FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 49Q5N

Calculation Name: 5Y0W-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5Y0W

Chain ID: A

ChEMBL ID:

UniProt ID: P03518

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 307
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4496370.469739
FMO2-HF: Nuclear repulsion 4369682.570952
FMO2-HF: Total energy -126687.898787
FMO2-MP2: Total energy -127042.550913


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:1:GLU)


Summations of interaction energy for fragment #1(A:1:GLU)
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.
-73.615-62.04716.107-11.778-15.8960.017
Interaction energy analysis for fragmet #1(A:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.928 / q_NPA : -0.975
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].
3A3PRO00.001-0.0073.436-6.928-4.7350.086-0.959-1.3210.006
4A4HIS00.0100.0302.851-11.209-8.5750.383-1.267-1.7510.013
5A5LEU00.0940.0582.484-8.688-6.2861.059-1.444-2.0160.013
6A6ARG10.7730.8804.916-25.206-25.110-0.001-0.003-0.0900.000
7A7ASN0-0.078-0.0566.089-3.985-3.9850.0000.0000.0000.000
8A8ARG10.7730.8666.692-28.006-28.0060.0000.0000.0000.000
9A9PRO00.0410.0418.221-1.309-1.3090.0000.0000.0000.000
10A10GLY0-0.004-0.01210.663-0.890-0.8900.0000.0000.0000.000
11A11LYS10.9190.96213.913-13.224-13.2240.0000.0000.0000.000
12A12GLY00.0700.04513.515-0.026-0.0260.0000.0000.0000.000
13A13HIS00.003-0.01114.1280.1820.1820.0000.0000.0000.000
14A14ASN0-0.029-0.03513.4050.2420.2420.0000.0000.0000.000
15A15TYR00.0760.03017.302-0.173-0.1730.0000.0000.0000.000
16A16ILE00.0560.03121.0500.0540.0540.0000.0000.0000.000
17A17ASP-1-0.789-0.90323.79711.03311.0330.0000.0000.0000.000
18A18GLY0-0.063-0.00526.772-0.277-0.2770.0000.0000.0000.000
19A19MET0-0.030-0.01725.709-0.254-0.2540.0000.0000.0000.000
20A20THR00.0710.04825.3990.3000.3000.0000.0000.0000.000
21A21GLN0-0.027-0.02826.0020.4210.4210.0000.0000.0000.000
22A22GLU-1-0.794-0.90021.14313.95513.9550.0000.0000.0000.000
23A23ASP-1-0.818-0.93021.83112.89212.8920.0000.0000.0000.000
24A24ALA0-0.093-0.03521.3780.3270.3270.0000.0000.0000.000
25A25THR00.019-0.00518.1020.1500.1500.0000.0000.0000.000
26A26CYS0-0.0510.01015.6450.0850.0850.0000.0000.0000.000
27A27LYS10.8660.96817.944-11.752-11.7520.0000.0000.0000.000
28A28PRO00.0140.01314.898-0.761-0.7610.0000.0000.0000.000
29A29VAL0-0.022-0.01711.514-0.462-0.4620.0000.0000.0000.000
30A30THR00.0220.01511.4020.6650.6650.0000.0000.0000.000
31A31TYR0-0.027-0.0487.068-1.019-1.0190.0000.0000.0000.000
32A32ALA0-0.076-0.03011.5010.0110.0110.0000.0000.0000.000
33A33GLY00.0440.02015.162-0.253-0.2530.0000.0000.0000.000
34A34ALA0-0.048-0.01815.7361.0311.0310.0000.0000.0000.000
35A36SER0-0.019-0.00316.7080.7150.7150.0000.0000.0000.000
36A37SER00.0190.01618.083-0.295-0.2950.0000.0000.0000.000
37A38PHE0-0.022-0.0158.6680.0690.0690.0000.0000.0000.000
38A39ASP-1-0.731-0.86412.82820.59220.5920.0000.0000.0000.000
39A40VAL0-0.019-0.02013.1281.0101.0100.0000.0000.0000.000
40A41LEU0-0.040-0.02010.920-0.067-0.0670.0000.0000.0000.000
41A42LEU00.0130.0077.1242.0662.0660.0000.0000.0000.000
42A43GLU-1-0.977-0.9609.82719.40719.4070.0000.0000.0000.000
43A44LYS11.0070.9949.859-23.301-23.3010.0000.0000.0000.000
44A45GLY0-0.024-0.00511.023-2.238-2.2380.0000.0000.0000.000
45A46LYS10.8880.93513.161-18.641-18.6410.0000.0000.0000.000
46A47PHE0-0.033-0.02011.3571.1441.1440.0000.0000.0000.000
47A48PRO00.0420.0349.8012.1692.1690.0000.0000.0000.000
48A49LEU0-0.037-0.0078.8153.1793.1790.0000.0000.0000.000
49A50PHE0-0.023-0.0238.5932.9682.9680.0000.0000.0000.000
50A51GLN0-0.042-0.0516.0383.4113.4110.0000.0000.0000.000
51A52SER0-0.0230.0054.30012.05712.264-0.001-0.008-0.1980.000
52A53TYR0-0.0220.0025.6322.4932.4930.0000.0000.0000.000
53A54ALA00.0650.0423.580-5.687-5.1040.012-0.185-0.4100.001
54A55HIS00.006-0.0081.917-2.445-3.3309.244-3.964-4.395-0.024
55A56HIS0-0.043-0.0095.413-2.538-2.5380.0000.0000.0000.000
56A57ARG10.7750.8868.846-18.951-18.9510.0000.0000.0000.000
57A58THR00.0230.01011.747-0.683-0.6830.0000.0000.0000.000
58A59LEU00.033-0.00313.478-0.781-0.7810.0000.0000.0000.000
59A60LEU0-0.032-0.03017.141-0.761-0.7610.0000.0000.0000.000
60A61GLU-1-0.690-0.80912.06622.70922.7090.0000.0000.0000.000
61A62ALA0-0.010-0.00216.377-0.561-0.5610.0000.0000.0000.000
62A63VAL0-0.028-0.01217.738-0.703-0.7030.0000.0000.0000.000
63A64HIS0-0.087-0.03619.639-0.769-0.7690.0000.0000.0000.000
64A65ASP-1-0.841-0.91816.36116.40516.4050.0000.0000.0000.000
65A66THR0-0.114-0.05919.839-0.397-0.3970.0000.0000.0000.000
66A67ILE0-0.0070.01116.805-0.251-0.2510.0000.0000.0000.000
67A68ILE0-0.038-0.02119.869-0.291-0.2910.0000.0000.0000.000
68A69ALA00.0470.02922.378-0.134-0.1340.0000.0000.0000.000
69A70LYS10.8690.89725.489-10.563-10.5630.0000.0000.0000.000
70A71ALA0-0.009-0.04127.135-0.251-0.2510.0000.0000.0000.000
71A72ASP-1-0.881-0.93329.5848.5998.5990.0000.0000.0000.000
72A73PRO0-0.051-0.02633.320-0.040-0.0400.0000.0000.0000.000
73A74PRO0-0.038-0.01229.9750.2050.2050.0000.0000.0000.000
74A75SER0-0.034-0.02229.2920.4000.4000.0000.0000.0000.000
75A76CYS0-0.0060.00331.185-0.221-0.2210.0000.0000.0000.000
76A77ASP-1-0.825-0.93232.9448.7808.7800.0000.0000.0000.000
77A78LEU0-0.015-0.02431.887-0.204-0.2040.0000.0000.0000.000
78A79GLN0-0.015-0.00936.135-0.129-0.1290.0000.0000.0000.000
79A80SER0-0.058-0.00739.222-0.208-0.2080.0000.0000.0000.000
80A81ALA00.0160.00141.583-0.026-0.0260.0000.0000.0000.000
81A82HIS0-0.019-0.01539.325-0.209-0.2090.0000.0000.0000.000
82A83GLY00.0780.05537.7260.1240.1240.0000.0000.0000.000
83A84ASN0-0.011-0.03536.3580.3840.3840.0000.0000.0000.000
84A85PRO0-0.0310.00134.9820.0910.0910.0000.0000.0000.000
85A87MET0-0.0030.02932.3190.3220.3220.0000.0000.0000.000
86A88LYS10.9920.98233.711-8.726-8.7260.0000.0000.0000.000
87A89GLU-1-0.831-0.93629.72610.61510.6150.0000.0000.0000.000
88A90LYS10.9110.96627.206-10.745-10.7450.0000.0000.0000.000
89A91LEU0-0.008-0.00329.7550.1980.1980.0000.0000.0000.000
90A92VAL0-0.069-0.01629.597-0.018-0.0180.0000.0000.0000.000
91A93MET0-0.0190.00523.7950.1650.1650.0000.0000.0000.000
92A94LYS10.9280.96926.299-11.253-11.2530.0000.0000.0000.000
93A95THR0-0.040-0.03523.7570.4970.4970.0000.0000.0000.000
94A96HIS00.012-0.01222.765-0.515-0.5150.0000.0000.0000.000
95A97CYS0-0.155-0.06722.7731.0431.0430.0000.0000.0000.000
96A98PRO0-0.007-0.00821.272-0.363-0.3630.0000.0000.0000.000
97A99ASN00.0560.03324.522-0.264-0.2640.0000.0000.0000.000
98A100ASP-1-0.892-0.94826.00211.36911.3690.0000.0000.0000.000
99A101TYR0-0.096-0.07520.0080.1710.1710.0000.0000.0000.000
100A102GLN00.0090.00826.811-0.120-0.1200.0000.0000.0000.000
101A103SER0-0.030-0.04525.326-0.439-0.4390.0000.0000.0000.000
102A104ALA00.0470.01823.8280.4220.4220.0000.0000.0000.000
103A105HIS00.0010.03718.580-1.162-1.1620.0000.0000.0000.000
104A106TYR0-0.018-0.01821.8640.5460.5460.0000.0000.0000.000
105A107LEU00.0280.01920.257-0.448-0.4480.0000.0000.0000.000
106A108ASN00.0480.03323.3170.0380.0380.0000.0000.0000.000
107A109ASN00.0150.01226.5370.4640.4640.0000.0000.0000.000
108A110ASP-1-0.924-0.98928.7789.9019.9010.0000.0000.0000.000
109A111GLY00.0040.02425.036-0.014-0.0140.0000.0000.0000.000
110A112LYS10.8250.93224.741-10.065-10.0650.0000.0000.0000.000
111A113MET00.0100.01222.4040.4140.4140.0000.0000.0000.000
112A114ALA0-0.0090.00424.801-0.476-0.4760.0000.0000.0000.000
113A115SER0-0.027-0.02925.7170.4590.4590.0000.0000.0000.000
114A116VAL0-0.0020.01327.461-0.484-0.4840.0000.0000.0000.000
115A117LYS10.9650.95828.654-9.656-9.6560.0000.0000.0000.000
116A118CYS00.0390.07431.1450.0460.0460.0000.0000.0000.000
117A119PRO00.0450.02133.3770.1570.1570.0000.0000.0000.000
118A120PRO00.008-0.02234.6220.1920.1920.0000.0000.0000.000
119A121LYS10.9390.95034.487-8.123-8.1230.0000.0000.0000.000
120A122TYR0-0.0040.00534.664-0.250-0.2500.0000.0000.0000.000
121A123GLU-1-0.794-0.88930.57510.23110.2310.0000.0000.0000.000
122A124LEU0-0.009-0.01727.364-0.260-0.2600.0000.0000.0000.000
123A125THR0-0.017-0.01129.9000.1070.1070.0000.0000.0000.000
124A126GLU-1-0.766-0.88628.18110.28910.2890.0000.0000.0000.000
125A127ASP-1-0.849-0.91827.36010.31710.3170.0000.0000.0000.000
126A129ASN0-0.008-0.01428.8330.1460.1460.0000.0000.0000.000
127A130PHE00.0200.00532.141-0.321-0.3210.0000.0000.0000.000
128A132ARG10.7950.89732.005-9.867-9.8670.0000.0000.0000.000
129A133GLN0-0.024-0.00735.6300.2310.2310.0000.0000.0000.000
130A134MET0-0.0130.01633.6580.1040.1040.0000.0000.0000.000
131A135THR00.0180.00234.132-0.178-0.1780.0000.0000.0000.000
132A136GLY00.0220.03933.054-0.091-0.0910.0000.0000.0000.000
133A137ALA0-0.022-0.02833.764-0.190-0.1900.0000.0000.0000.000
134A138SER0-0.049-0.02928.7190.0620.0620.0000.0000.0000.000
135A139LEU00.0340.02429.2950.0210.0210.0000.0000.0000.000
136A140LYS10.9130.95922.610-13.023-13.0230.0000.0000.0000.000
137A141LYS10.7990.88624.342-12.089-12.0890.0000.0000.0000.000
138A142GLY00.0450.02921.701-0.135-0.1350.0000.0000.0000.000
139A143SER0-0.038-0.03321.566-0.942-0.9420.0000.0000.0000.000
140A144TYR00.0430.00418.7851.0341.0340.0000.0000.0000.000
141A145PRO0-0.0300.00016.414-0.673-0.6730.0000.0000.0000.000
142A146LEU00.026-0.00318.9150.2830.2830.0000.0000.0000.000
143A147GLN0-0.093-0.05018.655-0.123-0.1230.0000.0000.0000.000
144A148ASP-1-0.811-0.90512.53524.38024.3800.0000.0000.0000.000
145A149LEU0-0.014-0.01613.737-0.663-0.6630.0000.0000.0000.000
146A150PHE00.0380.03010.7121.3971.3970.0000.0000.0000.000
147A151CYS0-0.055-0.02112.701-1.023-1.0230.0000.0000.0000.000
148A152GLN0-0.024-0.03112.9882.2452.2450.0000.0000.0000.000
149A153SER00.0560.03815.088-1.112-1.1120.0000.0000.0000.000
150A154SER0-0.057-0.06918.0700.2950.2950.0000.0000.0000.000
151A155GLU-1-0.811-0.91820.75611.72711.7270.0000.0000.0000.000
152A156ASP-1-0.878-0.91623.23811.77111.7710.0000.0000.0000.000
153A157ASP-1-0.807-0.90124.94810.20010.2000.0000.0000.0000.000
154A158GLY00.032-0.01427.1220.0860.0860.0000.0000.0000.000
155A159SER0-0.024-0.01628.080-0.115-0.1150.0000.0000.0000.000
156A160LYS10.8470.92931.376-9.250-9.2500.0000.0000.0000.000
157A161LEU0-0.0140.01026.213-0.160-0.1600.0000.0000.0000.000
158A162LYS10.9720.96630.025-9.013-9.0130.0000.0000.0000.000
159A163THR0-0.004-0.00528.9740.2120.2120.0000.0000.0000.000
160A164LYS10.8790.95029.621-9.706-9.7060.0000.0000.0000.000
161A165MET00.0340.02927.3480.2650.2650.0000.0000.0000.000
162A166LYS10.8920.91931.022-10.036-10.0360.0000.0000.0000.000
163A167GLY00.0260.02333.6000.0350.0350.0000.0000.0000.000
164A168VAL0-0.0050.01131.099-0.033-0.0330.0000.0000.0000.000
165A169CYS0-0.079-0.04634.539-0.064-0.0640.0000.0000.0000.000
166A170GLU-1-0.907-0.97934.6648.3828.3820.0000.0000.0000.000
167A171VAL00.0340.03228.0880.1420.1420.0000.0000.0000.000
168A172GLY00.0510.02829.5710.1160.1160.0000.0000.0000.000
169A173VAL0-0.054-0.03430.388-0.381-0.3810.0000.0000.0000.000
170A174GLN0-0.065-0.01729.003-0.445-0.4450.0000.0000.0000.000
171A175ALA00.0530.03033.3800.0510.0510.0000.0000.0000.000
172A176LEU0-0.077-0.03432.010-0.017-0.0170.0000.0000.0000.000
173A177LYS10.8300.89536.369-8.305-8.3050.0000.0000.0000.000
174A178LYS10.9470.97939.868-7.248-7.2480.0000.0000.0000.000
175A180ASP-1-0.830-0.90742.8766.7416.7410.0000.0000.0000.000
176A181GLY0-0.041-0.00344.924-0.085-0.0850.0000.0000.0000.000
177A182GLN00.001-0.00344.095-0.025-0.0250.0000.0000.0000.000
178A183LEU0-0.012-0.01338.9210.1270.1270.0000.0000.0000.000
179A184SER0-0.031-0.00635.548-0.001-0.0010.0000.0000.0000.000
180A185THR00.011-0.01534.7020.0670.0670.0000.0000.0000.000
181A186ALA00.0050.00530.653-0.053-0.0530.0000.0000.0000.000
182A187HIS00.0180.01427.4210.3000.3000.0000.0000.0000.000
183A188GLU-1-0.817-0.91325.80611.17611.1760.0000.0000.0000.000
184A189VAL0-0.045-0.02519.1210.0030.0030.0000.0000.0000.000
185A190VAL00.0050.00122.1130.1890.1890.0000.0000.0000.000
186A191PRO00.0190.01819.2380.2830.2830.0000.0000.0000.000
187A192PHE0-0.047-0.03619.788-0.910-0.9100.0000.0000.0000.000
188A193ALA00.0440.01919.8310.9380.9380.0000.0000.0000.000
189A194VAL0-0.0030.00920.894-0.824-0.8240.0000.0000.0000.000
190A195PHE00.0400.00321.4250.6760.6760.0000.0000.0000.000
191A196LYS10.9801.01223.776-11.196-11.1960.0000.0000.0000.000
192A197ASN0-0.073-0.02925.859-0.182-0.1820.0000.0000.0000.000
193A198SER0-0.045-0.03926.401-0.240-0.2400.0000.0000.0000.000
194A199LYS10.9821.00328.078-9.547-9.5470.0000.0000.0000.000
195A200LYS10.8630.94923.829-12.252-12.2520.0000.0000.0000.000
196A201VAL0-0.0250.00425.012-0.577-0.5770.0000.0000.0000.000
197A202TYR0-0.011-0.02424.5340.3900.3900.0000.0000.0000.000
198A203LEU00.016-0.01121.544-0.443-0.4430.0000.0000.0000.000
199A204ASP-1-0.849-0.92724.79411.08811.0880.0000.0000.0000.000
200A205LYS10.9030.94022.244-12.377-12.3770.0000.0000.0000.000
201A206LEU00.0250.01615.447-0.349-0.3490.0000.0000.0000.000
202A207ASP-1-0.875-0.92718.90715.66615.6660.0000.0000.0000.000
203A208LEU0-0.002-0.01013.591-0.693-0.6930.0000.0000.0000.000
204A209LYS10.9430.99115.493-15.059-15.0590.0000.0000.0000.000
205A210THR00.025-0.01810.360-0.887-0.8870.0000.0000.0000.000
206A211GLU-1-0.989-0.96113.56416.10316.1030.0000.0000.0000.000
207A212GLU-1-0.885-0.9538.58030.72030.7200.0000.0000.0000.000
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