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: 148YZ

Calculation Name: 1LRV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1LRV

Chain ID: A

ChEMBL ID:

UniProt ID: Q44534

Base Structure: X-ray

Registration Date: 2023-06-19

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 233
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2613518.689879
FMO2-HF: Nuclear repulsion 2519024.733593
FMO2-HF: Total energy -94493.956286
FMO2-MP2: Total energy -94769.345079


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:9:THR)


Summations of interaction energy for fragment #1(A:9:THR)
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.
-4.993-1.0770.118-1.905-2.1280.001
Interaction energy analysis for fragmet #1(A:9:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.014
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].
3A11ILE00.0340.0163.153-1.0191.9610.105-1.597-1.4880.000
4A12GLY00.0260.0064.9760.2260.248-0.001-0.002-0.0190.000
5A13ASP-1-0.820-0.9308.548-0.615-0.6150.0000.0000.0000.000
6A14CYS0-0.045-0.03410.7980.1350.1350.0000.0000.0000.000
7A15ARG10.9200.96813.3850.4600.4600.0000.0000.0000.000
8A16VAL00.0500.02016.0320.0490.0490.0000.0000.0000.000
9A17CYS0-0.0320.03014.0710.0660.0660.0000.0000.0000.000
10A18SER00.0580.01816.613-0.017-0.0170.0000.0000.0000.000
11A19PHE00.018-0.01815.9580.0030.0030.0000.0000.0000.000
12A20ARG10.9060.96216.6500.3020.3020.0000.0000.0000.000
13A21MET00.002-0.01817.518-0.008-0.0080.0000.0000.0000.000
14A22SER00.0190.01619.8700.0080.0080.0000.0000.0000.000
15A23LEU00.0200.01116.5890.0010.0010.0000.0000.0000.000
16A24LEU00.0420.00912.934-0.008-0.0080.0000.0000.0000.000
17A25LEU0-0.066-0.01916.114-0.021-0.0210.0000.0000.0000.000
18A26THR0-0.032-0.02718.4870.0180.0180.0000.0000.0000.000
19A27GLY0-0.0100.00715.8630.0210.0210.0000.0000.0000.000
20A28ARG10.9400.98415.8180.0880.0880.0000.0000.0000.000
21A29CYS0-0.034-0.00212.7940.0310.0310.0000.0000.0000.000
22A30THR0-0.011-0.0159.941-0.036-0.0360.0000.0000.0000.000
23A31PRO00.0300.0127.7410.0440.0440.0000.0000.0000.000
24A32GLY00.0190.0183.641-0.413-0.2810.004-0.040-0.0950.000
25A33ASP-1-0.904-0.9634.472-0.548-0.413-0.001-0.010-0.1240.000
26A34ALA00.0380.0217.2070.3540.3540.0000.0000.0000.000
27A35CYS0-0.061-0.0308.103-0.136-0.1360.0000.0000.0000.000
28A36VAL00.0960.04810.1030.1970.1970.0000.0000.0000.000
29A37ALA0-0.057-0.04411.4400.0620.0620.0000.0000.0000.000
30A38VAL00.0320.0105.739-0.141-0.1410.0000.0000.0000.000
31A39GLU-1-0.936-0.9508.8600.6360.6360.0000.0000.0000.000
32A40SER0-0.004-0.0044.8150.0830.0830.0000.0000.0000.000
33A41GLY00.1370.0647.229-0.374-0.3740.0000.0000.0000.000
34A42ARG10.9350.9724.834-1.979-1.9790.0000.0000.0000.000
35A43GLN0-0.017-0.0103.560-2.627-1.9800.011-0.256-0.4020.001
36A44ILE00.0100.0067.646-0.350-0.3500.0000.0000.0000.000
37A45ASP-1-0.867-0.93410.7290.3130.3130.0000.0000.0000.000
38A46ARG10.8470.9215.230-0.002-0.0020.0000.0000.0000.000
39A47PHE0-0.026-0.00611.698-0.117-0.1170.0000.0000.0000.000
40A48PHE00.011-0.00713.429-0.069-0.0690.0000.0000.0000.000
41A49ARG10.8740.95413.972-0.359-0.3590.0000.0000.0000.000
42A50ASN0-0.008-0.00614.462-0.012-0.0120.0000.0000.0000.000
43A51ASN0-0.065-0.01816.893-0.049-0.0490.0000.0000.0000.000
44A52PRO00.0590.02419.6300.0100.0100.0000.0000.0000.000
45A53HIS00.004-0.01321.0850.0100.0100.0000.0000.0000.000
46A54LEU00.0300.01819.223-0.007-0.0070.0000.0000.0000.000
47A55ALA00.0060.01320.1090.0050.0050.0000.0000.0000.000
48A56VAL00.0260.02021.0370.0100.0100.0000.0000.0000.000
49A57GLN0-0.052-0.03422.826-0.004-0.0040.0000.0000.0000.000
50A58TYR0-0.049-0.03917.884-0.009-0.0090.0000.0000.0000.000
51A59LEU00.0120.00821.0270.0250.0250.0000.0000.0000.000
52A60ALA00.0020.01023.4790.0050.0050.0000.0000.0000.000
53A61ASP-1-0.842-0.92117.9310.2130.2130.0000.0000.0000.000
54A62PRO00.0420.02519.3310.0220.0220.0000.0000.0000.000
55A63PHE0-0.0120.00311.7010.0050.0050.0000.0000.0000.000
56A64TRP00.1260.05614.6090.0160.0160.0000.0000.0000.000
57A65GLU-1-0.879-0.93611.8311.1051.1050.0000.0000.0000.000
58A66ARG10.8360.91812.303-0.348-0.3480.0000.0000.0000.000
59A67ARG10.7980.88915.276-0.293-0.2930.0000.0000.0000.000
60A68ALA00.026-0.00217.179-0.031-0.0310.0000.0000.0000.000
61A69ILE0-0.116-0.05013.110-0.030-0.0300.0000.0000.0000.000
62A70ALA00.0320.01616.672-0.042-0.0420.0000.0000.0000.000
63A71VAL00.0300.04019.208-0.039-0.0390.0000.0000.0000.000
64A72ARG10.8780.95315.158-0.503-0.5030.0000.0000.0000.000
65A73TYR0-0.057-0.05915.773-0.042-0.0420.0000.0000.0000.000
66A74SER0-0.021-0.00521.658-0.026-0.0260.0000.0000.0000.000
67A75PRO00.0100.02124.4550.0070.0070.0000.0000.0000.000
68A76VAL00.0550.00228.0360.0050.0050.0000.0000.0000.000
69A77GLU-1-0.842-0.91729.3500.1030.1030.0000.0000.0000.000
70A78ALA0-0.077-0.03728.103-0.002-0.0020.0000.0000.0000.000
71A79LEU00.0230.00925.2360.0060.0060.0000.0000.0000.000
72A80THR00.0280.02628.8780.0070.0070.0000.0000.0000.000
73A81PRO0-0.047-0.03929.8640.0020.0020.0000.0000.0000.000
74A82LEU00.008-0.00524.8880.0000.0000.0000.0000.0000.000
75A83ILE0-0.0440.00528.2880.0110.0110.0000.0000.0000.000
76A84ARG10.8880.93930.757-0.116-0.1160.0000.0000.0000.000
77A85ASP-1-0.762-0.87824.4480.2330.2330.0000.0000.0000.000
78A86SER0-0.003-0.00925.3920.0070.0070.0000.0000.0000.000
79A87ASP-1-0.850-0.92120.7730.4000.4000.0000.0000.0000.000
80A88GLU-1-0.865-0.94822.6250.3320.3320.0000.0000.0000.000
81A89VAL0-0.0230.00018.040-0.002-0.0020.0000.0000.0000.000
82A90VAL0-0.046-0.01920.5950.0040.0040.0000.0000.0000.000
83A91ARG10.8650.91822.239-0.235-0.2350.0000.0000.0000.000
84A92ARG10.8540.91721.569-0.382-0.3820.0000.0000.0000.000
85A93ALA0-0.038-0.01220.939-0.010-0.0100.0000.0000.0000.000
86A94VAL00.005-0.01022.847-0.021-0.0210.0000.0000.0000.000
87A95ALA00.0160.02626.089-0.020-0.0200.0000.0000.0000.000
88A96TYR0-0.032-0.02323.083-0.011-0.0110.0000.0000.0000.000
89A97ARG10.8090.87023.663-0.199-0.1990.0000.0000.0000.000
90A98LEU00.0130.03028.022-0.012-0.0120.0000.0000.0000.000
91A99PRO00.0410.03731.0540.0020.0020.0000.0000.0000.000
92A100ARG10.9760.96634.129-0.116-0.1160.0000.0000.0000.000
93A101GLU-1-0.787-0.90035.7660.0940.0940.0000.0000.0000.000
94A102GLN0-0.012-0.01135.0170.0050.0050.0000.0000.0000.000
95A103LEU0-0.104-0.03731.8950.0050.0050.0000.0000.0000.000
96A104SER0-0.068-0.08635.3360.0050.0050.0000.0000.0000.000
97A105ALA0-0.078-0.03335.3500.0000.0000.0000.0000.0000.000
98A106LEU0-0.004-0.00930.5630.0010.0010.0000.0000.0000.000
99A107MET0-0.039-0.00433.9290.0060.0060.0000.0000.0000.000
100A108PHE0-0.010-0.00636.3890.0000.0000.0000.0000.0000.000
101A109ASP-1-0.776-0.87330.3120.2010.2010.0000.0000.0000.000
102A110GLU-1-0.960-0.97630.2510.1850.1850.0000.0000.0000.000
103A111ASP-1-0.783-0.89026.5990.2950.2950.0000.0000.0000.000
104A112ARG10.9110.95029.095-0.243-0.2430.0000.0000.0000.000
105A113GLU-1-0.896-0.95624.9020.2900.2900.0000.0000.0000.000
106A114VAL00.0020.01926.916-0.004-0.0040.0000.0000.0000.000
107A115ARG10.7760.87128.686-0.182-0.1820.0000.0000.0000.000
108A116ILE0-0.011-0.00329.230-0.012-0.0120.0000.0000.0000.000
109A117THR0-0.021-0.00927.344-0.004-0.0040.0000.0000.0000.000
110A118VAL00.015-0.00629.891-0.012-0.0120.0000.0000.0000.000
111A119ALA00.0030.01332.872-0.012-0.0120.0000.0000.0000.000
112A120ASP-1-0.978-0.97231.4070.1650.1650.0000.0000.0000.000
113A121ARG10.7900.89630.299-0.176-0.1760.0000.0000.0000.000
114A122LEU0-0.056-0.03134.314-0.010-0.0100.0000.0000.0000.000
115A123PRO00.0100.01237.6520.0010.0010.0000.0000.0000.000
116A124LEU00.028-0.00240.869-0.001-0.0010.0000.0000.0000.000
117A125GLU-1-0.860-0.90642.9840.0850.0850.0000.0000.0000.000
118A126GLN00.1010.08041.1680.0050.0050.0000.0000.0000.000
119A127LEU00.0150.01939.0570.0020.0020.0000.0000.0000.000
120A128GLU-1-0.859-0.92641.5030.0920.0920.0000.0000.0000.000
121A129GLN0-0.044-0.01342.793-0.001-0.0010.0000.0000.0000.000
122A130MET0-0.043-0.02035.6730.0010.0010.0000.0000.0000.000
123A131ALA0-0.049-0.02840.9910.0050.0050.0000.0000.0000.000
124A132ALA0-0.0090.00243.300-0.001-0.0010.0000.0000.0000.000
125A133ASP-1-0.741-0.85337.1960.1540.1540.0000.0000.0000.000
126A134ARG11.0071.00035.751-0.160-0.1600.0000.0000.0000.000
127A135ASP-1-0.971-0.98733.9940.1920.1920.0000.0000.0000.000
128A136TYR00.1180.04233.1830.0010.0010.0000.0000.0000.000
129A137LEU00.0050.01230.579-0.004-0.0040.0000.0000.0000.000
130A138VAL0-0.0110.00633.945-0.002-0.0020.0000.0000.0000.000
131A139ARG10.8040.87135.827-0.132-0.1320.0000.0000.0000.000
132A140ALA0-0.0100.00036.284-0.007-0.0070.0000.0000.0000.000
133A141TYR00.003-0.00330.219-0.003-0.0030.0000.0000.0000.000
134A142VAL00.0110.00136.648-0.006-0.0060.0000.0000.0000.000
135A143VAL0-0.024-0.00840.007-0.006-0.0060.0000.0000.0000.000
136A144GLN0-0.038-0.00736.743-0.013-0.0130.0000.0000.0000.000
137A145ARG10.8230.87736.791-0.133-0.1330.0000.0000.0000.000
138A146ILE0-0.0190.01441.093-0.006-0.0060.0000.0000.0000.000
139A147PRO00.0160.00244.5120.0010.0010.0000.0000.0000.000
140A148PRO00.0770.01147.5440.0000.0000.0000.0000.0000.000
141A149GLY00.0480.02449.2020.0000.0000.0000.0000.0000.000
142A150ARG10.8500.90548.480-0.081-0.0810.0000.0000.0000.000
143A151LEU00.0240.02445.3130.0010.0010.0000.0000.0000.000
144A152PHE00.0310.02948.9380.0020.0020.0000.0000.0000.000
145A153ARG10.8930.95447.666-0.088-0.0880.0000.0000.0000.000
146A154PHE0-0.009-0.01344.2750.0010.0010.0000.0000.0000.000
147A155MET00.0070.00447.5130.0030.0030.0000.0000.0000.000
148A156ARG10.9070.96449.957-0.076-0.0760.0000.0000.0000.000
149A157ASP-1-0.776-0.87243.4390.1180.1180.0000.0000.0000.000
150A158GLU-1-0.859-0.92443.0030.1160.1160.0000.0000.0000.000
151A159ASP-1-0.838-0.91939.6300.1490.1490.0000.0000.0000.000
152A160ARG10.9400.96340.548-0.133-0.1330.0000.0000.0000.000
153A161GLN00.0110.02536.621-0.004-0.0040.0000.0000.0000.000
154A162VAL00.0250.01139.721-0.002-0.0020.0000.0000.0000.000
155A163ARG10.7620.84241.314-0.107-0.1070.0000.0000.0000.000
156A164LYS10.8200.90938.511-0.146-0.1460.0000.0000.0000.000
157A165LEU0-0.037-0.01737.845-0.003-0.0030.0000.0000.0000.000
158A166VAL0-0.010-0.00642.317-0.004-0.0040.0000.0000.0000.000
159A167ALA00.0380.01645.704-0.004-0.0040.0000.0000.0000.000
160A168LYS10.9280.97639.972-0.127-0.1270.0000.0000.0000.000
161A169ARG10.8420.89942.314-0.107-0.1070.0000.0000.0000.000
162A170LEU0-0.0330.00146.659-0.003-0.0030.0000.0000.0000.000
163A171PRO0-0.003-0.01150.0070.0000.0000.0000.0000.0000.000
164A172GLU-1-0.882-0.94352.8430.0660.0660.0000.0000.0000.000
165A173GLU-1-0.855-0.92654.4430.0630.0630.0000.0000.0000.000
166A174SER0-0.056-0.03655.183-0.001-0.0010.0000.0000.0000.000
167A175LEU00.013-0.00350.6160.0010.0010.0000.0000.0000.000
168A176GLY00.0530.04054.5580.0020.0020.0000.0000.0000.000
169A177LEU0-0.040-0.02255.1750.0000.0000.0000.0000.0000.000
170A178MET0-0.109-0.08349.0410.0020.0020.0000.0000.0000.000
171A179THR0-0.0140.01953.0330.0030.0030.0000.0000.0000.000
172A180GLN00.0400.02755.2180.0010.0010.0000.0000.0000.000
173A181ASP-1-0.837-0.87549.0210.0970.0970.0000.0000.0000.000
174A182PRO00.018-0.00549.6850.0000.0000.0000.0000.0000.000
175A183GLU-1-0.904-0.95944.8200.1150.1150.0000.0000.0000.000
176A184PRO00.0540.01647.011-0.001-0.0010.0000.0000.0000.000
177A185GLU-1-0.893-0.95640.9890.1320.1320.0000.0000.0000.000
178A186VAL0-0.014-0.00545.4740.0010.0010.0000.0000.0000.000
179A187ARG10.7930.88247.084-0.084-0.0840.0000.0000.0000.000
180A188ARG10.9320.97743.494-0.108-0.1080.0000.0000.0000.000
181A189ILE0-0.056-0.01744.3260.0000.0000.0000.0000.0000.000
182A190VAL00.012-0.00247.368-0.002-0.0020.0000.0000.0000.000
183A191ALA00.0220.00150.747-0.003-0.0030.0000.0000.0000.000
184A192SER0-0.093-0.02948.280-0.001-0.0010.0000.0000.0000.000
185A193ARG10.7930.86747.775-0.085-0.0850.0000.0000.0000.000
186A194LEU00.0480.03651.593-0.002-0.0020.0000.0000.0000.000
187A195ARG10.9100.95852.342-0.069-0.0690.0000.0000.0000.000
188A196GLY0-0.006-0.00757.905-0.001-0.0010.0000.0000.0000.000
189A197ASP-1-0.890-0.97061.4700.0500.0500.0000.0000.0000.000
190A198ASP-1-0.936-0.95058.9950.0590.0590.0000.0000.0000.000
191A199LEU0-0.044-0.02555.4520.0020.0020.0000.0000.0000.000
192A200LEU00.0090.00459.0510.0010.0010.0000.0000.0000.000
193A201GLU-1-0.883-0.93259.8200.0620.0620.0000.0000.0000.000
194A202LEU00.0280.00554.7890.0010.0010.0000.0000.0000.000
195A203LEU0-0.037-0.00457.3320.0010.0010.0000.0000.0000.000
196A204HIS10.8540.92859.228-0.056-0.0560.0000.0000.0000.000
197A205ASP-1-0.753-0.85754.3610.0770.0770.0000.0000.0000.000
198A206PRO0-0.021-0.01455.2090.0000.0000.0000.0000.0000.000
199A207ASP-1-0.866-0.89449.9930.0910.0910.0000.0000.0000.000
200A208TRP00.0620.00948.352-0.001-0.0010.0000.0000.0000.000
201A209THR0-0.015-0.01047.2250.0010.0010.0000.0000.0000.000
202A210VAL0-0.037-0.02350.0080.0010.0010.0000.0000.0000.000
203A211ARG10.8530.91951.533-0.070-0.0700.0000.0000.0000.000
204A212LEU0-0.007-0.00549.566-0.002-0.0020.0000.0000.0000.000
205A213ALA00.0050.00149.740-0.001-0.0010.0000.0000.0000.000
206A214ALA0-0.030-0.02151.535-0.002-0.0020.0000.0000.0000.000
207A215VAL0-0.042-0.04055.054-0.002-0.0020.0000.0000.0000.000
208A216GLU-1-0.939-0.95650.9720.0740.0740.0000.0000.0000.000
209A217HIS0-0.081-0.03751.252-0.003-0.0030.0000.0000.0000.000
210A218ALA00.0020.02456.426-0.002-0.0020.0000.0000.0000.000
211A219SER00.0400.01759.579-0.001-0.0010.0000.0000.0000.000
212A220LEU00.014-0.02062.5310.0000.0000.0000.0000.0000.000
213A221GLU-1-0.848-0.94864.5220.0430.0430.0000.0000.0000.000
214A222ALA00.0430.04263.294-0.001-0.0010.0000.0000.0000.000
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