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: NLYMQ

Calculation Name: 4XPU-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4XPU

Chain ID: A

ChEMBL ID:

UniProt ID: P68739

Base Structure: X-ray

Registration Date: 2025-10-05

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 208
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2425919.441844
FMO2-HF: Nuclear repulsion 2345104.318332
FMO2-HF: Total energy -80815.123512
FMO2-MP2: Total energy -81049.787711


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
54.87756.55711.96-4.235-9.405-0.033
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.841 / q_NPA : 0.917
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].
3A3LEU00.0540.0282.2641.6714.8032.584-1.869-3.847-0.013
4A4ALA00.0440.0031.9015.1523.6389.283-2.708-5.061-0.019
5A5SER00.0540.0253.2434.3764.4380.0930.342-0.497-0.001
6A6LEU00.0220.0225.6594.9744.9740.0000.0000.0000.000
7A7ARG10.8700.9305.72027.07027.0700.0000.0000.0000.000
8A8ALA00.0060.0047.2662.6302.6300.0000.0000.0000.000
9A9GLN00.1000.0419.2573.9673.9670.0000.0000.0000.000
10A10GLN00.0260.02610.5181.1031.1030.0000.0000.0000.000
11A11ILE0-0.027-0.02311.2301.5171.5170.0000.0000.0000.000
12A12GLU-1-0.911-0.93213.323-19.940-19.9400.0000.0000.0000.000
13A13LEU00.0240.01014.7811.1811.1810.0000.0000.0000.000
14A14ALA0-0.029-0.02715.9710.9830.9830.0000.0000.0000.000
15A15SER0-0.069-0.04217.1360.9440.9440.0000.0000.0000.000
16A16SER0-0.023-0.01519.1730.6920.6920.0000.0000.0000.000
17A17VAL0-0.056-0.01320.5030.4840.4840.0000.0000.0000.000
18A18ILE0-0.0190.00322.9880.2800.2800.0000.0000.0000.000
19A19ARG10.8400.89521.88712.19412.1940.0000.0000.0000.000
20A20GLU-1-0.799-0.88028.305-9.224-9.2240.0000.0000.0000.000
21A21ASP-1-0.754-0.84631.689-8.838-8.8380.0000.0000.0000.000
22A22ARG10.8300.89429.61010.15810.1580.0000.0000.0000.000
23A23LEU00.0380.01733.849-0.238-0.2380.0000.0000.0000.000
24A24ASP-1-0.873-0.91635.154-8.981-8.9810.0000.0000.0000.000
25A25LYS10.7640.85737.8617.8417.8410.0000.0000.0000.000
26A26ASP-1-0.883-0.92939.896-7.717-7.7170.0000.0000.0000.000
27A27PRO0-0.018-0.02141.8670.1520.1520.0000.0000.0000.000
28A28PRO0-0.031-0.00739.293-0.004-0.0040.0000.0000.0000.000
29A29ASP-1-0.831-0.90541.400-6.967-6.9670.0000.0000.0000.000
30A30LEU0-0.070-0.03639.2390.0960.0960.0000.0000.0000.000
31A31ILE0-0.003-0.00337.240-0.190-0.1900.0000.0000.0000.000
32A32ALA00.0320.00633.5000.0870.0870.0000.0000.0000.000
33A33GLY0-0.045-0.02033.340-0.019-0.0190.0000.0000.0000.000
34A34ALA0-0.023-0.01928.907-0.038-0.0380.0000.0000.0000.000
35A35ASP-1-0.865-0.93328.868-10.334-10.3340.0000.0000.0000.000
36A36VAL0-0.024-0.02223.317-0.240-0.2400.0000.0000.0000.000
37A37GLY00.0160.02125.5740.1090.1090.0000.0000.0000.000
38A38PHE0-0.041-0.03019.841-0.395-0.3950.0000.0000.0000.000
39A39GLU-1-0.750-0.84224.870-9.922-9.9220.0000.0000.0000.000
40A40GLN00.011-0.00525.578-0.363-0.3630.0000.0000.0000.000
41A41GLY00.0120.00825.442-0.292-0.2920.0000.0000.0000.000
42A42GLY0-0.043-0.01821.609-0.444-0.4440.0000.0000.0000.000
43A43GLU-1-0.911-0.94321.110-15.303-15.3030.0000.0000.0000.000
44A44VAL0-0.021-0.00322.717-0.085-0.0850.0000.0000.0000.000
45A45THR0-0.042-0.02121.259-0.139-0.1390.0000.0000.0000.000
46A46ARG10.8060.86823.6829.8399.8390.0000.0000.0000.000
47A47ALA00.0180.00325.943-0.280-0.2800.0000.0000.0000.000
48A48ALA0-0.0140.01027.8580.2590.2590.0000.0000.0000.000
49A49MET00.0000.00328.302-0.109-0.1090.0000.0000.0000.000
50A50VAL0-0.017-0.01432.5650.2760.2760.0000.0000.0000.000
51A51LEU00.0210.01135.673-0.176-0.1760.0000.0000.0000.000
52A52LEU0-0.005-0.01038.2380.1990.1990.0000.0000.0000.000
53A53LYS10.8820.93641.0726.5256.5250.0000.0000.0000.000
54A54TYR0-0.036-0.00141.942-0.038-0.0380.0000.0000.0000.000
55A55PRO00.0320.00544.0180.0630.0630.0000.0000.0000.000
56A56SER0-0.065-0.07446.119-0.040-0.0400.0000.0000.0000.000
57A57LEU0-0.020-0.01641.6850.0360.0360.0000.0000.0000.000
58A58GLU-1-0.823-0.85744.180-6.551-6.5510.0000.0000.0000.000
59A59LEU0-0.007-0.00340.436-0.132-0.1320.0000.0000.0000.000
60A60VAL0-0.035-0.02041.7380.1770.1770.0000.0000.0000.000
61A61GLU-1-0.779-0.83537.917-8.299-8.2990.0000.0000.0000.000
62A62TYR00.003-0.00137.112-0.105-0.1050.0000.0000.0000.000
63A63LYS10.8300.90833.9048.7368.7360.0000.0000.0000.000
64A64VAL00.0090.01131.790-0.206-0.2060.0000.0000.0000.000
65A65ALA00.0180.02028.1960.0930.0930.0000.0000.0000.000
66A66ARG10.7960.84527.3639.8269.8260.0000.0000.0000.000
67A67ILE00.0030.01221.5140.1050.1050.0000.0000.0000.000
68A68ALA00.0370.02122.3590.0110.0110.0000.0000.0000.000
69A69THR0-0.054-0.03917.635-0.395-0.3950.0000.0000.0000.000
70A70THR00.0180.01315.744-0.361-0.3610.0000.0000.0000.000
71A71MET0-0.0080.00710.418-1.627-1.6270.0000.0000.0000.000
72A72PRO00.0760.04811.6741.4341.4340.0000.0000.0000.000
73A73TYR00.032-0.00313.525-0.628-0.6280.0000.0000.0000.000
74A74ILE00.0190.0088.094-1.031-1.0310.0000.0000.0000.000
75A75PRO00.0170.00010.4100.6210.6210.0000.0000.0000.000
76A76GLY0-0.013-0.00710.888-1.209-1.2090.0000.0000.0000.000
77A77PHE00.013-0.0077.016-0.579-0.5790.0000.0000.0000.000
78A78LEU0-0.0080.00812.217-0.460-0.4600.0000.0000.0000.000
79A79SER00.0640.03015.676-0.071-0.0710.0000.0000.0000.000
80A80PHE0-0.028-0.02211.8080.1940.1940.0000.0000.0000.000
81A81ARG10.8180.91114.58017.29417.2940.0000.0000.0000.000
82A82GLU-1-0.859-0.94416.994-13.948-13.9480.0000.0000.0000.000
83A83TYR00.0390.02618.3250.6170.6170.0000.0000.0000.000
84A84PRO00.0170.00017.7850.6140.6140.0000.0000.0000.000
85A85ALA00.0210.02120.8260.5150.5150.0000.0000.0000.000
86A86LEU00.0220.00423.0170.5380.5380.0000.0000.0000.000
87A87LEU0-0.0110.00622.3620.4340.4340.0000.0000.0000.000
88A88ALA00.0220.00824.9060.4850.4850.0000.0000.0000.000
89A89ALA00.014-0.01026.8320.4340.4340.0000.0000.0000.000
90A90TRP00.0520.01127.8530.5070.5070.0000.0000.0000.000
91A91GLU-1-0.948-0.97227.200-11.238-11.2380.0000.0000.0000.000
92A92MET0-0.070-0.02530.3380.2750.2750.0000.0000.0000.000
93A93LEU0-0.055-0.01332.6280.3770.3770.0000.0000.0000.000
94A94SER0-0.065-0.07035.089-0.064-0.0640.0000.0000.0000.000
95A95GLN0-0.013-0.00237.9400.1560.1560.0000.0000.0000.000
96A96LYS10.8350.90632.0239.5639.5630.0000.0000.0000.000
97A97PRO0-0.054-0.01233.7490.2150.2150.0000.0000.0000.000
98A98ASP-1-0.728-0.87035.184-8.180-8.1800.0000.0000.0000.000
99A99LEU0-0.030-0.01633.399-0.126-0.1260.0000.0000.0000.000
100A100VAL0-0.011-0.00329.6810.1440.1440.0000.0000.0000.000
101A101PHE0-0.015-0.01631.334-0.108-0.1080.0000.0000.0000.000
102A102VAL00.016-0.00325.4880.0070.0070.0000.0000.0000.000
103A103ASP-1-0.817-0.90228.687-10.089-10.0890.0000.0000.0000.000
104A104GLY00.0220.00625.091-0.403-0.4030.0000.0000.0000.000
105A105HIS0-0.064-0.01722.3330.1290.1290.0000.0000.0000.000
106A106GLY00.0680.04323.027-0.301-0.3010.0000.0000.0000.000
107A107ILE00.0360.01721.695-0.585-0.5850.0000.0000.0000.000
108A108SER00.004-0.02122.164-0.193-0.1930.0000.0000.0000.000
109A109HIS00.0250.00815.1410.1540.1540.0000.0000.0000.000
110A110PRO0-0.014-0.02716.067-0.072-0.0720.0000.0000.0000.000
111A111ARG10.7650.8749.57121.34321.3430.0000.0000.0000.000
112A112ARG10.7550.88015.36812.42612.4260.0000.0000.0000.000
113A113LEU00.0370.02414.8000.1980.1980.0000.0000.0000.000
114A114GLY0-0.020-0.00317.120-0.577-0.5770.0000.0000.0000.000
115A115VAL00.0250.01119.802-0.117-0.1170.0000.0000.0000.000
116A116ALA00.0290.02421.053-0.003-0.0030.0000.0000.0000.000
117A117SER0-0.022-0.02720.7560.2410.2410.0000.0000.0000.000
118A118HIS0-0.035-0.00614.6680.0620.0620.0000.0000.0000.000
119A119PHE00.0430.00419.723-0.273-0.2730.0000.0000.0000.000
120A120GLY00.0340.01922.8640.0960.0960.0000.0000.0000.000
121A121LEU0-0.036-0.01719.5670.1930.1930.0000.0000.0000.000
122A122LEU0-0.051-0.03517.787-0.157-0.1570.0000.0000.0000.000
123A123VAL0-0.024-0.00622.2620.0760.0760.0000.0000.0000.000
124A124ASP-1-0.858-0.91125.576-10.749-10.7490.0000.0000.0000.000
125A125VAL00.0370.02127.3600.4820.4820.0000.0000.0000.000
126A126PRO0-0.0080.01828.999-0.312-0.3120.0000.0000.0000.000
127A127THR0-0.021-0.01726.7360.0890.0890.0000.0000.0000.000
128A128ILE0-0.022-0.00328.810-0.136-0.1360.0000.0000.0000.000
129A129GLY00.0280.01826.883-0.129-0.1290.0000.0000.0000.000
130A130VAL0-0.028-0.02027.7770.3140.3140.0000.0000.0000.000
131A131ALA00.0200.02826.8740.0630.0630.0000.0000.0000.000
132A132LYS10.8070.87428.8759.9399.9390.0000.0000.0000.000
133A133LYS10.9390.96827.4069.9639.9630.0000.0000.0000.000
134A134ARG10.9420.98424.60410.48310.4830.0000.0000.0000.000
135A135LEU0-0.0280.00319.782-0.137-0.1370.0000.0000.0000.000
136A136CYS0-0.074-0.04120.909-0.223-0.2230.0000.0000.0000.000
137A137GLY00.0740.03523.0010.3250.3250.0000.0000.0000.000
138A138LYS10.9050.94725.4929.5879.5870.0000.0000.0000.000
139A139PHE00.0480.02329.034-0.138-0.1380.0000.0000.0000.000
140A140GLU-1-0.883-0.93332.575-7.629-7.6290.0000.0000.0000.000
141A141PRO0-0.055-0.04336.043-0.014-0.0140.0000.0000.0000.000
142A142LEU0-0.0060.01137.0690.1520.1520.0000.0000.0000.000
143A143SER00.005-0.00939.747-0.012-0.0120.0000.0000.0000.000
144A144SER0-0.005-0.01542.758-0.124-0.1240.0000.0000.0000.000
145A145GLU-1-0.802-0.87444.740-6.658-6.6580.0000.0000.0000.000
146A146PRO0-0.054-0.03543.932-0.164-0.1640.0000.0000.0000.000
147A147GLY00.0320.00143.1180.1410.1410.0000.0000.0000.000
148A148ALA0-0.0080.01841.571-0.078-0.0780.0000.0000.0000.000
149A149LEU00.002-0.01037.364-0.195-0.1950.0000.0000.0000.000
150A150ALA00.0300.02435.9550.1100.1100.0000.0000.0000.000
151A151PRO00.0330.03232.870-0.190-0.1900.0000.0000.0000.000
152A152LEU0-0.074-0.03826.501-0.020-0.0200.0000.0000.0000.000
153A153MET00.0370.02328.620-0.306-0.3060.0000.0000.0000.000
154A154ASP-1-0.789-0.92021.750-12.398-12.3980.0000.0000.0000.000
155A155LYS10.8160.90519.08612.68312.6830.0000.0000.0000.000
156A156GLY00.0330.03624.617-0.010-0.0100.0000.0000.0000.000
157A157GLU-1-0.784-0.86123.382-11.822-11.8220.0000.0000.0000.000
158A158GLN00.012-0.01427.2370.0290.0290.0000.0000.0000.000
159A159LEU0-0.087-0.04123.172-0.194-0.1940.0000.0000.0000.000
160A160ALA00.002-0.01927.003-0.143-0.1430.0000.0000.0000.000
161A161TRP0-0.0080.00029.7100.1690.1690.0000.0000.0000.000
162A162VAL0-0.047-0.01931.518-0.150-0.1500.0000.0000.0000.000
163A163TRP00.0830.03633.9880.1860.1860.0000.0000.0000.000
164A164ARG10.7600.87137.2447.1597.1590.0000.0000.0000.000
165A165SER00.006-0.00638.9180.2080.2080.0000.0000.0000.000
166A166LYS10.9020.93440.7846.9136.9130.0000.0000.0000.000
167A167ALA00.0590.02042.891-0.075-0.0750.0000.0000.0000.000
168A168ARG10.9390.95844.1676.2266.2260.0000.0000.0000.000
169A169CYS0-0.0250.02139.738-0.088-0.0880.0000.0000.0000.000
170A170ASN00.0170.00735.5020.0750.0750.0000.0000.0000.000
171A171PRO00.0100.01634.4080.0270.0270.0000.0000.0000.000
172A172LEU0-0.0200.01333.381-0.207-0.2070.0000.0000.0000.000
173A173PHE0-0.011-0.01928.9010.0970.0970.0000.0000.0000.000
174A174ILE00.0030.01429.597-0.280-0.2800.0000.0000.0000.000
175A175ALA00.0280.00726.4870.0810.0810.0000.0000.0000.000
176A176THR00.0050.01226.742-0.054-0.0540.0000.0000.0000.000
177A177GLY00.0350.01224.971-0.413-0.4130.0000.0000.0000.000
178A178HIS0-0.012-0.02324.488-0.704-0.7040.0000.0000.0000.000
179A179ARG10.8030.90126.63810.42210.4220.0000.0000.0000.000
180A180VAL00.0220.02229.7960.4020.4020.0000.0000.0000.000
181A181SER0-0.002-0.01130.250-0.285-0.2850.0000.0000.0000.000
182A182VAL0-0.011-0.02730.656-0.004-0.0040.0000.0000.0000.000
183A183ASP-1-0.835-0.90632.217-8.251-8.2510.0000.0000.0000.000
184A184SER0-0.016-0.04235.5240.2330.2330.0000.0000.0000.000
185A185ALA0-0.0010.00832.0010.0690.0690.0000.0000.0000.000
186A186LEU0-0.031-0.01434.0130.0580.0580.0000.0000.0000.000
187A187ALA00.0230.01036.2770.1470.1470.0000.0000.0000.000
188A188TRP00.006-0.00336.0590.2660.2660.0000.0000.0000.000
189A189VAL00.017-0.00134.1460.0730.0730.0000.0000.0000.000
190A190GLN0-0.032-0.02837.3530.1990.1990.0000.0000.0000.000
191A191ARG10.8980.96040.8377.5737.5730.0000.0000.0000.000
192A192CYS0-0.0120.01038.8080.0860.0860.0000.0000.0000.000
193A193MET0-0.042-0.00538.513-0.060-0.0600.0000.0000.0000.000
194A194LYS11.0160.99942.4796.7286.7280.0000.0000.0000.000
195A195GLY0-0.0090.01645.1890.0350.0350.0000.0000.0000.000
196A196TYR0-0.025-0.00841.6530.0720.0720.0000.0000.0000.000
197A197ARG10.8330.88733.4928.5358.5350.0000.0000.0000.000
198A198LEU00.0190.03234.285-0.075-0.0750.0000.0000.0000.000
199A199PRO00.0230.02135.6320.2140.2140.0000.0000.0000.000
200A200GLU-1-0.753-0.86237.679-7.408-7.4080.0000.0000.0000.000
201A201PRO00.0270.02535.368-0.048-0.0480.0000.0000.0000.000
202A202THR00.0530.01031.907-0.014-0.0140.0000.0000.0000.000
203A203ARG10.7570.85434.4907.4147.4140.0000.0000.0000.000
204A204TRP00.017-0.00737.4750.1160.1160.0000.0000.0000.000
205A205ALA0-0.0180.00032.6650.0030.0030.0000.0000.0000.000
206A206ASP-1-0.815-0.91132.716-9.370-9.3700.0000.0000.0000.000
207A207ALA0-0.096-0.04134.5610.0710.0710.0000.0000.0000.000
208A208VAL-1-0.865-0.87834.894-8.817-8.8170.0000.0000.0000.000