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: R9N58

Calculation Name: 3HFD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HFD

Chain ID: A

ChEMBL ID:

UniProt ID:

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 OptHSide
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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2610615.434877
FMO2-HF: Nuclear repulsion 2520558.549626
FMO2-HF: Total energy -90056.885251
FMO2-MP2: Total energy -90325.40759


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:33:THR)


Summations of interaction energy for fragment #1(A:33:THR)
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.
-3.133-0.2040.004-1.469-1.4640
Interaction energy analysis for fragmet #1(A:33:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.077 / q_NPA : -0.073
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].
3A35LEU0-0.0090.0053.454-0.2842.6450.004-1.469-1.4640.000
4A36THR00.028-0.0215.818-0.313-0.3130.0000.0000.0000.000
5A37GLU-1-0.798-0.9158.4571.4541.4540.0000.0000.0000.000
6A38GLU-1-0.874-0.91510.5450.5930.5930.0000.0000.0000.000
7A39GLN00.0130.0108.4800.1660.1660.0000.0000.0000.000
8A40LYS10.8390.9155.321-1.413-1.4130.0000.0000.0000.000
9A41GLU-1-0.786-0.8778.4960.9370.9370.0000.0000.0000.000
10A42THR0-0.073-0.03711.474-0.185-0.1850.0000.0000.0000.000
11A43LEU00.0380.0255.866-0.135-0.1350.0000.0000.0000.000
12A44LYS10.8280.9019.989-1.179-1.1790.0000.0000.0000.000
13A45LYS10.9510.98711.986-0.896-0.8960.0000.0000.0000.000
14A46LEU00.0470.02411.961-0.108-0.1080.0000.0000.0000.000
15A47LYS10.9090.9479.159-1.700-1.7000.0000.0000.0000.000
16A48LEU0-0.025-0.01112.819-0.119-0.1190.0000.0000.0000.000
17A49TYR00.032-0.00716.205-0.062-0.0620.0000.0000.0000.000
18A50GLN0-0.0080.01514.673-0.059-0.0590.0000.0000.0000.000
19A51LYS10.8040.90116.773-0.544-0.5440.0000.0000.0000.000
20A52GLU-1-0.826-0.91718.2740.3610.3610.0000.0000.0000.000
21A53TYR0-0.095-0.05819.851-0.039-0.0390.0000.0000.0000.000
22A54TYR00.0230.00416.1890.0020.0020.0000.0000.0000.000
23A55ASP-1-0.834-0.89221.6020.4000.4000.0000.0000.0000.000
24A56TYR0-0.070-0.06324.345-0.050-0.0500.0000.0000.0000.000
25A57GLU-1-0.839-0.89522.8400.3550.3550.0000.0000.0000.000
26A58SER0-0.001-0.00824.960-0.026-0.0260.0000.0000.0000.000
27A59LYS10.8500.93326.994-0.334-0.3340.0000.0000.0000.000
28A60PHE00.0540.03329.487-0.022-0.0220.0000.0000.0000.000
29A61GLU-1-0.917-0.96127.9430.2300.2300.0000.0000.0000.000
30A62TYR0-0.033-0.01531.175-0.018-0.0180.0000.0000.0000.000
31A63GLU-1-0.921-0.96633.3390.1800.1800.0000.0000.0000.000
32A64LEU0-0.058-0.02633.172-0.015-0.0150.0000.0000.0000.000
33A65PHE0-0.020-0.02532.873-0.013-0.0130.0000.0000.0000.000
34A66LEU0-0.012-0.00336.850-0.011-0.0110.0000.0000.0000.000
35A67LEU0-0.035-0.00839.099-0.010-0.0100.0000.0000.0000.000
36A68ARG10.9740.97235.229-0.155-0.1550.0000.0000.0000.000
37A69GLN00.0090.01240.022-0.012-0.0120.0000.0000.0000.000
38A70LYS10.9540.98343.027-0.117-0.1170.0000.0000.0000.000
39A71TYR0-0.022-0.02944.720-0.004-0.0040.0000.0000.0000.000
40A72HIS0-0.040-0.01444.917-0.006-0.0060.0000.0000.0000.000
41A73ASP-1-0.873-0.93846.7230.0910.0910.0000.0000.0000.000
42A74LEU0-0.075-0.03448.568-0.004-0.0040.0000.0000.0000.000
43A75TYR0-0.037-0.01446.426-0.003-0.0030.0000.0000.0000.000
44A76GLY00.0650.04251.159-0.004-0.0040.0000.0000.0000.000
45A77PRO00.0590.02552.940-0.003-0.0030.0000.0000.0000.000
46A78ILE0-0.041-0.02153.919-0.004-0.0040.0000.0000.0000.000
47A79TYR00.0270.01049.795-0.003-0.0030.0000.0000.0000.000
48A80ASP-1-0.824-0.89356.1960.0610.0610.0000.0000.0000.000
49A81LYS10.9210.95758.568-0.064-0.0640.0000.0000.0000.000
50A82ARG10.8290.92454.724-0.063-0.0630.0000.0000.0000.000
51A83ARG10.8480.91158.010-0.057-0.0570.0000.0000.0000.000
52A84GLU-1-0.886-0.95761.2460.0480.0480.0000.0000.0000.000
53A85ALA0-0.034-0.01164.049-0.002-0.0020.0000.0000.0000.000
54A86LEU0-0.0230.00261.320-0.002-0.0020.0000.0000.0000.000
55A87VAL0-0.044-0.03063.250-0.002-0.0020.0000.0000.0000.000
56A88GLY00.0290.03166.239-0.001-0.0010.0000.0000.0000.000
57A89ASN0-0.068-0.04666.585-0.002-0.0020.0000.0000.0000.000
58A90GLY00.0390.03368.5770.0000.0000.0000.0000.0000.000
59A91GLU-1-0.983-1.00271.0780.0300.0300.0000.0000.0000.000
60A92ALA00.0270.01368.2530.0010.0010.0000.0000.0000.000
61A93LYS10.9080.95670.130-0.030-0.0300.0000.0000.0000.000
62A94ILE00.0010.00068.332-0.001-0.0010.0000.0000.0000.000
63A95GLY00.0570.03065.2100.0010.0010.0000.0000.0000.000
64A96THR0-0.079-0.04362.7550.0000.0000.0000.0000.0000.000
65A97PRO0-0.0110.00365.7980.0000.0000.0000.0000.0000.000
66A98ASN0-0.050-0.02268.384-0.002-0.0020.0000.0000.0000.000
67A99LEU0-0.078-0.03664.9260.0000.0000.0000.0000.0000.000
68A100PRO00.0300.01266.5970.0010.0010.0000.0000.0000.000
69A101GLU-1-0.852-0.91365.2350.0330.0330.0000.0000.0000.000
70A102PHE00.0120.00959.2960.0010.0010.0000.0000.0000.000
71A103TRP00.011-0.00655.4260.0020.0020.0000.0000.0000.000
72A104LEU00.0170.02359.0910.0010.0010.0000.0000.0000.000
73A105ARG10.9350.94059.933-0.034-0.0340.0000.0000.0000.000
74A106ALA0-0.0180.00257.7020.0000.0000.0000.0000.0000.000
75A107LEU0-0.049-0.04254.2400.0020.0020.0000.0000.0000.000
76A108ARG10.8040.88055.974-0.034-0.0340.0000.0000.0000.000
77A109ASN0-0.044-0.01257.951-0.002-0.0020.0000.0000.0000.000
78A110ASN0-0.038-0.01550.3370.0010.0010.0000.0000.0000.000
79A111ASN00.002-0.01551.5700.0000.0000.0000.0000.0000.000
80A112THR0-0.0150.00147.066-0.002-0.0020.0000.0000.0000.000
81A113VAL0-0.030-0.03250.247-0.001-0.0010.0000.0000.0000.000
82A114SER00.0030.00852.104-0.003-0.0030.0000.0000.0000.000
83A115HIS0-0.0120.00850.744-0.002-0.0020.0000.0000.0000.000
84A116VAL00.004-0.00450.368-0.002-0.0020.0000.0000.0000.000
85A117ILE0-0.084-0.02453.730-0.001-0.0010.0000.0000.0000.000
86A118GLU-1-0.846-0.92156.8990.0280.0280.0000.0000.0000.000
87A119ASP-1-0.853-0.94259.6180.0290.0290.0000.0000.0000.000
88A120HIS0-0.061-0.04659.543-0.001-0.0010.0000.0000.0000.000
89A121ASP-1-0.727-0.83358.2360.0340.0340.0000.0000.0000.000
90A122GLU-1-0.866-0.91261.4620.0340.0340.0000.0000.0000.000
91A123GLU-1-0.875-0.95263.5090.0270.0270.0000.0000.0000.000
92A124ILE0-0.022-0.02661.2540.0000.0000.0000.0000.0000.000
93A125LEU0-0.016-0.02357.5790.0010.0010.0000.0000.0000.000
94A126VAL00.0100.01861.5870.0010.0010.0000.0000.0000.000
95A127TYR0-0.043-0.01964.2340.0000.0000.0000.0000.0000.000
96A128LEU0-0.0430.00057.2550.0010.0010.0000.0000.0000.000
97A129ASN00.0400.00061.397-0.001-0.0010.0000.0000.0000.000
98A130ASP-1-0.879-0.96857.3340.0570.0570.0000.0000.0000.000
99A131ILE0-0.0210.00652.283-0.001-0.0010.0000.0000.0000.000
100A132ARG10.8930.95752.108-0.064-0.0640.0000.0000.0000.000
101A133CYS00.010-0.00145.7720.0010.0010.0000.0000.0000.000
102A134ASP-1-0.927-0.93446.9000.0750.0750.0000.0000.0000.000
103A135TYR00.0510.01841.1030.0030.0030.0000.0000.0000.000
104A136ILE00.0050.00040.443-0.004-0.0040.0000.0000.0000.000
105A137LYS10.9100.95841.560-0.083-0.0830.0000.0000.0000.000
106A138LYS10.8430.92337.034-0.109-0.1090.0000.0000.0000.000
107A139ASN0-0.0050.00439.2820.0050.0050.0000.0000.0000.000
108A140LYS10.8010.86731.367-0.176-0.1760.0000.0000.0000.000
109A141GLU-1-0.831-0.87732.4950.1710.1710.0000.0000.0000.000
110A142LYN0-0.017-0.00328.5170.0120.0120.0000.0000.0000.000
111A143LYS10.8810.94730.004-0.119-0.1190.0000.0000.0000.000
112A144GLU-1-0.740-0.88732.6750.1350.1350.0000.0000.0000.000
113A145GLY00.032-0.00436.149-0.003-0.0030.0000.0000.0000.000
114A146PHE0-0.041-0.03138.8420.0030.0030.0000.0000.0000.000
115A147ILE00.0020.01242.494-0.002-0.0020.0000.0000.0000.000
116A148LEU0-0.0080.01445.9550.0010.0010.0000.0000.0000.000
117A149SER0-0.018-0.02348.451-0.003-0.0030.0000.0000.0000.000
118A150PHE00.0290.00450.3490.0000.0000.0000.0000.0000.000
119A151HIS00.0110.00355.0370.0000.0000.0000.0000.0000.000
120A152PHE00.0320.00857.0280.0000.0000.0000.0000.0000.000
121A153ALA0-0.0130.00161.3680.0000.0000.0000.0000.0000.000
122A154PRO00.004-0.01964.995-0.001-0.0010.0000.0000.0000.000
123A155ASN00.0160.01863.185-0.002-0.0020.0000.0000.0000.000
124A156PRO0-0.020-0.01467.2340.0000.0000.0000.0000.0000.000
125A157PHE0-0.0120.00363.770-0.001-0.0010.0000.0000.0000.000
126A158PHE00.0370.00159.911-0.001-0.0010.0000.0000.0000.000
127A159SER0-0.0270.00162.8990.0010.0010.0000.0000.0000.000
128A160ASN0-0.026-0.00657.8040.0000.0000.0000.0000.0000.000
129A161SER00.0440.02160.4140.0000.0000.0000.0000.0000.000
130A162VAL0-0.034-0.03354.5210.0010.0010.0000.0000.0000.000
131A163LEU00.0040.03254.186-0.001-0.0010.0000.0000.0000.000
132A164THR00.002-0.01149.5700.0010.0010.0000.0000.0000.000
133A165LYS10.8220.90244.657-0.061-0.0610.0000.0000.0000.000
134A166THR0-0.050-0.03042.4360.0030.0030.0000.0000.0000.000
135A167TYR00.012-0.01539.991-0.001-0.0010.0000.0000.0000.000
136A168HIS0-0.056-0.03737.1070.0130.0130.0000.0000.0000.000
137A169MET00.0190.00234.501-0.003-0.0030.0000.0000.0000.000
138A170LYS10.9000.94926.581-0.195-0.1950.0000.0000.0000.000
139A178PRO00.012-0.02231.0970.0010.0010.0000.0000.0000.000
140A179VAL0-0.0060.01828.323-0.008-0.0080.0000.0000.0000.000
141A180LEU00.0230.01131.7690.0030.0030.0000.0000.0000.000
142A181LEU0-0.085-0.03531.158-0.001-0.0010.0000.0000.0000.000
143A182HIS0-0.014-0.01834.642-0.009-0.0090.0000.0000.0000.000
144A183THR00.0400.02438.2970.0040.0040.0000.0000.0000.000
145A184GLU-1-0.873-0.92941.8680.0690.0690.0000.0000.0000.000
146A185ALA00.0280.03745.0780.0030.0030.0000.0000.0000.000
147A186THR0-0.051-0.00648.585-0.001-0.0010.0000.0000.0000.000
148A187VAL00.010-0.01252.014-0.001-0.0010.0000.0000.0000.000
149A188ILE0-0.0060.01054.2200.0000.0000.0000.0000.0000.000
150A189ASP-1-0.896-0.93657.2310.0340.0340.0000.0000.0000.000
151A190TRP0-0.027-0.03957.680-0.001-0.0010.0000.0000.0000.000
152A191TYR0-0.0150.00262.463-0.001-0.0010.0000.0000.0000.000
153A192ASP-1-0.879-0.95766.0880.0200.0200.0000.0000.0000.000
154A193ASN0-0.113-0.05667.907-0.001-0.0010.0000.0000.0000.000
155A194LYS10.8400.93466.183-0.026-0.0260.0000.0000.0000.000
156A195ASN0-0.0120.00059.4510.0010.0010.0000.0000.0000.000
157A196ILE00.0600.04160.084-0.001-0.0010.0000.0000.0000.000
158A197LEU00.0210.03755.634-0.001-0.0010.0000.0000.0000.000
159A198LYS10.9000.95758.984-0.024-0.0240.0000.0000.0000.000
160A199LYS10.8310.93061.395-0.015-0.0150.0000.0000.0000.000
161A200ASN00.012-0.00364.2440.0000.0000.0000.0000.0000.000
162A201VAL00.0830.09167.545-0.001-0.0010.0000.0000.0000.000
163A202VAL0-0.049-0.04170.3390.0000.0000.0000.0000.0000.000
164A203LYS10.9000.90473.005-0.010-0.0100.0000.0000.0000.000
165A216VAL00.0240.00373.0510.0000.0000.0000.0000.0000.000
166A217GLN00.0710.07369.5670.0000.0000.0000.0000.0000.000
167A218GLN00.0150.00768.532-0.001-0.0010.0000.0000.0000.000
168A219THR00.0010.00063.8380.0010.0010.0000.0000.0000.000
169A220VAL00.047-0.00460.713-0.001-0.0010.0000.0000.0000.000
170A221ASN0-0.040-0.02856.4690.0010.0010.0000.0000.0000.000
171A222ARG10.8650.93358.239-0.025-0.0250.0000.0000.0000.000
172A223ASP-1-0.866-0.91453.7510.0280.0280.0000.0000.0000.000
173A224SER0-0.029-0.04855.1450.0000.0000.0000.0000.0000.000
174A225PHE00.1010.04452.2270.0010.0010.0000.0000.0000.000
175A226PHE0-0.031-0.03453.1780.0020.0020.0000.0000.0000.000
176A227HIS0-0.018-0.01351.4700.0010.0010.0000.0000.0000.000
177A228PHE00.0060.00746.8140.0020.0020.0000.0000.0000.000
178A229PHE0-0.051-0.01748.8350.0030.0030.0000.0000.0000.000
179A230THR0-0.027-0.00947.644-0.003-0.0030.0000.0000.0000.000
180A231SER0-0.004-0.00944.6570.0030.0030.0000.0000.0000.000
181A232HIS00.0280.01641.251-0.001-0.0010.0000.0000.0000.000
182A233LYS10.9060.92938.070-0.045-0.0450.0000.0000.0000.000
183A234VAL00.0910.03833.270-0.001-0.0010.0000.0000.0000.000
184A235PRO0-0.0160.02431.9550.0040.0040.0000.0000.0000.000
185A247GLU-1-0.950-0.98738.3240.0040.0040.0000.0000.0000.000
186A248VAL00.007-0.02633.6540.0040.0040.0000.0000.0000.000
187A249ALA00.0720.05937.1110.0050.0050.0000.0000.0000.000
188A250GLN00.0420.02538.7490.0040.0040.0000.0000.0000.000
189A251LEU0-0.053-0.03138.1600.0030.0030.0000.0000.0000.000
190A252GLU-1-0.935-0.96634.1670.0620.0620.0000.0000.0000.000
191A253MET00.000-0.00338.1870.0030.0030.0000.0000.0000.000
192A254ILE0-0.016-0.01341.2920.0010.0010.0000.0000.0000.000
193A255ILE0-0.044-0.02937.1090.0020.0020.0000.0000.0000.000
194A256GLU-1-0.933-0.96736.9280.0690.0690.0000.0000.0000.000
195A257GLY00.0090.01340.1980.0020.0020.0000.0000.0000.000
196A258ASP-1-0.818-0.87843.2260.0610.0610.0000.0000.0000.000
197A259TYR00.017-0.01538.1320.0030.0030.0000.0000.0000.000
198A260GLU-1-0.865-0.92042.0770.0640.0640.0000.0000.0000.000
199A261VAL00.0250.02043.5320.0010.0010.0000.0000.0000.000
200A262ALA0-0.012-0.00743.6840.0010.0010.0000.0000.0000.000
201A263LEU0-0.0170.00740.4700.0020.0020.0000.0000.0000.000
202A264THR0-0.007-0.01543.9810.0020.0020.0000.0000.0000.000
203A265ILE00.0180.00747.0970.0000.0000.0000.0000.0000.000
204A266LYS10.8530.91541.341-0.100-0.1000.0000.0000.0000.000
205A267GLU-1-0.899-0.95141.7880.1030.1030.0000.0000.0000.000
206A268ARG10.9240.95844.532-0.073-0.0730.0000.0000.0000.000
207A269ILE00.0030.01249.369-0.002-0.0020.0000.0000.0000.000
208A270ILE00.0060.01049.376-0.001-0.0010.0000.0000.0000.000
209A271PRO0-0.0040.00248.399-0.002-0.0020.0000.0000.0000.000
210A272TYR0-0.0020.00247.6860.0000.0000.0000.0000.0000.000
211A273ALA00.0010.02754.119-0.003-0.0030.0000.0000.0000.000
212A274VAL00.0660.00656.425-0.002-0.0020.0000.0000.0000.000
213A275ASP-1-0.885-0.92456.2880.0560.0560.0000.0000.0000.000
214A276TYR00.001-0.00851.4210.0000.0000.0000.0000.0000.000
215A277PHE0-0.033-0.01457.616-0.002-0.0020.0000.0000.0000.000
216A278LEU0-0.066-0.05261.046-0.002-0.0020.0000.0000.0000.000
217A279GLY0-0.0020.02360.211-0.001-0.0010.0000.0000.0000.000
218A280ILE0-0.070-0.03558.339-0.001-0.0010.0000.0000.0000.000
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