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: ML14Z

Calculation Name: 4DAP-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4DAP

Chain ID: A

ChEMBL ID:

UniProt ID: P0A823

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 234
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2889465.371315
FMO2-HF: Nuclear repulsion 2796910.681342
FMO2-HF: Total energy -92554.689973
FMO2-MP2: Total energy -92823.0567


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.
-169.624-167.78248.31-23.045-27.103-0.202
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 : 0.708 / q_NPA : 0.835
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].
3A3PHE0-0.065-0.0422.620-7.742-2.7951.322-2.750-3.519-0.027
4A4SER0-0.0020.0124.2204.3154.4020.000-0.011-0.0760.000
84A84TRP0-0.034-0.0332.953-6.568-3.9922.299-1.032-3.842-0.014
85A85ALA00.0200.0205.512-2.968-2.816-0.001-0.008-0.1430.000
87A87ARG10.9290.9642.67135.56934.6397.282-1.820-4.5310.025
88A88LEU00.003-0.0062.432-5.313-4.4841.249-0.460-1.618-0.003
89A89THR00.016-0.0024.856-0.738-0.712-0.001-0.007-0.0180.000
91A91GLU-1-0.866-0.9201.817-138.037-143.81123.896-10.703-7.419-0.126
223A223GLY00.0160.0074.106-5.692-5.5310.000-0.060-0.1010.000
224A224MET0-0.059-0.0102.61213.29015.8780.419-0.909-2.098-0.001
225A225ALA00.0260.0141.759-42.670-45.70311.843-5.207-3.602-0.056
226A226LEU0-0.037-0.0043.9309.79910.0120.002-0.078-0.1360.000
5A5PRO00.012-0.0117.0040.7910.7910.0000.0000.0000.000
6A6PRO00.0250.0047.843-1.611-1.6110.0000.0000.0000.000
7A7LEU0-0.058-0.0076.1812.4252.4250.0000.0000.0000.000
8A8GLN0-0.0050.0079.6141.8761.8760.0000.0000.0000.000
9A9ARG10.9730.98612.74114.31014.3100.0000.0000.0000.000
10A10ALA0-0.014-0.01515.1700.8060.8060.0000.0000.0000.000
11A11THR0-0.0060.00417.664-0.533-0.5330.0000.0000.0000.000
12A12LEU0-0.038-0.00518.4700.3160.3160.0000.0000.0000.000
13A13ILE00.0120.02320.5560.3780.3780.0000.0000.0000.000
14A14GLN00.001-0.02022.8950.4470.4470.0000.0000.0000.000
15A15ARG10.8390.91018.48113.47513.4750.0000.0000.0000.000
16A16TYR0-0.062-0.06021.4140.6700.6700.0000.0000.0000.000
17A17LYS10.9360.95522.16510.08610.0860.0000.0000.0000.000
18A18ARG10.9220.98920.23811.17711.1770.0000.0000.0000.000
19A19PHE00.0790.02917.855-0.297-0.2970.0000.0000.0000.000
20A20LEU0-0.043-0.00317.935-0.294-0.2940.0000.0000.0000.000
21A21ALA00.0460.01617.5870.1310.1310.0000.0000.0000.000
22A22ASP-1-0.794-0.83519.281-11.745-11.7450.0000.0000.0000.000
23A23VAL00.000-0.02017.538-0.146-0.1460.0000.0000.0000.000
24A24ILE00.0320.01820.8570.2550.2550.0000.0000.0000.000
25A25THR00.007-0.01519.056-0.584-0.5840.0000.0000.0000.000
26A26PRO0-0.037-0.03819.2880.5030.5030.0000.0000.0000.000
27A27ASP-1-0.842-0.90122.208-11.357-11.3570.0000.0000.0000.000
28A28GLY0-0.013-0.00124.8210.4610.4610.0000.0000.0000.000
29A29ARG10.8550.93524.68910.73410.7340.0000.0000.0000.000
30A30GLU-1-0.900-0.94524.055-10.558-10.5580.0000.0000.0000.000
31A31LEU0-0.048-0.02417.5540.0730.0730.0000.0000.0000.000
32A32THR0-0.041-0.03719.816-0.040-0.0400.0000.0000.0000.000
33A33LEU0-0.033-0.01513.963-0.358-0.3580.0000.0000.0000.000
34A34HIS0-0.026-0.02112.6651.1651.1650.0000.0000.0000.000
35A35CYS0-0.031-0.00913.756-1.217-1.2170.0000.0000.0000.000
36A36PRO0-0.0070.0059.9530.8580.8580.0000.0000.0000.000
37A37ASN00.003-0.01012.8830.6700.6700.0000.0000.0000.000
38A38THR0-0.002-0.01114.8670.6200.6200.0000.0000.0000.000
39A39GLY00.0410.03017.7960.7270.7270.0000.0000.0000.000
40A40ALA00.0300.01319.6370.1260.1260.0000.0000.0000.000
41A41MET0-0.051-0.01215.2370.1860.1860.0000.0000.0000.000
42A42THR00.0280.00618.7640.2280.2280.0000.0000.0000.000
43A43GLY00.0100.01219.867-0.461-0.4610.0000.0000.0000.000
44A44CYS0-0.056-0.02415.621-0.810-0.8100.0000.0000.0000.000
45A45ALA0-0.013-0.01116.689-0.683-0.6830.0000.0000.0000.000
46A46THR0-0.0030.00519.3180.7270.7270.0000.0000.0000.000
47A47PRO0-0.014-0.01221.618-0.355-0.3550.0000.0000.0000.000
48A48GLY00.0170.01023.2820.2050.2050.0000.0000.0000.000
49A49ASP-1-0.794-0.88018.283-14.255-14.2550.0000.0000.0000.000
50A50THR0-0.041-0.00715.6050.2720.2720.0000.0000.0000.000
51A51VAL0-0.032-0.01614.093-0.686-0.6860.0000.0000.0000.000
52A52TRP00.002-0.01310.1720.2200.2200.0000.0000.0000.000
53A53TYR0-0.020-0.02010.335-0.715-0.7150.0000.0000.0000.000
54A54SER00.003-0.0227.1620.0670.0670.0000.0000.0000.000
55A55THR00.020-0.0209.2601.6351.6350.0000.0000.0000.000
56A56SER0-0.043-0.01411.099-0.981-0.9810.0000.0000.0000.000
57A57ASP-1-0.868-0.93312.636-16.849-16.8490.0000.0000.0000.000
58A58ASN0-0.029-0.01115.1031.4821.4820.0000.0000.0000.000
59A59THR0-0.053-0.03215.7700.2430.2430.0000.0000.0000.000
60A60LYS10.9890.98317.94811.39711.3970.0000.0000.0000.000
61A61ARG10.8970.96412.19316.81816.8180.0000.0000.0000.000
62A62LYS10.9450.96719.71910.28010.2800.0000.0000.0000.000
63A63TYR00.0630.02817.6080.3900.3900.0000.0000.0000.000
64A64PRO00.0120.01315.523-0.577-0.5770.0000.0000.0000.000
65A65HIS00.0710.04613.177-1.642-1.6420.0000.0000.0000.000
66A66THR0-0.044-0.0169.6341.4131.4130.0000.0000.0000.000
67A67TRP00.017-0.00610.448-0.458-0.4580.0000.0000.0000.000
68A68GLU-1-0.763-0.8396.279-26.904-26.9040.0000.0000.0000.000
69A69LEU00.008-0.0076.215-0.403-0.4030.0000.0000.0000.000
70A70THR0-0.029-0.0289.9121.2411.2410.0000.0000.0000.000
71A71GLN0-0.0060.01013.509-1.167-1.1670.0000.0000.0000.000
72A72SER00.0180.00315.0921.2111.2110.0000.0000.0000.000
73A73GLN0-0.010-0.03118.4000.2610.2610.0000.0000.0000.000
74A74SER0-0.065-0.01920.5210.3100.3100.0000.0000.0000.000
75A75GLY00.0000.00219.0770.0140.0140.0000.0000.0000.000
76A76ALA0-0.0200.00016.783-1.096-1.0960.0000.0000.0000.000
77A77PHE00.0480.02310.8200.2750.2750.0000.0000.0000.000
78A78ILE00.0130.01612.191-0.186-0.1860.0000.0000.0000.000
79A79CYS0-0.0240.0006.078-0.083-0.0830.0000.0000.0000.000
80A80VAL0-0.0010.0029.1901.1551.1550.0000.0000.0000.000
81A81ASN0-0.009-0.0206.8482.5882.5880.0000.0000.0000.000
82A82THR00.018-0.0097.709-2.110-2.1100.0000.0000.0000.000
83A83LEU00.0010.0128.402-0.364-0.3640.0000.0000.0000.000
86A86ASN00.0220.0078.067-1.787-1.7870.0000.0000.0000.000
90A90LYS10.9350.9757.71525.00625.0060.0000.0000.0000.000
92A92ALA00.005-0.0015.9171.7021.7020.0000.0000.0000.000
93A93ILE00.0180.0197.6063.0923.0920.0000.0000.0000.000
94A94LEU0-0.048-0.0319.0141.6861.6860.0000.0000.0000.000
95A95ASN0-0.0350.0015.6234.4694.4690.0000.0000.0000.000
96A96GLU-1-0.891-0.9489.429-18.882-18.8820.0000.0000.0000.000
97A97SER0-0.041-0.0308.7691.0171.0170.0000.0000.0000.000
98A98ILE0-0.046-0.01610.3791.2161.2160.0000.0000.0000.000
99A99SER00.0380.01612.9751.0141.0140.0000.0000.0000.000
100A100GLU-1-0.824-0.89116.127-17.505-17.5050.0000.0000.0000.000
101A101LEU0-0.043-0.02514.1460.9720.9720.0000.0000.0000.000
102A102SER00.0470.03615.152-0.560-0.5600.0000.0000.0000.000
103A103GLY00.0220.01616.6941.0101.0100.0000.0000.0000.000
104A104TYR0-0.022-0.00818.2130.8790.8790.0000.0000.0000.000
105A105SER00.0290.01118.645-0.661-0.6610.0000.0000.0000.000
106A106SER0-0.041-0.01618.445-0.100-0.1000.0000.0000.0000.000
107A107LEU00.0290.01612.420-0.099-0.0990.0000.0000.0000.000
108A108LYS10.8520.92316.28213.22913.2290.0000.0000.0000.000
109A109SER00.008-0.01313.427-0.845-0.8450.0000.0000.0000.000
110A110GLU-1-0.864-0.91614.941-15.410-15.4100.0000.0000.0000.000
111A111VAL0-0.0080.01017.5580.7540.7540.0000.0000.0000.000
112A112LYS10.8080.88521.04510.21710.2170.0000.0000.0000.000
113A113TYR00.010-0.00123.770-0.017-0.0170.0000.0000.0000.000
114A114GLY00.0690.04826.4870.3040.3040.0000.0000.0000.000
115A115ALA00.0060.00929.5850.0500.0500.0000.0000.0000.000
116A116GLU-1-0.819-0.89529.276-9.991-9.9910.0000.0000.0000.000
117A117ARG10.8440.88426.9679.9869.9860.0000.0000.0000.000
118A118SER0-0.0120.01125.505-0.431-0.4310.0000.0000.0000.000
119A119ARG10.8110.87418.47014.06814.0680.0000.0000.0000.000
120A120ILE00.0050.02019.0840.1100.1100.0000.0000.0000.000
121A121ASP-1-0.825-0.88514.258-17.625-17.6250.0000.0000.0000.000
122A122PHE0-0.023-0.03310.574-1.221-1.2210.0000.0000.0000.000
123A123MET0-0.0120.01316.3720.8790.8790.0000.0000.0000.000
124A124LEU0-0.014-0.00415.237-0.530-0.5300.0000.0000.0000.000
125A125GLN00.019-0.00719.2290.4840.4840.0000.0000.0000.000
126A126ALA00.006-0.01921.721-0.587-0.5870.0000.0000.0000.000
127A127ASP-1-0.902-0.93224.240-11.223-11.2230.0000.0000.0000.000
128A128SER0-0.050-0.01727.1580.2660.2660.0000.0000.0000.000
129A129ARG10.8250.90120.72514.03214.0320.0000.0000.0000.000
130A130PRO00.0450.02826.713-0.073-0.0730.0000.0000.0000.000
131A131ASP-1-0.854-0.90424.185-12.446-12.4460.0000.0000.0000.000
132A132CYS0-0.048-0.02319.4250.1580.1580.0000.0000.0000.000
133A133TYR00.0140.00320.257-0.702-0.7020.0000.0000.0000.000
134A134ILE00.016-0.00615.165-0.038-0.0380.0000.0000.0000.000
135A135GLU-1-0.804-0.89617.234-14.189-14.1890.0000.0000.0000.000
136A136VAL0-0.030-0.02211.233-0.415-0.4150.0000.0000.0000.000
137A137LYS10.8030.89514.65215.90215.9020.0000.0000.0000.000
138A138SER00.0140.00411.930-1.522-1.5220.0000.0000.0000.000
139A139VAL0-0.024-0.01513.6261.3401.3400.0000.0000.0000.000
140A140THR00.0130.00112.869-0.956-0.9560.0000.0000.0000.000
141A141LEU00.0060.00915.5070.1590.1590.0000.0000.0000.000
142A142ALA00.0180.00118.854-0.256-0.2560.0000.0000.0000.000
143A143GLU-1-0.864-0.92220.723-11.043-11.0430.0000.0000.0000.000
144A144ASN0-0.047-0.03723.8860.1970.1970.0000.0000.0000.000
145A145GLU-1-0.817-0.89921.457-13.941-13.9410.0000.0000.0000.000
146A146GLN0-0.023-0.00121.551-0.352-0.3520.0000.0000.0000.000
147A147GLY00.0380.01119.637-0.119-0.1190.0000.0000.0000.000
148A148TYR00.007-0.00520.4520.5060.5060.0000.0000.0000.000
149A149PHE00.0020.01518.013-0.556-0.5560.0000.0000.0000.000
150A150PRO0-0.027-0.00221.2940.3260.3260.0000.0000.0000.000
151A151ASP-1-0.789-0.92520.655-13.576-13.5760.0000.0000.0000.000
152A152ALA0-0.009-0.01222.8150.4300.4300.0000.0000.0000.000
153A153VAL00.0060.00825.034-0.294-0.2940.0000.0000.0000.000
154A154THR0-0.028-0.01123.133-0.117-0.1170.0000.0000.0000.000
155A155GLU-1-0.892-0.94925.876-9.549-9.5490.0000.0000.0000.000
156A156ARG10.8980.94521.73612.24212.2420.0000.0000.0000.000
157A157GLY00.0350.02123.056-0.171-0.1710.0000.0000.0000.000
158A158GLN0-0.051-0.06023.8160.2240.2240.0000.0000.0000.000
159A159LYS0-0.0290.02526.0950.4780.4780.0000.0000.0000.000
160A160HIS0-0.036-0.02221.971-0.016-0.0160.0000.0000.0000.000
161A161LEU00.0880.04923.6830.0310.0310.0000.0000.0000.000
162A162ARG10.9160.95025.1799.8539.8530.0000.0000.0000.000
163A163GLU-1-0.856-0.92525.252-11.100-11.1000.0000.0000.0000.000
164A164LEU00.0150.00321.2980.1240.1240.0000.0000.0000.000
165A165MET0-0.048-0.02525.6700.3000.3000.0000.0000.0000.000
166A166SER0-0.063-0.01829.0950.3550.3550.0000.0000.0000.000
167A167VAL00.0280.01325.1360.1540.1540.0000.0000.0000.000
168A168ALA00.0090.01327.7770.0480.0480.0000.0000.0000.000
169A169ALA0-0.053-0.02329.2070.2360.2360.0000.0000.0000.000
170A170GLU-1-0.991-0.99631.052-9.458-9.4580.0000.0000.0000.000
171A171GLY0-0.026-0.00531.6500.0700.0700.0000.0000.0000.000
172A172GLN0-0.059-0.02426.436-0.146-0.1460.0000.0000.0000.000
173A173ARG10.7400.82020.13114.54114.5410.0000.0000.0000.000
174A174ALA00.0260.02123.344-0.542-0.5420.0000.0000.0000.000
175A175VAL00.0070.00018.4300.0420.0420.0000.0000.0000.000
176A176ILE0-0.015-0.00418.963-0.253-0.2530.0000.0000.0000.000
177A177PHE00.005-0.00410.702-0.176-0.1760.0000.0000.0000.000
178A178PHE00.013-0.00714.818-0.402-0.4020.0000.0000.0000.000
179A179ALA00.0390.0239.878-0.665-0.6650.0000.0000.0000.000
180A180VAL0-0.010-0.01811.8950.7420.7420.0000.0000.0000.000
181A181LEU00.005-0.0078.329-1.987-1.9870.0000.0000.0000.000
182A182HIS00.0700.03511.517-1.061-1.0610.0000.0000.0000.000
183A183SER00.002-0.02513.1950.6360.6360.0000.0000.0000.000
184A184ALA00.0190.01114.6100.3620.3620.0000.0000.0000.000
185A185ILE0-0.055-0.00216.4080.6510.6510.0000.0000.0000.000
186A186THR0-0.039-0.01617.372-0.971-0.9710.0000.0000.0000.000
187A187ARG10.8820.93419.79012.76412.7640.0000.0000.0000.000
188A188PHE0-0.003-0.00719.078-0.351-0.3510.0000.0000.0000.000
189A189SER00.0310.01221.2020.4310.4310.0000.0000.0000.000
190A190PRO0-0.0010.01123.134-0.398-0.3980.0000.0000.0000.000
191A191ALA00.007-0.00124.3940.3520.3520.0000.0000.0000.000
192A192ARG10.8650.91926.1739.7009.7000.0000.0000.0000.000
193A193HIS0-0.037-0.02526.6490.4870.4870.0000.0000.0000.000
194A194ILE0-0.035-0.00325.3440.1680.1680.0000.0000.0000.000
195A195ASP-1-0.778-0.90127.174-10.373-10.3730.0000.0000.0000.000
196A196GLU-1-0.820-0.89528.905-8.993-8.9930.0000.0000.0000.000
197A197LYS10.9080.96831.4148.9288.9280.0000.0000.0000.000
198A198TYR00.032-0.00821.357-0.009-0.0090.0000.0000.0000.000
199A199ALA00.0270.01827.579-0.194-0.1940.0000.0000.0000.000
200A200GLN0-0.031-0.01428.5950.1070.1070.0000.0000.0000.000
201A201LEU0-0.014-0.00628.7220.1460.1460.0000.0000.0000.000
202A202LEU00.0350.02423.170-0.082-0.0820.0000.0000.0000.000
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