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: 49Y4N

Calculation Name: 1BLN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1BLN

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2165658.025009
FMO2-HF: Nuclear repulsion 2082936.316923
FMO2-HF: Total energy -82721.708086
FMO2-MP2: Total energy -82962.694855


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:ASP)


Summations of interaction energy for fragment #1(A:1:ASP)
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.
-52.365-47.2172.482-3.187-4.4420.031
Interaction energy analysis for fragmet #1(A:1:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.919 / q_NPA : -0.966
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].
3A3LEU00.0180.0133.820-0.5940.721-0.004-0.546-0.7640.003
4A4MET0-0.017-0.0075.910-2.338-2.3380.0000.0000.0000.000
5A5THR0-0.006-0.0109.243-0.829-0.8290.0000.0000.0000.000
6A6GLN00.009-0.01912.0870.2220.2220.0000.0000.0000.000
7A7THR0-0.0640.00915.474-0.044-0.0440.0000.0000.0000.000
8A8PRO00.0440.01818.752-0.049-0.0490.0000.0000.0000.000
9A9VAL00.0860.03017.7000.1860.1860.0000.0000.0000.000
10A10SER0-0.0020.02120.1130.0830.0830.0000.0000.0000.000
11A11LEU00.015-0.00323.753-0.001-0.0010.0000.0000.0000.000
12A12SER00.0670.04626.300-0.189-0.1890.0000.0000.0000.000
13A13VAL0-0.042-0.02229.563-0.125-0.1250.0000.0000.0000.000
14A14SER00.0340.02631.740-0.161-0.1610.0000.0000.0000.000
15A15LEU00.012-0.00534.5950.1810.1810.0000.0000.0000.000
16A16GLY0-0.030-0.01535.962-0.169-0.1690.0000.0000.0000.000
17A17ASP-1-0.870-0.91734.0618.6488.6480.0000.0000.0000.000
18A18GLN0-0.050-0.04130.6080.1460.1460.0000.0000.0000.000
19A19ALA00.0110.00027.3020.0490.0490.0000.0000.0000.000
20A20SER0-0.064-0.04324.897-0.026-0.0260.0000.0000.0000.000
21A21ILE0-0.0170.01019.1180.0330.0330.0000.0000.0000.000
22A22SER00.0080.02119.1770.2420.2420.0000.0000.0000.000
23A23CYS0-0.044-0.02513.4560.6200.6200.0000.0000.0000.000
24A24ARG10.8470.93013.417-16.724-16.7240.0000.0000.0000.000
25A25SER00.018-0.0049.3010.5010.5010.0000.0000.0000.000
26A26SER00.0140.0076.161-1.000-1.0000.0000.0000.0000.000
27A27GLN00.0120.0005.2133.7973.7970.0000.0000.0000.000
28A27SER00.0140.0149.484-0.474-0.4740.0000.0000.0000.000
29A27ILE00.0200.0089.2661.0451.0450.0000.0000.0000.000
30A27VAL0-0.015-0.01512.165-0.215-0.2150.0000.0000.0000.000
31A27HIS0-0.025-0.01713.4131.2151.2150.0000.0000.0000.000
32A27SER0-0.005-0.00216.967-0.553-0.5530.0000.0000.0000.000
33A28THR00.009-0.00918.833-0.330-0.3300.0000.0000.0000.000
34A29GLY00.0370.01620.109-0.733-0.7330.0000.0000.0000.000
35A30ASN0-0.060-0.02417.6870.0060.0060.0000.0000.0000.000
36A31THR00.0750.06914.5271.1181.1180.0000.0000.0000.000
37A32TYR0-0.006-0.02013.138-1.263-1.2630.0000.0000.0000.000
38A33LEU00.0190.01512.2531.5431.5430.0000.0000.0000.000
39A34GLU-1-0.902-0.94014.26115.84815.8480.0000.0000.0000.000
40A35TRP00.0060.00515.5400.8470.8470.0000.0000.0000.000
41A36TYR0-0.026-0.04215.837-0.860-0.8600.0000.0000.0000.000
42A37LEU00.0030.00619.3960.1050.1050.0000.0000.0000.000
43A38GLN0-0.0150.00420.5850.3580.3580.0000.0000.0000.000
44A39LYS10.8130.90622.917-10.088-10.0880.0000.0000.0000.000
45A40PRO00.027-0.01126.4150.2180.2180.0000.0000.0000.000
46A41GLY00.0060.01227.007-0.299-0.2990.0000.0000.0000.000
47A42GLN0-0.0160.00126.468-0.127-0.1270.0000.0000.0000.000
48A43SER00.0310.00723.4050.4200.4200.0000.0000.0000.000
49A44PRO00.0000.00019.021-0.420-0.4200.0000.0000.0000.000
50A45LYS10.8720.95021.805-11.348-11.3480.0000.0000.0000.000
51A46LEU00.0320.02019.1460.2400.2400.0000.0000.0000.000
52A47LEU0-0.032-0.02021.378-0.768-0.7680.0000.0000.0000.000
53A48ILE00.0140.00020.543-0.475-0.4750.0000.0000.0000.000
54A49TYR00.0410.01018.8950.8270.8270.0000.0000.0000.000
55A50LYS10.9200.95718.020-14.159-14.1590.0000.0000.0000.000
56A51ILE00.0090.01517.076-0.522-0.5220.0000.0000.0000.000
57A52SER0-0.012-0.01418.909-0.321-0.3210.0000.0000.0000.000
58A53ASN0-0.067-0.01922.298-0.327-0.3270.0000.0000.0000.000
59A54ARG10.8640.92523.481-9.525-9.5250.0000.0000.0000.000
60A55PHE0-0.011-0.00323.938-0.227-0.2270.0000.0000.0000.000
61A56SER00.0660.01926.015-0.275-0.2750.0000.0000.0000.000
62A57GLY0-0.011-0.00628.8030.2400.2400.0000.0000.0000.000
63A58VAL0-0.079-0.02525.929-0.169-0.1690.0000.0000.0000.000
64A59PRO00.0520.02529.210-0.113-0.1130.0000.0000.0000.000
65A60ASP-1-0.798-0.90530.4989.4259.4250.0000.0000.0000.000
66A61ARG10.6960.83230.656-9.184-9.1840.0000.0000.0000.000
67A62PHE00.0320.01825.8330.1950.1950.0000.0000.0000.000
68A63SER0-0.015-0.00726.513-0.112-0.1120.0000.0000.0000.000
69A64GLY00.0470.02622.2480.1880.1880.0000.0000.0000.000
70A65SER0-0.014-0.00922.854-0.336-0.3360.0000.0000.0000.000
71A66GLY0-0.069-0.04019.0080.1680.1680.0000.0000.0000.000
72A67SER00.0360.00919.330-0.480-0.4800.0000.0000.0000.000
73A68GLY00.0090.02519.300-0.003-0.0030.0000.0000.0000.000
74A69THR0-0.015-0.01913.2890.4150.4150.0000.0000.0000.000
75A70ASP-1-0.848-0.91514.84717.03917.0390.0000.0000.0000.000
76A71PHE00.0020.00613.862-1.017-1.0170.0000.0000.0000.000
77A72THR00.041-0.00817.5520.1560.1560.0000.0000.0000.000
78A73LEU0-0.047-0.00220.589-0.366-0.3660.0000.0000.0000.000
79A74LYS10.9210.95622.308-10.073-10.0730.0000.0000.0000.000
80A75ILE00.0070.01325.688-0.156-0.1560.0000.0000.0000.000
81A76SER0-0.002-0.01428.581-0.175-0.1750.0000.0000.0000.000
82A77ARG10.9420.97232.042-8.525-8.5250.0000.0000.0000.000
83A78VAL00.0290.02130.2190.0410.0410.0000.0000.0000.000
84A79GLU-1-0.805-0.89932.5578.2788.2780.0000.0000.0000.000
85A80ALA00.0480.01832.7320.2670.2670.0000.0000.0000.000
86A81GLU-1-0.829-0.90332.8229.4989.4980.0000.0000.0000.000
87A82ASP-1-0.786-0.85728.93710.09910.0990.0000.0000.0000.000
88A83LEU0-0.0320.00427.8550.4700.4700.0000.0000.0000.000
89A84GLY00.0530.00025.465-0.077-0.0770.0000.0000.0000.000
90A85VAL0-0.0300.00019.075-0.081-0.0810.0000.0000.0000.000
91A86TYR0-0.003-0.01419.9500.1630.1630.0000.0000.0000.000
92A87TYR00.0120.00614.6540.2990.2990.0000.0000.0000.000
93A89PHE00.022-0.00310.3391.2681.2680.0000.0000.0000.000
94A90GLN00.0390.0115.498-3.270-3.2700.0000.0000.0000.000
95A91ALA00.017-0.0019.0991.4421.4420.0000.0000.0000.000
96A92SER0-0.051-0.02010.0650.2360.2360.0000.0000.0000.000
97A93HIS0-0.0050.0025.544-0.027-0.0270.0000.0000.0000.000
98A94ALA00.007-0.0036.6300.4390.4390.0000.0000.0000.000
99A95PRO00.0220.0232.555-12.568-9.1312.470-2.526-3.3810.028
100A96ARG10.8660.9394.135-30.964-30.8360.000-0.051-0.0770.000
101A97THR00.0050.0113.519-0.821-0.5530.016-0.064-0.2200.000
102A98PHE00.001-0.0166.580-3.056-3.0560.0000.0000.0000.000
103A99GLY00.0110.0209.0181.4891.4890.0000.0000.0000.000
104A100GLY0-0.026-0.02011.464-0.297-0.2970.0000.0000.0000.000
105A101GLY00.0260.01113.416-0.452-0.4520.0000.0000.0000.000
106A102THR0-0.057-0.04116.7500.0990.0990.0000.0000.0000.000
107A103LYS10.8180.90620.114-11.189-11.1890.0000.0000.0000.000
108A104LEU0-0.037-0.01823.234-0.187-0.1870.0000.0000.0000.000
109A105GLU-1-0.952-0.99126.24810.38610.3860.0000.0000.0000.000
110A106ILE00.0070.00329.553-0.035-0.0350.0000.0000.0000.000
111A107LYS10.8800.93532.369-9.336-9.3360.0000.0000.0000.000
112A108ARG10.8140.89735.298-7.770-7.7700.0000.0000.0000.000
113A109ALA00.0160.01238.8720.0300.0300.0000.0000.0000.000
114A110ASP-1-0.888-0.94541.1077.5207.5200.0000.0000.0000.000
115A111ALA0-0.054-0.02541.859-0.177-0.1770.0000.0000.0000.000
116A112ALA00.0210.01242.5100.1440.1440.0000.0000.0000.000
117A113PRO0-0.0040.01342.225-0.011-0.0110.0000.0000.0000.000
118A114THR00.003-0.00444.072-0.226-0.2260.0000.0000.0000.000
119A115VAL0-0.023-0.02645.1320.0810.0810.0000.0000.0000.000
120A116SER0-0.020-0.00246.366-0.240-0.2400.0000.0000.0000.000
121A117ILE0-0.0240.00346.7390.1730.1730.0000.0000.0000.000
122A118PHE0-0.013-0.01046.413-0.124-0.1240.0000.0000.0000.000
123A119PRO00.0200.01648.7780.1180.1180.0000.0000.0000.000
124A120PRO0-0.007-0.00349.0830.0630.0630.0000.0000.0000.000
125A121SER0-0.025-0.02449.698-0.091-0.0910.0000.0000.0000.000
126A122SER00.0620.01551.5120.0150.0150.0000.0000.0000.000
127A123GLU-1-0.828-0.90950.6506.1766.1760.0000.0000.0000.000
128A124GLN00.001-0.00146.3640.0770.0770.0000.0000.0000.000
129A125LEU00.0330.02349.7610.0370.0370.0000.0000.0000.000
130A126THR0-0.054-0.03152.508-0.084-0.0840.0000.0000.0000.000
131A127SER0-0.078-0.03348.983-0.017-0.0170.0000.0000.0000.000
132A128GLY0-0.0120.00449.7560.0900.0900.0000.0000.0000.000
133A129GLY0-0.042-0.02047.5390.0920.0920.0000.0000.0000.000
134A130ALA00.012-0.00347.576-0.124-0.1240.0000.0000.0000.000
135A131SER0-0.024-0.01743.3000.0770.0770.0000.0000.0000.000
136A132VAL0-0.0240.00045.745-0.102-0.1020.0000.0000.0000.000
137A133VAL00.0060.00942.2110.1780.1780.0000.0000.0000.000
138A134CYS0-0.078-0.03443.323-0.039-0.0390.0000.0000.0000.000
139A135PHE0-0.017-0.00841.5830.2290.2290.0000.0000.0000.000
140A136LEU00.022-0.00440.591-0.207-0.2070.0000.0000.0000.000
141A137ASN00.032-0.00240.3370.3580.3580.0000.0000.0000.000
142A138ASN0-0.023-0.03340.215-0.279-0.2790.0000.0000.0000.000
143A139PHE0-0.0060.02336.689-0.157-0.1570.0000.0000.0000.000
144A140TYR00.0190.00433.8760.2390.2390.0000.0000.0000.000
145A141PRO00.0790.04035.360-0.187-0.1870.0000.0000.0000.000
146A142LYS10.9190.94929.495-9.950-9.9500.0000.0000.0000.000
147A143ASP-1-0.934-0.96433.1109.1349.1340.0000.0000.0000.000
148A144ILE00.0060.01735.545-0.264-0.2640.0000.0000.0000.000
149A145ASN0-0.051-0.03737.7500.0510.0510.0000.0000.0000.000
150A146VAL00.0700.02339.470-0.152-0.1520.0000.0000.0000.000
151A147LYS10.7980.90341.474-7.264-7.2640.0000.0000.0000.000
152A148TRP00.0440.01342.463-0.196-0.1960.0000.0000.0000.000
153A149LYS10.7900.86146.306-6.201-6.2010.0000.0000.0000.000
154A150ILE00.0270.01348.582-0.052-0.0520.0000.0000.0000.000
155A151ASP-1-0.749-0.86751.8555.5495.5490.0000.0000.0000.000
156A152GLY0-0.019-0.00255.055-0.046-0.0460.0000.0000.0000.000
157A153SER0-0.065-0.03853.204-0.051-0.0510.0000.0000.0000.000
158A154GLU-1-0.849-0.91650.2076.1756.1750.0000.0000.0000.000
159A155ARG10.9580.99544.300-6.725-6.7250.0000.0000.0000.000
160A156GLN00.0730.04544.6010.2640.2640.0000.0000.0000.000
161A157ASN0-0.034-0.04240.4390.1130.1130.0000.0000.0000.000
162A158GLY00.0250.04539.7080.2080.2080.0000.0000.0000.000
163A159VAL0-0.038-0.02738.382-0.087-0.0870.0000.0000.0000.000
164A160LEU00.0160.02133.5390.2320.2320.0000.0000.0000.000
165A161ASN00.0030.01034.801-0.353-0.3530.0000.0000.0000.000
166A162SER00.0070.00632.7810.3510.3510.0000.0000.0000.000
167A163TRP00.0280.00931.506-0.204-0.2040.0000.0000.0000.000
168A164THR00.0190.02531.3480.2290.2290.0000.0000.0000.000
169A165ASP-1-0.832-0.92327.86610.74610.7460.0000.0000.0000.000
170A166GLN0-0.062-0.04830.5530.0140.0140.0000.0000.0000.000
171A167ASP-1-0.788-0.86932.2968.3518.3510.0000.0000.0000.000
172A168SER0-0.039-0.02833.131-0.160-0.1600.0000.0000.0000.000
173A169LYS10.8560.92534.931-7.915-7.9150.0000.0000.0000.000
174A170ASP-1-0.813-0.89138.7357.6447.6440.0000.0000.0000.000
175A171SER00.0020.00035.644-0.043-0.0430.0000.0000.0000.000
176A172THR0-0.096-0.04836.1690.1040.1040.0000.0000.0000.000
177A173TYR0-0.011-0.01131.0490.3860.3860.0000.0000.0000.000
178A174SER00.0420.02135.751-0.373-0.3730.0000.0000.0000.000
179A175MET0-0.0180.00335.7500.2860.2860.0000.0000.0000.000
180A176SER0-0.0290.00037.136-0.253-0.2530.0000.0000.0000.000
181A177SER0-0.026-0.02337.7930.1490.1490.0000.0000.0000.000
182A178THR00.021-0.00439.421-0.261-0.2610.0000.0000.0000.000
183A179LEU0-0.0030.01440.5460.1730.1730.0000.0000.0000.000
184A180THR00.0360.01241.091-0.161-0.1610.0000.0000.0000.000
185A181LEU0-0.046-0.00443.5710.0700.0700.0000.0000.0000.000
186A182THR00.038-0.01446.501-0.033-0.0330.0000.0000.0000.000
187A183LYS10.8760.94348.975-5.835-5.8350.0000.0000.0000.000
188A184ASP-1-0.810-0.90052.1525.7385.7380.0000.0000.0000.000
189A185GLU-1-0.843-0.89349.7536.1216.1210.0000.0000.0000.000
190A186TYR0-0.050-0.02451.012-0.014-0.0140.0000.0000.0000.000
191A187GLU-1-0.838-0.94552.8095.6365.6360.0000.0000.0000.000
192A188ARG10.7450.87853.534-5.953-5.9530.0000.0000.0000.000
193A189HIS10.7380.85152.986-5.874-5.8740.0000.0000.0000.000
194A190ASN00.0420.01056.638-0.066-0.0660.0000.0000.0000.000
195A191SER0-0.032-0.02056.007-0.009-0.0090.0000.0000.0000.000
196A192TYR00.0150.01550.1450.1580.1580.0000.0000.0000.000
197A193THR0-0.034-0.03050.594-0.073-0.0730.0000.0000.0000.000
198A195GLU-1-0.828-0.90846.6886.2086.2080.0000.0000.0000.000
199A196ALA00.0410.02343.6870.1780.1780.0000.0000.0000.000
200A197THR00.0000.00341.914-0.107-0.1070.0000.0000.0000.000
201A203SER0-0.025-0.02449.097-0.050-0.0500.0000.0000.0000.000
202A204PRO00.0140.01347.8170.0850.0850.0000.0000.0000.000
203A205ILE0-0.0030.00646.187-0.134-0.1340.0000.0000.0000.000
204A206VAL00.0060.00548.3320.1170.1170.0000.0000.0000.000
205A207LYS10.8820.93149.463-6.259-6.2590.0000.0000.0000.000
206A208SER00.0150.00150.9120.0850.0850.0000.0000.0000.000
207A209PHE00.0160.02350.596-0.056-0.0560.0000.0000.0000.000
208A210ASN0-0.022-0.02255.3780.0410.0410.0000.0000.0000.000
209A211ARG10.8950.94557.955-5.104-5.1040.0000.0000.0000.000
210A212ASN0-0.0080.01255.985-0.003-0.0030.0000.0000.0000.000
211A213GLU-1-0.825-0.90856.3835.2875.2870.0000.0000.0000.000