FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 52L6Z

Calculation Name: 5K9N-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 5K9N

Chain ID: A

ChEMBL ID:
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UniProt ID: Q9W469

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 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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2423921.225275
FMO2-HF: Nuclear repulsion 2342581.61515
FMO2-HF: Total energy -81339.610125
FMO2-MP2: Total energy -81577.07337


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:7:ASP)


Summations of interaction energy for fragment #1(A:7:ASP)
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.
-15.45-11.839-0.01-1.654-1.9450.003
Interaction energy analysis for fragmet #1(A:7:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.941 / q_NPA : -0.986
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].
3A9ILE0-0.092-0.0343.417-8.933-5.948-0.013-1.435-1.5370.002
4A10VAL00.0310.0184.5294.5514.671-0.001-0.010-0.1080.000
5A11VAL0-0.023-0.0057.131-2.828-2.8280.0000.0000.0000.000
6A12ARG10.9180.9649.140-18.171-18.1710.0000.0000.0000.000
7A13GLN0-0.007-0.01312.487-1.243-1.2430.0000.0000.0000.000
8A14VAL0-0.045-0.01416.0540.0800.0800.0000.0000.0000.000
9A15ASP-1-0.826-0.91218.57312.96412.9640.0000.0000.0000.000
10A16VAL0-0.022-0.03521.466-0.232-0.2320.0000.0000.0000.000
11A17GLY0-0.0170.00024.433-0.393-0.3930.0000.0000.0000.000
12A18GLU-1-0.919-0.95418.16215.94115.9410.0000.0000.0000.000
13A19THR00.0280.00421.5220.3730.3730.0000.0000.0000.000
14A20GLU-1-0.891-0.94023.73010.68910.6890.0000.0000.0000.000
15A21GLN0-0.007-0.01820.401-0.208-0.2080.0000.0000.0000.000
16A22LEU00.0230.02419.4680.3540.3540.0000.0000.0000.000
17A23MET00.0070.01021.2230.0140.0140.0000.0000.0000.000
18A24THR0-0.030-0.02223.346-0.260-0.2600.0000.0000.0000.000
19A25PHE0-0.051-0.01917.428-0.018-0.0180.0000.0000.0000.000
20A26LEU00.0160.01121.415-0.032-0.0320.0000.0000.0000.000
21A27LEU0-0.009-0.01223.279-0.270-0.2700.0000.0000.0000.000
22A28ALA0-0.042-0.01122.783-0.312-0.3120.0000.0000.0000.000
23A29HIS0-0.019-0.01820.294-0.131-0.1310.0000.0000.0000.000
24A30TYR0-0.014-0.01821.7930.4930.4930.0000.0000.0000.000
25A31TYR0-0.023-0.04523.843-0.150-0.1500.0000.0000.0000.000
26A32PRO0-0.0370.00626.167-0.337-0.3370.0000.0000.0000.000
27A33GLU-1-0.918-0.97424.81411.75311.7530.0000.0000.0000.000
28A34GLU-1-0.854-0.92727.17510.31810.3180.0000.0000.0000.000
29A35PRO0-0.008-0.01028.743-0.394-0.3940.0000.0000.0000.000
30A36LEU00.0290.01531.612-0.465-0.4650.0000.0000.0000.000
31A37THR0-0.007-0.00230.926-0.356-0.3560.0000.0000.0000.000
32A38ALA00.0200.01432.959-0.286-0.2860.0000.0000.0000.000
33A39GLY0-0.028-0.01134.629-0.249-0.2490.0000.0000.0000.000
34A40THR0-0.0200.00636.746-0.245-0.2450.0000.0000.0000.000
35A41HIS00.025-0.01038.4590.1740.1740.0000.0000.0000.000
36A42PRO00.0050.01939.873-0.050-0.0500.0000.0000.0000.000
37A43PRO0-0.0080.01336.6930.1500.1500.0000.0000.0000.000
38A44GLU-1-0.937-0.97234.1618.9998.9990.0000.0000.0000.000
39A45PRO0-0.033-0.00330.788-0.199-0.1990.0000.0000.0000.000
40A46GLU-1-0.851-0.95333.6777.8107.8100.0000.0000.0000.000
41A47ALA0-0.012-0.02833.9410.2810.2810.0000.0000.0000.000
42A48ALA00.0580.02333.7840.2090.2090.0000.0000.0000.000
43A49ASP-1-0.857-0.88730.91510.07210.0720.0000.0000.0000.000
44A50LYS10.9760.96429.348-9.369-9.3690.0000.0000.0000.000
45A51GLU-1-0.966-0.98629.0899.2579.2570.0000.0000.0000.000
46A52PHE00.0490.03029.2290.2280.2280.0000.0000.0000.000
47A53LEU0-0.0040.00125.0570.4180.4180.0000.0000.0000.000
48A54LEU0-0.023-0.02924.9130.4450.4450.0000.0000.0000.000
49A55SER0-0.046-0.01026.6980.2290.2290.0000.0000.0000.000
50A56ASN00.001-0.02024.8430.0430.0430.0000.0000.0000.000
51A57VAL00.002-0.00722.4100.3800.3800.0000.0000.0000.000
52A58PRO0-0.032-0.00923.5940.4540.4540.0000.0000.0000.000
53A59PHE0-0.0130.01124.980-0.059-0.0590.0000.0000.0000.000
54A60GLY00.0430.01821.2630.2720.2720.0000.0000.0000.000
55A61THR0-0.086-0.06619.9810.7910.7910.0000.0000.0000.000
56A62CYS0-0.0090.03819.329-0.020-0.0200.0000.0000.0000.000
57A63PHE00.0070.00613.7430.6360.6360.0000.0000.0000.000
58A64VAL00.0260.01413.660-0.639-0.6390.0000.0000.0000.000
59A65ALA00.006-0.0079.5671.8791.8790.0000.0000.0000.000
60A66LEU0-0.054-0.0269.660-1.777-1.7770.0000.0000.0000.000
61A67HIS00.0060.0018.6121.9071.9070.0000.0000.0000.000
62A68GLU-1-0.893-0.95710.02217.54517.5450.0000.0000.0000.000
63A69GLY0-0.016-0.00711.703-1.423-1.4230.0000.0000.0000.000
64A70ARG10.9330.97213.693-19.030-19.0300.0000.0000.0000.000
65A71ILE00.0040.00413.4321.5301.5300.0000.0000.0000.000
66A72VAL0-0.031-0.01710.746-0.676-0.6760.0000.0000.0000.000
67A73ALA0-0.021-0.02212.786-0.370-0.3700.0000.0000.0000.000
68A74ALA00.0220.01114.4930.5660.5660.0000.0000.0000.000
69A75VAL0-0.019-0.00515.946-0.314-0.3140.0000.0000.0000.000
70A76VAL00.0150.00118.1820.2010.2010.0000.0000.0000.000
71A77ALA00.0280.00521.108-0.283-0.2830.0000.0000.0000.000
72A78GLY00.0700.06122.7850.1370.1370.0000.0000.0000.000
73A79PRO0-0.090-0.03125.5510.0330.0330.0000.0000.0000.000
74A80LYS10.8560.92027.655-10.478-10.4780.0000.0000.0000.000
75A81ASP-1-0.768-0.92531.0479.1879.1870.0000.0000.0000.000
76A82SER0-0.044-0.03934.138-0.078-0.0780.0000.0000.0000.000
77A83HIS0-0.056-0.01937.214-0.233-0.2330.0000.0000.0000.000
78A84GLU-1-0.887-0.92733.0859.2459.2450.0000.0000.0000.000
79A85PRO0-0.034-0.01636.345-0.096-0.0960.0000.0000.0000.000
80A86GLU-1-0.945-0.97138.9157.3087.3080.0000.0000.0000.000
81A87HIS00.0200.01236.917-0.219-0.2190.0000.0000.0000.000
82A88MET00.0210.00334.613-0.073-0.0730.0000.0000.0000.000
83A89ALA0-0.035-0.01238.273-0.116-0.1160.0000.0000.0000.000
84A90GLU-1-0.897-0.95941.9126.8086.8080.0000.0000.0000.000
85A91GLU-1-0.955-0.98736.0828.5648.5640.0000.0000.0000.000
86A92ALA00.0070.00140.444-0.050-0.0500.0000.0000.0000.000
87A93ARG10.8380.93241.604-6.885-6.8850.0000.0000.0000.000
88A94LYS10.8550.92741.054-7.785-7.7850.0000.0000.0000.000
89A95TYR00.006-0.00339.214-0.082-0.0820.0000.0000.0000.000
90A96ALA0-0.0110.02942.9450.0350.0350.0000.0000.0000.000
91A97GLY0-0.006-0.01445.056-0.095-0.0950.0000.0000.0000.000
92A98GLY00.0170.01043.112-0.107-0.1070.0000.0000.0000.000
93A99LYS10.7880.87035.377-8.532-8.5320.0000.0000.0000.000
94A100TRP00.0810.02632.5300.0770.0770.0000.0000.0000.000
95A101GLY00.0490.03438.0020.0720.0720.0000.0000.0000.000
96A102SER0-0.043-0.01939.958-0.071-0.0710.0000.0000.0000.000
97A103ILE0-0.013-0.01233.6900.0140.0140.0000.0000.0000.000
98A104LEU00.0250.01335.5590.1070.1070.0000.0000.0000.000
99A105HIS0-0.052-0.01437.647-0.162-0.1620.0000.0000.0000.000
100A106LEU0-0.026-0.02134.903-0.045-0.0450.0000.0000.0000.000
101A107LEU00.0290.00432.0110.0420.0420.0000.0000.0000.000
102A108SER00.0160.01935.5810.0970.0970.0000.0000.0000.000
103A109ALA00.0100.00038.288-0.048-0.0480.0000.0000.0000.000
104A110VAL0-0.008-0.00533.373-0.053-0.0530.0000.0000.0000.000
105A111GLU-1-0.794-0.86133.3979.6199.6190.0000.0000.0000.000
106A112THR0-0.005-0.01035.936-0.101-0.1010.0000.0000.0000.000
107A113ALA0-0.048-0.01238.475-0.106-0.1060.0000.0000.0000.000
108A114THR0-0.154-0.11633.8080.0790.0790.0000.0000.0000.000
109A115ASP-1-0.838-0.91636.1858.3598.3590.0000.0000.0000.000
110A116VAL00.031-0.01030.995-0.052-0.0520.0000.0000.0000.000
111A117CYS0-0.0290.02433.5640.1030.1030.0000.0000.0000.000
112A118ARG10.9690.98034.888-8.101-8.1010.0000.0000.0000.000
113A119ARG10.8750.97735.647-8.783-8.7830.0000.0000.0000.000
114A120PHE0-0.030-0.03432.480-0.021-0.0210.0000.0000.0000.000
115A121SER0-0.076-0.01935.0870.0020.0020.0000.0000.0000.000
116A122VAL0-0.025-0.01431.0420.1150.1150.0000.0000.0000.000
117A123PRO0-0.036-0.01732.289-0.204-0.2040.0000.0000.0000.000
118A124SER0-0.002-0.02329.174-0.152-0.1520.0000.0000.0000.000
119A125CYS0-0.045-0.00127.6560.2590.2590.0000.0000.0000.000
120A126LEU0-0.0080.01421.151-0.090-0.0900.0000.0000.0000.000
121A127HIS00.0510.03124.9880.2800.2800.0000.0000.0000.000
122A128VAL0-0.027-0.03720.7370.2880.2880.0000.0000.0000.000
123A129HIS00.0250.01023.540-0.294-0.2940.0000.0000.0000.000
124A130ALA00.0070.01323.102-0.259-0.2590.0000.0000.0000.000
125A131LEU0-0.036-0.01816.2540.8050.8050.0000.0000.0000.000
126A132GLY00.0450.03218.762-0.622-0.6220.0000.0000.0000.000
127A133VAL0-0.072-0.05514.6411.3171.3170.0000.0000.0000.000
128A134ASP-1-0.778-0.87515.60615.42215.4220.0000.0000.0000.000
129A135PRO0-0.020-0.01515.5921.1631.1630.0000.0000.0000.000
130A136GLN0-0.056-0.03516.9330.0920.0920.0000.0000.0000.000
131A137LEU0-0.0110.00910.6960.6850.6850.0000.0000.0000.000
132A138ARG10.9660.97212.047-14.217-14.2170.0000.0000.0000.000
133A139GLY0-0.004-0.00711.1370.4590.4590.0000.0000.0000.000
134A140ARG10.9390.9756.472-29.521-29.5210.0000.0000.0000.000
135A141ASN0-0.018-0.0197.9750.1310.1310.0000.0000.0000.000
136A142LEU00.0580.0339.1120.9190.9190.0000.0000.0000.000
137A143GLY00.0740.04211.176-0.006-0.0060.0000.0000.0000.000
138A144GLY00.0080.00512.998-0.443-0.4430.0000.0000.0000.000
139A145ARG10.9360.9713.496-49.224-48.7180.004-0.209-0.3000.001
140A146LEU00.0150.03210.5450.0380.0380.0000.0000.0000.000
141A147MET00.0340.01113.010-0.792-0.7920.0000.0000.0000.000
142A148GLU-1-0.916-0.96612.20620.96020.9600.0000.0000.0000.000
143A149THR0-0.067-0.04111.4050.4210.4210.0000.0000.0000.000
144A150VAL0-0.015-0.01413.641-0.778-0.7780.0000.0000.0000.000
145A151ALA00.0100.01816.999-0.895-0.8950.0000.0000.0000.000
146A152GLN0-0.0010.00914.091-0.546-0.5460.0000.0000.0000.000
147A153ARG10.8660.94216.837-15.933-15.9330.0000.0000.0000.000
148A154GLY00.040-0.00818.346-0.862-0.8620.0000.0000.0000.000
149A155ARG10.8810.92716.407-18.791-18.7910.0000.0000.0000.000
150A156ASP-1-0.921-0.95317.57617.57217.5720.0000.0000.0000.000
151A157LEU0-0.098-0.05920.826-0.619-0.6190.0000.0000.0000.000
152A158GLY00.0050.02123.764-0.597-0.5970.0000.0000.0000.000
153A159HIS00.0130.02124.260-0.665-0.6650.0000.0000.0000.000
154A160GLN00.017-0.00725.3870.1920.1920.0000.0000.0000.000
155A161LEU0-0.024-0.00626.565-0.014-0.0140.0000.0000.0000.000
156A162VAL00.0220.01321.3960.2530.2530.0000.0000.0000.000
157A163SER0-0.003-0.02424.718-0.297-0.2970.0000.0000.0000.000
158A164VAL0-0.0070.00123.0550.3660.3660.0000.0000.0000.000
159A165ASP-1-0.758-0.85625.85910.14110.1410.0000.0000.0000.000
160A166CYS0-0.102-0.03725.3140.3620.3620.0000.0000.0000.000
161A167THR00.0740.04727.042-0.486-0.4860.0000.0000.0000.000
162A168SER00.0530.01924.707-0.136-0.1360.0000.0000.0000.000
163A169VAL00.0310.01025.2440.2000.2000.0000.0000.0000.000
164A170TYR0-0.002-0.00716.0410.4230.4230.0000.0000.0000.000
165A171SER00.0160.00521.6410.3820.3820.0000.0000.0000.000
166A172ALA00.1100.05522.5410.3680.3680.0000.0000.0000.000
167A173ARG10.9240.96221.396-11.994-11.9940.0000.0000.0000.000
168A174LEU0-0.046-0.02615.9350.4440.4440.0000.0000.0000.000
169A175VAL00.0650.02419.3280.5880.5880.0000.0000.0000.000
170A176GLN0-0.0020.00721.4110.1800.1800.0000.0000.0000.000
171A177ARG10.8600.93413.248-19.785-19.7850.0000.0000.0000.000
172A178LEU0-0.075-0.02815.2580.7900.7900.0000.0000.0000.000
173A179GLY0-0.0060.00219.0230.0250.0250.0000.0000.0000.000
174A180TYR0-0.026-0.00920.216-0.136-0.1360.0000.0000.0000.000
175A181GLN0-0.024-0.02124.602-0.282-0.2820.0000.0000.0000.000
176A182LEU0-0.043-0.01028.3700.0250.0250.0000.0000.0000.000
177A183ILE00.002-0.00130.520-0.298-0.2980.0000.0000.0000.000
178A184ASN0-0.025-0.01933.321-0.289-0.2890.0000.0000.0000.000
179A185THR0-0.014-0.01733.7260.3450.3450.0000.0000.0000.000
180A186LEU00.0370.04435.799-0.266-0.2660.0000.0000.0000.000
181A187ARG10.8630.90336.859-7.342-7.3420.0000.0000.0000.000
182A188TYR00.0430.02332.899-0.162-0.1620.0000.0000.0000.000
183A189VAL0-0.046-0.02539.453-0.149-0.1490.0000.0000.0000.000
184A190ASP-1-0.839-0.89741.9867.2247.2240.0000.0000.0000.000
185A191HIS0-0.0130.00640.686-0.033-0.0330.0000.0000.0000.000
186A192LEU0-0.033-0.00243.0810.0140.0140.0000.0000.0000.000
187A193ASP-1-0.768-0.89045.9036.6286.6280.0000.0000.0000.000
188A194ALA0-0.011-0.00947.331-0.105-0.1050.0000.0000.0000.000
189A195SER0-0.054-0.02750.567-0.180-0.1800.0000.0000.0000.000
190A196GLY0-0.037-0.01950.414-0.117-0.1170.0000.0000.0000.000
191A197GLN0-0.070-0.04748.6090.0730.0730.0000.0000.0000.000
192A198GLN0-0.059-0.03541.530-0.055-0.0550.0000.0000.0000.000
193A199VAL00.0130.01840.919-0.011-0.0110.0000.0000.0000.000
194A200ILE00.0240.01836.2750.0560.0560.0000.0000.0000.000
195A201ARG10.9010.93939.718-7.107-7.1070.0000.0000.0000.000
196A202PRO00.0310.03234.856-0.047-0.0470.0000.0000.0000.000
197A203PRO0-0.0100.00834.012-0.180-0.1800.0000.0000.0000.000
198A204PRO00.0110.01035.1850.1670.1670.0000.0000.0000.000
199A205PRO0-0.052-0.02931.1390.1010.1010.0000.0000.0000.000
200A206HIS0-0.002-0.01629.8460.4030.4030.0000.0000.0000.000
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