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: YY912

Calculation Name: 3ALZ-AB-Docking371-RPV(D507N)-SLAM: pose 1

Preferred Name:

Target Type:

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose

ligand 3-letter code: NAG

PDB ID: 3ALZ

Chain ID: AB

ChEMBL ID:

UniProt ID: P08362

Base Structure: Docking

Registration Date: 2023-03-09

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization BaseStructure_original
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Manual calculation
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 523
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -10699367.619171
FMO2-HF: Nuclear repulsion 10491986.391959
FMO2-HF: Total energy -207381.227212
FMO2-MP2: Total energy -207980.909174


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy (frag 1-109 : frag 110-523)
"
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.
-494.8624-426.696499.1538-60.0480-107.27180.0418


Interactive mode: IFIE and PIEDA for fragment #1(B:32:CYS)


Summations of interaction energy for fragment #1(B:32:CYS)
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.
10.33925.0215.717-10.483-19.9140.013
Interaction energy analysis for fragmet #1(B:32:CYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.783 / q_NPA : 0.877
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].
3B34LYS10.9490.9843.83933.29334.355-0.001-0.411-0.6500.001
16B47LEU00.0000.0025.129-2.923-2.789-0.002-0.009-0.1220.000
17B48THR0-0.0150.0163.689-10.071-9.8080.008-0.119-0.1520.000
39B70LEU0-0.018-0.0255.514-0.367-0.199-0.002-0.011-0.1550.000
86B117TRP0-0.038-0.0223.205-2.724-1.4590.330-0.292-1.303-0.002
87B118TYR0-0.010-0.0214.7584.3104.625-0.001-0.076-0.2390.000
88B119PHE00.004-0.0312.256-18.196-13.38510.453-6.612-8.652-0.010
89B120MET00.0100.0242.087-6.414-7.6183.880-0.283-2.3930.031
90B121THR0-0.029-0.0093.514-4.853-4.3280.0640.053-0.642-0.002
98B129GLN0-0.011-0.0025.2311.2411.234-0.0020.0000.0090.000
99B130ARG10.8280.9192.91219.65823.0920.299-1.757-1.976-0.001
102B134HIS00.002-0.0022.9991.8534.7780.562-0.788-2.699-0.003
103B135LEU00.0340.0394.6410.3910.411-0.002-0.013-0.0050.000
113A191SER0-0.023-0.0164.767-4.963-4.854-0.002-0.008-0.0990.000
114A192THR0-0.0170.0035.3904.1164.190-0.002-0.002-0.0690.000
467A548LEU00.0470.0353.697-2.998-2.2110.135-0.155-0.767-0.001
4B35ILE0-0.0040.0025.8523.6553.6550.0000.0000.0000.000
5B36VAL0-0.010-0.0088.7880.4070.4070.0000.0000.0000.000
6B37GLN0-0.008-0.01112.0331.4561.4560.0000.0000.0000.000
7B38GLN00.0380.02714.6820.5820.5820.0000.0000.0000.000
8B39LEU00.0030.01217.782-0.208-0.2080.0000.0000.0000.000
9B40GLY00.0160.01718.8790.6100.6100.0000.0000.0000.000
10B41SER0-0.058-0.03918.3500.2330.2330.0000.0000.0000.000
11B42ASP-1-0.822-0.91218.685-13.965-13.9650.0000.0000.0000.000
12B43VAL0-0.049-0.00513.545-0.484-0.4840.0000.0000.0000.000
13B44LEU00.027-0.00213.976-0.126-0.1260.0000.0000.0000.000
14B45LEU00.006-0.0197.783-0.928-0.9280.0000.0000.0000.000
15B46PRO0-0.034-0.0249.0510.7940.7940.0000.0000.0000.000
18B49HIS0-0.009-0.0175.3600.6750.6750.0000.0000.0000.000
19B50GLU-1-0.919-0.9806.919-22.508-22.5080.0000.0000.0000.000
20B51ARG10.9140.94710.32320.88820.8880.0000.0000.0000.000
21B52ILE00.0190.03013.3431.0551.0550.0000.0000.0000.000
22B53ASN00.0050.00010.036-0.003-0.0030.0000.0000.0000.000
23B54THR00.0420.03313.3180.3920.3920.0000.0000.0000.000
24B55SER0-0.036-0.01213.8581.0811.0810.0000.0000.0000.000
25B56MET00.0100.02314.093-0.669-0.6690.0000.0000.0000.000
26B57ASN0-0.015-0.00714.4840.6710.6710.0000.0000.0000.000
27B58LYS10.8760.95015.25212.54112.5410.0000.0000.0000.000
28B59SER00.012-0.00910.825-0.878-0.8780.0000.0000.0000.000
29B60ILE0-0.063-0.03312.927-0.193-0.1930.0000.0000.0000.000
30B61HIS00.0630.04313.1940.2520.2520.0000.0000.0000.000
31B62ILE00.0160.0098.782-1.021-1.0210.0000.0000.0000.000
32B63VAL00.0020.0138.5330.9530.9530.0000.0000.0000.000
33B64VAL0-0.0100.0046.925-1.048-1.0480.0000.0000.0000.000
34B65THR0-0.029-0.0446.5420.8350.8350.0000.0000.0000.000
35B66MET0-0.020-0.0066.641-1.607-1.6070.0000.0000.0000.000
36B67ALA0-0.0030.0137.4131.5321.5320.0000.0000.0000.000
37B68LYS10.9410.9728.79715.81915.8190.0000.0000.0000.000
38B69SER00.0090.01210.834-1.694-1.6940.0000.0000.0000.000
40B71GLU-1-0.936-0.9679.410-16.872-16.8720.0000.0000.0000.000
41B72ASN00.024-0.00512.9190.6390.6390.0000.0000.0000.000
42B73SER0-0.070-0.01310.3190.6650.6650.0000.0000.0000.000
43B74VAL00.0420.00711.5150.7970.7970.0000.0000.0000.000
44B75GLU-1-0.821-0.8697.530-19.494-19.4940.0000.0000.0000.000
45B76ASN00.0510.03710.9431.2901.2900.0000.0000.0000.000
46B77LYS10.8920.93910.94312.60912.6090.0000.0000.0000.000
47B78ILE0-0.0150.00010.2160.3630.3630.0000.0000.0000.000
48B79VAL00.008-0.01311.6220.7920.7920.0000.0000.0000.000
49B80SER00.0430.03311.617-0.685-0.6850.0000.0000.0000.000
50B81LEU0-0.045-0.02313.2090.5910.5910.0000.0000.0000.000
51B82ASP-1-0.747-0.87114.491-12.828-12.8280.0000.0000.0000.000
52B83PRO0-0.069-0.02114.7260.3680.3680.0000.0000.0000.000
53B84SER0-0.074-0.06917.4370.1290.1290.0000.0000.0000.000
54B85GLU-1-0.916-0.94120.525-9.627-9.6270.0000.0000.0000.000
55B86ALA0-0.015-0.01021.294-0.382-0.3820.0000.0000.0000.000
56B87GLY0-0.0140.00423.6900.0030.0030.0000.0000.0000.000
57B88PRO0-0.027-0.01421.114-0.420-0.4200.0000.0000.0000.000
58B89PRO00.0060.00616.5700.1850.1850.0000.0000.0000.000
59B90ARG10.9820.98418.51610.80210.8020.0000.0000.0000.000
60B91TYR00.004-0.01414.918-0.621-0.6210.0000.0000.0000.000
61B92LEU0-0.021-0.00115.6320.5330.5330.0000.0000.0000.000
62B93LYS10.8290.91617.16011.85111.8510.0000.0000.0000.000
63B94ASP-1-0.827-0.89418.126-11.942-11.9420.0000.0000.0000.000
64B95ARG10.8920.91116.14314.89214.8920.0000.0000.0000.000
65B96TYR0-0.017-0.00512.3810.0660.0660.0000.0000.0000.000
66B97ARG10.9380.98015.09314.43014.4300.0000.0000.0000.000
67B98PHE00.012-0.0029.412-0.946-0.9460.0000.0000.0000.000
68B99TYR0-0.023-0.00713.5641.4501.4500.0000.0000.0000.000
69B100LEU00.0020.00712.983-1.178-1.1780.0000.0000.0000.000
70B101GLU-1-0.814-0.94013.551-15.336-15.3360.0000.0000.0000.000
71B102ASN0-0.075-0.05913.6060.3500.3500.0000.0000.0000.000
72B103LEU0-0.0260.0018.079-1.860-1.8600.0000.0000.0000.000
73B104SER0-0.0040.0028.867-2.252-2.2520.0000.0000.0000.000
74B105LEU00.002-0.0039.2461.4831.4830.0000.0000.0000.000
75B106ALA0-0.033-0.02011.552-0.697-0.6970.0000.0000.0000.000
76B107ILE0-0.045-0.02111.0360.3170.3170.0000.0000.0000.000
77B108ARG10.9630.97615.31112.31212.3120.0000.0000.0000.000
78B109GLU-1-0.904-0.95419.081-11.760-11.7600.0000.0000.0000.000
79B110SER0-0.069-0.01816.173-0.157-0.1570.0000.0000.0000.000
80B111THR00.048-0.00317.5190.4620.4620.0000.0000.0000.000
81B112LYS10.9440.96916.49414.18114.1810.0000.0000.0000.000
82B113LYS10.8810.92916.17412.77712.7770.0000.0000.0000.000
83B114ASP-1-0.720-0.82213.667-16.660-16.6600.0000.0000.0000.000
84B115GLU-1-0.858-0.91611.339-21.701-21.7010.0000.0000.0000.000
85B116GLY00.0160.0099.2041.5601.5600.0000.0000.0000.000
91B122LEU00.0020.0095.8651.1781.1780.0000.0000.0000.000
92B123GLU-1-0.796-0.9017.996-16.058-16.0580.0000.0000.0000.000
93B124LYS10.9440.95211.17218.69818.6980.0000.0000.0000.000
94B125ASN0-0.004-0.01014.282-0.017-0.0170.0000.0000.0000.000
95B126ILE00.0370.02416.6370.2840.2840.0000.0000.0000.000
96B127SER0-0.045-0.02712.534-0.171-0.1710.0000.0000.0000.000
97B128VAL00.0240.0258.2280.2480.2480.0000.0000.0000.000
104B136LYS10.8230.9138.33126.63826.6380.0000.0000.0000.000
105B137LEU00.007-0.00911.002-0.220-0.2200.0000.0000.0000.000
106B138TYR0-0.0180.00014.7370.4270.4270.0000.0000.0000.000
107B139GLU-1-0.864-0.95417.507-13.307-13.3070.0000.0000.0000.000
108B140GLN0-0.038-0.03321.213-0.355-0.3550.0000.0000.0000.000
109B141NME00.0340.03923.6410.5100.5100.0000.0000.0000.000
110A606CYS0-0.057-0.0246.8897.0447.0440.0000.0000.0000.000
111A189THR00.0640.0285.6012.0422.0420.0000.0000.0000.000
112A190GLY00.0570.0295.394-4.893-4.8930.0000.0000.0000.000
115A193THR0-0.009-0.0256.619-0.413-0.4130.0000.0000.0000.000
116A194THR00.0000.0099.3770.8570.8570.0000.0000.0000.000
117A195LYS10.9270.96611.91116.52416.5240.0000.0000.0000.000
118A196GLY00.0260.02315.4030.0430.0430.0000.0000.0000.000
119A197GLN0-0.038-0.01618.307-0.151-0.1510.0000.0000.0000.000
120A198PHE00.0240.00420.5390.0830.0830.0000.0000.0000.000
121A199SER0-0.009-0.00424.4720.2270.2270.0000.0000.0000.000
122A200ASN00.0430.02028.082-0.146-0.1460.0000.0000.0000.000
123A201MET0-0.056-0.01230.8810.3090.3090.0000.0000.0000.000
124A202SER00.0200.00033.134-0.124-0.1240.0000.0000.0000.000
125A203LEU0-0.006-0.00535.5790.1860.1860.0000.0000.0000.000
126A204ALA00.0450.03536.3540.1240.1240.0000.0000.0000.000
127A205LEU00.0000.00638.3170.0190.0190.0000.0000.0000.000
128A206SER00.0210.00836.552-0.019-0.0190.0000.0000.0000.000
129A207GLY0-0.0090.01235.614-0.050-0.0500.0000.0000.0000.000
130A208ILE0-0.013-0.00536.4470.0300.0300.0000.0000.0000.000
131A209TYR00.011-0.00939.8810.0990.0990.0000.0000.0000.000
132A210SER0-0.003-0.01535.5560.0330.0330.0000.0000.0000.000
133A211GLY00.0210.02037.0140.0030.0030.0000.0000.0000.000
134A212ARG10.8250.90837.7716.9146.9140.0000.0000.0000.000
135A213GLY00.0080.01339.3070.1390.1390.0000.0000.0000.000
136A214TYR0-0.064-0.03040.3260.1360.1360.0000.0000.0000.000
137A215ASN0-0.003-0.00440.570-0.216-0.2160.0000.0000.0000.000
138A216ILE0-0.0010.00037.7170.0970.0970.0000.0000.0000.000
139A217SER00.0290.00637.829-0.211-0.2110.0000.0000.0000.000
140A218SER00.0250.00838.0530.0020.0020.0000.0000.0000.000
141A219MET0-0.046-0.01534.7040.0360.0360.0000.0000.0000.000
142A220ILE00.0350.03334.081-0.195-0.1950.0000.0000.0000.000
143A221THR0-0.043-0.03431.5260.0970.0970.0000.0000.0000.000
144A222ILE00.0180.01128.789-0.240-0.2400.0000.0000.0000.000
145A223THR00.009-0.00428.3680.1460.1460.0000.0000.0000.000
146A224GLU-1-0.774-0.89029.999-9.603-9.6030.0000.0000.0000.000
147A225LYS10.8720.91830.9279.0349.0340.0000.0000.0000.000
148A226GLY0-0.025-0.00231.581-0.146-0.1460.0000.0000.0000.000
149A227MET0-0.096-0.02332.4750.2420.2420.0000.0000.0000.000
150A228TYR0-0.026-0.04533.043-0.292-0.2920.0000.0000.0000.000
151A229GLY00.0440.01934.4380.2640.2640.0000.0000.0000.000
152A230SER0-0.057-0.03235.353-0.203-0.2030.0000.0000.0000.000
153A231THR00.0190.00937.4600.2250.2250.0000.0000.0000.000
154A232TYR0-0.055-0.04238.263-0.128-0.1280.0000.0000.0000.000
155A233LEU00.0020.03640.1850.1360.1360.0000.0000.0000.000
156A234VAL0-0.004-0.01041.831-0.134-0.1340.0000.0000.0000.000
157A235GLY00.0360.03044.3170.1590.1590.0000.0000.0000.000
158A236LYS10.8090.90246.5795.7865.7860.0000.0000.0000.000
159A237HIS00.0670.02648.8760.0550.0550.0000.0000.0000.000
160A238ASN0-0.027-0.02751.8600.1610.1610.0000.0000.0000.000
161A239GLN00.0080.00053.823-0.079-0.0790.0000.0000.0000.000
162A240GLY00.016-0.00456.7950.0880.0880.0000.0000.0000.000
163A241ALA0-0.061-0.00955.3110.0400.0400.0000.0000.0000.000
164A242ARG10.9500.96655.1965.0395.0390.0000.0000.0000.000
165A243ARG10.9490.96752.7775.1465.1460.0000.0000.0000.000
166A244PRO00.0940.08348.899-0.051-0.0510.0000.0000.0000.000
167A245SER0-0.072-0.06252.1150.0950.0950.0000.0000.0000.000
168A246THR00.0820.02653.728-0.048-0.0480.0000.0000.0000.000
169A247ALA0-0.044-0.00655.4050.0100.0100.0000.0000.0000.000
170A248TRP00.028-0.00554.7560.0200.0200.0000.0000.0000.000
171A249GLN00.0040.01449.0220.1410.1410.0000.0000.0000.000
172A250ARG10.8930.95151.6455.1935.1930.0000.0000.0000.000
173A251ASP-1-0.699-0.87346.114-6.353-6.3530.0000.0000.0000.000
174A252TYR0-0.046-0.02447.2720.2030.2030.0000.0000.0000.000
175A253ARG10.8970.94541.0266.6726.6720.0000.0000.0000.000
176A254VAL0-0.031-0.00742.6240.1200.1200.0000.0000.0000.000
177A255PHE00.0360.00942.313-0.146-0.1460.0000.0000.0000.000
178A256GLU-1-0.695-0.82538.928-7.369-7.3690.0000.0000.0000.000
179A257VAL0-0.012-0.00338.741-0.198-0.1980.0000.0000.0000.000
180A258GLY00.0570.02638.1320.1910.1910.0000.0000.0000.000
181A259ILE0-0.047-0.01736.190-0.147-0.1470.0000.0000.0000.000
182A260ILE0-0.0150.00530.0110.0670.0670.0000.0000.0000.000
183A261ARG10.8820.93533.4317.5957.5950.0000.0000.0000.000
184A262GLU-1-0.912-0.94931.108-9.961-9.9610.0000.0000.0000.000
185A263LEU0-0.035-0.02933.7880.2270.2270.0000.0000.0000.000
186A264GLY00.0330.01934.2060.1460.1460.0000.0000.0000.000
187A265VAL0-0.039-0.01732.294-0.078-0.0780.0000.0000.0000.000
188A266GLY00.0340.02229.026-0.129-0.1290.0000.0000.0000.000
189A267THR0-0.042-0.03827.387-0.473-0.4730.0000.0000.0000.000
190A268PRO0-0.0050.01627.1570.3320.3320.0000.0000.0000.000
191A269VAL0-0.014-0.00430.2260.0660.0660.0000.0000.0000.000
192A270PHE0-0.0030.00129.7180.0570.0570.0000.0000.0000.000
193A271HIS00.0210.01434.5610.0410.0410.0000.0000.0000.000
194A272MET00.0050.01438.311-0.031-0.0310.0000.0000.0000.000
195A273THR0-0.114-0.08840.7650.0430.0430.0000.0000.0000.000
196A274ASN0-0.042-0.03842.9340.2520.2520.0000.0000.0000.000
197A275TYR0-0.050-0.05743.477-0.153-0.1530.0000.0000.0000.000
198A276LEU00.0170.03245.6220.1410.1410.0000.0000.0000.000
199A277GLU-1-0.826-0.88646.536-6.162-6.1620.0000.0000.0000.000
200A278LEU00.0170.01048.6650.1420.1420.0000.0000.0000.000
201A279PRO0-0.0130.00249.579-0.083-0.0830.0000.0000.0000.000
202A280ARG10.7700.86147.3335.9305.9300.0000.0000.0000.000
203A281GLN0-0.008-0.00750.7860.0610.0610.0000.0000.0000.000
204A282PRO0-0.0170.00248.8720.0410.0410.0000.0000.0000.000
205A283GLU-1-0.938-0.98844.192-6.382-6.3820.0000.0000.0000.000
206A284LEU0-0.004-0.01744.066-0.124-0.1240.0000.0000.0000.000
207A285GLU-1-0.840-0.88144.497-6.111-6.1110.0000.0000.0000.000
208A286ILE00.0260.02737.769-0.112-0.1120.0000.0000.0000.000
209A287CYS0-0.106-0.05640.1960.0330.0330.0000.0000.0000.000
210A288MET00.0400.04138.250-0.207-0.2070.0000.0000.0000.000
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