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: G6G11

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 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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1898999.457778
FMO2-HF: Nuclear repulsion 1826772.323646
FMO2-HF: Total energy -72227.134132
FMO2-MP2: Total energy -72430.161104


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.
-21.568-11.84123.035-9.537-23.218-0.089
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 : -0.066 / q_NPA : -0.012
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].
3A3PRO00.0590.0323.100-0.9521.5330.125-1.250-1.359-0.001
4A4ASP-1-0.694-0.8575.2920.6840.814-0.001-0.006-0.1220.000
5A5ASP-1-0.901-0.9517.400-1.086-1.0860.0000.0000.0000.000
6A6GLU-1-0.844-0.9148.236-2.564-2.5640.0000.0000.0000.000
7A7PHE0-0.044-0.0085.2580.1040.1040.0000.0000.0000.000
8A8ILE00.015-0.00910.5560.1230.1230.0000.0000.0000.000
9A9LYS10.8290.90511.1830.6070.6070.0000.0000.0000.000
10A10ASN00.004-0.01915.5060.0130.0130.0000.0000.0000.000
11A11PRO00.0040.00218.8110.0200.0200.0000.0000.0000.000
12A12SER0-0.023-0.02921.3600.0240.0240.0000.0000.0000.000
13A13VAL0-0.058-0.01015.7230.0210.0210.0000.0000.0000.000
14A14PRO00.0150.01715.802-0.010-0.0100.0000.0000.0000.000
15A15GLY0-0.0120.01212.0450.0080.0080.0000.0000.0000.000
16A16PRO00.021-0.0137.739-0.056-0.0560.0000.0000.0000.000
17A17THR00.0070.0117.497-0.039-0.0390.0000.0000.0000.000
18A18ALA0-0.0100.0096.8000.2440.2440.0000.0000.0000.000
19A19MET00.0150.0052.096-0.9180.1772.803-0.903-2.9940.001
20A20GLU-1-0.764-0.8603.3464.3835.5721.332-0.727-1.794-0.013
21A21VAL00.0120.0046.027-0.165-0.094-0.001-0.010-0.0590.000
22A22ARG10.8120.8912.702-0.030-0.7705.999-1.539-3.7190.001
23A23CYS0-0.022-0.0162.243-6.632-5.2874.991-2.177-4.159-0.015
24A24LEU00.0260.0193.0670.729-1.2060.0932.160-0.3180.000
25A25ILE00.009-0.0025.168-0.325-0.3250.0000.0000.0000.000
26A26MET0-0.031-0.0242.560-0.683-0.2181.162-0.279-1.3470.000
27A27CYS0-0.056-0.0244.5040.1820.236-0.001-0.007-0.0460.000
28A28LEU0-0.003-0.0046.852-0.055-0.0550.0000.0000.0000.000
29A29ALA0-0.0150.0037.639-0.047-0.0470.0000.0000.0000.000
30A30GLU-1-0.906-0.9509.3450.2870.2870.0000.0000.0000.000
31A31PRO0-0.034-0.0146.973-0.042-0.0420.0000.0000.0000.000
32A32GLY00.0840.05310.2500.0590.0590.0000.0000.0000.000
33A33LYS10.9390.94712.863-0.147-0.1470.0000.0000.0000.000
34A34ASN0-0.048-0.03814.810-0.043-0.0430.0000.0000.0000.000
35A35ASP-1-0.764-0.86113.9050.0990.0990.0000.0000.0000.000
36A36VAL0-0.044-0.03415.519-0.033-0.0330.0000.0000.0000.000
37A37ALA00.0170.01112.1830.0230.0230.0000.0000.0000.000
38A38VAL00.001-0.00214.218-0.028-0.0280.0000.0000.0000.000
39A39ASP-1-0.823-0.90810.939-0.058-0.0580.0000.0000.0000.000
40A40VAL00.0230.00613.428-0.028-0.0280.0000.0000.0000.000
41A41GLY00.0040.00215.9330.0450.0450.0000.0000.0000.000
42A42CYS0-0.0110.00012.7250.0440.0440.0000.0000.0000.000
43A43GLY00.0300.02112.659-0.005-0.0050.0000.0000.0000.000
44A44THR0-0.068-0.06811.018-0.055-0.0550.0000.0000.0000.000
45A45GLY00.0690.03411.164-0.124-0.1240.0000.0000.0000.000
46A46GLY0-0.064-0.0377.340-0.165-0.1650.0000.0000.0000.000
47A47VAL00.020-0.0025.944-0.057-0.0570.0000.0000.0000.000
48A48THR00.022-0.0136.767-0.273-0.2730.0000.0000.0000.000
49A49LEU0-0.042-0.0136.324-0.024-0.0240.0000.0000.0000.000
50A50GLU-1-0.795-0.8952.348-13.454-8.9526.097-4.448-6.151-0.062
51A51LEU00.0330.0084.6130.3480.435-0.001-0.006-0.0800.000
52A52ALA00.0310.0257.6440.1450.1450.0000.0000.0000.000
53A53GLY0-0.0030.0137.7680.0940.0940.0000.0000.0000.000
54A54ARG10.7690.8692.748-2.133-1.1540.437-0.345-1.0700.000
55A55VAL0-0.0020.0149.5420.0810.0810.0000.0000.0000.000
56A56ARG10.8480.93212.288-0.032-0.0320.0000.0000.0000.000
57A57ARG10.7980.89015.4530.1450.1450.0000.0000.0000.000
58A58VAL00.0190.02011.2310.0230.0230.0000.0000.0000.000
59A59TYR00.006-0.01014.382-0.011-0.0110.0000.0000.0000.000
60A60ALA00.0270.01813.7650.0240.0240.0000.0000.0000.000
61A61ILE0-0.001-0.00215.461-0.003-0.0030.0000.0000.0000.000
62A62ASP-1-0.802-0.92117.388-0.014-0.0140.0000.0000.0000.000
63A63ARG10.8100.87319.559-0.017-0.0170.0000.0000.0000.000
64A64ASN0-0.046-0.02120.884-0.012-0.0120.0000.0000.0000.000
65A65PRO00.0670.03021.251-0.016-0.0160.0000.0000.0000.000
66A66GLU-1-0.828-0.86521.377-0.157-0.1570.0000.0000.0000.000
67A67ALA0-0.0040.02017.340-0.035-0.0350.0000.0000.0000.000
68A68ILE00.0240.02416.775-0.047-0.0470.0000.0000.0000.000
69A69SER00.0200.00717.829-0.053-0.0530.0000.0000.0000.000
70A70THR0-0.052-0.04814.261-0.045-0.0450.0000.0000.0000.000
71A71THR0-0.005-0.00612.749-0.090-0.0900.0000.0000.0000.000
72A72GLU-1-0.867-0.92613.724-0.422-0.4220.0000.0000.0000.000
73A73MET0-0.036-0.01115.837-0.062-0.0620.0000.0000.0000.000
74A74ASN00.0200.00910.718-0.195-0.1950.0000.0000.0000.000
75A75LEU00.0060.01511.195-0.211-0.2110.0000.0000.0000.000
76A76GLN00.020-0.00412.645-0.080-0.0800.0000.0000.0000.000
77A77ARG10.7750.88312.5010.5660.5660.0000.0000.0000.000
78A78HIS10.7620.8538.4011.6601.6600.0000.0000.0000.000
79A79GLY0-0.0200.01310.723-0.026-0.0260.0000.0000.0000.000
80A80LEU0-0.014-0.0068.3490.0270.0270.0000.0000.0000.000
81A81GLY00.0740.01912.8710.0050.0050.0000.0000.0000.000
82A82ASP-1-0.886-0.92215.437-0.302-0.3020.0000.0000.0000.000
83A83ASN0-0.114-0.06512.4320.0020.0020.0000.0000.0000.000
84A84VAL00.011-0.00213.0610.0190.0190.0000.0000.0000.000
85A85THR0-0.0100.00215.8880.0180.0180.0000.0000.0000.000
86A86LEU0-0.0090.00715.5420.0030.0030.0000.0000.0000.000
87A87MET0-0.047-0.02618.8370.0140.0140.0000.0000.0000.000
88A88GLU-1-0.853-0.93721.164-0.101-0.1010.0000.0000.0000.000
89A89GLY0-0.010-0.01223.0150.0040.0040.0000.0000.0000.000
90A90ASP-1-0.837-0.91123.8850.0090.0090.0000.0000.0000.000
91A91ALA00.0580.02921.605-0.004-0.0040.0000.0000.0000.000
92A92PRO00.0520.01623.151-0.002-0.0020.0000.0000.0000.000
93A93GLU-1-0.828-0.89525.638-0.026-0.0260.0000.0000.0000.000
94A94ALA0-0.025-0.02122.675-0.005-0.0050.0000.0000.0000.000
95A95LEU00.003-0.00119.624-0.005-0.0050.0000.0000.0000.000
96A96CYS0-0.053-0.01823.2330.0030.0030.0000.0000.0000.000
97A97LYS10.7940.88125.4480.0360.0360.0000.0000.0000.000
98A98ILE0-0.0250.00719.582-0.009-0.0090.0000.0000.0000.000
99A99PRO0-0.011-0.00221.9160.0090.0090.0000.0000.0000.000
100A100ASP-1-0.827-0.90122.4710.0260.0260.0000.0000.0000.000
101A101ILE0-0.068-0.03417.680-0.012-0.0120.0000.0000.0000.000
102A102ASP-1-0.825-0.89016.1810.0550.0550.0000.0000.0000.000
103A103ILE0-0.0100.00310.6220.0170.0170.0000.0000.0000.000
104A104ALA00.0280.01013.998-0.035-0.0350.0000.0000.0000.000
105A105VAL0-0.018-0.0059.0480.0470.0470.0000.0000.0000.000
106A106VAL00.0320.02312.372-0.044-0.0440.0000.0000.0000.000
107A107GLY00.0140.00213.7100.0770.0770.0000.0000.0000.000
108A108GLY0-0.0200.00814.488-0.001-0.0010.0000.0000.0000.000
109A109SER0-0.021-0.02817.655-0.029-0.0290.0000.0000.0000.000
110A110GLY00.0490.01619.802-0.008-0.0080.0000.0000.0000.000
111A111GLY0-0.032-0.00123.021-0.008-0.0080.0000.0000.0000.000
112A112GLU-1-0.833-0.89423.9920.0270.0270.0000.0000.0000.000
113A113LEU0-0.017-0.00819.180-0.001-0.0010.0000.0000.0000.000
114A114GLN00.0750.03822.789-0.007-0.0070.0000.0000.0000.000
115A115GLU-1-0.873-0.92025.6550.0480.0480.0000.0000.0000.000
116A116ILE0-0.030-0.02219.721-0.003-0.0030.0000.0000.0000.000
117A117LEU0-0.002-0.01318.9060.0000.0000.0000.0000.0000.000
118A118ARG10.8500.92022.254-0.064-0.0640.0000.0000.0000.000
119A119ILE00.0300.01524.301-0.001-0.0010.0000.0000.0000.000
120A120ILE0-0.027-0.01817.821-0.004-0.0040.0000.0000.0000.000
121A121LYS10.8920.94121.550-0.090-0.0900.0000.0000.0000.000
122A122ASP-1-0.964-0.98823.3190.0620.0620.0000.0000.0000.000
123A123LYS10.7960.89622.979-0.015-0.0150.0000.0000.0000.000
124A124LEU0-0.059-0.00417.665-0.006-0.0060.0000.0000.0000.000
125A125LYS10.7900.87620.104-0.025-0.0250.0000.0000.0000.000
126A126PRO00.008-0.02121.3910.0120.0120.0000.0000.0000.000
127A127GLY0-0.0040.01020.310-0.002-0.0020.0000.0000.0000.000
128A128GLY00.0060.01317.3070.0110.0110.0000.0000.0000.000
129A129ARG10.7630.87512.828-0.160-0.1600.0000.0000.0000.000
130A130ILE00.0260.01214.844-0.026-0.0260.0000.0000.0000.000
131A131ILE0-0.020-0.0129.2670.0430.0430.0000.0000.0000.000
132A132VAL0-0.002-0.00113.102-0.033-0.0330.0000.0000.0000.000
133A133THR0-0.027-0.01611.1040.1010.1010.0000.0000.0000.000
134A134ALA00.003-0.00513.112-0.067-0.0670.0000.0000.0000.000
135A135ILE0-0.023-0.01514.1610.0440.0440.0000.0000.0000.000
136A136LEU00.0160.00417.930-0.008-0.0080.0000.0000.0000.000
137A137LEU00.0220.01321.1700.0190.0190.0000.0000.0000.000
138A138GLU-1-0.838-0.93423.3460.1500.1500.0000.0000.0000.000
139A139THR00.011-0.00418.858-0.010-0.0100.0000.0000.0000.000
140A140LYS10.7650.86917.719-0.341-0.3410.0000.0000.0000.000
141A141PHE0-0.040-0.00320.6280.0090.0090.0000.0000.0000.000
142A142GLU-1-0.762-0.89723.3030.1130.1130.0000.0000.0000.000
143A143ALA0-0.014-0.01018.918-0.006-0.0060.0000.0000.0000.000
144A144MET0-0.031-0.01420.6590.0040.0040.0000.0000.0000.000
145A145GLU-1-0.897-0.92622.5740.1150.1150.0000.0000.0000.000
146A146CYS00.013-0.00523.922-0.010-0.0100.0000.0000.0000.000
147A147LEU0-0.020-0.01418.238-0.007-0.0070.0000.0000.0000.000
148A148ARG10.8790.93422.868-0.177-0.1770.0000.0000.0000.000
149A149ASP-1-0.902-0.94525.5660.1060.1060.0000.0000.0000.000
150A150LEU0-0.085-0.03423.968-0.010-0.0100.0000.0000.0000.000
151A151GLY0-0.038-0.01326.699-0.006-0.0060.0000.0000.0000.000
152A152PHE0-0.039-0.01721.5970.0000.0000.0000.0000.0000.000
153A153ASP-1-0.905-0.94522.1870.1750.1750.0000.0000.0000.000
154A154VAL0-0.052-0.03319.7940.0130.0130.0000.0000.0000.000
155A155ASN0-0.066-0.02416.759-0.005-0.0050.0000.0000.0000.000
156A156ILE00.0500.00616.6470.0030.0030.0000.0000.0000.000
157A157THR0-0.063-0.03013.1260.0160.0160.0000.0000.0000.000
158A158GLU-1-0.802-0.87614.1140.4410.4410.0000.0000.0000.000
159A159LEU0-0.022-0.0109.5920.0410.0410.0000.0000.0000.000
160A160ASN0-0.016-0.00913.639-0.056-0.0560.0000.0000.0000.000
161A161ILE00.0220.0169.8130.0220.0220.0000.0000.0000.000
162A162ALA00.006-0.00613.643-0.094-0.0940.0000.0000.0000.000
163A163ARG10.7290.8237.674-0.429-0.4290.0000.0000.0000.000
164A164GLY00.0590.01414.380-0.022-0.0220.0000.0000.0000.000
165A165ARG10.9310.97216.478-0.005-0.0050.0000.0000.0000.000
166A166ALA00.0340.01218.4020.0240.0240.0000.0000.0000.000
167A167LEU0-0.037-0.03220.539-0.016-0.0160.0000.0000.0000.000
168A168ASP-1-0.895-0.94124.053-0.069-0.0690.0000.0000.0000.000
169A169ARG10.9430.97127.2140.0210.0210.0000.0000.0000.000
170A170GLY00.0350.02825.3640.0120.0120.0000.0000.0000.000
171A171THR0-0.051-0.03119.098-0.014-0.0140.0000.0000.0000.000
172A172MET0-0.0170.00821.6470.0170.0170.0000.0000.0000.000
173A173MET00.0040.00616.148-0.027-0.0270.0000.0000.0000.000
174A174VAL0-0.055-0.02917.075-0.015-0.0150.0000.0000.0000.000
175A175SER00.0280.00216.0520.0220.0220.0000.0000.0000.000
176A176ARG10.8620.9429.904-0.293-0.2930.0000.0000.0000.000
177A177ASN00.017-0.00115.136-0.005-0.0050.0000.0000.0000.000
178A178PRO00.0150.00715.0370.0690.0690.0000.0000.0000.000
179A179VAL00.0010.01911.602-0.049-0.0490.0000.0000.0000.000
180A180ALA00.0200.02313.7250.0680.0680.0000.0000.0000.000
181A181LEU0-0.023-0.0078.4380.0210.0210.0000.0000.0000.000
182A182ILE00.006-0.01013.020-0.018-0.0180.0000.0000.0000.000
183A183TYR0-0.009-0.01713.258-0.010-0.0100.0000.0000.0000.000
184A184THR00.0440.03115.390-0.005-0.0050.0000.0000.0000.000
185A185GLY0-0.0020.00516.5910.0260.0260.0000.0000.0000.000
186A186VAL0-0.0190.00115.392-0.018-0.0180.0000.0000.0000.000