FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 855LY

Calculation Name: 5HXN-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 5HXN

Chain ID: A

ChEMBL ID:
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UniProt ID: B8XA40

Base Structure: X-ray

Registration Date: 2023-06-21

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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2745060.175974
FMO2-HF: Nuclear repulsion 2656169.347953
FMO2-HF: Total energy -88890.828021
FMO2-MP2: Total energy -89148.215029


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:76:LEU)


Summations of interaction energy for fragment #1(A:76:LEU)
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.
-10.061-7.5318.643-4.759-6.413-0.035
Interaction energy analysis for fragmet #1(A:76:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.008
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].
3A78PRO00.0010.0122.591-2.5040.0891.005-1.535-2.064-0.008
4A79LYS10.9600.9795.2690.9621.061-0.001-0.003-0.0940.000
5A80HIS0-0.041-0.0276.5920.3200.3200.0000.0000.0000.000
6A81ILE00.0160.0219.773-0.111-0.1110.0000.0000.0000.000
7A82ALA00.0170.01012.0290.1490.1490.0000.0000.0000.000
8A83LEU00.019-0.00615.572-0.038-0.0380.0000.0000.0000.000
9A84ILE0-0.028-0.00718.0780.0640.0640.0000.0000.0000.000
10A85MET00.0140.02621.582-0.009-0.0090.0000.0000.0000.000
11A86ASP-1-0.829-0.89023.400-0.231-0.2310.0000.0000.0000.000
12A87GLY00.0570.01625.332-0.016-0.0160.0000.0000.0000.000
13A88ASN00.0170.00926.2960.0180.0180.0000.0000.0000.000
14A89ARG10.7760.83829.7040.1860.1860.0000.0000.0000.000
15A90ARG10.8050.86730.7090.1600.1600.0000.0000.0000.000
16A91TRP00.005-0.00228.8870.0200.0200.0000.0000.0000.000
17A92ALA00.0540.03231.7190.0070.0070.0000.0000.0000.000
18A93LYS10.9270.95935.1930.1440.1440.0000.0000.0000.000
19A94ASP-1-0.801-0.87133.340-0.158-0.1580.0000.0000.0000.000
20A95LYS10.8410.93831.0290.1850.1850.0000.0000.0000.000
21A96GLY0-0.0090.00637.3500.0060.0060.0000.0000.0000.000
22A97LEU0-0.028-0.00936.8720.0050.0050.0000.0000.0000.000
23A98ASP-1-0.786-0.89139.282-0.130-0.1300.0000.0000.0000.000
24A99VAL0-0.097-0.05835.447-0.007-0.0070.0000.0000.0000.000
25A100SER00.012-0.00135.411-0.011-0.0110.0000.0000.0000.000
26A101GLU-1-0.848-0.91735.260-0.138-0.1380.0000.0000.0000.000
27A102GLY0-0.041-0.01232.514-0.006-0.0060.0000.0000.0000.000
28A103HIS0-0.054-0.06431.047-0.022-0.0220.0000.0000.0000.000
29A104LYS10.8890.91730.7680.1240.1240.0000.0000.0000.000
30A105HIS00.0050.01627.985-0.008-0.0080.0000.0000.0000.000
31A106LEU0-0.051-0.01025.644-0.017-0.0170.0000.0000.0000.000
32A107PHE00.0140.00725.159-0.026-0.0260.0000.0000.0000.000
33A108PRO00.0530.02624.835-0.019-0.0190.0000.0000.0000.000
34A109LYS10.8050.90122.1440.3150.3150.0000.0000.0000.000
35A110LEU00.009-0.00419.526-0.039-0.0390.0000.0000.0000.000
36A111LYS10.8130.90220.0020.1930.1930.0000.0000.0000.000
37A112GLU-1-0.821-0.88420.136-0.354-0.3540.0000.0000.0000.000
38A113ILE00.0160.00016.027-0.038-0.0380.0000.0000.0000.000
39A114CYS0-0.035-0.00215.800-0.088-0.0880.0000.0000.0000.000
40A115ASP-1-0.880-0.93515.882-0.327-0.3270.0000.0000.0000.000
41A116ILE0-0.051-0.00613.9720.0050.0050.0000.0000.0000.000
42A117SER00.007-0.02611.926-0.086-0.0860.0000.0000.0000.000
43A118SER0-0.043-0.03511.074-0.066-0.0660.0000.0000.0000.000
44A119LYS10.8420.91312.3630.3660.3660.0000.0000.0000.000
45A120LEU0-0.024-0.0048.9640.0600.0600.0000.0000.0000.000
46A121GLY0-0.0010.0017.745-0.210-0.2100.0000.0000.0000.000
47A122ILE0-0.048-0.0157.4720.0000.0000.0000.0000.0000.000
48A123GLN0-0.020-0.0177.9230.2120.2120.0000.0000.0000.000
49A124VAL0-0.040-0.02410.4350.1370.1370.0000.0000.0000.000
50A125ILE00.0280.01911.959-0.136-0.1360.0000.0000.0000.000
51A126THR0-0.003-0.00814.7130.1050.1050.0000.0000.0000.000
52A127ALA00.003-0.00617.494-0.041-0.0410.0000.0000.0000.000
53A128PHE0-0.083-0.03720.0230.0430.0430.0000.0000.0000.000
54A129ALA00.0060.00623.3450.0000.0000.0000.0000.0000.000
55A130PHE0-0.005-0.02026.3740.0170.0170.0000.0000.0000.000
56A131SER00.0320.00328.6040.0030.0030.0000.0000.0000.000
57A132THR00.033-0.00729.6150.0090.0090.0000.0000.0000.000
58A133GLU-1-0.875-0.90030.996-0.179-0.1790.0000.0000.0000.000
59A134ASN0-0.031-0.01030.3690.0060.0060.0000.0000.0000.000
60A135TRP00.0340.00634.0280.0060.0060.0000.0000.0000.000
61A136LYS10.8860.95635.9480.1520.1520.0000.0000.0000.000
62A137ARG10.8340.93131.7580.1880.1880.0000.0000.0000.000
63A138ALA00.0420.01738.8870.0050.0050.0000.0000.0000.000
64A139LYS10.8600.89840.9890.1040.1040.0000.0000.0000.000
65A140GLY00.0620.03741.911-0.002-0.0020.0000.0000.0000.000
66A141GLU-1-0.726-0.81635.692-0.162-0.1620.0000.0000.0000.000
67A142VAL0-0.024-0.00837.244-0.006-0.0060.0000.0000.0000.000
68A143ASP-1-0.785-0.87737.631-0.113-0.1130.0000.0000.0000.000
69A144PHE00.0160.00735.244-0.002-0.0020.0000.0000.0000.000
70A145LEU0-0.023-0.01332.175-0.004-0.0040.0000.0000.0000.000
71A146MET0-0.019-0.00734.043-0.005-0.0050.0000.0000.0000.000
72A147GLN00.0090.00235.727-0.001-0.0010.0000.0000.0000.000
73A148MET0-0.0120.00930.8100.0000.0000.0000.0000.0000.000
74A149PHE0-0.011-0.03029.869-0.009-0.0090.0000.0000.0000.000
75A150GLU-1-0.806-0.89831.698-0.123-0.1230.0000.0000.0000.000
76A151GLU-1-0.919-0.96732.139-0.151-0.1510.0000.0000.0000.000
77A152LEU0-0.033-0.01026.464-0.004-0.0040.0000.0000.0000.000
78A153TYR00.0300.00628.630-0.005-0.0050.0000.0000.0000.000
79A154ASP-1-0.836-0.91430.125-0.125-0.1250.0000.0000.0000.000
80A155GLU-1-0.805-0.88627.214-0.211-0.2110.0000.0000.0000.000
81A156PHE00.016-0.00721.752-0.011-0.0110.0000.0000.0000.000
82A157SER0-0.0220.02425.461-0.003-0.0030.0000.0000.0000.000
83A158ARG10.7960.87227.6380.1330.1330.0000.0000.0000.000
84A159SER0-0.014-0.01822.749-0.003-0.0030.0000.0000.0000.000
85A160GLY0-0.0080.00721.949-0.012-0.0120.0000.0000.0000.000
86A161VAL00.007-0.00118.307-0.008-0.0080.0000.0000.0000.000
87A162ARG10.8730.96417.4940.2690.2690.0000.0000.0000.000
88A163VAL00.011-0.00219.944-0.034-0.0340.0000.0000.0000.000
89A164SER0-0.008-0.01421.0400.0320.0320.0000.0000.0000.000
90A165ILE0-0.053-0.02523.083-0.019-0.0190.0000.0000.0000.000
91A166ILE0-0.0180.00021.7130.0090.0090.0000.0000.0000.000
92A167GLY0-0.006-0.02625.677-0.010-0.0100.0000.0000.0000.000
93A168CYS0-0.053-0.01228.7730.0090.0090.0000.0000.0000.000
94A169LYS10.8390.88727.4800.1830.1830.0000.0000.0000.000
95A170THR0-0.009-0.00933.0690.0030.0030.0000.0000.0000.000
96A171ASP-1-0.825-0.89036.061-0.123-0.1230.0000.0000.0000.000
97A172LEU0-0.034-0.00232.0040.0000.0000.0000.0000.0000.000
98A173PRO00.0390.01736.7120.0070.0070.0000.0000.0000.000
99A174MET00.0240.00237.951-0.004-0.0040.0000.0000.0000.000
100A175THR0-0.102-0.06938.9470.0020.0020.0000.0000.0000.000
101A176LEU00.0500.03532.254-0.002-0.0020.0000.0000.0000.000
102A177GLN0-0.052-0.03233.999-0.006-0.0060.0000.0000.0000.000
103A178LYS10.9390.96734.2100.0860.0860.0000.0000.0000.000
104A179CYS0-0.0050.02931.835-0.001-0.0010.0000.0000.0000.000
105A180ILE0-0.0030.00828.915-0.006-0.0060.0000.0000.0000.000
106A181ALA00.0300.01829.892-0.005-0.0050.0000.0000.0000.000
107A182LEU0-0.023-0.01231.1860.0020.0020.0000.0000.0000.000
108A183THR00.037-0.00526.7500.0020.0020.0000.0000.0000.000
109A184GLU-1-0.782-0.85626.083-0.190-0.1900.0000.0000.0000.000
110A185GLU-1-0.848-0.90327.093-0.103-0.1030.0000.0000.0000.000
111A186THR0-0.049-0.04929.3400.0030.0030.0000.0000.0000.000
112A187THR0-0.0180.00123.807-0.003-0.0030.0000.0000.0000.000
113A188LYS10.7930.88423.6450.0960.0960.0000.0000.0000.000
114A189GLY00.0030.00423.5010.0020.0020.0000.0000.0000.000
115A190ASN0-0.055-0.03220.9670.0270.0270.0000.0000.0000.000
116A191LYS10.8590.90217.7890.1040.1040.0000.0000.0000.000
117A192GLY00.0330.03815.8730.0050.0050.0000.0000.0000.000
118A193LEU00.0060.00512.8940.0070.0070.0000.0000.0000.000
119A194HIS0-0.0240.00514.5370.0820.0820.0000.0000.0000.000
120A195LEU00.0320.00715.796-0.064-0.0640.0000.0000.0000.000
121A196VAL0-0.001-0.00717.8330.0460.0460.0000.0000.0000.000
122A197ILE00.0230.00520.126-0.027-0.0270.0000.0000.0000.000
123A198ALA00.0000.00222.8600.0250.0250.0000.0000.0000.000
124A199LEU00.009-0.01624.456-0.002-0.0020.0000.0000.0000.000
125A200ASN0-0.036-0.01428.1640.0090.0090.0000.0000.0000.000
126A201TYR0-0.005-0.02423.462-0.002-0.0020.0000.0000.0000.000
127A202GLY00.0330.00027.250-0.001-0.0010.0000.0000.0000.000
128A203GLY00.0230.02225.4490.0070.0070.0000.0000.0000.000
129A204TYR0-0.031-0.03026.1300.0100.0100.0000.0000.0000.000
130A205TYR0-0.054-0.04728.5290.0160.0160.0000.0000.0000.000
131A206ASP-1-0.677-0.81424.085-0.220-0.2200.0000.0000.0000.000
132A207ILE00.0440.01825.2390.0110.0110.0000.0000.0000.000
133A208LEU0-0.030-0.00228.1610.0150.0150.0000.0000.0000.000
134A209GLN0-0.089-0.04927.3370.0220.0220.0000.0000.0000.000
135A210ALA00.0590.03727.4170.0100.0100.0000.0000.0000.000
136A211THR0-0.004-0.02529.4940.0110.0110.0000.0000.0000.000
137A212LYS10.9210.95932.0800.1210.1210.0000.0000.0000.000
138A213SER0-0.032-0.01931.1850.0120.0120.0000.0000.0000.000
139A214ILE00.0320.01628.7710.0080.0080.0000.0000.0000.000
140A215VAL00.0020.00033.1860.0070.0070.0000.0000.0000.000
141A216ASN0-0.061-0.04636.6050.0090.0090.0000.0000.0000.000
142A217LYS10.8340.90330.7460.1030.1030.0000.0000.0000.000
143A218ALA00.0400.03036.5670.0050.0050.0000.0000.0000.000
144A219MET0-0.079-0.04438.1910.0050.0050.0000.0000.0000.000
145A220ASN0-0.100-0.05139.7830.0050.0050.0000.0000.0000.000
146A221GLY00.0040.00640.8130.0030.0030.0000.0000.0000.000
147A222LEU0-0.079-0.04436.3060.0020.0020.0000.0000.0000.000
148A223LEU0-0.061-0.02332.268-0.002-0.0020.0000.0000.0000.000
149A224ASP-1-0.827-0.91435.691-0.044-0.0440.0000.0000.0000.000
150A225VAL0-0.060-0.05735.214-0.005-0.0050.0000.0000.0000.000
151A226GLU-1-0.977-0.98534.114-0.041-0.0410.0000.0000.0000.000
152A227ASP-1-0.832-0.89931.616-0.051-0.0510.0000.0000.0000.000
153A228ILE0-0.079-0.03330.073-0.010-0.0100.0000.0000.0000.000
154A229ASN0-0.009-0.01125.629-0.009-0.0090.0000.0000.0000.000
155A230LYS10.8690.90717.8790.2190.2190.0000.0000.0000.000
156A231ASN00.0520.01620.846-0.021-0.0210.0000.0000.0000.000
157A232LEU00.0220.02922.841-0.005-0.0050.0000.0000.0000.000
158A233PHE00.0520.01724.629-0.006-0.0060.0000.0000.0000.000
159A234ASP-1-0.815-0.89020.013-0.225-0.2250.0000.0000.0000.000
160A235GLN0-0.041-0.01621.503-0.009-0.0090.0000.0000.0000.000
161A236GLU-1-0.796-0.83924.348-0.110-0.1100.0000.0000.0000.000
162A237LEU0-0.0330.00222.527-0.001-0.0010.0000.0000.0000.000
163A238GLU-1-0.784-0.87623.819-0.194-0.1940.0000.0000.0000.000
164A239SER0-0.049-0.01019.092-0.021-0.0210.0000.0000.0000.000
165A240LYS10.7980.87318.5590.2070.2070.0000.0000.0000.000
166A241CYS0-0.031-0.00514.889-0.035-0.0350.0000.0000.0000.000
167A242PRO0-0.042-0.01710.4490.0450.0450.0000.0000.0000.000
168A243ASN00.0670.01312.5830.0040.0040.0000.0000.0000.000
169A244PRO0-0.0130.00111.018-0.073-0.0730.0000.0000.0000.000
170A245ASP-1-0.803-0.8766.667-1.627-1.6270.0000.0000.0000.000
171A246LEU0-0.009-0.0018.949-0.014-0.0140.0000.0000.0000.000
172A247LEU0-0.044-0.01711.2360.1310.1310.0000.0000.0000.000
173A248ILE00.0180.01112.696-0.018-0.0180.0000.0000.0000.000
174A249ARG10.7290.84416.1950.3780.3780.0000.0000.0000.000
175A250THR00.0220.01119.898-0.012-0.0120.0000.0000.0000.000
176A251GLY0-0.002-0.00922.0400.0180.0180.0000.0000.0000.000
177A252GLY0-0.054-0.02523.5420.0270.0270.0000.0000.0000.000
178A253ASP-1-0.809-0.88624.518-0.245-0.2450.0000.0000.0000.000
179A254GLN00.0020.00621.159-0.046-0.0460.0000.0000.0000.000
180A255ARG10.8310.90323.4240.2290.2290.0000.0000.0000.000
181A256VAL00.1100.05220.569-0.016-0.0160.0000.0000.0000.000
182A257SER0-0.054-0.04023.1870.0040.0040.0000.0000.0000.000
183A258ASN00.010-0.00426.806-0.002-0.0020.0000.0000.0000.000
184A259PHE00.0790.04218.9890.0120.0120.0000.0000.0000.000
185A260LEU00.0330.02017.6410.0250.0250.0000.0000.0000.000
186A261LEU0-0.057-0.03520.305-0.018-0.0180.0000.0000.0000.000
187A262TRP0-0.0110.00520.405-0.001-0.0010.0000.0000.0000.000
188A263GLN0-0.008-0.03017.241-0.013-0.0130.0000.0000.0000.000
189A264LEU00.002-0.00516.271-0.047-0.0470.0000.0000.0000.000
190A265ALA0-0.036-0.00217.068-0.028-0.0280.0000.0000.0000.000
191A266TYR0-0.031-0.02213.7940.0580.0580.0000.0000.0000.000
192A267THR0-0.063-0.02312.432-0.032-0.0320.0000.0000.0000.000
193A268GLU-1-0.776-0.8809.862-0.680-0.6800.0000.0000.0000.000
194A269PHE0-0.041-0.03512.229-0.014-0.0140.0000.0000.0000.000
195A270TYR0-0.034-0.03613.004-0.006-0.0060.0000.0000.0000.000
196A271PHE0-0.010-0.00815.0200.0270.0270.0000.0000.0000.000
197A272THR00.0580.03418.3210.0320.0320.0000.0000.0000.000
198A273LYS10.9540.95120.1800.2590.2590.0000.0000.0000.000
199A274THR0-0.0220.00520.7150.0370.0370.0000.0000.0000.000
200A275LEU0-0.010-0.00323.146-0.017-0.0170.0000.0000.0000.000
201A276PHE00.007-0.00820.663-0.003-0.0030.0000.0000.0000.000
202A277PRO00.028-0.00423.879-0.013-0.0130.0000.0000.0000.000
203A278ASP-1-0.850-0.91925.243-0.222-0.2220.0000.0000.0000.000
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