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: 9G3K2

Calculation Name: 1OY5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1OY5

Chain ID: A

ChEMBL ID:

UniProt ID: O67463

Base Structure: X-ray

Registration Date: 2023-06-20

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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2391688.903991
FMO2-HF: Nuclear repulsion 2304828.926788
FMO2-HF: Total energy -86859.977203
FMO2-MP2: Total energy -87116.082355


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:4:ASN)


Summations of interaction energy for fragment #1(A:4:ASN)
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.
-5.899-4.216-0.01-0.495-1.178-0.002
Interaction energy analysis for fragmet #1(A:4:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.055 / q_NPA : -0.052
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].
3A6LEU00.0080.0183.746-0.8560.316-0.012-0.404-0.756-0.002
4A7ARG10.8160.8784.1614.9095.047-0.001-0.010-0.1270.000
5A8PHE00.0470.0089.2720.2790.2790.0000.0000.0000.000
6A9PHE00.0180.00410.762-0.046-0.0460.0000.0000.0000.000
7A10VAL0-0.008-0.01115.5790.0920.0920.0000.0000.0000.000
8A11LEU00.0400.02818.9140.0130.0130.0000.0000.0000.000
9A12THR0-0.001-0.03821.9030.0430.0430.0000.0000.0000.000
10A13ILE00.0470.03424.838-0.013-0.0130.0000.0000.0000.000
11A14PHE0-0.026-0.01726.3530.0190.0190.0000.0000.0000.000
12A15PRO00.0370.01322.149-0.009-0.0090.0000.0000.0000.000
13A16HIS00.0500.01522.302-0.028-0.0280.0000.0000.0000.000
14A17ILE0-0.0050.01123.9970.0070.0070.0000.0000.0000.000
15A18ILE00.0230.01018.3290.0020.0020.0000.0000.0000.000
16A19SER00.0120.01118.921-0.027-0.0270.0000.0000.0000.000
17A20CYS0-0.0020.01019.7430.0060.0060.0000.0000.0000.000
18A21TYR0-0.033-0.04618.8840.0330.0330.0000.0000.0000.000
19A22SER0-0.012-0.03315.652-0.013-0.0130.0000.0000.0000.000
20A23GLU-1-0.889-0.91716.479-0.441-0.4410.0000.0000.0000.000
21A24TYR0-0.103-0.07118.9370.0620.0620.0000.0000.0000.000
22A25GLY00.0470.02218.321-0.027-0.0270.0000.0000.0000.000
23A26ILE0-0.003-0.01514.9710.0010.0010.0000.0000.0000.000
24A27VAL00.0750.05613.9420.0010.0010.0000.0000.0000.000
25A28LYS10.9200.98013.0970.2600.2600.0000.0000.0000.000
26A29GLN0-0.074-0.04813.300-0.063-0.0630.0000.0000.0000.000
27A30ALA00.023-0.00210.0790.0980.0980.0000.0000.0000.000
28A31ILE00.0540.0418.529-0.083-0.0830.0000.0000.0000.000
29A32LYS10.8770.9419.0260.3460.3460.0000.0000.0000.000
30A33LYS10.8240.9098.890-0.362-0.3620.0000.0000.0000.000
31A34GLY00.0190.0285.3630.7250.7250.0000.0000.0000.000
32A35LYS10.7800.8743.873-2.485-2.1120.003-0.081-0.2950.000
33A36VAL00.0230.0085.726-0.413-0.4130.0000.0000.0000.000
34A37GLU-1-0.800-0.8515.903-4.828-4.8280.0000.0000.0000.000
35A38VAL0-0.004-0.0119.3950.1030.1030.0000.0000.0000.000
36A39TYR0-0.013-0.0169.0390.1780.1780.0000.0000.0000.000
37A40PRO0-0.035-0.01214.9640.0590.0590.0000.0000.0000.000
38A41ILE0-0.011-0.00916.572-0.017-0.0170.0000.0000.0000.000
39A42ASP-1-0.758-0.86720.354-0.348-0.3480.0000.0000.0000.000
40A43LEU00.034-0.00224.0480.0040.0040.0000.0000.0000.000
41A44ARG10.8170.87126.1200.3540.3540.0000.0000.0000.000
42A45GLU-1-0.941-0.96224.949-0.363-0.3630.0000.0000.0000.000
43A46PHE0-0.003-0.00120.804-0.007-0.0070.0000.0000.0000.000
44A47ALA00.0060.01026.3650.0130.0130.0000.0000.0000.000
45A48PRO0-0.006-0.00229.7250.0170.0170.0000.0000.0000.000
46A49LYS10.8280.90731.8200.2220.2220.0000.0000.0000.000
47A50GLY00.0170.01533.0770.0120.0120.0000.0000.0000.000
48A51GLN0-0.028-0.00533.9430.0000.0000.0000.0000.0000.000
49A52VAL00.009-0.00829.879-0.007-0.0070.0000.0000.0000.000
50A53ASP-1-0.854-0.91832.540-0.237-0.2370.0000.0000.0000.000
51A54ASP-1-0.825-0.92035.394-0.171-0.1710.0000.0000.0000.000
52A55VAL00.0060.00538.778-0.001-0.0010.0000.0000.0000.000
53A56PRO0-0.0310.01440.123-0.001-0.0010.0000.0000.0000.000
54A57TYR00.015-0.01440.1930.0070.0070.0000.0000.0000.000
55A58GLY0-0.016-0.01443.692-0.001-0.0010.0000.0000.0000.000
56A59GLY0-0.028-0.00245.8180.0050.0050.0000.0000.0000.000
57A60LEU00.0050.00242.7530.0040.0040.0000.0000.0000.000
58A61PRO0-0.026-0.01644.751-0.003-0.0030.0000.0000.0000.000
59A62GLY00.006-0.00241.7190.0000.0000.0000.0000.0000.000
60A63MET0-0.078-0.03837.1970.0000.0000.0000.0000.0000.000
61A64VAL0-0.017-0.00534.965-0.003-0.0030.0000.0000.0000.000
62A65LEU00.004-0.00429.086-0.003-0.0030.0000.0000.0000.000
63A66LYS10.7740.87632.7100.2280.2280.0000.0000.0000.000
64A67PRO0-0.005-0.01030.409-0.018-0.0180.0000.0000.0000.000
65A68GLU-1-0.769-0.87929.225-0.252-0.2520.0000.0000.0000.000
66A69PRO00.0240.01728.063-0.017-0.0170.0000.0000.0000.000
67A70ILE0-0.025-0.00624.750-0.035-0.0350.0000.0000.0000.000
68A71TYR0-0.054-0.04124.238-0.032-0.0320.0000.0000.0000.000
69A72GLU-1-0.883-0.93424.112-0.371-0.3710.0000.0000.0000.000
70A73ALA0-0.012-0.00821.822-0.037-0.0370.0000.0000.0000.000
71A74TYR0-0.012-0.02819.667-0.090-0.0900.0000.0000.0000.000
72A75ASP-1-0.874-0.94519.389-0.470-0.4700.0000.0000.0000.000
73A76TYR00.0480.03716.830-0.073-0.0730.0000.0000.0000.000
74A77VAL0-0.024-0.01914.289-0.077-0.0770.0000.0000.0000.000
75A78VAL0-0.053-0.03415.047-0.108-0.1080.0000.0000.0000.000
76A79GLU-1-0.967-0.97816.130-0.513-0.5130.0000.0000.0000.000
77A80ASN0-0.104-0.05614.699-0.030-0.0300.0000.0000.0000.000
78A81TYR0-0.072-0.03910.054-0.224-0.2240.0000.0000.0000.000
79A82GLY00.0140.02710.846-0.177-0.1770.0000.0000.0000.000
80A83LYS10.8540.92913.4310.4520.4520.0000.0000.0000.000
81A84PRO0-0.012-0.00114.070-0.068-0.0680.0000.0000.0000.000
82A85PHE00.004-0.03014.8960.1260.1260.0000.0000.0000.000
83A86VAL0-0.003-0.00116.926-0.055-0.0550.0000.0000.0000.000
84A87LEU0-0.002-0.00119.4780.0620.0620.0000.0000.0000.000
85A88ILE00.0000.00421.249-0.025-0.0250.0000.0000.0000.000
86A89THR0-0.030-0.02223.4000.0080.0080.0000.0000.0000.000
87A90GLU-1-0.803-0.90726.078-0.215-0.2150.0000.0000.0000.000
88A91PRO0-0.039-0.02229.798-0.003-0.0030.0000.0000.0000.000
89A92TRP0-0.031-0.01132.0290.0110.0110.0000.0000.0000.000
90A93GLY00.1010.05329.9880.0150.0150.0000.0000.0000.000
91A94GLU-1-0.866-0.95027.615-0.211-0.2110.0000.0000.0000.000
92A95LYS10.7980.88428.1880.1280.1280.0000.0000.0000.000
93A96LEU0-0.0130.00121.8660.0020.0020.0000.0000.0000.000
94A97ASN00.010-0.02023.7570.0270.0270.0000.0000.0000.000
95A98GLN00.0590.00520.220-0.040-0.0400.0000.0000.0000.000
96A99LYS10.8610.93320.4230.1410.1410.0000.0000.0000.000
97A100LEU00.0530.03019.829-0.007-0.0070.0000.0000.0000.000
98A101VAL00.0190.01817.257-0.046-0.0460.0000.0000.0000.000
99A102ASN0-0.023-0.02015.8530.0000.0000.0000.0000.0000.000
100A103GLU-1-0.829-0.89214.908-0.187-0.1870.0000.0000.0000.000
101A104LEU0-0.053-0.01515.012-0.063-0.0630.0000.0000.0000.000
102A105SER0-0.009-0.02011.805-0.101-0.1010.0000.0000.0000.000
103A106LYS10.8730.94210.092-0.021-0.0210.0000.0000.0000.000
104A107LYS10.8860.94110.4630.5580.5580.0000.0000.0000.000
105A108GLU-1-0.795-0.8786.785-1.721-1.7210.0000.0000.0000.000
106A109ARG10.8340.9138.3380.9730.9730.0000.0000.0000.000
107A110ILE0-0.044-0.00611.0010.2660.2660.0000.0000.0000.000
108A111MET00.0070.02014.247-0.072-0.0720.0000.0000.0000.000
109A112ILE0-0.036-0.02217.0630.0590.0590.0000.0000.0000.000
110A113ILE00.0290.01819.986-0.007-0.0070.0000.0000.0000.000
111A114CYS0-0.039-0.01322.8450.0260.0260.0000.0000.0000.000
112A115GLY00.0240.01425.4510.0090.0090.0000.0000.0000.000
113A116ARG10.8420.89929.0520.2630.2630.0000.0000.0000.000
114A117TYR0-0.033-0.03231.9420.0020.0020.0000.0000.0000.000
115A118GLU-1-0.804-0.90535.680-0.168-0.1680.0000.0000.0000.000
116A119GLY0-0.0050.00933.6620.0060.0060.0000.0000.0000.000
117A120VAL0-0.027-0.01628.879-0.010-0.0100.0000.0000.0000.000
118A121ASP-1-0.754-0.84632.202-0.195-0.1950.0000.0000.0000.000
119A122GLU-1-0.757-0.89231.805-0.222-0.2220.0000.0000.0000.000
120A123ARG10.8260.89132.1780.1920.1920.0000.0000.0000.000
121A124VAL00.0340.03226.594-0.009-0.0090.0000.0000.0000.000
122A125LYS10.8130.90227.3380.2060.2060.0000.0000.0000.000
123A126LYS10.7490.87228.5630.2210.2210.0000.0000.0000.000
124A127ILE00.0030.01723.4260.0030.0030.0000.0000.0000.000
125A128VAL0-0.048-0.01423.045-0.041-0.0410.0000.0000.0000.000
126A129ASP-1-0.831-0.90219.901-0.447-0.4470.0000.0000.0000.000
127A130MET0-0.079-0.04121.2080.0230.0230.0000.0000.0000.000
128A131GLU-1-0.779-0.90223.702-0.262-0.2620.0000.0000.0000.000
129A132ILE0-0.103-0.03522.5800.0170.0170.0000.0000.0000.000
130A133SER00.0280.02126.5280.0090.0090.0000.0000.0000.000
131A134LEU00.0550.01730.123-0.001-0.0010.0000.0000.0000.000
132A135GLY0-0.033-0.01132.0900.0100.0100.0000.0000.0000.000
133A136ASP-1-0.893-0.91932.922-0.106-0.1060.0000.0000.0000.000
134A137PHE0-0.047-0.01931.2280.0060.0060.0000.0000.0000.000
135A138ILE00.0160.00835.011-0.005-0.0050.0000.0000.0000.000
136A139LEU0-0.023-0.00529.6810.0030.0030.0000.0000.0000.000
137A140SER00.003-0.00933.332-0.005-0.0050.0000.0000.0000.000
138A141GLY00.015-0.01530.500-0.002-0.0020.0000.0000.0000.000
139A142GLY00.0220.03027.0020.0090.0090.0000.0000.0000.000
140A143GLU-1-0.764-0.86024.260-0.348-0.3480.0000.0000.0000.000
141A144ILE0-0.009-0.00623.579-0.025-0.0250.0000.0000.0000.000
142A145VAL00.0360.02624.194-0.002-0.0020.0000.0000.0000.000
143A146ALA00.0290.01120.647-0.016-0.0160.0000.0000.0000.000
144A147LEU0-0.020-0.00719.331-0.047-0.0470.0000.0000.0000.000
145A148ALA0-0.0150.00419.623-0.003-0.0030.0000.0000.0000.000
146A149VAL0-0.012-0.01117.1600.0190.0190.0000.0000.0000.000
147A150ILE00.0150.01414.304-0.007-0.0070.0000.0000.0000.000
148A151ASP-1-0.869-0.90715.101-0.269-0.2690.0000.0000.0000.000
149A152ALA0-0.001-0.00916.5650.0430.0430.0000.0000.0000.000
150A153VAL0-0.007-0.00512.5160.0650.0650.0000.0000.0000.000
151A154SER00.009-0.01812.0010.0060.0060.0000.0000.0000.000
152A155ARG10.8760.93012.7620.1930.1930.0000.0000.0000.000
153A156VAL0-0.052-0.02413.9010.0730.0730.0000.0000.0000.000
154A157LEU00.0230.0368.0650.1160.1160.0000.0000.0000.000
155A158PRO00.0000.0007.7060.0390.0390.0000.0000.0000.000
156A159GLY00.0280.0098.8890.3650.3650.0000.0000.0000.000
157A160VAL0-0.0050.0159.954-0.098-0.0980.0000.0000.0000.000
158A161LEU00.0150.01412.057-0.094-0.0940.0000.0000.0000.000
159A162SER0-0.023-0.02215.3780.1030.1030.0000.0000.0000.000
160A163GLH0-0.026-0.01016.640-0.037-0.0370.0000.0000.0000.000
161A164PRO00.0190.02617.796-0.003-0.0030.0000.0000.0000.000
162A179TYR00.0150.00833.470-0.002-0.0020.0000.0000.0000.000
163A180PRO0-0.030-0.02036.029-0.001-0.0010.0000.0000.0000.000
164A181VAL00.0030.01132.9810.0070.0070.0000.0000.0000.000
165A182TYR00.0500.01336.124-0.006-0.0060.0000.0000.0000.000
166A183THR00.015-0.00433.8220.0080.0080.0000.0000.0000.000
167A184ARG10.9450.97636.033-0.051-0.0510.0000.0000.0000.000
168A185PRO00.010-0.01137.8780.0030.0030.0000.0000.0000.000
169A186ARG10.8530.92941.095-0.023-0.0230.0000.0000.0000.000
170A187GLU-1-0.818-0.90243.4840.0110.0110.0000.0000.0000.000
171A188TYR00.0150.00843.443-0.003-0.0030.0000.0000.0000.000
172A189ARG10.9130.94444.8700.0220.0220.0000.0000.0000.000
173A190GLY00.0640.04648.763-0.001-0.0010.0000.0000.0000.000
174A191MET0-0.0190.00344.6430.0010.0010.0000.0000.0000.000
175A192LYS10.8520.91346.326-0.014-0.0140.0000.0000.0000.000
176A193VAL0-0.023-0.01141.086-0.001-0.0010.0000.0000.0000.000
177A194PRO00.0130.01142.7730.0010.0010.0000.0000.0000.000
178A195GLU-1-0.756-0.87644.4850.0250.0250.0000.0000.0000.000
179A196GLU-1-0.899-0.95545.1580.0300.0300.0000.0000.0000.000
180A197LEU0-0.071-0.05039.7420.0050.0050.0000.0000.0000.000
181A198LEU0-0.063-0.02340.8800.0040.0040.0000.0000.0000.000
182A199SER0-0.022-0.02243.1490.0030.0030.0000.0000.0000.000
183A200GLY00.0520.00842.239-0.003-0.0030.0000.0000.0000.000
184A201HIS00.0600.04040.3760.0020.0020.0000.0000.0000.000
185A202HIS00.0060.00143.509-0.001-0.0010.0000.0000.0000.000
186A203LYS10.8540.95343.437-0.050-0.0500.0000.0000.0000.000
187A204LEU00.0110.01838.772-0.001-0.0010.0000.0000.0000.000
188A205ILE00.0090.01540.4510.0020.0020.0000.0000.0000.000
189A206GLU-1-0.853-0.94742.9520.0400.0400.0000.0000.0000.000
190A207LEU00.0140.00238.596-0.004-0.0040.0000.0000.0000.000
191A208TRP00.0520.01234.028-0.006-0.0060.0000.0000.0000.000
192A209LYN0-0.0110.04240.161-0.005-0.0050.0000.0000.0000.000
193A210LEU00.0550.03340.662-0.003-0.0030.0000.0000.0000.000
194A211TRP00.007-0.01032.344-0.003-0.0030.0000.0000.0000.000
195A212HIS10.8130.87935.870-0.053-0.0530.0000.0000.0000.000
196A213ARG10.8960.91340.344-0.035-0.0350.0000.0000.0000.000
197A214ILE00.0520.03841.629-0.004-0.0040.0000.0000.0000.000
198A215GLU-1-0.765-0.83035.0590.0290.0290.0000.0000.0000.000
199A216ASN00.008-0.01239.061-0.007-0.0070.0000.0000.0000.000
200A217THR0-0.101-0.05040.923-0.005-0.0050.0000.0000.0000.000
201A218VAL00.0720.02538.081-0.004-0.0040.0000.0000.0000.000
202A219LYS10.8670.92033.862-0.020-0.0200.0000.0000.0000.000
203A220LYS10.8950.95138.5320.0060.0060.0000.0000.0000.000
204A221ARG10.8720.94140.9440.0150.0150.0000.0000.0000.000
205A222PRO00.0200.02138.0370.0010.0010.0000.0000.0000.000
206A223ASP-1-0.839-0.91439.769-0.059-0.0590.0000.0000.0000.000
207A224LEU0-0.108-0.06942.8550.0040.0040.0000.0000.0000.000
208A225ILE00.0130.00746.6250.0030.0030.0000.0000.0000.000
209A226PRO0-0.017-0.02547.4110.0000.0000.0000.0000.0000.000
210A227LYS10.8290.91042.3390.0480.0480.0000.0000.0000.000
211A228ASP-1-0.803-0.89045.527-0.042-0.0420.0000.0000.0000.000
212A229LEU00.0570.03147.7850.0010.0010.0000.0000.0000.000
213A230THR0-0.048-0.02648.9510.0020.0020.0000.0000.0000.000
214A231GLU-1-0.871-0.92243.744-0.054-0.0540.0000.0000.0000.000
215A232LEU00.0170.00844.6800.0020.0020.0000.0000.0000.000
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