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: K9183

Calculation Name: 4TX1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4TX1

Chain ID: A

ChEMBL ID:

UniProt ID: Q7APD5

Base Structure: X-ray

Registration Date: 2023-09-20

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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2438329.935044
FMO2-HF: Nuclear repulsion 2356511.934282
FMO2-HF: Total energy -81818.000763
FMO2-MP2: Total energy -82052.337146


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.
-11.72-8.66611.354-3.658-10.75-0.032
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 : -0.045 / q_NPA : -0.005
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].
3A3THR00.0100.0103.4111.4194.3810.129-1.296-1.796-0.001
4A4VAL00.000-0.0055.075-0.317-0.266-0.001-0.007-0.0420.000
5A5LEU0-0.0090.0128.5800.2250.2250.0000.0000.0000.000
6A6CYS0-0.038-0.00711.659-0.058-0.0580.0000.0000.0000.000
7A7TYR00.010-0.00914.2180.0250.0250.0000.0000.0000.000
8A8GLY00.0760.01517.505-0.014-0.0140.0000.0000.0000.000
9A9ASP-1-0.754-0.85820.643-0.004-0.0040.0000.0000.0000.000
10A10SER0-0.006-0.01522.4020.0100.0100.0000.0000.0000.000
11A11LEU0-0.043-0.02623.7970.0090.0090.0000.0000.0000.000
12A12THR00.0150.01717.5330.0010.0010.0000.0000.0000.000
13A13TRP0-0.052-0.00918.8550.0180.0180.0000.0000.0000.000
14A14GLY00.0200.01320.6360.0150.0150.0000.0000.0000.000
15A15TYR0-0.042-0.02322.2560.0020.0020.0000.0000.0000.000
16A16ASP-1-0.778-0.87226.0590.0200.0200.0000.0000.0000.000
17A17ALA00.011-0.01028.162-0.001-0.0010.0000.0000.0000.000
18A18THR0-0.107-0.07030.736-0.002-0.0020.0000.0000.0000.000
19A19GLY0-0.009-0.01031.619-0.001-0.0010.0000.0000.0000.000
20A20SER0-0.087-0.03031.8260.0000.0000.0000.0000.0000.000
21A21GLY00.0460.02928.9610.0010.0010.0000.0000.0000.000
22A22ARG10.7820.88919.138-0.078-0.0780.0000.0000.0000.000
23A23HIS00.0250.01922.1860.0050.0050.0000.0000.0000.000
24A24ALA00.0640.04020.8560.0080.0080.0000.0000.0000.000
25A25LEU0-0.018-0.00914.225-0.001-0.0010.0000.0000.0000.000
26A26GLU-1-0.856-0.94915.4860.1030.1030.0000.0000.0000.000
27A27ASP-1-0.831-0.91116.5550.0440.0440.0000.0000.0000.000
28A28ARG10.8240.91016.617-0.108-0.1080.0000.0000.0000.000
29A29TRP00.0820.02214.7770.0230.0230.0000.0000.0000.000
30A30PRO00.0390.01212.843-0.003-0.0030.0000.0000.0000.000
31A31SER0-0.014-0.01411.5380.0570.0570.0000.0000.0000.000
32A32VAL0-0.065-0.01811.926-0.007-0.0070.0000.0000.0000.000
33A33LEU00.0460.02910.775-0.014-0.0140.0000.0000.0000.000
34A34GLN0-0.008-0.0074.5230.3430.458-0.001-0.003-0.1100.000
35A35LYS10.8820.9347.892-0.158-0.1580.0000.0000.0000.000
36A36ALA0-0.029-0.00410.396-0.022-0.0220.0000.0000.0000.000
37A37LEU00.007-0.0027.082-0.016-0.0160.0000.0000.0000.000
38A38GLY0-0.0020.0126.766-0.014-0.0140.0000.0000.0000.000
39A39SER0-0.026-0.0403.344-0.421-0.1140.014-0.060-0.2610.000
40A40ASP-1-0.923-0.9442.618-2.359-1.5321.802-0.865-1.764-0.011
41A41ALA0-0.012-0.0102.834-2.889-1.2182.091-1.416-2.347-0.012
42A42HIS00.0080.0142.900-0.821-3.1057.290-0.775-4.231-0.009
43A43VAL0-0.026-0.0114.044-0.811-1.4060.0300.764-0.1990.001
44A44ILE00.0100.0127.803-0.084-0.0840.0000.0000.0000.000
45A45ALA0-0.025-0.01810.311-0.119-0.1190.0000.0000.0000.000
46A46GLU-1-0.793-0.88813.7290.0090.0090.0000.0000.0000.000
47A47GLY00.0090.01116.549-0.028-0.0280.0000.0000.0000.000
48A48LEU0-0.019-0.01419.7200.0100.0100.0000.0000.0000.000
49A49ASN00.017-0.02523.111-0.008-0.0080.0000.0000.0000.000
50A50GLY0-0.003-0.00626.527-0.001-0.0010.0000.0000.0000.000
51A51ARG10.7900.90919.6320.0110.0110.0000.0000.0000.000
52A52THR0-0.023-0.03026.548-0.001-0.0010.0000.0000.0000.000
53A53THR0-0.006-0.04825.934-0.003-0.0030.0000.0000.0000.000
54A54ALA0-0.044-0.02226.144-0.006-0.0060.0000.0000.0000.000
55A55TYR0-0.038-0.02728.7430.0010.0010.0000.0000.0000.000
56A56ASP-1-0.777-0.85131.003-0.036-0.0360.0000.0000.0000.000
57A57ASP-1-0.792-0.87931.845-0.013-0.0130.0000.0000.0000.000
58A58HIS0-0.001-0.01632.4060.0020.0020.0000.0000.0000.000
59A59LEU0-0.052-0.02234.7160.0020.0020.0000.0000.0000.000
60A60ALA0-0.036-0.03831.3310.0030.0030.0000.0000.0000.000
61A61ASP-1-0.922-0.93931.3430.0010.0010.0000.0000.0000.000
62A62CYS0-0.067-0.04526.9570.0040.0040.0000.0000.0000.000
63A63ASP-1-0.740-0.82727.012-0.039-0.0390.0000.0000.0000.000
64A64ARG10.8230.90526.6190.0090.0090.0000.0000.0000.000
65A65ASN0-0.015-0.01427.639-0.007-0.0070.0000.0000.0000.000
66A66GLY00.0480.03224.229-0.002-0.0020.0000.0000.0000.000
67A67ALA00.0450.01623.449-0.008-0.0080.0000.0000.0000.000
68A68ARG10.7010.80624.9830.0340.0340.0000.0000.0000.000
69A69VAL0-0.004-0.00121.330-0.002-0.0020.0000.0000.0000.000
70A70LEU0-0.0030.01317.8160.0000.0000.0000.0000.0000.000
71A71PRO00.0380.01418.905-0.012-0.0120.0000.0000.0000.000
72A72THR00.0080.00219.007-0.017-0.0170.0000.0000.0000.000
73A73VAL0-0.0320.00415.666-0.003-0.0030.0000.0000.0000.000
74A74LEU0-0.007-0.00514.627-0.003-0.0030.0000.0000.0000.000
75A75HIS00.0200.01014.049-0.053-0.0530.0000.0000.0000.000
76A76THR0-0.115-0.06114.283-0.006-0.0060.0000.0000.0000.000
77A77HIS0-0.070-0.05210.5890.0500.0500.0000.0000.0000.000
78A78ALA00.0070.0409.320-0.062-0.0620.0000.0000.0000.000
79A79PRO00.001-0.0056.9020.0840.0840.0000.0000.0000.000
80A80LEU0-0.014-0.0317.461-0.054-0.0540.0000.0000.0000.000
81A81ASP-1-0.784-0.8796.182-3.219-3.2190.0000.0000.0000.000
82A82LEU0-0.027-0.0109.1250.2020.2020.0000.0000.0000.000
83A83ILE0-0.0230.00211.1430.0890.0890.0000.0000.0000.000
84A84VAL00.005-0.00413.154-0.001-0.0010.0000.0000.0000.000
85A85PHE00.0140.00615.8010.0350.0350.0000.0000.0000.000
86A86MET0-0.030-0.00619.2750.0010.0010.0000.0000.0000.000
87A87LEU0-0.032-0.00621.4670.0130.0130.0000.0000.0000.000
88A88GLY00.0960.05124.528-0.007-0.0070.0000.0000.0000.000
89A89SER00.0090.00327.7210.0000.0000.0000.0000.0000.000
90A90ASN0-0.025-0.03627.8930.0040.0040.0000.0000.0000.000
91A91ASP-1-0.739-0.83929.665-0.044-0.0440.0000.0000.0000.000
92A92MET0-0.065-0.01132.1740.0000.0000.0000.0000.0000.000
93A93LYS10.8820.95931.5810.0190.0190.0000.0000.0000.000
94A94PRO00.0530.01436.393-0.002-0.0020.0000.0000.0000.000
95A95ILE0-0.066-0.03237.368-0.001-0.0010.0000.0000.0000.000
96A96ILE0-0.086-0.02633.1500.0000.0000.0000.0000.0000.000
97A97HIS0-0.005-0.00932.797-0.001-0.0010.0000.0000.0000.000
98A98GLY00.0130.03436.4100.0010.0010.0000.0000.0000.000
99A99THR0-0.041-0.02736.369-0.001-0.0010.0000.0000.0000.000
100A100ALA00.0450.00033.398-0.002-0.0020.0000.0000.0000.000
101A101PHE00.0030.00233.114-0.004-0.0040.0000.0000.0000.000
102A102GLY00.0450.02033.816-0.004-0.0040.0000.0000.0000.000
103A103ALA00.0080.01630.028-0.003-0.0030.0000.0000.0000.000
104A104VAL00.0290.01929.167-0.005-0.0050.0000.0000.0000.000
105A105LYS10.8260.89229.1670.0700.0700.0000.0000.0000.000
106A106GLY00.0190.01128.797-0.004-0.0040.0000.0000.0000.000
107A107ILE0-0.012-0.02023.827-0.006-0.0060.0000.0000.0000.000
108A108GLU-1-0.767-0.84824.685-0.101-0.1010.0000.0000.0000.000
109A109ARG10.9130.96826.0090.0890.0890.0000.0000.0000.000
110A110LEU0-0.014-0.01021.797-0.007-0.0070.0000.0000.0000.000
111A111VAL00.0390.02021.138-0.018-0.0180.0000.0000.0000.000
112A112ASN0-0.052-0.04221.551-0.025-0.0250.0000.0000.0000.000
113A113LEU0-0.073-0.03621.730-0.006-0.0060.0000.0000.0000.000
114A114VAL00.0420.01616.157-0.008-0.0080.0000.0000.0000.000
115A115ARG10.8490.91018.4860.2370.2370.0000.0000.0000.000
116A116ARG10.8410.91520.5880.1820.1820.0000.0000.0000.000
117A117HIS0-0.021-0.00117.2540.0320.0320.0000.0000.0000.000
118A118ASP-1-0.960-0.96519.540-0.215-0.2150.0000.0000.0000.000
119A119TRP00.0420.00613.839-0.005-0.0050.0000.0000.0000.000
120A120PRO0-0.049-0.02013.6960.0190.0190.0000.0000.0000.000
121A121THR0-0.062-0.03313.3660.0180.0180.0000.0000.0000.000
122A122GLU-1-0.950-0.97415.634-0.283-0.2830.0000.0000.0000.000
123A123THR0-0.088-0.03212.835-0.031-0.0310.0000.0000.0000.000
124A124GLU-1-0.956-0.97112.687-0.374-0.3740.0000.0000.0000.000
125A125GLU-1-0.909-0.97412.608-0.523-0.5230.0000.0000.0000.000
126A126GLY0-0.025-0.00713.720-0.061-0.0610.0000.0000.0000.000
127A127PRO0-0.033-0.01412.306-0.018-0.0180.0000.0000.0000.000
128A128GLU-1-0.838-0.92613.027-0.295-0.2950.0000.0000.0000.000
129A129ILE0-0.055-0.03514.6260.0260.0260.0000.0000.0000.000
130A130LEU00.0050.00315.8230.0160.0160.0000.0000.0000.000
131A131ILE0-0.0010.00318.1760.0230.0230.0000.0000.0000.000
132A132VAL00.003-0.01419.0700.0040.0040.0000.0000.0000.000
133A133SER00.0130.00322.1330.0030.0030.0000.0000.0000.000
134A134PRO0-0.040-0.02324.8090.0040.0040.0000.0000.0000.000
135A135PRO0-0.026-0.02024.725-0.001-0.0010.0000.0000.0000.000
136A136PRO00.0050.02427.9410.0020.0020.0000.0000.0000.000
137A137LEU00.0360.02431.4840.0040.0040.0000.0000.0000.000
138A138CYS0-0.119-0.05833.8110.0000.0000.0000.0000.0000.000
139A139GLU-1-0.860-0.93636.735-0.012-0.0120.0000.0000.0000.000
140A140THR0-0.035-0.04738.3210.0020.0020.0000.0000.0000.000
141A141ALA0-0.013-0.00140.437-0.001-0.0010.0000.0000.0000.000
142A142ASN0-0.025-0.01637.7980.0000.0000.0000.0000.0000.000
143A143SER00.0260.00541.133-0.001-0.0010.0000.0000.0000.000
144A144ALA00.0190.01440.740-0.001-0.0010.0000.0000.0000.000
145A145PHE00.0120.00133.377-0.001-0.0010.0000.0000.0000.000
146A146ALA00.0170.00438.700-0.002-0.0020.0000.0000.0000.000
147A147ALA0-0.032-0.01341.084-0.001-0.0010.0000.0000.0000.000
148A148MET0-0.057-0.02136.296-0.002-0.0020.0000.0000.0000.000
149A149PHE00.003-0.01732.861-0.001-0.0010.0000.0000.0000.000
150A150ALA00.0330.02937.943-0.001-0.0010.0000.0000.0000.000
151A151GLY0-0.0010.00640.803-0.001-0.0010.0000.0000.0000.000
152A152GLY00.0510.01236.911-0.002-0.0020.0000.0000.0000.000
153A153VAL0-0.0420.00235.920-0.002-0.0020.0000.0000.0000.000
154A154GLU-1-0.870-0.95137.001-0.023-0.0230.0000.0000.0000.000
155A155GLN00.0190.01336.402-0.005-0.0050.0000.0000.0000.000
156A156SER00.026-0.01332.176-0.003-0.0030.0000.0000.0000.000
157A157ALA0-0.017-0.00132.488-0.003-0.0030.0000.0000.0000.000
158A158MET0-0.055-0.02934.118-0.003-0.0030.0000.0000.0000.000
159A159LEU0-0.012-0.00129.415-0.004-0.0040.0000.0000.0000.000
160A160ALA00.0250.01729.089-0.006-0.0060.0000.0000.0000.000
161A161PRO0-0.083-0.03729.700-0.006-0.0060.0000.0000.0000.000
162A162LEU00.0750.03431.230-0.005-0.0050.0000.0000.0000.000
163A163TYR0-0.027-0.05025.450-0.004-0.0040.0000.0000.0000.000
164A164ARG10.8530.93426.8390.0590.0590.0000.0000.0000.000
165A165ASP-1-0.901-0.95927.921-0.077-0.0770.0000.0000.0000.000
166A166LEU0-0.024-0.01526.575-0.005-0.0050.0000.0000.0000.000
167A167ALA0-0.047-0.02923.802-0.009-0.0090.0000.0000.0000.000
168A168ASP-1-0.951-0.95724.863-0.121-0.1210.0000.0000.0000.000
169A169GLU-1-0.971-0.98627.301-0.098-0.0980.0000.0000.0000.000
170A170LEU0-0.069-0.04525.035-0.003-0.0030.0000.0000.0000.000
171A171ASP-1-0.910-0.92622.354-0.221-0.2210.0000.0000.0000.000
172A172CYS0-0.061-0.01720.253-0.031-0.0310.0000.0000.0000.000
173A173GLY00.0540.02218.9820.0130.0130.0000.0000.0000.000
174A174PHE0-0.011-0.02219.9650.0130.0130.0000.0000.0000.000
175A175PHE0-0.016-0.01420.3740.0000.0000.0000.0000.0000.000
176A176ASP-1-0.765-0.86822.395-0.048-0.0480.0000.0000.0000.000
177A177GLY00.0510.03923.8640.0050.0050.0000.0000.0000.000
178A178GLY00.019-0.00824.6750.0060.0060.0000.0000.0000.000
179A179SER0-0.125-0.06525.9200.0020.0020.0000.0000.0000.000
180A180VAL0-0.041-0.02422.5140.0010.0010.0000.0000.0000.000
181A181ALA0-0.029-0.00324.6850.0060.0060.0000.0000.0000.000
182A182ARG10.9010.95326.7490.0030.0030.0000.0000.0000.000
183A183THR00.0310.00629.0550.0040.0040.0000.0000.0000.000
184A184THR0-0.003-0.00630.9890.0000.0000.0000.0000.0000.000
185A185PRO00.0680.02232.9930.0000.0000.0000.0000.0000.000
186A186ILE0-0.0460.00133.4030.0000.0000.0000.0000.0000.000
187A187ASP-1-0.782-0.88732.6200.0030.0030.0000.0000.0000.000
188A188GLY00.0390.03135.139-0.001-0.0010.0000.0000.0000.000
189A189VAL0-0.025-0.01830.336-0.003-0.0030.0000.0000.0000.000
190A190HIS10.8130.88427.605-0.005-0.0050.0000.0000.0000.000
191A191LEU00.0440.02623.753-0.003-0.0030.0000.0000.0000.000
192A192ASP-1-0.784-0.86627.1780.0150.0150.0000.0000.0000.000
193A193ALA00.0610.03723.7450.0000.0000.0000.0000.0000.000
194A194GLU-1-0.817-0.88722.9350.0190.0190.0000.0000.0000.000
195A195ASN0-0.002-0.03223.751-0.006-0.0060.0000.0000.0000.000
196A196THR0-0.046-0.03420.071-0.004-0.0040.0000.0000.0000.000
197A197ARG10.8520.90718.608-0.045-0.0450.0000.0000.0000.000
198A198ALA0-0.038-0.00919.375-0.002-0.0020.0000.0000.0000.000
199A199VAL00.0320.01419.372-0.007-0.0070.0000.0000.0000.000
200A200GLY00.003-0.00216.551-0.007-0.0070.0000.0000.0000.000
201A201ARG10.8070.87715.902-0.012-0.0120.0000.0000.0000.000
202A202GLY0-0.025-0.00517.828-0.010-0.0100.0000.0000.0000.000
203A203LEU00.0350.01515.864-0.013-0.0130.0000.0000.0000.000
204A204GLU-1-0.826-0.88712.909-0.076-0.0760.0000.0000.0000.000
205A205PRO0-0.025-0.01714.304-0.033-0.0330.0000.0000.0000.000
206A206VAL00.0190.01615.847-0.028-0.0280.0000.0000.0000.000
207A207VAL00.0420.02010.931-0.037-0.0370.0000.0000.0000.000
208A208ARG10.8050.8839.8490.0380.0380.0000.0000.0000.000
209A209MET0-0.055-0.01711.547-0.063-0.0630.0000.0000.0000.000
210A210MET0-0.0100.00713.384-0.017-0.0170.0000.0000.0000.000
211A211LEU0-0.0140.0017.231-0.060-0.0600.0000.0000.0000.000
212A212GLY00.0220.0278.338-0.231-0.2310.0000.0000.0000.000
213A213LEU0-0.092-0.0646.643-0.223-0.2230.0000.0000.0000.000