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: GNZ51

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 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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2238199.710022
FMO2-HF: Nuclear repulsion 2161244.817295
FMO2-HF: Total energy -76954.892727
FMO2-MP2: Total energy -77181.072492


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.
-11.424-6.6384.716-4.135-5.368-0.003
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 : -0.004 / 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].
3A3ASN00.0140.0012.281-4.580-1.1032.756-2.753-3.480-0.011
4A4LYS10.9320.9732.335-8.353-7.0441.960-1.382-1.8880.008
5A5LEU00.0790.0425.172-0.285-0.2850.0000.0000.0000.000
6A6SER00.0220.0257.3370.0610.0610.0000.0000.0000.000
7A7LEU00.007-0.0188.4120.0110.0110.0000.0000.0000.000
8A8LEU0-0.059-0.0239.996-0.044-0.0440.0000.0000.0000.000
9A9LEU0-0.019-0.01111.537-0.045-0.0450.0000.0000.0000.000
10A10LYS10.8520.92011.507-0.192-0.1920.0000.0000.0000.000
11A11ASP-1-0.838-0.90314.0140.4170.4170.0000.0000.0000.000
12A12ALA0-0.0230.00316.411-0.020-0.0200.0000.0000.0000.000
13A13GLY00.0420.01618.702-0.015-0.0150.0000.0000.0000.000
14A14ILE0-0.090-0.04519.009-0.010-0.0100.0000.0000.0000.000
15A15SER0-0.029-0.00319.2390.0150.0150.0000.0000.0000.000
16A16LEU00.016-0.02115.2530.0230.0230.0000.0000.0000.000
17A17THR00.0140.01118.2090.0020.0020.0000.0000.0000.000
18A18ASP-1-0.838-0.93416.3260.2280.2280.0000.0000.0000.000
19A19HIS0-0.0220.00515.7990.0440.0440.0000.0000.0000.000
20A20GLN00.0780.04316.5440.0340.0340.0000.0000.0000.000
21A21LYS10.8800.94510.512-0.529-0.5290.0000.0000.0000.000
22A22ASN0-0.036-0.03711.9660.1740.1740.0000.0000.0000.000
23A23GLN00.002-0.00112.4410.0850.0850.0000.0000.0000.000
24A24LEU00.0320.02011.5950.0890.0890.0000.0000.0000.000
25A25ILE0-0.046-0.0367.1170.3480.3480.0000.0000.0000.000
26A26ALA00.0250.0108.4970.3490.3490.0000.0000.0000.000
27A27TYR00.014-0.01710.4490.0280.0280.0000.0000.0000.000
28A28VAL0-0.003-0.0055.5110.0810.0810.0000.0000.0000.000
29A29ASN0-0.032-0.0155.4411.0171.0170.0000.0000.0000.000
30A30MET0-0.0090.0177.203-0.359-0.3590.0000.0000.0000.000
31A31LEU0-0.003-0.0049.913-0.156-0.1560.0000.0000.0000.000
32A32HIS0-0.026-0.0115.5650.0550.0550.0000.0000.0000.000
33A33LYS10.9300.9687.967-0.173-0.1730.0000.0000.0000.000
34A34TRP0-0.053-0.01110.226-0.082-0.0820.0000.0000.0000.000
35A35ASN0-0.063-0.02510.713-0.098-0.0980.0000.0000.0000.000
36A48GLU-1-0.842-0.9378.8600.0610.0610.0000.0000.0000.000
37A49MET00.0250.00910.0000.0810.0810.0000.0000.0000.000
38A50LEU00.0010.0107.6160.0400.0400.0000.0000.0000.000
39A51VAL00.0290.0027.5630.0700.0700.0000.0000.0000.000
40A52ARG10.9230.95410.140-0.164-0.1640.0000.0000.0000.000
41A53HIS00.0340.02213.373-0.026-0.0260.0000.0000.0000.000
42A54ILE0-0.0190.00610.793-0.013-0.0130.0000.0000.0000.000
43A55LEU00.0280.01413.847-0.026-0.0260.0000.0000.0000.000
44A56ASP-1-0.826-0.90515.4570.1410.1410.0000.0000.0000.000
45A57SER0-0.045-0.05117.213-0.025-0.0250.0000.0000.0000.000
46A58ILE0-0.002-0.00515.173-0.013-0.0130.0000.0000.0000.000
47A59VAL0-0.011-0.00119.082-0.022-0.0220.0000.0000.0000.000
48A60VAL00.014-0.00321.341-0.019-0.0190.0000.0000.0000.000
49A61ALA00.0300.01722.119-0.014-0.0140.0000.0000.0000.000
50A62PRO0-0.027-0.00923.751-0.011-0.0110.0000.0000.0000.000
51A63TYR0-0.006-0.00126.250-0.013-0.0130.0000.0000.0000.000
52A64LEU0-0.0410.00925.485-0.008-0.0080.0000.0000.0000.000
53A65GLN00.0010.00129.545-0.001-0.0010.0000.0000.0000.000
54A66GLY00.0170.00033.009-0.003-0.0030.0000.0000.0000.000
55A67GLU-1-0.966-0.98731.8230.0860.0860.0000.0000.0000.000
56A68ARG10.8620.95931.553-0.067-0.0670.0000.0000.0000.000
57A69PHE00.0010.00228.183-0.003-0.0030.0000.0000.0000.000
58A70ILE0-0.0020.01028.6320.0020.0020.0000.0000.0000.000
59A71ASP-1-0.794-0.87622.6630.1590.1590.0000.0000.0000.000
60A72VAL00.0310.01126.313-0.002-0.0020.0000.0000.0000.000
61A73GLY0-0.038-0.00425.995-0.001-0.0010.0000.0000.0000.000
62A74THR0-0.012-0.04121.9610.0100.0100.0000.0000.0000.000
63A75GLY00.0110.00720.5390.0190.0190.0000.0000.0000.000
64A76PRO0-0.073-0.05815.520-0.005-0.0050.0000.0000.0000.000
65A77GLY00.0490.03316.7300.0450.0450.0000.0000.0000.000
66A78LEU0-0.0700.00714.2720.0350.0350.0000.0000.0000.000
67A79PRO00.0470.00518.421-0.025-0.0250.0000.0000.0000.000
68A80GLY00.0570.00519.6060.0210.0210.0000.0000.0000.000
69A81ILE0-0.020-0.01016.113-0.001-0.0010.0000.0000.0000.000
70A82PRO0-0.012-0.00614.8960.0070.0070.0000.0000.0000.000
71A83LEU00.0090.00917.262-0.009-0.0090.0000.0000.0000.000
72A84SER0-0.045-0.01920.073-0.012-0.0120.0000.0000.0000.000
73A85ILE0-0.021-0.00315.5340.0000.0000.0000.0000.0000.000
74A86VAL0-0.025-0.02618.541-0.012-0.0120.0000.0000.0000.000
75A87ARG10.7650.87221.158-0.147-0.1470.0000.0000.0000.000
76A88PRO00.011-0.00723.002-0.006-0.0060.0000.0000.0000.000
77A89GLU-1-0.831-0.89625.3160.1250.1250.0000.0000.0000.000
78A90ALA00.0010.02127.420-0.010-0.0100.0000.0000.0000.000
79A91HIS0-0.031-0.02727.4440.0130.0130.0000.0000.0000.000
80A92PHE0-0.014-0.01724.859-0.001-0.0010.0000.0000.0000.000
81A93THR0-0.025-0.02726.4320.0050.0050.0000.0000.0000.000
82A94LEU0-0.040-0.01721.4730.0050.0050.0000.0000.0000.000
83A95LEU00.0500.03125.453-0.006-0.0060.0000.0000.0000.000
84A96ASP-1-0.758-0.86924.2180.0900.0900.0000.0000.0000.000
85A97SER00.0480.02526.613-0.008-0.0080.0000.0000.0000.000
86A98LEU0-0.039-0.01925.093-0.008-0.0080.0000.0000.0000.000
87A99GLY00.0580.03825.2480.0080.0080.0000.0000.0000.000
88A100LYS10.8860.93419.728-0.007-0.0070.0000.0000.0000.000
89A101ARG10.8910.93820.553-0.071-0.0710.0000.0000.0000.000
90A102VAL00.0610.03721.2010.0150.0150.0000.0000.0000.000
91A103ARG10.9450.96522.906-0.028-0.0280.0000.0000.0000.000
92A104PHE0-0.0210.00213.338-0.007-0.0070.0000.0000.0000.000
93A105LEU00.0470.01918.6630.0180.0180.0000.0000.0000.000
94A106ARG10.9290.96220.156-0.068-0.0680.0000.0000.0000.000
95A107GLN0-0.026-0.00117.7730.0080.0080.0000.0000.0000.000
96A108VAL00.002-0.00415.0660.0110.0110.0000.0000.0000.000
97A109GLN0-0.0070.00017.3910.0100.0100.0000.0000.0000.000
98A110HIS0-0.051-0.01220.165-0.004-0.0040.0000.0000.0000.000
99A111GLU-1-0.942-0.99915.5270.1460.1460.0000.0000.0000.000
100A112LEU0-0.098-0.04514.0010.0190.0190.0000.0000.0000.000
101A113LYS10.9390.97517.560-0.132-0.1320.0000.0000.0000.000
102A114LEU0-0.0140.00518.711-0.001-0.0010.0000.0000.0000.000
103A115GLU-1-0.923-0.97322.1200.1000.1000.0000.0000.0000.000
104A116ASN0-0.031-0.00523.959-0.001-0.0010.0000.0000.0000.000
105A117ILE0-0.002-0.00121.1950.0050.0050.0000.0000.0000.000
106A118GLU-1-0.842-0.90125.4230.0750.0750.0000.0000.0000.000
107A119PRO0-0.040-0.01523.401-0.004-0.0040.0000.0000.0000.000
108A120VAL00.0360.01625.788-0.011-0.0110.0000.0000.0000.000
109A121GLN0-0.072-0.04528.0980.0020.0020.0000.0000.0000.000
110A122SER00.0520.00129.469-0.006-0.0060.0000.0000.0000.000
111A123ARG10.8960.95531.023-0.032-0.0320.0000.0000.0000.000
112A124VAL00.0510.00532.4190.0010.0010.0000.0000.0000.000
113A125GLU-1-0.899-0.93734.2700.0410.0410.0000.0000.0000.000
114A126GLU-1-1.033-1.00035.6640.0330.0330.0000.0000.0000.000
115A127PHE0-0.014-0.00732.7280.0010.0010.0000.0000.0000.000
116A128PRO00.016-0.00135.8820.0000.0000.0000.0000.0000.000
117A129SER00.0320.00436.9670.0010.0010.0000.0000.0000.000
118A130GLU-1-0.952-0.94537.9230.0380.0380.0000.0000.0000.000
119A131PRO0-0.023-0.00837.710-0.001-0.0010.0000.0000.0000.000
120A132PRO00.0420.01737.6770.0040.0040.0000.0000.0000.000
121A133PHE0-0.012-0.00232.0740.0020.0020.0000.0000.0000.000
122A134ASP-1-0.783-0.89433.7890.0710.0710.0000.0000.0000.000
123A135GLY0-0.023-0.02531.725-0.001-0.0010.0000.0000.0000.000
124A136VAL0-0.0130.00430.7000.0040.0040.0000.0000.0000.000
125A137ILE0-0.017-0.00424.7080.0000.0000.0000.0000.0000.000
126A138SER00.037-0.01525.565-0.001-0.0010.0000.0000.0000.000
127A139ARG10.9450.97820.209-0.119-0.1190.0000.0000.0000.000
128A140ALA0-0.104-0.05824.312-0.003-0.0030.0000.0000.0000.000
129A141PHE00.0010.00426.076-0.008-0.0080.0000.0000.0000.000
130A142ALA0-0.0020.00528.4190.0040.0040.0000.0000.0000.000
131A143SER0-0.044-0.04730.2600.0000.0000.0000.0000.0000.000
132A144LEU00.019-0.00131.3250.0030.0030.0000.0000.0000.000
133A145ASN00.0050.00633.5390.0010.0010.0000.0000.0000.000
134A146ASP-1-0.850-0.89733.0820.0420.0420.0000.0000.0000.000
135A147MET0-0.038-0.02129.9710.0020.0020.0000.0000.0000.000
136A148VAL00.0130.01232.9740.0010.0010.0000.0000.0000.000
137A149SER00.0170.00636.091-0.002-0.0020.0000.0000.0000.000
138A150TRP0-0.058-0.03334.158-0.002-0.0020.0000.0000.0000.000
139A151CYS0-0.045-0.01832.5490.0020.0020.0000.0000.0000.000
140A152HIS10.9040.95235.263-0.040-0.0400.0000.0000.0000.000
141A153HIS0-0.015-0.01936.1470.0000.0000.0000.0000.0000.000
142A154LEU0-0.028-0.00333.0680.0010.0010.0000.0000.0000.000
143A155PRO0-0.0140.00135.8610.0020.0020.0000.0000.0000.000
144A156GLY00.0570.01637.536-0.004-0.0040.0000.0000.0000.000
145A157GLU-1-0.861-0.91640.3550.0390.0390.0000.0000.0000.000
146A158GLN0-0.018-0.04041.141-0.002-0.0020.0000.0000.0000.000
147A159GLY00.0260.03937.2170.0030.0030.0000.0000.0000.000
148A160ARG10.7770.85934.207-0.070-0.0700.0000.0000.0000.000
149A161PHE00.0160.00932.7140.0040.0040.0000.0000.0000.000
150A162TYR00.0180.00028.321-0.002-0.0020.0000.0000.0000.000
151A163ALA00.0360.00927.7110.0040.0040.0000.0000.0000.000
152A164LEU0-0.055-0.01121.770-0.002-0.0020.0000.0000.0000.000
153A165LYS10.8560.90825.445-0.064-0.0640.0000.0000.0000.000
154A166GLY00.0140.01125.1760.0070.0070.0000.0000.0000.000
155A167GLN0-0.001-0.02125.9870.0000.0000.0000.0000.0000.000
156A168MET00.0330.02429.3180.0040.0040.0000.0000.0000.000
157A169PRO0-0.0070.00231.086-0.003-0.0030.0000.0000.0000.000
158A170GLU-1-0.925-0.98033.1650.0370.0370.0000.0000.0000.000
159A171ASP-1-0.874-0.93336.2780.0310.0310.0000.0000.0000.000
160A172GLU-1-0.790-0.90631.3240.0550.0550.0000.0000.0000.000
161A173ILE0-0.031-0.01934.9350.0010.0010.0000.0000.0000.000
162A174ALA0-0.0030.00837.691-0.001-0.0010.0000.0000.0000.000
163A175LEU0-0.053-0.01938.611-0.002-0.0020.0000.0000.0000.000
164A176LEU0-0.037-0.00236.5560.0010.0010.0000.0000.0000.000
165A177PRO0-0.029-0.00840.071-0.001-0.0010.0000.0000.0000.000
166A178GLU-1-0.906-0.94643.1290.0320.0320.0000.0000.0000.000
167A179GLU-1-0.852-0.93044.5120.0320.0320.0000.0000.0000.000
168A180TYR0-0.079-0.04539.8360.0030.0030.0000.0000.0000.000
169A181GLN0-0.016-0.00641.1450.0000.0000.0000.0000.0000.000
170A182VAL00.006-0.01236.1400.0030.0030.0000.0000.0000.000
171A183GLU-1-0.803-0.86037.2410.0600.0600.0000.0000.0000.000
172A184SER0-0.030-0.03335.3350.0010.0010.0000.0000.0000.000
173A185VAL00.0160.00332.4140.0030.0030.0000.0000.0000.000
174A186VAL0-0.0200.00029.536-0.002-0.0020.0000.0000.0000.000
175A187LYS10.8850.95829.353-0.054-0.0540.0000.0000.0000.000
176A188LEU0-0.044-0.02924.3820.0020.0020.0000.0000.0000.000
177A189GLN0-0.009-0.01525.527-0.006-0.0060.0000.0000.0000.000
178A190VAL00.0220.00620.465-0.001-0.0010.0000.0000.0000.000
179A191PRO0-0.0190.00318.404-0.005-0.0050.0000.0000.0000.000
180A192ALA00.1510.10119.079-0.008-0.0080.0000.0000.0000.000
181A193LEU0-0.136-0.04116.2670.0100.0100.0000.0000.0000.000
182A194ASP-1-0.896-1.00120.4540.0420.0420.0000.0000.0000.000
183A195GLY0-0.085-0.03821.2130.0070.0070.0000.0000.0000.000
184A196GLU-1-0.831-0.90921.9860.0600.0600.0000.0000.0000.000
185A197ARG10.8100.88919.362-0.111-0.1110.0000.0000.0000.000
186A198HIS00.0090.00125.354-0.006-0.0060.0000.0000.0000.000
187A199LEU0-0.0200.00326.3910.0030.0030.0000.0000.0000.000
188A200VAL00.0160.00028.594-0.005-0.0050.0000.0000.0000.000
189A201VAL0-0.0050.00531.3800.0050.0050.0000.0000.0000.000
190A202ILE00.004-0.00233.645-0.005-0.0050.0000.0000.0000.000
191A203LYS10.8540.94236.343-0.051-0.0510.0000.0000.0000.000
192A204ALA00.0380.02239.139-0.002-0.0020.0000.0000.0000.000
193A205ASN0-0.020-0.00841.9730.0020.0020.0000.0000.0000.000
194A206LYS10.8310.90245.004-0.042-0.0420.0000.0000.0000.000
195A207ILE0-0.022-0.00447.728-0.002-0.0020.0000.0000.0000.000