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: 1N48Z

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 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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1927383.212606
FMO2-HF: Nuclear repulsion 1856502.705475
FMO2-HF: Total energy -70880.507131
FMO2-MP2: Total energy -71082.777843


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.
-0.2062.7210.046-1.314-1.66-0.001
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 : 0.023 / 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].
3A3GLU-1-0.786-0.8733.423-1.8710.0980.005-0.931-1.0430.001
4A4ASN0-0.023-0.0093.9300.4370.9570.001-0.153-0.3680.000
5A5LEU00.0610.0245.5140.0640.0640.0000.0000.0000.000
6A6TYR0-0.003-0.0127.8480.1960.1960.0000.0000.0000.000
7A7PHE0-0.040-0.0083.551-0.622-0.1840.040-0.230-0.249-0.002
8A8GLN0-0.034-0.0316.0330.3200.3200.0000.0000.0000.000
9A9GLY00.0530.0297.5360.1320.1320.0000.0000.0000.000
10A10HIS00.0060.0027.3250.2570.2570.0000.0000.0000.000
11A11MET0-0.024-0.01310.5140.1340.1340.0000.0000.0000.000
12A12ASP-1-0.821-0.89311.323-0.226-0.2260.0000.0000.0000.000
13A13VAL00.0350.02213.3380.0550.0550.0000.0000.0000.000
14A14LEU0-0.019-0.00814.6860.0450.0450.0000.0000.0000.000
15A15SER0-0.117-0.06716.6720.0390.0390.0000.0000.0000.000
16A16VAL00.0070.00417.6000.0230.0230.0000.0000.0000.000
17A17ALA00.0520.02519.4200.0200.0200.0000.0000.0000.000
18A18GLY00.0230.01221.1120.0140.0140.0000.0000.0000.000
19A19PRO0-0.072-0.05723.5970.0080.0080.0000.0000.0000.000
20A20PHE00.0330.02023.5730.0090.0090.0000.0000.0000.000
21A21MET00.0310.02822.1830.0030.0030.0000.0000.0000.000
22A22ARG10.9290.96525.9200.0940.0940.0000.0000.0000.000
23A23ARG10.8880.94429.2050.0360.0360.0000.0000.0000.000
24A24LEU00.0440.02826.1570.0040.0040.0000.0000.0000.000
25A25MET00.0050.03729.4140.0070.0070.0000.0000.0000.000
26A26LEU0-0.065-0.03730.9650.0040.0040.0000.0000.0000.000
27A27LEU0-0.039-0.02033.0430.0030.0030.0000.0000.0000.000
28A28SER00.028-0.00131.6170.0020.0020.0000.0000.0000.000
29A29GLY0-0.0120.00834.2150.0020.0020.0000.0000.0000.000
30A30GLU-1-0.751-0.86331.645-0.045-0.0450.0000.0000.0000.000
31A31THR0-0.040-0.04226.737-0.001-0.0010.0000.0000.0000.000
32A32VAL0-0.0030.01224.1240.0020.0020.0000.0000.0000.000
33A33ASN0-0.006-0.01922.299-0.023-0.0230.0000.0000.0000.000
34A34VAL00.0310.00317.0050.0160.0160.0000.0000.0000.000
35A35ALA00.0080.00316.369-0.026-0.0260.0000.0000.0000.000
36A36ILE00.0220.01710.3750.0230.0230.0000.0000.0000.000
37A37ARG10.8260.89111.652-0.263-0.2630.0000.0000.0000.000
38A38ASN0-0.006-0.0168.403-0.028-0.0280.0000.0000.0000.000
39A39GLY00.0080.0059.7900.0140.0140.0000.0000.0000.000
40A40ASN0-0.0060.00011.6780.0480.0480.0000.0000.0000.000
41A41GLU-1-0.791-0.86313.998-0.130-0.1300.0000.0000.0000.000
42A42ALA00.0100.00614.386-0.009-0.0090.0000.0000.0000.000
43A43VAL0-0.033-0.02113.356-0.003-0.0030.0000.0000.0000.000
44A44LEU0-0.0070.00115.647-0.016-0.0160.0000.0000.0000.000
45A45ILE0-0.007-0.00812.858-0.028-0.0280.0000.0000.0000.000
46A46GLY00.006-0.00616.282-0.008-0.0080.0000.0000.0000.000
47A47GLN0-0.073-0.05219.3710.0130.0130.0000.0000.0000.000
48A48LEU0-0.063-0.02823.114-0.001-0.0010.0000.0000.0000.000
49A49GLU-1-0.739-0.84126.584-0.085-0.0850.0000.0000.0000.000
50A50CYS0-0.093-0.02429.4120.0030.0030.0000.0000.0000.000
51A51LYS10.9440.94132.7280.0560.0560.0000.0000.0000.000
52A52SER00.0070.01935.8340.0030.0030.0000.0000.0000.000
53A53MET00.003-0.00936.241-0.003-0.0030.0000.0000.0000.000
54A54VAL00.0140.02536.964-0.001-0.0010.0000.0000.0000.000
55A55ARG10.8080.86331.5310.0810.0810.0000.0000.0000.000
56A56MET00.0330.07424.667-0.002-0.0020.0000.0000.0000.000
57A57CYS00.0210.01028.5080.0010.0010.0000.0000.0000.000
58A58ALA00.0240.01224.621-0.003-0.0030.0000.0000.0000.000
59A59PRO00.0410.03523.311-0.004-0.0040.0000.0000.0000.000
60A60LEU00.0240.01418.926-0.005-0.0050.0000.0000.0000.000
61A61GLY0-0.011-0.00316.828-0.002-0.0020.0000.0000.0000.000
62A62SER0-0.054-0.04717.8150.0040.0040.0000.0000.0000.000
63A63ARG10.7470.84912.7570.2410.2410.0000.0000.0000.000
64A64LEU00.0070.00418.5290.0190.0190.0000.0000.0000.000
65A65PRO00.0220.02319.2020.0020.0020.0000.0000.0000.000
66A66LEU00.0330.01515.691-0.001-0.0010.0000.0000.0000.000
67A67HIS0-0.016-0.01019.6340.0080.0080.0000.0000.0000.000
68A68ALA00.001-0.00322.9710.0020.0020.0000.0000.0000.000
69A69SER0-0.023-0.00621.753-0.007-0.0070.0000.0000.0000.000
70A70GLY0-0.002-0.01023.4900.0070.0070.0000.0000.0000.000
71A71ALA00.010-0.01419.9800.0080.0080.0000.0000.0000.000
72A72GLY0-0.002-0.00218.9880.0000.0000.0000.0000.0000.000
73A73LYS10.8170.86019.7870.0150.0150.0000.0000.0000.000
74A74ALA0-0.036-0.02420.9380.0160.0160.0000.0000.0000.000
75A75LEU0-0.043-0.02014.4100.0100.0100.0000.0000.0000.000
76A76LEU0-0.0170.00517.0770.0370.0370.0000.0000.0000.000
77A77TYR00.0630.03319.6150.0170.0170.0000.0000.0000.000
78A78PRO0-0.014-0.00618.4920.0080.0080.0000.0000.0000.000
79A79LEU0-0.043-0.00215.1530.0290.0290.0000.0000.0000.000
80A80ALA00.0180.01018.735-0.021-0.0210.0000.0000.0000.000
81A81GLU-1-0.858-0.94220.4560.1110.1110.0000.0000.0000.000
82A82GLU-1-0.886-0.94820.5240.1690.1690.0000.0000.0000.000
83A83GLU-1-0.829-0.88213.8660.4270.4270.0000.0000.0000.000
84A84LEU0-0.007-0.00718.034-0.009-0.0090.0000.0000.0000.000
85A85MET0-0.011-0.00220.363-0.020-0.0200.0000.0000.0000.000
86A86SER0-0.040-0.03016.909-0.009-0.0090.0000.0000.0000.000
87A87ILE0-0.049-0.02115.398-0.007-0.0070.0000.0000.0000.000
88A88ILE00.0040.00617.646-0.024-0.0240.0000.0000.0000.000
89A89LEU0-0.065-0.02220.346-0.017-0.0170.0000.0000.0000.000
90A90GLN0-0.066-0.04014.789-0.008-0.0080.0000.0000.0000.000
91A91THR0-0.027-0.02717.821-0.014-0.0140.0000.0000.0000.000
92A92GLY0-0.0190.01120.154-0.016-0.0160.0000.0000.0000.000
93A93LEU0-0.021-0.00723.1260.0020.0020.0000.0000.0000.000
94A94GLN00.0010.00324.8460.0000.0000.0000.0000.0000.000
95A95GLN0-0.003-0.00826.6370.0000.0000.0000.0000.0000.000
96A96PHE0-0.052-0.03424.145-0.006-0.0060.0000.0000.0000.000
97A97THR0-0.010-0.01230.045-0.002-0.0020.0000.0000.0000.000
98A98PRO0-0.030-0.02433.3130.0030.0030.0000.0000.0000.000
99A99THR00.016-0.00234.3540.0030.0030.0000.0000.0000.000
100A100THR0-0.038-0.01528.3130.0010.0010.0000.0000.0000.000
101A101LEU00.0060.01128.2470.0030.0030.0000.0000.0000.000
102A102VAL00.0210.00328.2490.0030.0030.0000.0000.0000.000
103A103ASP-1-0.856-0.90629.9650.0310.0310.0000.0000.0000.000
104A104MET00.0460.01323.429-0.004-0.0040.0000.0000.0000.000
105A105PRO0-0.005-0.00828.6430.0030.0030.0000.0000.0000.000
106A106THR0-0.022-0.03331.4320.0010.0010.0000.0000.0000.000
107A107LEU0-0.022-0.00323.889-0.001-0.0010.0000.0000.0000.000
108A108LEU00.001-0.00125.3110.0010.0010.0000.0000.0000.000
109A109LYS10.8210.89527.949-0.051-0.0510.0000.0000.0000.000
110A110ASP-1-0.825-0.89728.4730.0130.0130.0000.0000.0000.000
111A111LEU00.0120.00123.112-0.002-0.0020.0000.0000.0000.000
112A112GLU-1-0.811-0.90026.7570.0630.0630.0000.0000.0000.000
113A113GLN0-0.036-0.01428.875-0.004-0.0040.0000.0000.0000.000
114A114ALA0-0.001-0.01026.546-0.003-0.0030.0000.0000.0000.000
115A115ARG10.7940.89121.632-0.120-0.1200.0000.0000.0000.000
116A116GLU-1-0.967-0.96226.7660.0460.0460.0000.0000.0000.000
117A117LEU0-0.041-0.02130.226-0.003-0.0030.0000.0000.0000.000
118A118GLY00.0160.01226.405-0.004-0.0040.0000.0000.0000.000
119A119TYR0-0.037-0.01025.973-0.007-0.0070.0000.0000.0000.000
120A120THR00.0270.01724.4810.0030.0030.0000.0000.0000.000
121A121VAL00.0310.00027.482-0.008-0.0080.0000.0000.0000.000
122A122ASP-1-0.803-0.87427.271-0.030-0.0300.0000.0000.0000.000
123A123LYS10.8170.87729.263-0.006-0.0060.0000.0000.0000.000
124A124GLU-1-0.756-0.83932.573-0.021-0.0210.0000.0000.0000.000
125A125GLU-1-0.746-0.81129.0230.0010.0010.0000.0000.0000.000
126A126HIS0-0.007-0.00224.794-0.008-0.0080.0000.0000.0000.000
127A127VAL0-0.015-0.02828.159-0.003-0.0030.0000.0000.0000.000
128A128VAL00.0400.01430.9110.0020.0020.0000.0000.0000.000
129A129GLY0-0.015-0.00334.687-0.004-0.0040.0000.0000.0000.000
130A130LEU0-0.088-0.03328.558-0.003-0.0030.0000.0000.0000.000
131A131ASN00.0450.01131.9340.0040.0040.0000.0000.0000.000
132A132CYS0-0.067-0.04126.764-0.010-0.0100.0000.0000.0000.000
133A133ILE0-0.0090.01928.2750.0070.0070.0000.0000.0000.000
134A134ALA0-0.010-0.01423.109-0.011-0.0110.0000.0000.0000.000
135A135SER0-0.023-0.02523.2120.0120.0120.0000.0000.0000.000
136A136ALA00.0120.01718.922-0.017-0.0170.0000.0000.0000.000
137A137ILE0-0.026-0.01916.257-0.002-0.0020.0000.0000.0000.000
138A138TYR00.008-0.00916.1080.0090.0090.0000.0000.0000.000
139A139ASP-1-0.774-0.86512.6290.1780.1780.0000.0000.0000.000
140A140ASP-1-0.825-0.91615.2520.0690.0690.0000.0000.0000.000
141A141VAL0-0.102-0.04414.2370.0070.0070.0000.0000.0000.000
142A142GLY0-0.0060.01017.1100.0110.0110.0000.0000.0000.000
143A143SER0-0.102-0.06812.5570.0230.0230.0000.0000.0000.000
144A144VAL00.009-0.00114.835-0.038-0.0380.0000.0000.0000.000
145A145VAL0-0.058-0.03110.8790.0370.0370.0000.0000.0000.000
146A146ALA0-0.013-0.01011.925-0.093-0.0930.0000.0000.0000.000
147A147ALA00.0190.02214.6920.0470.0470.0000.0000.0000.000
148A148ILE0-0.023-0.00318.346-0.032-0.0320.0000.0000.0000.000
149A149SER0-0.011-0.01421.3490.0150.0150.0000.0000.0000.000
150A150ILE0-0.0130.00024.461-0.010-0.0100.0000.0000.0000.000
151A151SER00.037-0.00426.6830.0020.0020.0000.0000.0000.000
152A152GLY00.0160.00528.985-0.005-0.0050.0000.0000.0000.000
153A153PRO00.0070.00532.6310.0020.0020.0000.0000.0000.000
154A154SER00.000-0.01835.7480.0010.0010.0000.0000.0000.000
155A155SER0-0.028-0.01636.8560.0020.0020.0000.0000.0000.000
156A156ARG10.7250.81835.2680.0450.0450.0000.0000.0000.000
157A157LEU0-0.045-0.00831.5880.0010.0010.0000.0000.0000.000
158A158THR00.044-0.00435.9990.0000.0000.0000.0000.0000.000
159A159GLU-1-0.867-0.95337.860-0.013-0.0130.0000.0000.0000.000
160A160ASP-1-0.912-0.92938.846-0.013-0.0130.0000.0000.0000.000
161A161ARG10.7630.86735.8260.0300.0300.0000.0000.0000.000
162A162PHE0-0.0120.00234.538-0.001-0.0010.0000.0000.0000.000
163A163VAL00.0390.02933.9630.0000.0000.0000.0000.0000.000
164A164SER00.0270.01134.711-0.001-0.0010.0000.0000.0000.000
165A165GLN00.010-0.00732.641-0.005-0.0050.0000.0000.0000.000
166A166GLY00.0600.02530.398-0.004-0.0040.0000.0000.0000.000
167A167GLU-1-0.863-0.91029.8590.0040.0040.0000.0000.0000.000
168A168LEU0-0.0020.00830.532-0.001-0.0010.0000.0000.0000.000
169A169VAL0-0.0160.00125.713-0.005-0.0050.0000.0000.0000.000
170A170ARG10.7980.86326.016-0.009-0.0090.0000.0000.0000.000
171A171ASP-1-0.833-0.88226.0430.0000.0000.0000.0000.0000.000
172A172THR0-0.034-0.03425.046-0.003-0.0030.0000.0000.0000.000
173A173ALA00.0290.02121.997-0.009-0.0090.0000.0000.0000.000
174A174ARG10.8780.94921.931-0.005-0.0050.0000.0000.0000.000
175A175ASP-1-0.867-0.91823.489-0.020-0.0200.0000.0000.0000.000
176A176ILE0-0.019-0.01419.089-0.004-0.0040.0000.0000.0000.000
177A177SER00.019-0.00618.780-0.007-0.0070.0000.0000.0000.000
178A178THR0-0.065-0.04019.5800.0090.0090.0000.0000.0000.000
179A179ALA0-0.037-0.02721.4130.0030.0030.0000.0000.0000.000
180A180LEU0-0.024-0.00313.684-0.010-0.0100.0000.0000.0000.000
181A181GLY00.0360.03417.0210.0050.0050.0000.0000.0000.000
182A182LEU0-0.092-0.05219.1190.0120.0120.0000.0000.0000.000
183A183LYS10.8220.91217.590-0.047-0.0470.0000.0000.0000.000
184A184ALA0-0.033-0.01319.8050.0050.0050.0000.0000.0000.000