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: LZLM9

Calculation Name: 5H0J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5H0J

Chain ID: A

ChEMBL ID:

UniProt ID: C6Y1J8

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 234
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3163946.695935
FMO2-HF: Nuclear repulsion 3069093.049842
FMO2-HF: Total energy -94853.646093
FMO2-MP2: Total energy -95128.723796


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-6.283-4.87912.984-5.15-9.239-0.027
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.014
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].
3A3THR00.0110.0283.798-0.7970.624-0.017-0.542-0.8620.001
4A4PHE0-0.004-0.0143.918-1.316-1.1300.001-0.097-0.0900.000
5A5ALA00.0490.0135.797-0.195-0.1950.0000.0000.0000.000
6A6ASP-1-0.815-0.9102.010-2.293-6.96610.570-2.640-3.258-0.006
7A7LYS10.9150.9622.923-1.3530.9711.042-1.004-2.361-0.011
8A8VAL0-0.017-0.0023.6550.6580.7690.0150.066-0.1930.000
9A9ILE00.0060.0064.7910.2650.392-0.001-0.004-0.1220.000
10A10GLN0-0.037-0.0292.519-3.979-2.2821.376-0.919-2.154-0.011
11A11PHE00.002-0.0214.9180.6110.730-0.001-0.005-0.1130.000
12A12ASN0-0.013-0.0178.1240.3180.3180.0000.0000.0000.000
13A13LYS10.9100.9634.1993.0883.180-0.001-0.005-0.0860.000
14A14ASP-1-0.846-0.9157.212-0.246-0.2460.0000.0000.0000.000
15A15LEU0-0.114-0.0309.7290.1660.1660.0000.0000.0000.000
16A16SER0-0.008-0.01812.8690.0090.0090.0000.0000.0000.000
17A17TYR0-0.050-0.04916.0440.0180.0180.0000.0000.0000.000
18A18THR00.0280.01517.9220.0050.0050.0000.0000.0000.000
19A19GLY00.0120.01020.7090.0210.0210.0000.0000.0000.000
20A20SER0-0.0170.00423.7010.0110.0110.0000.0000.0000.000
21A21THR00.0160.00727.409-0.014-0.0140.0000.0000.0000.000
22A22LEU0-0.0090.00926.0950.0020.0020.0000.0000.0000.000
23A23PRO0-0.001-0.00730.0400.0070.0070.0000.0000.0000.000
24A24PRO00.0620.01732.896-0.007-0.0070.0000.0000.0000.000
25A25GLY00.0170.01334.445-0.002-0.0020.0000.0000.0000.000
26A26ILE0-0.057-0.02228.776-0.009-0.0090.0000.0000.0000.000
27A27ARG10.8870.94727.0930.1640.1640.0000.0000.0000.000
28A28ILE00.0390.01121.161-0.005-0.0050.0000.0000.0000.000
29A29MET0-0.0480.00121.924-0.004-0.0040.0000.0000.0000.000
30A30ASN00.0620.01115.288-0.047-0.0470.0000.0000.0000.000
31A31PRO00.0530.01417.4720.0000.0000.0000.0000.0000.000
32A32PHE00.009-0.00912.900-0.020-0.0200.0000.0000.0000.000
33A33LYS10.8560.92811.8120.5920.5920.0000.0000.0000.000
34A34GLU-1-0.971-0.96416.800-0.250-0.2500.0000.0000.0000.000
35A35HIS00.0090.00618.8050.0060.0060.0000.0000.0000.000
36A36GLU-1-0.864-0.93216.686-0.427-0.4270.0000.0000.0000.000
37A37GLN0-0.001-0.00316.026-0.056-0.0560.0000.0000.0000.000
38A38THR0-0.011-0.00315.239-0.045-0.0450.0000.0000.0000.000
39A39MET00.004-0.0058.549-0.014-0.0140.0000.0000.0000.000
40A40HIS00.0740.04811.676-0.202-0.2020.0000.0000.0000.000
41A41ILE0-0.0140.00213.749-0.022-0.0220.0000.0000.0000.000
42A42VAL0-0.035-0.0189.647-0.023-0.0230.0000.0000.0000.000
43A43GLU-1-0.948-0.9777.651-1.926-1.9260.0000.0000.0000.000
44A44ALA00.0090.00710.383-0.010-0.0100.0000.0000.0000.000
45A45PHE00.001-0.01613.4800.0430.0430.0000.0000.0000.000
46A46TYR0-0.018-0.0239.1240.0820.0820.0000.0000.0000.000
47A47HIS00.0390.0166.2060.1830.1830.0000.0000.0000.000
48A48LYS10.8310.93510.7920.5890.5890.0000.0000.0000.000
49A49TYR0-0.003-0.01213.4810.0840.0840.0000.0000.0000.000
50A50TYR0-0.065-0.0769.6170.0830.0830.0000.0000.0000.000
51A51ASN00.0290.0319.005-0.362-0.3620.0000.0000.0000.000
52A52ASP-1-0.763-0.8719.307-0.532-0.5320.0000.0000.0000.000
53A53ASN0-0.038-0.0536.824-0.223-0.2230.0000.0000.0000.000
54A54GLN0-0.040-0.01810.0270.1740.1740.0000.0000.0000.000
55A55SER0-0.0020.00812.005-0.111-0.1110.0000.0000.0000.000
56A56ARG10.7650.87212.1570.6670.6670.0000.0000.0000.000
57A57TYR00.0300.01915.2600.0410.0410.0000.0000.0000.000
58A58LEU00.0030.00515.401-0.041-0.0410.0000.0000.0000.000
59A59ILE0-0.007-0.00417.9450.0490.0490.0000.0000.0000.000
60A60LEU00.0040.00418.500-0.036-0.0360.0000.0000.0000.000
61A61GLY00.0130.00521.1460.0280.0280.0000.0000.0000.000
62A62ILE0-0.044-0.02623.2030.0150.0150.0000.0000.0000.000
63A63ASN00.028-0.00622.0420.0240.0240.0000.0000.0000.000
64A64PRO00.0000.02119.3610.0160.0160.0000.0000.0000.000
65A65GLY00.0210.00922.3280.0300.0300.0000.0000.0000.000
66A66ARG10.9860.98423.8610.2040.2040.0000.0000.0000.000
67A67PHE0-0.067-0.02825.027-0.009-0.0090.0000.0000.0000.000
68A68GLY00.0260.00625.178-0.012-0.0120.0000.0000.0000.000
69A69SER0-0.004-0.02120.942-0.016-0.0160.0000.0000.0000.000
70A70GLY0-0.025-0.00420.403-0.043-0.0430.0000.0000.0000.000
71A71LEU0-0.049-0.04320.980-0.006-0.0060.0000.0000.0000.000
72A72THR0-0.017-0.02319.142-0.020-0.0200.0000.0000.0000.000
73A73GLY0-0.0050.00516.010-0.060-0.0600.0000.0000.0000.000
74A74ILE0-0.0100.00714.506-0.066-0.0660.0000.0000.0000.000
75A75PRO00.005-0.00616.0450.0760.0760.0000.0000.0000.000
76A76PHE00.0190.00419.1790.0130.0130.0000.0000.0000.000
77A77THR00.0310.06320.0470.0270.0270.0000.0000.0000.000
78A78ASP-1-0.742-0.82421.721-0.298-0.2980.0000.0000.0000.000
79A79PRO00.0300.00823.698-0.006-0.0060.0000.0000.0000.000
80A80LYS10.9660.99224.7230.2040.2040.0000.0000.0000.000
81A81ARG10.8420.89724.5150.2620.2620.0000.0000.0000.000
82A82LEU00.0340.02018.515-0.006-0.0060.0000.0000.0000.000
83A83ILE0-0.018-0.00422.530-0.006-0.0060.0000.0000.0000.000
84A84THR0-0.109-0.07024.9440.0070.0070.0000.0000.0000.000
85A85GLU-1-0.866-0.92724.402-0.253-0.2530.0000.0000.0000.000
86A86CYS0-0.053-0.01519.716-0.018-0.0180.0000.0000.0000.000
87A87ASN0-0.0300.00721.035-0.014-0.0140.0000.0000.0000.000
88A88ILE0-0.0150.00516.708-0.020-0.0200.0000.0000.0000.000
89A89PRO00.005-0.01020.4400.0210.0210.0000.0000.0000.000
90A90TYR00.005-0.00221.137-0.037-0.0370.0000.0000.0000.000
91A91SER00.0010.00123.0540.0400.0400.0000.0000.0000.000
92A92GLY00.0380.01524.623-0.010-0.0100.0000.0000.0000.000
93A93LYS10.9270.97127.3130.2260.2260.0000.0000.0000.000
94A94LEU00.0710.02227.822-0.016-0.0160.0000.0000.0000.000
95A95SER0-0.019-0.00927.1770.0100.0100.0000.0000.0000.000
96A96HIS00.0360.01628.165-0.020-0.0200.0000.0000.0000.000
97A97GLU-1-0.797-0.89025.190-0.295-0.2950.0000.0000.0000.000
98A98PRO0-0.032-0.02929.096-0.005-0.0050.0000.0000.0000.000
99A99SER00.005-0.02027.2200.0040.0040.0000.0000.0000.000
100A100SER00.0280.01024.821-0.004-0.0040.0000.0000.0000.000
101A101VAL0-0.018-0.01126.868-0.003-0.0030.0000.0000.0000.000
102A102PHE00.0030.00128.7100.0010.0010.0000.0000.0000.000
103A103ILE00.0070.00123.2870.0050.0050.0000.0000.0000.000
104A104TYR00.078-0.00520.792-0.009-0.0090.0000.0000.0000.000
105A105GLU-1-0.866-0.92926.645-0.170-0.1700.0000.0000.0000.000
106A106MET0-0.072-0.01324.4440.0090.0090.0000.0000.0000.000
107A107ILE00.0060.00021.8900.0050.0050.0000.0000.0000.000
108A108ASN0-0.025-0.02425.864-0.006-0.0060.0000.0000.0000.000
109A109ALA0-0.030-0.00528.3360.0090.0090.0000.0000.0000.000
110A110PHE0-0.072-0.03823.4840.0090.0090.0000.0000.0000.000
111A111GLY00.0200.01527.0190.0060.0060.0000.0000.0000.000
112A112GLY00.0140.01925.185-0.003-0.0030.0000.0000.0000.000
113A113ALA0-0.001-0.01920.555-0.010-0.0100.0000.0000.0000.000
114A114GLU-1-0.937-0.96618.816-0.380-0.3800.0000.0000.0000.000
115A115ALA00.0470.02319.122-0.021-0.0210.0000.0000.0000.000
116A116PHE0-0.004-0.00820.274-0.007-0.0070.0000.0000.0000.000
117A117TYR0-0.005-0.02615.892-0.001-0.0010.0000.0000.0000.000
118A118LYS10.9160.99814.7470.3980.3980.0000.0000.0000.000
119A119GLN0-0.037-0.02316.5010.0090.0090.0000.0000.0000.000
120A120PHE0-0.031-0.01417.7640.0170.0170.0000.0000.0000.000
121A121TYR0-0.0040.00711.874-0.079-0.0790.0000.0000.0000.000
122A122ILE0-0.012-0.00215.4070.0630.0630.0000.0000.0000.000
123A123SER00.0540.02614.927-0.040-0.0400.0000.0000.0000.000
124A124SER0-0.033-0.04116.9410.0320.0320.0000.0000.0000.000
125A125PRO0-0.0100.01218.458-0.016-0.0160.0000.0000.0000.000
126A126CYS00.0040.02119.5460.0100.0100.0000.0000.0000.000
127A127PRO00.0200.02416.050-0.008-0.0080.0000.0000.0000.000
128A128LEU0-0.0040.00217.226-0.034-0.0340.0000.0000.0000.000
129A129GLY00.0470.02120.1510.0190.0190.0000.0000.0000.000
130A130PHE00.006-0.00523.5760.0090.0090.0000.0000.0000.000
131A131THR00.0120.01026.7950.0050.0050.0000.0000.0000.000
132A132SER00.0560.05529.3790.0070.0070.0000.0000.0000.000
133A133ILE0-0.032-0.01432.090-0.007-0.0070.0000.0000.0000.000
134A134ALA0-0.032-0.00335.1780.0070.0070.0000.0000.0000.000
135A135ALA00.0750.03438.888-0.002-0.0020.0000.0000.0000.000
136A136ASN00.006-0.00741.014-0.004-0.0040.0000.0000.0000.000
137A137GLY00.0600.03338.395-0.001-0.0010.0000.0000.0000.000
138A138LYS10.8900.96035.3670.1320.1320.0000.0000.0000.000
139A139GLU-1-0.863-0.94129.792-0.193-0.1930.0000.0000.0000.000
140A140LYS10.8710.93433.4750.1180.1180.0000.0000.0000.000
141A141ASN00.0400.01328.122-0.018-0.0180.0000.0000.0000.000
142A142TYR0-0.035-0.04129.1020.0130.0130.0000.0000.0000.000
143A143ASN0-0.032-0.01827.968-0.028-0.0280.0000.0000.0000.000
144A144TYR00.044-0.00725.2540.0210.0210.0000.0000.0000.000
145A145TYR0-0.015-0.01227.5670.0160.0160.0000.0000.0000.000
146A146ASP-1-0.862-0.93730.557-0.128-0.1280.0000.0000.0000.000
147A147SER0-0.025-0.01432.8420.0100.0100.0000.0000.0000.000
148A148LYS10.8760.92232.4820.0730.0730.0000.0000.0000.000
149A149ALA00.0370.02133.2560.0020.0020.0000.0000.0000.000
150A150LEU00.0090.01328.2790.0030.0030.0000.0000.0000.000
151A151GLU-1-0.821-0.91228.618-0.094-0.0940.0000.0000.0000.000
152A152LYS10.9340.96328.3360.0410.0410.0000.0000.0000.000
153A153ALA0-0.034-0.00428.6140.0060.0060.0000.0000.0000.000
154A154VAL00.014-0.00423.9830.0010.0010.0000.0000.0000.000
155A155TYR0-0.0100.00223.757-0.017-0.0170.0000.0000.0000.000
156A156GLU-1-0.844-0.94223.104-0.029-0.0290.0000.0000.0000.000
157A157PHE0-0.010-0.00217.699-0.007-0.0070.0000.0000.0000.000
158A158ILE0-0.030-0.01619.023-0.024-0.0240.0000.0000.0000.000
159A159ILE0-0.0070.00119.454-0.023-0.0230.0000.0000.0000.000
160A160GLU-1-0.855-0.93416.7040.0140.0140.0000.0000.0000.000
161A161ASN0-0.043-0.02214.865-0.063-0.0630.0000.0000.0000.000
162A162ILE0-0.013-0.01114.857-0.053-0.0530.0000.0000.0000.000
163A163ARG10.9380.97314.681-0.114-0.1140.0000.0000.0000.000
164A164LYS10.9390.9879.7960.4890.4890.0000.0000.0000.000
165A165GLN00.0140.02110.806-0.176-0.1760.0000.0000.0000.000
166A166LEU0-0.010-0.00412.119-0.071-0.0710.0000.0000.0000.000
167A167THR0-0.097-0.0598.849-0.018-0.0180.0000.0000.0000.000
168A168LEU0-0.023-0.0017.064-0.054-0.0540.0000.0000.0000.000
169A169GLY0-0.0190.0078.912-0.125-0.1250.0000.0000.0000.000
170A170ILE0-0.025-0.01611.304-0.024-0.0240.0000.0000.0000.000
171A171THR00.0080.00014.7850.0640.0640.0000.0000.0000.000
172A172THR00.0070.00117.534-0.012-0.0120.0000.0000.0000.000
173A173ASP-1-0.786-0.87020.012-0.082-0.0820.0000.0000.0000.000
174A174THR00.015-0.02822.8080.0160.0160.0000.0000.0000.000
175A175CYS0-0.0530.00721.550-0.030-0.0300.0000.0000.0000.000
176A176PHE00.0450.01122.3320.0210.0210.0000.0000.0000.000
177A177CYS0-0.0110.01523.257-0.019-0.0190.0000.0000.0000.000
178A178LEU00.0180.01724.0890.0140.0140.0000.0000.0000.000
179A179GLY0-0.029-0.04126.874-0.004-0.0040.0000.0000.0000.000
180A180THR00.0320.01629.9680.0010.0010.0000.0000.0000.000
181A181GLY00.0200.02332.7710.0090.0090.0000.0000.0000.000
182A182LYS10.9270.94832.2950.1000.1000.0000.0000.0000.000
183A183ASN00.0030.01225.1790.0090.0090.0000.0000.0000.000
184A184GLU-1-0.811-0.91328.383-0.109-0.1090.0000.0000.0000.000
185A185LYS10.8990.94830.2960.0930.0930.0000.0000.0000.000
186A186PHE0-0.0090.00524.3350.0110.0110.0000.0000.0000.000
187A187LEU00.0650.01323.3830.0070.0070.0000.0000.0000.000
188A188MET0-0.0050.00726.9220.0080.0080.0000.0000.0000.000
189A189LYS10.9260.97229.7350.0770.0770.0000.0000.0000.000
190A190VAL00.0050.00523.4860.0100.0100.0000.0000.0000.000
191A191ASN00.011-0.00424.5380.0080.0080.0000.0000.0000.000
192A192ALA0-0.029-0.01226.3470.0100.0100.0000.0000.0000.000
193A193GLN0-0.042-0.01027.3480.0100.0100.0000.0000.0000.000
194A194TYR0-0.006-0.01922.6820.0070.0070.0000.0000.0000.000
195A195LYS10.8980.95823.5680.0190.0190.0000.0000.0000.000
196A196PHE00.0250.02019.2400.0020.0020.0000.0000.0000.000
197A197PHE00.005-0.01018.969-0.010-0.0100.0000.0000.0000.000
198A198LYS10.9080.98123.0740.0560.0560.0000.0000.0000.000
199A199ARG10.8360.90725.7620.0950.0950.0000.0000.0000.000
200A200ILE00.0050.00025.218-0.014-0.0140.0000.0000.0000.000
201A201VAL00.0220.01926.8050.0120.0120.0000.0000.0000.000
202A202ALA00.0070.01227.520-0.017-0.0170.0000.0000.0000.000
203A203LEU0-0.002-0.00327.1720.0090.0090.0000.0000.0000.000
204A204GLU-1-0.806-0.89130.085-0.132-0.1320.0000.0000.0000.000
205A205HIS00.0510.04426.318-0.001-0.0010.0000.0000.0000.000
206A206PRO00.0990.04826.6570.0130.0130.0000.0000.0000.000
207A207ARG10.9310.97429.9970.1840.1840.0000.0000.0000.000
208A208PHE0-0.011-0.00831.7100.0090.0090.0000.0000.0000.000
209A209ILE00.0260.01931.5070.0090.0090.0000.0000.0000.000
210A210MET0-0.018-0.01232.4620.0080.0080.0000.0000.0000.000
211A211GLN0-0.076-0.01235.2100.0030.0030.0000.0000.0000.000
212A212TYR00.0040.00137.5600.0070.0070.0000.0000.0000.000
213A213LYS10.8910.95337.5830.1110.1110.0000.0000.0000.000
214A214THR00.0350.00937.9230.0010.0010.0000.0000.0000.000
215A215ALA00.0160.00339.212-0.003-0.0030.0000.0000.0000.000
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