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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: 2JVNR

Calculation Name: 2HL8-A-Xray372

Preferred Name:

Target Type:

Ligand Name: 3-sulfinoalanine

ligand 3-letter code: CSD

PDB ID: 2HL8

Chain ID: A

ChEMBL ID:

UniProt ID: Q02724

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 OptH
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 221
LigandCharge CSD=-1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2883373.39935
FMO2-HF: Nuclear repulsion 2792697.178892
FMO2-HF: Total energy -90676.220458
FMO2-MP2: Total energy -90938.495306


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:401:GLY)


Summations of interaction energy for fragment #1(A:401:GLY)
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.
0.7151.78-0.016-0.504-0.5460.001
Interaction energy analysis for fragmet #1(A:401:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : -0.012
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].
3A403LEU00.0290.0293.8340.5601.625-0.016-0.504-0.5460.001
4A404VAL0-0.0200.0076.8310.2370.2370.0000.0000.0000.000
5A405PRO00.0080.0008.687-0.319-0.3190.0000.0000.0000.000
6A406GLU-1-0.963-0.9759.694-0.669-0.6690.0000.0000.0000.000
7A407LEU0-0.057-0.02011.6500.0640.0640.0000.0000.0000.000
8A408ASN00.0520.03314.942-0.013-0.0130.0000.0000.0000.000
9A409GLU-1-0.843-0.94316.660-0.224-0.2240.0000.0000.0000.000
10A410LYS10.9090.96220.0780.1000.1000.0000.0000.0000.000
11A411ASP-1-0.902-0.96117.925-0.124-0.1240.0000.0000.0000.000
12A412ASP-1-0.854-0.94818.721-0.246-0.2460.0000.0000.0000.000
13A413ASP-1-0.824-0.90420.443-0.106-0.1060.0000.0000.0000.000
14A414GLN0-0.031-0.01623.1420.0070.0070.0000.0000.0000.000
15A415VAL0-0.006-0.00620.7190.0130.0130.0000.0000.0000.000
16A416GLN00.0420.01524.0420.0130.0130.0000.0000.0000.000
17A417LYS10.8420.90726.1080.1090.1090.0000.0000.0000.000
18A418ALA00.0050.00927.0070.0070.0070.0000.0000.0000.000
19A419LEU0-0.031-0.01824.7110.0060.0060.0000.0000.0000.000
20A420ALA00.010-0.00328.8720.0050.0050.0000.0000.0000.000
21A421SER0-0.0200.00631.5800.0080.0080.0000.0000.0000.000
22A422ARG10.8570.91433.4350.0710.0710.0000.0000.0000.000
23A423GLU-1-0.764-0.82734.333-0.040-0.0400.0000.0000.0000.000
24A424ASN0-0.195-0.16436.0590.0010.0010.0000.0000.0000.000
25A425THR0-0.071-0.03335.9870.0020.0020.0000.0000.0000.000
26A426GLN00.0710.03533.2260.0020.0020.0000.0000.0000.000
27A427LEU0-0.084-0.03927.671-0.002-0.0020.0000.0000.0000.000
28A428MET0-0.026-0.00925.9360.0000.0000.0000.0000.0000.000
29A429ASN0-0.037-0.01329.5810.0040.0040.0000.0000.0000.000
30A430ARG10.9440.97026.509-0.005-0.0050.0000.0000.0000.000
31A431ASP-1-0.883-0.91327.8750.0350.0350.0000.0000.0000.000
32A432ASN0-0.067-0.05930.1650.0040.0040.0000.0000.0000.000
33A433ILE00.0360.03626.721-0.001-0.0010.0000.0000.0000.000
34A434GLU-1-0.922-0.96530.184-0.021-0.0210.0000.0000.0000.000
35A435ILE00.0150.01426.078-0.003-0.0030.0000.0000.0000.000
36A436THR00.0660.03830.155-0.002-0.0020.0000.0000.0000.000
37A437VAL00.0610.03330.442-0.005-0.0050.0000.0000.0000.000
38A438ARG10.9490.97530.9120.0400.0400.0000.0000.0000.000
39A439ASP-1-0.773-0.87529.306-0.049-0.0490.0000.0000.0000.000
40A440PHE00.0220.03523.936-0.008-0.0080.0000.0000.0000.000
41A441LYN0-0.040-0.02026.502-0.012-0.0120.0000.0000.0000.000
42A442THR0-0.122-0.08927.637-0.007-0.0070.0000.0000.0000.000
43A443LEU00.0440.02421.146-0.006-0.0060.0000.0000.0000.000
44A444ALA0-0.0450.00123.231-0.022-0.0220.0000.0000.0000.000
45A445PRO00.025-0.00923.4220.0000.0000.0000.0000.0000.000
46A446ARG10.9010.94324.5950.1770.1770.0000.0000.0000.000
47A447ARG10.9100.98526.1900.1010.1010.0000.0000.0000.000
48A448TRP00.019-0.00326.232-0.010-0.0100.0000.0000.0000.000
49A449LEU0-0.012-0.00621.7920.0050.0050.0000.0000.0000.000
50A450ASN0-0.013-0.02126.4100.0060.0060.0000.0000.0000.000
51A451ASP-1-0.803-0.92727.378-0.030-0.0300.0000.0000.0000.000
52A452THR00.0080.01228.0180.0050.0050.0000.0000.0000.000
53A453ILE00.0100.01323.1520.0030.0030.0000.0000.0000.000
54A454ILE00.0010.00423.3520.0000.0000.0000.0000.0000.000
55A455GLU-1-0.902-0.95723.6480.0100.0100.0000.0000.0000.000
56A456PHE0-0.018-0.02620.2580.0120.0120.0000.0000.0000.000
57A457PHE00.026-0.00114.9630.0080.0080.0000.0000.0000.000
58A458MET0-0.0030.01019.8200.0200.0200.0000.0000.0000.000
59A459LYS10.8590.94221.601-0.020-0.0200.0000.0000.0000.000
60A460TYR00.0420.00213.7740.0110.0110.0000.0000.0000.000
61A461ILE0-0.0020.02715.6600.0170.0170.0000.0000.0000.000
62A462GLU-1-0.799-0.86718.2130.0920.0920.0000.0000.0000.000
63A463LYS10.7950.88020.761-0.031-0.0310.0000.0000.0000.000
64A464SER0-0.089-0.04315.4350.0130.0130.0000.0000.0000.000
65A465THR00.021-0.00615.5590.0470.0470.0000.0000.0000.000
66A466PRO0-0.0130.00316.503-0.030-0.0300.0000.0000.0000.000
67A467ASN0-0.030-0.02119.770-0.008-0.0080.0000.0000.0000.000
68A468THR00.0240.02219.3120.0040.0040.0000.0000.0000.000
69A469VAL0-0.044-0.01921.992-0.012-0.0120.0000.0000.0000.000
70A470ALA00.0250.00821.5170.0040.0040.0000.0000.0000.000
71A471PHE0-0.041-0.01423.622-0.008-0.0080.0000.0000.0000.000
72A472ASN00.020-0.00525.952-0.004-0.0040.0000.0000.0000.000
73A473SER00.0260.00028.0020.0060.0060.0000.0000.0000.000
74A474PHE00.0300.01329.4320.0010.0010.0000.0000.0000.000
75A475PHE0-0.0350.01030.1240.0010.0010.0000.0000.0000.000
76A476TYR00.019-0.01930.6670.0000.0000.0000.0000.0000.000
77A477THR00.0380.02032.6280.0000.0000.0000.0000.0000.000
78A478ASN0-0.045-0.04635.516-0.001-0.0010.0000.0000.0000.000
79A479LEU0-0.030-0.00333.4340.0010.0010.0000.0000.0000.000
80A480SER0-0.0280.00136.1000.0000.0000.0000.0000.0000.000
81A481GLU-1-0.941-0.96937.781-0.001-0.0010.0000.0000.0000.000
82A482ARG10.8620.92540.200-0.008-0.0080.0000.0000.0000.000
83A483GLY00.0510.03839.9440.0020.0020.0000.0000.0000.000
84A484TYR00.014-0.01436.456-0.002-0.0020.0000.0000.0000.000
85A485GLN00.008-0.01139.2310.0010.0010.0000.0000.0000.000
86A486GLY0-0.013-0.00540.512-0.001-0.0010.0000.0000.0000.000
87A487VAL0-0.032-0.01735.040-0.001-0.0010.0000.0000.0000.000
88A488ARG10.9560.99736.222-0.024-0.0240.0000.0000.0000.000
89A489ARG10.8740.93137.790-0.026-0.0260.0000.0000.0000.000
90A490TRP0-0.035-0.00531.1940.0030.0030.0000.0000.0000.000
91A491MET00.0920.06128.9830.0020.0020.0000.0000.0000.000
92A492LYS10.9740.99232.229-0.055-0.0550.0000.0000.0000.000
93A493ARG10.8850.93333.735-0.027-0.0270.0000.0000.0000.000
94A494LYS10.8580.93026.891-0.053-0.0530.0000.0000.0000.000
95A495LYS10.8700.93929.513-0.045-0.0450.0000.0000.0000.000
96A496THR00.0750.04427.9590.0040.0040.0000.0000.0000.000
97A497GLN0-0.112-0.06530.625-0.009-0.0090.0000.0000.0000.000
98A498ILE00.0850.04129.5990.0070.0070.0000.0000.0000.000
99A499ASP-1-0.828-0.91729.3310.0960.0960.0000.0000.0000.000
100A500LYS10.8370.91228.616-0.092-0.0920.0000.0000.0000.000
101A501LEU0-0.056-0.00525.0870.0070.0070.0000.0000.0000.000
102A502ASP-1-0.828-0.92820.5720.2320.2320.0000.0000.0000.000
103A503LYS10.8830.92917.168-0.297-0.2970.0000.0000.0000.000
104A504ILE0-0.039-0.01322.447-0.009-0.0090.0000.0000.0000.000
105A505PHE0-0.0020.00717.765-0.006-0.0060.0000.0000.0000.000
106A506THR0-0.031-0.04423.210-0.005-0.0050.0000.0000.0000.000
107A507PRO00.0130.03924.150-0.004-0.0040.0000.0000.0000.000
108A508ILE00.013-0.01925.5910.0020.0020.0000.0000.0000.000
109A509ASN00.0250.01528.226-0.011-0.0110.0000.0000.0000.000
110A510LEU00.0100.00130.1870.0050.0050.0000.0000.0000.000
111A511ASN0-0.011-0.03232.622-0.006-0.0060.0000.0000.0000.000
112A512GLN0-0.018-0.02134.336-0.002-0.0020.0000.0000.0000.000
113A513SER00.0130.03432.119-0.003-0.0030.0000.0000.0000.000
114A514HIS10.7960.87726.1280.0450.0450.0000.0000.0000.000
115A515TRP0-0.0190.00625.3880.0130.0130.0000.0000.0000.000
116A516ALA0-0.003-0.01024.509-0.008-0.0080.0000.0000.0000.000
117A517LEU0-0.028-0.01919.7670.0020.0020.0000.0000.0000.000
118A518GLY00.0260.02523.8520.0020.0020.0000.0000.0000.000
119A519ILE0-0.019-0.02218.9260.0030.0030.0000.0000.0000.000
120A520ILE00.0220.02323.1410.0000.0000.0000.0000.0000.000
121A521ASP-1-0.783-0.89620.5790.2260.2260.0000.0000.0000.000
122A522LEU0-0.012-0.01623.420-0.007-0.0070.0000.0000.0000.000
123A523LYS10.8410.92922.419-0.201-0.2010.0000.0000.0000.000
124A524LYS10.9180.95118.956-0.277-0.2770.0000.0000.0000.000
125A525LYS10.8110.92324.039-0.114-0.1140.0000.0000.0000.000
126A526THR0-0.0130.00323.857-0.005-0.0050.0000.0000.0000.000
127A527ILE00.020-0.00126.0360.0020.0020.0000.0000.0000.000
128A528GLY00.014-0.00223.546-0.006-0.0060.0000.0000.0000.000
129A529TYR0-0.055-0.03724.613-0.002-0.0020.0000.0000.0000.000
130A530VAL0-0.008-0.00619.0800.0010.0010.0000.0000.0000.000
131A531ASP-1-0.735-0.84822.504-0.050-0.0500.0000.0000.0000.000
132A532SER00.010-0.01420.3980.0030.0030.0000.0000.0000.000
133A533LEU0-0.038-0.02021.938-0.017-0.0170.0000.0000.0000.000
134A534SER00.0020.01524.7800.0100.0100.0000.0000.0000.000
135A535ASN00.010-0.00626.464-0.010-0.0100.0000.0000.0000.000
136A536GLY00.0010.01028.3050.0020.0020.0000.0000.0000.000
137A537PRO0-0.039-0.02328.8830.0000.0000.0000.0000.0000.000
138A538ASN00.0070.00431.162-0.001-0.0010.0000.0000.0000.000
139A539ALA00.0350.01133.9970.0030.0030.0000.0000.0000.000
140A540MET0-0.0050.00633.4700.0030.0030.0000.0000.0000.000
141A541SER00.019-0.03329.6510.0020.0020.0000.0000.0000.000
142A542PHE00.0440.01631.5200.0060.0060.0000.0000.0000.000
143A543ALA0-0.0080.01933.8840.0050.0050.0000.0000.0000.000
144A544ILE00.0170.02129.3910.0030.0030.0000.0000.0000.000
145A545LEU0-0.009-0.00827.8730.0050.0050.0000.0000.0000.000
146A546THR0-0.005-0.01331.5340.0050.0050.0000.0000.0000.000
147A547ASP-1-0.865-0.92834.2790.0230.0230.0000.0000.0000.000
148A548LEU0-0.026-0.01227.9030.0030.0030.0000.0000.0000.000
149A549GLN00.0380.00131.9370.0000.0000.0000.0000.0000.000
150A550LYS10.9260.95433.367-0.024-0.0240.0000.0000.0000.000
151A551TYR0-0.031-0.01130.9310.0010.0010.0000.0000.0000.000
152A552VAL0-0.004-0.00330.3000.0010.0010.0000.0000.0000.000
153A553MET0-0.0040.02533.1840.0020.0020.0000.0000.0000.000
154A554GLU-1-0.907-0.96336.6190.0380.0380.0000.0000.0000.000
155A555GLU-1-0.912-0.94533.1370.0540.0540.0000.0000.0000.000
156A556SER0-0.045-0.01934.2370.0010.0010.0000.0000.0000.000
157A557LYS10.8600.91536.049-0.051-0.0510.0000.0000.0000.000
158A558HIS0-0.026-0.00638.7440.0000.0000.0000.0000.0000.000
159A559THR0-0.075-0.03836.5120.0020.0020.0000.0000.0000.000
160A560ILE00.0230.00930.9350.0050.0050.0000.0000.0000.000
161A561GLY00.0510.00932.333-0.004-0.0040.0000.0000.0000.000
162A562GLU-1-0.922-0.96533.3890.0670.0670.0000.0000.0000.000
163A563ASP-1-0.853-0.92033.6710.0830.0830.0000.0000.0000.000
164A564PHE0-0.083-0.02628.3210.0070.0070.0000.0000.0000.000
165A565ASP-1-0.878-0.93727.5150.0790.0790.0000.0000.0000.000
166A566LEU0-0.058-0.02028.0800.0040.0040.0000.0000.0000.000
167A567ILE00.0070.00623.910-0.006-0.0060.0000.0000.0000.000
168A568HIS00.0390.04125.599-0.010-0.0100.0000.0000.0000.000
169A569LEU00.0040.00618.6070.0040.0040.0000.0000.0000.000
170A570ASP-1-0.925-0.94919.425-0.002-0.0020.0000.0000.0000.000
171A571CYS0-0.035-0.02516.9460.0210.0210.0000.0000.0000.000
172A572PRO0-0.0270.01213.697-0.002-0.0020.0000.0000.0000.000
173A573GLN00.003-0.00516.9290.0100.0100.0000.0000.0000.000
174A574GLN0-0.076-0.04819.516-0.030-0.0300.0000.0000.0000.000
175A575PRO0-0.020-0.01019.7560.0150.0150.0000.0000.0000.000
176A576ASN0-0.052-0.04422.6350.0240.0240.0000.0000.0000.000
177A577GLY00.0550.03825.3200.0040.0040.0000.0000.0000.000
178A578TYR0-0.002-0.00824.1860.0100.0100.0000.0000.0000.000
179A579ASP-1-0.804-0.87320.960-0.195-0.1950.0000.0000.0000.000
180A580CSD-1-0.766-0.84921.535-0.093-0.0930.0000.0000.0000.000
181A581GLY00.0530.01822.2290.0040.0040.0000.0000.0000.000
182A582ILE00.019-0.00217.6040.0090.0090.0000.0000.0000.000
183A583TYR00.0620.03117.452-0.027-0.0270.0000.0000.0000.000
184A584VAL0-0.0020.01217.9790.0150.0150.0000.0000.0000.000
185A585CYS0-0.047-0.01517.4900.0300.0300.0000.0000.0000.000
186A586MET0-0.0100.01211.1750.0240.0240.0000.0000.0000.000
187A587ASN00.052-0.00713.9770.0340.0340.0000.0000.0000.000
188A588THR0-0.030-0.01316.0820.0510.0510.0000.0000.0000.000
189A589LEU0-0.0090.00510.6110.0340.0340.0000.0000.0000.000
190A590TYR00.0240.0117.7600.0140.0140.0000.0000.0000.000
191A591GLY00.0380.02112.1170.1110.1110.0000.0000.0000.000
192A592SER0-0.116-0.08213.5460.0370.0370.0000.0000.0000.000
193A593ALA0-0.024-0.0029.5600.0220.0220.0000.0000.0000.000
194A594ASP-1-0.935-0.95611.1930.5600.5600.0000.0000.0000.000
195A595ALA0-0.030-0.0138.9630.1140.1140.0000.0000.0000.000
196A596PRO00.000-0.0159.467-0.173-0.1730.0000.0000.0000.000
197A597LEU0-0.043-0.01410.582-0.028-0.0280.0000.0000.0000.000
198A598ASP-1-0.911-0.9668.2940.0340.0340.0000.0000.0000.000
199A599PHE0-0.0270.0039.746-0.131-0.1310.0000.0000.0000.000
200A600ASP-1-0.816-0.92510.702-0.739-0.7390.0000.0000.0000.000
201A601TYR0-0.020-0.03612.854-0.006-0.0060.0000.0000.0000.000
202A602LYS10.9190.94912.8290.6190.6190.0000.0000.0000.000
203A603ASP-1-0.772-0.8649.259-1.263-1.2630.0000.0000.0000.000
204A604ALA00.0160.00211.7890.0640.0640.0000.0000.0000.000
205A605ILE0-0.053-0.03015.1060.0510.0510.0000.0000.0000.000
206A606ARG10.8340.9078.2771.3531.3530.0000.0000.0000.000
207A607MET00.0190.02113.5510.0380.0380.0000.0000.0000.000
208A608ARG10.7440.86315.2230.2310.2310.0000.0000.0000.000
209A609ARG10.8640.94316.5470.2620.2620.0000.0000.0000.000
210A610PHE00.0960.04813.0350.0260.0260.0000.0000.0000.000
211A611ILE00.0250.01116.0070.0430.0430.0000.0000.0000.000
212A612ALA0-0.0010.00118.6990.0260.0260.0000.0000.0000.000
213A613HIS00.0840.02616.8820.0080.0080.0000.0000.0000.000
214A614LEU0-0.0160.00615.6970.0290.0290.0000.0000.0000.000
215A615ILE0-0.050-0.03819.4470.0200.0200.0000.0000.0000.000
216A616LEU0-0.066-0.02322.8280.0120.0120.0000.0000.0000.000
217A617THR0-0.061-0.03620.2770.0120.0120.0000.0000.0000.000
218A618ASP-1-0.832-0.90322.7250.0100.0100.0000.0000.0000.000
219A619ALA00.0640.03119.2350.0130.0130.0000.0000.0000.000
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