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: K9763

Calculation Name: 5C59-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5C59

Chain ID: A

ChEMBL ID:

UniProt ID: Q0TJH0

Base Structure: X-ray

Registration Date: 2023-06-21

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 OptHSide
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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1999554.172742
FMO2-HF: Nuclear repulsion 1926546.406649
FMO2-HF: Total energy -73007.766093
FMO2-MP2: Total energy -73221.584175


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:14:ASN)


Summations of interaction energy for fragment #1(A:14: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.
-35.07-25.9141.947-5.175-5.9260.025
Interaction energy analysis for fragmet #1(A:14:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.076 / q_NPA : 0.045
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].
3A16ILE00.0100.0163.804-4.544-1.576-0.027-1.615-1.3260.001
4A17ASP-1-0.792-0.8576.0751.9981.9980.0000.0000.0000.000
5A18VAL0-0.035-0.0219.665-0.292-0.2920.0000.0000.0000.000
6A19TYR0-0.030-0.03812.2910.1200.1200.0000.0000.0000.000
7A20PRO0-0.044-0.01316.073-0.059-0.0590.0000.0000.0000.000
8A21GLY00.0570.03019.5570.0160.0160.0000.0000.0000.000
9A22ASN0-0.088-0.07519.898-0.012-0.0120.0000.0000.0000.000
10A23ASP-1-0.870-0.95917.331-0.093-0.0930.0000.0000.0000.000
11A24PHE0-0.025-0.01512.3560.0410.0410.0000.0000.0000.000
12A25GLY0-0.021-0.00418.354-0.014-0.0140.0000.0000.0000.000
13A26ASP-1-0.861-0.90821.1670.0740.0740.0000.0000.0000.000
14A27ASP-1-0.954-0.99323.0320.1280.1280.0000.0000.0000.000
15A28ASP-1-0.783-0.87425.0740.0900.0900.0000.0000.0000.000
16A29PRO0-0.061-0.04326.3440.0080.0080.0000.0000.0000.000
17A30GLN0-0.109-0.05328.047-0.001-0.0010.0000.0000.0000.000
18A31TYR0-0.006-0.01223.439-0.002-0.0020.0000.0000.0000.000
19A32GLN00.0100.01123.4960.0260.0260.0000.0000.0000.000
20A33GLN0-0.014-0.01323.8080.0200.0200.0000.0000.0000.000
21A34ALA00.0120.02021.748-0.004-0.0040.0000.0000.0000.000
22A35LEU0-0.0140.01516.620-0.021-0.0210.0000.0000.0000.000
23A36LYS10.9020.93420.487-0.131-0.1310.0000.0000.0000.000
24A37TYR00.048-0.00720.1970.0330.0330.0000.0000.0000.000
25A38ASP-1-0.878-0.94320.5520.1590.1590.0000.0000.0000.000
26A39ASP-1-0.787-0.89517.8240.0870.0870.0000.0000.0000.000
27A40LEU00.0010.01214.690-0.017-0.0170.0000.0000.0000.000
28A41ILE0-0.015-0.01116.466-0.001-0.0010.0000.0000.0000.000
29A42ALA0-0.056-0.03318.140-0.027-0.0270.0000.0000.0000.000
30A43ILE00.0030.00011.889-0.049-0.0490.0000.0000.0000.000
31A44GLN0-0.037-0.02913.504-0.104-0.1040.0000.0000.0000.000
32A45LYS10.9140.97714.553-0.015-0.0150.0000.0000.0000.000
33A46GLN0-0.0030.00413.030-0.094-0.0940.0000.0000.0000.000
34A47PRO00.0180.00012.6140.0160.0160.0000.0000.0000.000
35A48TRP00.0540.0247.060-0.025-0.0250.0000.0000.0000.000
36A49VAL00.0130.0317.510-0.209-0.2090.0000.0000.0000.000
37A50ALA0-0.051-0.0346.6870.0090.0090.0000.0000.0000.000
38A51SER0-0.043-0.0438.3080.1720.1720.0000.0000.0000.000
39A52ALA00.0630.0239.2690.0820.0820.0000.0000.0000.000
40A53THR0-0.0240.00610.292-0.193-0.1930.0000.0000.0000.000
41A54PRO00.0100.01012.4470.0290.0290.0000.0000.0000.000
42A55ALA00.0240.01015.1450.0920.0920.0000.0000.0000.000
43A56VAL00.0170.00316.809-0.082-0.0820.0000.0000.0000.000
44A57SER00.0190.01820.4450.0180.0180.0000.0000.0000.000
45A58GLN0-0.024-0.01423.667-0.003-0.0030.0000.0000.0000.000
46A59ASN00.0490.02327.1920.0080.0080.0000.0000.0000.000
47A60LEU0-0.048-0.02428.0660.0000.0000.0000.0000.0000.000
48A61ARG10.8610.91031.992-0.155-0.1550.0000.0000.0000.000
49A62LEU00.0140.02830.3300.0090.0090.0000.0000.0000.000
50A63ARG10.8810.92334.363-0.150-0.1500.0000.0000.0000.000
51A64TYR0-0.056-0.06036.1380.0040.0040.0000.0000.0000.000
52A65ASN00.0030.00638.151-0.007-0.0070.0000.0000.0000.000
53A66ASN0-0.020-0.02441.606-0.002-0.0020.0000.0000.0000.000
54A67VAL00.0130.03439.807-0.005-0.0050.0000.0000.0000.000
55A68ASP-1-0.805-0.89638.3820.1570.1570.0000.0000.0000.000
56A69VAL00.0180.03035.375-0.008-0.0080.0000.0000.0000.000
57A70ALA0-0.041-0.01635.9400.0090.0090.0000.0000.0000.000
58A71ALA00.0290.00331.718-0.003-0.0030.0000.0000.0000.000
59A72SER0-0.001-0.00927.088-0.003-0.0030.0000.0000.0000.000
60A73ALA0-0.0120.01325.7190.0060.0060.0000.0000.0000.000
61A74ASN0-0.017-0.01822.412-0.016-0.0160.0000.0000.0000.000
62A75GLY00.0480.01819.5500.0140.0140.0000.0000.0000.000
63A76VAL00.0000.01417.0300.0040.0040.0000.0000.0000.000
64A77SER00.0460.00711.3020.1160.1160.0000.0000.0000.000
65A78GLY00.000-0.00713.175-0.136-0.1360.0000.0000.0000.000
66A79ASP-1-0.835-0.93112.2420.6410.6410.0000.0000.0000.000
67A80TYR0-0.018-0.00814.986-0.104-0.1040.0000.0000.0000.000
68A81PHE00.0500.00517.530-0.055-0.0550.0000.0000.0000.000
69A82ASN0-0.0120.01016.180-0.077-0.0770.0000.0000.0000.000
70A83VAL0-0.0210.00614.363-0.053-0.0530.0000.0000.0000.000
71A84TYR0-0.059-0.04417.313-0.021-0.0210.0000.0000.0000.000
72A85GLY00.0150.02720.538-0.017-0.0170.0000.0000.0000.000
73A86MET0-0.090-0.05222.477-0.006-0.0060.0000.0000.0000.000
74A87THR00.0120.00523.6870.0130.0130.0000.0000.0000.000
75A88PHE0-0.025-0.03022.0620.0050.0050.0000.0000.0000.000
76A89SER0-0.056-0.01927.433-0.014-0.0140.0000.0000.0000.000
77A90GLU-1-0.760-0.88429.8670.1630.1630.0000.0000.0000.000
78A91GLY00.0210.00727.6100.0160.0160.0000.0000.0000.000
79A92ASN0-0.023-0.00522.443-0.023-0.0230.0000.0000.0000.000
80A93THR00.0450.02918.240-0.008-0.0080.0000.0000.0000.000
81A94PHE0-0.021-0.02016.734-0.004-0.0040.0000.0000.0000.000
82A95ASN00.0410.01015.7560.0690.0690.0000.0000.0000.000
83A96GLN00.0610.0027.488-0.060-0.0600.0000.0000.0000.000
84A97GLU-1-0.869-0.92113.0740.6980.6980.0000.0000.0000.000
85A98GLN00.0220.00315.389-0.022-0.0220.0000.0000.0000.000
86A99LEU0-0.0410.00311.487-0.043-0.0430.0000.0000.0000.000
87A100ASN0-0.0160.0029.7770.1190.1190.0000.0000.0000.000
88A101GLY00.0000.00913.599-0.079-0.0790.0000.0000.0000.000
89A102ARG10.8740.93713.291-1.102-1.1020.0000.0000.0000.000
90A103ALA00.0390.03518.246-0.077-0.0770.0000.0000.0000.000
91A104GLN0-0.044-0.03020.9790.0280.0280.0000.0000.0000.000
92A105VAL0-0.034-0.00521.430-0.039-0.0390.0000.0000.0000.000
93A106VAL0-0.018-0.02823.3230.0270.0270.0000.0000.0000.000
94A107VAL00.0150.02322.932-0.018-0.0180.0000.0000.0000.000
95A108LEU0-0.0010.00325.638-0.001-0.0010.0000.0000.0000.000
96A109ASP-1-0.712-0.82228.5370.1930.1930.0000.0000.0000.000
97A110SER00.0310.00429.916-0.007-0.0070.0000.0000.0000.000
98A111ASN00.004-0.01333.362-0.004-0.0040.0000.0000.0000.000
99A112THR00.030-0.02431.594-0.004-0.0040.0000.0000.0000.000
100A113ARG10.8070.90932.987-0.157-0.1570.0000.0000.0000.000
101A114ARG10.9450.96034.769-0.120-0.1200.0000.0000.0000.000
102A115GLN0-0.046-0.01937.527-0.011-0.0110.0000.0000.0000.000
103A116LEU0-0.023-0.00233.486-0.004-0.0040.0000.0000.0000.000
104A117PHE0-0.068-0.04733.765-0.003-0.0030.0000.0000.0000.000
105A118PRO0-0.015-0.00338.967-0.001-0.0010.0000.0000.0000.000
106A119HIS0-0.018-0.01341.9340.0010.0010.0000.0000.0000.000
107A120LYS10.9550.99239.180-0.132-0.1320.0000.0000.0000.000
108A121ALA00.0150.00839.6660.0020.0020.0000.0000.0000.000
109A122ASP-1-0.880-0.93035.1490.1410.1410.0000.0000.0000.000
110A123VAL0-0.029-0.02632.088-0.002-0.0020.0000.0000.0000.000
111A124VAL0-0.026-0.00628.9790.0120.0120.0000.0000.0000.000
112A125GLY0-0.001-0.00230.616-0.010-0.0100.0000.0000.0000.000
113A126GLU-1-0.846-0.90331.8470.1620.1620.0000.0000.0000.000
114A127VAL0-0.049-0.02931.4970.0210.0210.0000.0000.0000.000
115A128ILE00.0120.01829.875-0.016-0.0160.0000.0000.0000.000
116A129LEU0-0.008-0.01331.7960.0140.0140.0000.0000.0000.000
117A130VAL00.0380.01527.013-0.010-0.0100.0000.0000.0000.000
118A131GLY00.0310.01029.9500.0120.0120.0000.0000.0000.000
119A132ASN0-0.045-0.03031.459-0.020-0.0200.0000.0000.0000.000
120A133MET0-0.0500.00024.5800.0060.0060.0000.0000.0000.000
121A134PRO00.0020.00429.8150.0020.0020.0000.0000.0000.000
122A135ALA00.0060.00626.7310.0270.0270.0000.0000.0000.000
123A136ARG10.9310.97127.115-0.273-0.2730.0000.0000.0000.000
124A137VAL00.0200.01026.8950.0290.0290.0000.0000.0000.000
125A138ILE00.004-0.00422.104-0.013-0.0130.0000.0000.0000.000
126A139GLY00.0310.02126.2890.0010.0010.0000.0000.0000.000
127A140VAL0-0.101-0.04827.2230.0030.0030.0000.0000.0000.000
128A141ALA00.0500.03326.154-0.009-0.0090.0000.0000.0000.000
129A154LEU0-0.065-0.03132.6720.0000.0000.0000.0000.0000.000
130A155ARG10.9530.96426.034-0.212-0.2120.0000.0000.0000.000
131A156VAL00.0000.00827.003-0.005-0.0050.0000.0000.0000.000
132A157TRP00.0490.02121.7580.0030.0030.0000.0000.0000.000
133A158LEU0-0.007-0.01821.616-0.017-0.0170.0000.0000.0000.000
134A159PRO00.0550.04616.7820.0340.0340.0000.0000.0000.000
135A160TYR00.0580.0239.876-0.066-0.0660.0000.0000.0000.000
136A161SER0-0.082-0.05314.413-0.098-0.0980.0000.0000.0000.000
137A162THR0-0.015-0.01916.322-0.042-0.0420.0000.0000.0000.000
138A163MET00.000-0.00819.576-0.075-0.0750.0000.0000.0000.000
139A164SER0-0.020-0.02017.075-0.018-0.0180.0000.0000.0000.000
140A165GLY0-0.0210.00019.481-0.030-0.0300.0000.0000.0000.000
141A166ARG10.9100.95422.337-0.409-0.4090.0000.0000.0000.000
142A167VAL0-0.015-0.00121.308-0.035-0.0350.0000.0000.0000.000
143A168MET0-0.0020.00923.913-0.026-0.0260.0000.0000.0000.000
144A169GLY0-0.003-0.00327.6510.0000.0000.0000.0000.0000.000
145A170GLN0-0.004-0.00729.663-0.013-0.0130.0000.0000.0000.000
146A171SER0-0.0370.00025.1000.0020.0020.0000.0000.0000.000
147A172TRP0-0.028-0.00824.096-0.020-0.0200.0000.0000.0000.000
148A173LEU0-0.012-0.00718.4090.0400.0400.0000.0000.0000.000
149A174ASN0-0.063-0.04818.715-0.013-0.0130.0000.0000.0000.000
150A175SER00.0420.01414.5350.0420.0420.0000.0000.0000.000
151A176ILE0-0.038-0.02212.4850.0190.0190.0000.0000.0000.000
152A177THR00.0050.0077.551-0.022-0.0220.0000.0000.0000.000
153A178VAL0-0.028-0.0237.9950.1130.1130.0000.0000.0000.000
154A179ARG10.9120.9742.253-22.885-19.9851.399-2.031-2.2670.031
155A180VAL00.0480.0322.724-1.822-0.7290.253-0.444-0.9020.000
156A181LYS10.8140.9154.4690.2450.433-0.001-0.014-0.1730.000
157A182GLU-1-0.935-0.9805.978-1.529-1.5290.0000.0000.0000.000
158A183GLY00.0600.0366.9480.3310.3310.0000.0000.0000.000
159A184PHE0-0.080-0.0456.9390.2560.2560.0000.0000.0000.000
160A185ASP-1-0.848-0.9146.139-0.671-0.6710.0000.0000.0000.000
161A186SER00.007-0.0282.774-0.0830.4000.206-0.265-0.4240.000
162A187ALA00.0510.0304.635-0.222-0.214-0.001-0.0070.0000.000
163A188GLU-1-0.838-0.9207.846-0.347-0.3470.0000.0000.0000.000
164A189ALA0-0.0150.0056.1620.0850.0850.0000.0000.0000.000
165A190GLU-1-0.771-0.8617.171-0.682-0.6820.0000.0000.0000.000
166A191GLN00.0270.0148.6370.2390.2390.0000.0000.0000.000
167A192GLN0-0.065-0.02311.3980.0710.0710.0000.0000.0000.000
168A193LEU00.0080.0159.0140.1120.1120.0000.0000.0000.000
169A194THR0-0.014-0.01812.0600.1290.1290.0000.0000.0000.000
170A195ARG10.8360.88313.9960.3850.3850.0000.0000.0000.000
171A196LEU0-0.0210.00814.7120.0390.0390.0000.0000.0000.000
172A197LEU00.007-0.00114.0700.0430.0430.0000.0000.0000.000
173A198SER00.0230.01617.5570.0250.0250.0000.0000.0000.000
174A199LEU0-0.058-0.02019.5640.0140.0140.0000.0000.0000.000
175A200ARG10.8140.89018.989-0.046-0.0460.0000.0000.0000.000
176A201HIS10.7830.90119.745-0.043-0.0430.0000.0000.0000.000
177A202GLY0-0.0190.01423.6140.0070.0070.0000.0000.0000.000
178A203LYS10.8730.91824.101-0.053-0.0530.0000.0000.0000.000
179A204LYS10.9160.94417.2650.0660.0660.0000.0000.0000.000
180A205ASP-1-0.835-0.91321.4990.0510.0510.0000.0000.0000.000
181A206PHE0-0.0020.02214.7210.0240.0240.0000.0000.0000.000
182A207PHE0-0.0020.02214.874-0.036-0.0360.0000.0000.0000.000
183A208THR0-0.040-0.04310.0360.1130.1130.0000.0000.0000.000
184A209TRP00.0410.0179.1440.0630.0630.0000.0000.0000.000
185A210ASN0-0.054-0.0274.217-1.175-1.095-0.001-0.020-0.0590.000
186A211MET00.0080.0092.966-3.780-2.3440.119-0.779-0.775-0.007