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: 49R4N

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 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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2005041.096164
FMO2-HF: Nuclear repulsion 1932032.682896
FMO2-HF: Total energy -73008.413268
FMO2-MP2: Total energy -73222.253305


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.
-41.623-35.336.92-6.251-6.9620.031
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 : 0.089 / q_NPA : 0.065
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].
3A16ILE00.0150.0193.861-4.524-1.891-0.012-1.447-1.1730.004
4A17ASP-1-0.776-0.8406.5312.3792.3790.0000.0000.0000.000
5A18VAL0-0.019-0.0129.784-0.397-0.3970.0000.0000.0000.000
6A19TYR0-0.027-0.03612.4430.1440.1440.0000.0000.0000.000
7A20PRO0-0.0180.00416.253-0.081-0.0810.0000.0000.0000.000
8A21GLY00.0750.04119.9230.0300.0300.0000.0000.0000.000
9A22ASN0-0.078-0.05420.437-0.016-0.0160.0000.0000.0000.000
10A23ASP-1-0.863-0.94817.437-0.103-0.1030.0000.0000.0000.000
11A24PHE00.007-0.00312.3880.0500.0500.0000.0000.0000.000
12A25GLY0-0.029-0.00718.449-0.019-0.0190.0000.0000.0000.000
13A26ASP-1-0.858-0.91821.5350.0970.0970.0000.0000.0000.000
14A27ASP-1-0.938-0.97722.9420.1820.1820.0000.0000.0000.000
15A28ASP-1-0.802-0.87725.1910.1050.1050.0000.0000.0000.000
16A29PRO0-0.048-0.03926.6650.0080.0080.0000.0000.0000.000
17A30GLN0-0.118-0.05728.606-0.007-0.0070.0000.0000.0000.000
18A31TYR00.012-0.01023.727-0.012-0.0120.0000.0000.0000.000
19A32GLN0-0.0110.00823.9770.0350.0350.0000.0000.0000.000
20A33GLN0-0.032-0.02524.3060.0170.0170.0000.0000.0000.000
21A34ALA00.0680.03522.062-0.013-0.0130.0000.0000.0000.000
22A35LEU0-0.0240.02617.038-0.031-0.0310.0000.0000.0000.000
23A36LYS10.8770.92920.892-0.112-0.1120.0000.0000.0000.000
24A37TYR00.052-0.01020.5450.0220.0220.0000.0000.0000.000
25A38ASP-1-0.877-0.94220.7990.0790.0790.0000.0000.0000.000
26A39ASP-1-0.792-0.89218.1960.0020.0020.0000.0000.0000.000
27A40LEU0-0.0140.00714.698-0.033-0.0330.0000.0000.0000.000
28A41ILE00.0080.00016.708-0.028-0.0280.0000.0000.0000.000
29A42ALA0-0.052-0.02718.454-0.050-0.0500.0000.0000.0000.000
30A43ILE0-0.001-0.00412.317-0.073-0.0730.0000.0000.0000.000
31A44GLN0-0.051-0.03813.944-0.152-0.1520.0000.0000.0000.000
32A45LYS10.9350.99014.9750.1630.1630.0000.0000.0000.000
33A46GLN00.0150.00913.276-0.094-0.0940.0000.0000.0000.000
34A47PRO0-0.009-0.01312.799-0.048-0.0480.0000.0000.0000.000
35A48TRP00.0630.0317.367-0.130-0.1300.0000.0000.0000.000
36A49VAL00.0070.0257.894-0.447-0.4470.0000.0000.0000.000
37A50ALA0-0.062-0.0316.3510.0870.0870.0000.0000.0000.000
38A51SER0-0.021-0.0228.3210.3050.3050.0000.0000.0000.000
39A52ALA00.0350.0199.1720.1300.1300.0000.0000.0000.000
40A53THR0-0.0020.00010.368-0.161-0.1610.0000.0000.0000.000
41A54PRO00.0010.00712.6310.0430.0430.0000.0000.0000.000
42A55ALA00.0180.01115.2570.0780.0780.0000.0000.0000.000
43A56VAL00.003-0.00316.801-0.098-0.0980.0000.0000.0000.000
44A57SER0-0.0030.01520.2910.0290.0290.0000.0000.0000.000
45A58GLN0-0.014-0.02323.494-0.003-0.0030.0000.0000.0000.000
46A59ASN00.0060.01527.0280.0170.0170.0000.0000.0000.000
47A60LEU0-0.009-0.00727.901-0.005-0.0050.0000.0000.0000.000
48A61ARG10.8480.90031.760-0.183-0.1830.0000.0000.0000.000
49A62LEU00.0020.01630.1830.0130.0130.0000.0000.0000.000
50A63ARG10.8800.93734.115-0.178-0.1780.0000.0000.0000.000
51A64TYR0-0.025-0.04835.7320.0060.0060.0000.0000.0000.000
52A65ASN0-0.003-0.00337.846-0.009-0.0090.0000.0000.0000.000
53A66ASN0-0.014-0.01641.400-0.001-0.0010.0000.0000.0000.000
54A67VAL00.0100.03639.729-0.007-0.0070.0000.0000.0000.000
55A68ASP-1-0.806-0.90438.4110.1830.1830.0000.0000.0000.000
56A69VAL00.0260.02935.083-0.009-0.0090.0000.0000.0000.000
57A70ALA0-0.020-0.00835.6230.0110.0110.0000.0000.0000.000
58A71ALA00.002-0.00131.608-0.005-0.0050.0000.0000.0000.000
59A72SER0-0.020-0.01826.801-0.001-0.0010.0000.0000.0000.000
60A73ALA00.0090.00325.8940.0080.0080.0000.0000.0000.000
61A74ASN0-0.021-0.01722.327-0.022-0.0220.0000.0000.0000.000
62A75GLY00.0500.01719.4920.0250.0250.0000.0000.0000.000
63A76VAL0-0.0120.00316.840-0.009-0.0090.0000.0000.0000.000
64A77SER00.0430.01811.2080.1620.1620.0000.0000.0000.000
65A78GLY00.0070.00213.221-0.173-0.1730.0000.0000.0000.000
66A79ASP-1-0.814-0.90112.3740.9700.9700.0000.0000.0000.000
67A80TYR0-0.012-0.00314.922-0.142-0.1420.0000.0000.0000.000
68A81PHE00.032-0.00517.197-0.078-0.0780.0000.0000.0000.000
69A82ASN0-0.041-0.02315.748-0.120-0.1200.0000.0000.0000.000
70A83VAL0-0.030-0.00814.479-0.069-0.0690.0000.0000.0000.000
71A84TYR0-0.046-0.03417.252-0.033-0.0330.0000.0000.0000.000
72A85GLY00.0190.01920.681-0.024-0.0240.0000.0000.0000.000
73A86MET0-0.083-0.03622.488-0.012-0.0120.0000.0000.0000.000
74A87THR00.0070.00523.8890.0260.0260.0000.0000.0000.000
75A88PHE0-0.039-0.02421.981-0.002-0.0020.0000.0000.0000.000
76A89SER0-0.031-0.01827.154-0.025-0.0250.0000.0000.0000.000
77A90GLU-1-0.775-0.88829.4820.2320.2320.0000.0000.0000.000
78A91GLY0-0.012-0.00727.4900.0200.0200.0000.0000.0000.000
79A92ASN0-0.019-0.00822.188-0.022-0.0220.0000.0000.0000.000
80A93THR00.0340.00717.949-0.021-0.0210.0000.0000.0000.000
81A94PHE0-0.006-0.01316.810-0.008-0.0080.0000.0000.0000.000
82A95ASN00.018-0.00315.7250.1400.1400.0000.0000.0000.000
83A96GLN00.0630.0037.4870.1240.1240.0000.0000.0000.000
84A97GLU-1-0.866-0.90412.8031.0041.0040.0000.0000.0000.000
85A98GLN00.0370.01315.104-0.017-0.0170.0000.0000.0000.000
86A99LEU0-0.0080.01911.123-0.079-0.0790.0000.0000.0000.000
87A100ASN0-0.024-0.0089.5330.0310.0310.0000.0000.0000.000
88A101GLY0-0.015-0.00913.226-0.133-0.1330.0000.0000.0000.000
89A102ARG10.8680.93813.562-1.202-1.2020.0000.0000.0000.000
90A103ALA00.0390.03217.966-0.104-0.1040.0000.0000.0000.000
91A104GLN0-0.018-0.02420.7120.0170.0170.0000.0000.0000.000
92A105VAL0-0.037-0.00921.075-0.046-0.0460.0000.0000.0000.000
93A106VAL0-0.016-0.01922.8640.0330.0330.0000.0000.0000.000
94A107VAL00.0080.02822.752-0.016-0.0160.0000.0000.0000.000
95A108LEU00.0030.00125.429-0.006-0.0060.0000.0000.0000.000
96A109ASP-1-0.704-0.81328.1210.2510.2510.0000.0000.0000.000
97A110SER00.0450.00229.977-0.010-0.0100.0000.0000.0000.000
98A111ASN00.0190.00333.365-0.013-0.0130.0000.0000.0000.000
99A112THR00.022-0.01031.497-0.005-0.0050.0000.0000.0000.000
100A113ARG10.7700.87332.711-0.221-0.2210.0000.0000.0000.000
101A114ARG10.9140.94034.470-0.170-0.1700.0000.0000.0000.000
102A115GLN0-0.044-0.02137.091-0.018-0.0180.0000.0000.0000.000
103A116LEU0-0.0020.00133.829-0.007-0.0070.0000.0000.0000.000
104A117PHE0-0.051-0.04333.708-0.001-0.0010.0000.0000.0000.000
105A118PRO0-0.0190.00538.5540.0000.0000.0000.0000.0000.000
106A119HIS0-0.012-0.01741.4460.0010.0010.0000.0000.0000.000
107A120LYS10.9060.96838.941-0.186-0.1860.0000.0000.0000.000
108A121ALA00.0210.02639.5090.0030.0030.0000.0000.0000.000
109A122ASP-1-0.874-0.92034.9010.2110.2110.0000.0000.0000.000
110A123VAL0-0.047-0.03531.602-0.005-0.0050.0000.0000.0000.000
111A124VAL0-0.025-0.01228.4870.0140.0140.0000.0000.0000.000
112A125GLY00.0210.01530.559-0.010-0.0100.0000.0000.0000.000
113A126GLU-1-0.796-0.87231.5950.2170.2170.0000.0000.0000.000
114A127VAL0-0.062-0.02931.1880.0270.0270.0000.0000.0000.000
115A128ILE00.0060.01029.621-0.023-0.0230.0000.0000.0000.000
116A129LEU0-0.017-0.00731.3680.0180.0180.0000.0000.0000.000
117A130VAL00.0540.01526.830-0.013-0.0130.0000.0000.0000.000
118A131GLY00.0370.01330.0210.0090.0090.0000.0000.0000.000
119A132ASN0-0.065-0.03831.589-0.021-0.0210.0000.0000.0000.000
120A133MET0-0.0340.00324.6220.0090.0090.0000.0000.0000.000
121A134PRO0-0.0090.00829.7000.0040.0040.0000.0000.0000.000
122A135ALA00.0080.00126.2950.0280.0280.0000.0000.0000.000
123A136ARG10.8990.94627.084-0.352-0.3520.0000.0000.0000.000
124A137VAL00.0170.00126.6430.0380.0380.0000.0000.0000.000
125A138ILE0-0.017-0.01821.690-0.015-0.0150.0000.0000.0000.000
126A139GLY00.0520.02726.0590.0040.0040.0000.0000.0000.000
127A140VAL0-0.068-0.02526.957-0.003-0.0030.0000.0000.0000.000
128A141ALA00.0460.03425.753-0.017-0.0170.0000.0000.0000.000
129A154LEU0-0.051-0.02732.3670.0000.0000.0000.0000.0000.000
130A155ARG10.9230.95326.249-0.270-0.2700.0000.0000.0000.000
131A156VAL0-0.0050.00526.804-0.006-0.0060.0000.0000.0000.000
132A157TRP00.0360.01521.588-0.004-0.0040.0000.0000.0000.000
133A158LEU00.010-0.00421.242-0.025-0.0250.0000.0000.0000.000
134A159PRO00.0570.04216.2470.0430.0430.0000.0000.0000.000
135A160TYR00.020-0.0079.802-0.074-0.0740.0000.0000.0000.000
136A161SER0-0.072-0.03614.211-0.129-0.1290.0000.0000.0000.000
137A162THR0-0.010-0.01916.158-0.064-0.0640.0000.0000.0000.000
138A163MET00.006-0.00219.443-0.088-0.0880.0000.0000.0000.000
139A164SER0-0.021-0.01916.748-0.027-0.0270.0000.0000.0000.000
140A165GLY0-0.022-0.00619.168-0.050-0.0500.0000.0000.0000.000
141A166ARG10.8730.93822.067-0.475-0.4750.0000.0000.0000.000
142A167VAL00.0090.02521.514-0.035-0.0350.0000.0000.0000.000
143A168MET0-0.0130.00024.135-0.035-0.0350.0000.0000.0000.000
144A169GLY00.0070.00227.9030.0050.0050.0000.0000.0000.000
145A170GLN0-0.002-0.00429.744-0.015-0.0150.0000.0000.0000.000
146A171SER0-0.0300.00224.7550.0190.0190.0000.0000.0000.000
147A172TRP0-0.024-0.01223.853-0.030-0.0300.0000.0000.0000.000
148A173LEU0-0.018-0.00318.2400.0440.0440.0000.0000.0000.000
149A174ASN0-0.051-0.04318.551-0.006-0.0060.0000.0000.0000.000
150A175SER00.0560.00514.4670.0590.0590.0000.0000.0000.000
151A176ILE0-0.036-0.02212.441-0.020-0.0200.0000.0000.0000.000
152A177THR00.0120.0137.462-0.053-0.0530.0000.0000.0000.000
153A178VAL0-0.029-0.0158.4780.0460.0460.0000.0000.0000.000
154A179ARG10.8880.9381.903-27.409-27.8016.291-2.938-2.9610.039
155A180VAL00.0080.0042.896-1.647-0.4230.131-0.499-0.8560.001
156A181LYS10.8220.9124.4360.0410.247-0.001-0.017-0.1880.000
157A182GLU-1-0.921-0.9715.929-2.545-2.5450.0000.0000.0000.000
158A183GLY00.0710.0356.7670.5110.5110.0000.0000.0000.000
159A184PHE0-0.077-0.0427.2260.4550.4550.0000.0000.0000.000
160A185ASP-1-0.829-0.9066.183-1.814-1.8140.0000.0000.0000.000
161A186SER00.003-0.0302.618-0.1580.3580.209-0.249-0.477-0.001
162A187ALA00.0480.0454.6370.2180.230-0.001-0.008-0.0030.000
163A188GLU-1-0.768-0.8757.767-0.505-0.5050.0000.0000.0000.000
164A189ALA0-0.0060.0196.5440.1550.1550.0000.0000.0000.000
165A190GLU-1-0.749-0.8497.443-0.757-0.7570.0000.0000.0000.000
166A191GLN00.0250.0249.0470.3350.3350.0000.0000.0000.000
167A192GLN0-0.089-0.05611.8010.1530.1530.0000.0000.0000.000
168A193LEU00.0030.0099.5180.1470.1470.0000.0000.0000.000
169A194THR0-0.002-0.01212.6630.1690.1690.0000.0000.0000.000
170A195ARG10.7820.86114.6590.6500.6500.0000.0000.0000.000
171A196LEU0-0.037-0.01015.4600.0590.0590.0000.0000.0000.000
172A197LEU00.001-0.00314.6220.0600.0600.0000.0000.0000.000
173A198SER0-0.004-0.00918.1470.0380.0380.0000.0000.0000.000
174A199LEU0-0.0040.00020.5430.0270.0270.0000.0000.0000.000
175A200ARG10.8030.88019.5890.0560.0560.0000.0000.0000.000
176A201HIS10.7560.87620.6580.0240.0240.0000.0000.0000.000
177A202GLY0-0.0090.01124.1810.0150.0150.0000.0000.0000.000
178A203LYS10.8530.91724.267-0.015-0.0150.0000.0000.0000.000
179A204LYS10.8410.91917.6240.0700.0700.0000.0000.0000.000
180A205ASP-1-0.797-0.88221.8990.0300.0300.0000.0000.0000.000
181A206PHE0-0.017-0.00415.5170.0320.0320.0000.0000.0000.000
182A207PHE00.0120.02714.679-0.049-0.0490.0000.0000.0000.000
183A208THR0-0.043-0.05110.4020.1120.1120.0000.0000.0000.000
184A209TRP00.0370.0118.6260.1270.1270.0000.0000.0000.000
185A210ASN0-0.058-0.0474.204-1.453-1.368-0.001-0.019-0.0650.000
186A211MET0-0.0190.0032.747-4.923-2.9140.304-1.074-1.239-0.012