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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

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FMODB ID: R9KN8

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 OptAll
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 -1931694.060685
FMO2-HF: Nuclear repulsion 1854140.019809
FMO2-HF: Total energy -77554.040875
FMO2-MP2: Total energy -77781.874019


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.
-0.132.070.011-0.952-1.2580.003
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 : -0.021 / q_NPA : -0.019
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].
3L11ILE0-0.027-0.0083.8670.0751.597-0.010-0.735-0.7770.004
4L12SER0-0.021-0.0246.5030.7560.7560.0000.0000.0000.000
5L13VAL0-0.0090.00910.0050.0820.0820.0000.0000.0000.000
6L14ALA0-0.008-0.00212.7940.0370.0370.0000.0000.0000.000
7L15PRO0-0.011-0.01716.605-0.041-0.0410.0000.0000.0000.000
8L16GLY0-0.025-0.01019.2420.0650.0650.0000.0000.0000.000
9L17GLU-1-0.875-0.92214.706-0.748-0.7480.0000.0000.0000.000
10L18THR0-0.062-0.05214.3590.0420.0420.0000.0000.0000.000
11L19ALA00.0330.04910.517-0.045-0.0450.0000.0000.0000.000
12L20ARG10.8820.9119.6231.0611.0610.0000.0000.0000.000
13L21ILE00.0480.0375.266-0.485-0.4850.0000.0000.0000.000
14L22SER00.0030.0025.9860.6300.6300.0000.0000.0000.000
15L23CYS0-0.098-0.0325.865-0.335-0.3350.0000.0000.0000.000
16L24GLY00.0280.0098.2700.1720.1720.0000.0000.0000.000
17L25GLU-1-0.801-0.88710.1950.1260.1260.0000.0000.0000.000
18L26LYS10.8600.91912.774-0.388-0.3880.0000.0000.0000.000
19L27SER00.0190.00514.9800.0380.0380.0000.0000.0000.000
20L28LEU0-0.021-0.01218.0320.0420.0420.0000.0000.0000.000
21L29GLY00.0030.00821.3620.0140.0140.0000.0000.0000.000
22L30SER00.0140.00321.807-0.007-0.0070.0000.0000.0000.000
23L31ARG10.7330.84515.0560.1200.1200.0000.0000.0000.000
24L32ALA00.0400.03620.733-0.003-0.0030.0000.0000.0000.000
25L33VAL0-0.043-0.01714.5450.0030.0030.0000.0000.0000.000
26L34GLN00.0180.01917.2770.0010.0010.0000.0000.0000.000
27L35TRP00.019-0.0119.107-0.094-0.0940.0000.0000.0000.000
28L36TYR0-0.002-0.01113.5370.1310.1310.0000.0000.0000.000
29L37GLN00.0480.02912.925-0.102-0.1020.0000.0000.0000.000
30L38HIS0-0.007-0.00813.4000.1210.1210.0000.0000.0000.000
31L39ARG10.8520.91814.0600.6770.6770.0000.0000.0000.000
32L40ALA00.0630.03116.3170.0730.0730.0000.0000.0000.000
33L41GLY00.0320.01817.5010.0510.0510.0000.0000.0000.000
34L42GLN0-0.0100.01319.4850.0180.0180.0000.0000.0000.000
35L43ALA00.0210.00919.566-0.014-0.0140.0000.0000.0000.000
36L44PRO0-0.003-0.00916.566-0.045-0.0450.0000.0000.0000.000
37L45SER0-0.033-0.00817.4590.0780.0780.0000.0000.0000.000
38L46LEU0-0.019-0.01117.573-0.080-0.0800.0000.0000.0000.000
39L47ILE0-0.019-0.01514.2290.0240.0240.0000.0000.0000.000
40L48ILE0-0.017-0.00416.1830.0160.0160.0000.0000.0000.000
41L49TYR00.016-0.00518.779-0.013-0.0130.0000.0000.0000.000
42L50ASN0-0.030-0.02620.8870.0150.0150.0000.0000.0000.000
43L51ASN0-0.027-0.02218.3240.0130.0130.0000.0000.0000.000
44L52GLN0-0.079-0.06317.879-0.033-0.0330.0000.0000.0000.000
45L53ASP-1-0.830-0.87420.139-0.299-0.2990.0000.0000.0000.000
46L54ARG10.7990.86520.8670.4080.4080.0000.0000.0000.000
47L55PRO0-0.0110.00522.0020.0410.0410.0000.0000.0000.000
48L56SER00.003-0.01324.887-0.020-0.0200.0000.0000.0000.000
49L57GLY00.0150.01226.3780.0080.0080.0000.0000.0000.000
50L58ILE0-0.051-0.00420.344-0.024-0.0240.0000.0000.0000.000
51L59PRO0-0.0030.00821.5230.0350.0350.0000.0000.0000.000
52L60GLU-1-0.816-0.91621.859-0.426-0.4260.0000.0000.0000.000
53L61ARG10.7130.82317.8700.7470.7470.0000.0000.0000.000
54L62PHE00.0080.02015.234-0.093-0.0930.0000.0000.0000.000
55L63SER00.0170.00616.6000.1000.1000.0000.0000.0000.000
56L64GLY00.0510.02715.284-0.135-0.1350.0000.0000.0000.000
57L65SER0-0.0120.01114.8740.0380.0380.0000.0000.0000.000
58L66PRO00.0350.01916.680-0.003-0.0030.0000.0000.0000.000
59L66ASP-1-0.818-0.89318.358-0.171-0.1710.0000.0000.0000.000
60L66SER0-0.039-0.01420.3200.0390.0390.0000.0000.0000.000
61L66PRO00.000-0.01020.987-0.020-0.0200.0000.0000.0000.000
62L67PHE00.0240.01220.243-0.010-0.0100.0000.0000.0000.000
63L68GLY00.0240.02618.6920.0170.0170.0000.0000.0000.000
64L69THR0-0.046-0.03715.6870.0550.0550.0000.0000.0000.000
65L70THR0-0.018-0.0069.2670.0670.0670.0000.0000.0000.000
66L71ALA00.0230.03112.333-0.042-0.0420.0000.0000.0000.000
67L72THR0-0.016-0.0369.753-0.052-0.0520.0000.0000.0000.000
68L73LEU00.0090.03410.4740.1850.1850.0000.0000.0000.000
69L74THR0-0.029-0.02811.088-0.187-0.1870.0000.0000.0000.000
70L75ILE00.0110.02312.3110.1060.1060.0000.0000.0000.000
71L76THR00.019-0.01515.075-0.046-0.0460.0000.0000.0000.000
72L77SER00.002-0.00417.7920.0130.0130.0000.0000.0000.000
73L78VAL0-0.0210.00714.4150.0210.0210.0000.0000.0000.000
74L79GLU-1-0.826-0.89817.683-0.510-0.5100.0000.0000.0000.000
75L80ALA00.0530.01318.268-0.085-0.0850.0000.0000.0000.000
76L81GLY00.0140.01618.466-0.053-0.0530.0000.0000.0000.000
77L82ASP-1-0.739-0.83714.911-0.938-0.9380.0000.0000.0000.000
78L83GLU-1-0.740-0.84413.801-1.254-1.2540.0000.0000.0000.000
79L84ALA0-0.042-0.02312.6960.2030.2030.0000.0000.0000.000
80L85ASP-1-0.802-0.8659.373-2.186-2.1860.0000.0000.0000.000
81L86TYR0-0.059-0.0488.5080.6100.6100.0000.0000.0000.000
82L87TYR00.0040.0218.092-0.397-0.3970.0000.0000.0000.000
83L89HIS0-0.010-0.00212.2780.0550.0550.0000.0000.0000.000
84L90ILE0-0.018-0.01112.7950.0250.0250.0000.0000.0000.000
85L91TRP00.0250.01616.2070.0740.0740.0000.0000.0000.000
86L92ASP-1-0.704-0.85619.373-0.044-0.0440.0000.0000.0000.000
87L93SER00.001-0.00721.3550.0230.0230.0000.0000.0000.000
88L94ARG10.8110.89323.522-0.049-0.0490.0000.0000.0000.000
89L95VAL0-0.015-0.00418.9760.0340.0340.0000.0000.0000.000
90L95PRO0-0.0070.00722.103-0.024-0.0240.0000.0000.0000.000
91L95THR0-0.009-0.01521.112-0.005-0.0050.0000.0000.0000.000
92L95LYS10.9290.96612.6730.0430.0430.0000.0000.0000.000
93L96TRP0-0.007-0.01317.991-0.056-0.0560.0000.0000.0000.000
94L97VAL0-0.0090.00613.398-0.012-0.0120.0000.0000.0000.000
95L98PHE0-0.018-0.00912.4990.0310.0310.0000.0000.0000.000
96L99GLY00.0030.0039.6880.1040.1040.0000.0000.0000.000
97L100GLY00.008-0.0165.811-0.057-0.0570.0000.0000.0000.000
98L101GLY00.004-0.0176.4440.2690.2690.0000.0000.0000.000
99L102THR0-0.058-0.0163.0360.0920.6910.022-0.215-0.406-0.001
100L103THR00.018-0.0125.1510.8100.889-0.001-0.002-0.0750.000
101L104LEU0-0.080-0.0337.121-1.001-1.0010.0000.0000.0000.000
102L105THR0-0.020-0.0109.7840.5100.5100.0000.0000.0000.000
103L106VAL0-0.046-0.03111.898-0.049-0.0490.0000.0000.0000.000
104L107LEU00.0310.00512.9350.1390.1390.0000.0000.0000.000
105L108GLY0-0.007-0.01316.2490.0360.0360.0000.0000.0000.000
106L109GLN0-0.040-0.01317.4780.1070.1070.0000.0000.0000.000
107L110PRO0-0.019-0.00421.3260.0210.0210.0000.0000.0000.000
108L111LYS10.8350.90623.8990.2430.2430.0000.0000.0000.000
109L112ALA0-0.052-0.02224.7860.0210.0210.0000.0000.0000.000
110L113ALA00.0350.01526.183-0.009-0.0090.0000.0000.0000.000
111L114PRO0-0.0080.00727.603-0.008-0.0080.0000.0000.0000.000
112L115SER00.0200.01028.9750.0250.0250.0000.0000.0000.000
113L116VAL0-0.033-0.01931.0460.0020.0020.0000.0000.0000.000
114L117THR0-0.0120.00432.9740.0120.0120.0000.0000.0000.000
115L118LEU0-0.045-0.01635.119-0.003-0.0030.0000.0000.0000.000
116L119PHE0-0.0120.00036.3750.0030.0030.0000.0000.0000.000
117L120PRO00.0090.00339.9140.0020.0020.0000.0000.0000.000
118L121PRO00.0190.02942.353-0.004-0.0040.0000.0000.0000.000
119L122SER00.0220.01643.4750.0020.0020.0000.0000.0000.000
120L123SER00.031-0.01345.4970.0030.0030.0000.0000.0000.000
121L124GLU-1-0.914-0.94946.889-0.072-0.0720.0000.0000.0000.000
122L125GLU-1-0.824-0.90641.607-0.070-0.0700.0000.0000.0000.000
123L126LEU0-0.010-0.01045.8700.0050.0050.0000.0000.0000.000
124L127GLN0-0.057-0.02148.5170.0040.0040.0000.0000.0000.000
125L128ALA0-0.046-0.01246.7910.0030.0030.0000.0000.0000.000
126L129ASN0-0.055-0.03547.8040.0010.0010.0000.0000.0000.000
127L130LYS10.9300.96042.8460.0540.0540.0000.0000.0000.000
128L131ALA00.021-0.00543.443-0.001-0.0010.0000.0000.0000.000
129L132THR00.003-0.01237.0440.0040.0040.0000.0000.0000.000
130L133LEU0-0.0300.01038.598-0.004-0.0040.0000.0000.0000.000
131L134VAL00.0080.00134.577-0.003-0.0030.0000.0000.0000.000
132L135CYS0-0.059-0.01132.868-0.001-0.0010.0000.0000.0000.000
133L136LEU00.0490.02531.043-0.008-0.0080.0000.0000.0000.000
134L137ILE00.0000.00027.3520.0070.0070.0000.0000.0000.000
135L138SER00.021-0.00926.945-0.011-0.0110.0000.0000.0000.000
136L139ASP-1-0.775-0.87825.881-0.310-0.3100.0000.0000.0000.000
137L140PHE00.0040.02621.9850.0000.0000.0000.0000.0000.000
138L141TYR00.024-0.00817.226-0.016-0.0160.0000.0000.0000.000
139L142PRO00.0790.03318.1590.0330.0330.0000.0000.0000.000
140L143GLY00.0370.01618.2860.0480.0480.0000.0000.0000.000
141L144ALA0-0.0150.00118.6390.0280.0280.0000.0000.0000.000
142L145VAL0-0.007-0.00420.1760.0220.0220.0000.0000.0000.000
143L146THR0-0.049-0.01423.2230.0160.0160.0000.0000.0000.000
144L147VAL00.0470.01525.882-0.005-0.0050.0000.0000.0000.000
145L148ALA0-0.074-0.03629.2680.0150.0150.0000.0000.0000.000
146L149TRP00.0740.02432.507-0.006-0.0060.0000.0000.0000.000
147L150LYS10.8220.91435.8860.0550.0550.0000.0000.0000.000
148L151ALA00.0620.03839.534-0.004-0.0040.0000.0000.0000.000
149L152ASP-1-0.803-0.90042.935-0.038-0.0380.0000.0000.0000.000
150L153SER00.0020.00142.571-0.003-0.0030.0000.0000.0000.000
151L154SER00.0090.02141.8350.0020.0020.0000.0000.0000.000
152L155PRO0-0.027-0.01036.957-0.006-0.0060.0000.0000.0000.000
153L156VAL00.0050.00437.1760.0060.0060.0000.0000.0000.000
154L157LYS10.9130.94129.9780.0510.0510.0000.0000.0000.000
155L158ALA00.0400.02034.165-0.001-0.0010.0000.0000.0000.000
156L159GLY00.0510.02036.306-0.003-0.0030.0000.0000.0000.000
157L160VAL0-0.071-0.01931.110-0.007-0.0070.0000.0000.0000.000
158L161GLU-1-0.856-0.92129.207-0.070-0.0700.0000.0000.0000.000
159L162THR0-0.088-0.05225.794-0.008-0.0080.0000.0000.0000.000
160L163THR0-0.0060.00724.382-0.004-0.0040.0000.0000.0000.000
161L164THR00.012-0.00318.0710.0080.0080.0000.0000.0000.000
162L165PRO0-0.037-0.01419.342-0.015-0.0150.0000.0000.0000.000
163L166SER0-0.0210.00018.638-0.044-0.0440.0000.0000.0000.000
164L167LYS10.7910.88515.3990.9310.9310.0000.0000.0000.000
165L168GLN0-0.013-0.03618.7790.0320.0320.0000.0000.0000.000
166L169SER0-0.026-0.04220.447-0.032-0.0320.0000.0000.0000.000
167L170ASN0-0.043-0.01221.779-0.042-0.0420.0000.0000.0000.000
168L171ASN00.000-0.01918.6510.0060.0060.0000.0000.0000.000
169L172LYS10.8480.94519.4360.3200.3200.0000.0000.0000.000
170L173TYR00.0030.00715.015-0.049-0.0490.0000.0000.0000.000
171L174ALA0-0.0060.00121.7800.0380.0380.0000.0000.0000.000
172L175ALA0-0.004-0.00223.130-0.019-0.0190.0000.0000.0000.000
173L176SER0-0.0090.00725.4120.0140.0140.0000.0000.0000.000
174L177SER00.0030.00128.1010.0050.0050.0000.0000.0000.000
175L178TYR00.014-0.00729.7650.0010.0010.0000.0000.0000.000
176L179LEU00.0030.00633.7320.0060.0060.0000.0000.0000.000
177L180SER0-0.0060.00436.564-0.002-0.0020.0000.0000.0000.000
178L181LEU0-0.049-0.02239.0060.0060.0060.0000.0000.0000.000
179L182THR00.0450.01642.561-0.002-0.0020.0000.0000.0000.000
180L183PRO00.017-0.00346.012-0.001-0.0010.0000.0000.0000.000
181L184GLU-1-0.975-0.97648.419-0.025-0.0250.0000.0000.0000.000
182L185GLN00.0840.03744.416-0.003-0.0030.0000.0000.0000.000
183L186TRP00.0220.02944.076-0.001-0.0010.0000.0000.0000.000
184L187LYS10.9360.96146.4730.0410.0410.0000.0000.0000.000
185L188SER0-0.060-0.02247.7820.0020.0020.0000.0000.0000.000
186L189HIS0-0.046-0.01646.3720.0040.0040.0000.0000.0000.000
187L190ARG10.9220.94748.5480.0310.0310.0000.0000.0000.000
188L191SER0-0.034-0.03845.408-0.004-0.0040.0000.0000.0000.000
189L192TYR00.009-0.01741.0710.0040.0040.0000.0000.0000.000
190L193SER0-0.019-0.00838.843-0.004-0.0040.0000.0000.0000.000
191L195GLN0-0.007-0.03434.1490.0000.0000.0000.0000.0000.000
192L196VAL00.0310.01728.4880.0010.0010.0000.0000.0000.000
193L197THR0-0.0030.00528.0070.0030.0030.0000.0000.0000.000
194L198HIS0-0.011-0.02323.0560.0200.0200.0000.0000.0000.000
195L199GLU-1-0.839-0.91121.384-0.297-0.2970.0000.0000.0000.000
196L200GLY00.0160.01424.9950.0020.0020.0000.0000.0000.000
197L201SER0-0.035-0.01227.8710.0190.0190.0000.0000.0000.000
198L202THR0-0.006-0.02629.822-0.005-0.0050.0000.0000.0000.000
199L203VAL0-0.003-0.00132.2890.0030.0030.0000.0000.0000.000
200L204GLU-1-0.837-0.89234.188-0.077-0.0770.0000.0000.0000.000
201L205LYS10.8330.91036.3900.1350.1350.0000.0000.0000.000
202L206THR00.025-0.01138.5640.0010.0010.0000.0000.0000.000
203L207VAL0-0.0130.00141.573-0.003-0.0030.0000.0000.0000.000
204L208ALA00.0650.01843.9680.0040.0040.0000.0000.0000.000
205L209PRO0-0.075-0.01147.2870.0000.0000.0000.0000.0000.000