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: V5R81

Calculation Name: 2GHV-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GHV

Chain ID: E

ChEMBL ID:

UniProt ID: P59594

Base Structure: X-ray

Registration Date: 2023-06-21

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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1954404.428465
FMO2-HF: Nuclear repulsion 1880831.346437
FMO2-HF: Total energy -73573.082028
FMO2-MP2: Total energy -73785.945587


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(E:320:THR)


Summations of interaction energy for fragment #1(E:320:THR)
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.
-0.0861.1040.006-0.403-0.7930.001
Interaction energy analysis for fragmet #1(E:320:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.024
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].
3E322LEU00.0490.0423.7260.2121.0830.003-0.348-0.5260.001
4E323CYS0-0.066-0.0466.011-0.309-0.3090.0000.0000.0000.000
5E324PRO00.0170.0239.4830.2000.2000.0000.0000.0000.000
6E325PHE00.045-0.01412.0370.0310.0310.0000.0000.0000.000
7E326GLY00.0370.02213.9530.0340.0340.0000.0000.0000.000
8E327GLU-1-0.840-0.91413.453-0.449-0.4490.0000.0000.0000.000
9E328VAL0-0.0160.00316.9800.0010.0010.0000.0000.0000.000
10E329PHE00.002-0.01317.6680.0180.0180.0000.0000.0000.000
11E330ASN0-0.018-0.01118.8540.0340.0340.0000.0000.0000.000
12E331ALA00.0450.05120.7680.0090.0090.0000.0000.0000.000
13E332THR00.009-0.01321.8250.0100.0100.0000.0000.0000.000
14E333LYS10.9130.95024.8760.0680.0680.0000.0000.0000.000
15E334PHE00.0580.03323.399-0.012-0.0120.0000.0000.0000.000
16E335PRO00.0240.03425.8170.0110.0110.0000.0000.0000.000
17E336SER00.031-0.00128.8180.0110.0110.0000.0000.0000.000
18E337VAL00.0210.01331.250-0.010-0.0100.0000.0000.0000.000
19E338TYR0-0.007-0.00532.600-0.006-0.0060.0000.0000.0000.000
20E339ALA0-0.055-0.02830.874-0.006-0.0060.0000.0000.0000.000
21E340TRP0-0.0530.00725.688-0.013-0.0130.0000.0000.0000.000
22E341GLU-1-0.902-0.94623.599-0.182-0.1820.0000.0000.0000.000
23E342ARG10.8270.88021.2060.2600.2600.0000.0000.0000.000
24E343LYS10.8220.91113.5870.5090.5090.0000.0000.0000.000
25E344LYS10.8790.94514.8440.6070.6070.0000.0000.0000.000
26E345ILE0-0.0020.00011.657-0.078-0.0780.0000.0000.0000.000
27E346SER00.0370.01511.0690.0790.0790.0000.0000.0000.000
28E347ASN0-0.044-0.0097.518-0.159-0.1590.0000.0000.0000.000
29E348CYS0-0.0030.0085.029-0.775-0.7750.0000.0000.0000.000
30E349VAL00.0320.0294.1870.2440.5630.003-0.055-0.2670.000
31E350ALA00.015-0.0126.187-0.284-0.2840.0000.0000.0000.000
32E351ASP-1-0.817-0.9008.8230.9610.9610.0000.0000.0000.000
33E352TYR0-0.026-0.03210.552-0.121-0.1210.0000.0000.0000.000
34E353SER0-0.037-0.03113.201-0.082-0.0820.0000.0000.0000.000
35E354VAL0-0.0300.00211.295-0.016-0.0160.0000.0000.0000.000
36E355LEU0-0.055-0.01114.314-0.073-0.0730.0000.0000.0000.000
37E356TYR0-0.024-0.01416.9530.0320.0320.0000.0000.0000.000
38E357ASN0-0.0010.00320.475-0.020-0.0200.0000.0000.0000.000
39E358SER0-0.028-0.03722.775-0.015-0.0150.0000.0000.0000.000
40E359THR0-0.0080.01722.826-0.018-0.0180.0000.0000.0000.000
41E360PHE0-0.009-0.00824.5140.0050.0050.0000.0000.0000.000
42E361PHE00.006-0.00321.779-0.010-0.0100.0000.0000.0000.000
43E362SER00.0270.01227.7040.0050.0050.0000.0000.0000.000
44E363THR0-0.107-0.05829.756-0.002-0.0020.0000.0000.0000.000
45E364PHE00.0820.02822.137-0.004-0.0040.0000.0000.0000.000
46E365LYS10.9160.98128.0020.0410.0410.0000.0000.0000.000
47E366CYS0-0.062-0.00623.1610.0160.0160.0000.0000.0000.000
48E367TYR0-0.004-0.01427.3470.0130.0130.0000.0000.0000.000
49E368GLY00.1010.04827.366-0.010-0.0100.0000.0000.0000.000
50E369VAL0-0.0130.00724.610-0.008-0.0080.0000.0000.0000.000
51E370SER00.0160.00426.4660.0100.0100.0000.0000.0000.000
52E371ALA00.0610.00826.328-0.001-0.0010.0000.0000.0000.000
53E372THR0-0.011-0.01525.887-0.002-0.0020.0000.0000.0000.000
54E373LYS10.9090.95522.6170.1370.1370.0000.0000.0000.000
55E374LEU00.0540.03822.312-0.007-0.0070.0000.0000.0000.000
56E375ASN00.0150.00115.4630.0480.0480.0000.0000.0000.000
57E376ASP-1-0.869-0.93417.423-0.191-0.1910.0000.0000.0000.000
58E377LEU0-0.054-0.03718.458-0.013-0.0130.0000.0000.0000.000
59E378CYS0-0.062-0.02114.1040.0470.0470.0000.0000.0000.000
60E379PHE0-0.060-0.02914.1870.0070.0070.0000.0000.0000.000
61E380SER00.0470.02310.809-0.036-0.0360.0000.0000.0000.000
62E381ASN0-0.034-0.02711.469-0.236-0.2360.0000.0000.0000.000
63E382VAL0-0.0030.00714.0800.0800.0800.0000.0000.0000.000
64E383TYR0-0.0010.01616.421-0.080-0.0800.0000.0000.0000.000
65E384ALA00.0330.00418.5400.0380.0380.0000.0000.0000.000
66E385ASP-1-0.754-0.82120.325-0.234-0.2340.0000.0000.0000.000
67E386SER00.0130.00022.7020.0210.0210.0000.0000.0000.000
68E387PHE0-0.004-0.01425.243-0.003-0.0030.0000.0000.0000.000
69E388VAL00.0090.01828.8180.0070.0070.0000.0000.0000.000
70E389VAL0-0.022-0.01131.623-0.004-0.0040.0000.0000.0000.000
71E390LYS10.8590.93134.7560.0380.0380.0000.0000.0000.000
72E391GLY00.0360.01336.505-0.003-0.0030.0000.0000.0000.000
73E392ASP-1-0.891-0.96137.554-0.028-0.0280.0000.0000.0000.000
74E393ASP-1-0.842-0.90937.554-0.052-0.0520.0000.0000.0000.000
75E394VAL0-0.0080.00832.577-0.006-0.0060.0000.0000.0000.000
76E395ARG10.8610.92334.3660.0450.0450.0000.0000.0000.000
77E396GLN0-0.020-0.01536.651-0.005-0.0050.0000.0000.0000.000
78E397ILE0-0.0320.00329.962-0.007-0.0070.0000.0000.0000.000
79E398ALA00.013-0.01031.8600.0010.0010.0000.0000.0000.000
80E399PRO00.0310.02331.646-0.001-0.0010.0000.0000.0000.000
81E400GLY00.0410.02434.2170.0070.0070.0000.0000.0000.000
82E401GLN0-0.086-0.00536.6700.0100.0100.0000.0000.0000.000
83E402THR0-0.021-0.02538.951-0.003-0.0030.0000.0000.0000.000
84E403GLY00.0020.00441.3650.0040.0040.0000.0000.0000.000
85E404VAL00.0310.01341.125-0.004-0.0040.0000.0000.0000.000
86E405ILE0-0.0070.00535.347-0.005-0.0050.0000.0000.0000.000
87E406ALA00.0320.01736.221-0.007-0.0070.0000.0000.0000.000
88E407ASP-1-0.803-0.89737.301-0.075-0.0750.0000.0000.0000.000
89E408TYR0-0.015-0.02039.396-0.005-0.0050.0000.0000.0000.000
90E409ASN0-0.045-0.02435.311-0.002-0.0020.0000.0000.0000.000
91E410TYR00.029-0.03026.604-0.001-0.0010.0000.0000.0000.000
92E411LYS10.9330.99632.8340.0980.0980.0000.0000.0000.000
93E412LEU00.0000.01028.274-0.011-0.0110.0000.0000.0000.000
94E413PRO0-0.010-0.01129.6580.0090.0090.0000.0000.0000.000
95E414ASP-1-0.877-0.96532.491-0.087-0.0870.0000.0000.0000.000
96E415ASP-1-0.957-0.97231.523-0.131-0.1310.0000.0000.0000.000
97E416PHE0-0.068-0.02625.355-0.008-0.0080.0000.0000.0000.000
98E417MET00.0200.01023.8240.0150.0150.0000.0000.0000.000
99E418GLY00.0480.01323.338-0.024-0.0240.0000.0000.0000.000
100E420VAL0-0.0050.00024.685-0.014-0.0140.0000.0000.0000.000
101E421LEU0-0.0160.00122.0050.0150.0150.0000.0000.0000.000
102E422ALA00.003-0.00926.277-0.009-0.0090.0000.0000.0000.000
103E423TRP00.0290.00623.6510.0100.0100.0000.0000.0000.000
104E424ASN0-0.026-0.00829.488-0.005-0.0050.0000.0000.0000.000
105E425THR00.014-0.03728.8510.0060.0060.0000.0000.0000.000
106E426ARG10.9330.97431.949-0.007-0.0070.0000.0000.0000.000
107E427ASN0-0.028-0.03732.958-0.003-0.0030.0000.0000.0000.000
108E428ILE00.0000.00728.3330.0030.0030.0000.0000.0000.000
109E429ASP-1-0.733-0.78130.952-0.045-0.0450.0000.0000.0000.000
110E430ALA0-0.0210.00433.950-0.005-0.0050.0000.0000.0000.000
111E431THR0-0.009-0.00337.5840.0020.0020.0000.0000.0000.000
112E432SER00.007-0.00740.256-0.002-0.0020.0000.0000.0000.000
113E433THR00.0420.00942.9150.0000.0000.0000.0000.0000.000
114E434GLY0-0.0200.00242.662-0.002-0.0020.0000.0000.0000.000
115E435ASN0-0.061-0.03635.125-0.003-0.0030.0000.0000.0000.000
116E436TYR00.0460.00139.602-0.001-0.0010.0000.0000.0000.000
117E437ASN0-0.065-0.03535.030-0.006-0.0060.0000.0000.0000.000
118E438TYR0-0.081-0.04730.812-0.008-0.0080.0000.0000.0000.000
119E439LYS10.9140.94835.8470.0640.0640.0000.0000.0000.000
120E440TYR0-0.0200.00236.409-0.005-0.0050.0000.0000.0000.000
121E441ARG10.8240.89237.2590.0950.0950.0000.0000.0000.000
122E442TYR0-0.038-0.04140.4140.0010.0010.0000.0000.0000.000
123E443LEU0-0.0330.00543.7710.0020.0020.0000.0000.0000.000
124E444ARG10.8100.86938.3590.0980.0980.0000.0000.0000.000
125E445HIS0-0.0230.01644.4840.0020.0020.0000.0000.0000.000
126E446GLY00.0160.01243.611-0.003-0.0030.0000.0000.0000.000
127E447LYS10.8030.88540.6010.0690.0690.0000.0000.0000.000
128E448LEU0-0.079-0.01334.841-0.002-0.0020.0000.0000.0000.000
129E449ARG10.9350.95735.3570.1090.1090.0000.0000.0000.000
130E450PRO00.018-0.01931.855-0.002-0.0020.0000.0000.0000.000
131E451PHE0-0.027-0.00926.613-0.010-0.0100.0000.0000.0000.000
132E452GLU-1-0.797-0.86429.821-0.131-0.1310.0000.0000.0000.000
133E453ARG10.8520.90427.8280.1750.1750.0000.0000.0000.000
134E454ASP-1-0.772-0.85632.759-0.103-0.1030.0000.0000.0000.000
135E455ILE00.0140.00931.1510.0050.0050.0000.0000.0000.000
136E456SER0-0.036-0.01335.1720.0060.0060.0000.0000.0000.000
137E457ASN00.030-0.01038.6320.0030.0030.0000.0000.0000.000
138E458VAL00.0100.01141.2130.0020.0020.0000.0000.0000.000
139E459PRO0-0.011-0.00544.3850.0000.0000.0000.0000.0000.000
140E460PHE00.0120.00046.761-0.002-0.0020.0000.0000.0000.000
141E461SER00.0850.01048.7120.0040.0040.0000.0000.0000.000
142E462PRO00.002-0.01451.472-0.002-0.0020.0000.0000.0000.000
143E463ASP-1-0.819-0.88153.013-0.051-0.0510.0000.0000.0000.000
144E464GLY00.0000.00851.0380.0000.0000.0000.0000.0000.000
145E465LYS10.8230.91151.2990.0450.0450.0000.0000.0000.000
146E466PRO00.022-0.00450.650-0.001-0.0010.0000.0000.0000.000
147E467CYS0-0.0510.01450.8010.0000.0000.0000.0000.0000.000
148E468THR00.005-0.00251.320-0.002-0.0020.0000.0000.0000.000
149E469PRO00.0130.02750.1970.0020.0020.0000.0000.0000.000
150E470PRO0-0.010-0.00953.495-0.001-0.0010.0000.0000.0000.000
151E471ALA0-0.001-0.00756.0160.0020.0020.0000.0000.0000.000
152E472LEU00.031-0.00356.393-0.001-0.0010.0000.0000.0000.000
153E473ASN0-0.028-0.01356.254-0.002-0.0020.0000.0000.0000.000
154E475TYR0-0.007-0.01550.0930.0020.0020.0000.0000.0000.000
155E476TRP00.0570.02945.051-0.004-0.0040.0000.0000.0000.000
156E477PRO00.0200.01542.7990.0020.0020.0000.0000.0000.000
157E478LEU0-0.016-0.00238.577-0.002-0.0020.0000.0000.0000.000
158E479ASN0-0.011-0.01441.7860.0050.0050.0000.0000.0000.000
159E480ASP-1-0.845-0.91040.428-0.056-0.0560.0000.0000.0000.000
160E481TYR0-0.064-0.07136.3900.0010.0010.0000.0000.0000.000
161E482GLY00.0590.02340.7000.0000.0000.0000.0000.0000.000
162E483PHE0-0.059-0.02736.2060.0030.0030.0000.0000.0000.000
163E484TYR00.0510.04240.2790.0010.0010.0000.0000.0000.000
164E485THR0-0.031-0.02640.484-0.001-0.0010.0000.0000.0000.000
165E486THR0-0.020-0.01341.8430.0020.0020.0000.0000.0000.000
166E487THR00.0210.02342.927-0.002-0.0020.0000.0000.0000.000
167E488GLY00.0580.02943.1700.0020.0020.0000.0000.0000.000
168E489ILE00.0550.00738.303-0.003-0.0030.0000.0000.0000.000
169E490GLY00.0650.04139.357-0.002-0.0020.0000.0000.0000.000
170E491TYR0-0.003-0.00640.942-0.005-0.0050.0000.0000.0000.000
171E492GLN0-0.026-0.00137.3840.0000.0000.0000.0000.0000.000
172E493PRO00.0200.01833.894-0.003-0.0030.0000.0000.0000.000
173E494TYR0-0.0030.01031.9740.0090.0090.0000.0000.0000.000
174E495ARG10.8050.89925.8750.0410.0410.0000.0000.0000.000
175E496VAL0-0.010-0.01827.8320.0090.0090.0000.0000.0000.000
176E497VAL00.0170.00321.218-0.011-0.0110.0000.0000.0000.000
177E498VAL0-0.021-0.00624.5380.0150.0150.0000.0000.0000.000
178E499LEU0-0.0020.00818.795-0.027-0.0270.0000.0000.0000.000
179E500SER00.0070.00321.2830.0270.0270.0000.0000.0000.000
180E501PHE0-0.003-0.01619.583-0.031-0.0310.0000.0000.0000.000
181E502GLU-1-0.898-0.95317.844-0.449-0.4490.0000.0000.0000.000