FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: P9Y42

Calculation Name: 3HHT-B-Xray13

Preferred Name:

Target Type:

Ligand Name: 3-sulfinoalanine

ligand 3-letter code: CSD

PDB ID: 3HHT

Chain ID: B

ChEMBL ID:

UniProt ID: Q84FS5

Base Structure: X-ray

Registration Date: 2018-02-14

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water No
Procedure Auto-FMO protocol ver. 1.20181228
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 229
LigandCharge CL-=-1
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -2645798.199144
FMO2-HF: Nuclear repulsion 2553403.532019
FMO2-HF: Total energy -92394.667126
FMO2-MP2: Total energy -92662.785094


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(B:1:MET)


Summations of interaction energy for fragment #1(B:1:MET)
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.
-197.383-184.94924.295-16.553-20.17-0.15
Interaction energy analysis for fragmet #1(B:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.798 / q_NPA : 0.899
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].
3B3GLY00.0350.0202.5336.6879.3700.538-1.434-1.7870.004
4B4ILE00.005-0.0053.3452.7402.7490.0240.299-0.3310.000
5B5HIS00.0510.0242.5135.8976.9860.379-0.287-1.1800.001
6B6ASP-1-0.929-0.9405.575-40.054-40.0540.0000.0000.0000.000
7B7VAL00.030-0.0037.2091.3631.3630.0000.0000.0000.000
8B8GLY0-0.0170.00610.7452.2932.2930.0000.0000.0000.000
9B9GLY00.019-0.01612.873-1.011-1.0110.0000.0000.0000.000
10B10MET0-0.084-0.01511.539-0.168-0.1680.0000.0000.0000.000
11B11ASP-1-0.885-0.92815.161-15.076-15.0760.0000.0000.0000.000
12B12GLY0-0.036-0.03317.085-0.412-0.4120.0000.0000.0000.000
13B13PHE0-0.017-0.02111.8760.3070.3070.0000.0000.0000.000
14B14GLY0-0.030-0.00218.1000.3820.3820.0000.0000.0000.000
15B15LYS10.9430.96421.86210.28810.2880.0000.0000.0000.000
16B16VAL00.0590.02621.700-0.268-0.2680.0000.0000.0000.000
17B17MET0-0.045-0.02823.3820.6590.6590.0000.0000.0000.000
18B18TYR0-0.0090.00425.3550.0070.0070.0000.0000.0000.000
19B19VAL00.0210.01427.1260.2700.2700.0000.0000.0000.000
20B20LYS10.8540.92829.7548.4438.4430.0000.0000.0000.000
21B21GLU-1-0.852-0.93630.275-9.869-9.8690.0000.0000.0000.000
22B22GLU-1-1.012-0.99531.307-8.250-8.2500.0000.0000.0000.000
23B23GLU-1-0.943-0.98432.737-8.637-8.6370.0000.0000.0000.000
24B24ASP-1-0.939-0.95326.433-11.715-11.7150.0000.0000.0000.000
25B25ILE0-0.071-0.03328.622-0.102-0.1020.0000.0000.0000.000
26B26TYR00.0100.00326.259-0.190-0.1900.0000.0000.0000.000
27B27PHE0-0.031-0.02923.836-0.356-0.3560.0000.0000.0000.000
28B28THR00.000-0.00926.2300.3430.3430.0000.0000.0000.000
29B29HIS0-0.048-0.01224.8810.5010.5010.0000.0000.0000.000
30B30ASP-1-0.856-0.93426.611-9.877-9.8770.0000.0000.0000.000
31B31TRP0-0.044-0.02518.962-0.229-0.2290.0000.0000.0000.000
32B32GLU-1-0.817-0.92022.011-12.660-12.6600.0000.0000.0000.000
33B33ARG10.9620.98723.0339.7009.7000.0000.0000.0000.000
34B34LEU0-0.030-0.00823.929-0.108-0.1080.0000.0000.0000.000
35B35ALA00.0280.01019.303-0.230-0.2300.0000.0000.0000.000
36B36LEU0-0.008-0.01120.494-0.534-0.5340.0000.0000.0000.000
37B37GLY0-0.015-0.00422.060-0.106-0.1060.0000.0000.0000.000
38B38LEU0-0.024-0.01320.8300.0780.0780.0000.0000.0000.000
39B39VAL00.0330.01616.987-0.225-0.2250.0000.0000.0000.000
40B40ALA00.0080.01119.537-0.168-0.1680.0000.0000.0000.000
41B41GLY00.0260.01622.0120.2170.2170.0000.0000.0000.000
42B42CYS0-0.055-0.02320.0280.3630.3630.0000.0000.0000.000
43B43MET0-0.0040.00716.0940.1650.1650.0000.0000.0000.000
44B44ALA0-0.0120.00020.3150.1060.1060.0000.0000.0000.000
45B45GLN0-0.080-0.05123.5710.7450.7450.0000.0000.0000.000
46B46GLY0-0.0250.00420.7700.1720.1720.0000.0000.0000.000
47B47LEU00.0140.01320.838-0.277-0.2770.0000.0000.0000.000
48B48GLY00.0210.01717.190-0.207-0.2070.0000.0000.0000.000
49B49MET0-0.025-0.01514.880-1.725-1.7250.0000.0000.0000.000
50B50LYS10.8820.91616.40515.93715.9370.0000.0000.0000.000
51B51ALA00.0600.02215.9890.7010.7010.0000.0000.0000.000
52B52PHE00.003-0.01913.261-0.743-0.7430.0000.0000.0000.000
53B53ASP-1-0.889-0.93710.341-26.492-26.4920.0000.0000.0000.000
54B54GLU-1-0.756-0.8769.181-22.106-22.1060.0000.0000.0000.000
55B55PHE00.0190.01310.263-0.952-0.9520.0000.0000.0000.000
56B56ARG10.9360.9767.64625.17925.1790.0000.0000.0000.000
57B57ILE00.0160.0193.463-3.686-2.8910.399-0.248-0.946-0.001
58B58GLY00.0530.0315.410-0.607-0.437-0.001-0.011-0.1590.000
59B59ILE0-0.073-0.0377.8091.3051.3050.0000.0000.0000.000
60B60GLU-1-0.901-0.9523.063-59.606-58.2031.690-1.101-1.991-0.007
61B61LEU00.0020.0052.836-6.877-4.4691.764-1.283-2.889-0.013
62B62MET0-0.067-0.0033.8852.7642.8040.0050.055-0.1000.000
63B63ARG10.8950.9375.28216.17916.1790.0000.0000.0000.000
64B64PRO00.032-0.0075.7601.2421.2420.0000.0000.0000.000
65B65VAL00.0050.0038.0550.7730.7730.0000.0000.0000.000
66B66ASP-1-0.760-0.84810.203-17.172-17.1720.0000.0000.0000.000
67B67TYR0-0.038-0.0177.9540.4250.4250.0000.0000.0000.000
68B68LEU0-0.022-0.03610.0900.6090.6090.0000.0000.0000.000
69B69THR0-0.036-0.02212.6531.0451.0450.0000.0000.0000.000
70B70SER0-0.027-0.00613.9490.3490.3490.0000.0000.0000.000
71B71SER00.0190.01615.7180.8040.8040.0000.0000.0000.000
72B72TYR00.0570.02714.873-1.188-1.1880.0000.0000.0000.000
73B73TYR00.0830.02115.612-0.980-0.9800.0000.0000.0000.000
74B74GLY00.0430.01915.8790.0890.0890.0000.0000.0000.000
75B75HIS10.8570.92711.79620.39120.3910.0000.0000.0000.000
76B76TRP00.0230.01512.719-0.448-0.4480.0000.0000.0000.000
77B77ILE00.0100.01015.166-0.038-0.0380.0000.0000.0000.000
78B78ALA00.0040.01110.8800.0820.0820.0000.0000.0000.000
79B79THR0-0.018-0.02710.671-0.066-0.0660.0000.0000.0000.000
80B80VAL00.0150.00311.9670.0830.0830.0000.0000.0000.000
81B81ALA00.0090.01014.5540.3450.3450.0000.0000.0000.000
82B82TYR00.0130.0079.095-0.225-0.2250.0000.0000.0000.000
83B83ASN00.007-0.00911.141-0.194-0.1940.0000.0000.0000.000
84B84LEU0-0.034-0.02513.7990.6170.6170.0000.0000.0000.000
85B85VAL00.0110.01715.4310.6630.6630.0000.0000.0000.000
86B86ASP-1-0.899-0.92712.814-20.806-20.8060.0000.0000.0000.000
87B87THR0-0.094-0.05714.9830.5980.5980.0000.0000.0000.000
88B88GLY0-0.0110.00217.6630.6530.6530.0000.0000.0000.000
89B89VAL0-0.072-0.02420.0070.7200.7200.0000.0000.0000.000
90B90LEU0-0.045-0.03120.1040.6580.6580.0000.0000.0000.000
91B91ASP-1-0.822-0.91120.416-12.343-12.3430.0000.0000.0000.000
92B92GLU-1-0.909-0.95915.459-15.815-15.8150.0000.0000.0000.000
93B93LYS10.9370.97019.53011.24411.2440.0000.0000.0000.000
94B94GLU-1-0.944-0.96422.434-10.254-10.2540.0000.0000.0000.000
95B95LEU0-0.020-0.01517.9260.2770.2770.0000.0000.0000.000
96B96ASP-1-0.887-0.93818.757-13.418-13.4180.0000.0000.0000.000
97B97GLU-1-0.962-0.98921.433-9.847-9.8470.0000.0000.0000.000
98B98ARG10.9110.95324.75510.19910.1990.0000.0000.0000.000
99B99THR0-0.015-0.02620.3020.1380.1380.0000.0000.0000.000
100B100GLU-1-0.873-0.93223.354-10.169-10.1690.0000.0000.0000.000
101B101VAL0-0.090-0.04825.4210.3920.3920.0000.0000.0000.000
102B102PHE0-0.042-0.03425.8660.3440.3440.0000.0000.0000.000
103B103SER0-0.0020.02024.5270.1350.1350.0000.0000.0000.000
104B104LYS10.8930.95026.4639.3269.3260.0000.0000.0000.000
105B105LYS10.8720.93429.8478.4258.4250.0000.0000.0000.000
106B106PRO00.1110.06729.0060.0090.0090.0000.0000.0000.000
107B107ASP-1-0.917-0.94030.388-8.417-8.4170.0000.0000.0000.000
108B108THR0-0.134-0.07831.3510.3400.3400.0000.0000.0000.000
109B109LYS10.9230.95432.6017.5057.5050.0000.0000.0000.000
110B110ILE00.0380.02629.148-0.094-0.0940.0000.0000.0000.000
111B111PRO0-0.029-0.01031.1460.2520.2520.0000.0000.0000.000
112B112ARG10.9560.96632.9708.4238.4230.0000.0000.0000.000
113B113ARG10.9630.97432.2869.2119.2110.0000.0000.0000.000
114B114GLU-1-0.927-0.94734.956-7.888-7.8880.0000.0000.0000.000
115B115ASP-1-0.861-0.95433.878-8.842-8.8420.0000.0000.0000.000
116B116PRO00.0390.00734.916-0.232-0.2320.0000.0000.0000.000
117B117ALA00.0030.00836.040-0.069-0.0690.0000.0000.0000.000
118B118LEU00.0180.01828.577-0.176-0.1760.0000.0000.0000.000
119B119VAL0-0.009-0.00531.152-0.290-0.2900.0000.0000.0000.000
120B120LYS10.9200.97332.1348.0658.0650.0000.0000.0000.000
121B121LEU0-0.021-0.00127.645-0.097-0.0970.0000.0000.0000.000
122B122VAL00.032-0.00126.686-0.320-0.3200.0000.0000.0000.000
123B123GLU-1-0.906-0.96228.022-9.293-9.2930.0000.0000.0000.000
124B124LYS10.8990.96030.0079.5389.5380.0000.0000.0000.000
125B125ALA00.0230.01424.686-0.144-0.1440.0000.0000.0000.000
126B126LEU0-0.066-0.03624.912-0.388-0.3880.0000.0000.0000.000
127B127ASN0-0.050-0.02026.694-0.160-0.1600.0000.0000.0000.000
128B128ASP-1-0.926-0.96327.995-10.319-10.3190.0000.0000.0000.000
129B129GLY0-0.057-0.01123.873-0.241-0.2410.0000.0000.0000.000
130B130LEU00.000-0.01919.5190.0520.0520.0000.0000.0000.000
131B131SER0-0.0100.00820.427-1.029-1.0290.0000.0000.0000.000
132B132PRO00.0290.00917.5400.2300.2300.0000.0000.0000.000
133B133LEU00.0140.02419.541-0.447-0.4470.0000.0000.0000.000
134B134ARG10.7300.82320.55215.19915.1990.0000.0000.0000.000
135B135GLU-1-0.915-0.95223.118-10.945-10.9450.0000.0000.0000.000
136B136ILE0-0.056-0.03620.984-0.265-0.2650.0000.0000.0000.000
137B137SER0-0.017-0.01224.7890.5400.5400.0000.0000.0000.000
138B138ALA0-0.029-0.01023.7560.3930.3930.0000.0000.0000.000
139B139SER0-0.011-0.00525.8440.1750.1750.0000.0000.0000.000
140B140PRO0-0.0040.00122.958-0.329-0.3290.0000.0000.0000.000
141B141ARG10.9070.96719.03715.67915.6790.0000.0000.0000.000
142B142PHE0-0.035-0.01118.0060.2340.2340.0000.0000.0000.000
143B143LYS10.9520.97423.31911.35111.3510.0000.0000.0000.000
144B144VAL00.0380.00225.386-0.251-0.2510.0000.0000.0000.000
145B145GLY0-0.011-0.00626.0870.4730.4730.0000.0000.0000.000
146B146GLU-1-0.963-0.98324.120-12.489-12.4890.0000.0000.0000.000
147B147ARG10.9520.98223.53712.22412.2240.0000.0000.0000.000
148B148ILE0-0.012-0.00517.3990.2690.2690.0000.0000.0000.000
149B149LYS10.9270.95517.27116.44116.4410.0000.0000.0000.000
150B150THR0-0.040-0.02612.992-0.327-0.3270.0000.0000.0000.000
151B151LYS10.8950.95111.60022.24422.2440.0000.0000.0000.000
152B152ASN00.0680.03611.192-3.336-3.3360.0000.0000.0000.000
153B153ILE0-0.027-0.0097.6130.8540.8540.0000.0000.0000.000
154B154HIS00.004-0.0165.418-5.930-5.9300.0000.0000.0000.000
155B155PRO00.0240.0253.2431.6272.0720.011-0.101-0.3540.000
156B156THR00.001-0.0192.530-22.318-19.2761.466-2.346-2.162-0.024
157B157GLY00.0360.0402.525-5.044-2.1501.130-1.762-2.261-0.020
158B158HIS0-0.067-0.0661.683-45.315-48.66015.842-7.741-4.756-0.085
159B159THR0-0.048-0.0322.3343.0063.6701.050-0.556-1.157-0.005
160B160ARG10.9050.9604.58131.67431.687-0.001-0.0120.0000.000
161B161PHE00.0360.0396.1604.9564.9560.0000.0000.0000.000
162B162PRO00.0240.0116.199-6.001-6.0010.0000.0000.0000.000
163B163ARG10.9690.9586.32537.28937.2890.0000.0000.0000.000
164B164TYR0-0.0190.0008.4911.9301.9300.0000.0000.0000.000
165B165ALA00.0130.00611.0412.1982.1980.0000.0000.0000.000
166B166ARG10.7870.9083.94950.27650.400-0.001-0.025-0.0970.000
167B167ASP-1-0.911-0.95511.495-17.844-17.8440.0000.0000.0000.000
168B168LYS10.8650.95914.56821.35421.3540.0000.0000.0000.000
169B169TYR0-0.064-0.04616.859-0.072-0.0720.0000.0000.0000.000
170B170GLY00.0320.01619.475-0.131-0.1310.0000.0000.0000.000
171B171VAL0-0.051-0.02420.3690.3810.3810.0000.0000.0000.000
172B172ILE0-0.034-0.00120.057-0.369-0.3690.0000.0000.0000.000
173B173ASP-1-0.845-0.94122.178-11.995-11.9950.0000.0000.0000.000
174B174GLU-1-0.871-0.94022.747-12.086-12.0860.0000.0000.0000.000
175B175VAL0-0.036-0.02122.013-0.783-0.7830.0000.0000.0000.000
176B176TYR0-0.033-0.02418.8890.8550.8550.0000.0000.0000.000
177B177GLY00.0390.02522.0880.6230.6230.0000.0000.0000.000
178B178ALA0-0.015-0.00520.000-0.843-0.8430.0000.0000.0000.000
179B179HIS00.0260.00616.8501.0361.0360.0000.0000.0000.000
180B180VAL0-0.012-0.00914.457-0.603-0.6030.0000.0000.0000.000
181B181PHE0-0.0010.01210.092-1.227-1.2270.0000.0000.0000.000
182B182PRO00.0340.0128.679-0.822-0.8220.0000.0000.0000.000
183B183ASP-1-0.765-0.8586.692-43.813-43.8130.0000.0000.0000.000
184B184ASP-1-0.843-0.9047.696-26.305-26.3050.0000.0000.0000.000
185B185ALA00.003-0.00210.7300.7160.7160.0000.0000.0000.000
186B186ALA0-0.020-0.0197.9241.1291.1290.0000.0000.0000.000
187B187HIS0-0.041-0.0166.112-5.703-5.7030.0000.0000.0000.000
188B188ARG10.7640.85510.72822.34822.3480.0000.0000.0000.000
189B189LYS10.9190.96610.78526.84326.8430.0000.0000.0000.000
190B190GLY00.0410.03014.5160.8120.8120.0000.0000.0000.000
191B191GLU-1-0.840-0.91114.903-16.762-16.7620.0000.0000.0000.000
192B192ASN0-0.073-0.04714.7250.3940.3940.0000.0000.0000.000
193B193PRO00.0160.01016.092-0.928-0.9280.0000.0000.0000.000
194B194GLN00.0960.06313.2290.0520.0520.0000.0000.0000.000
195B195TYR0-0.025-0.02917.571-0.161-0.1610.0000.0000.0000.000
196B196LEU0-0.0180.00214.951-1.200-1.2000.0000.0000.0000.000
197B197TYR0-0.028-0.05017.0691.4811.4810.0000.0000.0000.000
198B198ARG10.8110.92217.39912.66812.6680.0000.0000.0000.000
199B199VAL0-0.026-0.02117.2250.8030.8030.0000.0000.0000.000
200B200ARG10.8240.90118.86111.80811.8080.0000.0000.0000.000
201B201PHE00.017-0.00215.7920.0040.0040.0000.0000.0000.000
202B202GLU-1-0.787-0.88820.325-12.114-12.1140.0000.0000.0000.000
203B203ALA00.0320.01421.760-0.545-0.5450.0000.0000.0000.000
204B204GLU-1-0.877-0.93422.607-12.112-12.1120.0000.0000.0000.000
205B205GLU-1-0.867-0.93319.487-15.204-15.2040.0000.0000.0000.000
206B206LEU0-0.069-0.03316.102-0.644-0.6440.0000.0000.0000.000
207B207TRP00.003-0.01015.578-0.974-0.9740.0000.0000.0000.000
208B208GLY00.0200.04020.6930.2850.2850.0000.0000.0000.000
209B209TYR0-0.071-0.04322.8320.6000.6000.0000.0000.0000.000
210B210LYS10.8520.90025.72911.34611.3460.0000.0000.0000.000
211B211GLN00.0230.03326.0520.3080.3080.0000.0000.0000.000
212B212LYS10.8860.93927.9389.4689.4680.0000.0000.0000.000
213B213ASP-1-0.843-0.91724.212-12.141-12.1410.0000.0000.0000.000
214B214SER0-0.063-0.04822.839-0.011-0.0110.0000.0000.0000.000
215B215VAL0-0.010-0.00316.738-0.120-0.1200.0000.0000.0000.000
216B216TYR00.0220.02619.4780.1550.1550.0000.0000.0000.000
217B217ILE0-0.030-0.01612.831-0.545-0.5450.0000.0000.0000.000
218B218ASP-1-0.793-0.87614.902-17.037-17.0370.0000.0000.0000.000
219B219LEU0-0.063-0.03911.368-2.348-2.3480.0000.0000.0000.000
220B220TRP00.0530.01111.4280.5670.5670.0000.0000.0000.000
221B221GLU-1-0.779-0.86813.737-16.067-16.0670.0000.0000.0000.000
222B222SER0-0.085-0.04412.168-0.451-0.4510.0000.0000.0000.000
223B223TYR0-0.039-0.0628.091-0.924-0.9240.0000.0000.0000.000
224B224MET0-0.035-0.00511.8220.2410.2410.0000.0000.0000.000
225B225GLU-1-0.942-0.97315.297-17.518-17.5180.0000.0000.0000.000
226B226PRO00.0120.01118.4560.1670.1670.0000.0000.0000.000
227B227VAL0-0.016-0.00821.859-0.199-0.1990.0000.0000.0000.000
228B0NME0-0.0120.00424.0260.3530.3530.0000.0000.0000.000
229B691CL--1-0.877-0.92524.371-13.171-13.1710.0000.0000.0000.000