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: QY73Y

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 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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1998620.905989
FMO2-HF: Nuclear repulsion 1925614.407057
FMO2-HF: Total energy -73006.498932
FMO2-MP2: Total energy -73220.419486


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.
-19.055-11.9520.888-3.575-4.415-0.011
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 : 0.041 / q_NPA : 0.027
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].
3A16ILE00.0130.0233.804-3.671-0.986-0.031-1.453-1.2010.001
4A17ASP-1-0.851-0.9186.0260.2650.2650.0000.0000.0000.000
5A18VAL0-0.029-0.0259.612-0.071-0.0710.0000.0000.0000.000
6A19TYR0-0.010-0.01311.9790.1290.1290.0000.0000.0000.000
7A20PRO0-0.051-0.01516.0240.0030.0030.0000.0000.0000.000
8A21GLY00.0330.01619.510-0.018-0.0180.0000.0000.0000.000
9A22ASN0-0.084-0.06719.8600.0000.0000.0000.0000.0000.000
10A23ASP-1-0.875-0.95117.351-0.289-0.2890.0000.0000.0000.000
11A24PHE0-0.038-0.03212.4130.0050.0050.0000.0000.0000.000
12A25GLY0-0.025-0.00918.3680.0160.0160.0000.0000.0000.000
13A26ASP-1-0.830-0.88121.186-0.080-0.0800.0000.0000.0000.000
14A27ASP-1-0.954-0.99723.044-0.100-0.1000.0000.0000.0000.000
15A28ASP-1-0.788-0.88225.084-0.034-0.0340.0000.0000.0000.000
16A29PRO0-0.060-0.04626.3080.0060.0060.0000.0000.0000.000
17A30GLN0-0.084-0.03327.9160.0220.0220.0000.0000.0000.000
18A31TYR0-0.023-0.01823.3430.0180.0180.0000.0000.0000.000
19A32GLN00.0420.01323.450-0.006-0.0060.0000.0000.0000.000
20A33GLN0-0.012-0.00623.7190.0200.0200.0000.0000.0000.000
21A34ALA0-0.0030.02021.7410.0200.0200.0000.0000.0000.000
22A35LEU0-0.0260.00716.5040.0160.0160.0000.0000.0000.000
23A36LYS10.8860.91420.443-0.088-0.0880.0000.0000.0000.000
24A37TYR00.040-0.02320.1550.0310.0310.0000.0000.0000.000
25A38ASP-1-0.884-0.95020.4740.2440.2440.0000.0000.0000.000
26A39ASP-1-0.837-0.91217.8430.1830.1830.0000.0000.0000.000
27A40LEU00.0170.01214.6550.0360.0360.0000.0000.0000.000
28A41ILE0-0.014-0.00416.4440.0790.0790.0000.0000.0000.000
29A42ALA0-0.063-0.04218.1190.0380.0380.0000.0000.0000.000
30A43ILE00.000-0.00111.9200.0130.0130.0000.0000.0000.000
31A44GLN0-0.024-0.02213.4810.0550.0550.0000.0000.0000.000
32A45LYS10.9180.97914.532-0.314-0.3140.0000.0000.0000.000
33A46GLN0-0.025-0.01313.131-0.044-0.0440.0000.0000.0000.000
34A47PRO00.0280.00612.5990.1210.1210.0000.0000.0000.000
35A48TRP00.0490.0317.3210.1770.1770.0000.0000.0000.000
36A49VAL00.0010.0217.4980.3970.3970.0000.0000.0000.000
37A50ALA0-0.043-0.0505.991-0.161-0.1610.0000.0000.0000.000
38A51SER0-0.071-0.0527.418-0.570-0.5700.0000.0000.0000.000
39A52ALA00.0550.0198.8700.1020.1020.0000.0000.0000.000
40A53THR0-0.031-0.00110.612-0.150-0.1500.0000.0000.0000.000
41A54PRO00.0070.01112.565-0.068-0.0680.0000.0000.0000.000
42A55ALA00.0360.01515.6060.0180.0180.0000.0000.0000.000
43A56VAL00.0000.00317.299-0.034-0.0340.0000.0000.0000.000
44A57SER00.0090.01120.888-0.033-0.0330.0000.0000.0000.000
45A58GLN00.0290.01624.2000.0230.0230.0000.0000.0000.000
46A59ASN00.0650.03027.705-0.014-0.0140.0000.0000.0000.000
47A60LEU0-0.054-0.03828.4020.0090.0090.0000.0000.0000.000
48A61ARG10.8590.93932.614-0.022-0.0220.0000.0000.0000.000
49A62LEU00.0090.02331.0540.0030.0030.0000.0000.0000.000
50A63ARG10.9220.95935.158-0.010-0.0100.0000.0000.0000.000
51A64TYR0-0.024-0.02036.9910.0000.0000.0000.0000.0000.000
52A65ASN00.0270.01339.0480.0020.0020.0000.0000.0000.000
53A66ASN0-0.039-0.02742.434-0.003-0.0030.0000.0000.0000.000
54A67VAL00.0100.03440.4530.0020.0020.0000.0000.0000.000
55A68ASP-1-0.801-0.94738.7160.0130.0130.0000.0000.0000.000
56A69VAL0-0.0090.03136.145-0.001-0.0010.0000.0000.0000.000
57A70ALA0-0.044-0.01836.6340.0040.0040.0000.0000.0000.000
58A71ALA00.0260.00332.414-0.006-0.0060.0000.0000.0000.000
59A72SER0-0.010-0.02227.7110.0120.0120.0000.0000.0000.000
60A73ALA0-0.0240.00726.402-0.011-0.0110.0000.0000.0000.000
61A74ASN00.0240.01323.0590.0220.0220.0000.0000.0000.000
62A75GLY00.0350.00920.215-0.018-0.0180.0000.0000.0000.000
63A76VAL00.0060.01017.8090.0170.0170.0000.0000.0000.000
64A77SER00.0560.01212.0340.0400.0400.0000.0000.0000.000
65A78GLY0-0.008-0.01413.8640.0000.0000.0000.0000.0000.000
66A79ASP-1-0.865-0.93811.641-0.736-0.7360.0000.0000.0000.000
67A80TYR0-0.026-0.02015.0440.0060.0060.0000.0000.0000.000
68A81PHE00.0510.00417.5310.0110.0110.0000.0000.0000.000
69A82ASN00.0260.02316.8260.0500.0500.0000.0000.0000.000
70A83VAL0-0.0210.01214.438-0.002-0.0020.0000.0000.0000.000
71A84TYR0-0.069-0.05517.3200.0190.0190.0000.0000.0000.000
72A85GLY00.0160.02720.5450.0220.0220.0000.0000.0000.000
73A86MET0-0.086-0.05222.4870.0290.0290.0000.0000.0000.000
74A87THR0-0.006-0.00323.659-0.017-0.0170.0000.0000.0000.000
75A88PHE0-0.013-0.02222.0540.0120.0120.0000.0000.0000.000
76A89SER0-0.068-0.03927.4860.0000.0000.0000.0000.0000.000
77A90GLU-1-0.795-0.91229.981-0.089-0.0890.0000.0000.0000.000
78A91GLY00.0100.00927.9670.0000.0000.0000.0000.0000.000
79A92ASN0-0.0140.00322.629-0.006-0.0060.0000.0000.0000.000
80A93THR00.0470.02118.3570.0400.0400.0000.0000.0000.000
81A94PHE0-0.031-0.02117.4520.0030.0030.0000.0000.0000.000
82A95ASN00.0970.04716.141-0.014-0.0140.0000.0000.0000.000
83A96GLN00.0720.0027.734-0.038-0.0380.0000.0000.0000.000
84A97GLU-1-0.938-0.96413.187-0.257-0.2570.0000.0000.0000.000
85A98GLN00.0090.00215.1660.0690.0690.0000.0000.0000.000
86A99LEU0-0.0210.01212.1110.0420.0420.0000.0000.0000.000
87A100ASN0-0.0180.0219.9990.2460.2460.0000.0000.0000.000
88A101GLY00.0110.00713.7120.0530.0530.0000.0000.0000.000
89A102ARG10.8610.93413.406-0.349-0.3490.0000.0000.0000.000
90A103ALA00.0520.04418.615-0.001-0.0010.0000.0000.0000.000
91A104GLN0-0.043-0.02021.2760.0180.0180.0000.0000.0000.000
92A105VAL0-0.033-0.00321.996-0.008-0.0080.0000.0000.0000.000
93A106VAL0-0.024-0.02624.1420.0120.0120.0000.0000.0000.000
94A107VAL00.0240.02523.550-0.010-0.0100.0000.0000.0000.000
95A108LEU0-0.007-0.00426.4290.0140.0140.0000.0000.0000.000
96A109ASP-1-0.720-0.84829.043-0.066-0.0660.0000.0000.0000.000
97A110SER00.0310.00630.3740.0060.0060.0000.0000.0000.000
98A111ASN0-0.011-0.02033.6910.0010.0010.0000.0000.0000.000
99A112THR00.040-0.00931.9630.0040.0040.0000.0000.0000.000
100A113ARG10.8980.95833.7550.0740.0740.0000.0000.0000.000
101A114ARG10.8950.94235.4430.0550.0550.0000.0000.0000.000
102A115GLN0-0.027-0.01138.2310.0060.0060.0000.0000.0000.000
103A116LEU00.0010.00934.4680.0040.0040.0000.0000.0000.000
104A117PHE0-0.011-0.02434.6110.0010.0010.0000.0000.0000.000
105A118PRO0-0.034-0.01239.797-0.004-0.0040.0000.0000.0000.000
106A119HIS0-0.020-0.01642.628-0.003-0.0030.0000.0000.0000.000
107A120LYS10.9010.96339.8200.0400.0400.0000.0000.0000.000
108A121ALA0-0.015-0.01040.175-0.002-0.0020.0000.0000.0000.000
109A122ASP-1-0.842-0.90435.520-0.095-0.0950.0000.0000.0000.000
110A123VAL0-0.043-0.03332.6530.0060.0060.0000.0000.0000.000
111A124VAL0-0.032-0.01429.2490.0040.0040.0000.0000.0000.000
112A125GLY0-0.017-0.00531.125-0.001-0.0010.0000.0000.0000.000
113A126GLU-1-0.911-0.95232.234-0.037-0.0370.0000.0000.0000.000
114A127VAL0-0.053-0.02632.007-0.001-0.0010.0000.0000.0000.000
115A128ILE00.0000.01030.6710.0040.0040.0000.0000.0000.000
116A129LEU0-0.014-0.01532.5540.0030.0030.0000.0000.0000.000
117A130VAL00.0410.01627.8930.0000.0000.0000.0000.0000.000
118A131GLY00.0170.01030.6500.0110.0110.0000.0000.0000.000
119A132ASN0-0.041-0.02932.071-0.009-0.0090.0000.0000.0000.000
120A133MET0-0.057-0.01225.2560.0070.0070.0000.0000.0000.000
121A134PRO00.0100.01030.303-0.005-0.0050.0000.0000.0000.000
122A135ALA00.0070.00627.5080.0050.0050.0000.0000.0000.000
123A136ARG10.9710.98627.6270.0470.0470.0000.0000.0000.000
124A137VAL00.0310.01627.529-0.005-0.0050.0000.0000.0000.000
125A138ILE00.005-0.00622.934-0.003-0.0030.0000.0000.0000.000
126A139GLY00.0360.02526.763-0.018-0.0180.0000.0000.0000.000
127A140VAL0-0.080-0.04327.7460.0170.0170.0000.0000.0000.000
128A141ALA00.0450.04726.386-0.008-0.0080.0000.0000.0000.000
129A154LEU0-0.053-0.01632.4570.0010.0010.0000.0000.0000.000
130A155ARG10.9240.95925.3680.0690.0690.0000.0000.0000.000
131A156VAL00.0130.01928.126-0.008-0.0080.0000.0000.0000.000
132A157TRP00.0460.01722.5710.0100.0100.0000.0000.0000.000
133A158LEU0-0.007-0.02322.503-0.008-0.0080.0000.0000.0000.000
134A159PRO00.0550.05017.7120.0100.0100.0000.0000.0000.000
135A160TYR00.0840.03010.7650.0780.0780.0000.0000.0000.000
136A161SER0-0.104-0.08815.0530.0240.0240.0000.0000.0000.000
137A162THR0-0.034-0.03916.9410.0160.0160.0000.0000.0000.000
138A163MET0-0.009-0.00720.228-0.008-0.0080.0000.0000.0000.000
139A164SER0-0.012-0.00617.4520.0260.0260.0000.0000.0000.000
140A165GLY0-0.0230.00019.8660.0160.0160.0000.0000.0000.000
141A166ARG10.8750.93222.661-0.131-0.1310.0000.0000.0000.000
142A167VAL00.0080.01721.447-0.016-0.0160.0000.0000.0000.000
143A168MET0-0.0080.00024.2920.0090.0090.0000.0000.0000.000
144A169GLY0-0.015-0.00527.962-0.012-0.0120.0000.0000.0000.000
145A170GLN0-0.007-0.00629.8450.0050.0050.0000.0000.0000.000
146A171SER0-0.0410.01025.164-0.008-0.0080.0000.0000.0000.000
147A172TRP0-0.018-0.00524.1160.0090.0090.0000.0000.0000.000
148A173LEU00.000-0.00318.6250.0140.0140.0000.0000.0000.000
149A174ASN0-0.069-0.04619.338-0.032-0.0320.0000.0000.0000.000
150A175SER00.0290.01014.241-0.014-0.0140.0000.0000.0000.000
151A176ILE0-0.032-0.01412.2300.0840.0840.0000.0000.0000.000
152A177THR00.0270.0327.755-0.071-0.0710.0000.0000.0000.000
153A178VAL0-0.020-0.0207.4100.3480.3480.0000.0000.0000.000
154A179ARG10.9210.9753.770-6.284-5.7520.001-0.191-0.3420.001
155A180VAL00.0590.0392.713-2.356-1.2510.254-0.462-0.8970.000
156A181LYS10.8560.9524.4530.2720.493-0.001-0.013-0.2070.000
157A182GLU-1-0.912-0.9705.9771.3801.3800.0000.0000.0000.000
158A183GLY00.0320.0256.951-0.338-0.3380.0000.0000.0000.000
159A184PHE0-0.074-0.0446.865-0.364-0.3640.0000.0000.0000.000
160A185ASP-1-0.848-0.9216.1761.2231.2230.0000.0000.0000.000
161A186SER00.019-0.0072.733-1.011-0.4720.200-0.282-0.4570.000
162A187ALA00.0630.0314.671-0.578-0.579-0.001-0.0050.0080.000
163A188GLU-1-0.918-0.9647.8710.1160.1160.0000.0000.0000.000
164A189ALA0-0.0130.0036.185-0.017-0.0170.0000.0000.0000.000
165A190GLU-1-0.809-0.9017.205-0.604-0.6040.0000.0000.0000.000
166A191GLN00.0080.0378.6340.0880.0880.0000.0000.0000.000
167A192GLN0-0.069-0.03911.4240.0550.0550.0000.0000.0000.000
168A193LEU00.0170.0199.1640.0440.0440.0000.0000.0000.000
169A194THR0-0.036-0.06312.0160.0010.0010.0000.0000.0000.000
170A195ARG10.9410.95514.142-0.106-0.1060.0000.0000.0000.000
171A196LEU0-0.0330.00514.7220.0100.0100.0000.0000.0000.000
172A197LEU00.0230.00514.1510.0060.0060.0000.0000.0000.000
173A198SER00.0160.02317.533-0.011-0.0110.0000.0000.0000.000
174A199LEU0-0.064-0.02219.552-0.001-0.0010.0000.0000.0000.000
175A200ARG10.8720.93519.110-0.206-0.2060.0000.0000.0000.000
176A201HIS10.8220.90619.375-0.088-0.0880.0000.0000.0000.000
177A202GLY0-0.0210.01423.587-0.005-0.0050.0000.0000.0000.000
178A203LYS10.9170.94924.058-0.030-0.0300.0000.0000.0000.000
179A204LYS10.9230.95816.3520.1410.1410.0000.0000.0000.000
180A205ASP-1-0.872-0.93921.4720.0000.0000.0000.0000.0000.000
181A206PHE0-0.0020.02114.7800.0060.0060.0000.0000.0000.000
182A207PHE0-0.0020.00814.759-0.001-0.0010.0000.0000.0000.000
183A208THR0-0.063-0.04410.0830.0760.0760.0000.0000.0000.000
184A209TRP00.0580.0148.9460.0530.0530.0000.0000.0000.000
185A210ASN0-0.0200.0014.002-1.586-1.4630.000-0.049-0.0740.000
186A211MET00.0170.0162.627-4.853-2.9540.466-1.120-1.245-0.013