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: 39YNL

Calculation Name: 1GGG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1GGG

Chain ID: A

ChEMBL ID:

UniProt ID: P0AEQ3

Base Structure: X-ray

Registration Date: 2023-09-20

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 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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2485123.973664
FMO2-HF: Nuclear repulsion 2401119.838063
FMO2-HF: Total energy -84004.135601
FMO2-MP2: Total energy -84253.491615


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(A:5:LEU)


Summations of interaction energy for fragment #1(A:5:LEU)
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.
-16.5-3.9819.395-7.818-14.098-0.04
Interaction energy analysis for fragmet #1(A:5:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : 0.005
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].
3A7VAL0-0.012-0.0053.830-0.0741.805-0.016-0.823-1.0400.004
4A8ALA00.006-0.0025.256-0.0160.002-0.001-0.002-0.0140.000
5A9THR0-0.047-0.0378.9650.1230.1230.0000.0000.0000.000
6A10ASP-1-0.798-0.90412.081-0.291-0.2910.0000.0000.0000.000
7A11THR0-0.069-0.04015.601-0.033-0.0330.0000.0000.0000.000
8A12ALA0-0.013-0.01718.0520.0020.0020.0000.0000.0000.000
9A13PHE00.0090.03218.4200.0280.0280.0000.0000.0000.000
10A14VAL0-0.0230.02020.067-0.001-0.0010.0000.0000.0000.000
11A15PRO0-0.044-0.02122.0110.0130.0130.0000.0000.0000.000
12A16PHE0-0.012-0.02317.1460.0090.0090.0000.0000.0000.000
13A17GLU-1-0.738-0.88814.948-0.298-0.2980.0000.0000.0000.000
14A18PHE0-0.027-0.01317.1160.0140.0140.0000.0000.0000.000
15A19LYS10.8960.96719.0820.3580.3580.0000.0000.0000.000
16A20GLN0-0.009-0.01520.0580.0440.0440.0000.0000.0000.000
17A21GLY0-0.0010.00821.467-0.009-0.0090.0000.0000.0000.000
18A22ASP-1-0.871-0.96620.277-0.371-0.3710.0000.0000.0000.000
19A23LEU0-0.0290.01016.466-0.049-0.0490.0000.0000.0000.000
20A24TYR0-0.026-0.04614.5420.0070.0070.0000.0000.0000.000
21A25VAL0-0.015-0.00315.986-0.006-0.0060.0000.0000.0000.000
22A26GLY00.0830.03317.635-0.008-0.0080.0000.0000.0000.000
23A27PHE0-0.022-0.01416.9700.0020.0020.0000.0000.0000.000
24A28ASP-1-0.738-0.87813.088-0.082-0.0820.0000.0000.0000.000
25A29VAL0-0.032-0.00912.1960.0010.0010.0000.0000.0000.000
26A30ASP-1-0.819-0.87812.349-0.192-0.1920.0000.0000.0000.000
27A31LEU0-0.040-0.01412.2230.0390.0390.0000.0000.0000.000
28A32TRP00.0410.0113.271-0.5270.1740.063-0.157-0.6080.001
29A33ALA00.0200.0258.3710.0860.0860.0000.0000.0000.000
30A34ALA0-0.016-0.0099.9370.0570.0570.0000.0000.0000.000
31A35ILE00.0540.0157.2200.0450.0450.0000.0000.0000.000
32A36ALA00.0180.0105.7400.1360.1360.0000.0000.0000.000
33A37LYS10.8330.9146.621-0.059-0.0590.0000.0000.0000.000
34A38GLU-1-0.888-0.9449.6260.2150.2150.0000.0000.0000.000
35A39LEU0-0.046-0.0176.2450.0120.0120.0000.0000.0000.000
36A40LYS10.7730.8987.492-0.184-0.1840.0000.0000.0000.000
37A41LEU0-0.0030.0072.511-0.756-0.1771.675-0.363-1.8920.001
38A42ASP-1-0.870-0.9244.534-0.964-0.617-0.001-0.072-0.2740.000
39A43TYR0-0.081-0.0662.135-6.682-3.1193.898-3.405-4.055-0.019
40A44GLU-1-0.832-0.9063.114-0.767-0.4680.0380.304-0.6410.001
41A45LEU00.0050.0105.822-0.148-0.1480.0000.0000.0000.000
42A46LYS10.8200.8948.3171.8581.8580.0000.0000.0000.000
43A47PRO00.0170.00310.3640.0950.0950.0000.0000.0000.000
44A48MET0-0.049-0.01910.9990.0170.0170.0000.0000.0000.000
45A49ASP-1-0.888-0.92815.452-0.256-0.2560.0000.0000.0000.000
46A50PHE00.0360.01216.5920.0050.0050.0000.0000.0000.000
47A51SER0-0.050-0.02717.2760.0030.0030.0000.0000.0000.000
48A52GLY00.003-0.00516.8160.0270.0270.0000.0000.0000.000
49A53ILE00.0030.00911.917-0.018-0.0180.0000.0000.0000.000
50A54ILE0-0.013-0.01713.0980.0100.0100.0000.0000.0000.000
51A55PRO00.004-0.01114.3690.0190.0190.0000.0000.0000.000
52A56ALA00.0470.02811.7800.0300.0300.0000.0000.0000.000
53A57LEU00.0350.0338.363-0.016-0.0160.0000.0000.0000.000
54A58GLN0-0.060-0.03010.7280.0730.0730.0000.0000.0000.000
55A59THR0-0.095-0.06913.4600.0580.0580.0000.0000.0000.000
56A60LYS10.8830.9438.404-0.106-0.1060.0000.0000.0000.000
57A61ASN0-0.0400.0138.6180.0410.0410.0000.0000.0000.000
58A62VAL00.0280.0066.408-0.234-0.2340.0000.0000.0000.000
59A63ASP-1-0.850-0.9072.464-6.188-2.9183.033-2.862-3.442-0.029
60A64LEU0-0.066-0.0402.988-0.4850.5330.262-0.216-1.064-0.001
61A65ALA00.000-0.0026.142-0.376-0.3760.0000.0000.0000.000
62A66LEU0-0.043-0.0128.0040.1690.1690.0000.0000.0000.000
63A67ALA00.0940.05411.201-0.058-0.0580.0000.0000.0000.000
64A68GLY00.000-0.00914.3860.0240.0240.0000.0000.0000.000
65A69ILE0-0.050-0.00313.2230.0050.0050.0000.0000.0000.000
66A70THR0-0.019-0.02117.1410.0230.0230.0000.0000.0000.000
67A71ILE00.0040.01916.805-0.004-0.0040.0000.0000.0000.000
68A72THR00.0300.00419.527-0.002-0.0020.0000.0000.0000.000
69A73ASP-1-0.811-0.91421.0060.0740.0740.0000.0000.0000.000
70A74GLU-1-0.867-0.95522.7210.0300.0300.0000.0000.0000.000
71A75ARG10.8890.95618.0810.0320.0320.0000.0000.0000.000
72A76LYS10.9020.95817.833-0.081-0.0810.0000.0000.0000.000
73A77LYS10.8440.93418.710-0.011-0.0110.0000.0000.0000.000
74A78ALA0-0.032-0.01017.4950.0090.0090.0000.0000.0000.000
75A79ILE0-0.019-0.00612.938-0.005-0.0050.0000.0000.0000.000
76A80ASP-1-0.826-0.89212.0520.2740.2740.0000.0000.0000.000
77A81PHE0-0.011-0.02312.196-0.010-0.0100.0000.0000.0000.000
78A82SER00.0140.01310.6360.0290.0290.0000.0000.0000.000
79A83ASP-1-0.904-0.95512.5480.2050.2050.0000.0000.0000.000
80A84GLY00.0150.01614.833-0.002-0.0020.0000.0000.0000.000
81A85TYR0-0.060-0.03413.5860.0310.0310.0000.0000.0000.000
82A86TYR00.0180.01716.678-0.017-0.0170.0000.0000.0000.000
83A87LYS10.8430.94419.633-0.001-0.0010.0000.0000.0000.000
84A88SER00.029-0.00122.893-0.009-0.0090.0000.0000.0000.000
85A89GLY00.0510.03124.6870.0100.0100.0000.0000.0000.000
86A90LEU0-0.069-0.02428.193-0.008-0.0080.0000.0000.0000.000
87A91LEU00.0720.02530.2590.0050.0050.0000.0000.0000.000
88A92VAL0-0.036-0.01133.224-0.003-0.0030.0000.0000.0000.000
89A93MET00.0170.01935.1070.0000.0000.0000.0000.0000.000
90A94VAL00.005-0.00637.8830.0000.0000.0000.0000.0000.000
91A95LYS10.8550.92340.8370.0290.0290.0000.0000.0000.000
92A96ALA00.0800.03041.2600.0030.0030.0000.0000.0000.000
93A97ASN0-0.052-0.02442.5470.0010.0010.0000.0000.0000.000
94A98ASN0-0.020-0.01345.1920.0010.0010.0000.0000.0000.000
95A99ASN0-0.005-0.00345.214-0.001-0.0010.0000.0000.0000.000
96A100ASP-1-0.856-0.92347.172-0.011-0.0110.0000.0000.0000.000
97A101VAL0-0.030-0.01042.6850.0010.0010.0000.0000.0000.000
98A102LYS10.9020.92641.0340.0070.0070.0000.0000.0000.000
99A103SER00.0160.01139.4840.0010.0010.0000.0000.0000.000
100A104VAL00.0050.02741.6030.0010.0010.0000.0000.0000.000
101A105LYS10.9100.94840.4760.0140.0140.0000.0000.0000.000
102A106ASP-1-0.801-0.90046.411-0.006-0.0060.0000.0000.0000.000
103A107LEU0-0.042-0.04448.650-0.002-0.0020.0000.0000.0000.000
104A108ASP-1-0.912-0.95151.379-0.009-0.0090.0000.0000.0000.000
105A109GLY0-0.045-0.02652.1050.0000.0000.0000.0000.0000.000
106A110LYS10.7800.91747.3700.0130.0130.0000.0000.0000.000
107A111VAL00.0110.00646.8440.0010.0010.0000.0000.0000.000
108A112VAL0-0.010-0.00940.937-0.001-0.0010.0000.0000.0000.000
109A113ALA00.0280.02441.7480.0000.0000.0000.0000.0000.000
110A114VAL00.017-0.00537.7200.0000.0000.0000.0000.0000.000
111A115LYS10.9290.95832.2490.0600.0600.0000.0000.0000.000
112A116SER0-0.006-0.03036.6770.0040.0040.0000.0000.0000.000
113A117GLY00.0000.00335.519-0.005-0.0050.0000.0000.0000.000
114A118THR00.002-0.00531.036-0.006-0.0060.0000.0000.0000.000
115A119GLY00.0790.04031.9410.0030.0030.0000.0000.0000.000
116A120SER00.007-0.00733.3340.0040.0040.0000.0000.0000.000
117A121VAL0-0.010-0.00835.5100.0020.0020.0000.0000.0000.000
118A122ASP-1-0.856-0.92835.790-0.018-0.0180.0000.0000.0000.000
119A123TYR00.0360.01635.5800.0020.0020.0000.0000.0000.000
120A124ALA0-0.013-0.01637.8120.0020.0020.0000.0000.0000.000
121A125LYS10.8560.93240.7600.0210.0210.0000.0000.0000.000
122A126ALA0-0.0350.00240.6100.0010.0010.0000.0000.0000.000
123A127ASN00.0060.00838.5780.0020.0020.0000.0000.0000.000
124A128ILE0-0.028-0.01240.3720.0000.0000.0000.0000.0000.000
125A129LYS10.9500.97144.4790.0070.0070.0000.0000.0000.000
126A130THR00.0090.01744.8650.0000.0000.0000.0000.0000.000
127A131LYS10.8340.91747.9170.0140.0140.0000.0000.0000.000
128A132ASP-1-0.869-0.94349.104-0.023-0.0230.0000.0000.0000.000
129A133LEU00.0150.01941.7680.0000.0000.0000.0000.0000.000
130A134ARG10.8190.90544.6990.0270.0270.0000.0000.0000.000
131A135GLN00.000-0.01241.083-0.001-0.0010.0000.0000.0000.000
132A136PHE00.0280.02240.011-0.001-0.0010.0000.0000.0000.000
133A137PRO00.0270.02338.9680.0000.0000.0000.0000.0000.000
134A138ASN0-0.012-0.00435.414-0.003-0.0030.0000.0000.0000.000
135A139ILE00.0670.01631.8270.0040.0040.0000.0000.0000.000
136A140ASP-1-0.841-0.90935.512-0.067-0.0670.0000.0000.0000.000
137A141ASN0-0.026-0.02637.0060.0010.0010.0000.0000.0000.000
138A142ALA0-0.0020.00338.1820.0030.0030.0000.0000.0000.000
139A143TYR00.020-0.00432.4170.0060.0060.0000.0000.0000.000
140A144MET00.0150.02139.5260.0030.0030.0000.0000.0000.000
141A145GLU-1-0.833-0.91742.667-0.030-0.0300.0000.0000.0000.000
142A146LEU0-0.053-0.02740.4040.0030.0030.0000.0000.0000.000
143A147GLY00.0370.02943.1880.0010.0010.0000.0000.0000.000
144A148THR0-0.052-0.01044.3760.0020.0020.0000.0000.0000.000
145A149ASN00.0420.01147.220-0.001-0.0010.0000.0000.0000.000
146A150ARG10.8460.92647.9470.0280.0280.0000.0000.0000.000
147A151ALA00.0340.02944.0480.0010.0010.0000.0000.0000.000
148A152ASP-1-0.796-0.88046.127-0.018-0.0180.0000.0000.0000.000
149A153ALA0-0.028-0.03041.2160.0000.0000.0000.0000.0000.000
150A154VAL0-0.0030.00136.664-0.001-0.0010.0000.0000.0000.000
151A155LEU0-0.067-0.02535.6870.0030.0030.0000.0000.0000.000
152A156HIS0-0.002-0.00530.0100.0020.0020.0000.0000.0000.000
153A157ASP-1-0.798-0.88227.336-0.056-0.0560.0000.0000.0000.000
154A158THR00.006-0.01126.393-0.005-0.0050.0000.0000.0000.000
155A159PRO00.0480.02623.7910.0000.0000.0000.0000.0000.000
156A160ASN0-0.024-0.03426.032-0.012-0.0120.0000.0000.0000.000
157A161ILE0-0.040-0.01628.399-0.002-0.0020.0000.0000.0000.000
158A162LEU0-0.014-0.00327.184-0.001-0.0010.0000.0000.0000.000
159A163TYR00.0500.01825.956-0.002-0.0020.0000.0000.0000.000
160A164PHE00.0310.02028.561-0.003-0.0030.0000.0000.0000.000
161A165ILE0-0.028-0.02731.7480.0000.0000.0000.0000.0000.000
162A166LYS10.8810.96426.9560.0770.0770.0000.0000.0000.000
163A167THR0-0.050-0.03328.969-0.001-0.0010.0000.0000.0000.000
164A168ALA0-0.009-0.00532.217-0.001-0.0010.0000.0000.0000.000
165A169GLY0-0.033-0.00235.1390.0030.0030.0000.0000.0000.000
166A170ASN0-0.033-0.01834.1560.0090.0090.0000.0000.0000.000
167A171GLY00.0000.00037.118-0.001-0.0010.0000.0000.0000.000
168A172GLN00.0120.01340.4860.0050.0050.0000.0000.0000.000
169A173PHE0-0.013-0.00338.0560.0030.0030.0000.0000.0000.000
170A174LYS10.8590.93137.4130.0180.0180.0000.0000.0000.000
171A175ALA00.0300.02334.3150.0000.0000.0000.0000.0000.000
172A176VAL0-0.051-0.03436.2300.0030.0030.0000.0000.0000.000
173A177GLY00.0050.00836.4180.0000.0000.0000.0000.0000.000
174A178ASP-1-0.772-0.88229.8790.0030.0030.0000.0000.0000.000
175A179SER0-0.056-0.03728.610-0.002-0.0020.0000.0000.0000.000
176A180LEU0-0.034-0.00630.6990.0050.0050.0000.0000.0000.000
177A181GLU-1-0.896-0.95730.8330.0040.0040.0000.0000.0000.000
178A182ALA0-0.020-0.01726.966-0.002-0.0020.0000.0000.0000.000
179A183GLN0-0.046-0.01323.9080.0010.0010.0000.0000.0000.000
180A184GLN00.024-0.00519.7670.0010.0010.0000.0000.0000.000
181A185TYR00.0090.00016.913-0.003-0.0030.0000.0000.0000.000
182A186GLY00.030-0.00314.6760.0270.0270.0000.0000.0000.000
183A187ILE00.0000.0127.884-0.047-0.0470.0000.0000.0000.000
184A188ALA0-0.0160.00610.8320.0640.0640.0000.0000.0000.000
185A189PHE00.0640.0115.399-0.039-0.0390.0000.0000.0000.000
186A190PRO00.0200.0137.029-0.074-0.0740.0000.0000.0000.000
187A191LYS10.8240.9189.927-0.070-0.0700.0000.0000.0000.000
188A192GLY00.0210.01611.4490.0080.0080.0000.0000.0000.000
189A193SER0-0.022-0.0247.1260.0880.0880.0000.0000.0000.000
190A194ASP-1-0.848-0.9278.8130.5370.5370.0000.0000.0000.000
191A195GLU-1-0.777-0.8678.5700.9460.9460.0000.0000.0000.000
192A196LEU0-0.009-0.0032.783-1.068-0.2230.444-0.222-1.0680.002
193A197ARG10.7770.8886.758-0.429-0.4290.0000.0000.0000.000
194A198ASP-1-0.849-0.9349.2500.4260.4260.0000.0000.0000.000
195A199LYS10.7880.8616.702-1.160-1.1600.0000.0000.0000.000
196A200VAL00.0140.0105.838-0.074-0.0740.0000.0000.0000.000
197A201ASN00.0200.0168.622-0.122-0.1220.0000.0000.0000.000
198A202GLY00.000-0.00312.085-0.069-0.0690.0000.0000.0000.000
199A203ALA00.0320.01510.291-0.061-0.0610.0000.0000.0000.000
200A204LEU0-0.044-0.02312.330-0.076-0.0760.0000.0000.0000.000
201A205LYS10.8310.91813.791-0.298-0.2980.0000.0000.0000.000
202A206THR00.0820.04615.187-0.017-0.0170.0000.0000.0000.000
203A207LEU0-0.028-0.01813.160-0.034-0.0340.0000.0000.0000.000
204A208ARG10.8530.91116.937-0.167-0.1670.0000.0000.0000.000
205A209GLU-1-0.944-0.96519.7500.1610.1610.0000.0000.0000.000
206A210ASN0-0.0130.00917.601-0.021-0.0210.0000.0000.0000.000
207A211GLY00.0310.01921.622-0.012-0.0120.0000.0000.0000.000
208A212THR0-0.022-0.02716.647-0.018-0.0180.0000.0000.0000.000
209A213TYR0-0.082-0.06517.001-0.019-0.0190.0000.0000.0000.000
210A214ASN0-0.030-0.02819.199-0.023-0.0230.0000.0000.0000.000
211A215GLU-1-0.794-0.89422.213-0.015-0.0150.0000.0000.0000.000
212A216ILE0-0.021-0.00916.129-0.014-0.0140.0000.0000.0000.000
213A217TYR0-0.004-0.00420.423-0.016-0.0160.0000.0000.0000.000
214A218LYS10.8120.89522.287-0.009-0.0090.0000.0000.0000.000
215A219LYS10.8230.90619.2270.1340.1340.0000.0000.0000.000
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