Manual

About

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: G6VR1

Calculation Name: 5C2M-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5C2M

Chain ID: A

ChEMBL ID:

UniProt ID: A7SDD2

Base Structure: X-ray

Registration Date: 2023-06-22

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 237
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3019015.222053
FMO2-HF: Nuclear repulsion 2927607.488994
FMO2-HF: Total energy -91407.733059
FMO2-MP2: Total energy -91681.246785


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:13:PHE)


Summations of interaction energy for fragment #1(A:13:PHE)
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.
-4.255-0.9580.234-1.431-2.0990
Interaction energy analysis for fragmet #1(A:13:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : -0.016
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].
3A15TYR0-0.008-0.0273.051-2.5650.4810.233-1.301-1.977-0.001
4A16ILE00.0300.0376.5480.0970.0970.0000.0000.0000.000
5A17PHE00.020-0.0139.128-0.067-0.0670.0000.0000.0000.000
6A18ALA00.0210.01412.5760.0410.0410.0000.0000.0000.000
7A19VAL00.0100.01315.821-0.015-0.0150.0000.0000.0000.000
8A20SER0-0.008-0.03819.1790.0140.0140.0000.0000.0000.000
9A21TYR00.0140.00521.529-0.007-0.0070.0000.0000.0000.000
10A22ASP-1-0.845-0.89024.039-0.029-0.0290.0000.0000.0000.000
11A23GLY0-0.078-0.04123.951-0.005-0.0050.0000.0000.0000.000
12A24GLU-1-0.857-0.91219.952-0.081-0.0810.0000.0000.0000.000
13A25LEU0-0.0080.00715.3720.0060.0060.0000.0000.0000.000
14A26PHE00.007-0.01314.043-0.016-0.0160.0000.0000.0000.000
15A27LYS10.9530.9966.4580.9300.9300.0000.0000.0000.000
16A28GLY00.0390.0088.2720.0550.0550.0000.0000.0000.000
17A29SER00.0080.0035.421-0.161-0.1610.0000.0000.0000.000
18A30PRO00.0060.0105.887-0.001-0.0010.0000.0000.0000.000
19A31PRO0-0.0190.0168.9060.0790.0790.0000.0000.0000.000
20A32GLU-1-0.798-0.9049.4060.8610.8610.0000.0000.0000.000
21A33SER0-0.030-0.01712.632-0.019-0.0190.0000.0000.0000.000
22A34ALA00.0400.03315.358-0.027-0.0270.0000.0000.0000.000
23A35GLN0-0.002-0.01418.766-0.020-0.0200.0000.0000.0000.000
24A36ALA0-0.0320.00415.442-0.015-0.0150.0000.0000.0000.000
25A37SER00.0380.03417.396-0.003-0.0030.0000.0000.0000.000
26A38TRP00.012-0.01910.547-0.010-0.0100.0000.0000.0000.000
27A39LEU00.0530.01813.950-0.008-0.0080.0000.0000.0000.000
28A40THR0-0.051-0.01815.734-0.015-0.0150.0000.0000.0000.000
29A41SER0-0.091-0.04310.8640.0060.0060.0000.0000.0000.000
30A42ALA0-0.0300.00310.9120.0140.0140.0000.0000.0000.000
31A43THR0-0.019-0.00810.1200.0000.0000.0000.0000.0000.000
32A44ARG10.8950.93612.8460.0610.0610.0000.0000.0000.000
33A45ILE0-0.018-0.00912.233-0.006-0.0060.0000.0000.0000.000
34A46GLY00.0480.02515.483-0.011-0.0110.0000.0000.0000.000
35A47THR0-0.058-0.04718.7660.0160.0160.0000.0000.0000.000
36A48LYS10.9190.94521.8380.0980.0980.0000.0000.0000.000
37A49GLY00.0320.00924.304-0.010-0.0100.0000.0000.0000.000
38A50TRP00.0360.00620.188-0.002-0.0020.0000.0000.0000.000
39A51ALA0-0.0040.01522.943-0.001-0.0010.0000.0000.0000.000
40A52ASN0-0.042-0.02524.9130.0100.0100.0000.0000.0000.000
41A53PHE0-0.0040.01523.2080.0020.0020.0000.0000.0000.000
42A54SER0-0.052-0.04826.0820.0050.0050.0000.0000.0000.000
43A55HIS00.0110.02024.247-0.001-0.0010.0000.0000.0000.000
44A56LEU0-0.018-0.01018.568-0.010-0.0100.0000.0000.0000.000
45A57LEU0-0.001-0.00318.2970.0110.0110.0000.0000.0000.000
46A58PHE00.017-0.00112.833-0.026-0.0260.0000.0000.0000.000
47A59ASN00.0350.03716.0160.0270.0270.0000.0000.0000.000
48A60PRO00.0120.01413.385-0.076-0.0760.0000.0000.0000.000
49A61ASP-1-0.904-0.93512.822-0.394-0.3940.0000.0000.0000.000
50A62GLY0-0.037-0.02512.273-0.080-0.0800.0000.0000.0000.000
51A63THR0-0.114-0.06412.902-0.012-0.0120.0000.0000.0000.000
52A64LEU0-0.064-0.02515.8520.0100.0100.0000.0000.0000.000
53A65TYR00.0660.00417.4690.0240.0240.0000.0000.0000.000
54A66GLY0-0.010-0.01020.9210.0010.0010.0000.0000.0000.000
55A67VAL0-0.0030.00923.3080.0020.0020.0000.0000.0000.000
56A68VAL00.023-0.00426.7970.0030.0030.0000.0000.0000.000
57A69ASN0-0.034-0.02628.7950.0020.0020.0000.0000.0000.000
58A70ASP-1-0.799-0.89431.986-0.045-0.0450.0000.0000.0000.000
59A71LYS10.8220.91331.2950.0650.0650.0000.0000.0000.000
60A72PHE0-0.022-0.00824.170-0.005-0.0050.0000.0000.0000.000
61A73TYR00.0480.01525.1900.0020.0020.0000.0000.0000.000
62A74LYS10.9340.97621.5220.1630.1630.0000.0000.0000.000
63A75GLY00.0470.02120.2970.0140.0140.0000.0000.0000.000
64A76PRO00.0440.02916.701-0.026-0.0260.0000.0000.0000.000
65A77THR00.0450.01911.9800.0220.0220.0000.0000.0000.000
66A78PRO0-0.0200.00915.124-0.007-0.0070.0000.0000.0000.000
67A79HIS0-0.023-0.02313.270-0.079-0.0790.0000.0000.0000.000
68A80ARG10.8070.89516.0030.1760.1760.0000.0000.0000.000
69A81THR00.0390.02618.7180.0050.0050.0000.0000.0000.000
70A82SER00.003-0.02121.144-0.001-0.0010.0000.0000.0000.000
71A83ALA00.0400.02223.339-0.010-0.0100.0000.0000.0000.000
72A84GLU-1-0.782-0.87024.242-0.095-0.0950.0000.0000.0000.000
73A85GLU-1-0.881-0.93424.912-0.133-0.1330.0000.0000.0000.000
74A86TRP0-0.084-0.05419.0970.0090.0090.0000.0000.0000.000
75A87ILE0-0.011-0.01423.644-0.004-0.0040.0000.0000.0000.000
76A88ALA0-0.059-0.01426.4060.0020.0020.0000.0000.0000.000
77A89GLN0-0.084-0.05524.655-0.009-0.0090.0000.0000.0000.000
78A90ALA0-0.0460.01923.993-0.010-0.0100.0000.0000.0000.000
79A91THR0-0.033-0.02624.8450.0090.0090.0000.0000.0000.000
80A92LEU0-0.0030.00126.583-0.004-0.0040.0000.0000.0000.000
81A93ILE0-0.068-0.04025.057-0.001-0.0010.0000.0000.0000.000
82A94GLY00.0500.01229.2130.0050.0050.0000.0000.0000.000
83A95ASP-1-0.827-0.89331.601-0.065-0.0650.0000.0000.0000.000
84A96GLY00.0300.02734.3910.0030.0030.0000.0000.0000.000
85A97GLY0-0.026-0.02135.329-0.001-0.0010.0000.0000.0000.000
86A98TRP00.007-0.00428.6040.0010.0010.0000.0000.0000.000
87A99GLY0-0.029-0.03230.7080.0000.0000.0000.0000.0000.000
88A100ALA0-0.024-0.01132.0200.0030.0030.0000.0000.0000.000
89A101PHE0-0.041-0.00629.3540.0050.0050.0000.0000.0000.000
90A102ARG10.8750.94729.928-0.015-0.0150.0000.0000.0000.000
91A103PHE0-0.031-0.02025.3970.0030.0030.0000.0000.0000.000
92A104LEU00.0470.01924.874-0.001-0.0010.0000.0000.0000.000
93A105PHE0-0.059-0.03720.803-0.007-0.0070.0000.0000.0000.000
94A106PHE00.0540.02818.5050.0030.0030.0000.0000.0000.000
95A107ASP-1-0.802-0.89319.026-0.017-0.0170.0000.0000.0000.000
96A108PRO00.007-0.01615.190-0.036-0.0360.0000.0000.0000.000
97A109HIS0-0.027-0.00316.250-0.037-0.0370.0000.0000.0000.000
98A110GLY0-0.0030.01818.851-0.019-0.0190.0000.0000.0000.000
99A111VAL0-0.007-0.00119.6880.0010.0010.0000.0000.0000.000
100A112LEU0-0.043-0.01822.5970.0050.0050.0000.0000.0000.000
101A113TYR0-0.028-0.04323.5440.0190.0190.0000.0000.0000.000
102A114GLY00.0360.00725.793-0.008-0.0080.0000.0000.0000.000
103A115VAL0-0.055-0.01628.4010.0050.0050.0000.0000.0000.000
104A116THR00.0390.01230.883-0.002-0.0020.0000.0000.0000.000
105A117GLU-1-0.892-0.93934.038-0.010-0.0100.0000.0000.0000.000
106A118ASP-1-0.762-0.87135.9090.0140.0140.0000.0000.0000.000
107A119LYS10.7990.90935.4160.0110.0110.0000.0000.0000.000
108A120LEU0-0.012-0.00228.062-0.003-0.0030.0000.0000.0000.000
109A121TYR00.0250.00330.9260.0030.0030.0000.0000.0000.000
110A122LYS10.9620.98425.8460.0040.0040.0000.0000.0000.000
111A123ARG10.7450.82727.4600.0690.0690.0000.0000.0000.000
112A124GLU-1-0.841-0.91224.958-0.100-0.1000.0000.0000.0000.000
113A125PRO00.0070.02123.0560.0080.0080.0000.0000.0000.000
114A126PRO00.0240.02626.2370.0000.0000.0000.0000.0000.000
115A127SER0-0.093-0.06726.601-0.020-0.0200.0000.0000.0000.000
116A128SER00.0500.02228.502-0.005-0.0050.0000.0000.0000.000
117A129ASP-1-0.916-0.95131.496-0.075-0.0750.0000.0000.0000.000
118A130GLU-1-0.931-0.96333.725-0.062-0.0620.0000.0000.0000.000
119A131ASP-1-0.852-0.87631.787-0.066-0.0660.0000.0000.0000.000
120A132HIS00.023-0.00233.950-0.003-0.0030.0000.0000.0000.000
121A133TRP0-0.016-0.02428.0310.0070.0070.0000.0000.0000.000
122A134LEU00.001-0.02233.3150.0030.0030.0000.0000.0000.000
123A135GLY0-0.0420.00335.3410.0040.0040.0000.0000.0000.000
124A136SER0-0.021-0.00634.9940.0010.0010.0000.0000.0000.000
125A137ALA0-0.0390.00032.272-0.001-0.0010.0000.0000.0000.000
126A138ASN0-0.042-0.03230.8990.0060.0060.0000.0000.0000.000
127A139LEU0-0.014-0.01032.5810.0010.0010.0000.0000.0000.000
128A140LEU0-0.044-0.03528.8630.0020.0020.0000.0000.0000.000
129A141GLY00.0160.00333.3120.0060.0060.0000.0000.0000.000
130A142ALA0-0.044-0.03035.233-0.004-0.0040.0000.0000.0000.000
131A143GLU-1-0.961-0.97137.6780.0140.0140.0000.0000.0000.000
132A144GLY00.0350.01236.9760.0030.0030.0000.0000.0000.000
133A145TRP00.006-0.01229.2690.0050.0050.0000.0000.0000.000
134A146GLY0-0.059-0.03832.247-0.001-0.0010.0000.0000.0000.000
135A147ASP-1-0.939-0.97334.4350.0310.0310.0000.0000.0000.000
136A148PHE0-0.034-0.00428.4520.0060.0060.0000.0000.0000.000
137A149GLU-1-0.845-0.93128.5980.0460.0460.0000.0000.0000.000
138A150PHE0-0.018-0.01823.018-0.002-0.0020.0000.0000.0000.000
139A151LEU00.006-0.00224.1730.0070.0070.0000.0000.0000.000
140A152PHE0-0.0270.00118.593-0.012-0.0120.0000.0000.0000.000
141A153PHE00.0610.01818.4850.0130.0130.0000.0000.0000.000
142A154ASP-1-0.788-0.87316.1270.2100.2100.0000.0000.0000.000
143A155PRO00.001-0.01911.937-0.052-0.0520.0000.0000.0000.000
144A156GLU-1-0.914-0.95814.0390.3820.3820.0000.0000.0000.000
145A157GLY0-0.0260.00216.906-0.033-0.0330.0000.0000.0000.000
146A158LYS10.7580.87019.416-0.157-0.1570.0000.0000.0000.000
147A159LEU0-0.0080.00320.802-0.001-0.0010.0000.0000.0000.000
148A160TYR0-0.069-0.07419.5960.0210.0210.0000.0000.0000.000
149A161GLY00.0390.00623.676-0.015-0.0150.0000.0000.0000.000
150A162VAL0-0.076-0.03525.1920.0110.0110.0000.0000.0000.000
151A163VAL00.0760.04927.899-0.009-0.0090.0000.0000.0000.000
152A164ASN0-0.027-0.01231.6920.0050.0050.0000.0000.0000.000
153A165GLY00.0090.01230.5070.0030.0030.0000.0000.0000.000
154A166LYS10.8440.91229.940-0.061-0.0610.0000.0000.0000.000
155A167LEU00.0180.02222.459-0.007-0.0070.0000.0000.0000.000
156A168HIS10.8550.93227.108-0.072-0.0720.0000.0000.0000.000
157A169LYS10.9910.99722.197-0.210-0.2100.0000.0000.0000.000
158A170GLY00.0410.01225.389-0.001-0.0010.0000.0000.0000.000
159A171ASP-1-0.831-0.90425.0900.1060.1060.0000.0000.0000.000
160A172PRO00.0220.02624.145-0.004-0.0040.0000.0000.0000.000
161A173PRO0-0.0020.01327.0000.0010.0010.0000.0000.0000.000
162A174LYS10.8400.89627.579-0.049-0.0490.0000.0000.0000.000
163A175ASP-1-0.819-0.90831.7660.0090.0090.0000.0000.0000.000
164A176ARG10.9420.97834.985-0.004-0.0040.0000.0000.0000.000
165A177HIS0-0.084-0.06037.3610.0000.0000.0000.0000.0000.000
166A178ASP-1-0.832-0.88532.8520.0410.0410.0000.0000.0000.000
167A179ALA0-0.001-0.00735.500-0.001-0.0010.0000.0000.0000.000
168A180TRP0-0.055-0.03526.7390.0020.0020.0000.0000.0000.000
169A181LEU00.0270.00831.6900.0070.0070.0000.0000.0000.000
170A182GLY0-0.0030.00533.5230.0060.0060.0000.0000.0000.000
171A183SER0-0.0130.00433.0750.0010.0010.0000.0000.0000.000
172A184SER0-0.092-0.02729.4270.0080.0080.0000.0000.0000.000
173A185THR0-0.033-0.02827.5290.0030.0030.0000.0000.0000.000
174A186LEU0-0.014-0.00228.2200.0020.0020.0000.0000.0000.000
175A187PHE0-0.011-0.01021.5620.0120.0120.0000.0000.0000.000
176A188LYS10.8470.90127.504-0.173-0.1730.0000.0000.0000.000
177A189GLY00.0290.01427.8660.0070.0070.0000.0000.0000.000
178A190GLU-1-0.899-0.95929.9270.0680.0680.0000.0000.0000.000
179A191LEU00.0250.01329.520-0.006-0.0060.0000.0000.0000.000
180A192TRP0-0.025-0.02521.8870.0030.0030.0000.0000.0000.000
181A193GLY00.0610.03626.1810.0000.0000.0000.0000.0000.000
182A194ASN0-0.065-0.03228.285-0.008-0.0080.0000.0000.0000.000
183A195PHE0-0.067-0.02022.1310.0040.0040.0000.0000.0000.000
184A196ARG10.9100.94423.439-0.027-0.0270.0000.0000.0000.000
185A197HIS0-0.022-0.01419.014-0.017-0.0170.0000.0000.0000.000
186A198LEU00.004-0.00719.2290.0210.0210.0000.0000.0000.000
187A199PHE0-0.0140.01012.627-0.019-0.0190.0000.0000.0000.000
188A200PHE00.0590.02313.5180.0450.0450.0000.0000.0000.000
189A201THR0-0.035-0.0217.963-0.075-0.0750.0000.0000.0000.000
190A202SER00.031-0.0016.632-0.069-0.0690.0000.0000.0000.000
191A203ASN0-0.048-0.0343.945-1.697-1.4460.001-0.130-0.1220.001
192A204GLY00.0550.0318.3200.0710.0710.0000.0000.0000.000
193A205HIS0-0.021-0.0168.991-0.205-0.2050.0000.0000.0000.000
194A206LEU0-0.0060.01512.176-0.080-0.0800.0000.0000.0000.000
195A207CYS0-0.041-0.02113.0000.0350.0350.0000.0000.0000.000
196A208GLY00.0520.02015.728-0.033-0.0330.0000.0000.0000.000
197A209ALA0-0.031-0.01018.3410.0120.0120.0000.0000.0000.000
198A210HIS00.0530.01320.349-0.018-0.0180.0000.0000.0000.000
199A211ASP-1-0.850-0.92123.1060.0460.0460.0000.0000.0000.000
200A212SER0-0.032-0.01121.652-0.004-0.0040.0000.0000.0000.000
201A213PHE00.000-0.00513.350-0.005-0.0050.0000.0000.0000.000
202A214TYR0-0.010-0.00218.3180.0140.0140.0000.0000.0000.000
203A215LYS10.8030.86810.469-0.700-0.7000.0000.0000.0000.000
204A216LYS10.8550.94715.538-0.405-0.4050.0000.0000.0000.000
205A217SER00.0420.02012.505-0.003-0.0030.0000.0000.0000.000
206A218PRO00.0150.01312.185-0.119-0.1190.0000.0000.0000.000
207A219PRO00.0130.01115.0630.0320.0320.0000.0000.0000.000
208A220ILE00.005-0.00515.138-0.021-0.0210.0000.0000.0000.000
209A221GLY0-0.0010.00818.750-0.026-0.0260.0000.0000.0000.000
210A222LEU0-0.007-0.02622.463-0.004-0.0040.0000.0000.0000.000
211A223ASP-1-0.857-0.90824.1640.1640.1640.0000.0000.0000.000
212A224TRP0-0.008-0.00523.9800.0080.0080.0000.0000.0000.000
213A225LEU00.0370.02618.2290.0120.0120.0000.0000.0000.000
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