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: 7661K

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 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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2159499.614548
FMO2-HF: Nuclear repulsion 2083793.206962
FMO2-HF: Total energy -75706.407585
FMO2-MP2: Total energy -75928.642335


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.
-2.584-0.4660.011-0.911-1.2180.003
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 : -0.022 / q_NPA : -0.016
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].
3A3HIS0-0.053-0.0173.530-1.2900.6400.013-0.907-1.0370.003
4A4TYR00.0140.0015.8640.6610.6610.0000.0000.0000.000
5A5LYS10.8350.9328.7740.8030.8030.0000.0000.0000.000
6A6LEU0-0.007-0.00212.0000.0550.0550.0000.0000.0000.000
7A7THR00.0120.01815.0890.0050.0050.0000.0000.0000.000
8A8TYR00.025-0.01918.4260.0340.0340.0000.0000.0000.000
9A9PHE00.0530.04021.586-0.009-0.0090.0000.0000.0000.000
10A10ASN00.0330.00923.268-0.001-0.0010.0000.0000.0000.000
11A11GLY0-0.003-0.01324.1980.0140.0140.0000.0000.0000.000
12A12ARG10.8730.93923.7580.0220.0220.0000.0000.0000.000
13A13GLY00.008-0.00824.046-0.011-0.0110.0000.0000.0000.000
14A14ALA00.006-0.01024.8930.0080.0080.0000.0000.0000.000
15A15GLY00.0430.03520.863-0.008-0.0080.0000.0000.0000.000
16A16GLU-1-0.734-0.84019.744-0.041-0.0410.0000.0000.0000.000
17A17CYS00.0130.02020.3140.0210.0210.0000.0000.0000.000
18A18ALA00.0600.02116.5100.0240.0240.0000.0000.0000.000
19A19ARG10.7660.86915.8800.1550.1550.0000.0000.0000.000
20A20GLN0-0.057-0.04416.2450.0480.0480.0000.0000.0000.000
21A21VAL0-0.024-0.01014.6100.0440.0440.0000.0000.0000.000
22A22PHE00.0310.01110.0610.0460.0460.0000.0000.0000.000
23A23ALA0-0.0150.01012.7370.1010.1010.0000.0000.0000.000
24A24LEU0-0.015-0.02315.1150.0600.0600.0000.0000.0000.000
25A25ALA0-0.039-0.01911.7860.0320.0320.0000.0000.0000.000
26A26ASP-1-0.896-0.92911.4100.6070.6070.0000.0000.0000.000
27A27GLN0-0.038-0.0104.7440.5390.641-0.0010.000-0.1000.000
28A28LYS10.9620.9794.7040.9241.010-0.001-0.004-0.0810.000
29A29TYR0-0.019-0.0147.291-0.168-0.1680.0000.0000.0000.000
30A30GLU-1-0.870-0.9439.508-0.824-0.8240.0000.0000.0000.000
31A31ASP-1-0.752-0.85911.836-0.176-0.1760.0000.0000.0000.000
32A32VAL00.004-0.00215.1490.0260.0260.0000.0000.0000.000
33A33ARG10.7990.88417.6160.1630.1630.0000.0000.0000.000
34A34LEU0-0.010-0.00821.2840.0060.0060.0000.0000.0000.000
35A35THR00.016-0.02423.7190.0130.0130.0000.0000.0000.000
36A36GLN00.018-0.00927.337-0.012-0.0120.0000.0000.0000.000
37A37GLU-1-0.815-0.89529.923-0.139-0.1390.0000.0000.0000.000
38A38THR0-0.026-0.01724.377-0.012-0.0120.0000.0000.0000.000
39A39PHE0-0.014-0.00625.434-0.015-0.0150.0000.0000.0000.000
40A40VAL0-0.0050.00926.771-0.008-0.0080.0000.0000.0000.000
41A41PRO0-0.013-0.01227.4840.0010.0010.0000.0000.0000.000
42A42LEU00.0290.01821.947-0.013-0.0130.0000.0000.0000.000
43A43LYS10.8680.96425.1950.1430.1430.0000.0000.0000.000
44A44ALA00.003-0.01827.107-0.001-0.0010.0000.0000.0000.000
45A45THR0-0.053-0.03322.519-0.013-0.0130.0000.0000.0000.000
46A46PHE00.0120.01320.735-0.026-0.0260.0000.0000.0000.000
47A47PRO00.0400.02321.5820.0260.0260.0000.0000.0000.000
48A48PHE00.006-0.00624.5600.0160.0160.0000.0000.0000.000
49A49GLY00.0110.02827.0220.0170.0170.0000.0000.0000.000
50A50GLN0-0.059-0.03526.2230.0110.0110.0000.0000.0000.000
51A51VAL00.0110.04321.559-0.021-0.0210.0000.0000.0000.000
52A52PRO0-0.048-0.03419.8040.0240.0240.0000.0000.0000.000
53A53VAL0-0.008-0.02318.0450.0150.0150.0000.0000.0000.000
54A54LEU0-0.033-0.00612.059-0.007-0.0070.0000.0000.0000.000
55A55GLU-1-0.816-0.91712.861-0.748-0.7480.0000.0000.0000.000
56A56VAL0-0.004-0.0129.338-0.051-0.0510.0000.0000.0000.000
57A57ASP-1-0.831-0.9166.220-3.541-3.5410.0000.0000.0000.000
58A58GLY0-0.006-0.0088.9460.1850.1850.0000.0000.0000.000
59A59GLN0-0.052-0.01212.1140.2950.2950.0000.0000.0000.000
60A60GLN0-0.014-0.02014.4850.0190.0190.0000.0000.0000.000
61A61LEU00.0000.01316.5610.0450.0450.0000.0000.0000.000
62A62ALA00.0130.00218.459-0.005-0.0050.0000.0000.0000.000
63A63GLN00.0380.01721.3340.0240.0240.0000.0000.0000.000
64A64SER0-0.009-0.01321.9140.0060.0060.0000.0000.0000.000
65A65GLN00.0510.01321.5470.0090.0090.0000.0000.0000.000
66A66ALA0-0.046-0.01921.7880.0160.0160.0000.0000.0000.000
67A67ILE00.0300.02516.4260.0060.0060.0000.0000.0000.000
68A68CYS0-0.050-0.02417.2080.0140.0140.0000.0000.0000.000
69A69ARG10.8700.92118.4200.0540.0540.0000.0000.0000.000
70A70TYR00.0250.00611.6270.0570.0570.0000.0000.0000.000
71A71LEU00.0110.02112.0960.0400.0400.0000.0000.0000.000
72A72ALA0-0.008-0.01014.5690.0780.0780.0000.0000.0000.000
73A73LYS10.8900.93517.151-0.022-0.0220.0000.0000.0000.000
74A74THR0-0.046-0.01610.6660.0140.0140.0000.0000.0000.000
75A75PHE0-0.009-0.0148.8330.0920.0920.0000.0000.0000.000
76A76GLY00.0010.02613.8720.0370.0370.0000.0000.0000.000
77A77PHE0-0.019-0.01215.136-0.018-0.0180.0000.0000.0000.000
78A78ALA00.002-0.02019.528-0.036-0.0360.0000.0000.0000.000
79A79GLY00.0460.02521.733-0.016-0.0160.0000.0000.0000.000
80A80ALA00.0090.00523.0600.0170.0170.0000.0000.0000.000
81A81THR00.0250.01125.181-0.002-0.0020.0000.0000.0000.000
82A82PRO00.022-0.00826.353-0.005-0.0050.0000.0000.0000.000
83A83PHE00.0360.01527.442-0.009-0.0090.0000.0000.0000.000
84A84GLU-1-0.822-0.91127.5620.1100.1100.0000.0000.0000.000
85A85SER00.0250.02524.608-0.004-0.0040.0000.0000.0000.000
86A86ALA0-0.0100.00626.293-0.010-0.0100.0000.0000.0000.000
87A87LEU0-0.014-0.00629.260-0.008-0.0080.0000.0000.0000.000
88A88ILE00.0130.02224.584-0.005-0.0050.0000.0000.0000.000
89A89ASP-1-0.802-0.88725.6080.0040.0040.0000.0000.0000.000
90A90SER0-0.045-0.02928.138-0.008-0.0080.0000.0000.0000.000
91A91LEU0-0.006-0.01030.156-0.005-0.0050.0000.0000.0000.000
92A92ALA0-0.018-0.00227.204-0.004-0.0040.0000.0000.0000.000
93A93ASP-1-0.878-0.94329.154-0.034-0.0340.0000.0000.0000.000
94A94ALA00.0130.01031.592-0.003-0.0030.0000.0000.0000.000
95A95TYR0-0.042-0.02929.224-0.004-0.0040.0000.0000.0000.000
96A96THR0-0.038-0.02930.223-0.007-0.0070.0000.0000.0000.000
97A97ASP-1-0.886-0.93532.544-0.027-0.0270.0000.0000.0000.000
98A98TYR0-0.038-0.03034.4660.0000.0000.0000.0000.0000.000
99A99ARG10.8630.92031.7630.0340.0340.0000.0000.0000.000
100A100ALA0-0.039-0.00735.400-0.003-0.0030.0000.0000.0000.000
101A101GLU-1-0.880-0.90137.511-0.014-0.0140.0000.0000.0000.000
102A102MET0-0.076-0.01136.0290.0010.0010.0000.0000.0000.000
103A118ASP-1-0.908-0.96745.257-0.017-0.0170.0000.0000.0000.000
104A119LYS10.9630.98447.0690.0190.0190.0000.0000.0000.000
105A120PRO00.0390.01243.9040.0010.0010.0000.0000.0000.000
106A121LYS10.8550.94543.8570.0070.0070.0000.0000.0000.000
107A122THR00.000-0.00844.8790.0020.0020.0000.0000.0000.000
108A123ASP-1-0.898-0.94947.910-0.015-0.0150.0000.0000.0000.000
109A124VAL0-0.006-0.02242.6370.0000.0000.0000.0000.0000.000
110A125LEU0-0.026-0.00939.0640.0020.0020.0000.0000.0000.000
111A126LEU00.0160.00442.0780.0020.0020.0000.0000.0000.000
112A127PRO00.0250.00744.3160.0030.0030.0000.0000.0000.000
113A128ALA00.0380.03440.6510.0020.0020.0000.0000.0000.000
114A129ARG10.8390.90339.462-0.004-0.0040.0000.0000.0000.000
115A130THR0-0.017-0.01240.7430.0040.0040.0000.0000.0000.000
116A131LYS10.8280.90241.9040.0120.0120.0000.0000.0000.000
117A132PHE00.0360.01332.9770.0030.0030.0000.0000.0000.000
118A133LEU00.0140.00636.4170.0040.0040.0000.0000.0000.000
119A134GLY00.0420.04839.0530.0050.0050.0000.0000.0000.000
120A135PHE0-0.086-0.05438.3670.0040.0040.0000.0000.0000.000
121A136ILE00.0520.02533.0430.0050.0050.0000.0000.0000.000
122A137THR00.008-0.01336.4860.0070.0070.0000.0000.0000.000
123A138LYS10.9080.96638.907-0.017-0.0170.0000.0000.0000.000
124A139PHE00.008-0.01233.9220.0020.0020.0000.0000.0000.000
125A140LEU00.0260.01532.8210.0050.0050.0000.0000.0000.000
126A141LYS10.8290.89936.072-0.032-0.0320.0000.0000.0000.000
127A142LYS10.8340.94736.614-0.043-0.0430.0000.0000.0000.000
128A143ASN0-0.038-0.02731.3800.0050.0050.0000.0000.0000.000
129A144SER00.0180.00335.392-0.001-0.0010.0000.0000.0000.000
130A145SER0-0.056-0.02530.630-0.001-0.0010.0000.0000.0000.000
131A146GLY0-0.026-0.00431.6360.0060.0060.0000.0000.0000.000
132A147PHE00.0240.01326.419-0.002-0.0020.0000.0000.0000.000
133A148LEU0-0.025-0.02128.897-0.006-0.0060.0000.0000.0000.000
134A149VAL0-0.044-0.03528.417-0.007-0.0070.0000.0000.0000.000
135A150GLY00.0580.04728.2570.0090.0090.0000.0000.0000.000
136A151ASP-1-0.901-0.94227.2390.1520.1520.0000.0000.0000.000
137A152LYS10.8700.93218.575-0.287-0.2870.0000.0000.0000.000
138A153ILE0-0.0210.01121.295-0.012-0.0120.0000.0000.0000.000
139A154SER0-0.009-0.04122.1620.0140.0140.0000.0000.0000.000
140A155TRP00.043-0.01420.267-0.014-0.0140.0000.0000.0000.000
141A156VAL00.0340.02022.061-0.015-0.0150.0000.0000.0000.000
142A157ASP-1-0.732-0.84125.1990.0820.0820.0000.0000.0000.000
143A158LEU00.0280.00919.751-0.005-0.0050.0000.0000.0000.000
144A159LEU0-0.031-0.00724.244-0.011-0.0110.0000.0000.0000.000
145A160VAL0-0.003-0.00525.904-0.008-0.0080.0000.0000.0000.000
146A161ALA0-0.0060.00427.174-0.006-0.0060.0000.0000.0000.000
147A162GLU-1-0.726-0.83025.5630.0020.0020.0000.0000.0000.000
148A163HIS00.0060.01527.842-0.006-0.0060.0000.0000.0000.000
149A164VAL00.0210.00830.697-0.003-0.0030.0000.0000.0000.000
150A165ALA00.0740.04130.017-0.002-0.0020.0000.0000.0000.000
151A166ASP-1-0.814-0.86530.522-0.028-0.0280.0000.0000.0000.000
152A167MET0-0.023-0.02332.462-0.004-0.0040.0000.0000.0000.000
153A168THR0-0.034-0.03535.4500.0000.0000.0000.0000.0000.000
154A169ASN0-0.057-0.03332.8840.0000.0000.0000.0000.0000.000
155A170ARG10.7520.87232.5270.0270.0270.0000.0000.0000.000
156A171VAL0-0.025-0.02038.417-0.001-0.0010.0000.0000.0000.000
157A172PRO00.0680.03640.5990.0020.0020.0000.0000.0000.000
158A173GLU-1-0.772-0.88141.6530.0010.0010.0000.0000.0000.000
159A174TYR0-0.056-0.04036.2440.0020.0020.0000.0000.0000.000
160A175ILE00.0190.01036.9140.0010.0010.0000.0000.0000.000
161A176GLU-1-0.919-0.94640.3710.0140.0140.0000.0000.0000.000
162A177GLY0-0.025-0.01744.007-0.002-0.0020.0000.0000.0000.000
163A178PHE0-0.021-0.01939.7680.0010.0010.0000.0000.0000.000
164A179PRO00.0420.02739.5630.0020.0020.0000.0000.0000.000
165A180GLU-1-0.822-0.92137.8710.0400.0400.0000.0000.0000.000
166A181VAL00.0210.01334.9120.0050.0050.0000.0000.0000.000
167A182LYS10.9430.97234.603-0.034-0.0340.0000.0000.0000.000
168A183ALA0-0.019-0.00934.6570.0030.0030.0000.0000.0000.000
169A184HIS0-0.113-0.06229.0760.0020.0020.0000.0000.0000.000
170A185MET00.0380.03030.4400.0050.0050.0000.0000.0000.000
171A186GLU-1-0.879-0.94629.8220.0500.0500.0000.0000.0000.000
172A187ARG10.8960.95628.635-0.077-0.0770.0000.0000.0000.000
173A188ILE0-0.014-0.01924.8540.0140.0140.0000.0000.0000.000
174A189GLN0-0.024-0.02925.1820.0070.0070.0000.0000.0000.000
175A190GLN00.0270.02626.2160.0050.0050.0000.0000.0000.000
176A191THR0-0.0230.00121.6500.0170.0170.0000.0000.0000.000
177A192PRO00.0180.00121.333-0.002-0.0020.0000.0000.0000.000
178A193ARG10.8110.89213.667-0.509-0.5090.0000.0000.0000.000
179A194ILE0-0.0060.00419.201-0.013-0.0130.0000.0000.0000.000
180A195LYS10.9010.96721.213-0.104-0.1040.0000.0000.0000.000
181A196LYS10.9971.00815.097-0.269-0.2690.0000.0000.0000.000
182A197TRP0-0.073-0.04017.097-0.021-0.0210.0000.0000.0000.000
183A198ILE0-0.020-0.02320.221-0.023-0.0230.0000.0000.0000.000
184A199GLU-1-0.950-0.98823.8500.0630.0630.0000.0000.0000.000
185A200THR0-0.064-0.04520.409-0.008-0.0080.0000.0000.0000.000
186A201ARG10.7290.87621.267-0.017-0.0170.0000.0000.0000.000
187A202PRO00.015-0.01121.2080.0010.0010.0000.0000.0000.000
188A203GLU-1-0.906-0.93624.411-0.021-0.0210.0000.0000.0000.000
189A204THR0-0.033-0.02226.127-0.007-0.0070.0000.0000.0000.000
190A205PRO00.0460.02128.9700.0070.0070.0000.0000.0000.000
191A206PHE00.0090.02327.3070.0050.0050.0000.0000.0000.000