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: LJV89

Calculation Name: 4BSZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4BSZ

Chain ID: A

ChEMBL ID:

UniProt ID: P05750

Base Structure: X-ray

Registration Date: 2023-03-14

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 187
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1576081.90964
FMO2-HF: Nuclear repulsion 1503810.241271
FMO2-HF: Total energy -72271.668369
FMO2-MP2: Total energy -72482.476973


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:12:VAL)


Summations of interaction energy for fragment #1(A:12:VAL)
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.
-6.872-0.7422.24-3.209-5.161-0.014
Interaction energy analysis for fragmet #1(A:12:VAL)
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 : -0.002
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].
3A14ASP-1-0.773-0.8902.576-5.804-2.6470.890-1.887-2.160-0.012
4A15GLY00.002-0.0035.2650.4090.473-0.001-0.002-0.0610.000
5A16VAL0-0.012-0.0087.8220.2520.2520.0000.0000.0000.000
6A17PHE00.0370.0126.7950.2150.2150.0000.0000.0000.000
7A18TYR00.002-0.0053.3820.0150.3520.013-0.058-0.2920.000
8A19ALA0-0.023-0.0038.3910.2100.2100.0000.0000.0000.000
9A20GLU-1-0.779-0.87511.895-0.588-0.5880.0000.0000.0000.000
10A21LEU0-0.036-0.0178.9210.1300.1300.0000.0000.0000.000
11A22ASN00.0090.02812.4330.1300.1300.0000.0000.0000.000
12A23GLU-1-0.952-0.96314.134-0.335-0.3350.0000.0000.0000.000
13A24PHE0-0.034-0.02515.9400.0450.0450.0000.0000.0000.000
14A25PHE00.043-0.00212.7720.0390.0390.0000.0000.0000.000
15A26THR0-0.023-0.02317.6080.0380.0380.0000.0000.0000.000
16A27ARG10.8600.93319.7940.1870.1870.0000.0000.0000.000
17A28GLU-1-0.914-0.93820.589-0.106-0.1060.0000.0000.0000.000
18A29LEU0-0.053-0.02618.3030.0190.0190.0000.0000.0000.000
19A30ALA00.0300.02322.2700.0080.0080.0000.0000.0000.000
20A31GLU-1-0.856-0.94024.704-0.055-0.0550.0000.0000.0000.000
21A32GLU-1-0.851-0.91822.988-0.036-0.0360.0000.0000.0000.000
22A33GLY0-0.0110.00823.5970.0120.0120.0000.0000.0000.000
23A34TYR0-0.003-0.02714.7240.0190.0190.0000.0000.0000.000
24A35SER0-0.033-0.02717.8690.0010.0010.0000.0000.0000.000
25A36GLY0-0.020-0.01014.199-0.013-0.0130.0000.0000.0000.000
26A37VAL0-0.0120.0019.6160.0240.0240.0000.0000.0000.000
27A38GLU-1-0.833-0.8886.5080.6200.6200.0000.0000.0000.000
28A39VAL0-0.012-0.0034.948-0.039-0.0390.0000.0000.0000.000
29A40ARG10.8160.8943.248-1.830-0.8650.052-0.371-0.646-0.002
30A41VAL00.0150.0032.365-2.733-1.3431.287-0.884-1.7930.000
31A42THR0-0.008-0.0014.3341.3701.587-0.001-0.007-0.2090.000
32A43PRO00.038-0.0087.072-0.470-0.4700.0000.0000.0000.000
33A44THR0-0.032-0.0169.370-0.111-0.1110.0000.0000.0000.000
34A45LYS10.8830.9539.004-0.393-0.3930.0000.0000.0000.000
35A46THR0-0.0030.0115.9460.2430.2430.0000.0000.0000.000
36A47GLU-1-0.851-0.9087.2620.8830.8830.0000.0000.0000.000
37A48VAL00.010-0.0147.663-0.009-0.0090.0000.0000.0000.000
38A49ILE0-0.0120.0029.763-0.012-0.0120.0000.0000.0000.000
39A50ILE00.0360.02111.680-0.049-0.0490.0000.0000.0000.000
40A51ARG10.7840.87510.098-0.205-0.2050.0000.0000.0000.000
41A52ALA00.0480.03115.763-0.036-0.0360.0000.0000.0000.000
42A53THR0-0.017-0.00519.4720.0240.0240.0000.0000.0000.000
43A54ARG10.7330.84322.7870.0170.0170.0000.0000.0000.000
44A55THR00.0680.02220.051-0.009-0.0090.0000.0000.0000.000
45A56GLN00.0250.01222.7510.0010.0010.0000.0000.0000.000
46A57ASP-1-0.800-0.88725.4060.0090.0090.0000.0000.0000.000
47A58VAL00.0270.00919.062-0.005-0.0050.0000.0000.0000.000
48A59LEU0-0.015-0.00520.885-0.001-0.0010.0000.0000.0000.000
49A60GLY00.0320.01023.269-0.008-0.0080.0000.0000.0000.000
50A61GLU-1-0.896-0.96026.7700.0420.0420.0000.0000.0000.000
51A62ASN0-0.063-0.03328.3930.0030.0030.0000.0000.0000.000
52A63GLY00.0330.03424.2530.0050.0050.0000.0000.0000.000
53A64ARG10.7980.87123.9110.0160.0160.0000.0000.0000.000
54A65ARG10.7310.85622.8310.0490.0490.0000.0000.0000.000
55A66ILE00.0740.03517.941-0.016-0.0160.0000.0000.0000.000
56A67ASN00.0100.01019.839-0.008-0.0080.0000.0000.0000.000
57A68GLU-1-0.811-0.86321.633-0.062-0.0620.0000.0000.0000.000
58A69LEU00.0170.00718.603-0.023-0.0230.0000.0000.0000.000
59A70THR0-0.009-0.01716.247-0.027-0.0270.0000.0000.0000.000
60A71LEU0-0.012-0.01017.670-0.033-0.0330.0000.0000.0000.000
61A72LEU0-0.0070.00420.314-0.027-0.0270.0000.0000.0000.000
62A73VAL00.0250.01413.625-0.036-0.0360.0000.0000.0000.000
63A74GLN00.015-0.00216.107-0.027-0.0270.0000.0000.0000.000
64A75LYS10.9020.95417.1920.1350.1350.0000.0000.0000.000
65A76ARG10.7650.86816.2480.4470.4470.0000.0000.0000.000
66A77PHE00.008-0.00613.264-0.027-0.0270.0000.0000.0000.000
67A78LYS10.9120.96214.2680.2590.2590.0000.0000.0000.000
68A79TYR00.0450.0387.4270.0080.0080.0000.0000.0000.000
69A80ALA00.0230.01514.1970.0530.0530.0000.0000.0000.000
70A81PRO00.003-0.00915.6910.0140.0140.0000.0000.0000.000
71A82GLY00.0470.04616.4970.0170.0170.0000.0000.0000.000
72A83THR0-0.066-0.05011.5900.0340.0340.0000.0000.0000.000
73A84ILE0-0.019-0.00710.0290.0250.0250.0000.0000.0000.000
74A85VAL0-0.017-0.00411.6290.0060.0060.0000.0000.0000.000
75A86LEU00.0010.01012.1460.0170.0170.0000.0000.0000.000
76A87TYR0-0.013-0.01112.287-0.016-0.0160.0000.0000.0000.000
77A88ALA00.013-0.00315.164-0.042-0.0420.0000.0000.0000.000
78A89GLU-1-0.849-0.91713.0570.3790.3790.0000.0000.0000.000
79A90ARG10.8830.94416.829-0.107-0.1070.0000.0000.0000.000
80A91VAL0-0.018-0.00716.2960.0190.0190.0000.0000.0000.000
81A92GLN0-0.020-0.00819.740-0.022-0.0220.0000.0000.0000.000
82A93ASP-1-0.738-0.86520.421-0.028-0.0280.0000.0000.0000.000
83A94ARG10.9520.96317.7630.0210.0210.0000.0000.0000.000
84A95GLY00.0290.01921.2590.0000.0000.0000.0000.0000.000
85A96LEU0-0.003-0.01224.4170.0040.0040.0000.0000.0000.000
86A97SER0-0.039-0.02123.5770.0060.0060.0000.0000.0000.000
87A98ALA00.0400.00725.563-0.003-0.0030.0000.0000.0000.000
88A99VAL0-0.0020.00024.589-0.002-0.0020.0000.0000.0000.000
89A100ALA00.0150.00821.4070.0020.0020.0000.0000.0000.000
90A101GLN00.024-0.01222.641-0.012-0.0120.0000.0000.0000.000
91A102ALA00.0070.01625.458-0.005-0.0050.0000.0000.0000.000
92A103GLU-1-0.789-0.87121.3920.0440.0440.0000.0000.0000.000
93A104SER0-0.029-0.00322.544-0.011-0.0110.0000.0000.0000.000
94A105MET0-0.039-0.01923.485-0.011-0.0110.0000.0000.0000.000
95A106LYS10.8490.89824.077-0.054-0.0540.0000.0000.0000.000
96A107PHE00.0430.01719.511-0.002-0.0020.0000.0000.0000.000
97A108LYS10.8760.94822.9540.0410.0410.0000.0000.0000.000
98A109LEU0-0.025-0.01625.853-0.004-0.0040.0000.0000.0000.000
99A110LEU0-0.027-0.01325.4930.0000.0000.0000.0000.0000.000
100A111ASN0-0.045-0.01822.395-0.005-0.0050.0000.0000.0000.000
101A112GLY00.0090.01826.104-0.008-0.0080.0000.0000.0000.000
102A113LEU0-0.041-0.01426.756-0.004-0.0040.0000.0000.0000.000
103A114ALA00.007-0.00629.5730.0060.0060.0000.0000.0000.000
104A115ILE00.0730.02132.615-0.004-0.0040.0000.0000.0000.000
105A116ARG10.9450.98233.0960.0330.0330.0000.0000.0000.000
106A117ARG10.9550.98330.9510.0590.0590.0000.0000.0000.000
107A118ALA00.0290.01528.722-0.005-0.0050.0000.0000.0000.000
108A119ALA00.0080.00629.170-0.001-0.0010.0000.0000.0000.000
109A120TYR00.012-0.00131.4140.0000.0000.0000.0000.0000.000
110A121GLY00.0160.01827.818-0.004-0.0040.0000.0000.0000.000
111A122VAL0-0.020-0.01226.081-0.004-0.0040.0000.0000.0000.000
112A123VAL00.030-0.00427.9130.0000.0000.0000.0000.0000.000
113A124ARG10.7820.85627.3790.1000.1000.0000.0000.0000.000
114A125TYR00.0250.02221.2500.0040.0040.0000.0000.0000.000
115A126VAL00.0060.00326.4440.0000.0000.0000.0000.0000.000
116A127MET0-0.032-0.01428.3000.0040.0040.0000.0000.0000.000
117A128GLU-1-0.829-0.86726.227-0.101-0.1010.0000.0000.0000.000
118A129SER0-0.034-0.02824.865-0.007-0.0070.0000.0000.0000.000
119A130GLY00.0160.01826.5810.0050.0050.0000.0000.0000.000
120A131ALA0-0.030-0.00530.0480.0060.0060.0000.0000.0000.000
121A132LYS10.9240.95931.6640.0150.0150.0000.0000.0000.000
122A133GLY0-0.005-0.01834.5290.0000.0000.0000.0000.0000.000
123A134CYS0-0.0460.00131.4520.0010.0010.0000.0000.0000.000
124A135GLU-1-0.854-0.91034.004-0.008-0.0080.0000.0000.0000.000
125A136VAL0-0.0070.00031.2320.0030.0030.0000.0000.0000.000
126A137VAL00.010-0.00434.180-0.002-0.0020.0000.0000.0000.000
127A138VAL0-0.0010.01333.3770.0030.0030.0000.0000.0000.000
128A139SER00.0100.00036.120-0.001-0.0010.0000.0000.0000.000
129A140GLY00.0520.02838.0360.0020.0020.0000.0000.0000.000
130A141LYS10.8790.92740.489-0.010-0.0100.0000.0000.0000.000
131A142LEU0-0.020-0.00238.019-0.001-0.0010.0000.0000.0000.000
132A143ARG10.8050.87141.0540.0110.0110.0000.0000.0000.000
133A144ALA00.0300.02244.2670.0020.0020.0000.0000.0000.000
134A145ALA00.018-0.00347.077-0.001-0.0010.0000.0000.0000.000
135A146ARG10.9800.99150.0280.0050.0050.0000.0000.0000.000
136A147ALA00.0510.03852.6720.0010.0010.0000.0000.0000.000
137A148LYS11.0261.00249.422-0.007-0.0070.0000.0000.0000.000
138A149ALA00.0310.02048.1110.0010.0010.0000.0000.0000.000
139A150MET0-0.0040.01948.2100.0020.0020.0000.0000.0000.000
140A151LYS10.8450.90443.421-0.011-0.0110.0000.0000.0000.000
141A152PHE00.0220.00443.039-0.001-0.0010.0000.0000.0000.000
142A153ALA00.030-0.00540.8650.0020.0020.0000.0000.0000.000
143A154ASP-1-0.804-0.84438.633-0.016-0.0160.0000.0000.0000.000
144A155GLY00.0240.00638.0930.0010.0010.0000.0000.0000.000
145A156PHE0-0.034-0.03535.718-0.003-0.0030.0000.0000.0000.000
146A157LEU00.0330.02236.4490.0010.0010.0000.0000.0000.000
147A158ILE00.004-0.00234.975-0.003-0.0030.0000.0000.0000.000
148A159HIS0-0.007-0.01037.7060.0040.0040.0000.0000.0000.000
149A160SER0-0.009-0.01739.1810.0020.0020.0000.0000.0000.000
150A161GLY00.0030.00741.064-0.001-0.0010.0000.0000.0000.000
151A162GLN0-0.001-0.00944.6600.0000.0000.0000.0000.0000.000
152A163PRO00.0680.03348.1050.0010.0010.0000.0000.0000.000
153A164VAL00.0270.01751.3060.0000.0000.0000.0000.0000.000
154A165ASN0-0.041-0.04847.3950.0010.0010.0000.0000.0000.000
155A166ASP-1-0.861-0.91950.807-0.005-0.0050.0000.0000.0000.000
156A167PHE0-0.054-0.04152.8290.0000.0000.0000.0000.0000.000
157A168ILE0-0.080-0.02250.6890.0010.0010.0000.0000.0000.000
158A169ASP-1-0.769-0.83054.2250.0020.0020.0000.0000.0000.000
159A170THR0-0.094-0.07052.2090.0020.0020.0000.0000.0000.000
160A171ALA00.0280.02155.5780.0000.0000.0000.0000.0000.000
161A172THR00.003-0.01453.6060.0010.0010.0000.0000.0000.000
162A173ARG10.8970.94756.934-0.012-0.0120.0000.0000.0000.000
163A174HIS00.0520.02555.5620.0000.0000.0000.0000.0000.000
164A175VAL00.0030.00459.164-0.001-0.0010.0000.0000.0000.000
165A176LEU00.0290.02361.1510.0010.0010.0000.0000.0000.000
166A177MET00.0240.00962.182-0.001-0.0010.0000.0000.0000.000
167A178ARG10.9700.96963.416-0.019-0.0190.0000.0000.0000.000
168A179GLN00.0100.01059.1320.0000.0000.0000.0000.0000.000
169A180GLY00.0500.03658.8750.0020.0020.0000.0000.0000.000
170A181VAL0-0.048-0.02857.593-0.001-0.0010.0000.0000.0000.000
171A182LEU00.0010.01256.9310.0010.0010.0000.0000.0000.000
172A183GLY00.0230.01854.916-0.001-0.0010.0000.0000.0000.000
173A184ILE0-0.002-0.00455.9630.0000.0000.0000.0000.0000.000
174A185LYS10.8990.94651.066-0.014-0.0140.0000.0000.0000.000
175A186VAL00.0260.02155.1970.0000.0000.0000.0000.0000.000
176A187LYS10.9640.96148.676-0.012-0.0120.0000.0000.0000.000
177A188ILE00.0290.01255.7100.0000.0000.0000.0000.0000.000
178A189MET0-0.0200.01152.185-0.001-0.0010.0000.0000.0000.000
179A190ARG10.8480.90456.8750.0000.0000.0000.0000.0000.000
180A191ASP-1-0.770-0.89058.493-0.003-0.0030.0000.0000.0000.000
181A192PRO00.0460.02257.1300.0000.0000.0000.0000.0000.000
182A193ALA0-0.044-0.02060.331-0.001-0.0010.0000.0000.0000.000
183A194LYS10.8740.92862.7470.0010.0010.0000.0000.0000.000
184A195SER0-0.002-0.01362.5730.0000.0000.0000.0000.0000.000
185A196ARG10.8930.96362.0070.0070.0070.0000.0000.0000.000
186A197THR00.0310.01264.6680.0010.0010.0000.0000.0000.000
187A198GLY0-0.0300.00267.369-0.001-0.0010.0000.0000.0000.000