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

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FMODB ID: Z6GRN

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 OptHSide
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 -1931259.406669
FMO2-HF: Nuclear repulsion 1853705.822866
FMO2-HF: Total energy -77553.583803
FMO2-MP2: Total energy -77781.335154


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.
-1.5481.8430.292-1.628-2.054-0.002
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 : -0.034 / q_NPA : -0.023
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].
3L11ILE00.0070.0053.810-0.5961.019-0.019-0.754-0.8420.005
4L12SER00.000-0.0186.5820.7600.7600.0000.0000.0000.000
5L13VAL0-0.0120.00410.1540.0760.0760.0000.0000.0000.000
6L14ALA0-0.0010.00912.8700.0690.0690.0000.0000.0000.000
7L15PRO00.003-0.00916.595-0.023-0.0230.0000.0000.0000.000
8L16GLY0-0.043-0.01718.9440.0600.0600.0000.0000.0000.000
9L17GLU-1-0.895-0.92515.238-0.859-0.8590.0000.0000.0000.000
10L18THR0-0.076-0.05614.1230.0380.0380.0000.0000.0000.000
11L19ALA00.0120.0249.761-0.086-0.0860.0000.0000.0000.000
12L20ARG10.8940.9208.9831.1671.1670.0000.0000.0000.000
13L21ILE00.0460.0364.802-0.588-0.5880.0000.0000.0000.000
14L22SER0-0.0010.0025.3010.7230.7230.0000.0000.0000.000
15L23CYS0-0.095-0.0305.6880.1690.1690.0000.0000.0000.000
16L24GLY00.0140.0047.9030.0550.0550.0000.0000.0000.000
17L25GLU-1-0.804-0.89310.2190.3490.3490.0000.0000.0000.000
18L26LYS10.9280.96112.731-0.414-0.4140.0000.0000.0000.000
19L27SER00.0000.00114.8240.0360.0360.0000.0000.0000.000
20L28LEU0-0.048-0.02817.8240.0290.0290.0000.0000.0000.000
21L29GLY0-0.032-0.02321.323-0.007-0.0070.0000.0000.0000.000
22L30SER00.007-0.00221.980-0.005-0.0050.0000.0000.0000.000
23L31ARG10.7270.82914.406-0.014-0.0140.0000.0000.0000.000
24L32ALA00.0170.02020.252-0.013-0.0130.0000.0000.0000.000
25L33VAL0-0.033-0.01613.8810.0130.0130.0000.0000.0000.000
26L34GLN00.0100.01816.624-0.034-0.0340.0000.0000.0000.000
27L35TRP00.024-0.0088.528-0.047-0.0470.0000.0000.0000.000
28L36TYR0-0.009-0.01613.0380.0850.0850.0000.0000.0000.000
29L37GLN00.0210.00612.503-0.063-0.0630.0000.0000.0000.000
30L38HIS0-0.008-0.01112.9670.1250.1250.0000.0000.0000.000
31L39ARG10.9070.96013.8070.6020.6020.0000.0000.0000.000
32L40ALA00.0430.02716.1510.0620.0620.0000.0000.0000.000
33L41GLY00.012-0.00517.2580.0350.0350.0000.0000.0000.000
34L42GLN0-0.033-0.01319.1170.0120.0120.0000.0000.0000.000
35L43ALA00.0080.00819.052-0.010-0.0100.0000.0000.0000.000
36L44PRO00.017-0.00216.171-0.034-0.0340.0000.0000.0000.000
37L45SER0-0.025-0.00217.3060.0550.0550.0000.0000.0000.000
38L46LEU0-0.025-0.01017.321-0.066-0.0660.0000.0000.0000.000
39L47ILE0-0.003-0.01013.7330.0150.0150.0000.0000.0000.000
40L48ILE0-0.012-0.00915.9050.0000.0000.0000.0000.0000.000
41L49TYR00.013-0.00118.1030.0000.0000.0000.0000.0000.000
42L50ASN0-0.026-0.01720.2170.0170.0170.0000.0000.0000.000
43L51ASN0-0.0210.00018.1880.0010.0010.0000.0000.0000.000
44L52GLN0-0.082-0.07317.812-0.035-0.0350.0000.0000.0000.000
45L53ASP-1-0.822-0.87320.061-0.258-0.2580.0000.0000.0000.000
46L54ARG10.8400.90720.6510.4060.4060.0000.0000.0000.000
47L55PRO0-0.0140.00921.4150.0350.0350.0000.0000.0000.000
48L56SER00.0370.00224.252-0.023-0.0230.0000.0000.0000.000
49L57GLY0-0.010-0.00125.7450.0010.0010.0000.0000.0000.000
50L58ILE0-0.060-0.01119.660-0.029-0.0290.0000.0000.0000.000
51L59PRO00.0100.00820.6610.0270.0270.0000.0000.0000.000
52L60GLU-1-0.860-0.94321.205-0.395-0.3950.0000.0000.0000.000
53L61ARG10.6990.81417.7860.7280.7280.0000.0000.0000.000
54L62PHE00.0330.03114.723-0.107-0.1070.0000.0000.0000.000
55L63SER00.002-0.00515.9670.1030.1030.0000.0000.0000.000
56L64GLY00.0660.04514.899-0.120-0.1200.0000.0000.0000.000
57L65SER0-0.002-0.00514.8160.0050.0050.0000.0000.0000.000
58L66PRO00.0280.01416.6620.0160.0160.0000.0000.0000.000
59L66ASP-1-0.840-0.91518.360-0.125-0.1250.0000.0000.0000.000
60L66SER0-0.0240.01620.2790.0370.0370.0000.0000.0000.000
61L66PRO0-0.005-0.01920.279-0.026-0.0260.0000.0000.0000.000
62L67PHE00.0280.00020.078-0.010-0.0100.0000.0000.0000.000
63L68GLY00.0130.01818.3820.0030.0030.0000.0000.0000.000
64L69THR0-0.057-0.02915.5500.0330.0330.0000.0000.0000.000
65L70THR00.000-0.0169.3090.0840.0840.0000.0000.0000.000
66L71ALA00.0030.02911.698-0.075-0.0750.0000.0000.0000.000
67L72THR0-0.009-0.0299.578-0.039-0.0390.0000.0000.0000.000
68L73LEU0-0.0170.0159.9800.1590.1590.0000.0000.0000.000
69L74THR0-0.030-0.02910.627-0.263-0.2630.0000.0000.0000.000
70L75ILE00.0110.02012.1100.1380.1380.0000.0000.0000.000
71L76THR00.015-0.01014.643-0.066-0.0660.0000.0000.0000.000
72L77SER00.000-0.01217.3750.0190.0190.0000.0000.0000.000
73L78VAL0-0.0010.01613.8910.0300.0300.0000.0000.0000.000
74L79GLU-1-0.834-0.90917.178-0.502-0.5020.0000.0000.0000.000
75L80ALA00.0700.02717.687-0.074-0.0740.0000.0000.0000.000
76L81GLY00.0130.01917.728-0.051-0.0510.0000.0000.0000.000
77L82ASP-1-0.753-0.84214.601-0.881-0.8810.0000.0000.0000.000
78L83GLU-1-0.776-0.85013.159-1.231-1.2310.0000.0000.0000.000
79L84ALA0-0.036-0.01711.9320.2120.2120.0000.0000.0000.000
80L85ASP-1-0.810-0.8698.978-1.831-1.8310.0000.0000.0000.000
81L86TYR0-0.055-0.0587.9800.5340.5340.0000.0000.0000.000
82L87TYR00.0000.0257.647-0.264-0.2640.0000.0000.0000.000
83L89HIS0-0.007-0.01011.7940.0830.0830.0000.0000.0000.000
84L90ILE0-0.025-0.01412.889-0.014-0.0140.0000.0000.0000.000
85L91TRP00.0170.01215.9800.0720.0720.0000.0000.0000.000
86L92ASP-1-0.668-0.83819.0060.0380.0380.0000.0000.0000.000
87L93SER00.0090.00620.9720.0230.0230.0000.0000.0000.000
88L94ARG10.8890.94223.304-0.094-0.0940.0000.0000.0000.000
89L95VAL0-0.051-0.02419.1310.0300.0300.0000.0000.0000.000
90L95PRO0-0.0010.00822.278-0.025-0.0250.0000.0000.0000.000
91L95THR0-0.015-0.01321.0910.0130.0130.0000.0000.0000.000
92L95LYS10.9200.97312.459-0.228-0.2280.0000.0000.0000.000
93L96TRP00.0390.00918.529-0.047-0.0470.0000.0000.0000.000
94L97VAL0-0.0280.00213.454-0.028-0.0280.0000.0000.0000.000
95L98PHE0-0.015-0.00712.4160.0140.0140.0000.0000.0000.000
96L99GLY00.0080.0049.8700.1340.1340.0000.0000.0000.000
97L100GLY00.005-0.0125.588-0.201-0.2010.0000.0000.0000.000
98L101GLY00.022-0.0126.5490.4080.4080.0000.0000.0000.000
99L102THR0-0.069-0.0262.411-1.2030.4550.312-0.855-1.115-0.007
100L103THR00.029-0.0044.5620.8490.967-0.001-0.019-0.0970.000
101L104LEU0-0.079-0.0316.902-0.986-0.9860.0000.0000.0000.000
102L105THR0-0.038-0.0189.3390.5550.5550.0000.0000.0000.000
103L106VAL0-0.031-0.02311.697-0.091-0.0910.0000.0000.0000.000
104L107LEU0-0.005-0.01112.9230.1550.1550.0000.0000.0000.000
105L108GLY00.014-0.00316.1030.0420.0420.0000.0000.0000.000
106L109GLN0-0.043-0.02017.1930.1140.1140.0000.0000.0000.000
107L110PRO0-0.0040.00021.2040.0200.0200.0000.0000.0000.000
108L111LYS10.8570.91623.8720.2570.2570.0000.0000.0000.000
109L112ALA0-0.069-0.03524.8290.0170.0170.0000.0000.0000.000
110L113ALA00.0300.01226.321-0.004-0.0040.0000.0000.0000.000
111L114PRO00.0240.01727.610-0.003-0.0030.0000.0000.0000.000
112L115SER0-0.035-0.00429.0810.0210.0210.0000.0000.0000.000
113L116VAL0-0.001-0.01831.3660.0000.0000.0000.0000.0000.000
114L117THR0-0.015-0.01333.4840.0080.0080.0000.0000.0000.000
115L118LEU0-0.017-0.00435.574-0.001-0.0010.0000.0000.0000.000
116L119PHE0-0.010-0.00836.6480.0020.0020.0000.0000.0000.000
117L120PRO00.0070.00740.0570.0020.0020.0000.0000.0000.000
118L121PRO00.0270.02742.559-0.003-0.0030.0000.0000.0000.000
119L122SER00.0330.02043.6580.0010.0010.0000.0000.0000.000
120L123SER00.034-0.01245.7540.0030.0030.0000.0000.0000.000
121L124GLU-1-0.917-0.95146.849-0.048-0.0480.0000.0000.0000.000
122L125GLU-1-0.813-0.89541.727-0.042-0.0420.0000.0000.0000.000
123L126LEU0-0.010-0.01445.9130.0050.0050.0000.0000.0000.000
124L127GLN0-0.065-0.02348.3490.0030.0030.0000.0000.0000.000
125L128ALA0-0.065-0.01146.8780.0030.0030.0000.0000.0000.000
126L129ASN0-0.063-0.04747.8730.0010.0010.0000.0000.0000.000
127L130LYS10.9420.96842.5170.0240.0240.0000.0000.0000.000
128L131ALA00.004-0.00643.423-0.002-0.0020.0000.0000.0000.000
129L132THR0-0.012-0.01337.2500.0040.0040.0000.0000.0000.000
130L133LEU0-0.042-0.00138.709-0.005-0.0050.0000.0000.0000.000
131L134VAL00.0110.00434.784-0.001-0.0010.0000.0000.0000.000
132L135CYS0-0.086-0.02033.072-0.004-0.0040.0000.0000.0000.000
133L136LEU00.0260.00631.252-0.005-0.0050.0000.0000.0000.000
134L137ILE0-0.0070.00227.6150.0020.0020.0000.0000.0000.000
135L138SER00.0160.00327.171-0.008-0.0080.0000.0000.0000.000
136L139ASP-1-0.797-0.91125.911-0.283-0.2830.0000.0000.0000.000
137L140PHE00.0020.01122.4700.0050.0050.0000.0000.0000.000
138L141TYR00.029-0.00217.117-0.011-0.0110.0000.0000.0000.000
139L142PRO00.0700.02218.3570.0280.0280.0000.0000.0000.000
140L143GLY00.0580.02818.4900.0430.0430.0000.0000.0000.000
141L144ALA0-0.038-0.00418.6860.0350.0350.0000.0000.0000.000
142L145VAL00.008-0.00320.4110.0060.0060.0000.0000.0000.000
143L146THR0-0.0190.00023.8210.0160.0160.0000.0000.0000.000
144L147VAL00.0200.00126.397-0.006-0.0060.0000.0000.0000.000
145L148ALA0-0.082-0.03729.5880.0150.0150.0000.0000.0000.000
146L149TRP00.0600.02632.812-0.006-0.0060.0000.0000.0000.000
147L150LYS10.8330.91936.0330.0450.0450.0000.0000.0000.000
148L151ALA00.0610.03939.592-0.004-0.0040.0000.0000.0000.000
149L152ASP-1-0.782-0.90142.931-0.028-0.0280.0000.0000.0000.000
150L153SER00.003-0.00343.067-0.003-0.0030.0000.0000.0000.000
151L154SER0-0.0060.00642.1410.0010.0010.0000.0000.0000.000
152L155PRO0-0.039-0.01937.078-0.004-0.0040.0000.0000.0000.000
153L156VAL00.0200.01237.5390.0060.0060.0000.0000.0000.000
154L157LYS10.9230.94830.7030.0240.0240.0000.0000.0000.000
155L158ALA00.0180.00634.4300.0010.0010.0000.0000.0000.000
156L159GLY00.0680.02735.861-0.004-0.0040.0000.0000.0000.000
157L160VAL0-0.050-0.01631.045-0.007-0.0070.0000.0000.0000.000
158L161GLU-1-0.887-0.92729.540-0.011-0.0110.0000.0000.0000.000
159L162THR0-0.028-0.02026.130-0.014-0.0140.0000.0000.0000.000
160L163THR0-0.025-0.00624.2270.0000.0000.0000.0000.0000.000
161L164THR00.006-0.00118.0700.0070.0070.0000.0000.0000.000
162L165PRO0-0.022-0.00719.510-0.010-0.0100.0000.0000.0000.000
163L166SER0-0.0130.00318.674-0.026-0.0260.0000.0000.0000.000
164L167LYS10.8060.90615.3570.8520.8520.0000.0000.0000.000
165L168GLN0-0.032-0.04518.6770.0400.0400.0000.0000.0000.000
166L169SER00.019-0.00920.033-0.037-0.0370.0000.0000.0000.000
167L170ASN0-0.055-0.01321.018-0.056-0.0560.0000.0000.0000.000
168L171ASN0-0.015-0.02818.1170.0000.0000.0000.0000.0000.000
169L172LYS10.8900.98019.8360.3080.3080.0000.0000.0000.000
170L173TYR0-0.0090.00815.135-0.040-0.0400.0000.0000.0000.000
171L174ALA00.0070.01221.9080.0260.0260.0000.0000.0000.000
172L175ALA0-0.010-0.01623.365-0.008-0.0080.0000.0000.0000.000
173L176SER00.0010.00025.6550.0100.0100.0000.0000.0000.000
174L177SER0-0.010-0.01628.3150.0080.0080.0000.0000.0000.000
175L178TYR00.0190.01330.124-0.002-0.0020.0000.0000.0000.000
176L179LEU00.0040.01433.8900.0060.0060.0000.0000.0000.000
177L180SER00.0000.00136.698-0.002-0.0020.0000.0000.0000.000
178L181LEU0-0.042-0.03038.9490.0040.0040.0000.0000.0000.000
179L182THR00.0280.01642.539-0.001-0.0010.0000.0000.0000.000
180L183PRO00.0360.00045.898-0.002-0.0020.0000.0000.0000.000
181L184GLU-1-0.969-0.98548.348-0.011-0.0110.0000.0000.0000.000
182L185GLN00.0740.03844.213-0.002-0.0020.0000.0000.0000.000
183L186TRP00.0080.01244.129-0.002-0.0020.0000.0000.0000.000
184L187LYS10.9400.96346.4630.0250.0250.0000.0000.0000.000
185L188SER0-0.060-0.00848.4340.0010.0010.0000.0000.0000.000
186L189HIS0-0.054-0.02246.1220.0020.0020.0000.0000.0000.000
187L190ARG10.9350.94948.5250.0240.0240.0000.0000.0000.000
188L191SER0-0.052-0.02145.637-0.004-0.0040.0000.0000.0000.000
189L192TYR00.012-0.00941.1600.0040.0040.0000.0000.0000.000
190L193SER00.0240.01939.233-0.005-0.0050.0000.0000.0000.000
191L195GLN0-0.045-0.04934.236-0.005-0.0050.0000.0000.0000.000
192L196VAL00.0260.01928.6830.0010.0010.0000.0000.0000.000
193L197THR0-0.015-0.00627.9010.0000.0000.0000.0000.0000.000
194L198HIS0-0.025-0.03023.2110.0190.0190.0000.0000.0000.000
195L199GLU-1-0.847-0.91421.784-0.313-0.3130.0000.0000.0000.000
196L200GLY0-0.004-0.00225.3820.0040.0040.0000.0000.0000.000
197L201SER0-0.0210.00228.3100.0180.0180.0000.0000.0000.000
198L202THR00.009-0.01330.084-0.005-0.0050.0000.0000.0000.000
199L203VAL0-0.0160.00132.4480.0050.0050.0000.0000.0000.000
200L204GLU-1-0.826-0.91134.553-0.064-0.0640.0000.0000.0000.000
201L205LYS10.8630.95036.5110.1170.1170.0000.0000.0000.000
202L206THR00.030-0.01138.8890.0020.0020.0000.0000.0000.000
203L207VAL0-0.022-0.00241.732-0.002-0.0020.0000.0000.0000.000
204L208ALA00.0250.00044.1160.0040.0040.0000.0000.0000.000
205L209PRO0-0.0140.01447.455-0.001-0.0010.0000.0000.0000.000