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: 17KRZ

Calculation Name: 1L3C-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1L3C

Chain ID: A

ChEMBL ID:

UniProt ID: O26249

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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1892773.106839
FMO2-HF: Nuclear repulsion 1820546.361635
FMO2-HF: Total energy -72226.745204
FMO2-MP2: Total energy -72429.755416


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-21.98-12.1722.876-9.667-23.015-0.09
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.058 / q_NPA : -0.008
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].
3A3PRO00.0900.0512.827-1.4251.4310.366-1.487-1.735-0.006
4A4ASP-1-0.705-0.8585.0411.0631.220-0.001-0.008-0.1480.000
5A5ASP-1-0.925-0.9777.309-1.057-1.0570.0000.0000.0000.000
6A6GLU-1-0.857-0.9038.029-2.431-2.4310.0000.0000.0000.000
7A7PHE0-0.055-0.0194.9340.0890.0890.0000.0000.0000.000
8A8ILE0-0.019-0.02510.3000.0910.0910.0000.0000.0000.000
9A9LYS10.8790.93011.0350.4570.4570.0000.0000.0000.000
10A10ASN0-0.001-0.02115.3170.0010.0010.0000.0000.0000.000
11A11PRO0-0.007-0.00418.4880.0240.0240.0000.0000.0000.000
12A12SER0-0.044-0.04221.0380.0250.0250.0000.0000.0000.000
13A13VAL0-0.053-0.00715.8420.0230.0230.0000.0000.0000.000
14A14PRO00.0280.02316.171-0.005-0.0050.0000.0000.0000.000
15A15GLY0-0.0100.01812.2460.0210.0210.0000.0000.0000.000
16A16PRO00.000-0.0287.782-0.095-0.0950.0000.0000.0000.000
17A17THR00.0130.0037.302-0.048-0.0480.0000.0000.0000.000
18A18ALA00.0170.0187.0450.2680.2680.0000.0000.0000.000
19A19MET00.002-0.0042.240-1.497-0.5993.833-1.154-3.5770.002
20A20GLU-1-0.751-0.8523.5054.1085.3800.830-0.625-1.478-0.009
21A21VAL0-0.005-0.0016.150-0.279-0.225-0.001-0.009-0.0430.000
22A22ARG10.8130.8952.437-1.817-2.3485.920-1.598-3.7900.002
23A23CYS0-0.034-0.0212.187-6.618-4.9534.659-2.432-3.891-0.016
24A24LEU00.0310.0193.0520.863-1.1730.0732.298-0.335-0.001
25A25ILE00.0080.0015.294-0.325-0.3250.0000.0000.0000.000
26A26MET0-0.034-0.0152.717-0.6340.0000.400-0.159-0.8750.000
27A27CYS0-0.063-0.0314.8540.1100.154-0.001-0.002-0.0400.000
28A28LEU0-0.019-0.0057.367-0.040-0.0400.0000.0000.0000.000
29A29ALA0-0.0010.0088.039-0.042-0.0420.0000.0000.0000.000
30A30GLU-1-0.920-0.9479.2110.2540.2540.0000.0000.0000.000
31A31PRO0-0.037-0.0217.337-0.037-0.0370.0000.0000.0000.000
32A32GLY00.0950.06110.5980.0400.0400.0000.0000.0000.000
33A33LYS10.9580.95513.189-0.041-0.0410.0000.0000.0000.000
34A34ASN0-0.063-0.03614.847-0.039-0.0390.0000.0000.0000.000
35A35ASP-1-0.792-0.89914.0770.0820.0820.0000.0000.0000.000
36A36VAL0-0.053-0.03615.428-0.033-0.0330.0000.0000.0000.000
37A37ALA00.0220.01112.4390.0230.0230.0000.0000.0000.000
38A38VAL00.002-0.00114.480-0.029-0.0290.0000.0000.0000.000
39A39ASP-1-0.834-0.91111.2260.1780.1780.0000.0000.0000.000
40A40VAL00.009-0.00313.665-0.028-0.0280.0000.0000.0000.000
41A41GLY0-0.0090.00415.5700.0460.0460.0000.0000.0000.000
42A42CYS0-0.010-0.01013.2040.0480.0480.0000.0000.0000.000
43A43GLY00.0480.03512.9500.0220.0220.0000.0000.0000.000
44A44THR0-0.055-0.05210.986-0.058-0.0580.0000.0000.0000.000
45A45GLY00.0610.03110.944-0.122-0.1220.0000.0000.0000.000
46A46GLY0-0.066-0.0377.002-0.130-0.1300.0000.0000.0000.000
47A47VAL00.0420.0036.1230.0120.0120.0000.0000.0000.000
48A48THR00.017-0.0097.225-0.277-0.2770.0000.0000.0000.000
49A49LEU0-0.054-0.0186.247-0.086-0.0860.0000.0000.0000.000
50A50GLU-1-0.822-0.9202.330-13.212-9.1235.933-4.122-5.900-0.063
51A51LEU00.0300.0064.7910.1450.211-0.001-0.004-0.0610.000
52A52ALA00.0430.0307.7530.0960.0960.0000.0000.0000.000
53A53GLY0-0.0120.0078.3100.0930.0930.0000.0000.0000.000
54A54ARG10.7820.8722.5480.0000.6420.866-0.365-1.1420.001
55A55VAL0-0.0140.0119.6530.0810.0810.0000.0000.0000.000
56A56ARG10.8590.94912.486-0.012-0.0120.0000.0000.0000.000
57A57ARG10.8700.93715.7460.0970.0970.0000.0000.0000.000
58A58VAL00.0450.03911.2130.0220.0220.0000.0000.0000.000
59A59TYR0-0.009-0.00414.495-0.018-0.0180.0000.0000.0000.000
60A60ALA00.0260.00814.3850.0240.0240.0000.0000.0000.000
61A61ILE00.0100.00415.972-0.013-0.0130.0000.0000.0000.000
62A62ASP-1-0.815-0.93717.7120.0930.0930.0000.0000.0000.000
63A63ARG10.8570.93420.037-0.070-0.0700.0000.0000.0000.000
64A64ASN0-0.002-0.00121.126-0.025-0.0250.0000.0000.0000.000
65A65PRO00.0830.04021.469-0.006-0.0060.0000.0000.0000.000
66A66GLU-1-0.831-0.87921.331-0.093-0.0930.0000.0000.0000.000
67A67ALA0-0.0090.01617.436-0.027-0.0270.0000.0000.0000.000
68A68ILE00.0290.02416.986-0.032-0.0320.0000.0000.0000.000
69A69SER00.0140.01017.975-0.046-0.0460.0000.0000.0000.000
70A70THR0-0.033-0.04214.322-0.044-0.0440.0000.0000.0000.000
71A71THR0-0.026-0.01412.655-0.065-0.0650.0000.0000.0000.000
72A72GLU-1-0.899-0.95413.809-0.326-0.3260.0000.0000.0000.000
73A73MET0-0.049-0.01615.923-0.062-0.0620.0000.0000.0000.000
74A74ASN00.0170.00210.556-0.191-0.1910.0000.0000.0000.000
75A75LEU00.0280.01711.165-0.179-0.1790.0000.0000.0000.000
76A76GLN00.0670.03412.694-0.082-0.0820.0000.0000.0000.000
77A77ARG10.7930.90212.6830.4590.4590.0000.0000.0000.000
78A78HIS10.7710.8698.4271.5191.5190.0000.0000.0000.000
79A79GLY0-0.0280.00110.837-0.040-0.0400.0000.0000.0000.000
80A80LEU0-0.0140.0018.2380.0240.0240.0000.0000.0000.000
81A81GLY00.0460.00212.7790.0240.0240.0000.0000.0000.000
82A82ASP-1-0.900-0.93115.171-0.285-0.2850.0000.0000.0000.000
83A83ASN0-0.127-0.08512.7480.0080.0080.0000.0000.0000.000
84A84VAL0-0.011-0.00812.9910.0180.0180.0000.0000.0000.000
85A85THR0-0.048-0.01516.0060.0020.0020.0000.0000.0000.000
86A86LEU00.0090.01116.0520.0180.0180.0000.0000.0000.000
87A87MET0-0.059-0.03719.2070.0070.0070.0000.0000.0000.000
88A88GLU-1-0.867-0.93721.463-0.042-0.0420.0000.0000.0000.000
89A89GLY0-0.010-0.00623.5640.0010.0010.0000.0000.0000.000
90A90ASP-1-0.887-0.97223.9620.0510.0510.0000.0000.0000.000
91A91ALA00.0380.01221.531-0.004-0.0040.0000.0000.0000.000
92A92PRO00.0480.02123.237-0.003-0.0030.0000.0000.0000.000
93A93GLU-1-0.808-0.88125.8170.0020.0020.0000.0000.0000.000
94A94ALA0-0.021-0.01423.212-0.005-0.0050.0000.0000.0000.000
95A95LEU00.0310.01119.820-0.006-0.0060.0000.0000.0000.000
96A96CYS0-0.024-0.00723.5410.0000.0000.0000.0000.0000.000
97A97LYS10.7600.87326.0870.0000.0000.0000.0000.0000.000
98A98ILE0-0.0380.00120.187-0.010-0.0100.0000.0000.0000.000
99A99PRO0-0.042-0.02021.9520.0070.0070.0000.0000.0000.000
100A100ASP-1-0.815-0.90122.6350.0420.0420.0000.0000.0000.000
101A101ILE0-0.061-0.04517.629-0.012-0.0120.0000.0000.0000.000
102A102ASP-1-0.804-0.87616.1460.0550.0550.0000.0000.0000.000
103A103ILE00.0040.00910.7320.0170.0170.0000.0000.0000.000
104A104ALA00.0300.01514.225-0.030-0.0300.0000.0000.0000.000
105A105VAL0-0.009-0.0019.1650.0430.0430.0000.0000.0000.000
106A106VAL0-0.003-0.00412.464-0.034-0.0340.0000.0000.0000.000
107A107GLY00.0530.02013.8930.0610.0610.0000.0000.0000.000
108A108GLY0-0.022-0.02014.396-0.011-0.0110.0000.0000.0000.000
109A109SER0-0.005-0.01517.691-0.037-0.0370.0000.0000.0000.000
110A110GLY0-0.0010.00020.053-0.018-0.0180.0000.0000.0000.000
111A111GLY0-0.031-0.00622.783-0.014-0.0140.0000.0000.0000.000
112A112GLU-1-0.822-0.89324.8430.0670.0670.0000.0000.0000.000
113A113LEU00.0070.00119.6710.0010.0010.0000.0000.0000.000
114A114GLN00.0710.03623.112-0.009-0.0090.0000.0000.0000.000
115A115GLU-1-0.893-0.93925.7530.0670.0670.0000.0000.0000.000
116A116ILE0-0.012-0.01020.134-0.004-0.0040.0000.0000.0000.000
117A117LEU0-0.007-0.01419.1590.0000.0000.0000.0000.0000.000
118A118ARG10.8700.93422.538-0.084-0.0840.0000.0000.0000.000
119A119ILE00.0310.01924.253-0.003-0.0030.0000.0000.0000.000
120A120ILE0-0.031-0.02918.182-0.004-0.0040.0000.0000.0000.000
121A121LYS10.8460.92021.997-0.101-0.1010.0000.0000.0000.000
122A122ASP-1-0.950-0.96923.7870.0690.0690.0000.0000.0000.000
123A123LYS10.7890.90222.670-0.038-0.0380.0000.0000.0000.000
124A124LEU0-0.068-0.00118.078-0.005-0.0050.0000.0000.0000.000
125A125LYS10.7880.88020.061-0.035-0.0350.0000.0000.0000.000
126A126PRO00.014-0.01921.4680.0110.0110.0000.0000.0000.000
127A127GLY0-0.020-0.00220.635-0.003-0.0030.0000.0000.0000.000
128A128GLY00.0060.01217.6130.0100.0100.0000.0000.0000.000
129A129ARG10.8060.90113.183-0.144-0.1440.0000.0000.0000.000
130A130ILE00.0410.02015.050-0.017-0.0170.0000.0000.0000.000
131A131ILE0-0.027-0.0199.4760.0380.0380.0000.0000.0000.000
132A132VAL00.0100.00713.206-0.013-0.0130.0000.0000.0000.000
133A133THR0-0.020-0.00511.5600.1040.1040.0000.0000.0000.000
134A134ALA0-0.018-0.01013.566-0.058-0.0580.0000.0000.0000.000
135A135ILE0-0.011-0.01814.0990.0450.0450.0000.0000.0000.000
136A136LEU00.0070.00917.938-0.018-0.0180.0000.0000.0000.000
137A137LEU00.014-0.00121.3040.0190.0190.0000.0000.0000.000
138A138GLU-1-0.848-0.94423.5520.1720.1720.0000.0000.0000.000
139A139THR00.0100.00618.961-0.003-0.0030.0000.0000.0000.000
140A140LYS10.8150.89418.243-0.352-0.3520.0000.0000.0000.000
141A141PHE0-0.033-0.00821.0090.0040.0040.0000.0000.0000.000
142A142GLU-1-0.798-0.91423.8920.1330.1330.0000.0000.0000.000
143A143ALA0-0.024-0.01319.527-0.007-0.0070.0000.0000.0000.000
144A144MET0-0.033-0.02420.800-0.001-0.0010.0000.0000.0000.000
145A145GLU-1-0.914-0.93622.7970.1250.1250.0000.0000.0000.000
146A146CYS00.0270.01523.940-0.011-0.0110.0000.0000.0000.000
147A147LEU0-0.002-0.00718.808-0.007-0.0070.0000.0000.0000.000
148A148ARG10.8920.94123.364-0.180-0.1800.0000.0000.0000.000
149A149ASP-1-0.905-0.94426.0270.1120.1120.0000.0000.0000.000
150A150LEU0-0.112-0.04624.251-0.011-0.0110.0000.0000.0000.000
151A151GLY0-0.014-0.00926.940-0.005-0.0050.0000.0000.0000.000
152A152PHE0-0.020-0.00121.8960.0000.0000.0000.0000.0000.000
153A153ASP-1-0.903-0.93522.7410.1640.1640.0000.0000.0000.000
154A154VAL0-0.054-0.04919.9770.0160.0160.0000.0000.0000.000
155A155ASN0-0.057-0.01617.281-0.010-0.0100.0000.0000.0000.000
156A156ILE00.0380.00116.8950.0110.0110.0000.0000.0000.000
157A157THR0-0.044-0.01313.630-0.004-0.0040.0000.0000.0000.000
158A158GLU-1-0.802-0.87814.7200.4310.4310.0000.0000.0000.000
159A159LEU0-0.018-0.0089.9680.0180.0180.0000.0000.0000.000
160A160ASN0-0.007-0.01514.140-0.056-0.0560.0000.0000.0000.000
161A161ILE00.0110.01110.038-0.009-0.0090.0000.0000.0000.000
162A162ALA00.0220.00213.767-0.073-0.0730.0000.0000.0000.000
163A163ARG10.6990.8068.140-0.601-0.6010.0000.0000.0000.000
164A164GLY00.0400.01314.182-0.017-0.0170.0000.0000.0000.000
165A165ARG10.9240.96115.796-0.019-0.0190.0000.0000.0000.000
166A166ALA00.0160.00018.2400.0220.0220.0000.0000.0000.000
167A167LEU0-0.052-0.03420.367-0.011-0.0110.0000.0000.0000.000
168A168ASP-1-0.903-0.95323.862-0.080-0.0800.0000.0000.0000.000
169A169ARG10.9530.97126.9990.0160.0160.0000.0000.0000.000
170A170GLY00.0390.02625.2080.0100.0100.0000.0000.0000.000
171A171THR0-0.011-0.00218.982-0.019-0.0190.0000.0000.0000.000
172A172MET0-0.0300.00421.4740.0200.0200.0000.0000.0000.000
173A173MET00.0200.01116.120-0.027-0.0270.0000.0000.0000.000
174A174VAL0-0.049-0.02816.971-0.008-0.0080.0000.0000.0000.000
175A175SER00.0260.00916.3930.0320.0320.0000.0000.0000.000
176A176ARG10.9000.95811.246-0.323-0.3230.0000.0000.0000.000
177A177ASN00.007-0.00415.198-0.018-0.0180.0000.0000.0000.000
178A178PRO00.0230.01014.9130.0760.0760.0000.0000.0000.000
179A179VAL0-0.032-0.00111.758-0.015-0.0150.0000.0000.0000.000
180A180ALA0-0.0020.01214.2570.0350.0350.0000.0000.0000.000
181A181LEU0-0.013-0.0088.8830.0250.0250.0000.0000.0000.000
182A182ILE00.002-0.00713.438-0.026-0.0260.0000.0000.0000.000
183A183TYR00.002-0.00913.520-0.002-0.0020.0000.0000.0000.000
184A184THR00.0400.02715.652-0.009-0.0090.0000.0000.0000.000
185A185GLY0-0.025-0.00616.8340.0160.0160.0000.0000.0000.000
186A186VAL0-0.0110.00515.305-0.019-0.0190.0000.0000.0000.000