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: 525KZ

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 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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2168011.608941
FMO2-HF: Nuclear repulsion 2085289.250944
FMO2-HF: Total energy -82722.357996
FMO2-MP2: Total energy -82963.349921


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.
-57.745-52.6492.903-3.443-4.5570.035
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 : -0.899 / q_NPA : -0.962
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].
3A3LEU00.0250.0263.883-1.867-0.529-0.006-0.557-0.7760.002
4A4MET0-0.008-0.0096.124-2.109-2.1090.0000.0000.0000.000
5A5THR00.013-0.0079.388-1.290-1.2900.0000.0000.0000.000
6A6GLN00.012-0.02312.289-0.114-0.1140.0000.0000.0000.000
7A7THR0-0.068-0.00915.354-0.079-0.0790.0000.0000.0000.000
8A8PRO00.0430.02318.702-0.134-0.1340.0000.0000.0000.000
9A9VAL00.0740.03017.4660.3250.3250.0000.0000.0000.000
10A10SER0-0.0100.00619.9670.0790.0790.0000.0000.0000.000
11A11LEU0-0.005-0.01023.582-0.017-0.0170.0000.0000.0000.000
12A12SER00.0680.05526.267-0.204-0.2040.0000.0000.0000.000
13A13VAL0-0.026-0.00929.903-0.080-0.0800.0000.0000.0000.000
14A14SER00.0080.01631.881-0.157-0.1570.0000.0000.0000.000
15A15LEU00.0220.00534.4910.1950.1950.0000.0000.0000.000
16A16GLY0-0.027-0.02036.241-0.184-0.1840.0000.0000.0000.000
17A17ASP-1-0.836-0.90133.7978.7878.7870.0000.0000.0000.000
18A18GLN0-0.047-0.03330.7550.1200.1200.0000.0000.0000.000
19A19ALA00.0490.03727.2670.0660.0660.0000.0000.0000.000
20A20SER0-0.071-0.06124.775-0.038-0.0380.0000.0000.0000.000
21A21ILE0-0.0060.01219.186-0.050-0.0500.0000.0000.0000.000
22A22SER00.0120.02519.1130.3240.3240.0000.0000.0000.000
23A23CYS0-0.041-0.02113.1610.5440.5440.0000.0000.0000.000
24A24ARG10.8320.92613.317-16.885-16.8850.0000.0000.0000.000
25A25SER00.0330.0019.4660.4420.4420.0000.0000.0000.000
26A26SER0-0.0070.0006.111-0.684-0.6840.0000.0000.0000.000
27A27GLN00.0170.0045.4274.2614.2610.0000.0000.0000.000
28A27SER00.0300.0229.575-0.738-0.7380.0000.0000.0000.000
29A27ILE00.0000.0119.0950.4790.4790.0000.0000.0000.000
30A27VAL00.002-0.00712.128-0.282-0.2820.0000.0000.0000.000
31A27HIS0-0.022-0.01513.6701.2621.2620.0000.0000.0000.000
32A27SER00.0110.00217.240-0.539-0.5390.0000.0000.0000.000
33A28THR0-0.029-0.02819.174-0.430-0.4300.0000.0000.0000.000
34A29GLY00.0670.03820.636-0.696-0.6960.0000.0000.0000.000
35A30ASN0-0.055-0.02117.9500.0490.0490.0000.0000.0000.000
36A31THR00.0600.03714.8881.1601.1600.0000.0000.0000.000
37A32TYR00.0090.00313.449-1.136-1.1360.0000.0000.0000.000
38A33LEU00.0180.02612.1531.7141.7140.0000.0000.0000.000
39A34GLU-1-0.884-0.93714.21015.73915.7390.0000.0000.0000.000
40A35TRP00.001-0.00715.4820.8060.8060.0000.0000.0000.000
41A36TYR0-0.019-0.02615.951-0.903-0.9030.0000.0000.0000.000
42A37LEU00.0000.00119.3620.2140.2140.0000.0000.0000.000
43A38GLN0-0.0150.00820.5390.4280.4280.0000.0000.0000.000
44A39LYS10.8480.92022.988-10.094-10.0940.0000.0000.0000.000
45A40PRO00.033-0.00426.1590.2900.2900.0000.0000.0000.000
46A41GLY00.0010.00927.034-0.296-0.2960.0000.0000.0000.000
47A42GLN0-0.0180.00026.538-0.062-0.0620.0000.0000.0000.000
48A43SER00.0480.01423.0800.3960.3960.0000.0000.0000.000
49A44PRO0-0.0110.00318.640-0.383-0.3830.0000.0000.0000.000
50A45LYS10.8550.93421.210-11.437-11.4370.0000.0000.0000.000
51A46LEU00.0180.01619.0030.0240.0240.0000.0000.0000.000
52A47LEU0-0.033-0.02021.284-0.762-0.7620.0000.0000.0000.000
53A48ILE0-0.010-0.00920.473-0.554-0.5540.0000.0000.0000.000
54A49TYR00.0470.01318.8420.7820.7820.0000.0000.0000.000
55A50LYS10.8950.94317.918-14.236-14.2360.0000.0000.0000.000
56A51ILE00.0010.01017.452-0.562-0.5620.0000.0000.0000.000
57A52SER0-0.003-0.01018.977-0.112-0.1120.0000.0000.0000.000
58A53ASN0-0.054-0.00622.354-0.413-0.4130.0000.0000.0000.000
59A54ARG10.8590.91423.500-9.548-9.5480.0000.0000.0000.000
60A55PHE00.0060.00223.782-0.221-0.2210.0000.0000.0000.000
61A56SER00.0470.00925.874-0.355-0.3550.0000.0000.0000.000
62A57GLY00.013-0.00128.4430.2370.2370.0000.0000.0000.000
63A58VAL0-0.069-0.00726.020-0.061-0.0610.0000.0000.0000.000
64A59PRO00.0400.01629.320-0.147-0.1470.0000.0000.0000.000
65A60ASP-1-0.806-0.90230.5239.4699.4690.0000.0000.0000.000
66A61ARG10.7310.83530.565-9.130-9.1300.0000.0000.0000.000
67A62PHE00.0310.02925.7760.1930.1930.0000.0000.0000.000
68A63SER0-0.017-0.01026.337-0.184-0.1840.0000.0000.0000.000
69A64GLY00.0500.02322.3020.2350.2350.0000.0000.0000.000
70A65SER0-0.010-0.00522.953-0.286-0.2860.0000.0000.0000.000
71A66GLY0-0.026-0.01319.2050.0700.0700.0000.0000.0000.000
72A67SER00.015-0.01319.690-0.256-0.2560.0000.0000.0000.000
73A68GLY00.0180.01019.2890.2150.2150.0000.0000.0000.000
74A69THR0-0.046-0.02713.4890.8300.8300.0000.0000.0000.000
75A70ASP-1-0.822-0.89815.11316.98116.9810.0000.0000.0000.000
76A71PHE0-0.0080.01613.596-1.178-1.1780.0000.0000.0000.000
77A72THR00.006-0.00617.4870.1870.1870.0000.0000.0000.000
78A73LEU0-0.0300.00120.358-0.353-0.3530.0000.0000.0000.000
79A74LYS10.9090.94522.010-10.142-10.1420.0000.0000.0000.000
80A75ILE00.0010.00325.055-0.073-0.0730.0000.0000.0000.000
81A76SER0-0.012-0.02428.354-0.181-0.1810.0000.0000.0000.000
82A77ARG10.9060.94231.785-8.633-8.6330.0000.0000.0000.000
83A78VAL00.0120.02230.246-0.006-0.0060.0000.0000.0000.000
84A79GLU-1-0.791-0.87732.7648.2998.2990.0000.0000.0000.000
85A80ALA00.0450.00932.7940.2690.2690.0000.0000.0000.000
86A81GLU-1-0.790-0.87632.7379.5669.5660.0000.0000.0000.000
87A82ASP-1-0.798-0.86228.85410.06810.0680.0000.0000.0000.000
88A83LEU0-0.0420.00527.6840.5300.5300.0000.0000.0000.000
89A84GLY00.0340.00625.667-0.073-0.0730.0000.0000.0000.000
90A85VAL0-0.044-0.01419.191-0.042-0.0420.0000.0000.0000.000
91A86TYR00.000-0.02020.1920.1460.1460.0000.0000.0000.000
92A87TYR00.013-0.00514.8570.4230.4230.0000.0000.0000.000
93A89PHE00.000-0.01410.2451.0681.0680.0000.0000.0000.000
94A90GLN00.007-0.0145.589-3.419-3.4190.0000.0000.0000.000
95A91ALA00.015-0.0018.7791.9831.9830.0000.0000.0000.000
96A92SER0-0.026-0.01510.320-0.166-0.1660.0000.0000.0000.000
97A93HIS0-0.011-0.0076.196-0.194-0.1940.0000.0000.0000.000
98A94ALA00.003-0.0016.458-0.278-0.2780.0000.0000.0000.000
99A95PRO00.0240.0232.465-13.552-10.1002.893-2.793-3.5520.033
100A96ARG10.8590.9464.555-33.249-33.155-0.001-0.027-0.0660.000
101A97THR0-0.008-0.0013.499-0.336-0.1240.017-0.066-0.1630.000
102A98PHE00.022-0.0036.552-2.868-2.8680.0000.0000.0000.000
103A99GLY00.0090.0119.2311.4971.4970.0000.0000.0000.000
104A100GLY0-0.032-0.02511.824-0.393-0.3930.0000.0000.0000.000
105A101GLY00.0140.01613.277-0.670-0.6700.0000.0000.0000.000
106A102THR0-0.050-0.04316.6820.1180.1180.0000.0000.0000.000
107A103LYS10.8170.91520.114-11.281-11.2810.0000.0000.0000.000
108A104LEU0-0.022-0.00623.247-0.230-0.2300.0000.0000.0000.000
109A105GLU-1-0.896-0.95126.10510.24610.2460.0000.0000.0000.000
110A106ILE0-0.007-0.00829.535-0.021-0.0210.0000.0000.0000.000
111A107LYS10.8700.91632.171-9.377-9.3770.0000.0000.0000.000
112A108ARG10.8120.89935.359-7.815-7.8150.0000.0000.0000.000
113A109ALA00.0280.01638.9260.0420.0420.0000.0000.0000.000
114A110ASP-1-0.888-0.94241.0117.5337.5330.0000.0000.0000.000
115A111ALA0-0.054-0.02741.578-0.160-0.1600.0000.0000.0000.000
116A112ALA00.0300.01542.3820.1330.1330.0000.0000.0000.000
117A113PRO00.0000.01442.042-0.012-0.0120.0000.0000.0000.000
118A114THR00.0180.00543.839-0.220-0.2200.0000.0000.0000.000
119A115VAL0-0.044-0.02944.8880.0460.0460.0000.0000.0000.000
120A116SER0-0.030-0.00746.062-0.246-0.2460.0000.0000.0000.000
121A117ILE0-0.030-0.01646.4190.1660.1660.0000.0000.0000.000
122A118PHE00.000-0.00546.019-0.128-0.1280.0000.0000.0000.000
123A119PRO00.0330.02848.4460.1230.1230.0000.0000.0000.000
124A120PRO0-0.0100.00648.3070.0820.0820.0000.0000.0000.000
125A121SER0-0.020-0.03749.298-0.093-0.0930.0000.0000.0000.000
126A122SER00.0580.01751.2350.0260.0260.0000.0000.0000.000
127A123GLU-1-0.813-0.88050.4226.1616.1610.0000.0000.0000.000
128A124GLN00.0020.02746.0840.0760.0760.0000.0000.0000.000
129A125LEU00.0380.02049.3850.0390.0390.0000.0000.0000.000
130A126THR0-0.050-0.04052.085-0.075-0.0750.0000.0000.0000.000
131A127SER0-0.081-0.04648.540-0.012-0.0120.0000.0000.0000.000
132A128GLY0-0.0030.00749.1090.1070.1070.0000.0000.0000.000
133A129GLY0-0.045-0.01846.8990.0620.0620.0000.0000.0000.000
134A130ALA00.030-0.00646.956-0.124-0.1240.0000.0000.0000.000
135A131SER0-0.034-0.03642.5650.0580.0580.0000.0000.0000.000
136A132VAL0-0.0100.00744.912-0.085-0.0850.0000.0000.0000.000
137A133VAL0-0.013-0.00442.2840.1950.1950.0000.0000.0000.000
138A134CYS0-0.074-0.02843.055-0.042-0.0420.0000.0000.0000.000
139A135PHE0-0.010-0.00641.2100.2310.2310.0000.0000.0000.000
140A136LEU00.031-0.00340.373-0.202-0.2020.0000.0000.0000.000
141A137ASN00.0320.00640.2360.3250.3250.0000.0000.0000.000
142A138ASN0-0.021-0.03340.126-0.269-0.2690.0000.0000.0000.000
143A139PHE00.0070.01636.312-0.150-0.1500.0000.0000.0000.000
144A140TYR0-0.001-0.00833.9120.2300.2300.0000.0000.0000.000
145A141PRO00.0670.04135.178-0.199-0.1990.0000.0000.0000.000
146A142LYS10.9200.95828.993-10.046-10.0460.0000.0000.0000.000
147A143ASP-1-0.918-0.96332.7379.2229.2220.0000.0000.0000.000
148A144ILE0-0.0110.01435.090-0.267-0.2670.0000.0000.0000.000
149A145ASN0-0.048-0.03637.1220.0490.0490.0000.0000.0000.000
150A146VAL00.0500.01738.831-0.155-0.1550.0000.0000.0000.000
151A147LYS10.8000.89540.818-7.349-7.3490.0000.0000.0000.000
152A148TRP00.0580.01442.243-0.156-0.1560.0000.0000.0000.000
153A149LYS10.7680.85746.242-6.178-6.1780.0000.0000.0000.000
154A150ILE00.0520.03248.542-0.036-0.0360.0000.0000.0000.000
155A151ASP-1-0.741-0.85851.7815.5815.5810.0000.0000.0000.000
156A152GLY00.0100.01654.411-0.063-0.0630.0000.0000.0000.000
157A153SER0-0.067-0.04952.860-0.034-0.0340.0000.0000.0000.000
158A154GLU-1-0.852-0.91049.9316.1786.1780.0000.0000.0000.000
159A155ARG10.9310.96644.643-6.669-6.6690.0000.0000.0000.000
160A156GLN00.0710.04044.5430.3040.3040.0000.0000.0000.000
161A157ASN0-0.035-0.03240.2520.1520.1520.0000.0000.0000.000
162A158GLY00.0500.05439.5560.2120.2120.0000.0000.0000.000
163A159VAL0-0.051-0.03238.137-0.106-0.1060.0000.0000.0000.000
164A160LEU00.0390.02933.3790.2280.2280.0000.0000.0000.000
165A161ASN00.0170.01334.687-0.346-0.3460.0000.0000.0000.000
166A162SER0-0.0050.00032.6200.3670.3670.0000.0000.0000.000
167A163TRP00.0300.00331.408-0.242-0.2420.0000.0000.0000.000
168A164THR0-0.003-0.00431.2490.2030.2030.0000.0000.0000.000
169A165ASP-1-0.807-0.90727.38410.91210.9120.0000.0000.0000.000
170A166GLN0-0.044-0.02630.119-0.047-0.0470.0000.0000.0000.000
171A167ASP-1-0.779-0.86632.2048.3418.3410.0000.0000.0000.000
172A168SER0-0.033-0.04332.998-0.128-0.1280.0000.0000.0000.000
173A169LYS10.8150.89834.950-7.935-7.9350.0000.0000.0000.000
174A170ASP-1-0.803-0.88238.5007.6437.6430.0000.0000.0000.000
175A171SER0-0.021-0.01135.620-0.064-0.0640.0000.0000.0000.000
176A172THR0-0.081-0.03436.2050.0990.0990.0000.0000.0000.000
177A173TYR0-0.045-0.04130.6110.3600.3600.0000.0000.0000.000
178A174SER00.0310.02035.619-0.383-0.3830.0000.0000.0000.000
179A175MET0-0.047-0.00335.5850.2750.2750.0000.0000.0000.000
180A176SER0-0.030-0.00436.785-0.244-0.2440.0000.0000.0000.000
181A177SER0-0.014-0.01937.4920.1520.1520.0000.0000.0000.000
182A178THR00.0280.01039.112-0.250-0.2500.0000.0000.0000.000
183A179LEU0-0.0080.01240.4970.1510.1510.0000.0000.0000.000
184A180THR00.0070.01141.303-0.129-0.1290.0000.0000.0000.000
185A181LEU0-0.050-0.00943.3500.0630.0630.0000.0000.0000.000
186A182THR00.029-0.01846.160-0.021-0.0210.0000.0000.0000.000
187A183LYS10.8540.92048.583-5.839-5.8390.0000.0000.0000.000
188A184ASP-1-0.799-0.88951.7725.7445.7440.0000.0000.0000.000
189A185GLU-1-0.861-0.89449.4076.1786.1780.0000.0000.0000.000
190A186TYR0-0.064-0.04050.907-0.019-0.0190.0000.0000.0000.000
191A187GLU-1-0.835-0.95452.6685.6265.6260.0000.0000.0000.000
192A188ARG10.7190.86852.866-6.000-6.0000.0000.0000.0000.000
193A189HIS10.7630.86152.587-5.874-5.8740.0000.0000.0000.000
194A190ASN00.0170.00756.452-0.060-0.0600.0000.0000.0000.000
195A191SER0-0.025-0.02655.922-0.021-0.0210.0000.0000.0000.000
196A192TYR00.0040.00750.0840.1580.1580.0000.0000.0000.000
197A193THR0-0.020-0.01650.366-0.084-0.0840.0000.0000.0000.000
198A195GLU-1-0.820-0.90346.0096.1846.1840.0000.0000.0000.000
199A196ALA00.0460.02443.3390.1740.1740.0000.0000.0000.000
200A197THR00.0000.00141.462-0.074-0.0740.0000.0000.0000.000
201A203SER0-0.014-0.02149.151-0.057-0.0570.0000.0000.0000.000
202A204PRO00.0090.01447.6340.1050.1050.0000.0000.0000.000
203A205ILE00.0020.00945.948-0.134-0.1340.0000.0000.0000.000
204A206VAL00.003-0.00147.7920.1280.1280.0000.0000.0000.000
205A207LYS10.8460.91849.477-6.270-6.2700.0000.0000.0000.000
206A208SER00.0190.00050.8220.0710.0710.0000.0000.0000.000
207A209PHE00.0060.01550.307-0.040-0.0400.0000.0000.0000.000
208A210ASN0-0.012-0.00955.1140.0170.0170.0000.0000.0000.000
209A211ARG10.9040.95957.789-5.095-5.0950.0000.0000.0000.000
210A212ASN0-0.032-0.00355.8590.0040.0040.0000.0000.0000.000
211A213GLU-1-0.798-0.88655.8545.3005.3000.0000.0000.0000.000