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: 2NNVR

Calculation Name: 1TW9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TW9

Chain ID: A

ChEMBL ID:

UniProt ID: Q9NJQ6

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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2164787.8142
FMO2-HF: Nuclear repulsion 2089080.763153
FMO2-HF: Total energy -75707.051046
FMO2-MP2: Total energy -75929.239382


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-1.69-0.010.002-0.782-0.90.003
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.012
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].
3A3HIS0-0.062-0.0383.702-0.5281.1520.002-0.782-0.9000.003
4A4TYR00.0250.0035.8960.4720.4720.0000.0000.0000.000
5A5LYS10.8260.9158.9340.6700.6700.0000.0000.0000.000
6A6LEU0-0.020-0.01412.2060.0430.0430.0000.0000.0000.000
7A7THR00.0180.01715.3670.0100.0100.0000.0000.0000.000
8A8TYR00.036-0.00818.5290.0320.0320.0000.0000.0000.000
9A9PHE00.0280.02821.705-0.011-0.0110.0000.0000.0000.000
10A10ASN00.0350.00923.5070.0060.0060.0000.0000.0000.000
11A11GLY00.012-0.00324.4650.0100.0100.0000.0000.0000.000
12A12ARG10.8540.92723.9770.0050.0050.0000.0000.0000.000
13A13GLY00.028-0.00524.090-0.009-0.0090.0000.0000.0000.000
14A14ALA0-0.004-0.00225.2130.0080.0080.0000.0000.0000.000
15A15GLY00.0530.04421.065-0.005-0.0050.0000.0000.0000.000
16A16GLU-1-0.727-0.83820.000-0.003-0.0030.0000.0000.0000.000
17A17CYS0-0.0090.00220.5480.0200.0200.0000.0000.0000.000
18A18ALA00.0350.01716.8750.0250.0250.0000.0000.0000.000
19A19ARG10.7570.87016.0930.1100.1100.0000.0000.0000.000
20A20GLN0-0.051-0.03216.3840.0480.0480.0000.0000.0000.000
21A21VAL00.001-0.00515.1460.0390.0390.0000.0000.0000.000
22A22PHE00.0070.00010.5640.0440.0440.0000.0000.0000.000
23A23ALA0-0.0030.00513.0340.1020.1020.0000.0000.0000.000
24A24LEU0-0.007-0.01315.4290.0480.0480.0000.0000.0000.000
25A25ALA0-0.021-0.00711.7930.0210.0210.0000.0000.0000.000
26A26ASP-1-0.866-0.90311.5630.5520.5520.0000.0000.0000.000
27A27GLN0-0.043-0.0095.0730.5450.5450.0000.0000.0000.000
28A28LYS10.9480.9745.0620.9740.9740.0000.0000.0000.000
29A29TYR0-0.0010.0007.370-0.144-0.1440.0000.0000.0000.000
30A30GLU-1-0.858-0.9329.768-0.719-0.7190.0000.0000.0000.000
31A31ASP-1-0.744-0.86112.238-0.128-0.1280.0000.0000.0000.000
32A32VAL00.0180.01515.4240.0220.0220.0000.0000.0000.000
33A33ARG10.7950.88517.8760.1080.1080.0000.0000.0000.000
34A34LEU00.0020.00621.3500.0050.0050.0000.0000.0000.000
35A35THR00.000-0.03623.8910.0130.0130.0000.0000.0000.000
36A36GLN00.025-0.00727.635-0.010-0.0100.0000.0000.0000.000
37A37GLU-1-0.842-0.89930.296-0.120-0.1200.0000.0000.0000.000
38A38THR00.004-0.00624.913-0.009-0.0090.0000.0000.0000.000
39A39PHE0-0.0030.00625.801-0.014-0.0140.0000.0000.0000.000
40A40VAL0-0.015-0.00727.336-0.006-0.0060.0000.0000.0000.000
41A41PRO0-0.009-0.00927.615-0.001-0.0010.0000.0000.0000.000
42A42LEU00.0340.02122.117-0.008-0.0080.0000.0000.0000.000
43A43LYS10.8720.96725.5340.1170.1170.0000.0000.0000.000
44A44ALA0-0.007-0.01427.9110.0040.0040.0000.0000.0000.000
45A45THR0-0.067-0.04222.851-0.012-0.0120.0000.0000.0000.000
46A46PHE00.0400.02020.945-0.025-0.0250.0000.0000.0000.000
47A47PRO00.0150.00421.9190.0220.0220.0000.0000.0000.000
48A48PHE00.0070.00124.8090.0140.0140.0000.0000.0000.000
49A49GLY00.0350.04027.5080.0140.0140.0000.0000.0000.000
50A50GLN0-0.060-0.02926.7380.0110.0110.0000.0000.0000.000
51A51VAL00.0360.03122.123-0.018-0.0180.0000.0000.0000.000
52A52PRO0-0.071-0.03420.4140.0190.0190.0000.0000.0000.000
53A53VAL0-0.017-0.02618.3270.0130.0130.0000.0000.0000.000
54A54LEU0-0.0190.00912.543-0.009-0.0090.0000.0000.0000.000
55A55GLU-1-0.821-0.90913.248-0.618-0.6180.0000.0000.0000.000
56A56VAL00.010-0.0059.2910.0050.0050.0000.0000.0000.000
57A57ASP-1-0.809-0.9036.363-3.281-3.2810.0000.0000.0000.000
58A58GLY0-0.0070.0039.1640.1620.1620.0000.0000.0000.000
59A59GLN0-0.060-0.03112.2700.2740.2740.0000.0000.0000.000
60A60GLN0-0.016-0.02314.6200.0400.0400.0000.0000.0000.000
61A61LEU0-0.0070.00917.0820.0380.0380.0000.0000.0000.000
62A62ALA00.011-0.00518.753-0.005-0.0050.0000.0000.0000.000
63A63GLN00.0120.00721.6460.0230.0230.0000.0000.0000.000
64A64SER0-0.027-0.02822.3780.0070.0070.0000.0000.0000.000
65A65GLN00.045-0.00221.9580.0120.0120.0000.0000.0000.000
66A66ALA0-0.0060.01122.3240.0160.0160.0000.0000.0000.000
67A67ILE00.0090.00816.8260.0080.0080.0000.0000.0000.000
68A68CYS0-0.043-0.02017.7710.0190.0190.0000.0000.0000.000
69A69ARG10.8380.90419.0030.0300.0300.0000.0000.0000.000
70A70TYR00.0180.00812.1070.0470.0470.0000.0000.0000.000
71A71LEU00.0140.01312.5310.0370.0370.0000.0000.0000.000
72A72ALA0-0.009-0.00415.1720.0750.0750.0000.0000.0000.000
73A73LYS10.8650.91717.746-0.051-0.0510.0000.0000.0000.000
74A74THR0-0.050-0.01511.0340.0000.0000.0000.0000.0000.000
75A75PHE0-0.008-0.0109.4850.1000.1000.0000.0000.0000.000
76A76GLY00.0110.03214.3530.0130.0130.0000.0000.0000.000
77A77PHE0-0.011-0.01015.625-0.017-0.0170.0000.0000.0000.000
78A78ALA00.024-0.01220.259-0.032-0.0320.0000.0000.0000.000
79A79GLY00.0230.01622.487-0.013-0.0130.0000.0000.0000.000
80A80ALA00.0160.02123.0980.0200.0200.0000.0000.0000.000
81A81THR0-0.034-0.03424.893-0.004-0.0040.0000.0000.0000.000
82A82PRO00.026-0.01126.310-0.004-0.0040.0000.0000.0000.000
83A83PHE00.0160.01327.473-0.008-0.0080.0000.0000.0000.000
84A84GLU-1-0.774-0.88327.8620.1120.1120.0000.0000.0000.000
85A85SER0-0.0200.00025.1330.0010.0010.0000.0000.0000.000
86A86ALA00.0170.01626.825-0.008-0.0080.0000.0000.0000.000
87A87LEU0-0.024-0.00330.009-0.007-0.0070.0000.0000.0000.000
88A88ILE00.0080.00125.035-0.005-0.0050.0000.0000.0000.000
89A89ASP-1-0.804-0.89125.7650.0330.0330.0000.0000.0000.000
90A90SER0-0.022-0.01728.384-0.008-0.0080.0000.0000.0000.000
91A91LEU00.004-0.00430.790-0.005-0.0050.0000.0000.0000.000
92A92ALA0-0.0100.00427.545-0.003-0.0030.0000.0000.0000.000
93A93ASP-1-0.806-0.89029.536-0.017-0.0170.0000.0000.0000.000
94A94ALA00.0270.01431.679-0.004-0.0040.0000.0000.0000.000
95A95TYR0-0.041-0.03029.616-0.004-0.0040.0000.0000.0000.000
96A96THR0-0.042-0.03230.477-0.006-0.0060.0000.0000.0000.000
97A97ASP-1-0.893-0.93832.852-0.015-0.0150.0000.0000.0000.000
98A98TYR0-0.052-0.04934.817-0.001-0.0010.0000.0000.0000.000
99A99ARG10.8490.90232.3660.0170.0170.0000.0000.0000.000
100A100ALA0-0.0210.01035.686-0.003-0.0030.0000.0000.0000.000
101A101GLU-1-0.859-0.88137.755-0.005-0.0050.0000.0000.0000.000
102A102MET0-0.084-0.02336.486-0.002-0.0020.0000.0000.0000.000
103A118ASP-1-0.860-0.93845.656-0.010-0.0100.0000.0000.0000.000
104A119LYS10.8480.90247.4240.0120.0120.0000.0000.0000.000
105A120PRO00.0260.00643.9400.0010.0010.0000.0000.0000.000
106A121LYS10.8740.93744.1390.0010.0010.0000.0000.0000.000
107A122THR00.001-0.01145.1270.0020.0020.0000.0000.0000.000
108A123ASP-1-0.843-0.89848.272-0.009-0.0090.0000.0000.0000.000
109A124VAL0-0.002-0.01043.3870.0000.0000.0000.0000.0000.000
110A125LEU0-0.0230.00039.4190.0020.0020.0000.0000.0000.000
111A126LEU00.0330.01942.4190.0020.0020.0000.0000.0000.000
112A127PRO00.0140.01844.7490.0030.0030.0000.0000.0000.000
113A128ALA00.0440.03040.9670.0020.0020.0000.0000.0000.000
114A129ARG10.7850.87139.725-0.010-0.0100.0000.0000.0000.000
115A130THR0-0.021-0.01940.8480.0040.0040.0000.0000.0000.000
116A131LYS10.8240.89841.9740.0030.0030.0000.0000.0000.000
117A132PHE00.0390.01833.2840.0030.0030.0000.0000.0000.000
118A133LEU00.0340.01636.5510.0040.0040.0000.0000.0000.000
119A134GLY00.0360.04139.2280.0040.0040.0000.0000.0000.000
120A135PHE0-0.086-0.05638.8010.0030.0030.0000.0000.0000.000
121A136ILE00.0590.03533.2810.0040.0040.0000.0000.0000.000
122A137THR00.016-0.00836.8140.0060.0060.0000.0000.0000.000
123A138LYS10.9050.96339.265-0.022-0.0220.0000.0000.0000.000
124A139PHE0-0.018-0.01634.4540.0000.0000.0000.0000.0000.000
125A140LEU00.0390.02233.0400.0040.0040.0000.0000.0000.000
126A141LYS10.8420.91536.259-0.034-0.0340.0000.0000.0000.000
127A142LYS10.8030.91436.906-0.049-0.0490.0000.0000.0000.000
128A143ASN0-0.035-0.02931.3110.0030.0030.0000.0000.0000.000
129A144SER00.0180.00734.5130.0000.0000.0000.0000.0000.000
130A145SER0-0.041-0.01729.933-0.001-0.0010.0000.0000.0000.000
131A146GLY0-0.0170.00031.4330.0030.0030.0000.0000.0000.000
132A147PHE00.0190.00126.4330.0000.0000.0000.0000.0000.000
133A148LEU0-0.032-0.01829.241-0.006-0.0060.0000.0000.0000.000
134A149VAL0-0.030-0.03529.034-0.008-0.0080.0000.0000.0000.000
135A150GLY00.0710.05528.4840.0080.0080.0000.0000.0000.000
136A151ASP-1-0.902-0.94126.4170.1520.1520.0000.0000.0000.000
137A152LYS10.8620.92418.271-0.282-0.2820.0000.0000.0000.000
138A153ILE0-0.0340.00521.791-0.008-0.0080.0000.0000.0000.000
139A154SER0-0.005-0.03622.7210.0150.0150.0000.0000.0000.000
140A155TRP00.043-0.01620.876-0.011-0.0110.0000.0000.0000.000
141A156VAL00.0230.01822.598-0.012-0.0120.0000.0000.0000.000
142A157ASP-1-0.739-0.84025.5830.0870.0870.0000.0000.0000.000
143A158LEU00.0240.01020.337-0.006-0.0060.0000.0000.0000.000
144A159LEU0-0.0130.00024.735-0.010-0.0100.0000.0000.0000.000
145A160VAL0-0.010-0.00226.433-0.009-0.0090.0000.0000.0000.000
146A161ALA00.0110.00927.694-0.005-0.0050.0000.0000.0000.000
147A162GLU-1-0.737-0.83525.9060.0220.0220.0000.0000.0000.000
148A163HIS00.0160.02528.174-0.006-0.0060.0000.0000.0000.000
149A164VAL00.0200.00831.073-0.003-0.0030.0000.0000.0000.000
150A165ALA00.0580.04030.355-0.002-0.0020.0000.0000.0000.000
151A166ASP-1-0.823-0.86930.655-0.014-0.0140.0000.0000.0000.000
152A167MET0-0.024-0.01532.630-0.005-0.0050.0000.0000.0000.000
153A168THR0-0.037-0.04035.775-0.001-0.0010.0000.0000.0000.000
154A169ASN0-0.071-0.04833.638-0.001-0.0010.0000.0000.0000.000
155A170ARG10.7430.85832.5380.0130.0130.0000.0000.0000.000
156A171VAL0-0.024-0.01738.716-0.002-0.0020.0000.0000.0000.000
157A172PRO00.0630.03740.7180.0020.0020.0000.0000.0000.000
158A173GLU-1-0.757-0.87641.7370.0060.0060.0000.0000.0000.000
159A174TYR0-0.051-0.03036.4190.0020.0020.0000.0000.0000.000
160A175ILE00.0080.00037.3360.0010.0010.0000.0000.0000.000
161A176GLU-1-0.921-0.95340.6770.0180.0180.0000.0000.0000.000
162A177GLY00.0080.00244.424-0.002-0.0020.0000.0000.0000.000
163A178PHE0-0.028-0.01540.0800.0010.0010.0000.0000.0000.000
164A179PRO00.0470.02439.8040.0020.0020.0000.0000.0000.000
165A180GLU-1-0.822-0.91938.4020.0420.0420.0000.0000.0000.000
166A181VAL00.0270.01435.1310.0050.0050.0000.0000.0000.000
167A182LYS10.8850.93834.979-0.038-0.0380.0000.0000.0000.000
168A183ALA0-0.001-0.00735.0700.0030.0030.0000.0000.0000.000
169A184HIS0-0.114-0.06429.3960.0020.0020.0000.0000.0000.000
170A185MET00.0170.01230.8280.0050.0050.0000.0000.0000.000
171A186GLU-1-0.802-0.88930.2240.0570.0570.0000.0000.0000.000
172A187ARG10.8930.96528.776-0.080-0.0800.0000.0000.0000.000
173A188ILE0-0.0110.00225.0960.0140.0140.0000.0000.0000.000
174A189GLN0-0.023-0.03025.5570.0060.0060.0000.0000.0000.000
175A190GLN00.0170.00326.4800.0060.0060.0000.0000.0000.000
176A191THR0-0.044-0.02222.1710.0140.0140.0000.0000.0000.000
177A192PRO00.009-0.00521.3350.0040.0040.0000.0000.0000.000
178A193ARG10.7980.88412.744-0.506-0.5060.0000.0000.0000.000
179A194ILE0-0.0020.00919.296-0.008-0.0080.0000.0000.0000.000
180A195LYS10.8960.96521.409-0.100-0.1000.0000.0000.0000.000
181A196LYS10.9260.95414.901-0.293-0.2930.0000.0000.0000.000
182A197TRP0-0.052-0.02517.175-0.015-0.0150.0000.0000.0000.000
183A198ILE0-0.028-0.02420.337-0.022-0.0220.0000.0000.0000.000
184A199GLU-1-0.918-0.97324.0370.0670.0670.0000.0000.0000.000
185A200THR0-0.073-0.05020.496-0.007-0.0070.0000.0000.0000.000
186A201ARG10.7500.87021.402-0.037-0.0370.0000.0000.0000.000
187A202PRO00.000-0.01221.4790.0000.0000.0000.0000.0000.000
188A203GLU-1-0.891-0.93024.628-0.010-0.0100.0000.0000.0000.000
189A204THR0-0.021-0.01726.318-0.008-0.0080.0000.0000.0000.000
190A205PRO00.0240.02429.2230.0060.0060.0000.0000.0000.000
191A206PHE00.0210.02827.3150.0060.0060.0000.0000.0000.000