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

tag_button

FMODB ID: 179YZ

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 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 237
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3016596.120564
FMO2-HF: Nuclear repulsion 2925189.877744
FMO2-HF: Total energy -91406.24282
FMO2-MP2: Total energy -91679.787507


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.
-3.684-0.3170.377-1.446-2.299-0.002
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 : 0.001 / q_NPA : -0.013
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].
3A15TYR0-0.012-0.0202.925-2.5930.5690.377-1.362-2.177-0.002
4A16ILE00.0280.0426.5380.1000.1000.0000.0000.0000.000
5A17PHE00.009-0.0219.099-0.067-0.0670.0000.0000.0000.000
6A18ALA00.0230.01712.5780.0450.0450.0000.0000.0000.000
7A19VAL00.0160.01215.798-0.016-0.0160.0000.0000.0000.000
8A20SER00.0440.01419.1690.0160.0160.0000.0000.0000.000
9A21TYR0-0.001-0.01321.496-0.008-0.0080.0000.0000.0000.000
10A22ASP-1-0.889-0.92524.152-0.035-0.0350.0000.0000.0000.000
11A23GLY0-0.089-0.05023.951-0.005-0.0050.0000.0000.0000.000
12A24GLU-1-0.870-0.92219.737-0.091-0.0910.0000.0000.0000.000
13A25LEU0-0.0120.00415.3770.0060.0060.0000.0000.0000.000
14A26PHE0-0.001-0.02014.034-0.018-0.0180.0000.0000.0000.000
15A27LYS10.9701.0016.5621.0441.0440.0000.0000.0000.000
16A28GLY00.0430.0078.1970.0620.0620.0000.0000.0000.000
17A29SER00.0150.0095.630-0.192-0.1920.0000.0000.0000.000
18A30PRO0-0.0130.0005.971-0.006-0.0060.0000.0000.0000.000
19A31PRO0-0.0070.0158.8870.1100.1100.0000.0000.0000.000
20A32GLU-1-0.820-0.9179.5700.8540.8540.0000.0000.0000.000
21A33SER0-0.041-0.01912.679-0.019-0.0190.0000.0000.0000.000
22A34ALA00.0480.03415.601-0.027-0.0270.0000.0000.0000.000
23A35GLN0-0.012-0.01818.961-0.027-0.0270.0000.0000.0000.000
24A36ALA0-0.0260.00415.837-0.014-0.0140.0000.0000.0000.000
25A37SER00.0310.03617.807-0.008-0.0080.0000.0000.0000.000
26A38TRP00.023-0.01710.355-0.008-0.0080.0000.0000.0000.000
27A39LEU00.0510.01713.833-0.005-0.0050.0000.0000.0000.000
28A40THR0-0.053-0.01715.632-0.018-0.0180.0000.0000.0000.000
29A41SER0-0.095-0.03911.1300.0090.0090.0000.0000.0000.000
30A42ALA0-0.0240.00410.7990.0210.0210.0000.0000.0000.000
31A43THR0-0.025-0.01210.115-0.001-0.0010.0000.0000.0000.000
32A44ARG10.9090.94512.8020.0780.0780.0000.0000.0000.000
33A45ILE0-0.033-0.01412.267-0.009-0.0090.0000.0000.0000.000
34A46GLY00.0510.02315.507-0.011-0.0110.0000.0000.0000.000
35A47THR0-0.066-0.04918.7930.0200.0200.0000.0000.0000.000
36A48LYS11.0491.01621.8490.1110.1110.0000.0000.0000.000
37A49GLY00.0400.01424.332-0.011-0.0110.0000.0000.0000.000
38A50TRP00.0350.01020.300-0.002-0.0020.0000.0000.0000.000
39A51ALA0-0.0120.00822.969-0.002-0.0020.0000.0000.0000.000
40A52ASN0-0.037-0.02524.9240.0130.0130.0000.0000.0000.000
41A53PHE0-0.0120.00923.2770.0020.0020.0000.0000.0000.000
42A54SER0-0.048-0.03926.1270.0060.0060.0000.0000.0000.000
43A55HIS00.0080.01024.302-0.001-0.0010.0000.0000.0000.000
44A56LEU0-0.017-0.01618.862-0.010-0.0100.0000.0000.0000.000
45A57LEU0-0.010-0.00518.3690.0090.0090.0000.0000.0000.000
46A58PHE00.018-0.00412.974-0.030-0.0300.0000.0000.0000.000
47A59ASN00.0430.04116.0180.0320.0320.0000.0000.0000.000
48A60PRO00.0110.01613.326-0.086-0.0860.0000.0000.0000.000
49A61ASP-1-0.899-0.93412.778-0.436-0.4360.0000.0000.0000.000
50A62GLY0-0.047-0.02912.314-0.079-0.0790.0000.0000.0000.000
51A63THR0-0.096-0.04912.939-0.016-0.0160.0000.0000.0000.000
52A64LEU0-0.071-0.03216.1710.0080.0080.0000.0000.0000.000
53A65TYR00.0610.00717.4520.0170.0170.0000.0000.0000.000
54A66GLY0-0.019-0.02020.916-0.001-0.0010.0000.0000.0000.000
55A67VAL00.0020.01323.3390.0030.0030.0000.0000.0000.000
56A68VAL00.012-0.01326.8610.0030.0030.0000.0000.0000.000
57A69ASN0-0.026-0.01928.8610.0030.0030.0000.0000.0000.000
58A70ASP-1-0.796-0.89732.067-0.056-0.0560.0000.0000.0000.000
59A71LYS10.9370.99431.3740.0790.0790.0000.0000.0000.000
60A72PHE0-0.029-0.00624.247-0.007-0.0070.0000.0000.0000.000
61A73TYR00.0330.01225.0470.0030.0030.0000.0000.0000.000
62A74LYS10.9440.98021.5340.1800.1800.0000.0000.0000.000
63A75GLY00.0470.02120.2830.0170.0170.0000.0000.0000.000
64A76PRO00.0390.03316.677-0.029-0.0290.0000.0000.0000.000
65A77THR00.0520.00712.0710.0560.0560.0000.0000.0000.000
66A78PRO0-0.0320.00615.074-0.005-0.0050.0000.0000.0000.000
67A79HIS00.008-0.00513.477-0.103-0.1030.0000.0000.0000.000
68A80ARG10.8190.90015.9280.2150.2150.0000.0000.0000.000
69A81THR00.0420.03318.7570.0070.0070.0000.0000.0000.000
70A82SER00.0250.01221.187-0.001-0.0010.0000.0000.0000.000
71A83ALA00.0560.02323.397-0.012-0.0120.0000.0000.0000.000
72A84GLU-1-0.958-0.98424.297-0.102-0.1020.0000.0000.0000.000
73A85GLU-1-0.915-0.96124.872-0.148-0.1480.0000.0000.0000.000
74A86TRP0-0.077-0.05719.0750.0100.0100.0000.0000.0000.000
75A87ILE0-0.014-0.01223.667-0.004-0.0040.0000.0000.0000.000
76A88ALA0-0.052-0.01126.3950.0020.0020.0000.0000.0000.000
77A89GLN0-0.058-0.03324.583-0.008-0.0080.0000.0000.0000.000
78A90ALA0-0.0490.01723.919-0.011-0.0110.0000.0000.0000.000
79A91THR0-0.031-0.02524.8410.0100.0100.0000.0000.0000.000
80A92LEU0-0.0010.00126.578-0.006-0.0060.0000.0000.0000.000
81A93ILE0-0.071-0.04725.1020.0000.0000.0000.0000.0000.000
82A94GLY00.0360.00329.2230.0050.0050.0000.0000.0000.000
83A95ASP-1-0.921-0.96531.604-0.076-0.0760.0000.0000.0000.000
84A96GLY00.0330.02934.3800.0040.0040.0000.0000.0000.000
85A97GLY0-0.023-0.01735.325-0.001-0.0010.0000.0000.0000.000
86A98TRP00.014-0.00228.8660.0000.0000.0000.0000.0000.000
87A99GLY0-0.028-0.02630.780-0.001-0.0010.0000.0000.0000.000
88A100ALA0-0.016-0.00732.0740.0030.0030.0000.0000.0000.000
89A101PHE0-0.051-0.00929.2900.0060.0060.0000.0000.0000.000
90A102ARG10.8950.96029.912-0.002-0.0020.0000.0000.0000.000
91A103PHE0-0.035-0.02225.2790.0020.0020.0000.0000.0000.000
92A104LEU00.0480.01324.7020.0010.0010.0000.0000.0000.000
93A105PHE0-0.073-0.03920.710-0.009-0.0090.0000.0000.0000.000
94A106PHE00.0610.03418.4000.0060.0060.0000.0000.0000.000
95A107ASP-1-0.835-0.92218.950-0.053-0.0530.0000.0000.0000.000
96A108PRO00.002-0.01415.191-0.035-0.0350.0000.0000.0000.000
97A109HIS0-0.041-0.00916.184-0.036-0.0360.0000.0000.0000.000
98A110GLY00.0140.02718.826-0.018-0.0180.0000.0000.0000.000
99A111VAL0-0.015-0.00919.6310.0030.0030.0000.0000.0000.000
100A112LEU0-0.049-0.02122.5280.0020.0020.0000.0000.0000.000
101A113TYR00.007-0.01323.8550.0210.0210.0000.0000.0000.000
102A114GLY00.0280.00025.783-0.009-0.0090.0000.0000.0000.000
103A115VAL0-0.057-0.01528.4010.0060.0060.0000.0000.0000.000
104A116THR00.0320.01030.883-0.002-0.0020.0000.0000.0000.000
105A117GLU-1-0.949-0.98134.038-0.019-0.0190.0000.0000.0000.000
106A118ASP-1-0.793-0.88435.9370.0040.0040.0000.0000.0000.000
107A119LYS10.8980.96935.4160.0180.0180.0000.0000.0000.000
108A120LEU0-0.0150.00127.936-0.004-0.0040.0000.0000.0000.000
109A121TYR00.0250.00430.8490.0040.0040.0000.0000.0000.000
110A122LYS10.9670.98626.6610.0160.0160.0000.0000.0000.000
111A123ARG10.7240.81827.3950.0820.0820.0000.0000.0000.000
112A124GLU-1-0.849-0.91624.515-0.123-0.1230.0000.0000.0000.000
113A125PRO00.0000.01423.0000.0080.0080.0000.0000.0000.000
114A126PRO00.0280.02426.2600.0010.0010.0000.0000.0000.000
115A127SER0-0.090-0.06726.392-0.022-0.0220.0000.0000.0000.000
116A128SER00.0330.01428.541-0.005-0.0050.0000.0000.0000.000
117A129ASP-1-0.887-0.93731.522-0.086-0.0860.0000.0000.0000.000
118A130GLU-1-0.934-0.96133.739-0.068-0.0680.0000.0000.0000.000
119A131ASP-1-0.871-0.89132.041-0.075-0.0750.0000.0000.0000.000
120A132HIS00.0320.00233.982-0.004-0.0040.0000.0000.0000.000
121A133TRP0-0.017-0.01928.1240.0080.0080.0000.0000.0000.000
122A134LEU00.006-0.02133.3550.0030.0030.0000.0000.0000.000
123A135GLY0-0.051-0.00135.2800.0050.0050.0000.0000.0000.000
124A136SER0-0.017-0.00434.9430.0010.0010.0000.0000.0000.000
125A137ALA0-0.040-0.00232.137-0.001-0.0010.0000.0000.0000.000
126A138ASN0-0.023-0.01830.7340.0080.0080.0000.0000.0000.000
127A139LEU0-0.019-0.01232.5060.0000.0000.0000.0000.0000.000
128A140LEU0-0.048-0.03828.7690.0020.0020.0000.0000.0000.000
129A141GLY00.0250.00633.2300.0060.0060.0000.0000.0000.000
130A142ALA0-0.049-0.03535.148-0.004-0.0040.0000.0000.0000.000
131A143GLU-1-0.961-0.97337.6300.0080.0080.0000.0000.0000.000
132A144GLY00.0380.01336.9760.0030.0030.0000.0000.0000.000
133A145TRP00.003-0.01029.2500.0030.0030.0000.0000.0000.000
134A146GLY0-0.058-0.03832.247-0.002-0.0020.0000.0000.0000.000
135A147ASP-1-0.951-0.98034.4120.0210.0210.0000.0000.0000.000
136A148PHE0-0.0390.01328.5230.0060.0060.0000.0000.0000.000
137A149GLU-1-0.842-0.93528.5420.0340.0340.0000.0000.0000.000
138A150PHE0-0.026-0.02023.142-0.003-0.0030.0000.0000.0000.000
139A151LEU0-0.001-0.01124.1580.0080.0080.0000.0000.0000.000
140A152PHE0-0.0200.01018.550-0.014-0.0140.0000.0000.0000.000
141A153PHE00.0580.01818.3340.0160.0160.0000.0000.0000.000
142A154ASP-1-0.797-0.88616.0610.1760.1760.0000.0000.0000.000
143A155PRO00.001-0.02811.711-0.042-0.0420.0000.0000.0000.000
144A156GLU-1-0.918-0.95113.9470.3320.3320.0000.0000.0000.000
145A157GLY0-0.026-0.00316.815-0.028-0.0280.0000.0000.0000.000
146A158LYS10.8430.93419.327-0.141-0.1410.0000.0000.0000.000
147A159LEU0-0.0030.00520.708-0.004-0.0040.0000.0000.0000.000
148A160TYR0-0.078-0.07119.4700.0230.0230.0000.0000.0000.000
149A161GLY00.0450.00223.638-0.015-0.0150.0000.0000.0000.000
150A162VAL0-0.065-0.02825.1460.0110.0110.0000.0000.0000.000
151A163VAL00.0990.04927.862-0.008-0.0080.0000.0000.0000.000
152A164ASN0-0.027-0.00631.6560.0040.0040.0000.0000.0000.000
153A165GLY00.0290.01230.4730.0040.0040.0000.0000.0000.000
154A166LYS10.8950.95429.900-0.051-0.0510.0000.0000.0000.000
155A167LEU00.0180.02222.535-0.008-0.0080.0000.0000.0000.000
156A168HIS10.8530.93127.071-0.059-0.0590.0000.0000.0000.000
157A169LYS11.0121.00422.758-0.181-0.1810.0000.0000.0000.000
158A170GLY00.0200.00025.3110.0010.0010.0000.0000.0000.000
159A171ASP-1-0.874-0.93524.9980.0860.0860.0000.0000.0000.000
160A172PRO0-0.028-0.00924.029-0.004-0.0040.0000.0000.0000.000
161A173PRO0-0.0260.00426.9100.0020.0020.0000.0000.0000.000
162A174LYS10.8990.91926.140-0.021-0.0210.0000.0000.0000.000
163A175ASP-1-0.847-0.92031.6810.0020.0020.0000.0000.0000.000
164A176ARG10.9330.95834.9020.0040.0040.0000.0000.0000.000
165A177HIS0-0.074-0.04137.2750.0000.0000.0000.0000.0000.000
166A178ASP-1-0.806-0.86433.0330.0280.0280.0000.0000.0000.000
167A179ALA00.008-0.00335.409-0.002-0.0020.0000.0000.0000.000
168A180TRP0-0.059-0.03526.5570.0030.0030.0000.0000.0000.000
169A181LEU00.0230.00231.7820.0070.0070.0000.0000.0000.000
170A182GLY0-0.011-0.00233.4840.0060.0060.0000.0000.0000.000
171A183SER0-0.0120.00332.7820.0020.0020.0000.0000.0000.000
172A184SER0-0.100-0.02429.3820.0080.0080.0000.0000.0000.000
173A185THR0-0.035-0.02727.4920.0040.0040.0000.0000.0000.000
174A186LEU0-0.031-0.00928.1830.0010.0010.0000.0000.0000.000
175A187PHE00.002-0.00321.6930.0090.0090.0000.0000.0000.000
176A188LYS10.9200.95827.469-0.151-0.1510.0000.0000.0000.000
177A189GLY00.0300.01627.8320.0060.0060.0000.0000.0000.000
178A190GLU-1-0.949-0.99129.8940.0630.0630.0000.0000.0000.000
179A191LEU00.0180.00729.473-0.006-0.0060.0000.0000.0000.000
180A192TRP0-0.032-0.03721.8310.0020.0020.0000.0000.0000.000
181A193GLY00.0410.02726.148-0.001-0.0010.0000.0000.0000.000
182A194ASN0-0.042-0.01728.265-0.010-0.0100.0000.0000.0000.000
183A195PHE0-0.084-0.02522.4970.0040.0040.0000.0000.0000.000
184A196ARG10.9350.96123.588-0.015-0.0150.0000.0000.0000.000
185A197HIS0-0.038-0.01118.909-0.020-0.0200.0000.0000.0000.000
186A198LEU00.009-0.01019.2020.0220.0220.0000.0000.0000.000
187A199PHE0-0.0150.00712.536-0.021-0.0210.0000.0000.0000.000
188A200PHE00.0580.02313.4700.0470.0470.0000.0000.0000.000
189A201THR0-0.023-0.0078.241-0.078-0.0780.0000.0000.0000.000
190A202SER00.028-0.0026.587-0.068-0.0680.0000.0000.0000.000
191A203ASN0-0.028-0.0204.068-1.241-1.0360.000-0.084-0.1220.000
192A204GLY00.0420.0248.2980.0910.0910.0000.0000.0000.000
193A205HIS0-0.016-0.0089.082-0.160-0.1600.0000.0000.0000.000
194A206LEU00.0000.01712.141-0.080-0.0800.0000.0000.0000.000
195A207CYS0-0.036-0.02112.9370.0370.0370.0000.0000.0000.000
196A208GLY00.0510.01915.695-0.034-0.0340.0000.0000.0000.000
197A209ALA0-0.033-0.00718.3140.0150.0150.0000.0000.0000.000
198A210HIS00.0590.02320.322-0.018-0.0180.0000.0000.0000.000
199A211ASP-1-0.850-0.92723.0840.0390.0390.0000.0000.0000.000
200A212SER0-0.042-0.01321.631-0.002-0.0020.0000.0000.0000.000
201A213PHE00.005-0.00513.395-0.009-0.0090.0000.0000.0000.000
202A214TYR00.0210.01218.3160.0170.0170.0000.0000.0000.000
203A215LYS10.8110.87010.219-0.718-0.7180.0000.0000.0000.000
204A216LYS10.8810.96415.511-0.387-0.3870.0000.0000.0000.000
205A217SER00.0130.00512.233-0.009-0.0090.0000.0000.0000.000
206A218PRO00.0220.01812.077-0.110-0.1100.0000.0000.0000.000
207A219PRO0-0.0020.00515.0340.0360.0360.0000.0000.0000.000
208A220ILE00.011-0.00615.118-0.016-0.0160.0000.0000.0000.000
209A221GLY0-0.0040.00318.718-0.023-0.0230.0000.0000.0000.000
210A222LEU0-0.010-0.02622.431-0.007-0.0070.0000.0000.0000.000
211A223ASP-1-0.903-0.94423.8020.1700.1700.0000.0000.0000.000
212A224TRP0-0.022-0.02123.9470.0060.0060.0000.0000.0000.000
213A225LEU00.0410.03018.1710.0120.0120.0000.0000.0000.000
214A226ALA0-0.0090.01121.6700.0180.0180.0000.0000.0000.000
215A227HIS0-0.0060.00623.031-0.022-0.0220.0000.0000.0000.000
216A228GLU-1-0.865-0.95322.8920.1470.1470.0000.0000.0000.000
217A229SER0-0.072-0.04322.1580.0070.0070.0000.0000.0000.000
218A230ASN0-0.020-0.00818.6130.0520.0520.0000.0000.0000.000
219A231MET0-0.0070.01818.0250.0080.0080.0000.0000.0000.000
220A232VAL0-0.031-0.01714.0100.0140.0140.0000.0000.0000.000
221A233GLY0-0.018-0.01916.0860.0030.0030.0000.0000.0000.000
222A234HIS0-0.0110.00218.338-0.010-0.0100.0000.0000.0000.000
223A235GLY00.0340.01022.139-0.007-0.0070.0000.0000.0000.000
224A236GLY0-0.001-0.01221.9800.0050.0050.0000.0000.0000.000
225A237TRP00.002-0.00614.448-0.013-0.0130.0000.0000.0000.000
226A238HIS00.0160.01421.424-0.007-0.0070.0000.0000.0000.000
227A239MET0-0.033-0.01021.117-0.006-0.0060.0000.0000.0000.000
228A240PHE0-0.018-0.01517.776-0.016-0.0160.0000.0000.0000.000
229A241LYS10.8860.95421.3370.0790.0790.0000.0000.0000.000
230A242LEU0-0.006-0.00118.6320.0070.0070.0000.0000.0000.000
231A243LEU0-0.018-0.00215.617-0.010-0.0100.0000.0000.0000.000
232A244ILE00.0120.01314.3840.0180.0180.0000.0000.0000.000
233A245SER0-0.030-0.0559.543-0.025-0.0250.0000.0000.0000.000
234A246PRO00.0080.0379.1770.0820.0820.0000.0000.0000.000
235A247LEU00.0360.02910.389-0.015-0.0150.0000.0000.0000.000
236A248PRO00.002-0.0058.533-0.145-0.1450.0000.0000.0000.000
237A249GLN00.0090.01010.4950.1610.1610.0000.0000.0000.000