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: LZ8L9

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 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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2497443.59989
FMO2-HF: Nuclear repulsion 2413438.440128
FMO2-HF: Total energy -84005.159762
FMO2-MP2: Total energy -84254.563185


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.
-13.651-1.9066.998-6.735-12.005-0.034
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 : 0.010 / 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].
3A7VAL00.0060.0033.8810.1051.801-0.011-0.764-0.9210.004
4A8ALA0-0.011-0.0125.4810.0690.0690.0000.0000.0000.000
5A9THR0-0.016-0.0259.1100.1070.1070.0000.0000.0000.000
6A10ASP-1-0.777-0.89812.255-0.312-0.3120.0000.0000.0000.000
7A11THR0-0.059-0.02015.667-0.043-0.0430.0000.0000.0000.000
8A12ALA0-0.022-0.02618.126-0.006-0.0060.0000.0000.0000.000
9A13PHE0-0.0140.02318.5100.0330.0330.0000.0000.0000.000
10A14VAL00.0150.02720.1170.0050.0050.0000.0000.0000.000
11A15PRO0-0.037-0.01722.1290.0130.0130.0000.0000.0000.000
12A16PHE0-0.027-0.01617.2540.0070.0070.0000.0000.0000.000
13A17GLU-1-0.765-0.89715.219-0.328-0.3280.0000.0000.0000.000
14A18PHE0-0.002-0.01017.3060.0220.0220.0000.0000.0000.000
15A19LYS10.8490.92518.9640.3740.3740.0000.0000.0000.000
16A20GLN0-0.019-0.01820.1070.0460.0460.0000.0000.0000.000
17A21GLY0-0.012-0.00421.549-0.009-0.0090.0000.0000.0000.000
18A22ASP-1-0.843-0.92320.411-0.380-0.3800.0000.0000.0000.000
19A23LEU00.0070.02816.793-0.048-0.0480.0000.0000.0000.000
20A24TYR0-0.013-0.04514.7640.0070.0070.0000.0000.0000.000
21A25VAL0-0.038-0.01816.2780.0000.0000.0000.0000.0000.000
22A26GLY00.0910.03717.798-0.006-0.0060.0000.0000.0000.000
23A27PHE0-0.030-0.01616.966-0.004-0.0040.0000.0000.0000.000
24A28ASP-1-0.720-0.86213.264-0.114-0.1140.0000.0000.0000.000
25A29VAL0-0.0190.00212.391-0.012-0.0120.0000.0000.0000.000
26A30ASP-1-0.802-0.87312.520-0.179-0.1790.0000.0000.0000.000
27A31LEU0-0.022-0.00912.5130.0350.0350.0000.0000.0000.000
28A32TRP00.0300.0093.451-0.2740.2170.014-0.096-0.4090.001
29A33ALA00.0200.0178.8640.0800.0800.0000.0000.0000.000
30A34ALA0-0.032-0.01810.4490.0690.0690.0000.0000.0000.000
31A35ILE00.0450.0117.4300.0540.0540.0000.0000.0000.000
32A36ALA00.0170.0155.6680.1470.1470.0000.0000.0000.000
33A37LYS10.8500.9226.781-0.015-0.0150.0000.0000.0000.000
34A38GLU-1-0.865-0.9419.5720.2200.2200.0000.0000.0000.000
35A39LEU0-0.052-0.0166.1590.0160.0160.0000.0000.0000.000
36A40LYS10.7530.8817.324-0.198-0.1980.0000.0000.0000.000
37A41LEU0-0.0140.0062.385-0.654-0.2641.826-0.368-1.8480.002
38A42ASP-1-0.877-0.9324.773-0.704-0.511-0.001-0.016-0.1760.000
39A43TYR0-0.071-0.0502.444-3.768-0.6500.657-1.607-2.168-0.008
40A44GLU-1-0.827-0.8883.517-1.373-0.7870.007-0.085-0.5070.000
41A45LEU00.0160.0085.715-0.267-0.2670.0000.0000.0000.000
42A46LYS10.7780.8608.4781.8631.8630.0000.0000.0000.000
43A47PRO00.0180.01510.4750.0890.0890.0000.0000.0000.000
44A48MET0-0.067-0.01711.1980.0140.0140.0000.0000.0000.000
45A49ASP-1-0.858-0.92715.660-0.276-0.2760.0000.0000.0000.000
46A50PHE00.010-0.00316.678-0.005-0.0050.0000.0000.0000.000
47A51SER0-0.070-0.03917.2460.0010.0010.0000.0000.0000.000
48A52GLY00.0210.01216.5950.0260.0260.0000.0000.0000.000
49A53ILE00.0230.01111.598-0.011-0.0110.0000.0000.0000.000
50A54ILE0-0.006-0.00512.8330.0060.0060.0000.0000.0000.000
51A55PRO00.0190.00014.1920.0240.0240.0000.0000.0000.000
52A56ALA00.0430.03211.1630.0260.0260.0000.0000.0000.000
53A57LEU00.0270.0328.243-0.007-0.0070.0000.0000.0000.000
54A58GLN0-0.062-0.04510.6960.0810.0810.0000.0000.0000.000
55A59THR0-0.053-0.04512.9790.0550.0550.0000.0000.0000.000
56A60LYS10.8270.9177.948-0.016-0.0160.0000.0000.0000.000
57A61ASN0-0.0400.0038.5390.0300.0300.0000.0000.0000.000
58A62VAL0-0.006-0.0016.382-0.248-0.2480.0000.0000.0000.000
59A63ASP-1-0.839-0.9062.367-6.616-3.0133.578-3.364-3.816-0.035
60A64LEU0-0.055-0.0362.984-0.2970.6070.216-0.196-0.9240.000
61A65ALA00.009-0.0026.188-0.429-0.4290.0000.0000.0000.000
62A66LEU0-0.065-0.0258.3560.1850.1850.0000.0000.0000.000
63A67ALA00.0760.03011.364-0.080-0.0800.0000.0000.0000.000
64A68GLY00.0040.00414.7340.0240.0240.0000.0000.0000.000
65A69ILE0-0.036-0.00412.9590.0160.0160.0000.0000.0000.000
66A70THR0-0.038-0.02416.9940.0270.0270.0000.0000.0000.000
67A71ILE00.0160.02517.039-0.006-0.0060.0000.0000.0000.000
68A72THR00.020-0.00419.552-0.003-0.0030.0000.0000.0000.000
69A73ASP-1-0.809-0.91021.1150.0660.0660.0000.0000.0000.000
70A74GLU-1-0.822-0.90322.4940.0200.0200.0000.0000.0000.000
71A75ARG10.8990.95418.0310.0470.0470.0000.0000.0000.000
72A76LYS10.8650.93217.950-0.077-0.0770.0000.0000.0000.000
73A77LYS10.7930.89718.727-0.006-0.0060.0000.0000.0000.000
74A78ALA0-0.0150.00417.8430.0100.0100.0000.0000.0000.000
75A79ILE0-0.005-0.00613.169-0.006-0.0060.0000.0000.0000.000
76A80ASP-1-0.826-0.90112.0850.2770.2770.0000.0000.0000.000
77A81PHE0-0.007-0.02012.498-0.035-0.0350.0000.0000.0000.000
78A82SER00.0130.01311.0390.0380.0380.0000.0000.0000.000
79A83ASP-1-0.850-0.92412.8170.1980.1980.0000.0000.0000.000
80A84GLY0-0.024-0.00415.295-0.006-0.0060.0000.0000.0000.000
81A85TYR0-0.072-0.04813.9060.0260.0260.0000.0000.0000.000
82A86TYR00.0220.01816.768-0.015-0.0150.0000.0000.0000.000
83A87LYS10.8300.92019.8250.0020.0020.0000.0000.0000.000
84A88SER00.026-0.00323.161-0.010-0.0100.0000.0000.0000.000
85A89GLY00.0460.01724.9920.0100.0100.0000.0000.0000.000
86A90LEU0-0.0390.00228.423-0.009-0.0090.0000.0000.0000.000
87A91LEU00.0340.00730.8300.0060.0060.0000.0000.0000.000
88A92VAL0-0.025-0.00833.676-0.003-0.0030.0000.0000.0000.000
89A93MET0-0.0020.01735.2420.0010.0010.0000.0000.0000.000
90A94VAL00.021-0.01437.9640.0010.0010.0000.0000.0000.000
91A95LYS10.8690.92940.9910.0320.0320.0000.0000.0000.000
92A96ALA00.0360.01741.6370.0030.0030.0000.0000.0000.000
93A97ASN0-0.021-0.01443.0690.0010.0010.0000.0000.0000.000
94A98ASN0-0.045-0.01845.6720.0020.0020.0000.0000.0000.000
95A99ASN00.0270.00145.475-0.001-0.0010.0000.0000.0000.000
96A100ASP-1-0.826-0.89047.167-0.012-0.0120.0000.0000.0000.000
97A101VAL0-0.008-0.00143.0040.0020.0020.0000.0000.0000.000
98A102LYS10.8440.90141.8580.0080.0080.0000.0000.0000.000
99A103SER00.0290.03439.7660.0020.0020.0000.0000.0000.000
100A104VAL00.0160.01141.685-0.001-0.0010.0000.0000.0000.000
101A105LYS10.8990.93041.0870.0140.0140.0000.0000.0000.000
102A106ASP-1-0.836-0.91346.535-0.008-0.0080.0000.0000.0000.000
103A107LEU0-0.061-0.06248.803-0.001-0.0010.0000.0000.0000.000
104A108ASP-1-0.908-0.94451.643-0.011-0.0110.0000.0000.0000.000
105A109GLY0-0.007-0.00352.3700.0000.0000.0000.0000.0000.000
106A110LYS10.7800.91747.9990.0150.0150.0000.0000.0000.000
107A111VAL00.0060.00246.8660.0000.0000.0000.0000.0000.000
108A112VAL0-0.007-0.00241.3180.0000.0000.0000.0000.0000.000
109A113ALA00.0080.01142.0170.0000.0000.0000.0000.0000.000
110A114VAL00.011-0.00537.6570.0000.0000.0000.0000.0000.000
111A115LYS10.9190.95731.8930.0660.0660.0000.0000.0000.000
112A116SER00.031-0.00536.4620.0040.0040.0000.0000.0000.000
113A117GLY00.0000.01335.646-0.005-0.0050.0000.0000.0000.000
114A118THR00.017-0.02031.044-0.008-0.0080.0000.0000.0000.000
115A119GLY00.0750.05232.2280.0030.0030.0000.0000.0000.000
116A120SER0-0.010-0.00633.6700.0040.0040.0000.0000.0000.000
117A121VAL0-0.027-0.01935.7460.0030.0030.0000.0000.0000.000
118A122ASP-1-0.865-0.94035.963-0.025-0.0250.0000.0000.0000.000
119A123TYR00.0250.01535.7050.0030.0030.0000.0000.0000.000
120A124ALA0-0.023-0.02338.1850.0030.0030.0000.0000.0000.000
121A125LYS10.8210.91241.1650.0250.0250.0000.0000.0000.000
122A126ALA0-0.0180.00841.1020.0010.0010.0000.0000.0000.000
123A127ASN0-0.007-0.00438.3190.0030.0030.0000.0000.0000.000
124A128ILE0-0.012-0.01240.5010.0000.0000.0000.0000.0000.000
125A129LYS10.9120.96444.5440.0090.0090.0000.0000.0000.000
126A130THR0-0.0110.00245.3920.0010.0010.0000.0000.0000.000
127A131LYS10.8640.92348.4450.0170.0170.0000.0000.0000.000
128A132ASP-1-0.803-0.88648.958-0.026-0.0260.0000.0000.0000.000
129A133LEU0-0.016-0.00741.9250.0010.0010.0000.0000.0000.000
130A134ARG10.8090.89444.5630.0290.0290.0000.0000.0000.000
131A135GLN00.0390.02241.3500.0010.0010.0000.0000.0000.000
132A136PHE00.0420.02440.1350.0000.0000.0000.0000.0000.000
133A137PRO00.0080.00338.823-0.001-0.0010.0000.0000.0000.000
134A138ASN0-0.0100.00135.421-0.004-0.0040.0000.0000.0000.000
135A139ILE00.0690.01731.7500.0050.0050.0000.0000.0000.000
136A140ASP-1-0.834-0.90635.922-0.069-0.0690.0000.0000.0000.000
137A141ASN0-0.018-0.01437.5080.0010.0010.0000.0000.0000.000
138A142ALA0-0.0040.00338.5720.0040.0040.0000.0000.0000.000
139A143TYR00.0390.00132.6440.0060.0060.0000.0000.0000.000
140A144MET00.0120.01039.7690.0040.0040.0000.0000.0000.000
141A145GLU-1-0.843-0.91642.965-0.033-0.0330.0000.0000.0000.000
142A146LEU0-0.034-0.00340.4950.0030.0030.0000.0000.0000.000
143A147GLY00.0250.02143.5570.0010.0010.0000.0000.0000.000
144A148THR0-0.0220.00244.4440.0020.0020.0000.0000.0000.000
145A149ASN00.0060.00047.248-0.001-0.0010.0000.0000.0000.000
146A150ARG10.8320.90947.9150.0300.0300.0000.0000.0000.000
147A151ALA00.0420.02944.5200.0010.0010.0000.0000.0000.000
148A152ASP-1-0.803-0.88646.076-0.021-0.0210.0000.0000.0000.000
149A153ALA0-0.013-0.02041.4890.0000.0000.0000.0000.0000.000
150A154VAL0-0.0180.00236.756-0.001-0.0010.0000.0000.0000.000
151A155LEU0-0.068-0.01336.0770.0020.0020.0000.0000.0000.000
152A156HIS0-0.008-0.01229.7040.0020.0020.0000.0000.0000.000
153A157ASP-1-0.785-0.88027.415-0.067-0.0670.0000.0000.0000.000
154A158THR00.002-0.01326.938-0.004-0.0040.0000.0000.0000.000
155A159PRO00.0420.02524.0120.0000.0000.0000.0000.0000.000
156A160ASN0-0.019-0.03626.345-0.010-0.0100.0000.0000.0000.000
157A161ILE0-0.047-0.01728.511-0.001-0.0010.0000.0000.0000.000
158A162LEU00.0110.00128.1560.0010.0010.0000.0000.0000.000
159A163TYR00.0470.02325.979-0.002-0.0020.0000.0000.0000.000
160A164PHE00.0430.03028.766-0.002-0.0020.0000.0000.0000.000
161A165ILE0-0.025-0.00532.0360.0010.0010.0000.0000.0000.000
162A166LYS10.8530.93926.9510.0810.0810.0000.0000.0000.000
163A167THR0-0.072-0.05228.970-0.002-0.0020.0000.0000.0000.000
164A168ALA0-0.018-0.00732.345-0.002-0.0020.0000.0000.0000.000
165A169GLY0-0.031-0.01435.2670.0030.0030.0000.0000.0000.000
166A170ASN0-0.002-0.00534.4370.0100.0100.0000.0000.0000.000
167A171GLY00.0110.00537.4130.0000.0000.0000.0000.0000.000
168A172GLN0-0.025-0.01140.3590.0060.0060.0000.0000.0000.000
169A173PHE0-0.016-0.01038.1970.0020.0020.0000.0000.0000.000
170A174LYS10.8550.92537.4550.0200.0200.0000.0000.0000.000
171A175ALA00.0470.03034.399-0.001-0.0010.0000.0000.0000.000
172A176VAL0-0.050-0.03136.4330.0030.0030.0000.0000.0000.000
173A177GLY00.0060.00636.5930.0000.0000.0000.0000.0000.000
174A178ASP-1-0.778-0.86930.016-0.003-0.0030.0000.0000.0000.000
175A179SER0-0.051-0.05428.706-0.001-0.0010.0000.0000.0000.000
176A180LEU00.0050.02030.8140.0050.0050.0000.0000.0000.000
177A181GLU-1-0.896-0.96331.155-0.003-0.0030.0000.0000.0000.000
178A182ALA0-0.052-0.00327.686-0.003-0.0030.0000.0000.0000.000
179A183GLN0-0.031-0.02024.3740.0000.0000.0000.0000.0000.000
180A184GLN00.025-0.00119.8400.0010.0010.0000.0000.0000.000
181A185TYR00.0300.03417.222-0.002-0.0020.0000.0000.0000.000
182A186GLY00.0360.00114.8730.0250.0250.0000.0000.0000.000
183A187ILE0-0.006-0.0068.059-0.042-0.0420.0000.0000.0000.000
184A188ALA00.0060.01511.0980.0790.0790.0000.0000.0000.000
185A189PHE00.0590.0065.521-0.023-0.0230.0000.0000.0000.000
186A190PRO00.0290.0237.104-0.080-0.0800.0000.0000.0000.000
187A191LYS10.8170.9169.955-0.050-0.0500.0000.0000.0000.000
188A192GLY00.0240.02011.775-0.007-0.0070.0000.0000.0000.000
189A193SER0-0.026-0.0286.8020.0830.0830.0000.0000.0000.000
190A194ASP-1-0.831-0.9068.4120.6120.6120.0000.0000.0000.000
191A195GLU-1-0.799-0.8768.3971.0931.0930.0000.0000.0000.000
192A196LEU0-0.0160.0062.543-0.988-0.2240.712-0.239-1.2360.002
193A197ARG10.7540.8556.700-0.454-0.4540.0000.0000.0000.000
194A198ASP-1-0.825-0.9149.1340.4190.4190.0000.0000.0000.000
195A199LYS10.7980.8636.412-1.345-1.3450.0000.0000.0000.000
196A200VAL00.0040.0045.925-0.096-0.0960.0000.0000.0000.000
197A201ASN00.0160.0008.736-0.142-0.1420.0000.0000.0000.000
198A202GLY0-0.0020.00612.109-0.071-0.0710.0000.0000.0000.000
199A203ALA00.0400.02010.317-0.069-0.0690.0000.0000.0000.000
200A204LEU0-0.028-0.00912.217-0.083-0.0830.0000.0000.0000.000
201A205LYS10.8320.92713.757-0.302-0.3020.0000.0000.0000.000
202A206THR00.0730.03715.452-0.020-0.0200.0000.0000.0000.000
203A207LEU0-0.041-0.02413.316-0.033-0.0330.0000.0000.0000.000
204A208ARG10.7970.89316.717-0.165-0.1650.0000.0000.0000.000
205A209GLU-1-0.905-0.95719.7980.1760.1760.0000.0000.0000.000
206A210ASN00.0110.01917.552-0.022-0.0220.0000.0000.0000.000
207A211GLY00.0220.01521.711-0.012-0.0120.0000.0000.0000.000
208A212THR0-0.031-0.03616.929-0.018-0.0180.0000.0000.0000.000
209A213TYR0-0.074-0.06717.181-0.021-0.0210.0000.0000.0000.000
210A214ASN0-0.025-0.01719.375-0.023-0.0230.0000.0000.0000.000
211A215GLU-1-0.794-0.89622.531-0.016-0.0160.0000.0000.0000.000
212A216ILE0-0.0090.00216.488-0.016-0.0160.0000.0000.0000.000
213A217TYR00.0180.00920.774-0.016-0.0160.0000.0000.0000.000
214A218LYS10.7790.86822.787-0.008-0.0080.0000.0000.0000.000
215A219LYS10.8100.89319.2620.1420.1420.0000.0000.0000.000
216A220TRP0-0.037-0.03119.604-0.011-0.0110.0000.0000.0000.000
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