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: LZ6V9

Calculation Name: 4XHJ-C-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 4XHJ

Chain ID: C

ChEMBL ID:

UniProt ID: Q775J3

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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2122291.103646
FMO2-HF: Nuclear repulsion 2040875.060375
FMO2-HF: Total energy -81416.043271
FMO2-MP2: Total energy -81654.284785


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(C:1:ASP)


Summations of interaction energy for fragment #1(C:1:ASP)
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.
-81.301-90.00123.911-9.919-5.2920.074
Interaction energy analysis for fragmet #1(C:1:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.853 / q_NPA : -0.909
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].
3C3GLN00.0320.0333.863-2.216-0.580-0.010-0.696-0.9300.004
4C4MET00.0070.0345.535-2.059-2.0590.0000.0000.0000.000
5C5THR0-0.049-0.0418.834-0.978-0.9780.0000.0000.0000.000
6C6GLN00.028-0.00612.3290.8520.8520.0000.0000.0000.000
7C7SER0-0.0240.00915.816-0.391-0.3910.0000.0000.0000.000
8C8PRO00.0920.04019.430-0.079-0.0790.0000.0000.0000.000
9C9SER00.0070.03118.5780.3580.3580.0000.0000.0000.000
10C10PHE0-0.009-0.01820.2570.1710.1710.0000.0000.0000.000
11C11LEU0-0.0100.00423.863-0.178-0.1780.0000.0000.0000.000
12C12SER00.0420.01126.903-0.089-0.0890.0000.0000.0000.000
13C13ALA0-0.0120.01830.389-0.176-0.1760.0000.0000.0000.000
14C14SER00.012-0.00632.629-0.063-0.0630.0000.0000.0000.000
15C15VAL0-0.043-0.02035.2520.1090.1090.0000.0000.0000.000
16C16GLY00.0360.02036.051-0.335-0.3350.0000.0000.0000.000
17C17ASP-1-0.771-0.85033.8058.6618.6610.0000.0000.0000.000
18C18ARG10.9130.96530.445-9.169-9.1690.0000.0000.0000.000
19C19VAL0-0.0040.00926.1960.0420.0420.0000.0000.0000.000
20C20THR00.003-0.01024.7290.0120.0120.0000.0000.0000.000
21C21ILE0-0.0210.00519.655-0.062-0.0620.0000.0000.0000.000
22C22THR0-0.021-0.01018.6940.2830.2830.0000.0000.0000.000
23C23CYS0-0.021-0.00413.6120.3590.3590.0000.0000.0000.000
24C24ARG10.8500.92013.765-17.459-17.4590.0000.0000.0000.000
25C25ALA00.0560.0189.4061.2931.2930.0000.0000.0000.000
26C26SER0-0.037-0.0416.500-1.724-1.7240.0000.0000.0000.000
27C27GLN0-0.026-0.0156.503-0.212-0.2120.0000.0000.0000.000
28C28GLY0-0.017-0.0129.6910.0420.0420.0000.0000.0000.000
29C29LEU00.0240.0108.0181.0101.0100.0000.0000.0000.000
30C30ASP-1-0.903-0.95411.58816.28116.2810.0000.0000.0000.000
31C31ASN00.0520.00915.332-0.537-0.5370.0000.0000.0000.000
32C32PHE0-0.018-0.01112.567-0.553-0.5530.0000.0000.0000.000
33C33LEU0-0.020-0.01012.3922.0272.0270.0000.0000.0000.000
34C34ALA0-0.0130.01314.396-1.283-1.2830.0000.0000.0000.000
35C35TRP00.012-0.00915.8450.8670.8670.0000.0000.0000.000
36C36TYR0-0.014-0.02415.358-1.325-1.3250.0000.0000.0000.000
37C37GLN0-0.010-0.01519.743-0.202-0.2020.0000.0000.0000.000
38C38GLN0-0.001-0.00320.1770.5310.5310.0000.0000.0000.000
39C39LYS10.8660.93922.905-10.670-10.6700.0000.0000.0000.000
40C40PRO00.0450.01425.9200.2670.2670.0000.0000.0000.000
41C41GLY00.0030.00726.466-0.320-0.3200.0000.0000.0000.000
42C42LYS10.9130.96626.079-10.408-10.4080.0000.0000.0000.000
43C43ALA00.0490.02622.7100.4600.4600.0000.0000.0000.000
44C44PRO0-0.006-0.00918.532-0.542-0.5420.0000.0000.0000.000
45C45LYS10.8760.94521.485-11.313-11.3130.0000.0000.0000.000
46C46LEU0-0.0030.00318.8480.0480.0480.0000.0000.0000.000
47C47LEU0-0.051-0.03121.444-0.776-0.7760.0000.0000.0000.000
48C48ILE00.000-0.01220.795-0.688-0.6880.0000.0000.0000.000
49C49TYR0-0.001-0.00619.4850.6140.6140.0000.0000.0000.000
50C50ALA00.0280.03018.1600.6750.6750.0000.0000.0000.000
51C51ALA00.0160.01618.251-0.262-0.2620.0000.0000.0000.000
52C52SER0-0.011-0.01019.333-0.270-0.2700.0000.0000.0000.000
53C53THR00.0000.00422.560-0.458-0.4580.0000.0000.0000.000
54C54LEU00.0140.01723.7890.3890.3890.0000.0000.0000.000
55C55GLN00.0700.04324.275-0.620-0.6200.0000.0000.0000.000
56C56ARG10.8670.91426.264-10.994-10.9940.0000.0000.0000.000
57C57GLY00.0610.02929.1280.1510.1510.0000.0000.0000.000
58C58VAL0-0.049-0.00126.0380.0190.0190.0000.0000.0000.000
59C59PRO00.0140.00529.366-0.217-0.2170.0000.0000.0000.000
60C60SER00.0290.00130.4830.2520.2520.0000.0000.0000.000
61C61ARG10.7570.86031.098-9.720-9.7200.0000.0000.0000.000
62C62PHE0-0.0070.01025.8220.0540.0540.0000.0000.0000.000
63C63GLY00.0410.01726.809-0.235-0.2350.0000.0000.0000.000
64C64GLY00.0100.00422.9970.2570.2570.0000.0000.0000.000
65C65SER0-0.029-0.00722.394-0.444-0.4440.0000.0000.0000.000
66C66GLY00.0520.01319.2340.3660.3660.0000.0000.0000.000
67C67SER0-0.0030.00717.784-0.289-0.2890.0000.0000.0000.000
68C68GLY00.0250.02114.668-0.048-0.0480.0000.0000.0000.000
69C69THR0-0.017-0.00312.1351.2521.2520.0000.0000.0000.000
70C70GLU-1-0.827-0.88614.06515.45015.4500.0000.0000.0000.000
71C71PHE00.0250.01213.614-0.630-0.6300.0000.0000.0000.000
72C72THR0-0.074-0.04718.215-0.034-0.0340.0000.0000.0000.000
73C73LEU00.0000.01420.877-0.171-0.1710.0000.0000.0000.000
74C74THR0-0.042-0.03322.509-0.286-0.2860.0000.0000.0000.000
75C75ILE00.0120.00326.095-0.072-0.0720.0000.0000.0000.000
76C76SER0-0.034-0.04528.729-0.352-0.3520.0000.0000.0000.000
77C77SER0-0.018-0.02731.886-0.313-0.3130.0000.0000.0000.000
78C78LEU0-0.0060.01629.7690.0690.0690.0000.0000.0000.000
79C79GLN0-0.025-0.03732.795-0.544-0.5440.0000.0000.0000.000
80C80PRO00.0380.01533.2440.2770.2770.0000.0000.0000.000
81C81GLU-1-0.843-0.90732.1879.8549.8540.0000.0000.0000.000
82C82ASP-1-0.776-0.86529.22210.46610.4660.0000.0000.0000.000
83C83PHE00.0090.03028.1640.4330.4330.0000.0000.0000.000
84C84ALA0-0.046-0.01924.7490.0250.0250.0000.0000.0000.000
85C85THR0-0.013-0.00320.329-0.181-0.1810.0000.0000.0000.000
86C86TYR00.004-0.01320.286-0.101-0.1010.0000.0000.0000.000
87C87TYR00.0180.01714.8760.2020.2020.0000.0000.0000.000
88C89GLN00.0170.00411.070-0.723-0.7230.0000.0000.0000.000
89C90GLN00.0590.0294.722-2.912-2.826-0.001-0.003-0.0830.000
90C91LEU0-0.020-0.0209.9000.1080.1080.0000.0000.0000.000
91C92ASN0-0.056-0.03010.4100.2050.2050.0000.0000.0000.000
92C93SER00.0350.0175.7600.5860.5860.0000.0000.0000.000
93C94TYR00.0140.0006.476-2.340-2.3400.0000.0000.0000.000
94C95SER0-0.043-0.0371.556-26.766-37.58423.917-9.135-3.9640.070
95C96LEU0-0.033-0.0064.5141.4191.550-0.001-0.028-0.1010.000
96C97THR0-0.0010.0043.586-4.287-4.0220.006-0.057-0.2140.000
97C98PHE00.012-0.0066.724-3.841-3.8410.0000.0000.0000.000
98C99GLY00.0080.0049.1431.3521.3520.0000.0000.0000.000
99C100PRO0-0.051-0.03811.321-0.604-0.6040.0000.0000.0000.000
100C101GLY00.0040.01713.466-0.798-0.7980.0000.0000.0000.000
101C102THR0-0.060-0.04816.6430.0120.0120.0000.0000.0000.000
102C103LYS10.9320.96320.106-13.631-13.6310.0000.0000.0000.000
103C104VAL0-0.006-0.00323.221-0.139-0.1390.0000.0000.0000.000
104C105GLU-1-0.841-0.90426.5459.6249.6240.0000.0000.0000.000
105C106ILE0-0.049-0.03330.004-0.015-0.0150.0000.0000.0000.000
106C107LYS10.8790.93533.041-9.311-9.3110.0000.0000.0000.000
107C108ARG10.8490.91036.162-7.493-7.4930.0000.0000.0000.000
108C109ARG10.8880.93639.532-7.636-7.6360.0000.0000.0000.000
109C110THR00.0070.00842.532-0.093-0.0930.0000.0000.0000.000
110C111VAL00.0280.03043.3310.1630.1630.0000.0000.0000.000
111C112ALA0-0.032-0.01743.911-0.106-0.1060.0000.0000.0000.000
112C113ALA00.0620.02845.3490.1160.1160.0000.0000.0000.000
113C114PRO0-0.0160.00545.5560.0240.0240.0000.0000.0000.000
114C115SER00.0230.01447.096-0.213-0.2130.0000.0000.0000.000
115C116VAL00.0070.00748.3400.1010.1010.0000.0000.0000.000
116C117PHE0-0.036-0.01549.271-0.197-0.1970.0000.0000.0000.000
117C118ILE00.0200.00349.8410.1000.1000.0000.0000.0000.000
118C119PHE0-0.009-0.00548.606-0.087-0.0870.0000.0000.0000.000
119C120PRO0-0.003-0.00152.4160.0360.0360.0000.0000.0000.000
120C121PRO0-0.036-0.01353.944-0.049-0.0490.0000.0000.0000.000
121C122SER00.0920.03753.2770.1400.1400.0000.0000.0000.000
122C123ASP-1-0.862-0.92054.5815.3835.3830.0000.0000.0000.000
123C124GLU-1-0.905-0.94553.6355.7705.7700.0000.0000.0000.000
124C125GLN00.0300.04349.0390.0040.0040.0000.0000.0000.000
125C126LEU00.0250.03753.3680.0030.0030.0000.0000.0000.000
126C127LYS10.8240.89156.448-5.492-5.4920.0000.0000.0000.000
127C128SER0-0.064-0.04352.6960.0260.0260.0000.0000.0000.000
128C129GLY00.0040.00953.9170.0620.0620.0000.0000.0000.000
129C130THR0-0.076-0.04249.8440.1070.1070.0000.0000.0000.000
130C131ALA00.0320.01851.852-0.076-0.0760.0000.0000.0000.000
131C132SER0-0.016-0.04348.0310.1420.1420.0000.0000.0000.000
132C133VAL0-0.035-0.00549.742-0.099-0.0990.0000.0000.0000.000
133C134VAL00.0240.02245.3500.0330.0330.0000.0000.0000.000
134C135CYS0-0.049-0.00446.850-0.055-0.0550.0000.0000.0000.000
135C136LEU0-0.023-0.00943.7310.1790.1790.0000.0000.0000.000
136C137LEU00.0040.00543.673-0.197-0.1970.0000.0000.0000.000
137C138ASN0-0.021-0.02843.1220.0800.0800.0000.0000.0000.000
138C139ASN0-0.001-0.02541.876-0.118-0.1180.0000.0000.0000.000
139C140PHE0-0.0040.02440.304-0.134-0.1340.0000.0000.0000.000
140C141TYR00.0680.01736.0330.1740.1740.0000.0000.0000.000
141C142PRO00.018-0.00539.076-0.211-0.2110.0000.0000.0000.000
142C143ARG11.0131.01733.327-9.021-9.0210.0000.0000.0000.000
143C144GLU-1-0.902-0.96337.2968.1648.1640.0000.0000.0000.000
144C145ALA0-0.021-0.00240.521-0.232-0.2320.0000.0000.0000.000
145C146LYS10.7900.88640.010-7.495-7.4950.0000.0000.0000.000
146C147VAL00.0120.00343.992-0.157-0.1570.0000.0000.0000.000
147C148GLN0-0.029-0.01046.160-0.001-0.0010.0000.0000.0000.000
148C149TRP0-0.009-0.01446.963-0.121-0.1210.0000.0000.0000.000
149C150LYS10.8120.88051.669-5.717-5.7170.0000.0000.0000.000
150C151VAL0-0.0090.00753.000-0.102-0.1020.0000.0000.0000.000
151C152ASP-1-0.814-0.90151.4416.2556.2550.0000.0000.0000.000
152C153ASN0-0.062-0.03647.2500.1150.1150.0000.0000.0000.000
153C154ALA00.004-0.00146.5460.1680.1680.0000.0000.0000.000
154C155LEU00.029-0.01040.8400.0040.0040.0000.0000.0000.000
155C156GLN0-0.0020.01144.385-0.027-0.0270.0000.0000.0000.000
156C157SER00.0210.00547.064-0.086-0.0860.0000.0000.0000.000
157C158GLY00.0480.02543.613-0.012-0.0120.0000.0000.0000.000
158C159ASN00.0500.02143.3540.1650.1650.0000.0000.0000.000
159C160SER0-0.0070.00039.4940.0190.0190.0000.0000.0000.000
160C161GLN0-0.069-0.02739.1450.3710.3710.0000.0000.0000.000
161C162GLU-1-0.828-0.90438.2907.5747.5740.0000.0000.0000.000
162C163SER0-0.0090.01336.3440.3570.3570.0000.0000.0000.000
163C164VAL0-0.011-0.03134.940-0.252-0.2520.0000.0000.0000.000
164C165THR0-0.043-0.01734.2490.1740.1740.0000.0000.0000.000
165C166GLU-1-0.859-0.94228.21910.80910.8090.0000.0000.0000.000
166C167GLN0-0.014-0.01432.148-0.038-0.0380.0000.0000.0000.000
167C168ASP-1-0.757-0.84933.7268.3728.3720.0000.0000.0000.000
168C169SER0-0.039-0.02833.646-0.111-0.1110.0000.0000.0000.000
169C170LYS10.7970.86435.143-8.268-8.2680.0000.0000.0000.000
170C171ASP-1-0.770-0.84638.5557.5727.5720.0000.0000.0000.000
171C172SER0-0.021-0.01035.765-0.123-0.1230.0000.0000.0000.000
172C173THR0-0.106-0.05837.3400.0550.0550.0000.0000.0000.000
173C174TYR0-0.042-0.04433.5480.1510.1510.0000.0000.0000.000
174C175SER00.0270.01438.247-0.351-0.3510.0000.0000.0000.000
175C176LEU0-0.0090.00138.6000.2400.2400.0000.0000.0000.000
176C177SER0-0.004-0.00940.418-0.177-0.1770.0000.0000.0000.000
177C178SER0-0.0010.01341.5240.0930.0930.0000.0000.0000.000
178C179THR0-0.009-0.01942.424-0.168-0.1680.0000.0000.0000.000
179C180LEU0-0.0010.03244.5570.0660.0660.0000.0000.0000.000
180C181THR0-0.001-0.01745.4460.0110.0110.0000.0000.0000.000
181C182LEU00.0090.01248.0110.0460.0460.0000.0000.0000.000
182C183SER0-0.011-0.00748.964-0.054-0.0540.0000.0000.0000.000
183C184LYS10.9430.94550.910-6.235-6.2350.0000.0000.0000.000
184C185ALA00.0070.01254.322-0.094-0.0940.0000.0000.0000.000
185C186ASP-1-0.811-0.88653.6385.8315.8310.0000.0000.0000.000
186C187TYR0-0.018-0.01454.724-0.041-0.0410.0000.0000.0000.000
187C188GLU-1-0.773-0.86356.0125.0675.0670.0000.0000.0000.000
188C189LYS10.7670.87753.325-5.996-5.9960.0000.0000.0000.000
189C190HIS0-0.002-0.00357.294-0.062-0.0620.0000.0000.0000.000
190C191LYS10.8200.88959.386-5.048-5.0480.0000.0000.0000.000
191C192VAL0-0.035-0.01958.868-0.053-0.0530.0000.0000.0000.000
192C193TYR00.0170.01753.0840.1100.1100.0000.0000.0000.000
193C194ALA0-0.004-0.02154.271-0.097-0.0970.0000.0000.0000.000
194C196GLU-1-0.810-0.89050.8795.7245.7240.0000.0000.0000.000
195C197VAL00.0150.00247.0880.1570.1570.0000.0000.0000.000
196C198THR00.0070.00347.061-0.081-0.0810.0000.0000.0000.000
197C199HIS00.033-0.00442.767-0.003-0.0030.0000.0000.0000.000
198C200GLN00.0210.00842.609-0.156-0.1560.0000.0000.0000.000
199C201GLY0-0.021-0.01147.029-0.072-0.0720.0000.0000.0000.000
200C202LEU0-0.038-0.02348.347-0.081-0.0810.0000.0000.0000.000
201C203SER0-0.011-0.00651.6350.0120.0120.0000.0000.0000.000
202C204SER0-0.017-0.00654.338-0.087-0.0870.0000.0000.0000.000
203C205PRO00.0240.00651.7980.0650.0650.0000.0000.0000.000
204C206VAL0-0.0130.01852.176-0.138-0.1380.0000.0000.0000.000
205C207THR00.005-0.00452.7710.0940.0940.0000.0000.0000.000
206C208LYS10.8570.92953.256-5.987-5.9870.0000.0000.0000.000
207C209SER00.022-0.01154.4590.1290.1290.0000.0000.0000.000
208C210PHE0-0.003-0.00455.831-0.050-0.0500.0000.0000.0000.000
209C211ASN00.0290.01558.0940.0730.0730.0000.0000.0000.000
210C212ARG10.9991.01660.615-5.306-5.3060.0000.0000.0000.000