Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 148NZ

Calculation Name: 1JSX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JSX

Chain ID: A

ChEMBL ID:

UniProt ID: P0A6U5

Base Structure: X-ray

Registration Date: 2023-06-19

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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2237879.256431
FMO2-HF: Nuclear repulsion 2160925.505825
FMO2-HF: Total energy -76953.750606
FMO2-MP2: Total energy -77180.022144


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.
-13.854-9.5885.126-3.987-5.4040.01
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 : 0.015 / q_NPA : -0.013
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].
3A3ASN00.0110.0072.578-4.456-0.0390.461-2.216-2.662-0.004
4A4LYS10.9400.9892.279-9.538-9.6894.665-1.771-2.7420.014
5A5LEU00.0800.0404.881-0.434-0.4340.0000.0000.0000.000
6A6SER00.0320.0247.422-0.035-0.0350.0000.0000.0000.000
7A7LEU0-0.001-0.0178.511-0.009-0.0090.0000.0000.0000.000
8A8LEU0-0.047-0.01210.004-0.067-0.0670.0000.0000.0000.000
9A9LEU0-0.019-0.01311.536-0.073-0.0730.0000.0000.0000.000
10A10LYS10.8980.94312.135-0.328-0.3280.0000.0000.0000.000
11A11ASP-1-0.876-0.93013.9380.5300.5300.0000.0000.0000.000
12A12ALA0-0.036-0.00116.464-0.032-0.0320.0000.0000.0000.000
13A13GLY00.0290.01018.702-0.022-0.0220.0000.0000.0000.000
14A14ILE0-0.072-0.03818.844-0.019-0.0190.0000.0000.0000.000
15A15SER0-0.051-0.01319.2470.0230.0230.0000.0000.0000.000
16A16LEU00.049-0.00415.1500.0260.0260.0000.0000.0000.000
17A17THR00.0010.02418.2170.0010.0010.0000.0000.0000.000
18A18ASP-1-0.837-0.94016.3280.3150.3150.0000.0000.0000.000
19A19HIS0-0.028-0.00815.8080.0630.0630.0000.0000.0000.000
20A20GLN00.0870.03816.5570.0570.0570.0000.0000.0000.000
21A21LYS10.9630.9919.651-0.908-0.9080.0000.0000.0000.000
22A22ASN0-0.002-0.01011.9790.2250.2250.0000.0000.0000.000
23A23GLN0-0.0020.00112.4560.0940.0940.0000.0000.0000.000
24A24LEU00.0340.02111.7490.1000.1000.0000.0000.0000.000
25A25ILE0-0.078-0.0487.0800.3700.3700.0000.0000.0000.000
26A26ALA00.0540.0308.5170.3550.3550.0000.0000.0000.000
27A27TYR00.007-0.01510.4050.0120.0120.0000.0000.0000.000
28A28VAL0-0.011-0.0065.5960.0790.0790.0000.0000.0000.000
29A29ASN0-0.075-0.0405.0320.0730.0730.0000.0000.0000.000
30A30MET00.0050.0157.163-0.397-0.3970.0000.0000.0000.000
31A31LEU0-0.014-0.0089.827-0.169-0.1690.0000.0000.0000.000
32A32HIS0-0.050-0.0285.7450.0650.0650.0000.0000.0000.000
33A33LYS10.9360.9727.958-0.167-0.1670.0000.0000.0000.000
34A34TRP0-0.074-0.02010.215-0.091-0.0910.0000.0000.0000.000
35A35ASN0-0.022-0.00110.157-0.104-0.1040.0000.0000.0000.000
36A48GLU-1-0.922-0.9669.0220.0960.0960.0000.0000.0000.000
37A49MET00.016-0.00910.0570.0880.0880.0000.0000.0000.000
38A50LEU00.0090.0137.6090.0460.0460.0000.0000.0000.000
39A51VAL00.011-0.0067.6990.0790.0790.0000.0000.0000.000
40A52ARG10.9660.98310.233-0.217-0.2170.0000.0000.0000.000
41A53HIS00.0390.02913.466-0.029-0.0290.0000.0000.0000.000
42A54ILE0-0.0220.00010.852-0.016-0.0160.0000.0000.0000.000
43A55LEU00.0220.00913.944-0.032-0.0320.0000.0000.0000.000
44A56ASP-1-0.860-0.93515.5590.2000.2000.0000.0000.0000.000
45A57SER0-0.056-0.05717.443-0.036-0.0360.0000.0000.0000.000
46A58ILE00.0080.00415.182-0.019-0.0190.0000.0000.0000.000
47A59VAL0-0.015-0.00419.123-0.028-0.0280.0000.0000.0000.000
48A60VAL0-0.014-0.01321.444-0.024-0.0240.0000.0000.0000.000
49A61ALA00.0370.02222.134-0.018-0.0180.0000.0000.0000.000
50A62PRO0-0.033-0.01423.668-0.015-0.0150.0000.0000.0000.000
51A63TYR0-0.009-0.00226.381-0.016-0.0160.0000.0000.0000.000
52A64LEU0-0.0550.00425.530-0.011-0.0110.0000.0000.0000.000
53A65GLN00.0070.00029.550-0.001-0.0010.0000.0000.0000.000
54A66GLY00.011-0.00333.009-0.004-0.0040.0000.0000.0000.000
55A67GLU-1-0.964-0.98531.8060.1120.1120.0000.0000.0000.000
56A68ARG10.8700.96231.553-0.084-0.0840.0000.0000.0000.000
57A69PHE0-0.0010.00028.163-0.004-0.0040.0000.0000.0000.000
58A70ILE00.0010.00828.6450.0020.0020.0000.0000.0000.000
59A71ASP-1-0.812-0.89422.6860.1950.1950.0000.0000.0000.000
60A72VAL00.0350.00826.339-0.004-0.0040.0000.0000.0000.000
61A73GLY0-0.042-0.01126.051-0.001-0.0010.0000.0000.0000.000
62A74THR0-0.007-0.02521.7360.0110.0110.0000.0000.0000.000
63A75GLY00.0110.00120.5420.0220.0220.0000.0000.0000.000
64A76PRO0-0.077-0.06415.509-0.006-0.0060.0000.0000.0000.000
65A77GLY00.0540.02716.7070.0500.0500.0000.0000.0000.000
66A78LEU0-0.0710.00614.2380.0440.0440.0000.0000.0000.000
67A79PRO00.0450.00118.497-0.030-0.0300.0000.0000.0000.000
68A80GLY00.0630.01519.6060.0260.0260.0000.0000.0000.000
69A81ILE0-0.017-0.00416.125-0.002-0.0020.0000.0000.0000.000
70A82PRO0-0.021-0.01214.9590.0100.0100.0000.0000.0000.000
71A83LEU00.0140.00817.262-0.008-0.0080.0000.0000.0000.000
72A84SER0-0.046-0.01920.071-0.014-0.0140.0000.0000.0000.000
73A85ILE0-0.021-0.00315.662-0.001-0.0010.0000.0000.0000.000
74A86VAL0-0.032-0.02818.602-0.012-0.0120.0000.0000.0000.000
75A87ARG10.7610.87021.158-0.187-0.1870.0000.0000.0000.000
76A88PRO0-0.005-0.01922.964-0.008-0.0080.0000.0000.0000.000
77A89GLU-1-0.843-0.90225.3340.1600.1600.0000.0000.0000.000
78A90ALA00.0020.02127.405-0.012-0.0120.0000.0000.0000.000
79A91HIS0-0.003-0.01327.4440.0150.0150.0000.0000.0000.000
80A92PHE0-0.015-0.01324.853-0.001-0.0010.0000.0000.0000.000
81A93THR0-0.0100.00526.3970.0050.0050.0000.0000.0000.000
82A94LEU0-0.039-0.02421.4680.0060.0060.0000.0000.0000.000
83A95LEU00.0550.03625.425-0.008-0.0080.0000.0000.0000.000
84A96ASP-1-0.763-0.87924.0630.1100.1100.0000.0000.0000.000
85A97SER00.0470.03026.595-0.010-0.0100.0000.0000.0000.000
86A98LEU0-0.044-0.02424.977-0.010-0.0100.0000.0000.0000.000
87A99GLY00.0830.04525.2310.0090.0090.0000.0000.0000.000
88A100LYS10.8830.93019.9890.0020.0020.0000.0000.0000.000
89A101ARG10.9080.95620.474-0.084-0.0840.0000.0000.0000.000
90A102VAL00.0690.05121.1770.0170.0170.0000.0000.0000.000
91A103ARG10.9160.95222.752-0.031-0.0310.0000.0000.0000.000
92A104PHE0-0.0190.00513.317-0.011-0.0110.0000.0000.0000.000
93A105LEU00.0460.01518.6310.0200.0200.0000.0000.0000.000
94A106ARG10.9790.99020.125-0.076-0.0760.0000.0000.0000.000
95A107GLN0-0.039-0.00717.3920.0150.0150.0000.0000.0000.000
96A108VAL00.0130.00615.1220.0130.0130.0000.0000.0000.000
97A109GLN00.0090.00417.3510.0120.0120.0000.0000.0000.000
98A110HIS0-0.036-0.00720.3450.0010.0010.0000.0000.0000.000
99A111GLU-1-0.942-0.98915.2210.1840.1840.0000.0000.0000.000
100A112LEU0-0.110-0.05814.0230.0250.0250.0000.0000.0000.000
101A113LYS10.9430.97617.578-0.164-0.1640.0000.0000.0000.000
102A114LEU0-0.025-0.00218.6230.0000.0000.0000.0000.0000.000
103A115GLU-1-0.936-0.97722.1270.1290.1290.0000.0000.0000.000
104A116ASN0-0.0250.00123.843-0.004-0.0040.0000.0000.0000.000
105A117ILE0-0.011-0.00821.3530.0040.0040.0000.0000.0000.000
106A118GLU-1-0.911-0.96625.3840.0890.0890.0000.0000.0000.000
107A119PRO0-0.067-0.02723.453-0.004-0.0040.0000.0000.0000.000
108A120VAL00.0380.02025.756-0.013-0.0130.0000.0000.0000.000
109A121GLN0-0.082-0.05528.0740.0020.0020.0000.0000.0000.000
110A122SER00.0580.00429.446-0.007-0.0070.0000.0000.0000.000
111A123ARG10.8870.94631.005-0.040-0.0400.0000.0000.0000.000
112A124VAL00.0360.00132.5050.0010.0010.0000.0000.0000.000
113A125GLU-1-0.899-0.94534.2530.0520.0520.0000.0000.0000.000
114A126GLU-1-1.039-0.99135.5580.0420.0420.0000.0000.0000.000
115A127PHE0-0.041-0.02333.0520.0020.0020.0000.0000.0000.000
116A128PRO00.0250.00435.8490.0000.0000.0000.0000.0000.000
117A129SER00.022-0.00736.9510.0010.0010.0000.0000.0000.000
118A130GLU-1-0.926-0.92537.8950.0480.0480.0000.0000.0000.000
119A131PRO0-0.073-0.03037.651-0.001-0.0010.0000.0000.0000.000
120A132PRO00.0670.02537.6770.0050.0050.0000.0000.0000.000
121A133PHE00.0060.00331.9740.0030.0030.0000.0000.0000.000
122A134ASP-1-0.784-0.89233.7960.0910.0910.0000.0000.0000.000
123A135GLY0-0.028-0.03231.745-0.001-0.0010.0000.0000.0000.000
124A136VAL0-0.0060.01030.7520.0050.0050.0000.0000.0000.000
125A137ILE0-0.0140.00024.5720.0010.0010.0000.0000.0000.000
126A138SER00.024-0.02225.624-0.002-0.0020.0000.0000.0000.000
127A139ARG10.9540.98620.227-0.150-0.1500.0000.0000.0000.000
128A140ALA0-0.090-0.05124.380-0.004-0.0040.0000.0000.0000.000
129A141PHE0-0.0050.00426.141-0.010-0.0100.0000.0000.0000.000
130A142ALA0-0.0090.00328.4880.0050.0050.0000.0000.0000.000
131A143SER0-0.043-0.03430.3240.0010.0010.0000.0000.0000.000
132A144LEU00.005-0.01531.4680.0030.0030.0000.0000.0000.000
133A145ASN00.000-0.01033.6180.0010.0010.0000.0000.0000.000
134A146ASP-1-0.838-0.90533.1700.0520.0520.0000.0000.0000.000
135A147MET0-0.030-0.01830.3450.0030.0030.0000.0000.0000.000
136A148VAL00.0040.00933.0490.0010.0010.0000.0000.0000.000
137A149SER00.0160.00236.170-0.003-0.0030.0000.0000.0000.000
138A150TRP0-0.065-0.02534.225-0.002-0.0020.0000.0000.0000.000
139A151CYS0-0.043-0.01432.5380.0030.0030.0000.0000.0000.000
140A152HIS10.9010.93235.338-0.051-0.0510.0000.0000.0000.000
141A153HIS0-0.007-0.00536.274-0.001-0.0010.0000.0000.0000.000
142A154LEU0-0.0190.00433.0630.0010.0010.0000.0000.0000.000
143A155PRO0-0.025-0.01035.6590.0030.0030.0000.0000.0000.000
144A156GLY00.0630.02437.580-0.004-0.0040.0000.0000.0000.000
145A157GLU-1-0.928-0.96540.3550.0510.0510.0000.0000.0000.000
146A158GLN00.022-0.02041.214-0.001-0.0010.0000.0000.0000.000
147A159GLY0-0.0030.02737.2300.0040.0040.0000.0000.0000.000
148A160ARG10.7890.86234.251-0.090-0.0900.0000.0000.0000.000
149A161PHE00.0120.02132.8090.0050.0050.0000.0000.0000.000
150A162TYR00.0400.00828.427-0.002-0.0020.0000.0000.0000.000
151A163ALA00.0380.00727.7910.0050.0050.0000.0000.0000.000
152A164LEU0-0.050-0.00921.854-0.002-0.0020.0000.0000.0000.000
153A165LYS10.8760.94025.530-0.086-0.0860.0000.0000.0000.000
154A166GLY00.0090.00625.2610.0100.0100.0000.0000.0000.000
155A167GLN00.0120.00926.0700.0000.0000.0000.0000.0000.000
156A168MET0-0.002-0.01029.4010.0050.0050.0000.0000.0000.000
157A169PRO0-0.0150.00331.224-0.004-0.0040.0000.0000.0000.000
158A170GLU-1-0.920-0.98233.2480.0480.0480.0000.0000.0000.000
159A171ASP-1-0.864-0.92836.3740.0400.0400.0000.0000.0000.000
160A172GLU-1-0.807-0.92531.5410.0710.0710.0000.0000.0000.000
161A173ILE0-0.042-0.01735.2550.0010.0010.0000.0000.0000.000
162A174ALA0-0.0010.00837.775-0.001-0.0010.0000.0000.0000.000
163A175LEU0-0.046-0.01538.288-0.003-0.0030.0000.0000.0000.000
164A176LEU0-0.0340.00336.9040.0010.0010.0000.0000.0000.000
165A177PRO0-0.030-0.00640.070-0.002-0.0020.0000.0000.0000.000
166A178GLU-1-0.898-0.94143.2130.0420.0420.0000.0000.0000.000
167A179GLU-1-0.856-0.93244.5620.0420.0420.0000.0000.0000.000
168A180TYR0-0.075-0.04239.9030.0040.0040.0000.0000.0000.000
169A181GLN0-0.014-0.00941.1580.0000.0000.0000.0000.0000.000
170A182VAL0-0.002-0.01136.3660.0040.0040.0000.0000.0000.000
171A183GLU-1-0.820-0.88737.6630.0760.0760.0000.0000.0000.000
172A184SER0-0.047-0.03635.2130.0010.0010.0000.0000.0000.000
173A185VAL00.0330.01132.4990.0030.0030.0000.0000.0000.000
174A186VAL0-0.0120.00629.315-0.003-0.0030.0000.0000.0000.000
175A187LYS10.9790.99629.451-0.072-0.0720.0000.0000.0000.000
176A188LEU0-0.030-0.02224.4100.0020.0020.0000.0000.0000.000
177A189GLN0-0.049-0.03625.660-0.005-0.0050.0000.0000.0000.000
178A190VAL00.0280.01420.340-0.002-0.0020.0000.0000.0000.000
179A191PRO00.0030.01718.957-0.004-0.0040.0000.0000.0000.000
180A192ALA00.1310.09219.102-0.011-0.0110.0000.0000.0000.000
181A193LEU0-0.131-0.05816.3770.0150.0150.0000.0000.0000.000
182A194ASP-1-0.891-0.98520.4960.0590.0590.0000.0000.0000.000
183A195GLY0-0.085-0.04421.1920.0100.0100.0000.0000.0000.000
184A196GLU-1-0.852-0.92922.0720.0810.0810.0000.0000.0000.000
185A197ARG10.8090.90219.725-0.144-0.1440.0000.0000.0000.000
186A198HIS00.0110.01125.446-0.007-0.0070.0000.0000.0000.000
187A199LEU0-0.0160.00426.5140.0040.0040.0000.0000.0000.000
188A200VAL00.0140.00128.690-0.007-0.0070.0000.0000.0000.000
189A201VAL0-0.0180.00031.4740.0060.0060.0000.0000.0000.000
190A202ILE00.0200.00433.740-0.006-0.0060.0000.0000.0000.000
191A203LYS10.8440.95736.435-0.067-0.0670.0000.0000.0000.000
192A204ALA00.0520.02939.230-0.002-0.0020.0000.0000.0000.000
193A205ASN0-0.029-0.01342.0620.0030.0030.0000.0000.0000.000
194A206LYS10.8550.91344.620-0.055-0.0550.0000.0000.0000.000
195A207ILE00.0240.02047.818-0.002-0.0020.0000.0000.0000.000