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: JLJM9

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 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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2483988.904172
FMO2-HF: Nuclear repulsion 2399986.694614
FMO2-HF: Total energy -84002.209558
FMO2-MP2: Total energy -84251.699754


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.
-11.341-1.68.758-6.026-12.475-0.023
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 : -0.018 / q_NPA : -0.013
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].
3A7VAL0-0.013-0.0043.830-0.4101.008-0.015-0.511-0.8920.002
4A8ALA00.013-0.0045.2900.1050.124-0.001-0.003-0.0160.000
5A9THR0-0.038-0.0258.9970.0480.0480.0000.0000.0000.000
6A10ASP-1-0.799-0.90712.115-0.110-0.1100.0000.0000.0000.000
7A11THR0-0.060-0.03315.636-0.015-0.0150.0000.0000.0000.000
8A12ALA0-0.057-0.04918.0870.0010.0010.0000.0000.0000.000
9A13PHE00.0020.05618.1270.0180.0180.0000.0000.0000.000
10A14VAL0-0.0230.01720.100-0.008-0.0080.0000.0000.0000.000
11A15PRO0-0.044-0.02722.0430.0080.0080.0000.0000.0000.000
12A16PHE0-0.012-0.02117.166-0.002-0.0020.0000.0000.0000.000
13A17GLU-1-0.781-0.91815.038-0.208-0.2080.0000.0000.0000.000
14A18PHE0-0.019-0.01517.1500.0180.0180.0000.0000.0000.000
15A19LYS10.9931.00418.9810.1100.1100.0000.0000.0000.000
16A20GLN0-0.018-0.00819.9570.0180.0180.0000.0000.0000.000
17A21GLY0-0.016-0.00721.369-0.006-0.0060.0000.0000.0000.000
18A22ASP-1-0.910-0.97219.601-0.113-0.1130.0000.0000.0000.000
19A23LEU0-0.0570.00216.456-0.017-0.0170.0000.0000.0000.000
20A24TYR0-0.010-0.03014.3660.0180.0180.0000.0000.0000.000
21A25VAL0-0.012-0.00215.894-0.018-0.0180.0000.0000.0000.000
22A26GLY00.0720.02617.5470.0050.0050.0000.0000.0000.000
23A27PHE0-0.031-0.01916.714-0.011-0.0110.0000.0000.0000.000
24A28ASP-1-0.721-0.87013.095-0.160-0.1600.0000.0000.0000.000
25A29VAL0-0.050-0.02212.113-0.027-0.0270.0000.0000.0000.000
26A30ASP-1-0.818-0.89512.282-0.231-0.2310.0000.0000.0000.000
27A31LEU0-0.053-0.01912.3470.0020.0020.0000.0000.0000.000
28A32TRP00.0300.0073.203-0.4230.1090.035-0.112-0.4550.001
29A33ALA00.0460.0388.233-0.009-0.0090.0000.0000.0000.000
30A34ALA0-0.020-0.0199.840-0.001-0.0010.0000.0000.0000.000
31A35ILE00.0530.0107.1960.0140.0140.0000.0000.0000.000
32A36ALA00.0210.0105.7110.0480.0480.0000.0000.0000.000
33A37LYS10.8590.9466.5590.1240.1240.0000.0000.0000.000
34A38GLU-1-0.971-0.9939.610-0.117-0.1170.0000.0000.0000.000
35A39LEU0-0.045-0.0216.1090.0320.0320.0000.0000.0000.000
36A40LYS10.8110.9287.5130.2100.2100.0000.0000.0000.000
37A41LEU0-0.0080.0032.250-0.558-0.6342.614-0.439-2.0990.002
38A42ASP-1-0.863-0.9214.661-1.030-0.720-0.001-0.037-0.2720.000
39A43TYR0-0.099-0.0771.939-5.340-3.0394.501-3.078-3.725-0.007
40A44GLU-1-0.897-0.9492.9842.1092.0310.0300.721-0.6740.000
41A45LEU0-0.017-0.0035.453-0.222-0.2220.0000.0000.0000.000
42A46LYS10.8910.9488.2350.4190.4190.0000.0000.0000.000
43A47PRO00.0100.00210.3640.0160.0160.0000.0000.0000.000
44A48MET0-0.042-0.01610.8200.0440.0440.0000.0000.0000.000
45A49ASP-1-0.899-0.93015.483-0.080-0.0800.0000.0000.0000.000
46A50PHE00.0560.01816.6240.0070.0070.0000.0000.0000.000
47A51SER0-0.038-0.02117.3010.0020.0020.0000.0000.0000.000
48A52GLY00.0150.00016.8400.0140.0140.0000.0000.0000.000
49A53ILE00.0060.00612.1940.0030.0030.0000.0000.0000.000
50A54ILE0-0.009-0.01613.115-0.001-0.0010.0000.0000.0000.000
51A55PRO0-0.012-0.01714.5650.0110.0110.0000.0000.0000.000
52A56ALA00.0530.02911.7110.0200.0200.0000.0000.0000.000
53A57LEU00.0290.0288.6920.0150.0150.0000.0000.0000.000
54A58GLN0-0.035-0.02410.8820.0300.0300.0000.0000.0000.000
55A59THR0-0.121-0.06413.4020.0200.0200.0000.0000.0000.000
56A60LYS10.9290.9698.771-0.077-0.0770.0000.0000.0000.000
57A61ASN0-0.0370.0008.6120.0420.0420.0000.0000.0000.000
58A62VAL00.0240.0016.385-0.005-0.0050.0000.0000.0000.000
59A63ASP-1-0.859-0.9252.663-4.179-0.5981.161-2.177-2.565-0.021
60A64LEU0-0.065-0.0372.699-0.8010.1460.338-0.210-1.074-0.001
61A65ALA0-0.004-0.0056.272-0.155-0.1550.0000.0000.0000.000
62A66LEU0-0.031-0.0028.4840.0750.0750.0000.0000.0000.000
63A67ALA00.0720.04011.227-0.022-0.0220.0000.0000.0000.000
64A68GLY00.003-0.02214.4150.0220.0220.0000.0000.0000.000
65A69ILE0-0.050-0.00113.2290.0130.0130.0000.0000.0000.000
66A70THR0-0.029-0.02017.1630.0030.0030.0000.0000.0000.000
67A71ILE0-0.0070.00317.1620.0030.0030.0000.0000.0000.000
68A72THR00.0340.00619.5390.0020.0020.0000.0000.0000.000
69A73ASP-1-0.835-0.92021.316-0.009-0.0090.0000.0000.0000.000
70A74GLU-1-0.966-1.01223.010-0.008-0.0080.0000.0000.0000.000
71A75ARG10.9270.97518.3460.0510.0510.0000.0000.0000.000
72A76LYS10.9300.96918.1230.0110.0110.0000.0000.0000.000
73A77LYS10.8860.96018.9760.0080.0080.0000.0000.0000.000
74A78ALA0-0.032-0.01317.7220.0060.0060.0000.0000.0000.000
75A79ILE0-0.037-0.00913.1840.0040.0040.0000.0000.0000.000
76A80ASP-1-0.844-0.92012.2750.0420.0420.0000.0000.0000.000
77A81PHE0-0.004-0.01712.503-0.009-0.0090.0000.0000.0000.000
78A82SER0-0.0020.00310.6340.0090.0090.0000.0000.0000.000
79A83ASP-1-0.953-0.97012.591-0.015-0.0150.0000.0000.0000.000
80A84GLY00.0040.00514.899-0.006-0.0060.0000.0000.0000.000
81A85TYR0-0.063-0.03713.8010.0090.0090.0000.0000.0000.000
82A86TYR00.0190.01416.764-0.007-0.0070.0000.0000.0000.000
83A87LYS10.8880.98019.7110.0520.0520.0000.0000.0000.000
84A88SER00.0410.00522.935-0.002-0.0020.0000.0000.0000.000
85A89GLY00.0520.03024.7460.0040.0040.0000.0000.0000.000
86A90LEU0-0.063-0.01928.244-0.003-0.0030.0000.0000.0000.000
87A91LEU00.0700.02630.5860.0010.0010.0000.0000.0000.000
88A92VAL0-0.034-0.00733.2890.0010.0010.0000.0000.0000.000
89A93MET00.0150.01535.200-0.001-0.0010.0000.0000.0000.000
90A94VAL00.012-0.00737.9530.0020.0020.0000.0000.0000.000
91A95LYS10.8600.92240.9130.0250.0250.0000.0000.0000.000
92A96ALA00.0850.02841.3380.0010.0010.0000.0000.0000.000
93A97ASN0-0.053-0.00742.6340.0000.0000.0000.0000.0000.000
94A98ASN00.0220.00745.2760.0010.0010.0000.0000.0000.000
95A99ASN0-0.011-0.01545.301-0.001-0.0010.0000.0000.0000.000
96A100ASP-1-0.888-0.92947.262-0.021-0.0210.0000.0000.0000.000
97A101VAL0-0.056-0.02142.8450.0010.0010.0000.0000.0000.000
98A102LYS10.9390.94041.3650.0230.0230.0000.0000.0000.000
99A103SER00.0090.00639.6030.0000.0000.0000.0000.0000.000
100A104VAL00.0080.03441.6720.0010.0010.0000.0000.0000.000
101A105LYS10.9440.93840.4090.0240.0240.0000.0000.0000.000
102A106ASP-1-0.799-0.90646.473-0.017-0.0170.0000.0000.0000.000
103A107LEU0-0.037-0.05148.7050.0000.0000.0000.0000.0000.000
104A108ASP-1-0.896-0.93551.503-0.016-0.0160.0000.0000.0000.000
105A109GLY0-0.056-0.02952.1320.0000.0000.0000.0000.0000.000
106A110LYS10.8110.96347.3640.0200.0200.0000.0000.0000.000
107A111VAL00.0090.00846.6110.0010.0010.0000.0000.0000.000
108A112VAL0-0.031-0.01340.948-0.001-0.0010.0000.0000.0000.000
109A113ALA00.0220.01841.6170.0010.0010.0000.0000.0000.000
110A114VAL00.0190.00437.809-0.001-0.0010.0000.0000.0000.000
111A115LYS10.9570.97932.0790.0370.0370.0000.0000.0000.000
112A116SER0-0.009-0.02636.7050.0010.0010.0000.0000.0000.000
113A117GLY0-0.006-0.00735.544-0.002-0.0020.0000.0000.0000.000
114A118THR0-0.0100.00431.572-0.002-0.0020.0000.0000.0000.000
115A119GLY00.1010.04431.9650.0020.0020.0000.0000.0000.000
116A120SER0-0.010-0.02133.3560.0020.0020.0000.0000.0000.000
117A121VAL0-0.016-0.01235.5350.0010.0010.0000.0000.0000.000
118A122ASP-1-0.869-0.93536.047-0.020-0.0200.0000.0000.0000.000
119A123TYR00.0400.01235.7580.0010.0010.0000.0000.0000.000
120A124ALA0-0.006-0.01137.8430.0010.0010.0000.0000.0000.000
121A125LYS10.8660.93640.7950.0180.0180.0000.0000.0000.000
122A126ALA0-0.0180.00940.6360.0010.0010.0000.0000.0000.000
123A127ASN00.0000.00338.6560.0010.0010.0000.0000.0000.000
124A128ILE0-0.020-0.00940.632-0.001-0.0010.0000.0000.0000.000
125A129LYS10.9290.97944.5240.0160.0160.0000.0000.0000.000
126A130THR0-0.0050.00045.0420.0000.0000.0000.0000.0000.000
127A131LYS10.8520.93047.9610.0150.0150.0000.0000.0000.000
128A132ASP-1-0.882-0.95849.137-0.017-0.0170.0000.0000.0000.000
129A133LEU0-0.0140.00441.884-0.001-0.0010.0000.0000.0000.000
130A134ARG10.8700.95344.7680.0210.0210.0000.0000.0000.000
131A135GLN0-0.006-0.01441.050-0.001-0.0010.0000.0000.0000.000
132A136PHE00.0270.02139.9910.0010.0010.0000.0000.0000.000
133A137PRO00.0060.00538.995-0.001-0.0010.0000.0000.0000.000
134A138ASN00.0240.00135.746-0.002-0.0020.0000.0000.0000.000
135A139ILE00.0470.01432.1610.0020.0020.0000.0000.0000.000
136A140ASP-1-0.862-0.92335.549-0.039-0.0390.0000.0000.0000.000
137A141ASN00.009-0.00837.0380.0010.0010.0000.0000.0000.000
138A142ALA0-0.022-0.01038.2030.0010.0010.0000.0000.0000.000
139A143TYR00.018-0.00132.6430.0020.0020.0000.0000.0000.000
140A144MET00.0130.02839.5570.0010.0010.0000.0000.0000.000
141A145GLU-1-0.844-0.94042.700-0.021-0.0210.0000.0000.0000.000
142A146LEU0-0.054-0.02540.3950.0010.0010.0000.0000.0000.000
143A147GLY00.0170.01843.2330.0000.0000.0000.0000.0000.000
144A148THR0-0.0300.01044.4070.0010.0010.0000.0000.0000.000
145A149ASN00.0230.00147.251-0.001-0.0010.0000.0000.0000.000
146A150ARG10.8680.93847.9810.0210.0210.0000.0000.0000.000
147A151ALA00.0190.01744.0860.0010.0010.0000.0000.0000.000
148A152ASP-1-0.818-0.90446.155-0.021-0.0210.0000.0000.0000.000
149A153ALA0-0.034-0.03341.241-0.001-0.0010.0000.0000.0000.000
150A154VAL0-0.0050.00336.7200.0010.0010.0000.0000.0000.000
151A155LEU0-0.058-0.02535.8820.0000.0000.0000.0000.0000.000
152A156HIS00.0190.00330.7820.0030.0030.0000.0000.0000.000
153A157ASP-1-0.792-0.88327.289-0.054-0.0540.0000.0000.0000.000
154A158THR0-0.005-0.01626.6530.0000.0000.0000.0000.0000.000
155A159PRO00.0460.01623.961-0.001-0.0010.0000.0000.0000.000
156A160ASN0-0.017-0.02026.097-0.005-0.0050.0000.0000.0000.000
157A161ILE0-0.052-0.01628.4280.0010.0010.0000.0000.0000.000
158A162LEU0-0.018-0.01126.9110.0010.0010.0000.0000.0000.000
159A163TYR00.0440.01725.895-0.002-0.0020.0000.0000.0000.000
160A164PHE00.0230.02128.5910.0000.0000.0000.0000.0000.000
161A165ILE0-0.030-0.02731.7790.0020.0020.0000.0000.0000.000
162A166LYS10.8730.95426.4830.0830.0830.0000.0000.0000.000
163A167THR0-0.058-0.03829.0180.0010.0010.0000.0000.0000.000
164A168ALA0-0.014-0.00732.1650.0010.0010.0000.0000.0000.000
165A169GLY0-0.040-0.00735.1700.0030.0030.0000.0000.0000.000
166A170ASN00.0140.00434.6660.0040.0040.0000.0000.0000.000
167A171GLY0-0.034-0.01237.0760.0010.0010.0000.0000.0000.000
168A172GLN00.0540.02940.5650.0010.0010.0000.0000.0000.000
169A173PHE0-0.033-0.00638.0520.0020.0020.0000.0000.0000.000
170A174LYS10.8320.89837.5020.0280.0280.0000.0000.0000.000
171A175ALA00.0390.02934.4160.0010.0010.0000.0000.0000.000
172A176VAL0-0.058-0.03536.3120.0010.0010.0000.0000.0000.000
173A177GLY00.0010.00436.5020.0000.0000.0000.0000.0000.000
174A178ASP-1-0.821-0.91529.824-0.045-0.0450.0000.0000.0000.000
175A179SER0-0.045-0.02728.5850.0000.0000.0000.0000.0000.000
176A180LEU0-0.036-0.01630.7690.0020.0020.0000.0000.0000.000
177A181GLU-1-0.912-0.96130.886-0.026-0.0260.0000.0000.0000.000
178A182ALA0-0.022-0.02126.991-0.002-0.0020.0000.0000.0000.000
179A183GLN0-0.0180.00723.5810.0030.0030.0000.0000.0000.000
180A184GLN00.002-0.02119.845-0.006-0.0060.0000.0000.0000.000
181A185TYR0-0.0020.00116.8330.0060.0060.0000.0000.0000.000
182A186GLY00.024-0.00714.7200.0080.0080.0000.0000.0000.000
183A187ILE0-0.0050.0107.975-0.015-0.0150.0000.0000.0000.000
184A188ALA0-0.0080.00710.8380.0320.0320.0000.0000.0000.000
185A189PHE00.0600.0085.554-0.046-0.0460.0000.0000.0000.000
186A190PRO00.0160.0097.2300.0060.0060.0000.0000.0000.000
187A191LYS10.8610.92710.139-0.009-0.0090.0000.0000.0000.000
188A192GLY00.0030.00611.5920.0140.0140.0000.0000.0000.000
189A193SER0-0.0110.0017.4020.0290.0290.0000.0000.0000.000
190A194ASP-1-0.898-0.9619.0600.0860.0860.0000.0000.0000.000
191A195GLU-1-0.771-0.8848.6260.0530.0530.0000.0000.0000.000
192A196LEU0-0.033-0.0163.164-0.885-0.0980.096-0.180-0.7030.001
193A197ARG10.8810.9666.901-0.048-0.0480.0000.0000.0000.000
194A198ASP-1-0.897-0.9599.2750.0310.0310.0000.0000.0000.000
195A199LYS10.8120.8946.551-0.081-0.0810.0000.0000.0000.000
196A200VAL00.0040.0076.052-0.028-0.0280.0000.0000.0000.000
197A201ASN00.0440.0218.722-0.044-0.0440.0000.0000.0000.000
198A202GLY0-0.012-0.00812.164-0.015-0.0150.0000.0000.0000.000
199A203ALA00.0360.01410.442-0.015-0.0150.0000.0000.0000.000
200A204LEU0-0.030-0.01512.347-0.020-0.0200.0000.0000.0000.000
201A205LYS10.9280.96313.9110.0100.0100.0000.0000.0000.000
202A206THR00.0820.04615.0960.0000.0000.0000.0000.0000.000
203A207LEU0-0.015-0.01813.229-0.005-0.0050.0000.0000.0000.000
204A208ARG10.8440.91816.8830.0480.0480.0000.0000.0000.000
205A209GLU-1-0.972-0.97419.794-0.040-0.0400.0000.0000.0000.000
206A210ASN0-0.0110.02917.7170.0010.0010.0000.0000.0000.000
207A211GLY00.0360.01821.595-0.002-0.0020.0000.0000.0000.000
208A212THR0-0.017-0.03716.678-0.005-0.0050.0000.0000.0000.000
209A213TYR0-0.081-0.06017.186-0.004-0.0040.0000.0000.0000.000
210A214ASN0-0.015-0.01619.208-0.003-0.0030.0000.0000.0000.000
211A215GLU-1-0.866-0.93721.934-0.074-0.0740.0000.0000.0000.000
212A216ILE0-0.0110.00015.974-0.001-0.0010.0000.0000.0000.000
213A217TYR00.015-0.00320.283-0.001-0.0010.0000.0000.0000.000
214A218LYS10.8330.91222.3820.0650.0650.0000.0000.0000.000
215A219LYS10.8510.92319.3150.1550.1550.0000.0000.0000.000
216A220TRP0-0.026-0.02119.3890.0070.0070.0000.0000.0000.000
217A221PHE0-0.005-0.01021.2050.0040.0040.0000.0000.0000.000
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