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: 82J5Y

Calculation Name: 4H63-H-Xray321

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4H63

Chain ID: H

ChEMBL ID:

UniProt ID: Q9P6Q0

Base Structure: X-ray

Registration Date: 2021-09-07

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 179
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1343280.978666
FMO2-HF: Nuclear repulsion 1272167.161776
FMO2-HF: Total energy -71113.81689
FMO2-MP2: Total energy -71323.511714


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(H:2:ACE )


Summations of interaction energy for fragment #1(H:2:ACE )
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.
0.3651.4991.721-0.99-1.866-0.004
Interaction energy analysis for fragmet #1(H:2:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.015
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].
3H4ILE 00.0990.0523.8490.6741.454-0.004-0.305-0.4710.000
4H5SER 0-0.014-0.0172.667-0.846-0.1230.918-0.801-0.840-0.005
5H6THR 00.0050.0142.5060.5620.1320.8070.126-0.5030.001
6H7GLU -1-0.850-0.9104.752-0.417-0.3560.000-0.010-0.0520.000
7H8LYS 10.9800.9907.413-0.165-0.1650.0000.0000.0000.000
8H9THR 0-0.049-0.0266.2130.0170.0170.0000.0000.0000.000
9H10VAL 00.0270.0318.7050.0200.0200.0000.0000.0000.000
10H11GLU -1-0.924-0.96610.693-0.087-0.0870.0000.0000.0000.000
11H12SER 0-0.062-0.04211.6530.0380.0380.0000.0000.0000.000
12H13LEU 00.024-0.00411.2300.0060.0060.0000.0000.0000.000
13H14GLU -1-0.945-0.96514.498-0.071-0.0710.0000.0000.0000.000
14H15ALA 00.0060.00916.5510.0060.0060.0000.0000.0000.000
15H16ILE 0-0.008-0.00615.3360.0050.0050.0000.0000.0000.000
16H17ARG 10.9380.96318.2920.0570.0570.0000.0000.0000.000
17H18HIS 0-0.036-0.01320.051-0.004-0.0040.0000.0000.0000.000
18H19ARG 10.9520.97622.108-0.015-0.0150.0000.0000.0000.000
19H20ILE 00.0230.00320.6120.0010.0010.0000.0000.0000.000
20H21ALA 00.0000.00624.190-0.001-0.0010.0000.0000.0000.000
21H22GLN 0-0.026-0.02526.0930.0030.0030.0000.0000.0000.000
22H23ILE 00.0390.03326.9190.0000.0000.0000.0000.0000.000
23H24VAL 00.0300.01827.6290.0000.0000.0000.0000.0000.000
24H25GLN 00.0130.01030.113-0.002-0.0020.0000.0000.0000.000
25H26SER 0-0.044-0.03032.2880.0010.0010.0000.0000.0000.000
26H27LEU 00.0060.00131.0040.0010.0010.0000.0000.0000.000
27H28THR 0-0.023-0.00933.783-0.001-0.0010.0000.0000.0000.000
28H29HIS 00.0130.00736.180-0.001-0.0010.0000.0000.0000.000
29H30PHE 0-0.003-0.00137.7560.0000.0000.0000.0000.0000.000
30H31LEU 00.004-0.00737.2200.0000.0000.0000.0000.0000.000
31H32ALA 00.0080.01040.3910.0000.0000.0000.0000.0000.000
32H33ILE 0-0.043-0.03341.7300.0000.0000.0000.0000.0000.000
33H34LEU 0-0.063-0.03041.7260.0000.0000.0000.0000.0000.000
34H35HIS 00.0190.01042.4960.0010.0010.0000.0000.0000.000
35H36GLN 0-0.110-0.04246.035-0.001-0.0010.0000.0000.0000.000
36H37SER 0-0.052-0.03749.0960.0000.0000.0000.0000.0000.000
37H38GLU -1-0.929-0.93850.1380.0010.0010.0000.0000.0000.000
38H39SER 00.026-0.02151.6030.0000.0000.0000.0000.0000.000
39H40LEU 0-0.049-0.00247.5020.0000.0000.0000.0000.0000.000
40H41SER 00.0710.03147.6440.0000.0000.0000.0000.0000.000
41H42PRO 0-0.0010.00549.4620.0010.0010.0000.0000.0000.000
42H43TRP 00.0870.04445.7130.0000.0000.0000.0000.0000.000
43H44PRO 00.013-0.00847.4810.0010.0010.0000.0000.0000.000
44H45THR 00.0200.00744.9970.0010.0010.0000.0000.0000.000
45H46ILE 00.0360.03243.9270.0000.0000.0000.0000.0000.000
46H47HIS 00.0190.01542.6040.0010.0010.0000.0000.0000.000
47H48LYS 10.9300.96241.622-0.004-0.0040.0000.0000.0000.000
48H49ASN 0-0.011-0.03539.3540.0000.0000.0000.0000.0000.000
49H50PHE 00.0370.02938.1120.0010.0010.0000.0000.0000.000
50H51ASN 0-0.003-0.00237.0770.0030.0030.0000.0000.0000.000
51H52ILE 0-0.060-0.01435.0060.0010.0010.0000.0000.0000.000
52H53LEU 00.0370.01933.3710.0010.0010.0000.0000.0000.000
53H54LEU 00.0130.01732.3300.0020.0020.0000.0000.0000.000
54H55SER 00.001-0.00931.9670.0040.0040.0000.0000.0000.000
55H56GLN 00.0130.01429.4860.0010.0010.0000.0000.0000.000
56H57ILE 00.006-0.01127.7930.0020.0020.0000.0000.0000.000
57H58HIS 00.0170.02427.2630.0070.0070.0000.0000.0000.000
58H59SER 0-0.036-0.02325.9290.0040.0040.0000.0000.0000.000
59H60LEU 0-0.015-0.01122.3880.0060.0060.0000.0000.0000.000
60H61SER 00.0450.01822.4920.0070.0070.0000.0000.0000.000
61H62ASN 0-0.015-0.00822.7850.0140.0140.0000.0000.0000.000
62H63ASN 0-0.045-0.03118.9540.0120.0120.0000.0000.0000.000
63H64LEU 00.0140.00118.0780.0120.0120.0000.0000.0000.000
64H65ALA 00.0100.00617.8180.0240.0240.0000.0000.0000.000
65H66ALA 0-0.031-0.00518.3500.0190.0190.0000.0000.0000.000
66H67HIS 0-0.019-0.01213.1580.0120.0120.0000.0000.0000.000
67H68SER 00.0260.02213.8350.0240.0240.0000.0000.0000.000
68H69HIS 00.0080.00810.2520.0000.0000.0000.0000.0000.000
69H70THR 0-0.009-0.0038.8700.0470.0470.0000.0000.0000.000
70H71LEU 00.0240.0229.3540.0530.0530.0000.0000.0000.000
71H72GLN 00.0280.01711.6740.0300.0300.0000.0000.0000.000
72H73THR 0-0.118-0.0578.2300.0530.0530.0000.0000.0000.000
73H74THR 0-0.063-0.0496.7790.1930.1930.0000.0000.0000.000
74H75SER 00.0270.0079.250-0.080-0.0800.0000.0000.0000.000
75H76ILE 0-0.0180.00311.065-0.047-0.0470.0000.0000.0000.000
76H77TYR 0-0.013-0.0098.984-0.022-0.0220.0000.0000.0000.000
77H78PRO 0-0.0090.00515.140-0.027-0.0270.0000.0000.0000.000
78H79SER 00.0520.02915.263-0.005-0.0050.0000.0000.0000.000
79H80LEU 0-0.004-0.02715.9320.0200.0200.0000.0000.0000.000
80H81GLU -1-0.931-0.95618.574-0.167-0.1670.0000.0000.0000.000
81H82PHE 0-0.029-0.01420.0840.0130.0130.0000.0000.0000.000
82H83PRO 00.0260.03321.8400.0040.0040.0000.0000.0000.000
83H84VAL 0-0.030-0.04921.8140.0090.0090.0000.0000.0000.000
84H85LYS 10.9150.96125.0120.0600.0600.0000.0000.0000.000
85H86GLU -1-0.922-0.96028.486-0.036-0.0360.0000.0000.0000.000
86H87GLN 0-0.007-0.00627.6850.0070.0070.0000.0000.0000.000
87H88GLU -1-0.867-0.93025.738-0.008-0.0080.0000.0000.0000.000
88H89PRO 00.019-0.00926.2470.0040.0040.0000.0000.0000.000
89H90LEU 00.0020.01425.3400.0040.0040.0000.0000.0000.000
90H91LEU 0-0.0020.01120.1420.0010.0010.0000.0000.0000.000
91H92THR 0-0.022-0.02922.7810.0070.0070.0000.0000.0000.000
92H93THR 0-0.032-0.01224.3800.0080.0080.0000.0000.0000.000
93H94LEU 0-0.058-0.03121.5560.0040.0040.0000.0000.0000.000
94H95LEU 0-0.016-0.00517.6890.0040.0040.0000.0000.0000.000
95H96ARG 10.9250.96820.965-0.019-0.0190.0000.0000.0000.000
96H97THR 00.0160.00321.0640.0010.0010.0000.0000.0000.000
97H98LYS 10.8540.95222.851-0.040-0.0400.0000.0000.0000.000
98H99ALA 00.0910.05026.579-0.004-0.0040.0000.0000.0000.000
99H100LEU 0-0.019-0.02228.587-0.004-0.0040.0000.0000.0000.000
100H101PRO 00.0350.01331.9940.0020.0020.0000.0000.0000.000
101H102GLU -1-0.878-0.94234.9700.0270.0270.0000.0000.0000.000
102H103VAL 0-0.052-0.02730.2350.0000.0000.0000.0000.0000.000
103H104GLU -1-0.918-0.96531.0610.0510.0510.0000.0000.0000.000
104H105GLU -1-0.925-0.96533.6390.0320.0320.0000.0000.0000.000
105H106TRP 0-0.0150.00632.3600.0010.0010.0000.0000.0000.000
106H107GLU -1-0.935-0.95329.8260.0690.0690.0000.0000.0000.000
107H108ALA 0-0.015-0.01034.6000.0000.0000.0000.0000.0000.000
108H109ASN 0-0.021-0.01637.1030.0000.0000.0000.0000.0000.000
109H110THR 0-0.030-0.04136.4990.0010.0010.0000.0000.0000.000
110H111LEU 0-0.015-0.00733.4660.0010.0010.0000.0000.0000.000
111H112GLN 0-0.0210.00037.858-0.001-0.0010.0000.0000.0000.000
112H113GLU -1-0.939-0.98741.4070.0360.0360.0000.0000.0000.000
113H114TYR 0-0.050-0.00738.083-0.001-0.0010.0000.0000.0000.000
114H115GLU -1-0.891-0.95538.7920.0550.0550.0000.0000.0000.000
115H116ALA 0-0.079-0.03042.636-0.002-0.0020.0000.0000.0000.000
116H117SER 0-0.108-0.05743.760-0.001-0.0010.0000.0000.0000.000
117H118ILE 0-0.075-0.02141.723-0.001-0.0010.0000.0000.0000.000
118H119NME 0-0.021-0.00645.267-0.002-0.0020.0000.0000.0000.000
119H126ACE 00.0330.00738.268-0.001-0.0010.0000.0000.0000.000
120H127ALA 00.004-0.01035.0910.0040.0040.0000.0000.0000.000
121H128ASN 0-0.047-0.02035.7230.0020.0020.0000.0000.0000.000
122H129ASP -1-0.829-0.92538.1940.0520.0520.0000.0000.0000.000
123H130ALA 0-0.071-0.02734.979-0.002-0.0020.0000.0000.0000.000
124H131TYR 00.0400.02233.5330.0010.0010.0000.0000.0000.000
125H132GLN 00.0220.00635.804-0.004-0.0040.0000.0000.0000.000
126H133LYS 10.9430.96838.945-0.049-0.0490.0000.0000.0000.000
127H134ASP -1-0.863-0.92933.3530.0650.0650.0000.0000.0000.000
128H135GLN 0-0.029-0.01936.836-0.001-0.0010.0000.0000.0000.000
129H136LEU 0-0.036-0.01338.223-0.003-0.0030.0000.0000.0000.000
130H137TRP 0-0.002-0.00537.878-0.004-0.0040.0000.0000.0000.000
131H138ASP -1-0.876-0.92135.7900.0510.0510.0000.0000.0000.000
132H139GLN 00.0540.01138.2060.0000.0000.0000.0000.0000.000
133H140ALA 0-0.0240.00341.647-0.003-0.0030.0000.0000.0000.000
134H141ARG 10.8520.91836.383-0.048-0.0480.0000.0000.0000.000
135H142ILE 0-0.018-0.01038.204-0.002-0.0020.0000.0000.0000.000
136H143ILE 00.0300.01441.878-0.002-0.0020.0000.0000.0000.000
137H144PHE 0-0.020-0.01143.660-0.002-0.0020.0000.0000.0000.000
138H145MET 0-0.065-0.05638.638-0.001-0.0010.0000.0000.0000.000
139H146GLU -1-0.938-0.94543.9710.0280.0280.0000.0000.0000.000
140H147GLU -1-0.887-0.94846.5460.0200.0200.0000.0000.0000.000
141H148ARG 10.8510.93044.022-0.023-0.0230.0000.0000.0000.000
142H149GLU -1-0.941-0.97845.9670.0190.0190.0000.0000.0000.000
143H150ASN 0-0.045-0.01549.5190.0000.0000.0000.0000.0000.000
144H151TYR 0-0.059-0.02052.277-0.001-0.0010.0000.0000.0000.000
145H152SER 0-0.011-0.00452.6810.0000.0000.0000.0000.0000.000
146H153TRP 0-0.031-0.01150.196-0.001-0.0010.0000.0000.0000.000
147H154PHE 0-0.051-0.03548.4960.0000.0000.0000.0000.0000.000
148H155NME 00.0150.02554.7060.0000.0000.0000.0000.0000.000
149H170ACE 00.0260.00063.0910.0000.0000.0000.0000.0000.000
150H171ARG 10.9510.96357.733-0.005-0.0050.0000.0000.0000.000
151H172GLN 00.0190.00763.7370.0000.0000.0000.0000.0000.000
152H173LEU 00.0620.03666.5500.0000.0000.0000.0000.0000.000
153H174GLU -1-0.965-0.98964.0790.0030.0030.0000.0000.0000.000
154H175ILE 0-0.0020.00364.9110.0000.0000.0000.0000.0000.000
155H176ASP -1-0.879-0.94468.8790.0030.0030.0000.0000.0000.000
156H177ARG 10.9410.96670.556-0.003-0.0030.0000.0000.0000.000
157H178ALA 00.0080.02369.4550.0000.0000.0000.0000.0000.000
158H179THR 0-0.053-0.04771.5970.0000.0000.0000.0000.0000.000
159H180GLU -1-0.972-0.98074.0270.0010.0010.0000.0000.0000.000
160H181GLU -1-0.917-0.95573.2020.0000.0000.0000.0000.0000.000
161H182GLN 0-0.045-0.02172.9200.0000.0000.0000.0000.0000.000
162H183ASN 0-0.019-0.01376.0410.0000.0000.0000.0000.0000.000
163H184ALA 00.0970.04979.3520.0000.0000.0000.0000.0000.000
164H185ASN 0-0.0020.00175.9150.0000.0000.0000.0000.0000.000
165H186GLN 0-0.0340.00879.8330.0000.0000.0000.0000.0000.000
166H187MET 00.0170.01281.4240.0000.0000.0000.0000.0000.000
167H188LEU 0-0.018-0.01381.5920.0000.0000.0000.0000.0000.000
168H189THR 0-0.075-0.07482.0580.0000.0000.0000.0000.0000.000
169H190ASP -1-0.850-0.91684.549-0.001-0.0010.0000.0000.0000.000
170H191ILE 00.0130.02887.4670.0000.0000.0000.0000.0000.000
171H192LEU 0-0.007-0.00585.0590.0000.0000.0000.0000.0000.000
172H193SER 0-0.063-0.04889.4810.0000.0000.0000.0000.0000.000
173H194PHE 00.0020.02491.2220.0000.0000.0000.0000.0000.000
174H195MET 0-0.009-0.00490.0650.0000.0000.0000.0000.0000.000
175H196LYS 10.9100.97392.2450.0020.0020.0000.0000.0000.000
176H197SER 0-0.124-0.08694.1440.0000.0000.0000.0000.0000.000
177H198GLY 00.0320.01595.5090.0000.0000.0000.0000.0000.000
178H199LYS 10.8640.92792.0560.0020.0020.0000.0000.0000.000
179H200ARG 00.0910.06092.9210.0000.0000.0000.0000.0000.000