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: J34Y9

Calculation Name: 3ALZ-AB-Docking371-PPRV(D506N)-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 -10999178.733048
FMO2-HF: Nuclear repulsion 10787969.688537
FMO2-HF: Total energy -211209.044512
FMO2-MP2: Total energy -211817.364073


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.
-932.5817-1953.62172952.5912-1791.4987-140.05250.2924


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.
-40.998-26.96215.49-10.391-19.1360.022
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 : 0.812 / q_NPA : 0.889
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].
3B34LYS10.9490.9843.83833.83234.884-0.001-0.412-0.6390.002
16B47LEU0-0.007-0.0025.128-2.685-2.555-0.002-0.009-0.1190.000
17B48THR00.0050.0283.689-9.791-9.5320.008-0.115-0.1530.000
39B70LEU00.002-0.0135.668-0.170-0.006-0.002-0.009-0.1520.000
86B117TRP0-0.013-0.0063.205-1.932-0.6800.328-0.284-1.297-0.002
87B118TYR0-0.036-0.0374.7624.5724.894-0.001-0.076-0.2450.000
88B119PHE00.023-0.0162.256-17.148-12.28610.397-6.621-8.638-0.006
89B120MET0-0.0040.0142.087-6.930-7.9563.831-0.365-2.4400.033
90B121THR0-0.023-0.0023.510-4.869-4.3370.0650.060-0.658-0.001
98B129GLN00.2730.2615.220-0.066-0.079-0.002-0.0060.0220.000
99B130ARG10.8390.9172.91519.97023.4170.302-1.762-1.986-0.002
102B134HIS00.0130.0033.0002.4375.3600.571-0.772-2.723-0.002
103B135LEU00.0230.0334.6360.5880.604-0.002-0.013-0.0010.000
467A548SER0-0.016-0.0225.773-3.613-3.497-0.002-0.007-0.1070.000
4B35ILE0-0.0040.0025.8553.8063.8060.0000.0000.0000.000
5B36VAL0-0.010-0.0098.7870.5050.5050.0000.0000.0000.000
6B37GLN0-0.007-0.01112.0391.4931.4930.0000.0000.0000.000
7B38GLN00.0370.02614.6840.5970.5970.0000.0000.0000.000
8B39LEU00.0000.01117.783-0.184-0.1840.0000.0000.0000.000
9B40GLY00.0110.01418.8750.6030.6030.0000.0000.0000.000
10B41SER0-0.054-0.03718.3510.2420.2420.0000.0000.0000.000
11B42ASP-1-0.825-0.91618.685-13.853-13.8530.0000.0000.0000.000
12B43VAL0-0.047-0.00413.547-0.441-0.4410.0000.0000.0000.000
13B44LEU00.026-0.00313.979-0.092-0.0920.0000.0000.0000.000
14B45LEU00.005-0.0197.784-0.789-0.7890.0000.0000.0000.000
15B46PRO0-0.031-0.0239.0510.8670.8670.0000.0000.0000.000
18B49HIS0-0.013-0.0185.3560.9850.9850.0000.0000.0000.000
19B50GLU-1-0.913-0.9776.920-22.492-22.4920.0000.0000.0000.000
20B51ARG10.9060.94210.32420.82020.8200.0000.0000.0000.000
21B52ILE00.0180.02913.3461.0681.0680.0000.0000.0000.000
22B53ASN00.0120.00410.0320.0060.0060.0000.0000.0000.000
23B54THR00.0340.02713.3210.4140.4140.0000.0000.0000.000
24B55SER0-0.031-0.00913.8561.0761.0760.0000.0000.0000.000
25B56MET00.0020.01814.089-0.655-0.6550.0000.0000.0000.000
26B57ASN0-0.010-0.00514.4870.6880.6880.0000.0000.0000.000
27B58LYS10.8540.93815.25612.61812.6180.0000.0000.0000.000
28B59SER00.0460.01110.822-0.842-0.8420.0000.0000.0000.000
29B60ILE0-0.064-0.03212.919-0.134-0.1340.0000.0000.0000.000
30B61HIS00.0740.04913.1950.2250.2250.0000.0000.0000.000
31B62ILE00.0230.0138.778-1.013-1.0130.0000.0000.0000.000
32B63VAL00.0060.0148.5330.9700.9700.0000.0000.0000.000
33B64VAL0-0.017-0.0016.925-0.984-0.9840.0000.0000.0000.000
34B65THR0-0.016-0.0406.5410.8250.8250.0000.0000.0000.000
35B66MET0-0.046-0.0206.641-1.249-1.2490.0000.0000.0000.000
36B67ALA00.0150.0237.4141.5561.5560.0000.0000.0000.000
37B68LYS10.9040.9508.79615.93215.9320.0000.0000.0000.000
38B69SER0-0.0010.00610.833-1.595-1.5950.0000.0000.0000.000
40B71GLU-1-0.909-0.9519.409-16.828-16.8280.0000.0000.0000.000
41B72ASN00.014-0.01212.9170.6980.6980.0000.0000.0000.000
42B73SER0-0.059-0.00710.3160.7160.7160.0000.0000.0000.000
43B74VAL00.010-0.01311.5130.8990.8990.0000.0000.0000.000
44B75GLU-1-0.797-0.8477.531-19.387-19.3870.0000.0000.0000.000
45B76ASN00.0070.01210.9421.4281.4280.0000.0000.0000.000
46B77LYS10.8970.93010.94312.67712.6770.0000.0000.0000.000
47B78ILE0-0.063-0.03210.2110.5370.5370.0000.0000.0000.000
48B79VAL00.000-0.01811.6190.8090.8090.0000.0000.0000.000
49B80SER00.0510.04011.617-0.632-0.6320.0000.0000.0000.000
50B81LEU0-0.057-0.03013.2110.6140.6140.0000.0000.0000.000
51B82ASP-1-0.703-0.84314.490-12.785-12.7850.0000.0000.0000.000
52B83PRO0-0.066-0.01814.7260.4040.4040.0000.0000.0000.000
53B84SER0-0.097-0.08517.4400.1650.1650.0000.0000.0000.000
54B85GLU-1-0.911-0.93820.528-9.603-9.6030.0000.0000.0000.000
55B86ALA0-0.012-0.00821.296-0.380-0.3800.0000.0000.0000.000
56B87GLY0-0.0150.00323.6900.0050.0050.0000.0000.0000.000
57B88PRO0-0.029-0.01521.114-0.421-0.4210.0000.0000.0000.000
58B89PRO00.0220.01516.5700.1930.1930.0000.0000.0000.000
59B90ARG10.9770.98118.51610.80410.8040.0000.0000.0000.000
60B91TYR00.0230.00014.916-0.583-0.5830.0000.0000.0000.000
61B92LEU0-0.026-0.00515.6340.5600.5600.0000.0000.0000.000
62B93LYS10.8200.90917.15711.77111.7710.0000.0000.0000.000
63B94ASP-1-0.899-0.93718.126-11.824-11.8240.0000.0000.0000.000
64B95ARG10.8920.91316.15114.80414.8040.0000.0000.0000.000
65B96TYR0-0.019-0.00312.3810.2360.2360.0000.0000.0000.000
66B97ARG10.9380.98215.09414.33714.3370.0000.0000.0000.000
67B98PHE00.0190.0019.410-0.840-0.8400.0000.0000.0000.000
68B99TYR0-0.025-0.00813.5671.4641.4640.0000.0000.0000.000
69B100LEU00.0080.01012.986-1.156-1.1560.0000.0000.0000.000
70B101GLU-1-0.810-0.93813.555-15.258-15.2580.0000.0000.0000.000
71B102ASN0-0.077-0.05913.6230.3600.3600.0000.0000.0000.000
72B103LEU0-0.0130.0098.079-1.785-1.7850.0000.0000.0000.000
73B104SER00.0020.0058.875-2.161-2.1610.0000.0000.0000.000
74B105LEU0-0.005-0.0079.2421.5621.5620.0000.0000.0000.000
75B106ALA0-0.028-0.01611.557-0.655-0.6550.0000.0000.0000.000
76B107ILE0-0.057-0.02811.0360.4060.4060.0000.0000.0000.000
77B108ARG10.9660.97815.31412.23612.2360.0000.0000.0000.000
78B109GLU-1-0.910-0.95719.085-11.675-11.6750.0000.0000.0000.000
79B110SER0-0.069-0.01716.169-0.138-0.1380.0000.0000.0000.000
80B111THR00.036-0.01017.5060.4670.4670.0000.0000.0000.000
81B112LYS10.9620.97916.49114.14614.1460.0000.0000.0000.000
82B113LYS10.8510.91216.16912.78912.7890.0000.0000.0000.000
83B114ASP-1-0.726-0.82613.668-16.407-16.4070.0000.0000.0000.000
84B115GLU-1-0.847-0.90911.341-21.361-21.3610.0000.0000.0000.000
85B116GLY00.0080.0059.2041.6161.6160.0000.0000.0000.000
91B122LEU00.0020.0055.8651.2341.2340.0000.0000.0000.000
92B123GLU-1-0.811-0.9157.999-16.163-16.1630.0000.0000.0000.000
93B124LYS0-0.009-0.02111.1730.8760.8760.0000.0000.0000.000
94B125ASN0-0.010-0.01514.2840.0330.0330.0000.0000.0000.000
95B126ILE00.0220.01316.6160.3240.3240.0000.0000.0000.000
96B127SER0-0.029-0.01512.537-0.137-0.1370.0000.0000.0000.000
97B128VAL00.0350.0228.2140.2810.2810.0000.0000.0000.000
104B136LYS10.8270.9158.32726.52926.5290.0000.0000.0000.000
105B137LEU00.001-0.01311.005-0.141-0.1410.0000.0000.0000.000
106B138TYR0-0.0120.00314.7400.4410.4410.0000.0000.0000.000
107B139GLU-1-0.870-0.95817.506-13.223-13.2230.0000.0000.0000.000
108B140GLN0-0.037-0.03221.212-0.350-0.3500.0000.0000.0000.000
109B141NME00.0360.04023.6500.5050.5050.0000.0000.0000.000
110A606CYS0-0.052-0.0187.3666.7066.7060.0000.0000.0000.000
111A189LEU00.0520.0246.1332.1232.1230.0000.0000.0000.000
112A190GLY00.0400.0195.840-5.142-5.1420.0000.0000.0000.000
113A191ARG0-0.297-0.2615.568-3.608-3.6080.0000.0000.0000.000
114A192THR0-0.002-0.0046.0613.1583.1580.0000.0000.0000.000
115A193ILE00.017-0.0087.362-0.474-0.4740.0000.0000.0000.000
116A194THR0-0.0020.01710.1440.2820.2820.0000.0000.0000.000
117A195ARG10.9370.96712.29315.08615.0860.0000.0000.0000.000
118A196ALA00.0480.02115.853-0.084-0.0840.0000.0000.0000.000
119A197HIS0-0.042-0.01918.950-0.012-0.0120.0000.0000.0000.000
120A198PHE00.0220.01320.791-0.149-0.1490.0000.0000.0000.000
121A199SER0-0.007-0.01225.1110.2510.2510.0000.0000.0000.000
122A200GLU-1-0.893-0.94728.700-8.659-8.6590.0000.0000.0000.000
123A201LEU0-0.050-0.02231.9030.2000.2000.0000.0000.0000.000
124A202THR0-0.002-0.02033.542-0.149-0.1490.0000.0000.0000.000
125A203LEU0-0.032-0.02136.1300.1910.1910.0000.0000.0000.000
126A204THR0-0.007-0.00436.4400.0880.0880.0000.0000.0000.000
127A205LEU0-0.0090.00239.0750.0170.0170.0000.0000.0000.000
128A206MET00.0160.02233.7100.0210.0210.0000.0000.0000.000
129A207ASP-1-0.836-0.91734.152-8.432-8.4320.0000.0000.0000.000
130A208LEU00.0440.02636.7940.0060.0060.0000.0000.0000.000
131A209ASP-1-0.834-0.93540.094-6.693-6.6930.0000.0000.0000.000
132A210LEU0-0.022-0.01934.5700.0570.0570.0000.0000.0000.000
133A211GLU-1-1.012-0.99237.445-7.543-7.5430.0000.0000.0000.000
134A212MET0-0.077-0.05138.2970.0590.0590.0000.0000.0000.000
135A213LYS10.8800.94638.0997.2877.2870.0000.0000.0000.000
136A214HIS00.0310.03640.7970.1520.1520.0000.0000.0000.000
137A215ASN0-0.009-0.01241.112-0.222-0.2220.0000.0000.0000.000
138A216VAL0-0.036-0.01538.2970.1010.1010.0000.0000.0000.000
139A217SER00.027-0.01038.081-0.186-0.1860.0000.0000.0000.000
140A218SER0-0.035-0.02338.4120.0100.0100.0000.0000.0000.000
141A219VAL00.0150.01234.4490.0770.0770.0000.0000.0000.000
142A220LEU0-0.065-0.02933.065-0.201-0.2010.0000.0000.0000.000
143A221THR0-0.014-0.01131.2370.1540.1540.0000.0000.0000.000
144A222VAL00.002-0.00330.309-0.222-0.2220.0000.0000.0000.000
145A223VAL0-0.0050.00427.5890.1980.1980.0000.0000.0000.000
146A224GLU-1-0.852-0.92930.044-10.050-10.0500.0000.0000.0000.000
147A225GLU-1-0.890-0.95131.342-8.175-8.1750.0000.0000.0000.000
148A226GLY0-0.054-0.02931.301-0.289-0.2890.0000.0000.0000.000
149A227LEU0-0.066-0.02432.6480.1900.1900.0000.0000.0000.000
150A228PHE0-0.010-0.00132.869-0.304-0.3040.0000.0000.0000.000
151A229GLY00.0430.02234.5580.2750.2750.0000.0000.0000.000
152A230ARG10.8050.89232.7928.1658.1650.0000.0000.0000.000
153A231THR0-0.019-0.00437.5170.2360.2360.0000.0000.0000.000
154A232TYR0-0.055-0.02938.522-0.221-0.2210.0000.0000.0000.000
155A233THR00.0300.01440.3720.1540.1540.0000.0000.0000.000
156A234VAL00.0090.00642.076-0.124-0.1240.0000.0000.0000.000
157A235TRP00.0280.01844.4630.1210.1210.0000.0000.0000.000
158A236ARG10.8340.88646.7145.8155.8150.0000.0000.0000.000
159A237SER00.0320.03349.3710.0320.0320.0000.0000.0000.000
160A238ASP-1-0.812-0.89252.439-5.403-5.4030.0000.0000.0000.000
161A239ALA0-0.019-0.01654.279-0.030-0.0300.0000.0000.0000.000
162A240ARG10.8500.91257.0935.0265.0260.0000.0000.0000.000
163A241ASP-1-0.917-0.95454.426-5.376-5.3760.0000.0000.0000.000
164A242PRO0-0.0310.02054.9830.0440.0440.0000.0000.0000.000
165A243SER0-0.021-0.03452.969-0.124-0.1240.0000.0000.0000.000
166A244THR00.0690.02649.568-0.115-0.1150.0000.0000.0000.000
167A245ASP-1-0.949-0.95352.787-5.114-5.1140.0000.0000.0000.000
168A246LEU0-0.007-0.00150.524-0.082-0.0820.0000.0000.0000.000
169A247GLY0-0.022-0.01854.4670.0690.0690.0000.0000.0000.000
170A248ILE0-0.051-0.03554.8180.0840.0840.0000.0000.0000.000
171A249GLY00.0550.02651.613-0.060-0.0600.0000.0000.0000.000
172A250HIS0-0.050-0.02451.858-0.049-0.0490.0000.0000.0000.000
173A251PHE00.0420.01447.673-0.093-0.0930.0000.0000.0000.000
174A252LEU0-0.029-0.00747.8040.1000.1000.0000.0000.0000.000
175A253ARG10.8300.91840.9586.7346.7340.0000.0000.0000.000
176A254VAL00.0140.01343.0120.1250.1250.0000.0000.0000.000
177A255PHE00.017-0.00842.479-0.163-0.1630.0000.0000.0000.000
178A256GLU-1-0.756-0.90239.374-7.342-7.3420.0000.0000.0000.000
179A257ILE0-0.002-0.00138.856-0.184-0.1840.0000.0000.0000.000
180A258GLY00.0460.02038.2080.2010.2010.0000.0000.0000.000
181A259LEU0-0.040-0.00836.218-0.139-0.1390.0000.0000.0000.000
182A260VAL00.0200.00930.1860.0730.0730.0000.0000.0000.000
183A261ARG10.8860.94033.5797.6297.6290.0000.0000.0000.000
184A262ASP-1-0.847-0.92132.027-9.699-9.6990.0000.0000.0000.000
185A263LEU0-0.014-0.02033.9520.2720.2720.0000.0000.0000.000
186A264GLY0-0.031-0.01434.8480.1930.1930.0000.0000.0000.000
187A265LEU0-0.018-0.01333.792-0.077-0.0770.0000.0000.0000.000
188A266GLY0-0.0250.00329.937-0.092-0.0920.0000.0000.0000.000
189A267PRO0-0.041-0.02028.207-0.428-0.4280.0000.0000.0000.000
190A268PRO0-0.029-0.00727.5610.2820.2820.0000.0000.0000.000
191A269VAL00.0080.00030.5790.0510.0510.0000.0000.0000.000
192A270PHE00.0250.02029.665-0.032-0.0320.0000.0000.0000.000
193A271HIS00.0000.00934.8020.0560.0560.0000.0000.0000.000
194A272MET0-0.0040.01338.542-0.033-0.0330.0000.0000.0000.000
195A273THR0-0.109-0.09140.9740.0400.0400.0000.0000.0000.000
196A274ASN0-0.050-0.03643.1760.2740.2740.0000.0000.0000.000
197A275TYR00.009-0.00543.637-0.129-0.1290.0000.0000.0000.000
198A276LEU00.0170.03045.7450.1320.1320.0000.0000.0000.000
199A277THR00.004-0.00146.749-0.168-0.1680.0000.0000.0000.000
200A278VAL00.0140.00748.7250.1300.1300.0000.0000.0000.000
201A279ASN00.0260.01449.868-0.139-0.1390.0000.0000.0000.000
202A280MET0-0.068-0.00845.669-0.026-0.0260.0000.0000.0000.000
203A281SER0-0.022-0.02151.3360.0650.0650.0000.0000.0000.000
204A282ASP-1-0.830-0.91648.788-5.886-5.8860.0000.0000.0000.000
205A283ASP-1-0.865-0.93344.933-6.296-6.2960.0000.0000.0000.000
206A284TYR00.0160.00444.206-0.166-0.1660.0000.0000.0000.000
207A285ARG10.7940.89443.9075.7595.7590.0000.0000.0000.000
208A286ARG10.8560.92539.5776.9216.9210.0000.0000.0000.000
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