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: 1742Z

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 OptAll
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 -1958291.053248
FMO2-HF: Nuclear repulsion 1884717.701362
FMO2-HF: Total energy -73573.351886
FMO2-MP2: Total energy -73786.363016


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.
-0.4051.050.019-0.55-0.9230.002
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 : -0.001 / q_NPA : -0.019
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].
3E322LEU00.0590.0433.791-0.1140.8640.001-0.401-0.5770.001
4E323CYS0-0.060-0.0306.259-0.401-0.4010.0000.0000.0000.000
5E324PRO00.0310.0299.5780.2090.2090.0000.0000.0000.000
6E325PHE00.047-0.01112.1940.0300.0300.0000.0000.0000.000
7E326GLY00.0290.01914.1890.0310.0310.0000.0000.0000.000
8E327GLU-1-0.839-0.91813.702-0.381-0.3810.0000.0000.0000.000
9E328VAL0-0.0340.00017.188-0.003-0.0030.0000.0000.0000.000
10E329PHE00.011-0.01317.5950.0150.0150.0000.0000.0000.000
11E330ASN0-0.039-0.02218.9670.0390.0390.0000.0000.0000.000
12E331ALA00.0680.06220.9010.0140.0140.0000.0000.0000.000
13E332THR00.019-0.00821.9870.0030.0030.0000.0000.0000.000
14E333LYS10.9070.95725.2410.0440.0440.0000.0000.0000.000
15E334PHE00.0500.02923.623-0.010-0.0100.0000.0000.0000.000
16E335PRO00.0270.03325.9730.0110.0110.0000.0000.0000.000
17E336SER00.018-0.00728.9920.0080.0080.0000.0000.0000.000
18E337VAL00.0110.01731.625-0.009-0.0090.0000.0000.0000.000
19E338TYR0-0.033-0.01532.618-0.007-0.0070.0000.0000.0000.000
20E339ALA0-0.044-0.01831.019-0.005-0.0050.0000.0000.0000.000
21E340TRP0-0.0540.00825.912-0.012-0.0120.0000.0000.0000.000
22E341GLU-1-0.903-0.94923.622-0.160-0.1600.0000.0000.0000.000
23E342ARG10.8290.88621.1440.2580.2580.0000.0000.0000.000
24E343LYS10.8190.91013.6170.4550.4550.0000.0000.0000.000
25E344LYS10.8290.90315.0880.6120.6120.0000.0000.0000.000
26E345ILE0-0.013-0.00511.768-0.054-0.0540.0000.0000.0000.000
27E346SER00.0400.01411.5250.1280.1280.0000.0000.0000.000
28E347ASN0-0.049-0.0077.962-0.090-0.0900.0000.0000.0000.000
29E348CYS0-0.0040.0075.363-0.643-0.6430.0000.0000.0000.000
30E349VAL00.0300.0183.875-0.0950.3820.018-0.149-0.3460.001
31E350ALA00.022-0.0055.8990.1320.1320.0000.0000.0000.000
32E351ASP-1-0.832-0.8958.8580.8540.8540.0000.0000.0000.000
33E352TYR0-0.024-0.02710.409-0.121-0.1210.0000.0000.0000.000
34E353SER0-0.050-0.04413.138-0.088-0.0880.0000.0000.0000.000
35E354VAL0-0.051-0.01411.346-0.027-0.0270.0000.0000.0000.000
36E355LEU0-0.0280.00114.305-0.071-0.0710.0000.0000.0000.000
37E356TYR0-0.029-0.01617.1310.0290.0290.0000.0000.0000.000
38E357ASN00.0340.01720.730-0.029-0.0290.0000.0000.0000.000
39E358SER0-0.004-0.02422.898-0.013-0.0130.0000.0000.0000.000
40E359THR0-0.027-0.00122.531-0.018-0.0180.0000.0000.0000.000
41E360PHE0-0.014-0.00624.673-0.003-0.0030.0000.0000.0000.000
42E361PHE00.012-0.00321.683-0.009-0.0090.0000.0000.0000.000
43E362SER0-0.037-0.01727.4550.0000.0000.0000.0000.0000.000
44E363THR0-0.040-0.02429.719-0.002-0.0020.0000.0000.0000.000
45E364PHE00.0820.04021.941-0.004-0.0040.0000.0000.0000.000
46E365LYS10.8920.95527.6450.0560.0560.0000.0000.0000.000
47E366CYS0-0.063-0.02122.9460.0130.0130.0000.0000.0000.000
48E367TYR00.0270.00427.3010.0160.0160.0000.0000.0000.000
49E368GLY00.0870.04427.282-0.012-0.0120.0000.0000.0000.000
50E369VAL0-0.029-0.00324.281-0.007-0.0070.0000.0000.0000.000
51E370SER00.0400.01726.2910.0130.0130.0000.0000.0000.000
52E371ALA00.0780.02026.184-0.006-0.0060.0000.0000.0000.000
53E372THR0-0.030-0.01125.678-0.008-0.0080.0000.0000.0000.000
54E373LYS10.8840.93322.4380.1880.1880.0000.0000.0000.000
55E374LEU00.0220.02522.111-0.008-0.0080.0000.0000.0000.000
56E375ASN0-0.011-0.00516.4420.0170.0170.0000.0000.0000.000
57E376ASP-1-0.819-0.91017.444-0.276-0.2760.0000.0000.0000.000
58E377LEU0-0.039-0.02418.031-0.017-0.0170.0000.0000.0000.000
59E378CYS0-0.056-0.02313.6890.0400.0400.0000.0000.0000.000
60E379PHE0-0.058-0.04213.895-0.003-0.0030.0000.0000.0000.000
61E380SER00.0340.01810.872-0.021-0.0210.0000.0000.0000.000
62E381ASN0-0.025-0.04211.608-0.239-0.2390.0000.0000.0000.000
63E382VAL0-0.0100.02314.3590.0880.0880.0000.0000.0000.000
64E383TYR0-0.042-0.04116.782-0.064-0.0640.0000.0000.0000.000
65E384ALA00.0280.00718.7790.0350.0350.0000.0000.0000.000
66E385ASP-1-0.757-0.81320.516-0.224-0.2240.0000.0000.0000.000
67E386SER00.0160.00022.5100.0180.0180.0000.0000.0000.000
68E387PHE0-0.006-0.01925.0490.0000.0000.0000.0000.0000.000
69E388VAL00.0080.01328.6120.0070.0070.0000.0000.0000.000
70E389VAL0-0.009-0.00231.589-0.003-0.0030.0000.0000.0000.000
71E390LYS10.8410.90834.8480.0400.0400.0000.0000.0000.000
72E391GLY00.0400.01836.812-0.004-0.0040.0000.0000.0000.000
73E392ASP-1-0.876-0.94237.648-0.033-0.0330.0000.0000.0000.000
74E393ASP-1-0.823-0.90337.336-0.055-0.0550.0000.0000.0000.000
75E394VAL0-0.0020.00932.463-0.007-0.0070.0000.0000.0000.000
76E395ARG10.8080.90134.2840.0520.0520.0000.0000.0000.000
77E396GLN0-0.027-0.01836.567-0.004-0.0040.0000.0000.0000.000
78E397ILE0-0.0200.00229.953-0.007-0.0070.0000.0000.0000.000
79E398ALA00.005-0.01331.749-0.001-0.0010.0000.0000.0000.000
80E399PRO00.0460.02931.6950.0000.0000.0000.0000.0000.000
81E400GLY0-0.009-0.00634.4320.0070.0070.0000.0000.0000.000
82E401GLN0-0.093-0.01436.4170.0100.0100.0000.0000.0000.000
83E402THR00.001-0.00438.772-0.003-0.0030.0000.0000.0000.000
84E403GLY00.005-0.00141.3290.0040.0040.0000.0000.0000.000
85E404VAL00.0240.00840.943-0.004-0.0040.0000.0000.0000.000
86E405ILE0-0.014-0.00135.401-0.004-0.0040.0000.0000.0000.000
87E406ALA00.0390.02136.339-0.006-0.0060.0000.0000.0000.000
88E407ASP-1-0.779-0.88737.424-0.077-0.0770.0000.0000.0000.000
89E408TYR0-0.031-0.02639.418-0.003-0.0030.0000.0000.0000.000
90E409ASN0-0.041-0.02435.2250.0000.0000.0000.0000.0000.000
91E410TYR00.029-0.03926.769-0.002-0.0020.0000.0000.0000.000
92E411LYS10.8710.96833.3320.1050.1050.0000.0000.0000.000
93E412LEU00.0080.01028.125-0.011-0.0110.0000.0000.0000.000
94E413PRO0-0.014-0.01229.3390.0090.0090.0000.0000.0000.000
95E414ASP-1-0.826-0.92032.506-0.097-0.0970.0000.0000.0000.000
96E415ASP-1-0.921-0.96131.711-0.144-0.1440.0000.0000.0000.000
97E416PHE0-0.042-0.01625.398-0.009-0.0090.0000.0000.0000.000
98E417MET00.0200.00823.5510.0130.0130.0000.0000.0000.000
99E418GLY00.0400.01323.392-0.026-0.0260.0000.0000.0000.000
100E420VAL0-0.013-0.00424.732-0.012-0.0120.0000.0000.0000.000
101E421LEU0-0.0140.00421.6540.0130.0130.0000.0000.0000.000
102E422ALA00.011-0.00425.934-0.006-0.0060.0000.0000.0000.000
103E423TRP00.0100.00123.9040.0060.0060.0000.0000.0000.000
104E424ASN0-0.009-0.00129.837-0.002-0.0020.0000.0000.0000.000
105E425THR00.007-0.03129.0000.0060.0060.0000.0000.0000.000
106E426ARG10.9100.95832.114-0.006-0.0060.0000.0000.0000.000
107E427ASN0-0.008-0.02032.865-0.002-0.0020.0000.0000.0000.000
108E428ILE0-0.0190.00028.4180.0040.0040.0000.0000.0000.000
109E429ASP-1-0.732-0.77630.918-0.037-0.0370.0000.0000.0000.000
110E430ALA0-0.0070.00733.905-0.005-0.0050.0000.0000.0000.000
111E431THR0-0.013-0.00737.6300.0030.0030.0000.0000.0000.000
112E432SER00.0150.00840.347-0.002-0.0020.0000.0000.0000.000
113E433THR00.0310.00743.1700.0000.0000.0000.0000.0000.000
114E434GLY0-0.0040.00742.640-0.002-0.0020.0000.0000.0000.000
115E435ASN0-0.074-0.04335.364-0.001-0.0010.0000.0000.0000.000
116E436TYR00.0590.01539.791-0.002-0.0020.0000.0000.0000.000
117E437ASN0-0.060-0.04034.935-0.005-0.0050.0000.0000.0000.000
118E438TYR0-0.068-0.04230.754-0.007-0.0070.0000.0000.0000.000
119E439LYS10.8460.90535.7150.0520.0520.0000.0000.0000.000
120E440TYR0-0.0130.00036.267-0.005-0.0050.0000.0000.0000.000
121E441ARG10.8200.88637.2320.0880.0880.0000.0000.0000.000
122E442TYR0-0.060-0.04740.3720.0000.0000.0000.0000.0000.000
123E443LEU0-0.0300.00643.7770.0020.0020.0000.0000.0000.000
124E444ARG10.7770.84838.0350.0950.0950.0000.0000.0000.000
125E445HIS0-0.0320.00744.2670.0000.0000.0000.0000.0000.000
126E446GLY00.0190.00743.559-0.003-0.0030.0000.0000.0000.000
127E447LYS10.8020.89041.0400.0700.0700.0000.0000.0000.000
128E448LEU0-0.058-0.00134.890-0.002-0.0020.0000.0000.0000.000
129E449ARG10.9430.96035.5460.1080.1080.0000.0000.0000.000
130E450PRO00.021-0.01132.067-0.001-0.0010.0000.0000.0000.000
131E451PHE0-0.023-0.00826.663-0.011-0.0110.0000.0000.0000.000
132E452GLU-1-0.786-0.86130.237-0.122-0.1220.0000.0000.0000.000
133E453ARG10.8510.90127.6700.1610.1610.0000.0000.0000.000
134E454ASP-1-0.767-0.84432.389-0.096-0.0960.0000.0000.0000.000
135E455ILE00.0340.02530.9940.0050.0050.0000.0000.0000.000
136E456SER0-0.039-0.03234.8290.0070.0070.0000.0000.0000.000
137E457ASN00.041-0.00238.3740.0020.0020.0000.0000.0000.000
138E458VAL00.0200.01641.2330.0030.0030.0000.0000.0000.000
139E459PRO0-0.019-0.01244.1420.0000.0000.0000.0000.0000.000
140E460PHE00.0200.00946.677-0.001-0.0010.0000.0000.0000.000
141E461SER00.0810.00748.6840.0040.0040.0000.0000.0000.000
142E462PRO0-0.015-0.02651.265-0.003-0.0030.0000.0000.0000.000
143E463ASP-1-0.834-0.88152.850-0.048-0.0480.0000.0000.0000.000
144E464GLY00.0070.01550.661-0.001-0.0010.0000.0000.0000.000
145E465LYS10.8430.91751.1400.0420.0420.0000.0000.0000.000
146E466PRO00.013-0.00650.443-0.001-0.0010.0000.0000.0000.000
147E467CYS0-0.0420.01750.4900.0000.0000.0000.0000.0000.000
148E468THR0-0.011-0.01250.986-0.001-0.0010.0000.0000.0000.000
149E469PRO00.0210.02450.1380.0020.0020.0000.0000.0000.000
150E470PRO0-0.011-0.00453.4140.0000.0000.0000.0000.0000.000
151E471ALA00.0050.00055.9350.0010.0010.0000.0000.0000.000
152E472LEU00.034-0.00256.309-0.001-0.0010.0000.0000.0000.000
153E473ASN0-0.023-0.01056.084-0.001-0.0010.0000.0000.0000.000
154E475TYR00.002-0.00449.9260.0020.0020.0000.0000.0000.000
155E476TRP00.0520.02145.163-0.003-0.0030.0000.0000.0000.000
156E477PRO00.0070.01642.6490.0020.0020.0000.0000.0000.000
157E478LEU0-0.007-0.00538.649-0.003-0.0030.0000.0000.0000.000
158E479ASN00.002-0.00941.7190.0050.0050.0000.0000.0000.000
159E480ASP-1-0.792-0.88440.491-0.048-0.0480.0000.0000.0000.000
160E481TYR0-0.070-0.06636.3680.0010.0010.0000.0000.0000.000
161E482GLY00.0450.02540.5740.0010.0010.0000.0000.0000.000
162E483PHE0-0.007-0.00836.0180.0030.0030.0000.0000.0000.000
163E484TYR00.0300.03240.3770.0020.0020.0000.0000.0000.000
164E485THR0-0.041-0.02440.302-0.001-0.0010.0000.0000.0000.000
165E486THR0-0.014-0.00841.7050.0020.0020.0000.0000.0000.000
166E487THR00.0270.01142.623-0.002-0.0020.0000.0000.0000.000
167E488GLY00.0510.03243.4050.0020.0020.0000.0000.0000.000
168E489ILE00.0460.00438.569-0.002-0.0020.0000.0000.0000.000
169E490GLY00.0690.04239.751-0.002-0.0020.0000.0000.0000.000
170E491TYR0-0.010-0.01241.183-0.005-0.0050.0000.0000.0000.000
171E492GLN0-0.0250.00537.7770.0000.0000.0000.0000.0000.000
172E493PRO00.0200.01234.128-0.003-0.0030.0000.0000.0000.000
173E494TYR00.010-0.00532.3170.0080.0080.0000.0000.0000.000
174E495ARG10.7760.88425.8440.0320.0320.0000.0000.0000.000
175E496VAL0-0.012-0.01627.8440.0070.0070.0000.0000.0000.000
176E497VAL00.0150.00421.199-0.008-0.0080.0000.0000.0000.000
177E498VAL0-0.032-0.01724.2400.0120.0120.0000.0000.0000.000
178E499LEU0-0.0040.01418.735-0.023-0.0230.0000.0000.0000.000
179E500SER00.0240.00221.5530.0180.0180.0000.0000.0000.000
180E501PHE00.006-0.01019.802-0.034-0.0340.0000.0000.0000.000
181E502GLU-1-0.820-0.86617.523-0.505-0.5050.0000.0000.0000.000