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: Z9RLN

Calculation Name: 4L72-B-Xray547

Preferred Name: Dipeptidyl peptidase IV

Target Type: SINGLE PROTEIN

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

Ligand 3-letter code: NAG | BMA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4L72

Chain ID: B

ChEMBL ID: CHEMBL284

UniProt ID: P27487

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 200
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2214478.774025
FMO2-HF: Nuclear repulsion 2134163.736858
FMO2-HF: Total energy -80315.037166
FMO2-MP2: Total energy -80544.230545


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(B:382:GLU)


Summations of interaction energy for fragment #1(B:382:GLU)
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.
-31.933-21.3755.77-7.4-8.928-0.035
Interaction energy analysis for fragmet #1(B:382:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.136 / q_NPA : -0.060
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].
3B384ASP-1-0.821-0.9263.29616.74619.0330.308-0.855-1.7410.004
4B385PHE0-0.0200.0174.5863.6783.895-0.001-0.014-0.2020.000
26B408ASN00.0240.0112.076-10.479-7.5914.556-3.580-3.864-0.027
27B409TYR00.008-0.0082.740-1.9120.9710.830-1.893-1.820-0.021
28B410ASN00.0680.0405.192-1.706-1.600-0.001-0.003-0.1010.000
31B413LYS10.8410.9273.190-31.262-29.0850.078-1.055-1.2000.009
5B386SER00.0720.0196.8322.3322.3320.0000.0000.0000.000
6B387PRO00.0060.0149.2630.1980.1980.0000.0000.0000.000
7B388LEU0-0.0360.00712.166-0.441-0.4410.0000.0000.0000.000
8B389LEU00.0040.00010.008-0.203-0.2030.0000.0000.0000.000
9B390SER0-0.046-0.03513.809-0.314-0.3140.0000.0000.0000.000
10B391GLY00.0530.03116.409-0.045-0.0450.0000.0000.0000.000
11B392THR00.0150.01319.7900.1640.1640.0000.0000.0000.000
12B393PRO0-0.0110.01318.899-0.107-0.1070.0000.0000.0000.000
13B394PRO0-0.0030.01420.190-0.104-0.1040.0000.0000.0000.000
14B395GLN00.0440.01823.3460.0850.0850.0000.0000.0000.000
15B396VAL00.0060.00224.906-0.041-0.0410.0000.0000.0000.000
16B397TYR0-0.055-0.04625.869-0.024-0.0240.0000.0000.0000.000
17B398ASN0-0.041-0.01125.472-0.127-0.1270.0000.0000.0000.000
18B399PHE00.0040.02020.8770.0770.0770.0000.0000.0000.000
19B400LYS10.9230.96916.970-0.745-0.7450.0000.0000.0000.000
20B401ARG10.8580.90917.2040.2490.2490.0000.0000.0000.000
21B402LEU0-0.032-0.01011.1340.0750.0750.0000.0000.0000.000
22B403VAL00.016-0.00512.8660.0640.0640.0000.0000.0000.000
23B404PHE00.006-0.0017.1640.2160.2160.0000.0000.0000.000
24B405THR00.0200.0118.6780.6220.6220.0000.0000.0000.000
25B406ASN00.0340.0117.3900.1420.1420.0000.0000.0000.000
29B411LEU00.0310.0197.1760.9110.9110.0000.0000.0000.000
30B412THR0-0.013-0.0348.976-0.388-0.3880.0000.0000.0000.000
32B414LEU0-0.039-0.0237.339-0.057-0.0570.0000.0000.0000.000
33B415LEU00.0130.0119.837-1.205-1.2050.0000.0000.0000.000
34B416SER00.0220.00112.674-0.318-0.3180.0000.0000.0000.000
35B417LEU0-0.0170.00610.714-0.318-0.3180.0000.0000.0000.000
36B418PHE0-0.018-0.01313.362-0.420-0.4200.0000.0000.0000.000
37B419SER0-0.0060.00717.231-0.088-0.0880.0000.0000.0000.000
38B420VAL00.018-0.00217.591-0.142-0.1420.0000.0000.0000.000
39B421ASN0-0.053-0.02320.460-0.122-0.1220.0000.0000.0000.000
40B422ASP-1-0.815-0.90322.8630.7830.7830.0000.0000.0000.000
41B423PHE00.014-0.00616.5220.1700.1700.0000.0000.0000.000
42B424THR00.0230.03521.834-0.116-0.1160.0000.0000.0000.000
43B425CYS0-0.090-0.03718.3480.1160.1160.0000.0000.0000.000
44B426SER00.0210.00923.213-0.044-0.0440.0000.0000.0000.000
45B427GLN0-0.007-0.02023.237-0.034-0.0340.0000.0000.0000.000
46B428ILE00.0060.01517.779-0.105-0.1050.0000.0000.0000.000
47B429SER00.0250.01721.4980.0870.0870.0000.0000.0000.000
48B430PRO00.0890.02819.043-0.056-0.0560.0000.0000.0000.000
49B431ALA00.0100.00317.4610.1460.1460.0000.0000.0000.000
50B432ALA0-0.0020.01116.915-0.006-0.0060.0000.0000.0000.000
51B433ILE0-0.015-0.01914.561-0.155-0.1550.0000.0000.0000.000
52B434ALA0-0.034-0.01912.9390.0660.0660.0000.0000.0000.000
53B435SER0-0.035-0.01512.1510.1730.1730.0000.0000.0000.000
54B436ASN0-0.034-0.01913.058-0.292-0.2920.0000.0000.0000.000
55B585CYS-1-0.784-0.8816.499-2.486-2.4860.0000.0000.0000.000
56B438TYR0-0.019-0.02910.9310.3560.3560.0000.0000.0000.000
57B439SER0-0.022-0.00611.551-0.717-0.7170.0000.0000.0000.000
58B440SER0-0.048-0.02112.406-0.363-0.3630.0000.0000.0000.000
59B441LEU00.0280.0219.1260.3960.3960.0000.0000.0000.000
60B442ILE0-0.042-0.02012.371-0.109-0.1090.0000.0000.0000.000
61B443LEU00.0190.00311.0400.2710.2710.0000.0000.0000.000
62B444ASP-1-0.778-0.85514.4220.3400.3400.0000.0000.0000.000
63B445TYR00.0260.00014.9280.2270.2270.0000.0000.0000.000
64B446PHE0-0.004-0.00517.915-0.156-0.1560.0000.0000.0000.000
65B447SER00.010-0.00321.2690.1660.1660.0000.0000.0000.000
66B448TYR0-0.061-0.08023.587-0.158-0.1580.0000.0000.0000.000
67B449PRO00.0120.03125.4750.0920.0920.0000.0000.0000.000
68B450LEU00.022-0.02324.844-0.063-0.0630.0000.0000.0000.000
69B451SER0-0.029-0.00728.550-0.038-0.0380.0000.0000.0000.000
70B452MET00.0140.01730.537-0.068-0.0680.0000.0000.0000.000
71B453LYS10.8600.92427.333-0.968-0.9680.0000.0000.0000.000
72B454SER0-0.058-0.03129.742-0.031-0.0310.0000.0000.0000.000
73B455ASP-1-0.826-0.90131.8800.4580.4580.0000.0000.0000.000
74B456LEU0-0.0340.00123.764-0.044-0.0440.0000.0000.0000.000
75B457SER00.0350.00527.1480.0300.0300.0000.0000.0000.000
76B458VAL00.012-0.01126.277-0.043-0.0430.0000.0000.0000.000
77B459SER0-0.031-0.01528.965-0.061-0.0610.0000.0000.0000.000
78B460SER0-0.0410.00031.504-0.029-0.0290.0000.0000.0000.000
79B461ALA00.0290.02333.279-0.029-0.0290.0000.0000.0000.000
80B462GLY00.0670.04934.646-0.015-0.0150.0000.0000.0000.000
81B463PRO00.0220.00334.675-0.021-0.0210.0000.0000.0000.000
82B464ILE0-0.0160.00428.571-0.014-0.0140.0000.0000.0000.000
83B465SER00.006-0.02230.214-0.006-0.0060.0000.0000.0000.000
84B466GLN0-0.057-0.02031.211-0.064-0.0640.0000.0000.0000.000
85B467PHE00.0230.00233.416-0.040-0.0400.0000.0000.0000.000
86B468ASN0-0.054-0.03028.8740.0380.0380.0000.0000.0000.000
87B469TYR00.012-0.01820.6340.0160.0160.0000.0000.0000.000
88B470LYS10.9680.99626.492-0.031-0.0310.0000.0000.0000.000
89B471GLN00.0300.01221.251-0.066-0.0660.0000.0000.0000.000
90B472SER0-0.025-0.02422.806-0.019-0.0190.0000.0000.0000.000
91B473PHE00.007-0.00524.5820.0680.0680.0000.0000.0000.000
92B474SER0-0.018-0.00425.8870.0130.0130.0000.0000.0000.000
93B475ASN0-0.031-0.01120.633-0.111-0.1110.0000.0000.0000.000
94B476PRO0-0.0010.00119.5980.1060.1060.0000.0000.0000.000
95B477THR00.0090.00719.708-0.056-0.0560.0000.0000.0000.000
96B479LEU00.0210.01920.266-0.003-0.0030.0000.0000.0000.000
97B480ILE0-0.0220.00016.257-0.008-0.0080.0000.0000.0000.000
98B481LEU00.0050.00820.356-0.013-0.0130.0000.0000.0000.000
99B482ALA0-0.003-0.00219.3220.0570.0570.0000.0000.0000.000
100B483THR00.0330.00221.266-0.105-0.1050.0000.0000.0000.000
101B484VAL00.0180.01219.2620.2420.2420.0000.0000.0000.000
102B485PRO0-0.029-0.00419.176-0.206-0.2060.0000.0000.0000.000
103B486HIS00.046-0.00420.7170.2370.2370.0000.0000.0000.000
104B487ASN0-0.0310.00018.317-0.166-0.1660.0000.0000.0000.000
105B488LEU0-0.041-0.00914.9040.2590.2590.0000.0000.0000.000
106B489THR00.012-0.00417.927-0.147-0.1470.0000.0000.0000.000
107B490THR0-0.083-0.04115.023-0.257-0.2570.0000.0000.0000.000
108B491ILE00.0140.02715.475-0.142-0.1420.0000.0000.0000.000
109B492THR0-0.007-0.01819.136-0.132-0.1320.0000.0000.0000.000
110B493LYS10.8510.89622.773-1.384-1.3840.0000.0000.0000.000
111B494PRO0-0.0130.00624.940-0.065-0.0650.0000.0000.0000.000
112B495LEU00.017-0.00727.8070.0070.0070.0000.0000.0000.000
113B496LYS10.8390.92530.904-0.616-0.6160.0000.0000.0000.000
114B497TYR00.0350.01025.9530.0650.0650.0000.0000.0000.000
115B498SER0-0.011-0.01229.587-0.077-0.0770.0000.0000.0000.000
116B499TYR0-0.006-0.01329.9750.0260.0260.0000.0000.0000.000
117B500ILE00.0050.00432.116-0.024-0.0240.0000.0000.0000.000
118B501ASN0-0.007-0.00234.530-0.026-0.0260.0000.0000.0000.000
119B502LYS10.9030.93637.473-0.190-0.1900.0000.0000.0000.000
120B503CYS0-0.0430.00634.564-0.006-0.0060.0000.0000.0000.000
121B504SER0-0.002-0.03438.481-0.014-0.0140.0000.0000.0000.000
122B505ARG10.8450.93541.6880.0040.0040.0000.0000.0000.000
123B506LEU0-0.0130.02043.9940.0060.0060.0000.0000.0000.000
124B507LEU00.004-0.00547.239-0.013-0.0130.0000.0000.0000.000
125B508SER00.0370.00749.6210.0090.0090.0000.0000.0000.000
126B509ASP-1-0.808-0.87352.4610.0230.0230.0000.0000.0000.000
127B510ASP-1-0.903-0.95852.8520.0600.0600.0000.0000.0000.000
128B511ARG10.8590.93453.718-0.029-0.0290.0000.0000.0000.000
129B512THR0-0.070-0.06249.5170.0090.0090.0000.0000.0000.000
130B513GLU-1-0.800-0.86644.8420.1340.1340.0000.0000.0000.000
131B514VAL0-0.021-0.01643.271-0.007-0.0070.0000.0000.0000.000
132B515PRO00.0320.01540.7800.0010.0010.0000.0000.0000.000
133B516GLN0-0.092-0.05737.781-0.040-0.0400.0000.0000.0000.000
134B517LEU00.0200.01135.3280.0260.0260.0000.0000.0000.000
135B518VAL0-0.036-0.00929.208-0.036-0.0360.0000.0000.0000.000
136B519ASN0-0.020-0.01630.2270.0020.0020.0000.0000.0000.000
137B520ALA0-0.007-0.01426.3610.0360.0360.0000.0000.0000.000
138B521ASN0-0.034-0.01822.177-0.031-0.0310.0000.0000.0000.000
139B522GLN00.0010.01724.497-0.016-0.0160.0000.0000.0000.000
140B523TYR00.002-0.01822.5100.0430.0430.0000.0000.0000.000
141B524SER00.0260.01628.118-0.061-0.0610.0000.0000.0000.000
142B525PRO00.0590.01731.5890.0110.0110.0000.0000.0000.000
143B527VAL00.0180.01429.0030.0230.0230.0000.0000.0000.000
144B528SER0-0.099-0.05032.2680.0110.0110.0000.0000.0000.000
145B529ILE0-0.045-0.03034.783-0.009-0.0090.0000.0000.0000.000
146B530VAL0-0.0080.01633.5700.0110.0110.0000.0000.0000.000
147B531PRO00.0370.03533.1680.0070.0070.0000.0000.0000.000
148B532SER0-0.011-0.01128.2180.0180.0180.0000.0000.0000.000
149B533THR0-0.034-0.03629.1210.1120.1120.0000.0000.0000.000
150B534VAL0-0.0110.01331.654-0.036-0.0360.0000.0000.0000.000
151B535TRP0-0.0080.01135.1100.0500.0500.0000.0000.0000.000
152B536GLU-1-0.908-0.98037.7970.5130.5130.0000.0000.0000.000
153B537ASP-1-0.840-0.92138.6080.4590.4590.0000.0000.0000.000
154B538GLY00.0390.03639.870-0.008-0.0080.0000.0000.0000.000
155B539ASP-1-0.851-0.91139.4540.3610.3610.0000.0000.0000.000
156B540TYR0-0.022-0.02540.536-0.010-0.0100.0000.0000.0000.000
157B541TYR0-0.007-0.00937.878-0.003-0.0030.0000.0000.0000.000
158B542ARG10.9350.95941.754-0.191-0.1910.0000.0000.0000.000
159B543LYS10.9150.96539.047-0.025-0.0250.0000.0000.0000.000
160B544GLN00.0150.01643.656-0.003-0.0030.0000.0000.0000.000
161B545LEU0-0.069-0.02742.317-0.001-0.0010.0000.0000.0000.000
162B546SER00.012-0.00444.663-0.008-0.0080.0000.0000.0000.000
163B547PRO00.016-0.02347.041-0.004-0.0040.0000.0000.0000.000
164B548LEU00.0100.00144.929-0.004-0.0040.0000.0000.0000.000
165B549GLU-1-0.858-0.89941.395-0.029-0.0290.0000.0000.0000.000
166B550GLY00.0280.00943.7550.0110.0110.0000.0000.0000.000
167B551GLY0-0.021-0.00946.1720.0080.0080.0000.0000.0000.000
168B552GLY00.0260.01147.7000.0030.0030.0000.0000.0000.000
169B553TRP0-0.011-0.00246.2080.0080.0080.0000.0000.0000.000
170B554LEU0-0.007-0.00238.089-0.011-0.0110.0000.0000.0000.000
171B555VAL0-0.005-0.01542.2460.0100.0100.0000.0000.0000.000
172B556ALA00.0220.00637.752-0.003-0.0030.0000.0000.0000.000
173B557SER0-0.058-0.04839.1660.0010.0010.0000.0000.0000.000
174B558GLY00.0100.00936.6660.0030.0030.0000.0000.0000.000
175B559SER0-0.0080.01435.971-0.022-0.0220.0000.0000.0000.000
176B560THR0-0.107-0.06234.0840.0360.0360.0000.0000.0000.000
177B561VAL00.0010.00432.186-0.013-0.0130.0000.0000.0000.000
178B562ALA00.0280.01532.8700.0360.0360.0000.0000.0000.000
179B563MET0-0.0080.00627.3220.0710.0710.0000.0000.0000.000
180B564THR00.0290.03328.449-0.014-0.0140.0000.0000.0000.000
181B565GLU-1-0.800-0.89629.1821.2421.2420.0000.0000.0000.000
182B566GLN0-0.036-0.03024.8450.0720.0720.0000.0000.0000.000
183B567LEU0-0.0180.00722.0820.0770.0770.0000.0000.0000.000
184B568GLN0-0.012-0.00423.5350.0560.0560.0000.0000.0000.000
185B569MET00.0310.01117.1400.0200.0200.0000.0000.0000.000
186B570GLY00.0260.01921.343-0.023-0.0230.0000.0000.0000.000
187B571PHE0-0.014-0.02115.8260.1360.1360.0000.0000.0000.000
188B572GLY00.0020.01518.277-0.119-0.1190.0000.0000.0000.000
189B573ILE0-0.014-0.01314.2160.0920.0920.0000.0000.0000.000
190B574THR0-0.028-0.01716.731-0.072-0.0720.0000.0000.0000.000
191B575VAL0-0.0070.01013.797-0.085-0.0850.0000.0000.0000.000
192B576GLN00.0240.02215.5200.1930.1930.0000.0000.0000.000
193B577TYR00.0360.01615.662-0.258-0.2580.0000.0000.0000.000
194B578GLY0-0.0060.01917.3360.1060.1060.0000.0000.0000.000
195B579THR0-0.034-0.03317.690-0.205-0.2050.0000.0000.0000.000
196B580ASP-1-0.876-0.94719.224-1.648-1.6480.0000.0000.0000.000
197B581THR0-0.028-0.01615.182-0.146-0.1460.0000.0000.0000.000
198B582ASN00.002-0.00413.359-0.330-0.3300.0000.0000.0000.000
199B583SER0-0.017-0.0139.558-0.225-0.2250.0000.0000.0000.000
200B584VAL0-0.0200.0046.788-2.112-2.1120.0000.0000.0000.000