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: VRM51

Calculation Name: 4H63-H-Xray372

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: 2023-06-20

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 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 174
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1326957.23718
FMO2-HF: Nuclear repulsion 1256337.115977
FMO2-HF: Total energy -70620.121203
FMO2-MP2: Total energy -70828.293229


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:3:ASP)


Summations of interaction energy for fragment #1(H:3:ASP)
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.
57.06961.0862.712-2.503-4.2240.018
Interaction energy analysis for fragmet #1(H:3:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.913 / q_NPA : -0.956
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].
3H5SER0-0.033-0.0263.306-4.024-1.6560.073-1.047-1.3940.005
4H6THR00.0220.0152.537-12.964-11.5202.639-1.417-2.6650.013
5H7GLU-1-0.861-0.9144.82029.41129.6160.000-0.039-0.1650.000
6H8LYS10.9730.9866.938-30.129-30.1290.0000.0000.0000.000
7H9THR0-0.050-0.0267.678-2.464-2.4640.0000.0000.0000.000
8H10VAL00.0250.0308.233-2.833-2.8330.0000.0000.0000.000
9H11GLU-1-0.925-0.96810.57320.32920.3290.0000.0000.0000.000
10H12SER0-0.065-0.04412.433-1.618-1.6180.0000.0000.0000.000
11H13LEU00.025-0.00412.091-1.561-1.5610.0000.0000.0000.000
12H14GLU-1-0.948-0.96614.83413.97213.9720.0000.0000.0000.000
13H15ALA00.0060.00916.717-1.136-1.1360.0000.0000.0000.000
14H16ILE0-0.012-0.00716.503-1.052-1.0520.0000.0000.0000.000
15H17ARG10.9400.96318.766-14.722-14.7220.0000.0000.0000.000
16H18HIS0-0.038-0.01520.574-0.542-0.5420.0000.0000.0000.000
17H19ARG10.9520.97622.778-12.825-12.8250.0000.0000.0000.000
18H20ILE00.0220.00421.764-0.550-0.5500.0000.0000.0000.000
19H21ALA00.0000.00624.724-0.472-0.4720.0000.0000.0000.000
20H22GLN0-0.021-0.02326.473-0.303-0.3030.0000.0000.0000.000
21H23ILE00.0310.03027.954-0.429-0.4290.0000.0000.0000.000
22H24VAL00.0300.01828.455-0.396-0.3960.0000.0000.0000.000
23H25GLN00.0140.01130.875-0.282-0.2820.0000.0000.0000.000
24H26SER0-0.042-0.02932.791-0.261-0.2610.0000.0000.0000.000
25H27LEU00.0030.00132.167-0.315-0.3150.0000.0000.0000.000
26H28THR0-0.024-0.01134.304-0.276-0.2760.0000.0000.0000.000
27H29HIS00.0120.00736.806-0.241-0.2410.0000.0000.0000.000
28H30PHE0-0.002-0.00138.561-0.260-0.2600.0000.0000.0000.000
29H31LEU00.003-0.00738.138-0.222-0.2220.0000.0000.0000.000
30H32ALA00.0080.00941.031-0.201-0.2010.0000.0000.0000.000
31H33ILE0-0.038-0.03142.416-0.210-0.2100.0000.0000.0000.000
32H34LEU0-0.067-0.03242.864-0.193-0.1930.0000.0000.0000.000
33H35HIS00.0200.01143.275-0.205-0.2050.0000.0000.0000.000
34H36GLN0-0.111-0.04246.493-0.201-0.2010.0000.0000.0000.000
35H37SER0-0.051-0.03749.654-0.060-0.0600.0000.0000.0000.000
36H38GLU-1-0.931-0.94051.0996.0216.0210.0000.0000.0000.000
37H39SER00.025-0.02152.694-0.172-0.1720.0000.0000.0000.000
38H40LEU0-0.047-0.00148.8680.0630.0630.0000.0000.0000.000
39H41SER00.0680.03048.751-0.071-0.0710.0000.0000.0000.000
40H42PRO00.0000.00650.435-0.033-0.0330.0000.0000.0000.000
41H43TRP00.0870.04347.1790.1400.1400.0000.0000.0000.000
42H44PRO00.011-0.00948.6700.1390.1390.0000.0000.0000.000
43H45THR00.0190.00745.9220.1280.1280.0000.0000.0000.000
44H46ILE00.0320.03144.9690.1940.1940.0000.0000.0000.000
45H47HIS00.0230.01543.8110.1730.1730.0000.0000.0000.000
46H48LYS10.9310.96342.318-6.967-6.9670.0000.0000.0000.000
47H49ASN0-0.010-0.03540.2720.3760.3760.0000.0000.0000.000
48H50PHE00.0360.02939.2230.2030.2030.0000.0000.0000.000
49H51ASN0-0.003-0.00238.3270.2780.2780.0000.0000.0000.000
50H52ILE0-0.061-0.01535.9030.1770.1770.0000.0000.0000.000
51H53LEU00.0380.02034.5090.2780.2780.0000.0000.0000.000
52H54LEU00.0120.01633.5500.2950.2950.0000.0000.0000.000
53H55SER00.000-0.01033.2310.3420.3420.0000.0000.0000.000
54H56GLN00.0140.01430.2900.5710.5710.0000.0000.0000.000
55H57ILE00.004-0.01128.9270.4200.4200.0000.0000.0000.000
56H58HIS00.0170.02328.6730.3250.3250.0000.0000.0000.000
57H59SER0-0.036-0.02326.8120.3070.3070.0000.0000.0000.000
58H60LEU0-0.016-0.01123.8430.5140.5140.0000.0000.0000.000
59H61SER00.0440.01723.9390.4020.4020.0000.0000.0000.000
60H62ASN0-0.014-0.00824.4080.2450.2450.0000.0000.0000.000
61H63ASN0-0.046-0.03119.9080.9570.9570.0000.0000.0000.000
62H64LEU00.0170.00219.7720.7060.7060.0000.0000.0000.000
63H65ALA00.0080.00519.5770.6010.6010.0000.0000.0000.000
64H66ALA0-0.033-0.00619.4680.2520.2520.0000.0000.0000.000
65H67HIS0-0.014-0.00914.5770.8970.8970.0000.0000.0000.000
66H68SER00.0190.01915.6680.4940.4940.0000.0000.0000.000
67H69HIS00.0080.00811.9580.4650.4650.0000.0000.0000.000
68H70THR0-0.0030.00010.3520.2630.2630.0000.0000.0000.000
69H71LEU00.0230.02311.4781.2701.2700.0000.0000.0000.000
70H72GLN00.0220.01314.0280.5800.5800.0000.0000.0000.000
71H73THR0-0.116-0.05610.7710.4290.4290.0000.0000.0000.000
72H74THR0-0.052-0.0418.9402.5982.5980.0000.0000.0000.000
73H75SER00.0250.00611.491-2.114-2.1140.0000.0000.0000.000
74H76ILE0-0.0170.00312.5791.2451.2450.0000.0000.0000.000
75H77TYR0-0.012-0.00910.276-0.843-0.8430.0000.0000.0000.000
76H78PRO0-0.0130.00315.8300.5720.5720.0000.0000.0000.000
77H79SER00.0560.03215.0510.5480.5480.0000.0000.0000.000
78H80LEU0-0.004-0.02615.208-1.022-1.0220.0000.0000.0000.000
79H81GLU-1-0.933-0.95718.21815.93915.9390.0000.0000.0000.000
80H82PHE0-0.029-0.01320.226-0.683-0.6830.0000.0000.0000.000
81H83PRO00.0230.03221.915-0.171-0.1710.0000.0000.0000.000
82H84VAL0-0.027-0.04822.511-0.518-0.5180.0000.0000.0000.000
83H85LYS10.9150.96025.579-11.441-11.4410.0000.0000.0000.000
84H86GLU-1-0.925-0.96229.0479.6329.6320.0000.0000.0000.000
85H87GLN0-0.009-0.00727.991-0.455-0.4550.0000.0000.0000.000
86H88GLU-1-0.865-0.92826.57911.42911.4290.0000.0000.0000.000
87H89PRO00.014-0.01127.1720.2450.2450.0000.0000.0000.000
88H90LEU00.0020.01326.016-0.023-0.0230.0000.0000.0000.000
89H91LEU00.0010.01320.8940.2920.2920.0000.0000.0000.000
90H92THR0-0.021-0.02823.8610.2240.2240.0000.0000.0000.000
91H93THR0-0.038-0.01525.780-0.036-0.0360.0000.0000.0000.000
92H94LEU0-0.055-0.03022.5780.0460.0460.0000.0000.0000.000
93H95LEU0-0.010-0.00218.8550.3650.3650.0000.0000.0000.000
94H96ARG10.9240.96922.403-9.977-9.9770.0000.0000.0000.000
95H97THR00.0280.00723.0580.1880.1880.0000.0000.0000.000
96H98LYS10.8360.94324.838-9.388-9.3880.0000.0000.0000.000
97H99ALA00.0910.05228.6280.0940.0940.0000.0000.0000.000
98H100LEU0-0.016-0.02030.701-0.133-0.1330.0000.0000.0000.000
99H101PRO00.0340.01334.016-0.012-0.0120.0000.0000.0000.000
100H102GLU-1-0.881-0.94437.0557.4617.4610.0000.0000.0000.000
101H103VAL0-0.051-0.02632.455-0.074-0.0740.0000.0000.0000.000
102H104GLU-1-0.918-0.96533.2649.1419.1410.0000.0000.0000.000
103H105GLU-1-0.925-0.96535.9487.1757.1750.0000.0000.0000.000
104H106TRP0-0.0180.00534.505-0.030-0.0300.0000.0000.0000.000
105H107GLU-1-0.934-0.95432.2459.3719.3710.0000.0000.0000.000
106H108ALA0-0.016-0.01137.056-0.113-0.1130.0000.0000.0000.000
107H109ASN0-0.021-0.01639.594-0.146-0.1460.0000.0000.0000.000
108H110THR0-0.029-0.04138.924-0.060-0.0600.0000.0000.0000.000
109H111LEU0-0.013-0.00636.068-0.033-0.0330.0000.0000.0000.000
110H112GLN0-0.0210.00040.419-0.144-0.1440.0000.0000.0000.000
111H113GLU-1-0.942-0.98843.9906.7596.7590.0000.0000.0000.000
112H114TYR0-0.051-0.00840.574-0.120-0.1200.0000.0000.0000.000
113H115GLU-1-0.894-0.95841.4167.4697.4690.0000.0000.0000.000
114H116ALA0-0.099-0.03545.245-0.152-0.1520.0000.0000.0000.000
115H117SER0-0.112-0.05646.316-0.142-0.1420.0000.0000.0000.000
116H118ILE0-0.059-0.01444.228-0.178-0.1780.0000.0000.0000.000
117H127ALA00.0260.00737.169-0.027-0.0270.0000.0000.0000.000
118H128ASN0-0.045-0.03537.7160.1150.1150.0000.0000.0000.000
119H129ASP-1-0.826-0.92440.1447.0617.0610.0000.0000.0000.000
120H130ALA0-0.056-0.02437.047-0.039-0.0390.0000.0000.0000.000
121H131TYR00.0300.01935.1870.1170.1170.0000.0000.0000.000
122H132GLN00.0220.00637.603-0.121-0.1210.0000.0000.0000.000
123H133LYS10.9420.96840.877-7.120-7.1200.0000.0000.0000.000
124H134ASP-1-0.863-0.92935.1758.4368.4360.0000.0000.0000.000
125H135GLN0-0.029-0.02038.585-0.007-0.0070.0000.0000.0000.000
126H136LEU0-0.037-0.01339.770-0.146-0.1460.0000.0000.0000.000
127H137TRP0-0.003-0.00639.573-0.184-0.1840.0000.0000.0000.000
128H138ASP-1-0.874-0.92037.0988.1868.1860.0000.0000.0000.000
129H139GLN00.0530.01139.6360.0990.0990.0000.0000.0000.000
130H140ALA0-0.0240.00342.989-0.142-0.1420.0000.0000.0000.000
131H141ARG10.8510.91837.650-8.162-8.1620.0000.0000.0000.000
132H142ILE0-0.016-0.01039.307-0.023-0.0230.0000.0000.0000.000
133H143ILE00.0290.01443.029-0.108-0.1080.0000.0000.0000.000
134H144PHE0-0.020-0.01144.825-0.106-0.1060.0000.0000.0000.000
135H145MET0-0.064-0.05539.571-0.004-0.0040.0000.0000.0000.000
136H146GLU-1-0.938-0.94545.0086.5796.5790.0000.0000.0000.000
137H147GLU-1-0.889-0.94947.5205.7775.7770.0000.0000.0000.000
138H148ARG10.8510.93044.798-6.882-6.8820.0000.0000.0000.000
139H149GLU-1-0.941-0.97946.7206.5626.5620.0000.0000.0000.000
140H150ASN0-0.046-0.01550.317-0.012-0.0120.0000.0000.0000.000
141H151TYR0-0.059-0.01953.234-0.213-0.2130.0000.0000.0000.000
142H152SER0-0.013-0.00653.4350.1230.1230.0000.0000.0000.000
143H153TRP0-0.029-0.00750.990-0.108-0.1080.0000.0000.0000.000
144H154PHE0-0.034-0.01249.1070.0030.0030.0000.0000.0000.000
145H171ARG10.9770.97558.039-5.277-5.2770.0000.0000.0000.000
146H172GLN00.0240.00063.6210.0850.0850.0000.0000.0000.000
147H173LEU00.0630.03466.555-0.040-0.0400.0000.0000.0000.000
148H174GLU-1-0.972-0.99264.0874.9014.9010.0000.0000.0000.000
149H175ILE00.0010.00464.708-0.027-0.0270.0000.0000.0000.000
150H176ASP-1-0.878-0.94468.6734.4034.4030.0000.0000.0000.000
151H177ARG10.9380.96570.680-4.438-4.4380.0000.0000.0000.000
152H178ALA00.0090.02469.196-0.030-0.0300.0000.0000.0000.000
153H179THR0-0.052-0.04771.322-0.055-0.0550.0000.0000.0000.000
154H180GLU-1-0.972-0.98173.6374.0884.0880.0000.0000.0000.000
155H181GLU-1-0.916-0.95472.8694.3094.3090.0000.0000.0000.000
156H182GLN0-0.043-0.01972.204-0.084-0.0840.0000.0000.0000.000
157H183ASN0-0.020-0.01475.482-0.072-0.0720.0000.0000.0000.000
158H184ALA00.0950.04878.798-0.062-0.0620.0000.0000.0000.000
159H185ASN00.0050.00575.363-0.083-0.0830.0000.0000.0000.000
160H186GLN0-0.0320.01079.0600.0100.0100.0000.0000.0000.000
161H187MET00.0100.00880.689-0.042-0.0420.0000.0000.0000.000
162H188LEU0-0.013-0.01280.946-0.064-0.0640.0000.0000.0000.000
163H189THR0-0.067-0.06981.266-0.030-0.0300.0000.0000.0000.000
164H190ASP-1-0.866-0.92583.7143.7373.7370.0000.0000.0000.000
165H191ILE00.0030.02386.823-0.063-0.0630.0000.0000.0000.000
166H192LEU00.0060.00284.163-0.054-0.0540.0000.0000.0000.000
167H193SER0-0.062-0.04588.613-0.047-0.0470.0000.0000.0000.000
168H194PHE0-0.0160.01090.264-0.059-0.0590.0000.0000.0000.000
169H195MET00.0040.00289.462-0.049-0.0490.0000.0000.0000.000
170H196LYS10.9210.98191.198-3.510-3.5100.0000.0000.0000.000
171H197SER0-0.111-0.07993.104-0.027-0.0270.0000.0000.0000.000
172H198GLY00.0460.02494.541-0.040-0.0400.0000.0000.0000.000
173H199LYS10.9000.94890.810-3.538-3.5380.0000.0000.0000.000
174H200ARG11.0181.01991.423-3.239-3.2390.0000.0000.0000.000