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: YZY62

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 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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1952705.008391
FMO2-HF: Nuclear repulsion 1879132.896862
FMO2-HF: Total energy -73572.111528
FMO2-MP2: Total energy -73784.924019


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.
0.5251.7880.002-0.469-0.7940.001
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 : 0.014 / q_NPA : -0.018
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].
3E322LEU00.0510.0413.8330.1391.059-0.002-0.408-0.5090.001
4E323CYS00.0020.0145.993-0.402-0.4020.0000.0000.0000.000
5E324PRO00.0180.0279.4590.1850.1850.0000.0000.0000.000
6E325PHE00.052-0.01212.0170.0370.0370.0000.0000.0000.000
7E326GLY00.0420.02413.9330.0390.0390.0000.0000.0000.000
8E327GLU-1-0.952-0.99013.490-0.559-0.5590.0000.0000.0000.000
9E328VAL0-0.0300.00116.8110.0050.0050.0000.0000.0000.000
10E329PHE0-0.002-0.01917.7420.0210.0210.0000.0000.0000.000
11E330ASN0-0.017-0.00718.6520.0370.0370.0000.0000.0000.000
12E331ALA00.0580.05720.749-0.001-0.0010.0000.0000.0000.000
13E332THR00.009-0.01121.8090.0150.0150.0000.0000.0000.000
14E333LYS10.9070.94624.8290.1220.1220.0000.0000.0000.000
15E334PHE00.0610.03623.443-0.014-0.0140.0000.0000.0000.000
16E335PRO00.0400.03825.8750.0090.0090.0000.0000.0000.000
17E336SER00.015-0.00528.9560.0160.0160.0000.0000.0000.000
18E337VAL00.0270.01331.431-0.011-0.0110.0000.0000.0000.000
19E338TYR0-0.010-0.00532.548-0.005-0.0050.0000.0000.0000.000
20E339ALA0-0.050-0.03431.056-0.006-0.0060.0000.0000.0000.000
21E340TRP0-0.0600.00625.572-0.016-0.0160.0000.0000.0000.000
22E341GLU-1-0.913-0.94723.718-0.224-0.2240.0000.0000.0000.000
23E342ARG10.8630.91720.9770.2410.2410.0000.0000.0000.000
24E343LYS10.9280.97813.5050.6420.6420.0000.0000.0000.000
25E344LYS10.9520.97714.5370.7290.7290.0000.0000.0000.000
26E345ILE00.008-0.00111.341-0.108-0.1080.0000.0000.0000.000
27E346SER00.0210.00310.9050.1180.1180.0000.0000.0000.000
28E347ASN0-0.065-0.0287.408-0.156-0.1560.0000.0000.0000.000
29E348CYS0-0.103-0.0464.826-0.642-0.6420.0000.0000.0000.000
30E349VAL00.0650.0344.0530.3400.6830.004-0.061-0.2850.000
31E350ALA00.028-0.0035.886-0.387-0.3870.0000.0000.0000.000
32E351ASP-1-0.846-0.9348.6921.2701.2700.0000.0000.0000.000
33E352TYR0-0.027-0.03510.542-0.140-0.1400.0000.0000.0000.000
34E353SER0-0.021-0.00613.474-0.119-0.1190.0000.0000.0000.000
35E354VAL0-0.0180.01311.380-0.040-0.0400.0000.0000.0000.000
36E355LEU0-0.055-0.01314.302-0.099-0.0990.0000.0000.0000.000
37E356TYR0-0.033-0.01816.9380.0250.0250.0000.0000.0000.000
38E357ASN0-0.0040.00520.460-0.013-0.0130.0000.0000.0000.000
39E358SER0-0.030-0.04722.762-0.019-0.0190.0000.0000.0000.000
40E359THR0-0.0050.01922.825-0.026-0.0260.0000.0000.0000.000
41E360PHE0-0.012-0.00424.5000.0140.0140.0000.0000.0000.000
42E361PHE00.001-0.00621.798-0.015-0.0150.0000.0000.0000.000
43E362SER00.0280.01327.6810.0070.0070.0000.0000.0000.000
44E363THR0-0.114-0.05429.600-0.003-0.0030.0000.0000.0000.000
45E364PHE00.0840.02121.959-0.005-0.0050.0000.0000.0000.000
46E365LYS10.9130.97627.708-0.008-0.0080.0000.0000.0000.000
47E366CYS0-0.0710.00122.9070.0190.0190.0000.0000.0000.000
48E367TYR0-0.010-0.01427.1080.0080.0080.0000.0000.0000.000
49E368GLY00.1010.04527.142-0.005-0.0050.0000.0000.0000.000
50E369VAL0-0.0030.01124.719-0.001-0.0010.0000.0000.0000.000
51E370SER00.0130.00526.2700.0040.0040.0000.0000.0000.000
52E371ALA00.0430.00326.1400.0070.0070.0000.0000.0000.000
53E372THR0-0.012-0.02525.7160.0100.0100.0000.0000.0000.000
54E373LYS10.9310.97522.451-0.009-0.0090.0000.0000.0000.000
55E374LEU00.0650.03822.122-0.007-0.0070.0000.0000.0000.000
56E375ASN00.0150.00215.1480.0710.0710.0000.0000.0000.000
57E376ASP-1-0.880-0.93517.2170.0130.0130.0000.0000.0000.000
58E377LEU0-0.060-0.04218.225-0.021-0.0210.0000.0000.0000.000
59E378CYS0-0.067-0.02713.8340.0400.0400.0000.0000.0000.000
60E379PHE0-0.043-0.01813.9230.0080.0080.0000.0000.0000.000
61E380SER00.0310.01410.533-0.074-0.0740.0000.0000.0000.000
62E381ASN0-0.054-0.04011.266-0.209-0.2090.0000.0000.0000.000
63E382VAL00.0200.02413.8940.0670.0670.0000.0000.0000.000
64E383TYR0-0.0170.00416.216-0.105-0.1050.0000.0000.0000.000
65E384ALA00.0280.00418.3200.0450.0450.0000.0000.0000.000
66E385ASP-1-0.765-0.84420.081-0.218-0.2180.0000.0000.0000.000
67E386SER00.0200.00422.7290.0260.0260.0000.0000.0000.000
68E387PHE0-0.015-0.01925.157-0.009-0.0090.0000.0000.0000.000
69E388VAL00.0190.02028.8130.0110.0110.0000.0000.0000.000
70E389VAL0-0.023-0.00831.604-0.005-0.0050.0000.0000.0000.000
71E390LYS10.9650.98734.7000.0310.0310.0000.0000.0000.000
72E391GLY00.0340.01036.434-0.001-0.0010.0000.0000.0000.000
73E392ASP-1-0.924-0.98137.491-0.007-0.0070.0000.0000.0000.000
74E393ASP-1-0.880-0.91837.255-0.037-0.0370.0000.0000.0000.000
75E394VAL0-0.0060.00632.306-0.005-0.0050.0000.0000.0000.000
76E395ARG10.9040.95434.0880.0180.0180.0000.0000.0000.000
77E396GLN00.0130.00136.383-0.004-0.0040.0000.0000.0000.000
78E397ILE0-0.0330.00429.684-0.007-0.0070.0000.0000.0000.000
79E398ALA00.020-0.01031.5950.0060.0060.0000.0000.0000.000
80E399PRO00.0260.01831.399-0.005-0.0050.0000.0000.0000.000
81E400GLY00.0260.01433.9840.0060.0060.0000.0000.0000.000
82E401GLN0-0.104-0.02236.4660.0060.0060.0000.0000.0000.000
83E402THR0-0.027-0.02738.708-0.004-0.0040.0000.0000.0000.000
84E403GLY0-0.020-0.00641.1130.0040.0040.0000.0000.0000.000
85E404VAL00.0290.01540.800-0.003-0.0030.0000.0000.0000.000
86E405ILE0-0.0040.00835.131-0.006-0.0060.0000.0000.0000.000
87E406ALA00.0290.01335.984-0.007-0.0070.0000.0000.0000.000
88E407ASP-1-0.883-0.95037.064-0.056-0.0560.0000.0000.0000.000
89E408TYR0-0.029-0.03239.178-0.006-0.0060.0000.0000.0000.000
90E409ASN0-0.051-0.02835.077-0.007-0.0070.0000.0000.0000.000
91E410TYR00.024-0.03226.300-0.002-0.0020.0000.0000.0000.000
92E411LYS10.9421.00432.6210.0700.0700.0000.0000.0000.000
93E412LEU0-0.0020.01028.176-0.011-0.0110.0000.0000.0000.000
94E413PRO0-0.010-0.01029.4510.0060.0060.0000.0000.0000.000
95E414ASP-1-0.901-0.96832.281-0.043-0.0430.0000.0000.0000.000
96E415ASP-1-0.964-0.97731.105-0.068-0.0680.0000.0000.0000.000
97E416PHE0-0.054-0.02125.146-0.001-0.0010.0000.0000.0000.000
98E417MET00.0280.01224.2990.0190.0190.0000.0000.0000.000
99E418GLY00.0500.01523.097-0.021-0.0210.0000.0000.0000.000
100E420VAL0-0.001-0.00124.419-0.018-0.0180.0000.0000.0000.000
101E421LEU0-0.015-0.00421.6970.0180.0180.0000.0000.0000.000
102E422ALA00.010-0.00225.983-0.016-0.0160.0000.0000.0000.000
103E423TRP00.0300.00423.7170.0170.0170.0000.0000.0000.000
104E424ASN0-0.024-0.00629.472-0.011-0.0110.0000.0000.0000.000
105E425THR00.009-0.04228.8540.0070.0070.0000.0000.0000.000
106E426ARG10.9680.98931.932-0.017-0.0170.0000.0000.0000.000
107E427ASN0-0.049-0.04132.821-0.005-0.0050.0000.0000.0000.000
108E428ILE0-0.010-0.00128.3480.0000.0000.0000.0000.0000.000
109E429ASP-1-0.737-0.80431.036-0.057-0.0570.0000.0000.0000.000
110E430ALA0-0.0220.00433.930-0.005-0.0050.0000.0000.0000.000
111E431THR0-0.0080.00437.5650.0000.0000.0000.0000.0000.000
112E432SER0-0.027-0.02940.237-0.001-0.0010.0000.0000.0000.000
113E433THR00.0520.00742.7280.0010.0010.0000.0000.0000.000
114E434GLY0-0.0160.00942.634-0.001-0.0010.0000.0000.0000.000
115E435ASN0-0.075-0.04835.115-0.007-0.0070.0000.0000.0000.000
116E436TYR00.035-0.02939.6010.0020.0020.0000.0000.0000.000
117E437ASN0-0.020-0.00235.041-0.005-0.0050.0000.0000.0000.000
118E438TYR0-0.103-0.05730.847-0.010-0.0100.0000.0000.0000.000
119E439LYS10.9830.99635.9840.0910.0910.0000.0000.0000.000
120E440TYR0-0.015-0.00536.565-0.003-0.0030.0000.0000.0000.000
121E441ARG10.8330.89937.6330.0970.0970.0000.0000.0000.000
122E442TYR0-0.022-0.02940.5210.0040.0040.0000.0000.0000.000
123E443LEU0-0.0310.00843.6650.0030.0030.0000.0000.0000.000
124E444ARG10.8600.89638.9070.0890.0890.0000.0000.0000.000
125E445HIS0-0.0030.03144.3570.0040.0040.0000.0000.0000.000
126E446GLY00.0210.01543.435-0.004-0.0040.0000.0000.0000.000
127E447LYS10.9210.96040.3140.0500.0500.0000.0000.0000.000
128E448LEU0-0.057-0.00734.610-0.002-0.0020.0000.0000.0000.000
129E449ARG10.9380.96635.1730.0910.0910.0000.0000.0000.000
130E450PRO00.017-0.02131.670-0.003-0.0030.0000.0000.0000.000
131E451PHE0-0.031-0.00926.548-0.010-0.0100.0000.0000.0000.000
132E452GLU-1-0.873-0.91829.646-0.128-0.1280.0000.0000.0000.000
133E453ARG10.8590.91028.5890.1890.1890.0000.0000.0000.000
134E454ASP-1-0.776-0.86632.672-0.110-0.1100.0000.0000.0000.000
135E455ILE00.0140.00831.4240.0050.0050.0000.0000.0000.000
136E456SER0-0.048-0.01335.4660.0030.0030.0000.0000.0000.000
137E457ASN00.011-0.01638.9380.0060.0060.0000.0000.0000.000
138E458VAL00.0240.01941.4860.0000.0000.0000.0000.0000.000
139E459PRO0-0.016-0.01044.6820.0020.0020.0000.0000.0000.000
140E460PHE00.009-0.00246.828-0.001-0.0010.0000.0000.0000.000
141E461SER00.073-0.00449.0010.0040.0040.0000.0000.0000.000
142E462PRO0-0.003-0.01251.620-0.002-0.0020.0000.0000.0000.000
143E463ASP-1-0.868-0.91952.978-0.052-0.0520.0000.0000.0000.000
144E464GLY0-0.0070.00051.1290.0000.0000.0000.0000.0000.000
145E465LYS10.8750.95551.4810.0450.0450.0000.0000.0000.000
146E466PRO00.0250.00050.960-0.001-0.0010.0000.0000.0000.000
147E467CYS0-0.0200.03551.1170.0010.0010.0000.0000.0000.000
148E468THR0-0.008-0.01251.628-0.003-0.0030.0000.0000.0000.000
149E469PRO00.0060.02650.4590.0030.0030.0000.0000.0000.000
150E470PRO00.003-0.00353.754-0.002-0.0020.0000.0000.0000.000
151E471ALA0-0.004-0.00956.2590.0020.0020.0000.0000.0000.000
152E472LEU00.026-0.00656.6500.0000.0000.0000.0000.0000.000
153E473ASN0-0.039-0.02956.561-0.001-0.0010.0000.0000.0000.000
154E475TYR0-0.002-0.00550.3250.0020.0020.0000.0000.0000.000
155E476TRP00.0520.02445.412-0.005-0.0050.0000.0000.0000.000
156E477PRO00.0180.01343.1210.0030.0030.0000.0000.0000.000
157E478LEU0-0.034-0.01738.9100.0000.0000.0000.0000.0000.000
158E479ASN0-0.015-0.01041.9550.0020.0020.0000.0000.0000.000
159E480ASP-1-0.862-0.92540.550-0.065-0.0650.0000.0000.0000.000
160E481TYR0-0.109-0.10536.4650.0030.0030.0000.0000.0000.000
161E482GLY00.0590.02740.781-0.002-0.0020.0000.0000.0000.000
162E483PHE0-0.058-0.02536.2260.0050.0050.0000.0000.0000.000
163E484TYR00.0570.06740.260-0.001-0.0010.0000.0000.0000.000
164E485THR0-0.044-0.03240.3220.0020.0020.0000.0000.0000.000
165E486THR0-0.009-0.01041.8250.0040.0040.0000.0000.0000.000
166E487THR00.0230.02543.020-0.002-0.0020.0000.0000.0000.000
167E488GLY00.0470.02343.1530.0030.0030.0000.0000.0000.000
168E489ILE00.0550.00938.520-0.003-0.0030.0000.0000.0000.000
169E490GLY00.0610.04039.341-0.002-0.0020.0000.0000.0000.000
170E491TYR0-0.030-0.01740.924-0.005-0.0050.0000.0000.0000.000
171E492GLN0-0.030-0.00537.392-0.001-0.0010.0000.0000.0000.000
172E493PRO00.0190.02133.885-0.001-0.0010.0000.0000.0000.000
173E494TYR00.0010.01031.9220.0100.0100.0000.0000.0000.000
174E495ARG10.8030.90925.7950.0500.0500.0000.0000.0000.000
175E496VAL0-0.002-0.01327.6340.0160.0160.0000.0000.0000.000
176E497VAL00.0170.00320.903-0.017-0.0170.0000.0000.0000.000
177E498VAL0-0.017-0.00324.2660.0240.0240.0000.0000.0000.000
178E499LEU0-0.012-0.00418.335-0.031-0.0310.0000.0000.0000.000
179E500SER00.0140.00721.0380.0300.0300.0000.0000.0000.000
180E501PHE0-0.012-0.02119.368-0.022-0.0220.0000.0000.0000.000
181E502GLU-1-0.934-0.96017.352-0.255-0.2550.0000.0000.0000.000