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: 4LNKN

Calculation Name: 1O65-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1O65

Chain ID: A

ChEMBL ID:

UniProt ID: P32157

Base Structure: X-ray

Registration Date: 2023-09-26

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 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2774250.862643
FMO2-HF: Nuclear repulsion 2685417.468019
FMO2-HF: Total energy -88833.394624
FMO2-MP2: Total energy -89092.430762


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:3:LYS)


Summations of interaction energy for fragment #1(A:3:LYS)
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.
-78.828-74.6420.581-1.762-3.004-0.007
Interaction energy analysis for fragmet #1(A:3:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.969 / q_NPA : 0.976
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].
3A5LEU0-0.0040.0002.487-0.5803.4140.582-1.749-2.826-0.007
4A6VAL00.0420.0104.8443.3523.544-0.001-0.013-0.1780.000
5A7GLU-1-0.843-0.9056.971-22.856-22.8560.0000.0000.0000.000
6A8ARG10.8900.9408.45926.05326.0530.0000.0000.0000.000
7A9GLU-1-0.951-0.9678.456-28.277-28.2770.0000.0000.0000.000
8A10GLN0-0.069-0.02611.1912.1102.1100.0000.0000.0000.000
9A11MET00.0210.01711.3870.4450.4450.0000.0000.0000.000
10A12ARG10.9570.97514.27915.97915.9790.0000.0000.0000.000
11A13TYR0-0.018-0.01914.175-0.614-0.6140.0000.0000.0000.000
12A14PRO00.0180.00420.1700.3460.3460.0000.0000.0000.000
13A15VAL0-0.064-0.02123.626-0.272-0.2720.0000.0000.0000.000
14A16ASP-1-0.803-0.87525.490-10.276-10.2760.0000.0000.0000.000
15A17VAL00.012-0.01228.024-0.268-0.2680.0000.0000.0000.000
16A18TYR00.012-0.00530.1230.2760.2760.0000.0000.0000.000
17A19THR0-0.031-0.01932.004-0.107-0.1070.0000.0000.0000.000
18A20GLY00.0410.01934.6460.1610.1610.0000.0000.0000.000
19A21LYS10.8290.93437.2157.6637.6630.0000.0000.0000.000
20A34ALA00.0410.02437.5250.0060.0060.0000.0000.0000.000
21A35LYS10.7550.89331.7649.1759.1750.0000.0000.0000.000
22A36ILE00.009-0.01236.599-0.019-0.0190.0000.0000.0000.000
23A37GLN0-0.003-0.00332.859-0.383-0.3830.0000.0000.0000.000
24A38VAL0-0.055-0.02533.6760.2840.2840.0000.0000.0000.000
25A39ASP-1-0.862-0.93533.930-8.708-8.7080.0000.0000.0000.000
26A40GLY0-0.0150.00235.041-0.082-0.0820.0000.0000.0000.000
27A41GLU-1-0.938-0.98833.301-9.067-9.0670.0000.0000.0000.000
28A42LEU0-0.050-0.03031.9050.3050.3050.0000.0000.0000.000
29A43MET0-0.043-0.00432.021-0.259-0.2590.0000.0000.0000.000
30A44LEU00.0180.02125.9230.0900.0900.0000.0000.0000.000
31A45THR0-0.005-0.01230.238-0.116-0.1160.0000.0000.0000.000
32A46GLU-1-0.918-0.97428.977-9.442-9.4420.0000.0000.0000.000
33A47LEU0-0.034-0.04429.007-0.201-0.2010.0000.0000.0000.000
34A48GLY00.0620.04329.787-0.002-0.0020.0000.0000.0000.000
35A49LEU0-0.014-0.00529.0800.0670.0670.0000.0000.0000.000
36A50GLU-1-0.931-0.96832.174-7.758-7.7580.0000.0000.0000.000
37A51GLY00.0430.02635.755-0.013-0.0130.0000.0000.0000.000
38A52ASP-1-0.769-0.89432.540-8.887-8.8870.0000.0000.0000.000
39A53GLU-1-1.035-1.02635.621-7.529-7.5290.0000.0000.0000.000
40A54GLN00.0400.03535.415-0.031-0.0310.0000.0000.0000.000
41A55ALA00.0290.00737.3560.0570.0570.0000.0000.0000.000
42A56GLU-1-0.688-0.80238.878-7.228-7.2280.0000.0000.0000.000
43A57LYS10.7740.86339.0997.0917.0910.0000.0000.0000.000
44A58LYS10.8430.88038.2477.3377.3370.0000.0000.0000.000
45A59VAL0-0.055-0.00633.467-0.069-0.0690.0000.0000.0000.000
46A60HIS00.0780.04233.410-0.210-0.2100.0000.0000.0000.000
47A61GLY00.0240.00029.692-0.112-0.1120.0000.0000.0000.000
48A62GLY0-0.020-0.00628.852-0.245-0.2450.0000.0000.0000.000
49A63PRO00.0900.03927.968-0.122-0.1220.0000.0000.0000.000
50A64ASP-1-0.871-0.93124.686-11.323-11.3230.0000.0000.0000.000
51A65ARG10.8280.90224.8228.9618.9610.0000.0000.0000.000
52A66ALA00.0250.04326.5670.2290.2290.0000.0000.0000.000
53A67LEU00.0170.01424.5100.2030.2030.0000.0000.0000.000
54A68CYS0-0.035-0.01124.778-0.493-0.4930.0000.0000.0000.000
55A69HIS00.0850.05320.8670.2560.2560.0000.0000.0000.000
56A70TYR0-0.016-0.02023.592-0.145-0.1450.0000.0000.0000.000
57A71PRO0-0.026-0.00120.6170.1780.1780.0000.0000.0000.000
58A72ARG10.9310.95623.09912.03212.0320.0000.0000.0000.000
59A73GLU-1-0.823-0.90520.971-14.192-14.1920.0000.0000.0000.000
60A74HIS10.7250.84121.37213.51513.5150.0000.0000.0000.000
61A75TYR00.046-0.00526.0410.3440.3440.0000.0000.0000.000
62A76LEU0-0.0120.01326.5260.3260.3260.0000.0000.0000.000
63A77TYR0-0.071-0.03827.0820.0500.0500.0000.0000.0000.000
64A78TRP00.0570.00328.1020.2060.2060.0000.0000.0000.000
65A79ALA00.0380.02431.6890.2810.2810.0000.0000.0000.000
66A80ARG10.8900.94128.10011.00711.0070.0000.0000.0000.000
67A81GLU-1-0.962-0.98031.476-9.667-9.6670.0000.0000.0000.000
68A82PHE0-0.038-0.02034.2610.1930.1930.0000.0000.0000.000
69A83PRO00.0190.01637.3640.0370.0370.0000.0000.0000.000
70A84GLU-1-0.951-0.99239.054-7.244-7.2440.0000.0000.0000.000
71A85GLN0-0.0190.00938.9100.1610.1610.0000.0000.0000.000
72A86ALA00.001-0.00937.066-0.193-0.1930.0000.0000.0000.000
73A87GLU-1-0.912-0.96736.935-7.823-7.8230.0000.0000.0000.000
74A88LEU0-0.021-0.00137.770-0.056-0.0560.0000.0000.0000.000
75A89PHE0-0.068-0.03532.643-0.274-0.2740.0000.0000.0000.000
76A90VAL00.0050.00432.861-0.254-0.2540.0000.0000.0000.000
77A91ALA0-0.0150.03029.9530.0460.0460.0000.0000.0000.000
78A92PRO0-0.038-0.01231.3620.2130.2130.0000.0000.0000.000
79A93ALA00.0330.00932.3760.0840.0840.0000.0000.0000.000
80A94PHE00.001-0.01029.3250.1270.1270.0000.0000.0000.000
81A95GLY0-0.029-0.02230.649-0.107-0.1070.0000.0000.0000.000
82A96GLU-1-0.826-0.90627.086-10.285-10.2850.0000.0000.0000.000
83A97ASN0-0.043-0.04227.6720.0950.0950.0000.0000.0000.000
84A98LEU00.0030.01423.1140.1030.1030.0000.0000.0000.000
85A99SER00.0200.01225.337-0.225-0.2250.0000.0000.0000.000
86A100THR00.0550.02821.404-0.021-0.0210.0000.0000.0000.000
87A101ASP-1-0.868-0.91022.395-12.426-12.4260.0000.0000.0000.000
88A102GLY0-0.016-0.02518.578-0.284-0.2840.0000.0000.0000.000
89A103LEU0-0.031-0.00815.164-1.349-1.3490.0000.0000.0000.000
90A104THR0-0.004-0.01615.9390.9740.9740.0000.0000.0000.000
91A105GLU-1-0.720-0.87215.544-15.229-15.2290.0000.0000.0000.000
92A106SER0-0.008-0.00613.651-0.274-0.2740.0000.0000.0000.000
93A107ASN0-0.045-0.02410.958-0.786-0.7860.0000.0000.0000.000
94A108VAL00.0150.03011.491-0.889-0.8890.0000.0000.0000.000
95A109TYR0-0.051-0.0436.960-0.961-0.9610.0000.0000.0000.000
96A110MET0-0.043-0.00311.3871.2301.2300.0000.0000.0000.000
97A111GLY00.0530.03312.372-0.910-0.9100.0000.0000.0000.000
98A112ASP-1-0.755-0.86810.537-23.016-23.0160.0000.0000.0000.000
99A113ILE0-0.008-0.00113.2281.3461.3460.0000.0000.0000.000
100A114PHE00.011-0.01214.835-1.107-1.1070.0000.0000.0000.000
101A115ARG10.8740.93817.44514.84514.8450.0000.0000.0000.000
102A116TRP0-0.010-0.01520.201-0.363-0.3630.0000.0000.0000.000
103A117GLY00.0410.03223.2720.4680.4680.0000.0000.0000.000
104A118GLU-1-0.960-0.98625.354-10.436-10.4360.0000.0000.0000.000
105A119ALA0-0.059-0.01725.2620.0680.0680.0000.0000.0000.000
106A120LEU0-0.025-0.02119.384-0.612-0.6120.0000.0000.0000.000
107A121ILE0-0.0010.01319.6860.5390.5390.0000.0000.0000.000
108A122GLN0-0.014-0.01915.348-0.160-0.1600.0000.0000.0000.000
109A123VAL0-0.0400.00815.7030.7810.7810.0000.0000.0000.000
110A124SER00.0240.00317.372-0.378-0.3780.0000.0000.0000.000
111A125GLN0-0.018-0.01619.6440.3680.3680.0000.0000.0000.000
112A126PRO00.0650.04618.7890.0300.0300.0000.0000.0000.000
113A127ARG10.8460.93120.89310.88410.8840.0000.0000.0000.000
114A128SER0-0.002-0.02924.445-0.187-0.1870.0000.0000.0000.000
115A129PRO0-0.0220.02326.5670.3710.3710.0000.0000.0000.000
116A130CYS0-0.046-0.02629.5800.2610.2610.0000.0000.0000.000
117A131TYR00.0870.03933.1150.0860.0860.0000.0000.0000.000
118A132LYS10.8850.92336.4387.9417.9410.0000.0000.0000.000
119A133LEU00.0230.01130.9980.1100.1100.0000.0000.0000.000
120A134ASN00.0370.02535.693-0.137-0.1370.0000.0000.0000.000
121A135TYR0-0.042-0.02538.0100.1310.1310.0000.0000.0000.000
122A136HIS0-0.058-0.01036.8800.2190.2190.0000.0000.0000.000
123A137PHE0-0.009-0.01333.1990.0200.0200.0000.0000.0000.000
124A138ASP-1-0.932-0.95538.607-7.000-7.0000.0000.0000.0000.000
125A139ILE00.0080.02636.6650.0230.0230.0000.0000.0000.000
126A140SER00.010-0.02138.284-0.096-0.0960.0000.0000.0000.000
127A141ASP-1-0.914-0.95736.230-8.408-8.4080.0000.0000.0000.000
128A142ILE00.0830.05432.410-0.317-0.3170.0000.0000.0000.000
129A143ALA0-0.049-0.02931.803-0.380-0.3800.0000.0000.0000.000
130A144GLN0-0.029-0.01630.779-0.101-0.1010.0000.0000.0000.000
131A145LEU00.0480.02930.338-0.443-0.4430.0000.0000.0000.000
132A146MET0-0.037-0.01027.362-0.318-0.3180.0000.0000.0000.000
133A147GLN00.0530.02126.177-0.343-0.3430.0000.0000.0000.000
134A148ASN00.0040.01325.604-0.491-0.4910.0000.0000.0000.000
135A149THR0-0.041-0.01825.346-0.479-0.4790.0000.0000.0000.000
136A150GLY00.0160.01621.898-0.593-0.5930.0000.0000.0000.000
137A151LYS10.8430.94721.70812.06712.0670.0000.0000.0000.000
138A152VAL0-0.031-0.02021.8540.5750.5750.0000.0000.0000.000
139A153GLY00.0640.02921.6080.4330.4330.0000.0000.0000.000
140A154TRP0-0.076-0.05418.665-0.191-0.1910.0000.0000.0000.000
141A155LEU0-0.041-0.01621.2710.4480.4480.0000.0000.0000.000
142A156TYR00.018-0.01018.250-0.891-0.8910.0000.0000.0000.000
143A157SER00.0120.00921.4780.4520.4520.0000.0000.0000.000
144A158VAL0-0.011-0.01722.508-0.453-0.4530.0000.0000.0000.000
145A159ILE0-0.055-0.02219.5570.2570.2570.0000.0000.0000.000
146A160ALA0-0.005-0.02023.0070.3130.3130.0000.0000.0000.000
147A161PRO0-0.009-0.00825.297-0.138-0.1380.0000.0000.0000.000
148A162GLY00.0420.01828.486-0.004-0.0040.0000.0000.0000.000
149A163LYS10.9330.97329.7568.5978.5970.0000.0000.0000.000
150A164VAL0-0.0060.02626.911-0.331-0.3310.0000.0000.0000.000
151A165SER00.038-0.01828.4910.2970.2970.0000.0000.0000.000
152A166ALA00.0540.03628.446-0.383-0.3830.0000.0000.0000.000
153A167ASP-1-0.909-0.93428.897-9.929-9.9290.0000.0000.0000.000
154A168ALA0-0.085-0.02825.796-0.334-0.3340.0000.0000.0000.000
155A169PRO0-0.017-0.01021.527-0.078-0.0780.0000.0000.0000.000
156A170LEU00.0070.00019.335-0.092-0.0920.0000.0000.0000.000
157A171GLU-1-0.851-0.94617.462-15.016-15.0160.0000.0000.0000.000
158A172LEU0-0.064-0.0069.9530.1450.1450.0000.0000.0000.000
159A173VAL0-0.027-0.01813.801-0.562-0.5620.0000.0000.0000.000
160A174SER0-0.046-0.02510.847-0.132-0.1320.0000.0000.0000.000
161A175ARG10.8080.9015.97428.71128.7110.0000.0000.0000.000
162A176VAL0-0.012-0.0147.603-1.057-1.0570.0000.0000.0000.000
163A177SER0-0.061-0.0408.7951.1281.1280.0000.0000.0000.000
164A178ASP-1-0.908-0.9606.232-26.060-26.0600.0000.0000.0000.000
165A179VAL00.0130.0137.7480.2150.2150.0000.0000.0000.000
166A180THR0-0.0090.00210.0081.1431.1430.0000.0000.0000.000
167A181VAL00.0520.01512.0051.1621.1620.0000.0000.0000.000
168A182GLN0-0.006-0.00514.9140.0970.0970.0000.0000.0000.000
169A183GLU-1-0.773-0.87010.974-21.056-21.0560.0000.0000.0000.000
170A184ALA00.0210.01015.5670.8910.8910.0000.0000.0000.000
171A185ALA0-0.003-0.00417.5140.8150.8150.0000.0000.0000.000
172A186ALA00.0200.00918.5290.7110.7110.0000.0000.0000.000
173A187ILE0-0.004-0.01716.2890.6620.6620.0000.0000.0000.000
174A188ALA0-0.058-0.03220.4970.6200.6200.0000.0000.0000.000
175A189TRP0-0.051-0.04523.2020.4990.4990.0000.0000.0000.000
176A190HIS0-0.053-0.03122.508-0.014-0.0140.0000.0000.0000.000
177A191MET0-0.0240.01621.062-0.078-0.0780.0000.0000.0000.000
178A192PRO0-0.012-0.00924.2100.2960.2960.0000.0000.0000.000
179A193PHE0-0.029-0.01025.137-0.326-0.3260.0000.0000.0000.000
180A194ASP-1-0.771-0.88620.773-13.140-13.1400.0000.0000.0000.000
181A195ASP-1-0.822-0.88522.842-11.475-11.4750.0000.0000.0000.000
182A196ASP-1-0.863-0.92118.990-13.219-13.2190.0000.0000.0000.000
183A197GLN0-0.038-0.03716.397-1.390-1.3900.0000.0000.0000.000
184A198TYR0-0.006-0.00818.564-0.125-0.1250.0000.0000.0000.000
185A199HIS0-0.050-0.02617.6300.4020.4020.0000.0000.0000.000
186A200ARG10.8630.92610.29020.14220.1420.0000.0000.0000.000
187A201LEU00.0010.00015.427-0.397-0.3970.0000.0000.0000.000
188A202LEU0-0.088-0.05517.2210.0700.0700.0000.0000.0000.000
189A203SER0-0.038-0.00914.8590.4090.4090.0000.0000.0000.000
190A204ALA0-0.042-0.00913.392-0.701-0.7010.0000.0000.0000.000
191A205ALA00.012-0.00313.4160.9300.9300.0000.0000.0000.000
192A206GLY00.0310.00615.098-0.238-0.2380.0000.0000.0000.000
193A207LEU0-0.0550.00018.0090.4900.4900.0000.0000.0000.000
194A208SER00.0200.00719.5970.4890.4890.0000.0000.0000.000
195A209LYS10.9570.95523.13310.42410.4240.0000.0000.0000.000
196A210SER0-0.065-0.03025.9560.1350.1350.0000.0000.0000.000
197A211TRP00.1050.04720.8600.1000.1000.0000.0000.0000.000
198A212THR00.0420.02422.875-0.114-0.1140.0000.0000.0000.000
199A213ARG10.9030.95724.0699.0219.0210.0000.0000.0000.000
200A214THR0-0.040-0.01826.1360.3250.3250.0000.0000.0000.000
201A215MET00.0570.04021.8700.1860.1860.0000.0000.0000.000
202A216GLN00.017-0.00324.9390.2840.2840.0000.0000.0000.000
203A217LYS10.8600.91426.6728.9798.9790.0000.0000.0000.000
204A218ARG10.7620.85625.16211.06011.0600.0000.0000.0000.000
205A219ARG10.8350.88323.27611.69611.6960.0000.0000.0000.000
206A220LEU0-0.045-0.01327.7120.2320.2320.0000.0000.0000.000
207A221SER0-0.091-0.03231.2000.2750.2750.0000.0000.0000.000
208A222GLY00.0360.02430.5400.2250.2250.0000.0000.0000.000
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210A224ILE00.0430.02327.839-0.161-0.1610.0000.0000.0000.000
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