Manual

About

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: 76L5K

Calculation Name: 4HYN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4HYN

Chain ID: A

ChEMBL ID:

UniProt ID: G4FDE4

Base Structure: X-ray

Registration Date: 2023-09-24

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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2210531.546292
FMO2-HF: Nuclear repulsion 2131428.335286
FMO2-HF: Total energy -79103.211006
FMO2-MP2: Total energy -79327.441849


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:ALA)


Summations of interaction energy for fragment #1(A:1:ALA)
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.
-4.868-2.9460.06-0.966-1.015-0.002
Interaction energy analysis for fragmet #1(A:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.064 / q_NPA : -0.055
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].
3A24VAL0-0.069-0.0523.342-2.513-0.8990.013-0.882-0.745-0.002
4A25LEU0-0.040-0.0016.0620.4480.4480.0000.0000.0000.000
5A26THR0-0.041-0.0548.8310.2040.2040.0000.0000.0000.000
6A27PRO0-0.030-0.03210.7890.0110.0110.0000.0000.0000.000
7A28GLU-1-0.794-0.87413.401-0.151-0.1510.0000.0000.0000.000
8A29GLU-1-0.822-0.88811.892-0.563-0.5630.0000.0000.0000.000
9A30LYS10.8220.9079.2620.2280.2280.0000.0000.0000.000
10A31ASP-1-0.879-0.94315.3900.0070.0070.0000.0000.0000.000
11A32MET0-0.0460.00417.3250.0050.0050.0000.0000.0000.000
12A33ILE0-0.019-0.02116.7410.0080.0080.0000.0000.0000.000
13A34GLY00.0580.03019.5160.0130.0130.0000.0000.0000.000
14A35GLU-1-0.966-0.97921.523-0.053-0.0530.0000.0000.0000.000
15A36ILE0-0.026-0.02321.8600.0050.0050.0000.0000.0000.000
16A37GLY00.0320.02723.3580.0010.0010.0000.0000.0000.000
17A38ASN0-0.016-0.04024.4260.0120.0120.0000.0000.0000.000
18A39ILE0-0.023-0.00127.2720.0040.0040.0000.0000.0000.000
19A40ALA0-0.0110.00126.8960.0040.0040.0000.0000.0000.000
20A41MET00.0210.00127.1540.0000.0000.0000.0000.0000.000
21A42GLY00.0630.04429.2320.0070.0070.0000.0000.0000.000
22A43SER0-0.016-0.00431.9140.0050.0050.0000.0000.0000.000
23A44ALA00.004-0.00231.3300.0030.0030.0000.0000.0000.000
24A45ALA00.001-0.00132.8900.0030.0030.0000.0000.0000.000
25A46THR0-0.029-0.01734.5390.0050.0050.0000.0000.0000.000
26A47THR0-0.025-0.01836.5240.0030.0030.0000.0000.0000.000
27A48LEU0-0.012-0.01335.5710.0020.0020.0000.0000.0000.000
28A49SER0-0.011-0.02037.9660.0030.0030.0000.0000.0000.000
29A50MET0-0.040-0.02040.1310.0020.0020.0000.0000.0000.000
30A51ILE0-0.066-0.02839.5630.0010.0010.0000.0000.0000.000
31A52LEU0-0.049-0.01640.0450.0020.0020.0000.0000.0000.000
32A53GLY0-0.029-0.01543.9060.0000.0000.0000.0000.0000.000
33A54ARG10.7850.89341.9430.0090.0090.0000.0000.0000.000
34A55ASP-1-0.856-0.92040.507-0.016-0.0160.0000.0000.0000.000
35A56ILE0-0.067-0.03834.8810.0010.0010.0000.0000.0000.000
36A57HIS0-0.0110.01931.605-0.005-0.0050.0000.0000.0000.000
37A58ILE00.001-0.01328.3430.0000.0000.0000.0000.0000.000
38A59THR0-0.046-0.02026.3400.0030.0030.0000.0000.0000.000
39A60VAL00.0190.01421.103-0.002-0.0020.0000.0000.0000.000
40A61PRO0-0.078-0.02422.3630.0050.0050.0000.0000.0000.000
41A62THR0-0.026-0.02916.5850.0250.0250.0000.0000.0000.000
42A63VAL00.0050.00714.939-0.026-0.0260.0000.0000.0000.000
43A64ARG10.7340.84111.185-0.008-0.0080.0000.0000.0000.000
44A65GLU-1-0.727-0.8497.309-1.241-1.2410.0000.0000.0000.000
45A66GLU-1-0.834-0.8868.1200.1580.1580.0000.0000.0000.000
46A67LYS10.8660.9253.1980.9801.2880.047-0.084-0.2700.000
47A68MET0-0.0030.0088.0330.1580.1580.0000.0000.0000.000
48A69LYS10.7800.8637.9610.0970.0970.0000.0000.0000.000
49A70ASN0-0.070-0.0468.4600.0540.0540.0000.0000.0000.000
50A71VAL00.0570.04512.1600.0380.0380.0000.0000.0000.000
51A72LYS10.7860.88814.4830.0580.0580.0000.0000.0000.000
52A73SER0-0.039-0.04314.5820.0130.0130.0000.0000.0000.000
53A74ASP-1-0.833-0.88014.2570.0260.0260.0000.0000.0000.000
54A75PHE0-0.056-0.02417.3190.0040.0040.0000.0000.0000.000
55A76SER00.002-0.00220.9770.0060.0060.0000.0000.0000.000
56A77GLY0-0.0080.00424.005-0.004-0.0040.0000.0000.0000.000
57A78GLU-1-0.893-0.93626.976-0.026-0.0260.0000.0000.0000.000
58A79GLN0-0.030-0.02624.309-0.001-0.0010.0000.0000.0000.000
59A80VAL00.0060.01128.013-0.004-0.0040.0000.0000.0000.000
60A81VAL0-0.035-0.01723.797-0.002-0.0020.0000.0000.0000.000
61A82VAL00.023-0.00126.1100.0030.0030.0000.0000.0000.000
62A83SER0-0.025-0.00624.964-0.009-0.0090.0000.0000.0000.000
63A84VAL0-0.001-0.00125.4840.0100.0100.0000.0000.0000.000
64A85GLU-1-0.887-0.94724.083-0.202-0.2020.0000.0000.0000.000
65A86TYR0-0.026-0.01822.8120.0190.0190.0000.0000.0000.000
66A87THR0-0.019-0.04926.134-0.011-0.0110.0000.0000.0000.000
67A88GLU-1-0.803-0.87428.241-0.111-0.1110.0000.0000.0000.000
68A89GLY00.0290.03527.3020.0030.0030.0000.0000.0000.000
69A90LEU0-0.055-0.03821.608-0.019-0.0190.0000.0000.0000.000
70A91GLU-1-0.953-0.97422.580-0.184-0.1840.0000.0000.0000.000
71A92GLY00.0140.00820.826-0.033-0.0330.0000.0000.0000.000
72A93LEU0-0.0210.00620.6440.0180.0180.0000.0000.0000.000
73A94ASN0-0.027-0.02620.310-0.033-0.0330.0000.0000.0000.000
74A95VAL0-0.018-0.01420.8950.0170.0170.0000.0000.0000.000
75A96LEU00.0260.01521.784-0.004-0.0040.0000.0000.0000.000
76A97VAL0-0.037-0.02221.3970.0000.0000.0000.0000.0000.000
77A98LEU00.0480.01524.5320.0060.0060.0000.0000.0000.000
78A99ASP-1-0.794-0.89827.704-0.008-0.0080.0000.0000.0000.000
79A100LYS10.8890.93429.1680.0140.0140.0000.0000.0000.000
80A101LYS10.8530.91032.635-0.005-0.0050.0000.0000.0000.000
81A102LEU00.0130.00929.579-0.001-0.0010.0000.0000.0000.000
82A103VAL0-0.013-0.00931.592-0.002-0.0020.0000.0000.0000.000
83A104ALA0-0.012-0.00534.130-0.001-0.0010.0000.0000.0000.000
84A105VAL0-0.023-0.00336.0610.0000.0000.0000.0000.0000.000
85A106ILE00.010-0.00432.9950.0000.0000.0000.0000.0000.000
86A107ALA0-0.002-0.00637.345-0.001-0.0010.0000.0000.0000.000
87A108ASP-1-0.855-0.94139.461-0.012-0.0120.0000.0000.0000.000
88A109LEU0-0.025-0.00839.2550.0000.0000.0000.0000.0000.000
89A110MET0-0.026-0.00938.923-0.002-0.0020.0000.0000.0000.000
90A111MET0-0.093-0.04342.143-0.001-0.0010.0000.0000.0000.000
91A112GLY0-0.047-0.01245.0090.0010.0010.0000.0000.0000.000
92A113GLY0-0.036-0.00145.7320.0020.0020.0000.0000.0000.000
93A114SER0-0.132-0.09545.251-0.001-0.0010.0000.0000.0000.000
94A115GLY00.0710.02541.1910.0000.0000.0000.0000.0000.000
95A116GLU-1-0.880-0.93240.496-0.002-0.0020.0000.0000.0000.000
96A117VAL0-0.0170.00740.1800.0000.0000.0000.0000.0000.000
97A118GLU-1-0.984-0.99640.1950.0020.0020.0000.0000.0000.000
98A119THR0-0.099-0.07639.9840.0000.0000.0000.0000.0000.000
99A120GLU-1-0.812-0.90433.704-0.001-0.0010.0000.0000.0000.000
100A121GLU-1-0.903-0.91936.606-0.008-0.0080.0000.0000.0000.000
101A122LEU0-0.023-0.00233.960-0.001-0.0010.0000.0000.0000.000
102A123ASP-1-0.802-0.90938.722-0.022-0.0220.0000.0000.0000.000
103A124GLU-1-0.859-0.95038.429-0.037-0.0370.0000.0000.0000.000
104A125ILE0-0.071-0.01440.731-0.002-0.0020.0000.0000.0000.000
105A126LYS10.8970.93038.9380.0150.0150.0000.0000.0000.000
106A127LEU0-0.006-0.00634.668-0.001-0.0010.0000.0000.0000.000
107A128SER0-0.014-0.00336.900-0.004-0.0040.0000.0000.0000.000
108A129ALA0-0.031-0.00739.357-0.002-0.0020.0000.0000.0000.000
109A130VAL00.0190.00133.637-0.001-0.0010.0000.0000.0000.000
110A131GLY00.0120.00534.794-0.004-0.0040.0000.0000.0000.000
111A132GLU-1-0.836-0.91235.656-0.051-0.0510.0000.0000.0000.000
112A133ALA00.002-0.00235.814-0.001-0.0010.0000.0000.0000.000
113A134MET0-0.034-0.01630.149-0.004-0.0040.0000.0000.0000.000
114A135ASN0-0.081-0.03732.926-0.010-0.0100.0000.0000.0000.000
115A136GLN00.002-0.01634.958-0.006-0.0060.0000.0000.0000.000
116A137MET0-0.0430.00831.8220.0010.0010.0000.0000.0000.000
117A138MET00.017-0.00926.842-0.002-0.0020.0000.0000.0000.000
118A139GLY00.0380.03230.969-0.007-0.0070.0000.0000.0000.000
119A140SER0-0.012-0.00533.416-0.004-0.0040.0000.0000.0000.000
120A141ALA00.0040.01328.262-0.002-0.0020.0000.0000.0000.000
121A142ALA00.0240.01028.749-0.006-0.0060.0000.0000.0000.000
122A143THR0-0.020-0.01929.782-0.004-0.0040.0000.0000.0000.000
123A144SER0-0.012-0.01531.146-0.001-0.0010.0000.0000.0000.000
124A145LEU0-0.0040.00024.200-0.002-0.0020.0000.0000.0000.000
125A146SER0-0.011-0.01128.112-0.008-0.0080.0000.0000.0000.000
126A147GLU-1-0.938-0.96630.360-0.068-0.0680.0000.0000.0000.000
127A148LEU0-0.036-0.00925.8310.0000.0000.0000.0000.0000.000
128A149LEU00.0230.00323.484-0.002-0.0020.0000.0000.0000.000
129A150GLY0-0.096-0.03727.186-0.002-0.0020.0000.0000.0000.000
130A151ILE0-0.051-0.02126.7370.0010.0010.0000.0000.0000.000
131A152THR0-0.017-0.01530.0770.0010.0010.0000.0000.0000.000
132A153ILE00.0030.01026.319-0.010-0.0100.0000.0000.0000.000
133A154ASN0-0.060-0.02829.5830.0130.0130.0000.0000.0000.000
134A155ILE00.001-0.00928.340-0.012-0.0120.0000.0000.0000.000
135A156SER0-0.0270.00429.8010.0040.0040.0000.0000.0000.000
136A157PRO0-0.001-0.00731.5900.0010.0010.0000.0000.0000.000
137A158PRO00.0280.00730.474-0.006-0.0060.0000.0000.0000.000
138A159LYS10.7880.88627.0960.1080.1080.0000.0000.0000.000
139A160VAL00.0070.00429.435-0.004-0.0040.0000.0000.0000.000
140A161GLU-1-0.831-0.89426.949-0.092-0.0920.0000.0000.0000.000
141A162ILE00.004-0.00329.5170.0010.0010.0000.0000.0000.000
142A163LEU0-0.015-0.00122.918-0.002-0.0020.0000.0000.0000.000
143A164ASN00.001-0.01827.0490.0070.0070.0000.0000.0000.000
144A165PHE00.0160.01120.396-0.005-0.0050.0000.0000.0000.000
145A166ASP-1-0.815-0.90223.6530.0110.0110.0000.0000.0000.000
146A167ASP-1-0.837-0.90026.048-0.024-0.0240.0000.0000.0000.000
147A168PRO0-0.046-0.01823.795-0.006-0.0060.0000.0000.0000.000
148A169ASN0-0.109-0.07723.354-0.008-0.0080.0000.0000.0000.000
149A170THR0-0.017-0.00724.445-0.011-0.0110.0000.0000.0000.000
150A171GLN0-0.031-0.01720.625-0.011-0.0110.0000.0000.0000.000
151A172PHE00.0500.02718.1020.0080.0080.0000.0000.0000.000
152A173PRO00.0340.01919.925-0.013-0.0130.0000.0000.0000.000
153A174PRO0-0.0030.00018.540-0.015-0.0150.0000.0000.0000.000
154A175VAL0-0.0040.00515.827-0.012-0.0120.0000.0000.0000.000
155A176THR00.010-0.01111.747-0.017-0.0170.0000.0000.0000.000
156A177ASP-1-0.867-0.91115.208-0.431-0.4310.0000.0000.0000.000
157A178ASN0-0.007-0.01711.5200.0060.0060.0000.0000.0000.000
158A179PRO00.0310.01111.810-0.058-0.0580.0000.0000.0000.000
159A180GLU-1-0.796-0.8856.510-0.263-0.2630.0000.0000.0000.000
160A181LYS10.7620.8756.8720.2870.2870.0000.0000.0000.000
161A182ASP-1-0.836-0.9335.726-1.949-1.9490.0000.0000.0000.000
162A183VAL0-0.037-0.0128.6610.1300.1300.0000.0000.0000.000
163A184ALA00.0190.01210.859-0.041-0.0410.0000.0000.0000.000
164A185VAL0-0.006-0.00513.2760.0270.0270.0000.0000.0000.000
165A186VAL0-0.003-0.00415.5230.0270.0270.0000.0000.0000.000
166A187GLU-1-0.793-0.86118.6150.0300.0300.0000.0000.0000.000
167A188PHE0-0.001-0.01221.236-0.001-0.0010.0000.0000.0000.000
168A189GLU-1-0.881-0.93524.8630.0210.0210.0000.0000.0000.000
169A190MET0-0.013-0.00927.517-0.007-0.0070.0000.0000.0000.000
170A191GLU-1-0.881-0.93531.0330.0100.0100.0000.0000.0000.000
171A192ILE00.0510.01834.409-0.003-0.0030.0000.0000.0000.000
172A193GLU-1-0.864-0.92337.753-0.004-0.0040.0000.0000.0000.000
173A194GLY0-0.018-0.01141.160-0.001-0.0010.0000.0000.0000.000
174A195LEU0-0.0030.00438.4400.0000.0000.0000.0000.0000.000
175A196PRO0-0.051-0.02435.9190.0020.0020.0000.0000.0000.000
176A197LYS10.7890.88630.549-0.018-0.0180.0000.0000.0000.000
177A198SER0-0.030-0.00731.1740.0000.0000.0000.0000.0000.000
178A199LYS10.8650.91223.415-0.021-0.0210.0000.0000.0000.000
179A200PHE0-0.0050.01425.5300.0020.0020.0000.0000.0000.000
180A201TYR0-0.025-0.03519.9120.0060.0060.0000.0000.0000.000
181A202GLN00.0270.02520.8560.0050.0050.0000.0000.0000.000
182A203VAL0-0.053-0.01615.458-0.005-0.0050.0000.0000.0000.000
183A204ILE00.0730.02916.5420.0100.0100.0000.0000.0000.000
184A205SER00.0500.02413.893-0.036-0.0360.0000.0000.0000.000
185A206ALA00.004-0.00710.1320.0310.0310.0000.0000.0000.000
186A207ASP-1-0.859-0.92412.064-0.659-0.6590.0000.0000.0000.000
187A208LEU00.0140.01114.0220.0420.0420.0000.0000.0000.000
188A209VAL00.0340.01614.0760.0420.0420.0000.0000.0000.000
189A210LYS10.9350.96012.7270.5320.5320.0000.0000.0000.000
190A211LYS10.7890.89615.0680.3070.3070.0000.0000.0000.000
191A212MET0-0.0010.00218.5830.0360.0360.0000.0000.0000.000
192A213TYR00.007-0.03615.6820.0350.0350.0000.0000.0000.000
193A214GLU-1-0.836-0.88618.205-0.301-0.3010.0000.0000.0000.000
194A215TYR0-0.075-0.06120.2930.0210.0210.0000.0000.0000.000
195A216PHE00.0220.01620.6400.0160.0160.0000.0000.0000.000
196A217THR00.020-0.00819.0280.0190.0190.0000.0000.0000.000
197A218LYS10.7850.89322.2670.1260.1260.0000.0000.0000.000
198A219LYS10.8490.89725.0730.1110.1110.0000.0000.0000.000
199A220GLN0-0.022-0.00222.6170.0020.0020.0000.0000.0000.000
200A221SER0-0.055-0.03224.8510.0100.0100.0000.0000.0000.000
201A222GLU-1-0.911-0.92127.222-0.088-0.0880.0000.0000.0000.000
202A223ALA0-0.038-0.01430.2750.0060.0060.0000.0000.0000.000