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: KR6R3

Calculation Name: 1HJP-A-Xray308

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1HJP

Chain ID: A

ChEMBL ID:

UniProt ID: P0A809

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 188
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1828484.151897
FMO2-HF: Nuclear repulsion 1756499.005469
FMO2-HF: Total energy -71985.146428
FMO2-MP2: Total energy -72194.752925


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.
-0.9641.6011.07-1.148-2.4860.006
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 : 0.039 / q_NPA : 0.006
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].
3A3GLY 00.0050.0123.7160.1371.269-0.002-0.383-0.7460.002
4A4ARG 10.9240.9476.1310.7890.7890.0000.0000.0000.000
5A5LEU 00.0240.0397.973-0.124-0.1240.0000.0000.0000.000
6A6ARG 10.8830.93010.7030.2860.2860.0000.0000.0000.000
7A7GLY 00.0150.01313.953-0.023-0.0230.0000.0000.0000.000
8A8ILE 00.0450.03616.0530.0150.0150.0000.0000.0000.000
9A9ILE 0-0.0050.01518.401-0.002-0.0020.0000.0000.0000.000
10A10ILE 00.0340.01918.7310.0080.0080.0000.0000.0000.000
11A11GLU -1-0.901-0.96620.857-0.037-0.0370.0000.0000.0000.000
12A12LYS 10.7700.87721.3620.0610.0610.0000.0000.0000.000
13A13GLN 0-0.023-0.01222.5160.0090.0090.0000.0000.0000.000
14A14PRO 0-0.0340.04322.3240.0080.0080.0000.0000.0000.000
15A15PRO 00.028-0.01519.3810.0030.0030.0000.0000.0000.000
16A16LEU 0-0.004-0.01217.3140.0040.0040.0000.0000.0000.000
17A17VAL 00.009-0.00317.040-0.012-0.0120.0000.0000.0000.000
18A18LEU 00.0040.01515.7470.0060.0060.0000.0000.0000.000
19A19ILE 0-0.032-0.01814.215-0.008-0.0080.0000.0000.0000.000
20A20GLU -1-0.918-0.95714.201-0.159-0.1590.0000.0000.0000.000
21A21VAL 0-0.033-0.02510.574-0.009-0.0090.0000.0000.0000.000
22A22GLY 0-0.030-0.01112.407-0.034-0.0340.0000.0000.0000.000
23A23GLY 00.0580.02514.0920.0260.0260.0000.0000.0000.000
24A24VAL 0-0.054-0.0219.6480.0110.0110.0000.0000.0000.000
25A25GLY 00.0490.02612.883-0.008-0.0080.0000.0000.0000.000
26A26TYR 0-0.032-0.0267.157-0.053-0.0530.0000.0000.0000.000
27A27GLU -1-0.880-0.93512.3280.0160.0160.0000.0000.0000.000
28A28VAL 0-0.077-0.03712.2100.0540.0540.0000.0000.0000.000
29A29HIS 00.0230.01013.428-0.031-0.0310.0000.0000.0000.000
30A30MET 0-0.026-0.01614.3250.0070.0070.0000.0000.0000.000
31A31PRO 00.0060.00616.0190.0050.0050.0000.0000.0000.000
32A32MET 00.002-0.00919.181-0.009-0.0090.0000.0000.0000.000
33A33THR 0-0.055-0.03922.258-0.008-0.0080.0000.0000.0000.000
34A34CYS 0-0.037-0.01018.417-0.002-0.0020.0000.0000.0000.000
35A35PHE 00.003-0.00520.323-0.008-0.0080.0000.0000.0000.000
36A36TYR 0-0.036-0.02921.798-0.002-0.0020.0000.0000.0000.000
37A37GLU -1-0.903-0.94622.356-0.061-0.0610.0000.0000.0000.000
38A38LEU 0-0.125-0.04318.676-0.010-0.0100.0000.0000.0000.000
39A39PRO 00.0920.05021.5170.0060.0060.0000.0000.0000.000
40A40GLU -1-0.868-0.93024.453-0.070-0.0700.0000.0000.0000.000
41A41ALA 0-0.008-0.01424.002-0.006-0.0060.0000.0000.0000.000
42A42GLY 0-0.026-0.01223.5090.0040.0040.0000.0000.0000.000
43A43GLN 0-0.038-0.01223.801-0.008-0.0080.0000.0000.0000.000
44A44GLU -1-0.909-0.96318.411-0.184-0.1840.0000.0000.0000.000
45A45ALA 00.0240.02117.9020.0090.0090.0000.0000.0000.000
46A46ILE 0-0.044-0.04514.491-0.036-0.0360.0000.0000.0000.000
47A47VAL 00.0010.01312.0920.0230.0230.0000.0000.0000.000
48A48PHE 0-0.027-0.03710.827-0.100-0.1000.0000.0000.0000.000
49A49THR 00.024-0.0106.425-0.033-0.0330.0000.0000.0000.000
50A50HIS 00.0150.0086.060-0.286-0.2860.0000.0000.0000.000
51A51PHE 00.0180.0162.750-1.574-0.2181.072-0.763-1.6660.004
52A52VAL 0-0.052-0.0355.346-0.349-0.2720.000-0.002-0.0740.000
53A53VAL 00.0080.0055.3030.0280.0280.0000.0000.0000.000
54A54ARG 10.8600.9308.238-0.337-0.3370.0000.0000.0000.000
55A55GLU -1-0.939-0.96411.5050.1910.1910.0000.0000.0000.000
56A56ASP -1-0.877-0.94013.8450.1620.1620.0000.0000.0000.000
57A57ALA 00.0040.00612.779-0.026-0.0260.0000.0000.0000.000
58A58GLN 00.003-0.0126.365-0.004-0.0040.0000.0000.0000.000
59A59LEU 00.0100.0139.585-0.109-0.1090.0000.0000.0000.000
60A60LEU 00.0400.0266.7200.3290.3290.0000.0000.0000.000
61A61TYR 00.0010.0099.218-0.155-0.1550.0000.0000.0000.000
62A62GLY 00.019-0.00710.110-0.010-0.0100.0000.0000.0000.000
63A63PHE 0-0.004-0.02210.8400.0070.0070.0000.0000.0000.000
64A64ASN 00.0790.03614.538-0.023-0.0230.0000.0000.0000.000
65A65ASN 0-0.005-0.00716.156-0.023-0.0230.0000.0000.0000.000
66A66LYS 10.9550.95612.4100.2990.2990.0000.0000.0000.000
67A67GLN 00.0260.02814.2630.0000.0000.0000.0000.0000.000
68A68GLU -1-0.721-0.86616.340-0.082-0.0820.0000.0000.0000.000
69A69ARG 10.8520.9528.5600.4670.4670.0000.0000.0000.000
70A70THR 0-0.041-0.01912.4490.0040.0040.0000.0000.0000.000
71A71LEU 00.0530.04613.8170.0190.0190.0000.0000.0000.000
72A72PHE 00.0100.01111.0430.0210.0210.0000.0000.0000.000
73A73LYS 10.8260.8846.3430.3790.3790.0000.0000.0000.000
74A74GLU -1-0.877-0.95512.413-0.049-0.0490.0000.0000.0000.000
75A75LEU 0-0.015-0.02015.8020.0150.0150.0000.0000.0000.000
76A76ILE 0-0.066-0.03310.9040.0150.0150.0000.0000.0000.000
77A77LYS 10.8740.96013.2970.0660.0660.0000.0000.0000.000
78A78THR 0-0.075-0.00916.3210.0040.0040.0000.0000.0000.000
79A79ASN 00.0620.02119.9600.0080.0080.0000.0000.0000.000
80A80GLY 0-0.017-0.01521.356-0.006-0.0060.0000.0000.0000.000
81A81VAL 0-0.018-0.00718.717-0.001-0.0010.0000.0000.0000.000
82A82GLY 00.0550.03616.5560.0060.0060.0000.0000.0000.000
83A83PRO 00.0150.00112.952-0.017-0.0170.0000.0000.0000.000
84A84LYS 11.0141.00815.276-0.062-0.0620.0000.0000.0000.000
85A85LEU 00.0030.00618.451-0.011-0.0110.0000.0000.0000.000
86A86ALA 00.0390.01816.384-0.010-0.0100.0000.0000.0000.000
87A87LEU 0-0.014-0.00415.903-0.011-0.0110.0000.0000.0000.000
88A88ALA 00.0170.00818.496-0.011-0.0110.0000.0000.0000.000
89A89ILE 0-0.005-0.00521.179-0.007-0.0070.0000.0000.0000.000
90A90LEU 0-0.003-0.00717.360-0.005-0.0050.0000.0000.0000.000
91A91SER 0-0.036-0.01121.320-0.007-0.0070.0000.0000.0000.000
92A92GLY 0-0.042-0.00923.365-0.003-0.0030.0000.0000.0000.000
93A93MET 0-0.030-0.00524.953-0.002-0.0020.0000.0000.0000.000
94A94SER 00.0450.02723.862-0.001-0.0010.0000.0000.0000.000
95A95ALA 00.0630.01820.4740.0030.0030.0000.0000.0000.000
96A96GLN 00.0770.02922.4390.0060.0060.0000.0000.0000.000
97A97GLN 0-0.0030.00425.6160.0040.0040.0000.0000.0000.000
98A98PHE 00.0170.00722.2850.0040.0040.0000.0000.0000.000
99A99VAL 00.0380.01122.9850.0030.0030.0000.0000.0000.000
100A100ASN 0-0.016-0.00525.5190.0030.0030.0000.0000.0000.000
101A101ALA 00.001-0.01028.4310.0020.0020.0000.0000.0000.000
102A102VAL 0-0.049-0.01024.7680.0030.0030.0000.0000.0000.000
103A103GLU -1-0.798-0.91827.750-0.024-0.0240.0000.0000.0000.000
104A104ARG 10.8220.91630.1540.0190.0190.0000.0000.0000.000
105A105GLU -1-0.910-0.95631.575-0.006-0.0060.0000.0000.0000.000
106A106GLU -1-0.894-0.95031.956-0.013-0.0130.0000.0000.0000.000
107A107VAL 00.0080.00031.5430.0010.0010.0000.0000.0000.000
108A108GLY 0-0.020-0.02732.7620.0020.0020.0000.0000.0000.000
109A109ALA 00.0190.01131.3290.0010.0010.0000.0000.0000.000
110A110LEU 00.0550.01925.8330.0000.0000.0000.0000.0000.000
111A111VAL 0-0.086-0.03329.1470.0030.0030.0000.0000.0000.000
112A112LYS 10.8750.92631.7030.0030.0030.0000.0000.0000.000
113A113LEU 0-0.0010.01925.7710.0010.0010.0000.0000.0000.000
114A114PRO 00.0330.00926.8980.0020.0020.0000.0000.0000.000
115A115GLY 0-0.005-0.01125.9360.0030.0030.0000.0000.0000.000
116A116ILE 00.0260.03924.4830.0030.0030.0000.0000.0000.000
117A117GLY 00.000-0.00827.1630.0010.0010.0000.0000.0000.000
118A118LYS 10.9310.95130.818-0.013-0.0130.0000.0000.0000.000
119A119LYS 11.0501.02231.575-0.012-0.0120.0000.0000.0000.000
120A120THR 00.0280.01325.227-0.001-0.0010.0000.0000.0000.000
121A121ALA 00.0190.02527.101-0.001-0.0010.0000.0000.0000.000
122A122GLU -1-0.884-0.95628.4560.0050.0050.0000.0000.0000.000
123A123ARG 10.8810.95522.914-0.024-0.0240.0000.0000.0000.000
124A124LEU 00.007-0.00821.734-0.001-0.0010.0000.0000.0000.000
125A125ILE 00.0010.02524.967-0.004-0.0040.0000.0000.0000.000
126A126VAL 00.0100.01227.256-0.003-0.0030.0000.0000.0000.000
127A127GLU -1-0.888-0.96823.1820.0120.0120.0000.0000.0000.000
128A128MET 0-0.089-0.04219.304-0.002-0.0020.0000.0000.0000.000
129A129LYS 10.8610.94423.4480.0100.0100.0000.0000.0000.000
130A130ASP -1-0.971-0.97725.108-0.014-0.0140.0000.0000.0000.000
131A131ARG 10.8830.93518.8110.0070.0070.0000.0000.0000.000
132A132PHE 0-0.002-0.01420.689-0.008-0.0080.0000.0000.0000.000
133A133LYS 10.9210.98423.1800.0150.0150.0000.0000.0000.000
134A134GLY 00.0040.00822.707-0.001-0.0010.0000.0000.0000.000
135A135LEU 0-0.087-0.03817.177-0.010-0.0100.0000.0000.0000.000
136A136HIS 0-0.005-0.01515.3000.0010.0010.0000.0000.0000.000
137A137GLY 00.0360.01720.0430.0090.0090.0000.0000.0000.000
138A138ASP -1-0.916-0.95021.693-0.092-0.0920.0000.0000.0000.000
139A139LEU 0-0.097-0.05220.1570.0020.0020.0000.0000.0000.000
140A140PHE 0-0.007-0.01918.0220.0040.0040.0000.0000.0000.000
141A141NME 00.0260.04123.8690.0050.0050.0000.0000.0000.000
142A157ACE 0-0.018-0.02121.486-0.003-0.0030.0000.0000.0000.000
143A158ASP -1-0.864-0.95021.996-0.052-0.0520.0000.0000.0000.000
144A159ALA 00.0130.01422.624-0.005-0.0050.0000.0000.0000.000
145A160GLU -1-0.835-0.92622.995-0.039-0.0390.0000.0000.0000.000
146A161GLN 00.0410.00721.8760.0050.0050.0000.0000.0000.000
147A162GLU -1-0.962-0.96717.782-0.145-0.1450.0000.0000.0000.000
148A163ALA 00.021-0.00718.842-0.003-0.0030.0000.0000.0000.000
149A164VAL 00.0080.00420.8510.0060.0060.0000.0000.0000.000
150A165ALA 00.0110.00816.6780.0040.0040.0000.0000.0000.000
151A166ALA 0-0.017-0.00815.946-0.001-0.0010.0000.0000.0000.000
152A167LEU 00.003-0.00616.9640.0100.0100.0000.0000.0000.000
153A168VAL 0-0.049-0.01817.4290.0100.0100.0000.0000.0000.000
154A169ALA 0-0.063-0.02513.3510.0060.0060.0000.0000.0000.000
155A170LEU 0-0.052-0.03115.1430.0150.0150.0000.0000.0000.000
156A171GLY 0-0.0090.00817.1910.0160.0160.0000.0000.0000.000
157A172TYR 0-0.0210.00719.3200.0060.0060.0000.0000.0000.000
158A173LYS 10.9230.96121.269-0.006-0.0060.0000.0000.0000.000
159A174PRO 00.0750.02021.649-0.001-0.0010.0000.0000.0000.000
160A175GLN 00.0150.03223.739-0.001-0.0010.0000.0000.0000.000
161A176GLU -1-0.881-0.97425.6890.0010.0010.0000.0000.0000.000
162A177ALA 00.0300.01922.9110.0010.0010.0000.0000.0000.000
163A178SER 00.010-0.02624.893-0.004-0.0040.0000.0000.0000.000
164A179ARG 10.9020.96127.0200.0090.0090.0000.0000.0000.000
165A180MET 0-0.031-0.01425.5800.0000.0000.0000.0000.0000.000
166A181VAL 0-0.064-0.01224.2390.0010.0010.0000.0000.0000.000
167A182SER 00.0620.01127.672-0.001-0.0010.0000.0000.0000.000
168A183LYS 10.8700.95431.2890.0090.0090.0000.0000.0000.000
169A184ILE 0-0.004-0.00129.3070.0010.0010.0000.0000.0000.000
170A185ALA 0-0.0040.01429.818-0.002-0.0020.0000.0000.0000.000
171A186ARG 10.8890.94330.6110.0330.0330.0000.0000.0000.000
172A187PRO 0-0.004-0.01231.058-0.003-0.0030.0000.0000.0000.000
173A188ASP -1-0.910-0.94630.636-0.040-0.0400.0000.0000.0000.000
174A189ALA 00.0170.00528.8170.0020.0020.0000.0000.0000.000
175A190SER 00.0240.01923.899-0.002-0.0020.0000.0000.0000.000
176A191SER 00.0600.02019.6810.0090.0090.0000.0000.0000.000
177A192GLU -1-0.898-0.94619.017-0.074-0.0740.0000.0000.0000.000
178A193THR 0-0.110-0.05821.7180.0110.0110.0000.0000.0000.000
179A194LEU 00.0650.05024.4570.0060.0060.0000.0000.0000.000
180A195ILE 00.0170.01618.6990.0050.0050.0000.0000.0000.000
181A196ARG 10.8820.93922.8470.0330.0330.0000.0000.0000.000
182A197GLU -1-0.957-0.99324.670-0.010-0.0100.0000.0000.0000.000
183A198ALA 0-0.036-0.02625.1450.0040.0040.0000.0000.0000.000
184A199LEU 0-0.025-0.01821.1320.0040.0040.0000.0000.0000.000
185A200ARG 10.9370.97825.6260.0070.0070.0000.0000.0000.000
186A201ALA 0-0.037-0.01028.6610.0030.0030.0000.0000.0000.000
187A202ALA 0-0.047-0.03827.782-0.002-0.0020.0000.0000.0000.000
188A203LEU -1-0.978-0.95825.1100.0160.0160.0000.0000.0000.000