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: 17Z1Z

Calculation Name: 2HLC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2HLC

Chain ID: A

ChEMBL ID:

UniProt ID: P08897

Base Structure: X-ray

Registration Date: 2023-09-20

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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2866409.909884
FMO2-HF: Nuclear repulsion 2777417.23068
FMO2-HF: Total energy -88992.679205
FMO2-MP2: Total energy -89251.45296


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:16:ILE)


Summations of interaction energy for fragment #1(A:16:ILE)
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.
-34.936-17.25124.887-13.851-28.726-0.103
Interaction energy analysis for fragmet #1(A:16:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.049 / q_NPA : -0.028
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].
3A18ASN0-0.069-0.0572.819-1.0931.0790.453-1.117-1.507-0.006
4A19GLY00.0180.0122.681-0.9960.1240.907-0.708-1.319-0.002
5A20TYR0-0.083-0.0333.0990.215-0.4440.1270.809-0.2780.000
6A21GLU-1-0.819-0.8885.8051.2301.2300.0000.0000.0000.000
7A22ALA0-0.027-0.0197.340-0.221-0.2210.0000.0000.0000.000
8A23TYR0-0.017-0.0078.852-0.012-0.0120.0000.0000.0000.000
9A24THR00.005-0.01312.2090.0130.0130.0000.0000.0000.000
10A25GLY00.0990.05013.858-0.022-0.0220.0000.0000.0000.000
11A26LEU0-0.108-0.0289.607-0.020-0.0200.0000.0000.0000.000
12A27PHE00.009-0.0087.246-0.005-0.0050.0000.0000.0000.000
13A28PRO00.0170.01711.427-0.018-0.0180.0000.0000.0000.000
14A29TYR00.0570.0379.219-0.030-0.0300.0000.0000.0000.000
15A30GLN0-0.037-0.0096.4490.0200.0200.0000.0000.0000.000
16A31ALA00.0060.00110.2640.0120.0120.0000.0000.0000.000
17A32GLY00.0350.0199.630-0.054-0.0540.0000.0000.0000.000
18A33LEU0-0.064-0.03311.2100.0500.0500.0000.0000.0000.000
19A34ASP-1-0.704-0.82213.207-0.126-0.1260.0000.0000.0000.000
20A35ILE0-0.0110.00013.7860.0340.0340.0000.0000.0000.000
21A36THR0-0.020-0.01017.217-0.001-0.0010.0000.0000.0000.000
22A37LEU00.0130.01018.0110.0100.0100.0000.0000.0000.000
23A37GLN0-0.024-0.02821.4260.0170.0170.0000.0000.0000.000
24A37ASP-1-0.868-0.90622.371-0.154-0.1540.0000.0000.0000.000
25A37GLN0-0.054-0.04123.9370.0060.0060.0000.0000.0000.000
26A38ARG10.8460.91518.7510.2110.2110.0000.0000.0000.000
27A39ARG10.8380.88916.3300.0640.0640.0000.0000.0000.000
28A40VAL0-0.008-0.01013.082-0.025-0.0250.0000.0000.0000.000
29A41TRP00.0040.0157.8800.1440.1440.0000.0000.0000.000
30A42CYS0-0.072-0.0119.270-0.188-0.1880.0000.0000.0000.000
31A43GLY00.0700.0387.2310.0850.0850.0000.0000.0000.000
32A44GLY00.0190.0008.2390.0170.0170.0000.0000.0000.000
33A45SER0-0.0120.0019.8780.0520.0520.0000.0000.0000.000
34A46LEU0-0.0050.00712.115-0.018-0.0180.0000.0000.0000.000
35A47ILE0-0.033-0.01715.4490.0130.0130.0000.0000.0000.000
36A48ASP-1-0.768-0.89717.9570.0180.0180.0000.0000.0000.000
37A49ASN0-0.051-0.01320.478-0.007-0.0070.0000.0000.0000.000
38A50LYS10.7830.90022.579-0.016-0.0160.0000.0000.0000.000
39A51TRP0-0.004-0.00520.178-0.012-0.0120.0000.0000.0000.000
40A52ILE00.0320.02414.0220.0110.0110.0000.0000.0000.000
41A53LEU0-0.024-0.01014.413-0.009-0.0090.0000.0000.0000.000
42A54THR00.019-0.00711.409-0.010-0.0100.0000.0000.0000.000
43A55ALA00.0500.03111.7680.0260.0260.0000.0000.0000.000
44A56ALA0-0.023-0.00813.5800.0020.0020.0000.0000.0000.000
45A57HIS0-0.046-0.03611.210-0.072-0.0720.0000.0000.0000.000
46A59VAL0-0.016-0.03414.8280.0220.0220.0000.0000.0000.000
47A59HIS0-0.050-0.01918.1510.0370.0370.0000.0000.0000.000
48A60ASP-1-0.857-0.92320.011-0.182-0.1820.0000.0000.0000.000
49A61ALA0-0.009-0.00819.5870.0010.0010.0000.0000.0000.000
50A62VAL0-0.065-0.02021.6380.0130.0130.0000.0000.0000.000
51A63SER0-0.038-0.02622.5130.0130.0130.0000.0000.0000.000
52A64VAL00.004-0.00616.376-0.015-0.0150.0000.0000.0000.000
53A65VAL0-0.0180.00518.6250.0160.0160.0000.0000.0000.000
54A66VAL0-0.005-0.00815.561-0.019-0.0190.0000.0000.0000.000
55A67TYR0-0.057-0.02513.8990.0200.0200.0000.0000.0000.000
56A68LEU00.0430.00413.939-0.007-0.0070.0000.0000.0000.000
57A69GLY00.0820.03214.7370.0000.0000.0000.0000.0000.000
58A70SER0-0.058-0.03514.3450.0160.0160.0000.0000.0000.000
59A71ALA00.0140.00710.226-0.012-0.0120.0000.0000.0000.000
60A72VAL0-0.0060.01110.0190.1400.1400.0000.0000.0000.000
61A73GLN00.0210.0038.4880.0310.0310.0000.0000.0000.000
62A74TYR0-0.091-0.04711.275-0.030-0.0300.0000.0000.0000.000
63A75GLU-1-0.878-0.92314.2130.2000.2000.0000.0000.0000.000
64A76GLY0-0.016-0.03815.059-0.002-0.0020.0000.0000.0000.000
65A80GLU-1-0.860-0.87317.3010.1180.1180.0000.0000.0000.000
66A81ALA0-0.020-0.01219.058-0.014-0.0140.0000.0000.0000.000
67A82VAL00.0030.00318.1320.0030.0030.0000.0000.0000.000
68A83VAL0-0.036-0.01019.895-0.002-0.0020.0000.0000.0000.000
69A84ASN00.0100.00120.405-0.002-0.0020.0000.0000.0000.000
70A85SER00.0100.00220.4340.0010.0010.0000.0000.0000.000
71A86GLU-1-0.872-0.91722.143-0.011-0.0110.0000.0000.0000.000
72A87ARG10.9080.94623.9450.0410.0410.0000.0000.0000.000
73A88ILE00.0530.03720.0440.0010.0010.0000.0000.0000.000
74A89ILE0-0.075-0.04121.3360.0060.0060.0000.0000.0000.000
75A90SER00.0960.04620.148-0.009-0.0090.0000.0000.0000.000
76A91HIS00.0110.00920.5020.0100.0100.0000.0000.0000.000
77A92SER0-0.025-0.02022.407-0.007-0.0070.0000.0000.0000.000
78A93MET0-0.030-0.01624.9180.0020.0020.0000.0000.0000.000
79A94PHE00.0250.02417.981-0.001-0.0010.0000.0000.0000.000
80A95ASN0-0.030-0.00821.6120.0020.0020.0000.0000.0000.000
81A96PRO00.014-0.00119.812-0.010-0.0100.0000.0000.0000.000
82A97ASP-1-0.910-0.93619.820-0.163-0.1630.0000.0000.0000.000
83A98THR0-0.045-0.05620.609-0.002-0.0020.0000.0000.0000.000
84A99TYR0-0.0250.00313.6050.0040.0040.0000.0000.0000.000
85A100LEU00.0400.03517.8440.0090.0090.0000.0000.0000.000
86A101ASN0-0.031-0.02820.1460.0040.0040.0000.0000.0000.000
87A102ASP-1-0.670-0.78514.041-0.263-0.2630.0000.0000.0000.000
88A103VAL0-0.054-0.00615.245-0.005-0.0050.0000.0000.0000.000
89A104ALA00.006-0.00816.1920.0050.0050.0000.0000.0000.000
90A105LEU0-0.028-0.00216.7000.0050.0050.0000.0000.0000.000
91A106ILE00.000-0.00216.530-0.006-0.0060.0000.0000.0000.000
92A107LYS10.7790.88719.4070.0200.0200.0000.0000.0000.000
93A108ILE00.0180.00318.928-0.006-0.0060.0000.0000.0000.000
94A109PRO00.0440.01322.6120.0030.0030.0000.0000.0000.000
95A111HIS0-0.064-0.06023.755-0.003-0.0030.0000.0000.0000.000
96A112VAL00.0100.01620.5730.0020.0020.0000.0000.0000.000
97A113GLU-1-0.884-0.93323.1000.0450.0450.0000.0000.0000.000
98A114TYR0-0.004-0.00620.5030.0030.0030.0000.0000.0000.000
99A115THR0-0.030-0.04720.868-0.002-0.0020.0000.0000.0000.000
100A116ASP-1-0.923-0.95620.9080.1180.1180.0000.0000.0000.000
101A117ASN0-0.083-0.05716.9400.0360.0360.0000.0000.0000.000
102A118ILE0-0.023-0.00216.3080.0080.0080.0000.0000.0000.000
103A119GLN0-0.015-0.02916.905-0.019-0.0190.0000.0000.0000.000
104A120PRO0-0.0130.01316.4330.0030.0030.0000.0000.0000.000
105A121ILE0-0.014-0.00712.7580.0120.0120.0000.0000.0000.000
106A122ARG10.7500.84715.612-0.087-0.0870.0000.0000.0000.000
107A123LEU00.0450.01116.7290.0040.0040.0000.0000.0000.000
108A124PRO00.0040.00017.9950.0030.0030.0000.0000.0000.000
109A125SER0-0.017-0.01620.847-0.007-0.0070.0000.0000.0000.000
110A125GLY00.0390.00824.6770.0040.0040.0000.0000.0000.000
111A125GLU-1-0.839-0.92326.5380.0130.0130.0000.0000.0000.000
112A126GLU-1-0.802-0.85121.3840.0580.0580.0000.0000.0000.000
113A127LEU0-0.023-0.01921.9100.0000.0000.0000.0000.0000.000
114A128ASN0-0.023-0.02823.701-0.008-0.0080.0000.0000.0000.000
115A129ASN0-0.064-0.01321.427-0.001-0.0010.0000.0000.0000.000
116A130LYS10.8960.92720.4840.0080.0080.0000.0000.0000.000
117A131PHE00.012-0.00216.6150.0010.0010.0000.0000.0000.000
118A132GLU-1-0.780-0.87816.9690.0070.0070.0000.0000.0000.000
119A133ASN0-0.042-0.03217.188-0.002-0.0020.0000.0000.0000.000
120A134ILE0-0.0260.00915.5020.0060.0060.0000.0000.0000.000
121A135TRP00.003-0.0049.839-0.002-0.0020.0000.0000.0000.000
122A136ALA0-0.0060.00310.385-0.017-0.0170.0000.0000.0000.000
123A137THR0-0.008-0.0106.8800.0600.0600.0000.0000.0000.000
124A138VAL0-0.0140.0002.733-1.056-0.2290.329-0.223-0.9340.002
125A139SER0-0.022-0.0292.758-0.7380.4820.648-0.611-1.257-0.002
126A140GLY0-0.016-0.0072.918-1.438-0.8140.6970.013-1.335-0.004
127A141TRP0-0.033-0.0253.5200.5111.1020.043-0.072-0.562-0.001
128A142GLY0-0.0140.0043.0240.4150.8440.026-0.144-0.3120.000
129A143GLN0-0.022-0.0293.2831.3192.3830.151-0.530-0.685-0.003
130A144SER00.0770.0482.026-9.451-9.1076.297-3.301-3.340-0.016
131A145ASN0-0.063-0.0483.622-0.587-0.2790.019-0.087-0.2400.000
132A146THR0-0.027-0.0196.6940.0570.0570.0000.0000.0000.000
133A147ASP-1-0.922-0.9567.6190.4720.4720.0000.0000.0000.000
134A152THR0-0.056-0.0457.128-0.095-0.0950.0000.0000.0000.000
135A153VAL00.0160.0088.7230.0290.0290.0000.0000.0000.000
136A154ILE0-0.044-0.0148.739-0.180-0.1800.0000.0000.0000.000
137A155LEU0-0.063-0.0185.1750.4570.4570.0000.0000.0000.000
138A156GLN00.0810.0452.138-2.001-1.2792.667-1.096-2.2940.001
139A157TYR0-0.027-0.0352.587-2.729-1.2181.399-0.844-2.066-0.009
140A158THR00.0080.0082.374-0.832-0.4602.649-0.304-2.716-0.001
141A159TYR0-0.013-0.0053.697-0.270-0.1730.0060.061-0.1640.000
142A160ASN0-0.044-0.0465.5770.1440.1440.0000.0000.0000.000
143A161LEU0-0.0180.0078.615-0.009-0.0090.0000.0000.0000.000
144A162VAL00.0350.01712.402-0.029-0.0290.0000.0000.0000.000
145A163ILE0-0.057-0.02913.639-0.005-0.0050.0000.0000.0000.000
146A164ASP-1-0.828-0.91316.363-0.025-0.0250.0000.0000.0000.000
147A165ASN00.021-0.00719.154-0.001-0.0010.0000.0000.0000.000
148A166ASP-1-0.924-0.95320.226-0.049-0.0490.0000.0000.0000.000
149A167ARG10.8350.90916.4640.0100.0100.0000.0000.0000.000
150A168CYS0-0.015-0.02112.658-0.045-0.0450.0000.0000.0000.000
151A169ALA00.0230.00518.355-0.019-0.0190.0000.0000.0000.000
152A170GLN0-0.097-0.04921.1950.0010.0010.0000.0000.0000.000
153A170GLU-1-0.860-0.89817.217-0.136-0.1360.0000.0000.0000.000
154A171TYR0-0.028-0.03113.021-0.042-0.0420.0000.0000.0000.000
155A172PRO0-0.009-0.00419.9010.0150.0150.0000.0000.0000.000
156A173PRO00.017-0.01022.4190.0010.0010.0000.0000.0000.000
157A174GLY0-0.015-0.00124.345-0.003-0.0030.0000.0000.0000.000
158A175ILE0-0.0060.00617.8220.0000.0000.0000.0000.0000.000
159A176ILE0-0.054-0.00916.936-0.005-0.0050.0000.0000.0000.000
160A177VAL00.0200.00820.1030.0090.0090.0000.0000.0000.000
161A178GLU-1-0.895-0.96020.786-0.054-0.0540.0000.0000.0000.000
162A179SER0-0.049-0.03020.3770.0070.0070.0000.0000.0000.000
163A180THR00.0310.02515.679-0.003-0.0030.0000.0000.0000.000
164A181ILE0-0.036-0.00512.8980.0180.0180.0000.0000.0000.000
165A183GLY00.0320.0249.9780.0390.0390.0000.0000.0000.000
166A184ASP-1-0.825-0.90710.480-0.101-0.1010.0000.0000.0000.000
167A185THR00.0080.0057.4660.0770.0770.0000.0000.0000.000
168A186SER0-0.046-0.0349.415-0.046-0.0460.0000.0000.0000.000
169A186ASP-1-0.891-0.93610.0060.0810.0810.0000.0000.0000.000
170A187GLY00.0140.0078.9680.0340.0340.0000.0000.0000.000
171A188LYS10.8160.9224.750-0.377-0.314-0.001-0.007-0.0550.000
172A189SER00.031-0.0093.7950.0810.4200.001-0.073-0.2680.000
173A190PRO0-0.0140.0122.110-3.621-0.9833.041-2.577-3.103-0.009
174A191CYS0-0.0440.0053.1360.9170.7570.0340.836-0.7090.000
175A192PHE00.035-0.0114.792-0.0880.030-0.001-0.003-0.1140.000
176A193GLY00.0330.0225.822-0.255-0.2550.0000.0000.0000.000
177A194ASP-1-0.749-0.8832.259-14.969-11.1345.397-3.867-5.366-0.053
178A195SER0-0.033-0.0334.9550.5020.551-0.001-0.004-0.0440.000
179A196GLY00.009-0.0108.1830.0300.0300.0000.0000.0000.000
180A197GLY0-0.0040.0085.4960.0860.0860.0000.0000.0000.000
181A198PRO0-0.025-0.0025.7990.0520.0520.0000.0000.0000.000
182A199PHE00.0350.0096.3990.1050.1050.0000.0000.0000.000
183A200VAL00.0170.0018.729-0.069-0.0690.0000.0000.0000.000
184A201LEU00.0150.01710.9440.0360.0360.0000.0000.0000.000
185A202SER00.0480.00712.012-0.015-0.0150.0000.0000.0000.000
186A203ASP-1-0.895-0.93914.0390.1520.1520.0000.0000.0000.000
187A206LYS10.7810.88417.053-0.091-0.0910.0000.0000.0000.000
188A207ASN00.016-0.00315.7280.0010.0010.0000.0000.0000.000
189A208LEU0-0.044-0.00615.682-0.014-0.0140.0000.0000.0000.000
190A209LEU00.0230.02210.9450.0190.0190.0000.0000.0000.000
191A210ILE0-0.044-0.03112.470-0.020-0.0200.0000.0000.0000.000
192A211GLY0-0.015-0.01812.067-0.022-0.0220.0000.0000.0000.000
193A212VAL0-0.0130.0049.8250.0300.0300.0000.0000.0000.000
194A213VAL0-0.019-0.0034.795-0.0480.013-0.001-0.002-0.0580.000
195A214SER0-0.059-0.0448.255-0.062-0.0620.0000.0000.0000.000
196A215PHE00.0330.00110.851-0.049-0.0490.0000.0000.0000.000
197A216VAL00.0470.0187.4770.0300.0300.0000.0000.0000.000
198A217SER00.0500.03310.6210.0490.0490.0000.0000.0000.000
199A217GLY00.0280.00912.709-0.066-0.0660.0000.0000.0000.000
200A218ALA0-0.075-0.03315.0480.0020.0020.0000.0000.0000.000
201A219GLY00.0270.01411.2460.0030.0030.0000.0000.0000.000
202A221GLU-1-0.822-0.9007.551-0.771-0.7710.0000.0000.0000.000
203A222SER0-0.095-0.0579.9310.1410.1410.0000.0000.0000.000
204A223GLY0-0.0040.00211.6150.0570.0570.0000.0000.0000.000
205A224LYS10.7670.87212.5690.2320.2320.0000.0000.0000.000
206A225PRO00.0300.01711.350-0.044-0.0440.0000.0000.0000.000
207A226VAL00.0050.0336.755-0.049-0.0490.0000.0000.0000.000
208A227GLY00.0380.0189.9730.0860.0860.0000.0000.0000.000
209A228PHE0-0.021-0.0206.714-0.063-0.0630.0000.0000.0000.000
210A229SER00.004-0.01411.8630.0130.0130.0000.0000.0000.000
211A230ARG10.8040.88914.2800.0350.0350.0000.0000.0000.000
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