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: K9V63

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 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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2165481.03122
FMO2-HF: Nuclear repulsion 2082760.164038
FMO2-HF: Total energy -82720.867182
FMO2-MP2: Total energy -82961.928972


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.
-46.111-42.7982.213-2.161-3.3650.011
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 : -0.935 / q_NPA : -0.971
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].
3A3LEU00.0190.0023.820-0.5960.883-0.004-0.649-0.8250.003
4A4MET0-0.030-0.0045.801-2.807-2.8070.0000.0000.0000.000
5A5THR0-0.005-0.0109.005-0.710-0.7100.0000.0000.0000.000
6A6GLN00.001-0.02512.0320.1810.1810.0000.0000.0000.000
7A7THR0-0.0610.01915.289-0.016-0.0160.0000.0000.0000.000
8A8PRO00.0380.01118.702-0.061-0.0610.0000.0000.0000.000
9A9VAL00.0830.02017.7150.1970.1970.0000.0000.0000.000
10A10SER00.0040.02320.0080.1190.1190.0000.0000.0000.000
11A11LEU00.006-0.00723.639-0.006-0.0060.0000.0000.0000.000
12A12SER00.0500.03926.147-0.182-0.1820.0000.0000.0000.000
13A13VAL0-0.059-0.03329.816-0.131-0.1310.0000.0000.0000.000
14A14SER00.0290.02431.554-0.159-0.1590.0000.0000.0000.000
15A15LEU00.015-0.00334.3850.1830.1830.0000.0000.0000.000
16A16GLY0-0.036-0.01835.730-0.170-0.1700.0000.0000.0000.000
17A17ASP-1-0.868-0.92533.6048.5808.5800.0000.0000.0000.000
18A18GLN0-0.049-0.03330.2650.1080.1080.0000.0000.0000.000
19A19ALA0-0.003-0.01026.9280.0540.0540.0000.0000.0000.000
20A20SER0-0.040-0.02824.812-0.020-0.0200.0000.0000.0000.000
21A21ILE0-0.0300.00818.7990.0450.0450.0000.0000.0000.000
22A22SER00.0010.01518.9210.2060.2060.0000.0000.0000.000
23A23CYS0-0.051-0.02713.3190.5920.5920.0000.0000.0000.000
24A24ARG10.8760.94113.492-16.888-16.8880.0000.0000.0000.000
25A25SER00.0470.0039.3550.6940.6940.0000.0000.0000.000
26A26SER0-0.0110.0035.887-1.541-1.5410.0000.0000.0000.000
27A27GLN00.011-0.0015.0453.4953.527-0.001-0.001-0.0290.000
28A27SER00.0110.0039.468-0.418-0.4180.0000.0000.0000.000
29A27ILE00.0190.0079.2851.0481.0480.0000.0000.0000.000
30A27VAL0-0.010-0.01412.246-0.233-0.2330.0000.0000.0000.000
31A27HIS0-0.030-0.01913.4830.9220.9220.0000.0000.0000.000
32A27SER0-0.018-0.00716.963-0.505-0.5050.0000.0000.0000.000
33A28THR00.015-0.00418.638-0.333-0.3330.0000.0000.0000.000
34A29GLY00.0290.00920.091-0.691-0.6910.0000.0000.0000.000
35A30ASN0-0.062-0.02117.4960.0250.0250.0000.0000.0000.000
36A31THR00.0740.06914.5850.9790.9790.0000.0000.0000.000
37A32TYR0-0.007-0.01813.197-1.267-1.2670.0000.0000.0000.000
38A33LEU00.0300.01712.6201.5341.5340.0000.0000.0000.000
39A34GLU-1-0.912-0.96214.50615.96815.9680.0000.0000.0000.000
40A35TRP0-0.0110.00515.7260.8820.8820.0000.0000.0000.000
41A36TYR0-0.017-0.02815.622-0.944-0.9440.0000.0000.0000.000
42A37LEU00.0210.01019.3200.1340.1340.0000.0000.0000.000
43A38GLN0-0.031-0.00720.7440.2270.2270.0000.0000.0000.000
44A39LYS10.8210.92922.741-10.133-10.1330.0000.0000.0000.000
45A40PRO00.025-0.00726.2700.2360.2360.0000.0000.0000.000
46A41GLY00.0100.01426.902-0.307-0.3070.0000.0000.0000.000
47A42GLN0-0.015-0.00126.355-0.178-0.1780.0000.0000.0000.000
48A43SER00.0230.00123.2660.4230.4230.0000.0000.0000.000
49A44PRO0-0.009-0.00318.864-0.428-0.4280.0000.0000.0000.000
50A45LYS10.8770.95521.614-11.448-11.4480.0000.0000.0000.000
51A46LEU00.0240.01019.4220.2690.2690.0000.0000.0000.000
52A47LEU0-0.024-0.01121.556-0.760-0.7600.0000.0000.0000.000
53A48ILE00.0070.00220.565-0.497-0.4970.0000.0000.0000.000
54A49TYR00.016-0.00119.1040.7810.7810.0000.0000.0000.000
55A50LYS10.9350.96218.201-13.978-13.9780.0000.0000.0000.000
56A51ILE00.0230.02517.205-0.487-0.4870.0000.0000.0000.000
57A52SER0-0.022-0.02219.114-0.312-0.3120.0000.0000.0000.000
58A53ASN0-0.053-0.00922.520-0.076-0.0760.0000.0000.0000.000
59A54ARG10.8910.98123.704-9.575-9.5750.0000.0000.0000.000
60A55PHE0-0.025-0.00824.196-0.234-0.2340.0000.0000.0000.000
61A56SER00.0710.01426.232-0.262-0.2620.0000.0000.0000.000
62A57GLY00.008-0.00129.0340.2490.2490.0000.0000.0000.000
63A58VAL0-0.069-0.02026.200-0.160-0.1600.0000.0000.0000.000
64A59PRO00.0540.02329.410-0.120-0.1200.0000.0000.0000.000
65A60ASP-1-0.833-0.96030.6669.3159.3150.0000.0000.0000.000
66A61ARG10.6840.83830.799-9.223-9.2230.0000.0000.0000.000
67A62PHE00.0480.02625.7330.1860.1860.0000.0000.0000.000
68A63SER0-0.028-0.01626.760-0.118-0.1180.0000.0000.0000.000
69A64GLY00.0700.02922.5130.1990.1990.0000.0000.0000.000
70A65SER0-0.017-0.01123.084-0.357-0.3570.0000.0000.0000.000
71A66GLY0-0.067-0.03519.2630.1500.1500.0000.0000.0000.000
72A67SER00.0400.00919.548-0.468-0.4680.0000.0000.0000.000
73A68GLY00.0120.02819.2850.0190.0190.0000.0000.0000.000
74A69THR0-0.004-0.01213.3340.2760.2760.0000.0000.0000.000
75A70ASP-1-0.862-0.92414.84717.05517.0550.0000.0000.0000.000
76A71PHE0-0.0030.00214.064-1.015-1.0150.0000.0000.0000.000
77A72THR00.044-0.00617.7420.2200.2200.0000.0000.0000.000
78A73LEU0-0.059-0.00620.623-0.387-0.3870.0000.0000.0000.000
79A74LYS10.9400.97222.313-10.008-10.0080.0000.0000.0000.000
80A75ILE00.0040.00925.424-0.164-0.1640.0000.0000.0000.000
81A76SER00.005-0.01528.469-0.188-0.1880.0000.0000.0000.000
82A77ARG10.9430.97231.973-8.531-8.5310.0000.0000.0000.000
83A78VAL00.0210.01930.1120.0470.0470.0000.0000.0000.000
84A79GLU-1-0.822-0.91932.3288.2798.2790.0000.0000.0000.000
85A80ALA00.0500.01832.5160.2730.2730.0000.0000.0000.000
86A81GLU-1-0.850-0.92932.6409.6409.6400.0000.0000.0000.000
87A82ASP-1-0.821-0.87828.70910.09110.0910.0000.0000.0000.000
88A83LEU0-0.0250.00327.6450.4610.4610.0000.0000.0000.000
89A84GLY00.048-0.00425.288-0.073-0.0730.0000.0000.0000.000
90A85VAL0-0.0250.00018.912-0.076-0.0760.0000.0000.0000.000
91A86TYR00.0120.00519.7370.1270.1270.0000.0000.0000.000
92A87TYR00.0130.01414.4090.3570.3570.0000.0000.0000.000
93A89PHE00.028-0.00210.1901.3081.3080.0000.0000.0000.000
94A90GLN00.0620.0336.085-3.150-3.1500.0000.0000.0000.000
95A91ALA00.003-0.0169.2891.5691.5690.0000.0000.0000.000
96A92SER0-0.064-0.03110.1070.2020.2020.0000.0000.0000.000
97A93HIS00.0120.0195.479-0.168-0.1680.0000.0000.0000.000
98A94ALA0-0.012-0.0166.7480.6940.6940.0000.0000.0000.000
99A95PRO00.0200.0212.311-6.929-5.5392.193-1.398-2.1860.008
100A96ARG10.8960.9564.252-29.486-29.405-0.001-0.037-0.0440.000
101A97THR00.0030.0133.302-0.583-0.2520.026-0.076-0.2810.000
102A98PHE00.003-0.0176.477-3.496-3.4960.0000.0000.0000.000
103A99GLY00.0070.0168.8411.6321.6320.0000.0000.0000.000
104A100GLY0-0.021-0.01911.270-0.273-0.2730.0000.0000.0000.000
105A101GLY00.0270.01313.312-0.473-0.4730.0000.0000.0000.000
106A102THR0-0.060-0.03116.6060.0870.0870.0000.0000.0000.000
107A103LYS10.8220.90819.955-11.388-11.3880.0000.0000.0000.000
108A104LEU0-0.037-0.01623.097-0.184-0.1840.0000.0000.0000.000
109A105GLU-1-0.932-0.97826.08110.55410.5540.0000.0000.0000.000
110A106ILE00.0090.00729.407-0.056-0.0560.0000.0000.0000.000
111A107LYS10.8980.93531.876-9.485-9.4850.0000.0000.0000.000
112A108ARG10.8550.92835.147-7.762-7.7620.0000.0000.0000.000
113A109ALA00.0100.01338.7260.0290.0290.0000.0000.0000.000
114A110ASP-1-0.883-0.94640.9157.6137.6130.0000.0000.0000.000
115A111ALA0-0.060-0.02941.747-0.183-0.1830.0000.0000.0000.000
116A112ALA00.0170.01142.4380.1470.1470.0000.0000.0000.000
117A113PRO0-0.0280.00642.131-0.017-0.0170.0000.0000.0000.000
118A114THR00.0250.00344.027-0.230-0.2300.0000.0000.0000.000
119A115VAL0-0.022-0.02944.9960.0820.0820.0000.0000.0000.000
120A116SER0-0.050-0.02546.366-0.235-0.2350.0000.0000.0000.000
121A117ILE0-0.0200.00846.7550.1750.1750.0000.0000.0000.000
122A118PHE0-0.022-0.01346.543-0.126-0.1260.0000.0000.0000.000
123A119PRO00.0120.01448.8370.1210.1210.0000.0000.0000.000
124A120PRO0-0.0010.00349.2390.0700.0700.0000.0000.0000.000
125A121SER00.0410.01949.080-0.102-0.1020.0000.0000.0000.000
126A122SER00.0700.01051.5300.0320.0320.0000.0000.0000.000
127A123GLU-1-0.891-0.93550.6676.2146.2140.0000.0000.0000.000
128A124GLN0-0.039-0.01945.8450.1570.1570.0000.0000.0000.000
129A125LEU00.0250.01649.5850.0410.0410.0000.0000.0000.000
130A126THR0-0.047-0.03752.371-0.082-0.0820.0000.0000.0000.000
131A127SER0-0.065-0.02948.618-0.020-0.0200.0000.0000.0000.000
132A128GLY0-0.0150.00449.4190.0910.0910.0000.0000.0000.000
133A129GLY0-0.024-0.01247.3750.0960.0960.0000.0000.0000.000
134A130ALA00.019-0.00747.576-0.125-0.1250.0000.0000.0000.000
135A131SER00.0170.02043.7800.1510.1510.0000.0000.0000.000
136A132VAL0-0.0220.00345.847-0.107-0.1070.0000.0000.0000.000
137A133VAL00.0130.01142.3190.1760.1760.0000.0000.0000.000
138A134CYS0-0.082-0.03443.371-0.046-0.0460.0000.0000.0000.000
139A135PHE0-0.009-0.00541.1590.2350.2350.0000.0000.0000.000
140A136LEU00.015-0.00640.566-0.210-0.2100.0000.0000.0000.000
141A137ASN00.030-0.00440.3100.3800.3800.0000.0000.0000.000
142A138ASN0-0.026-0.02940.136-0.249-0.2490.0000.0000.0000.000
143A139PHE0-0.0060.02336.862-0.167-0.1670.0000.0000.0000.000
144A140TYR0-0.003-0.00434.1700.2360.2360.0000.0000.0000.000
145A141PRO00.0870.04535.345-0.185-0.1850.0000.0000.0000.000
146A142LYS10.9230.95329.406-10.131-10.1310.0000.0000.0000.000
147A143ASP-1-0.931-0.96533.3379.2829.2820.0000.0000.0000.000
148A144ILE00.0110.02135.528-0.271-0.2710.0000.0000.0000.000
149A145ASN0-0.063-0.03937.7680.0860.0860.0000.0000.0000.000
150A146VAL00.0690.02139.673-0.163-0.1630.0000.0000.0000.000
151A147LYS10.7940.90441.682-7.281-7.2810.0000.0000.0000.000
152A148TRP00.0250.00442.435-0.217-0.2170.0000.0000.0000.000
153A149LYS10.8090.87046.296-6.270-6.2700.0000.0000.0000.000
154A150ILE00.0390.01948.618-0.052-0.0520.0000.0000.0000.000
155A151ASP-1-0.742-0.88751.8305.6005.6000.0000.0000.0000.000
156A152GLY0-0.027-0.00655.033-0.046-0.0460.0000.0000.0000.000
157A153SER0-0.068-0.03953.207-0.052-0.0520.0000.0000.0000.000
158A154GLU-1-0.884-0.94150.2366.2566.2560.0000.0000.0000.000
159A155ARG10.9590.99543.801-6.865-6.8650.0000.0000.0000.000
160A156GLN00.0650.03944.5580.2760.2760.0000.0000.0000.000
161A157ASN0-0.019-0.04040.3590.0950.0950.0000.0000.0000.000
162A158GLY00.0230.04639.6800.2130.2130.0000.0000.0000.000
163A159VAL0-0.040-0.02338.327-0.087-0.0870.0000.0000.0000.000
164A160LEU00.0320.02733.9180.2460.2460.0000.0000.0000.000
165A161ASN00.0050.00534.837-0.378-0.3780.0000.0000.0000.000
166A162SER00.0030.00032.8210.3650.3650.0000.0000.0000.000
167A163TRP00.0230.01031.445-0.196-0.1960.0000.0000.0000.000
168A164THR00.0370.02931.3340.2520.2520.0000.0000.0000.000
169A165ASP-1-0.841-0.93528.25810.84610.8460.0000.0000.0000.000
170A166GLN0-0.077-0.04530.4780.0140.0140.0000.0000.0000.000
171A167ASP-1-0.762-0.86332.1768.4398.4390.0000.0000.0000.000
172A168SER0-0.013-0.00633.138-0.157-0.1570.0000.0000.0000.000
173A169LYS10.8330.90434.772-8.009-8.0090.0000.0000.0000.000
174A170ASP-1-0.793-0.89138.5767.6977.6970.0000.0000.0000.000
175A171SER0-0.008-0.01335.495-0.047-0.0470.0000.0000.0000.000
176A172THR0-0.100-0.04536.0480.1080.1080.0000.0000.0000.000
177A173TYR00.000-0.01130.0650.2980.2980.0000.0000.0000.000
178A174SER00.0350.02435.700-0.376-0.3760.0000.0000.0000.000
179A175MET0-0.0240.00235.7220.2910.2910.0000.0000.0000.000
180A176SER0-0.037-0.00437.156-0.272-0.2720.0000.0000.0000.000
181A177SER0-0.002-0.00637.8330.1530.1530.0000.0000.0000.000
182A178THR00.016-0.00639.494-0.279-0.2790.0000.0000.0000.000
183A179LEU0-0.0120.01240.6430.1730.1730.0000.0000.0000.000
184A180THR00.018-0.00541.861-0.068-0.0680.0000.0000.0000.000
185A181LEU0-0.045-0.01243.6960.0680.0680.0000.0000.0000.000
186A182THR00.0500.00146.594-0.010-0.0100.0000.0000.0000.000
187A183LYS10.9300.96748.925-5.900-5.9000.0000.0000.0000.000
188A184ASP-1-0.850-0.92652.0855.8505.8500.0000.0000.0000.000
189A185GLU-1-0.836-0.89949.8406.1656.1650.0000.0000.0000.000
190A186TYR0-0.056-0.01751.129-0.022-0.0220.0000.0000.0000.000
191A187GLU-1-0.865-0.94952.9435.6515.6510.0000.0000.0000.000
192A188ARG10.7470.87753.278-6.037-6.0370.0000.0000.0000.000
193A189HIS10.7460.87753.620-5.938-5.9380.0000.0000.0000.000
194A190ASN00.0590.02956.683-0.034-0.0340.0000.0000.0000.000
195A191SER0-0.025-0.00256.069-0.010-0.0100.0000.0000.0000.000
196A192TYR00.0110.01250.1210.1580.1580.0000.0000.0000.000
197A193THR0-0.037-0.02950.612-0.081-0.0810.0000.0000.0000.000
198A195GLU-1-0.851-0.92246.7316.2586.2580.0000.0000.0000.000
199A196ALA00.0460.02643.7390.1830.1830.0000.0000.0000.000
200A197THR00.0010.00441.934-0.099-0.0990.0000.0000.0000.000
201A203SER0-0.039-0.02649.9560.0140.0140.0000.0000.0000.000
202A204PRO00.0260.01347.8320.0860.0860.0000.0000.0000.000
203A205ILE00.0030.01346.090-0.141-0.1410.0000.0000.0000.000
204A206VAL00.0090.00848.3440.1200.1200.0000.0000.0000.000
205A207LYS10.9080.94949.500-6.292-6.2920.0000.0000.0000.000
206A208SER00.0380.00750.9510.0910.0910.0000.0000.0000.000
207A209PHE0-0.0070.01950.859-0.059-0.0590.0000.0000.0000.000
208A210ASN0-0.025-0.03255.4300.0360.0360.0000.0000.0000.000
209A211ARG10.9330.97558.025-5.191-5.1910.0000.0000.0000.000
210A212ASN0-0.004-0.00156.2320.0190.0190.0000.0000.0000.000
211A213GLU-1-0.890-0.95256.4745.3715.3710.0000.0000.0000.000