FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: VZZL1

Calculation Name: 1QWO-A-Xray547

Preferred Name:

Target Type:

Ligand Name: n1-phosphonohistidine | 2-acetamido-2-deoxy-beta-d-glucopyranose

Ligand 3-letter code: NEP | NAG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1QWO

Chain ID: A

ChEMBL ID:

UniProt ID: O00092

Base Structure: X-ray

Registration Date: 2025-10-06

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 430
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -7997578.111041
FMO2-HF: Nuclear repulsion 7829021.835108
FMO2-HF: Total energy -168556.275933
FMO2-MP2: Total energy -169047.404992


3D Structure Molmil
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(A:8:CYS)


Summations of interaction energy for fragment #1(A:8: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.
-32.198-13.65611.676-12.439-17.781-0.055
Interaction energy analysis for fragmet #1(A:8:CYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.792 / q_NPA : 0.913
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].
3A10THR0-0.063-0.0253.411-3.806-1.683-0.006-1.117-1.000-0.002
8A15TYR0-0.045-0.0592.562-20.784-12.9565.036-5.083-7.782-0.043
11A19PRO00.0740.0532.532-5.859-1.4481.150-2.523-3.0390.027
12A20ALA0-0.024-0.0165.0300.2670.396-0.002-0.012-0.1150.000
14A22SER00.0530.0144.0922.2982.700-0.002-0.198-0.2020.000
15A23HIS10.8290.9373.62136.89937.086-0.0020.005-0.1900.000
24A32PHE0-0.045-0.0225.216-5.841-5.884-0.002-0.0100.0550.000
100A108PHE0-0.0010.0114.515-1.513-1.360-0.002-0.014-0.1370.000
242A251ASP-1-0.810-0.8903.365-58.641-58.0160.003-0.136-0.492-0.001
243A252ALA0-0.005-0.0032.769-21.213-18.5860.316-1.582-1.360-0.018
244A253SER0-0.058-0.0502.642-5.767-4.7825.114-3.524-2.576-0.013
245A254GLN0-0.0070.0103.7206.7445.8590.0731.755-0.943-0.005
4A11VAL00.0470.0216.0122.2442.2440.0000.0000.0000.000
5A12ASP-1-0.882-0.9399.773-23.779-23.7790.0000.0000.0000.000
6A13LEU00.0390.0105.8341.6921.6920.0000.0000.0000.000
7A14GLY00.0520.0565.8290.2490.2490.0000.0000.0000.000
13A21THR0-0.015-0.0077.3861.7361.7360.0000.0000.0000.000
16A24LEU0-0.075-0.0238.5552.0712.0710.0000.0000.0000.000
17A25TRP00.053-0.0027.056-0.117-0.1170.0000.0000.0000.000
18A26GLY00.0620.02412.9350.5800.5800.0000.0000.0000.000
19A27GLN00.0170.00113.538-1.484-1.4840.0000.0000.0000.000
20A28TYR0-0.014-0.00413.6000.3370.3370.0000.0000.0000.000
21A29SER0-0.034-0.0269.334-0.873-0.8730.0000.0000.0000.000
22A30PRO00.003-0.0066.1841.4401.4400.0000.0000.0000.000
23A31PHE0-0.0180.0118.3430.3410.3410.0000.0000.0000.000
25A33SER0-0.058-0.0516.8433.7993.7990.0000.0000.0000.000
26A34LEU00.010-0.0058.530-0.528-0.5280.0000.0000.0000.000
27A35GLU-1-0.761-0.81511.392-15.479-15.4790.0000.0000.0000.000
28A36ASP-1-0.922-0.98012.648-15.967-15.9670.0000.0000.0000.000
29A37GLU-1-0.949-0.96011.873-16.285-16.2850.0000.0000.0000.000
30A38LEU0-0.033-0.02514.1130.3900.3900.0000.0000.0000.000
31A39SER00.0080.00016.8000.3630.3630.0000.0000.0000.000
32A40VAL0-0.0070.01418.7330.2010.2010.0000.0000.0000.000
33A41SER00.007-0.00417.661-0.392-0.3920.0000.0000.0000.000
34A42SER00.001-0.03416.3310.7880.7880.0000.0000.0000.000
35A43LYS10.9110.96716.76816.09616.0960.0000.0000.0000.000
36A44LEU00.0110.01120.7600.3970.3970.0000.0000.0000.000
37A45PRO00.000-0.00224.2870.1030.1030.0000.0000.0000.000
38A46LYS10.9140.93626.5959.4609.4600.0000.0000.0000.000
39A47ASP-1-0.888-0.93929.257-8.948-8.9480.0000.0000.0000.000
40A48CYS0-0.0340.00328.8340.0320.0320.0000.0000.0000.000
41A49ARG10.9660.97429.7579.1219.1210.0000.0000.0000.000
42A50ILE00.0180.01925.3480.2900.2900.0000.0000.0000.000
43A51THR0-0.085-0.05929.1520.1150.1150.0000.0000.0000.000
44A52LEU0-0.0170.00129.2090.2230.2230.0000.0000.0000.000
45A53VAL0-0.027-0.00723.628-0.184-0.1840.0000.0000.0000.000
46A54GLN0-0.0100.00925.5450.6020.6020.0000.0000.0000.000
47A55VAL0-0.015-0.01220.183-0.395-0.3950.0000.0000.0000.000
48A56LEU0-0.0190.01321.6170.5600.5600.0000.0000.0000.000
49A57SER0-0.001-0.00818.261-1.055-1.0550.0000.0000.0000.000
50A58ARG10.7730.87315.36219.83219.8320.0000.0000.0000.000
51A59HIS00.013-0.00816.5820.3230.3230.0000.0000.0000.000
52A60GLY00.0350.00513.820-0.875-0.8750.0000.0000.0000.000
53A61ALA0-0.051-0.01110.5211.3351.3350.0000.0000.0000.000
54A62ARG10.9090.95712.51517.38117.3810.0000.0000.0000.000
55A63TYR00.0520.03414.941-0.879-0.8790.0000.0000.0000.000
56A64PRO0-0.040-0.00916.9730.2620.2620.0000.0000.0000.000
57A65THR00.0600.03219.568-0.028-0.0280.0000.0000.0000.000
58A66SER00.016-0.00422.9390.1680.1680.0000.0000.0000.000
59A67SER0-0.012-0.00525.466-0.011-0.0110.0000.0000.0000.000
60A68LYS10.9070.95721.62514.04114.0410.0000.0000.0000.000
61A69SER00.0140.00621.4380.0100.0100.0000.0000.0000.000
62A70LYS10.9650.98423.09210.07510.0750.0000.0000.0000.000
63A71LYS10.8240.91025.39411.57311.5730.0000.0000.0000.000
64A72TYR0-0.029-0.06719.3170.1040.1040.0000.0000.0000.000
65A73LYS10.9841.00823.35312.06012.0600.0000.0000.0000.000
66A74LYS10.9420.98725.1089.9899.9890.0000.0000.0000.000
67A75LEU00.0040.01823.3800.2360.2360.0000.0000.0000.000
68A76VAL0-0.004-0.00621.5250.1000.1000.0000.0000.0000.000
69A77THR0-0.024-0.02824.6690.2100.2100.0000.0000.0000.000
70A78ALA00.000-0.00328.1420.3140.3140.0000.0000.0000.000
71A79ILE0-0.022-0.01823.8450.2090.2090.0000.0000.0000.000
72A80GLN0-0.093-0.07324.1340.3810.3810.0000.0000.0000.000
73A81ALA0-0.0380.00028.4250.2080.2080.0000.0000.0000.000
74A82ASN0-0.023-0.00931.1200.2670.2670.0000.0000.0000.000
75A83ALA0-0.048-0.01128.4430.1980.1980.0000.0000.0000.000
76A84THR0-0.047-0.04230.4570.0470.0470.0000.0000.0000.000
77A85ASP-1-0.866-0.94229.267-9.524-9.5240.0000.0000.0000.000
78A86PHE0-0.016-0.01324.589-0.243-0.2430.0000.0000.0000.000
79A87LYS10.9470.98625.3748.9548.9540.0000.0000.0000.000
80A88GLY00.021-0.00222.651-0.275-0.2750.0000.0000.0000.000
81A89LYS10.9590.97016.26413.49313.4930.0000.0000.0000.000
82A90PHE00.0560.02618.595-0.610-0.6100.0000.0000.0000.000
83A91ALA0-0.0170.00621.1140.1020.1020.0000.0000.0000.000
84A92PHE00.0270.00217.1690.2510.2510.0000.0000.0000.000
85A93LEU00.0140.01119.879-0.029-0.0290.0000.0000.0000.000
86A94LYS10.8730.95821.91111.50811.5080.0000.0000.0000.000
87A95THR00.017-0.00321.4720.3910.3910.0000.0000.0000.000
88A96TYR0-0.092-0.04916.2690.0580.0580.0000.0000.0000.000
89A97ASN00.0460.02220.7190.7770.7770.0000.0000.0000.000
90A98TYR0-0.005-0.03120.259-0.809-0.8090.0000.0000.0000.000
91A99THR0-0.015-0.01918.3720.2510.2510.0000.0000.0000.000
92A100LEU0-0.0380.00015.416-0.299-0.2990.0000.0000.0000.000
93A101GLY00.0680.03818.4010.8550.8550.0000.0000.0000.000
94A102ALA0-0.015-0.02020.3310.0970.0970.0000.0000.0000.000
95A103ASP-1-0.760-0.86121.233-13.357-13.3570.0000.0000.0000.000
96A104ASP-1-0.850-0.90919.134-15.225-15.2250.0000.0000.0000.000
97A105LEU0-0.041-0.03015.153-0.670-0.6700.0000.0000.0000.000
98A106THR0-0.044-0.02810.7100.4800.4800.0000.0000.0000.000
99A107PRO00.0530.01211.240-0.951-0.9510.0000.0000.0000.000
101A109GLY0-0.020-0.0178.817-1.654-1.6540.0000.0000.0000.000
102A110GLU-1-0.864-0.95011.483-19.840-19.8400.0000.0000.0000.000
103A111GLN00.0110.0017.5282.3162.3160.0000.0000.0000.000
104A112GLN0-0.019-0.0288.5661.8881.8880.0000.0000.0000.000
105A113LEU0-0.061-0.01510.2390.9420.9420.0000.0000.0000.000
106A114VAL00.0320.03611.9221.3021.3020.0000.0000.0000.000
107A115ASN0-0.017-0.0267.0483.7153.7150.0000.0000.0000.000
108A116SER0-0.021-0.00711.5341.3081.3080.0000.0000.0000.000
109A117GLY00.0420.02714.4791.2501.2500.0000.0000.0000.000
110A118ILE0-0.039-0.01512.5471.2911.2910.0000.0000.0000.000
111A119LYS10.8040.89611.54925.35425.3540.0000.0000.0000.000
112A120PHE0-0.021-0.00415.6831.2781.2780.0000.0000.0000.000
113A121TYR0-0.019-0.03719.0381.1911.1910.0000.0000.0000.000
114A122GLN0-0.032-0.03314.8720.2250.2250.0000.0000.0000.000
115A123ARG10.7870.87617.53116.66816.6680.0000.0000.0000.000
116A124TYR0-0.014-0.03220.2350.6240.6240.0000.0000.0000.000
117A125LYS10.9590.99722.06914.65914.6590.0000.0000.0000.000
118A126ALA0-0.054-0.03924.4370.3990.3990.0000.0000.0000.000
119A127LEU00.0130.02127.5220.4410.4410.0000.0000.0000.000
120A128ALA00.0580.02224.4870.2720.2720.0000.0000.0000.000
121A129ARG10.7900.86526.08112.04212.0420.0000.0000.0000.000
122A130SER0-0.026-0.01627.9580.3380.3380.0000.0000.0000.000
123A131VAL00.0150.00629.2360.2890.2890.0000.0000.0000.000
124A132VAL0-0.0040.00328.571-0.466-0.4660.0000.0000.0000.000
125A133PRO0-0.034-0.02325.2840.2920.2920.0000.0000.0000.000
126A134PHE00.0190.01928.376-0.037-0.0370.0000.0000.0000.000
127A135ILE0-0.019-0.01223.978-0.300-0.3000.0000.0000.0000.000
128A136ARG10.7560.82627.35811.24211.2420.0000.0000.0000.000
129A137ALA00.0070.00125.368-0.650-0.6500.0000.0000.0000.000
130A138SER00.020-0.01526.1420.7400.7400.0000.0000.0000.000
131A139GLY0-0.0120.00326.648-0.419-0.4190.0000.0000.0000.000
132A140SER0-0.009-0.00524.382-0.095-0.0950.0000.0000.0000.000
133A141ASP-1-0.833-0.91924.195-12.871-12.8710.0000.0000.0000.000
134A142ARG10.8030.88619.11814.31814.3180.0000.0000.0000.000
135A143VAL0-0.044-0.01319.597-1.165-1.1650.0000.0000.0000.000
136A144ILE00.0340.01621.879-0.371-0.3710.0000.0000.0000.000
137A145ALA00.0720.03919.702-0.282-0.2820.0000.0000.0000.000
138A146SER0-0.052-0.04317.587-1.450-1.4500.0000.0000.0000.000
139A147GLY00.0510.01818.425-0.649-0.6490.0000.0000.0000.000
140A148GLU-1-0.928-0.97020.823-14.244-14.2440.0000.0000.0000.000
141A149LYS10.8260.91315.23119.07819.0780.0000.0000.0000.000
142A150PHE00.0110.01216.687-0.676-0.6760.0000.0000.0000.000
143A151ILE0-0.006-0.00318.1300.0920.0920.0000.0000.0000.000
144A152GLU-1-0.839-0.91017.083-18.244-18.2440.0000.0000.0000.000
145A153GLY0-0.012-0.00616.036-0.068-0.0680.0000.0000.0000.000
146A154PHE0-0.025-0.01916.6500.3960.3960.0000.0000.0000.000
147A155GLN0-0.003-0.02819.8730.5200.5200.0000.0000.0000.000
148A156GLN0-0.0150.00414.451-0.241-0.2410.0000.0000.0000.000
149A157ALA0-0.004-0.00817.3340.3060.3060.0000.0000.0000.000
150A158LYS10.8390.93118.98012.96112.9610.0000.0000.0000.000
151A159LEU0-0.048-0.01821.9900.7560.7560.0000.0000.0000.000
152A160ALA00.0080.01119.3600.4370.4370.0000.0000.0000.000
153A161ASP-1-0.724-0.80021.299-12.890-12.8900.0000.0000.0000.000
154A162PRO00.0180.00023.5510.4860.4860.0000.0000.0000.000
155A163GLY0-0.031-0.01926.8400.4590.4590.0000.0000.0000.000
156A164ALA0-0.040-0.00926.2140.2120.2120.0000.0000.0000.000
157A165THR0-0.029-0.01728.2830.0900.0900.0000.0000.0000.000
158A167ASN00.0080.00930.8430.1560.1560.0000.0000.0000.000
159A168ARG10.8590.90626.05211.52011.5200.0000.0000.0000.000
160A169ALA00.0180.02828.293-0.243-0.2430.0000.0000.0000.000
161A170ALA00.0150.00326.103-0.278-0.2780.0000.0000.0000.000
162A171PRO0-0.023-0.00324.8670.3970.3970.0000.0000.0000.000
163A172ALA00.0500.01826.323-0.403-0.4030.0000.0000.0000.000
164A173ILE0-0.015-0.01523.8530.0720.0720.0000.0000.0000.000
165A174SER0-0.052-0.01428.0060.3970.3970.0000.0000.0000.000
166A175VAL0-0.027-0.01630.7650.4270.4270.0000.0000.0000.000
167A176ILE00.0190.01928.642-0.462-0.4620.0000.0000.0000.000
168A177ILE0-0.015-0.00830.5160.4620.4620.0000.0000.0000.000
169A178PRO0-0.006-0.01131.197-0.321-0.3210.0000.0000.0000.000
170A179GLU-1-0.750-0.82327.413-12.220-12.2200.0000.0000.0000.000
171A180SER0-0.009-0.01732.1690.1490.1490.0000.0000.0000.000
172A181GLU-1-0.914-0.94635.452-8.459-8.4590.0000.0000.0000.000
173A182THR0-0.021-0.01237.3930.1620.1620.0000.0000.0000.000
174A183PHE0-0.051-0.03335.9520.1920.1920.0000.0000.0000.000
175A184ASN0-0.023-0.01136.358-0.201-0.2010.0000.0000.0000.000
176A185ASN00.032-0.00730.146-0.123-0.1230.0000.0000.0000.000
177A186THR0-0.026-0.02331.509-0.085-0.0850.0000.0000.0000.000
178A187LEU0-0.046-0.02426.706-0.347-0.3470.0000.0000.0000.000
179A188ASP-1-0.904-0.95327.092-12.209-12.2090.0000.0000.0000.000
180A189HIS10.7850.88828.34711.08811.0880.0000.0000.0000.000
181A190GLY00.0640.01731.571-0.151-0.1510.0000.0000.0000.000
182A191VAL0-0.0060.00234.6140.1780.1780.0000.0000.0000.000
183A192CYS0-0.105-0.02036.2040.1020.1020.0000.0000.0000.000
184A193THR00.0710.02337.611-0.185-0.1850.0000.0000.0000.000
185A194LYS10.8770.94839.3057.3597.3590.0000.0000.0000.000
186A195PHE0-0.049-0.02930.173-0.117-0.1170.0000.0000.0000.000
187A196GLU-1-0.777-0.86732.962-10.095-10.0950.0000.0000.0000.000
188A197ALA0-0.0010.01135.263-0.064-0.0640.0000.0000.0000.000
189A198SER0-0.037-0.00733.8180.0580.0580.0000.0000.0000.000
190A199GLN00.009-0.00933.612-0.329-0.3290.0000.0000.0000.000
191A200LEU0-0.0220.00632.238-0.186-0.1860.0000.0000.0000.000
192A201GLY00.0320.00528.915-0.111-0.1110.0000.0000.0000.000
193A202ASP-1-0.896-0.94828.447-10.956-10.9560.0000.0000.0000.000
194A203GLU-1-0.933-0.97029.787-8.604-8.6040.0000.0000.0000.000
195A204VAL0-0.059-0.03428.1600.0720.0720.0000.0000.0000.000
196A205ALA00.0170.01225.784-0.146-0.1460.0000.0000.0000.000
197A206ALA0-0.0010.01027.206-0.181-0.1810.0000.0000.0000.000
198A207ASN00.008-0.00529.5360.0630.0630.0000.0000.0000.000
199A208PHE0-0.011-0.00622.978-0.045-0.0450.0000.0000.0000.000
200A209THR0-0.045-0.05224.941-0.287-0.2870.0000.0000.0000.000
201A210ALA0-0.0030.00626.725-0.061-0.0610.0000.0000.0000.000
202A211LEU0-0.040-0.00128.0540.2250.2250.0000.0000.0000.000
203A212PHE0-0.085-0.05821.309-0.126-0.1260.0000.0000.0000.000
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