.014-0.01826.3910.0030.0030.0000.0000.0000.000
152A152GLY00.0060.00428.785-0.005-0.0050.0000.0000.0000.000
153A153PRO00.0080.00432.2610.0030.0030.0000.0000.0000.000
154A154SER00.0460.02435.485-0.001-0.0010.0000.0000.0000.000
155A155SER0-0.036-0.01436.7550.0010.0010.0000.0000.0000.000
156A156ARG10.7480.83635.0270.0550.0550.0000.0000.0000.000
157A157LEU0-0.038-0.01131.6230.0000.0000.0000.0000.0000.000
158A158THR00.017-0.03336.1620.0000.0000.0000.0000.0000.000
159A159GLU-1-0.849-0.94437.820-0.019-0.0190.0000.0000.0000.000
160A160ASP-1-0.921-0.92038.869-0.024-0.0240.0000.0000.0000.000
161A161ARG10.8210.90536.1600.0420.0420.0000.0000.0000.000
162A162PHE0-0.0010.00034.540-0.002-0.0020.0000.0000.0000.000
163A163VAL00.0430.03533.920-0.002-0.0020.0000.0000.0000.000
164A164SER00.0100.00434.765-0.003-0.0030.0000.0000.0000.000
165A165GLN00.018-0.01332.428-0.008-0.0080.0000.0000.0000.000
166A166GLY00.0620.03430.245-0.006-0.0060.0000.0000.0000.000
167A167GLU-1-0.970-0.98929.749-0.028-0.0280.0000.0000.0000.000
168A168LEU00.0030.01430.695-0.004-0.0040.0000.0000.0000.000
169A169VAL0-0.018-0.01125.603-0.009-0.0090.0000.0000.0000.000
170A170ARG10.9070.96525.9860.0230.0230.0000.0000.0000.000
171A171ASP-1-0.882-0.93626.099-0.050-0.0500.0000.0000.0000.000
172A172THR0-0.029-0.02824.761-0.006-0.0060.0000.0000.0000.000
173A173ALA00.0100.00921.867-0.014-0.0140.0000.0000.0000.000
174A174ARG10.8940.95021.9750.0350.0350.0000.0000.0000.000
175A175ASP-1-0.898-0.95523.484-0.082-0.0820.0000.0000.0000.000
176A176ILE0-0.057-0.03318.923-0.010-0.0100.0000.0000.0000.000
177A177SER00.0190.01218.789-0.019-0.0190.0000.0000.0000.000
178A178THR0-0.029-0.01219.6330.0000.0000.0000.0000.0000.000
179A179ALA0-0.043-0.03021.4330.0000.0000.0000.0000.0000.000
180A180LEU0-0.034-0.01113.961-0.011-0.0110.0000.0000.0000.000
181A181GLY00.0770.05617.168-0.013-0.0130.0000.0000.0000.000
182A182LEU0-0.112-0.05418.9350.0210.0210.0000.0000.0000.000
183A183LYS10.9130.95718.8270.0730.0730.0000.0000.0000.000
184A184ALA0-0.0110.00220.1800.0150.0150.0000.0000.0000.000