Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

tag_button

FMODB ID: 6NRLZ

Calculation Name: 4FQ1-L-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 4FQ1

Chain ID: L

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1930993.771527
FMO2-HF: Nuclear repulsion 1853440.89019
FMO2-HF: Total energy -77552.881336
FMO2-MP2: Total energy -77780.598985


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(L:9:SER)


Summations of interaction energy for fragment #1(L:9:SER)
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.
-3.1120.0670000000000010.502-1.609-2.072-0.01
Interaction energy analysis for fragmet #1(L:9:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.038 / q_NPA : -0.050
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].
3L11ILE00.0020.0023.782-0.2360.811-0.010-0.455-0.5820.001
4L12SER0-0.010-0.0176.1670.4630.4630.0000.0000.0000.000
5L13VAL0-0.0070.0069.6860.0400.0400.0000.0000.0000.000
6L14ALA00.0020.01112.4510.0240.0240.0000.0000.0000.000
7L15PRO00.005-0.00916.1460.0070.0070.0000.0000.0000.000
8L16GLY0-0.038-0.01218.7660.0210.0210.0000.0000.0000.000
9L17GLU-1-0.926-0.94515.061-0.336-0.3360.0000.0000.0000.000
10L18THR0-0.081-0.05915.2750.0020.0020.0000.0000.0000.000
11L19ALA00.0310.0369.927-0.040-0.0400.0000.0000.0000.000
12L20ARG10.8960.9269.6190.1140.1140.0000.0000.0000.000
13L21ILE00.0410.0344.6020.0300.054-0.001-0.003-0.0200.000
14L22SER0-0.024-0.0105.753-0.194-0.1940.0000.0000.0000.000
15L23CYS0-0.109-0.0475.7440.3430.3430.0000.0000.0000.000
16L24GLY00.005-0.0117.918-0.045-0.0450.0000.0000.0000.000
17L25GLU-1-0.893-0.9409.8500.3570.3570.0000.0000.0000.000
18L26LYS10.9070.95512.183-0.339-0.3390.0000.0000.0000.000
19L27SER0-0.0040.00014.640-0.011-0.0110.0000.0000.0000.000
20L28LEU0-0.048-0.02317.6910.0020.0020.0000.0000.0000.000
21L29GLY0-0.026-0.02321.064-0.010-0.0100.0000.0000.0000.000
22L30SER00.0270.01221.9620.0060.0060.0000.0000.0000.000
23L31ARG10.8140.90213.995-0.168-0.1680.0000.0000.0000.000
24L32ALA00.0240.02320.267-0.008-0.0080.0000.0000.0000.000
25L33VAL0-0.037-0.00813.8750.0000.0000.0000.0000.0000.000
26L34GLN00.0030.00916.630-0.011-0.0110.0000.0000.0000.000
27L35TRP00.031-0.0028.758-0.003-0.0030.0000.0000.0000.000
28L36TYR0-0.002-0.01213.0270.0180.0180.0000.0000.0000.000
29L37GLN00.0110.00512.482-0.030-0.0300.0000.0000.0000.000
30L38HIS0-0.018-0.01012.9420.0470.0470.0000.0000.0000.000
31L39ARG10.9470.97413.7860.1910.1910.0000.0000.0000.000
32L40ALA00.0590.03216.1160.0260.0260.0000.0000.0000.000
33L41GLY0-0.007-0.01517.2360.0160.0160.0000.0000.0000.000
34L42GLN0-0.036-0.01419.1070.0140.0140.0000.0000.0000.000
35L43ALA00.0070.00719.054-0.005-0.0050.0000.0000.0000.000
36L44PRO00.018-0.00116.264-0.013-0.0130.0000.0000.0000.000
37L45SER0-0.0180.00217.2950.0260.0260.0000.0000.0000.000
38L46LEU0-0.025-0.01117.298-0.022-0.0220.0000.0000.0000.000
39L47ILE0-0.004-0.01013.6620.0040.0040.0000.0000.0000.000
40L48ILE0-0.018-0.01216.1120.0070.0070.0000.0000.0000.000
41L49TYR00.004-0.00718.077-0.001-0.0010.0000.0000.0000.000
42L50ASN00.0030.01220.1920.0090.0090.0000.0000.0000.000
43L51ASN0-0.015-0.00118.1710.0100.0100.0000.0000.0000.000
44L52GLN0-0.102-0.08517.766-0.002-0.0020.0000.0000.0000.000
45L53ASP-1-0.835-0.89020.005-0.036-0.0360.0000.0000.0000.000
46L54ARG10.8990.93220.1450.0830.0830.0000.0000.0000.000
47L55PRO0-0.0180.01121.3190.0080.0080.0000.0000.0000.000
48L56SER00.0380.00124.189-0.007-0.0070.0000.0000.0000.000
49L57GLY0-0.0080.00125.679-0.001-0.0010.0000.0000.0000.000
50L58ILE0-0.061-0.01219.594-0.013-0.0130.0000.0000.0000.000
51L59PRO0-0.0090.00720.3840.0130.0130.0000.0000.0000.000
52L60GLU-1-0.907-0.98421.108-0.088-0.0880.0000.0000.0000.000
53L61ARG10.7850.89918.0960.2390.2390.0000.0000.0000.000
54L62PHE00.0510.04214.418-0.023-0.0230.0000.0000.0000.000
55L63SER00.015-0.01016.0230.0220.0220.0000.0000.0000.000
56L64GLY00.0480.04714.909-0.009-0.0090.0000.0000.0000.000
57L65SER0-0.009-0.01215.2280.0060.0060.0000.0000.0000.000
58L66PRO00.0220.01416.922-0.003-0.0030.0000.0000.0000.000
59L66ASP-1-0.871-0.94218.6670.0640.0640.0000.0000.0000.000
60L66SER0-0.0390.01420.5030.0040.0040.0000.0000.0000.000
61L66PRO00.000-0.02520.999-0.006-0.0060.0000.0000.0000.000
62L67PHE00.0260.00020.5170.0080.0080.0000.0000.0000.000
63L68GLY00.0130.02118.3610.0000.0000.0000.0000.0000.000
64L69THR0-0.048-0.02515.8950.0310.0310.0000.0000.0000.000
65L70THR00.026-0.0019.504-0.010-0.0100.0000.0000.0000.000
66L71ALA0-0.0060.01911.666-0.029-0.0290.0000.0000.0000.000
67L72THR0-0.009-0.0219.9730.1240.1240.0000.0000.0000.000
68L73LEU0-0.0160.01610.062-0.037-0.0370.0000.0000.0000.000
69L74THR0-0.030-0.03210.8580.0020.0020.0000.0000.0000.000
70L75ILE00.0160.02312.1570.0150.0150.0000.0000.0000.000
71L76THR00.004-0.01414.780-0.029-0.0290.0000.0000.0000.000
72L77SER00.004-0.01217.680-0.003-0.0030.0000.0000.0000.000
73L78VAL0-0.0010.02314.2460.0070.0070.0000.0000.0000.000
74L79GLU-1-0.888-0.95317.242-0.183-0.1830.0000.0000.0000.000
75L80ALA00.0540.02017.573-0.030-0.0300.0000.0000.0000.000
76L81GLY00.0130.01817.631-0.025-0.0250.0000.0000.0000.000
77L82ASP-1-0.806-0.89314.542-0.301-0.3010.0000.0000.0000.000
78L83GLU-1-0.769-0.86613.068-0.536-0.5360.0000.0000.0000.000
79L84ALA0-0.058-0.02411.8630.0960.0960.0000.0000.0000.000
80L85ASP-1-0.805-0.8498.942-0.892-0.8920.0000.0000.0000.000
81L86TYR0-0.038-0.0567.9540.3020.3020.0000.0000.0000.000
82L87TYR00.0050.0197.640-0.131-0.1310.0000.0000.0000.000
83L89HIS0-0.032-0.03111.8100.0080.0080.0000.0000.0000.000
84L90ILE0-0.014-0.01412.690-0.001-0.0010.0000.0000.0000.000
85L91TRP00.0160.01516.0170.0110.0110.0000.0000.0000.000
86L92ASP-1-0.674-0.86018.9540.1160.1160.0000.0000.0000.000
87L93SER0-0.0020.00720.9490.0000.0000.0000.0000.0000.000
88L94ARG10.9000.94723.071-0.099-0.0990.0000.0000.0000.000
89L95VAL0-0.034-0.02218.9570.0080.0080.0000.0000.0000.000
90L95PRO0-0.0070.00821.820-0.010-0.0100.0000.0000.0000.000
91L95THR0-0.008-0.00620.9080.0080.0080.0000.0000.0000.000
92L95LYS10.9640.99711.586-0.119-0.1190.0000.0000.0000.000
93L96TRP00.0260.00518.607-0.017-0.0170.0000.0000.0000.000
94L97VAL0-0.0050.01413.353-0.014-0.0140.0000.0000.0000.000
95L98PHE00.0120.00212.4350.0160.0160.0000.0000.0000.000
96L99GLY0-0.035-0.0309.9570.0440.0440.0000.0000.0000.000
97L100GLY00.0120.0015.6540.0010.0010.0000.0000.0000.000
98L101GLY00.021-0.0036.6120.1290.1290.0000.0000.0000.000
99L102THR0-0.029-0.0102.387-3.112-1.1000.514-1.138-1.388-0.011
100L103THR00.019-0.0044.5420.6770.773-0.001-0.013-0.0820.000
101L104LEU0-0.089-0.0356.811-0.553-0.5530.0000.0000.0000.000
102L105THR0-0.004-0.0049.2370.2960.2960.0000.0000.0000.000
103L106VAL0-0.045-0.02711.697-0.037-0.0370.0000.0000.0000.000
104L107LEU00.002-0.01512.8800.0630.0630.0000.0000.0000.000
105L108GLY00.010-0.00515.7580.0270.0270.0000.0000.0000.000
106L109GLN0-0.0330.00117.1650.0640.0640.0000.0000.0000.000
107L110PRO0-0.0070.00120.9950.0050.0050.0000.0000.0000.000
108L111LYS10.9430.97323.8160.1180.1180.0000.0000.0000.000
109L112ALA0-0.062-0.03224.8540.0090.0090.0000.0000.0000.000
110L113ALA00.0140.00326.306-0.002-0.0020.0000.0000.0000.000
111L114PRO00.0230.02027.6080.0000.0000.0000.0000.0000.000
112L115SER0-0.030-0.00329.0680.0080.0080.0000.0000.0000.000
113L116VAL00.008-0.01731.3760.0010.0010.0000.0000.0000.000
114L117THR0-0.020-0.01733.4730.0030.0030.0000.0000.0000.000
115L118LEU0-0.023-0.00635.5650.0000.0000.0000.0000.0000.000
116L119PHE0-0.008-0.00537.0390.0010.0010.0000.0000.0000.000
117L120PRO00.0040.00440.0480.0010.0010.0000.0000.0000.000
118L121PRO00.0340.02742.553-0.001-0.0010.0000.0000.0000.000
119L122SER00.0400.01943.6510.0000.0000.0000.0000.0000.000
120L123SER00.021-0.01745.7500.0010.0010.0000.0000.0000.000
121L124GLU-1-0.923-0.95346.809-0.014-0.0140.0000.0000.0000.000
122L125GLU-1-0.816-0.89141.542-0.012-0.0120.0000.0000.0000.000
123L126LEU0-0.032-0.02745.9110.0020.0020.0000.0000.0000.000
124L127GLN0-0.0220.01048.3440.0010.0010.0000.0000.0000.000
125L128ALA0-0.086-0.03246.8580.0010.0010.0000.0000.0000.000
126L129ASN0-0.067-0.04347.8710.0010.0010.0000.0000.0000.000
127L130LYS10.9360.95742.1940.0040.0040.0000.0000.0000.000
128L131ALA00.013-0.00343.424-0.001-0.0010.0000.0000.0000.000
129L132THR0-0.0030.00037.3070.0020.0020.0000.0000.0000.000
130L133LEU0-0.049-0.00638.319-0.002-0.0020.0000.0000.0000.000
131L134VAL00.0200.01434.6260.0000.0000.0000.0000.0000.000
132L135CYS0-0.081-0.02332.995-0.002-0.0020.0000.0000.0000.000
133L136LEU00.000-0.00931.235-0.001-0.0010.0000.0000.0000.000
134L137ILE00.0130.01327.471-0.001-0.0010.0000.0000.0000.000
135L138SER00.0150.00427.170-0.005-0.0050.0000.0000.0000.000
136L139ASP-1-0.837-0.93025.961-0.111-0.1110.0000.0000.0000.000
137L140PHE0-0.025-0.00222.2190.0010.0010.0000.0000.0000.000
138L141TYR00.024-0.00516.814-0.004-0.0040.0000.0000.0000.000
139L142PRO00.0800.03018.6540.0100.0100.0000.0000.0000.000
140L143GLY00.0480.02518.4730.0210.0210.0000.0000.0000.000
141L144ALA0-0.024-0.00118.8900.0200.0200.0000.0000.0000.000
142L145VAL00.0190.00620.434-0.001-0.0010.0000.0000.0000.000
143L146THR0-0.057-0.01823.8000.0110.0110.0000.0000.0000.000
144L147VAL00.0530.01926.402-0.004-0.0040.0000.0000.0000.000
145L148ALA0-0.088-0.04129.5680.0070.0070.0000.0000.0000.000
146L149TRP00.0650.02432.632-0.003-0.0030.0000.0000.0000.000
147L150LYS10.8880.94436.0140.0230.0230.0000.0000.0000.000
148L151ALA00.0700.04639.572-0.001-0.0010.0000.0000.0000.000
149L152ASP-1-0.830-0.93942.911-0.014-0.0140.0000.0000.0000.000
150L153SER0-0.008-0.01643.176-0.002-0.0020.0000.0000.0000.000
151L154SER0-0.032-0.01042.3210.0000.0000.0000.0000.0000.000
152L155PRO0-0.047-0.02337.327-0.001-0.0010.0000.0000.0000.000
153L156VAL00.0220.01837.5420.0030.0030.0000.0000.0000.000
154L157LYS10.9180.94631.2000.0090.0090.0000.0000.0000.000
155L158ALA00.0230.00934.4120.0020.0020.0000.0000.0000.000
156L159GLY00.0660.02735.856-0.002-0.0020.0000.0000.0000.000
157L160VAL0-0.047-0.01731.040-0.003-0.0030.0000.0000.0000.000
158L161GLU-1-0.897-0.93129.9700.0100.0100.0000.0000.0000.000
159L162THR00.0020.02125.963-0.008-0.0080.0000.0000.0000.000
160L163THR00.0080.02424.1790.0040.0040.0000.0000.0000.000
161L164THR0-0.018-0.01718.0010.0040.0040.0000.0000.0000.000
162L165PRO0-0.032-0.00719.380-0.004-0.0040.0000.0000.0000.000
163L166SER0-0.0130.00218.671-0.007-0.0070.0000.0000.0000.000
164L167LYS10.8450.92215.2530.3790.3790.0000.0000.0000.000
165L168GLN0-0.018-0.04818.6780.0190.0190.0000.0000.0000.000
166L169SER00.0340.00219.992-0.019-0.0190.0000.0000.0000.000
167L170ASN0-0.0580.00220.960-0.023-0.0230.0000.0000.0000.000
168L171ASN0-0.007-0.02118.2020.0030.0030.0000.0000.0000.000
169L172LYS10.9070.97919.8320.1290.1290.0000.0000.0000.000
170L173TYR0-0.0150.00515.130-0.023-0.0230.0000.0000.0000.000
171L174ALA00.0190.01621.9020.0100.0100.0000.0000.0000.000
172L175ALA0-0.033-0.02823.360-0.001-0.0010.0000.0000.0000.000
173L176SER0-0.006-0.00425.6480.0020.0020.0000.0000.0000.000
174L177SER0-0.026-0.05828.3060.0040.0040.0000.0000.0000.000
175L178TYR00.0230.01930.428-0.002-0.0020.0000.0000.0000.000
176L179LEU0-0.0050.01333.8810.0030.0030.0000.0000.0000.000
177L180SER00.0080.00236.686-0.001-0.0010.0000.0000.0000.000
178L181LEU0-0.045-0.03338.9390.0010.0010.0000.0000.0000.000
179L182THR00.0400.02242.5280.0000.0000.0000.0000.0000.000
180L183PRO00.0390.00145.888-0.001-0.0010.0000.0000.0000.000
181L184GLU-1-0.968-0.98948.338-0.004-0.0040.0000.0000.0000.000
182L185GLN00.0580.02944.349-0.001-0.0010.0000.0000.0000.000
183L186TRP00.0100.00443.896-0.001-0.0010.0000.0000.0000.000
184L187LYS10.9360.95846.4500.0090.0090.0000.0000.0000.000
185L188SER0-0.058-0.00248.4570.0000.0000.0000.0000.0000.000
186L189HIS0-0.048-0.02045.9980.0000.0000.0000.0000.0000.000
187L190ARG10.9410.96648.5070.0120.0120.0000.0000.0000.000
188L191SER0-0.047-0.01845.594-0.002-0.0020.0000.0000.0000.000
189L192TYR00.0430.01740.9990.0020.0020.0000.0000.0000.000
190L193SER00.0260.01039.487-0.002-0.0020.0000.0000.0000.000
191L195GLN0-0.069-0.06534.215-0.003-0.0030.0000.0000.0000.000
192L196VAL00.0360.02228.5370.0010.0010.0000.0000.0000.000
193L197THR0-0.020-0.01027.795-0.002-0.0020.0000.0000.0000.000
194L198HIS0-0.034-0.04523.0350.0100.0100.0000.0000.0000.000
195L199GLU-1-0.908-0.96122.067-0.157-0.1570.0000.0000.0000.000
196L200GLY0-0.020-0.00925.7270.0010.0010.0000.0000.0000.000
197L201SER0-0.034-0.00628.6950.0080.0080.0000.0000.0000.000
198L202THR00.0240.01030.398-0.002-0.0020.0000.0000.0000.000
199L203VAL0-0.008-0.00232.1200.0020.0020.0000.0000.0000.000
200L204GLU-1-0.843-0.91034.608-0.030-0.0300.0000.0000.0000.000
201L205LYS10.8730.95636.6010.0480.0480.0000.0000.0000.000
202L206THR00.0410.00238.8730.0010.0010.0000.0000.0000.000
203L207VAL0-0.028-0.00141.741-0.001-0.0010.0000.0000.0000.000
204L208ALA00.0310.00044.1020.0010.0010.0000.0000.0000.000
205L209PRO0-0.0260.01047.4410.0000.0000.0000.0000.0000.000