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: 8J1KY

Calculation Name: 1LRV-A-Xray315

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 235
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2620937.891573
FMO2-HF: Nuclear repulsion 2526273.068394
FMO2-HF: Total energy -94664.82318
FMO2-MP2: Total energy -94940.726975


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:8:ACE )


Summations of interaction energy for fragment #1(A:8:ACE )
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.
2.1132.947-0.005-0.389-0.440
Interaction energy analysis for fragmet #1(A:8:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.033 / q_NPA : 0.007
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].
3A10PRO 00.0330.0313.8450.9331.767-0.005-0.389-0.4400.000
4A11ILE 00.0360.0197.1520.0110.0110.0000.0000.0000.000
5A12GLY 00.0260.0069.7380.0610.0610.0000.0000.0000.000
6A13ASP -1-0.822-0.93113.292-0.073-0.0730.0000.0000.0000.000
7A14CYS 0-0.042-0.03315.8340.0130.0130.0000.0000.0000.000
8A15ARG 10.9170.96818.3140.0560.0560.0000.0000.0000.000
9A16VAL 00.0510.02020.3090.0120.0120.0000.0000.0000.000
10A17CYS 0-0.0350.02919.6510.0040.0040.0000.0000.0000.000
11A18SER 00.0610.01921.7700.0040.0040.0000.0000.0000.000
12A19PHE 00.018-0.01921.6830.0060.0060.0000.0000.0000.000
13A20ARG 10.9050.96222.0410.0780.0780.0000.0000.0000.000
14A21MET 00.004-0.01622.9470.0060.0060.0000.0000.0000.000
15A22SER 00.0160.01525.5430.0020.0020.0000.0000.0000.000
16A23LEU 00.0220.01122.5250.0020.0020.0000.0000.0000.000
17A24LEU 00.0450.01018.283-0.004-0.0040.0000.0000.0000.000
18A25LEU 0-0.067-0.01821.7470.0020.0020.0000.0000.0000.000
19A26THR 0-0.033-0.02824.0860.0120.0120.0000.0000.0000.000
20A27GLY 0-0.0110.00621.3190.0020.0020.0000.0000.0000.000
21A28ARG 10.9380.98321.4540.0930.0930.0000.0000.0000.000
22A29CYS 0-0.037-0.00318.756-0.010-0.0100.0000.0000.0000.000
23A30THR 0-0.004-0.01415.1610.0290.0290.0000.0000.0000.000
24A31PRO 00.0240.01013.004-0.057-0.0570.0000.0000.0000.000
25A32GLY 00.0200.0199.5480.0160.0160.0000.0000.0000.000
26A33ASP -1-0.900-0.96110.169-0.442-0.4420.0000.0000.0000.000
27A34ALA 00.0380.02112.906-0.026-0.0260.0000.0000.0000.000
28A35CYS 0-0.055-0.02913.9520.0630.0630.0000.0000.0000.000
29A36VAL 00.0830.04415.563-0.036-0.0360.0000.0000.0000.000
30A37ALA 0-0.056-0.04416.6840.0000.0000.0000.0000.0000.000
31A38VAL 00.0350.01110.2840.0080.0080.0000.0000.0000.000
32A39GLU -1-0.934-0.95012.260-0.322-0.3220.0000.0000.0000.000
33A40SER 0-0.006-0.0069.777-0.045-0.0450.0000.0000.0000.000
34A41GLY 00.1380.06511.8480.0560.0560.0000.0000.0000.000
35A42ARG 10.9370.9739.7770.7100.7100.0000.0000.0000.000
36A43GLN 0-0.016-0.0098.9610.2430.2430.0000.0000.0000.000
37A44ILE 00.0050.00413.5280.0820.0820.0000.0000.0000.000
38A45ASP -1-0.859-0.93216.376-0.210-0.2100.0000.0000.0000.000
39A46ARG 10.8460.92111.0920.5690.5690.0000.0000.0000.000
40A47PHE 0-0.025-0.00617.6590.0390.0390.0000.0000.0000.000
41A48PHE 00.003-0.00919.3330.0300.0300.0000.0000.0000.000
42A49ARG 10.8800.95719.9940.2260.2260.0000.0000.0000.000
43A50ASN 0-0.008-0.00520.2070.0300.0300.0000.0000.0000.000
44A51ASN 0-0.063-0.01922.7910.0330.0330.0000.0000.0000.000
45A52PRO 00.0550.02325.545-0.001-0.0010.0000.0000.0000.000
46A53HIS 00.007-0.01127.022-0.004-0.0040.0000.0000.0000.000
47A54LEU 00.0290.01624.9740.0050.0050.0000.0000.0000.000
48A55ALA 00.0060.01325.542-0.002-0.0020.0000.0000.0000.000
49A56VAL 00.0260.02126.5290.0000.0000.0000.0000.0000.000
50A57GLN 0-0.051-0.03328.0400.0070.0070.0000.0000.0000.000
51A58TYR 0-0.048-0.03922.703-0.005-0.0050.0000.0000.0000.000
52A59LEU 00.0070.00725.736-0.006-0.0060.0000.0000.0000.000
53A60ALA 00.0050.01128.1550.0040.0040.0000.0000.0000.000
54A61ASP -1-0.842-0.92121.941-0.177-0.1770.0000.0000.0000.000
55A62PRO 00.0440.02622.7080.0000.0000.0000.0000.0000.000
56A63PHE 0-0.0140.00215.1260.0000.0000.0000.0000.0000.000
57A64TRP 00.1250.05617.463-0.008-0.0080.0000.0000.0000.000
58A65GLU -1-0.878-0.93715.641-0.356-0.3560.0000.0000.0000.000
59A66ARG 10.8350.91916.5450.2570.2570.0000.0000.0000.000
60A67ARG 10.8000.89019.8810.1420.1420.0000.0000.0000.000
61A68ALA 00.026-0.00221.4820.0110.0110.0000.0000.0000.000
62A69ILE 0-0.115-0.05017.8340.0090.0090.0000.0000.0000.000
63A70ALA 00.0310.01521.7390.0110.0110.0000.0000.0000.000
64A71VAL 00.0300.04024.4560.0130.0130.0000.0000.0000.000
65A72ARG 10.8800.95520.3520.2190.2190.0000.0000.0000.000
66A73TYR 0-0.060-0.06021.5480.0120.0120.0000.0000.0000.000
67A74SER 0-0.023-0.00827.3690.0080.0080.0000.0000.0000.000
68A75PRO 00.0100.02130.0180.0010.0010.0000.0000.0000.000
69A76VAL 00.0550.00333.637-0.002-0.0020.0000.0000.0000.000
70A77GLU -1-0.842-0.91734.760-0.073-0.0730.0000.0000.0000.000
71A78ALA 0-0.074-0.03633.3740.0020.0020.0000.0000.0000.000
72A79LEU 00.0250.00930.373-0.003-0.0030.0000.0000.0000.000
73A80THR 00.0270.02533.8160.0000.0000.0000.0000.0000.000
74A81PRO 0-0.049-0.03934.4490.0020.0020.0000.0000.0000.000
75A82LEU 00.010-0.00429.3210.0000.0000.0000.0000.0000.000
76A83ILE 0-0.0460.00432.439-0.002-0.0020.0000.0000.0000.000
77A84ARG 10.8890.93934.8340.0640.0640.0000.0000.0000.000
78A85ASP -1-0.763-0.87928.035-0.113-0.1130.0000.0000.0000.000
79A86SER 0-0.002-0.00828.5330.0000.0000.0000.0000.0000.000
80A87ASP -1-0.850-0.92223.742-0.146-0.1460.0000.0000.0000.000
81A88GLU -1-0.866-0.94925.135-0.114-0.1140.0000.0000.0000.000
82A89VAL 0-0.0230.00021.5400.0010.0010.0000.0000.0000.000
83A90VAL 0-0.044-0.01824.632-0.005-0.0050.0000.0000.0000.000
84A91ARG 10.8650.91926.2620.0880.0880.0000.0000.0000.000
85A92ARG 10.8570.91824.0270.1220.1220.0000.0000.0000.000
86A93ALA 0-0.041-0.01325.3520.0020.0020.0000.0000.0000.000
87A94VAL 00.010-0.00927.3050.0050.0050.0000.0000.0000.000
88A95ALA 00.0160.02730.6760.0060.0060.0000.0000.0000.000
89A96TYR 0-0.035-0.02427.1160.0040.0040.0000.0000.0000.000
90A97ARG 10.8070.86928.9700.1110.1110.0000.0000.0000.000
91A98LEU 00.0110.02833.0950.0030.0030.0000.0000.0000.000
92A99PRO 00.0430.03735.9780.0010.0010.0000.0000.0000.000
93A100ARG 10.9770.96539.2300.0570.0570.0000.0000.0000.000
94A101GLU -1-0.784-0.89840.623-0.052-0.0520.0000.0000.0000.000
95A102GLN 0-0.014-0.01139.768-0.002-0.0020.0000.0000.0000.000
96A103LEU 0-0.103-0.03836.346-0.002-0.0020.0000.0000.0000.000
97A104SER 0-0.074-0.08739.696-0.001-0.0010.0000.0000.0000.000
98A105ALA 0-0.077-0.03239.5400.0010.0010.0000.0000.0000.000
99A106LEU 0-0.001-0.00934.5010.0000.0000.0000.0000.0000.000
100A107MET 0-0.040-0.00437.5350.0000.0000.0000.0000.0000.000
101A108PHE 0-0.010-0.00639.9780.0020.0020.0000.0000.0000.000
102A109ASP -1-0.776-0.87433.413-0.075-0.0750.0000.0000.0000.000
103A110GLU -1-0.960-0.97632.873-0.064-0.0640.0000.0000.0000.000
104A111ASP -1-0.783-0.89129.138-0.094-0.0940.0000.0000.0000.000
105A112ARG 10.9110.95030.9000.0670.0670.0000.0000.0000.000
106A113GLU -1-0.896-0.95627.310-0.087-0.0870.0000.0000.0000.000
107A114VAL 00.0010.01930.200-0.001-0.0010.0000.0000.0000.000
108A115ARG 10.7800.87232.0270.0580.0580.0000.0000.0000.000
109A116ILE 0-0.016-0.00531.7060.0030.0030.0000.0000.0000.000
110A117THR 0-0.021-0.00931.1570.0000.0000.0000.0000.0000.000
111A118VAL 00.020-0.00533.5550.0030.0030.0000.0000.0000.000
112A119ALA 00.0050.01436.7630.0040.0040.0000.0000.0000.000
113A120ASP -1-0.978-0.97135.401-0.064-0.0640.0000.0000.0000.000
114A121ARG 10.7850.89534.8130.0780.0780.0000.0000.0000.000
115A122LEU 0-0.059-0.03338.5600.0020.0020.0000.0000.0000.000
116A123PRO 00.0130.01341.8430.0010.0010.0000.0000.0000.000
117A124LEU 00.029-0.00245.1870.0010.0010.0000.0000.0000.000
118A125GLU -1-0.859-0.90646.872-0.037-0.0370.0000.0000.0000.000
119A126GLN 00.1010.08145.433-0.002-0.0020.0000.0000.0000.000
120A127LEU 00.0150.01742.4330.0000.0000.0000.0000.0000.000
121A128GLU -1-0.859-0.92445.172-0.032-0.0320.0000.0000.0000.000
122A129GLN 0-0.045-0.01346.3290.0010.0010.0000.0000.0000.000
123A130MET 0-0.041-0.02038.9710.0000.0000.0000.0000.0000.000
124A131ALA 0-0.049-0.02843.7500.0000.0000.0000.0000.0000.000
125A132ALA 0-0.0070.00246.0030.0010.0010.0000.0000.0000.000
126A133ASP -1-0.744-0.85439.723-0.049-0.0490.0000.0000.0000.000
127A134ARG 11.0091.00137.2700.0440.0440.0000.0000.0000.000
128A135ASP -1-0.972-0.98835.684-0.052-0.0520.0000.0000.0000.000
129A136TYR 00.1170.04234.271-0.002-0.0020.0000.0000.0000.000
130A137LEU 00.0060.01232.4020.0010.0010.0000.0000.0000.000
131A138VAL 0-0.0100.00636.536-0.001-0.0010.0000.0000.0000.000
132A139ARG 10.8010.87138.3660.0360.0360.0000.0000.0000.000
133A140ALA 0-0.0100.00038.4950.0010.0010.0000.0000.0000.000
134A141TYR 00.000-0.00433.0000.0000.0000.0000.0000.0000.000
135A142VAL 00.0160.00239.5030.0010.0010.0000.0000.0000.000
136A143VAL 0-0.025-0.00843.0090.0010.0010.0000.0000.0000.000
137A144GLN 0-0.036-0.00639.3950.0040.0040.0000.0000.0000.000
138A145ARG 10.8200.87640.3940.0510.0510.0000.0000.0000.000
139A146ILE 0-0.0170.01344.4600.0010.0010.0000.0000.0000.000
140A147PRO 00.0150.00247.8860.0000.0000.0000.0000.0000.000
141A148PRO 00.0770.01150.9230.0000.0000.0000.0000.0000.000
142A149GLY 00.0490.02552.2120.0010.0010.0000.0000.0000.000
143A150ARG 10.8490.90551.6130.0290.0290.0000.0000.0000.000
144A151LEU 00.0230.02448.0690.0000.0000.0000.0000.0000.000
145A152PHE 00.0320.02951.5680.0000.0000.0000.0000.0000.000
146A153ARG 10.8930.95550.4320.0290.0290.0000.0000.0000.000
147A154PHE 0-0.007-0.01346.7190.0000.0000.0000.0000.0000.000
148A155MET 00.0060.00449.3880.0000.0000.0000.0000.0000.000
149A156ARG 10.9060.96451.4800.0200.0200.0000.0000.0000.000
150A157ASP -1-0.776-0.87344.983-0.032-0.0320.0000.0000.0000.000
151A158GLU -1-0.857-0.92344.315-0.030-0.0300.0000.0000.0000.000
152A159ASP -1-0.840-0.92140.629-0.035-0.0350.0000.0000.0000.000
153A160ARG 10.9380.96340.5000.0240.0240.0000.0000.0000.000
154A161GLN 00.0120.02537.7000.0000.0000.0000.0000.0000.000
155A162VAL 00.0210.01041.014-0.001-0.0010.0000.0000.0000.000
156A163ARG 10.7690.84543.0610.0240.0240.0000.0000.0000.000
157A164LYS 10.8200.90839.4970.0330.0330.0000.0000.0000.000
158A165LEU 0-0.040-0.01840.0030.0000.0000.0000.0000.0000.000
159A166VAL 0-0.009-0.00544.3210.0000.0000.0000.0000.0000.000
160A167ALA 00.0410.01847.8040.0010.0010.0000.0000.0000.000
161A168LYS 10.9260.97541.7980.0340.0340.0000.0000.0000.000
162A169ARG 10.8410.89845.0690.0350.0350.0000.0000.0000.000
163A170LEU 0-0.0310.00049.1700.0000.0000.0000.0000.0000.000
164A171PRO 0-0.003-0.01252.4120.0000.0000.0000.0000.0000.000
165A172GLU -1-0.884-0.94355.424-0.018-0.0180.0000.0000.0000.000
166A173GLU -1-0.854-0.92556.780-0.020-0.0200.0000.0000.0000.000
167A174SER 0-0.057-0.03757.4970.0010.0010.0000.0000.0000.000
168A175LEU 00.015-0.00252.5080.0000.0000.0000.0000.0000.000
169A176GLY 00.0530.04056.2230.0000.0000.0000.0000.0000.000
170A177LEU 0-0.039-0.02056.9960.0000.0000.0000.0000.0000.000
171A178MET 0-0.111-0.08450.595-0.001-0.0010.0000.0000.0000.000
172A179THR 0-0.0160.01854.2010.0000.0000.0000.0000.0000.000
173A180GLN 00.0430.02756.3360.0010.0010.0000.0000.0000.000
174A181ASP -1-0.837-0.87649.869-0.022-0.0220.0000.0000.0000.000
175A182PRO 00.018-0.00550.2590.0000.0000.0000.0000.0000.000
176A183GLU -1-0.904-0.95945.130-0.021-0.0210.0000.0000.0000.000
177A184PRO 00.0530.01647.1070.0000.0000.0000.0000.0000.000
178A185GLU -1-0.894-0.95641.624-0.027-0.0270.0000.0000.0000.000
179A186VAL 0-0.017-0.00746.066-0.001-0.0010.0000.0000.0000.000
180A187ARG 10.7970.88448.0810.0150.0150.0000.0000.0000.000
181A188ARG 10.9310.97743.7930.0200.0200.0000.0000.0000.000
182A189ILE 0-0.058-0.01845.6670.0000.0000.0000.0000.0000.000
183A190VAL 00.015-0.00148.6420.0000.0000.0000.0000.0000.000
184A191ALA 00.0210.00152.1590.0000.0000.0000.0000.0000.000
185A192SER 0-0.093-0.02949.7500.0000.0000.0000.0000.0000.000
186A193ARG 10.7900.86649.7710.0240.0240.0000.0000.0000.000
187A194LEU 00.0470.03653.3640.0000.0000.0000.0000.0000.000
188A195ARG 10.9110.95854.1370.0180.0180.0000.0000.0000.000
189A196GLY 0-0.005-0.00859.6160.0000.0000.0000.0000.0000.000
190A197ASP -1-0.892-0.97162.787-0.012-0.0120.0000.0000.0000.000
191A198ASP -1-0.935-0.94960.540-0.015-0.0150.0000.0000.0000.000
192A199LEU 0-0.045-0.02556.6950.0000.0000.0000.0000.0000.000
193A200LEU 00.0110.00460.0780.0000.0000.0000.0000.0000.000
194A201GLU -1-0.881-0.93160.568-0.013-0.0130.0000.0000.0000.000
195A202LEU 00.0270.00455.6690.0000.0000.0000.0000.0000.000
196A203LEU 0-0.038-0.00457.7750.0000.0000.0000.0000.0000.000
197A204HIS 10.8540.92759.7000.0110.0110.0000.0000.0000.000
198A205ASP -1-0.754-0.85854.523-0.014-0.0140.0000.0000.0000.000
199A206PRO 0-0.019-0.01255.1250.0010.0010.0000.0000.0000.000
200A207ASP -1-0.867-0.89549.733-0.013-0.0130.0000.0000.0000.000
201A208TRP 00.0600.00847.695-0.001-0.0010.0000.0000.0000.000
202A209THR 0-0.014-0.00947.023-0.001-0.0010.0000.0000.0000.000
203A210VAL 0-0.035-0.02250.041-0.001-0.0010.0000.0000.0000.000
204A211ARG 10.8530.91951.9300.0100.0100.0000.0000.0000.000
205A212LEU 0-0.010-0.00649.6460.0000.0000.0000.0000.0000.000
206A213ALA 00.0060.00150.4400.0000.0000.0000.0000.0000.000
207A214ALA 0-0.028-0.02152.2480.0000.0000.0000.0000.0000.000
208A215VAL 0-0.040-0.04055.7390.0000.0000.0000.0000.0000.000
209A216GLU -1-0.944-0.95751.704-0.015-0.0150.0000.0000.0000.000
210A217HIS 0-0.078-0.03652.5630.0000.0000.0000.0000.0000.000
211A218ALA 00.0030.02357.6980.0000.0000.0000.0000.0000.000
212A219SER 00.0380.01660.6820.0000.0000.0000.0000.0000.000
213A220LEU 00.014-0.02063.4530.0000.0000.0000.0000.0000.000
214A221GLU -1-0.848-0.94765.421-0.009-0.0090.0000.0000.0000.000
215A222ALA 00.0440.04264.1500.0000.0000.0000.0000.0000.000
216A223LEU 0-0.009-0.00560.4990.0000.0000.0000.0000.0000.000
217A224ARG 10.7770.88764.2810.0090.0090.0000.0000.0000.000
218A225GLU -1-0.938-0.95566.951-0.009-0.0090.0000.0000.0000.000
219A226LEU 0-0.050-0.02961.8560.0000.0000.0000.0000.0000.000
220A227ASP -1-0.965-0.95665.196-0.005-0.0050.0000.0000.0000.000
221A228GLU -1-0.799-0.90758.091-0.009-0.0090.0000.0000.0000.000
222A229PRO 00.000-0.00558.7900.0010.0010.0000.0000.0000.000
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