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: 4YV2N

Calculation Name: 4EFC-A-Xray547

Preferred Name:

Target Type:

Ligand Name: adenosine monophosphate

Ligand 3-letter code: AMP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4EFC

Chain ID: A

ChEMBL ID:

UniProt ID: Q38EJ2

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 457
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -7781093.853959
FMO2-HF: Nuclear repulsion 7599292.61859
FMO2-HF: Total energy -181801.235369
FMO2-MP2: Total energy -182329.984611


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:12:VAL)


Summations of interaction energy for fragment #1(A:12:VAL)
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.
42.32747.7464.492-2.86-7.052-0.031
Interaction energy analysis for fragmet #1(A:12:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.817 / q_NPA : 0.906
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].
3A14TYR0-0.012-0.0202.695-5.762-1.3943.019-2.252-5.136-0.024
4A15SER0-0.053-0.0374.3076.0026.1400.000-0.020-0.1170.000
10A21PHE00.0080.0032.500-4.630-3.7171.473-0.588-1.799-0.007
5A16VAL00.0130.0125.6013.0993.0990.0000.0000.0000.000
6A17ASP-1-0.869-0.9247.552-22.665-22.6650.0000.0000.0000.000
7A18ASN0-0.019-0.0227.1752.5432.5430.0000.0000.0000.000
8A19PRO0-0.057-0.0349.108-0.380-0.3800.0000.0000.0000.000
9A20LEU0-0.021-0.0207.3190.9520.9520.0000.0000.0000.000
11A22ALA0-0.0330.0007.1430.5840.5840.0000.0000.0000.000
12A23LEU00.0440.02410.7720.6190.6190.0000.0000.0000.000
13A24SER00.0260.02512.1191.2931.2930.0000.0000.0000.000
14A25PRO00.032-0.00114.982-0.265-0.2650.0000.0000.0000.000
15A26LEU0-0.025-0.01015.9570.2790.2790.0000.0000.0000.000
16A27ASP-1-0.812-0.87715.105-15.239-15.2390.0000.0000.0000.000
17A28GLY00.0370.01813.153-0.744-0.7440.0000.0000.0000.000
18A29ARG10.9090.95313.83115.61415.6140.0000.0000.0000.000
19A30TYR00.0250.00315.6200.5820.5820.0000.0000.0000.000
20A31LYS10.9911.01914.75618.09518.0950.0000.0000.0000.000
21A32ARG10.9090.94218.50813.13213.1320.0000.0000.0000.000
22A33GLN00.0780.02121.3060.0160.0160.0000.0000.0000.000
23A34THR00.002-0.00119.9580.4150.4150.0000.0000.0000.000
24A35LYS10.9090.96020.60912.52712.5270.0000.0000.0000.000
25A36ALA00.0240.01522.2710.0210.0210.0000.0000.0000.000
26A37LEU00.0770.03624.6290.1980.1980.0000.0000.0000.000
27A38ARG10.8180.89516.12115.41815.4180.0000.0000.0000.000
28A39ALA00.0160.03223.981-0.065-0.0650.0000.0000.0000.000
29A40PHE0-0.016-0.00427.3070.1970.1970.0000.0000.0000.000
30A41PHE00.0480.00325.5760.0460.0460.0000.0000.0000.000
31A42SER0-0.051-0.02621.818-0.424-0.4240.0000.0000.0000.000
32A43GLU-1-0.830-0.91722.064-12.592-12.5920.0000.0000.0000.000
33A44TYR0-0.028-0.02123.2520.3070.3070.0000.0000.0000.000
34A45GLY00.0400.02124.9450.4170.4170.0000.0000.0000.000
35A46PHE00.021-0.00626.9270.4350.4350.0000.0000.0000.000
36A47PHE0-0.016-0.02224.9880.4360.4360.0000.0000.0000.000
37A48ARG10.9621.00829.1369.7629.7620.0000.0000.0000.000
38A49TYR0-0.048-0.06931.0610.2280.2280.0000.0000.0000.000
39A50ARG10.7660.86228.73710.30110.3010.0000.0000.0000.000
40A51VAL00.000-0.00232.5400.2690.2690.0000.0000.0000.000
41A52LEU00.0060.01435.0020.2310.2310.0000.0000.0000.000
42A53VAL00.0110.00637.0230.2450.2450.0000.0000.0000.000
43A54GLU-1-0.774-0.89137.205-7.658-7.6580.0000.0000.0000.000
44A55VAL00.0040.01338.3210.2210.2210.0000.0000.0000.000
45A56GLU-1-0.828-0.89740.811-6.983-6.9830.0000.0000.0000.000
46A57TYR0-0.038-0.03542.4840.2620.2620.0000.0000.0000.000
47A58PHE00.0260.00443.5830.1830.1830.0000.0000.0000.000
48A59THR00.007-0.00644.5160.1640.1640.0000.0000.0000.000
49A60ALA00.0230.01746.8180.1640.1640.0000.0000.0000.000
50A61LEU0-0.060-0.03447.4500.1780.1780.0000.0000.0000.000
51A62CYS0-0.041-0.01248.7180.1310.1310.0000.0000.0000.000
52A63LYS10.8020.89150.9146.0686.0680.0000.0000.0000.000
53A64ASP-1-0.810-0.89651.662-5.877-5.8770.0000.0000.0000.000
54A65VAL0-0.040-0.00652.2520.0840.0840.0000.0000.0000.000
55A66PRO00.0860.04954.809-0.010-0.0100.0000.0000.0000.000
56A67THR0-0.027-0.01857.5070.0930.0930.0000.0000.0000.000
57A68ILE0-0.0060.00951.6480.0480.0480.0000.0000.0000.000
58A69VAL00.005-0.00655.729-0.029-0.0290.0000.0000.0000.000
59A70PRO00.003-0.00653.2490.0160.0160.0000.0000.0000.000
60A71LEU00.0430.00949.439-0.032-0.0320.0000.0000.0000.000
61A72ARG10.8380.91853.2585.2575.2570.0000.0000.0000.000
62A73SER0-0.047-0.01755.0420.0310.0310.0000.0000.0000.000
63A74VAL0-0.0180.00649.365-0.028-0.0280.0000.0000.0000.000
64A75THR00.000-0.02552.1390.0250.0250.0000.0000.0000.000
65A76ASP-1-0.771-0.88350.366-6.135-6.1350.0000.0000.0000.000
66A77GLU-1-0.856-0.91048.744-6.168-6.1680.0000.0000.0000.000
67A78GLN0-0.035-0.01347.198-0.090-0.0900.0000.0000.0000.000
68A79LEU00.002-0.00245.574-0.207-0.2070.0000.0000.0000.000
69A80GLN0-0.032-0.01544.407-0.215-0.2150.0000.0000.0000.000
70A81LYS10.8370.91142.3497.0667.0660.0000.0000.0000.000
71A82LEU00.0770.02140.680-0.228-0.2280.0000.0000.0000.000
72A83ARG10.8390.92839.6806.9616.9610.0000.0000.0000.000
73A84LYS11.0021.00838.4157.3807.3800.0000.0000.0000.000
74A85ILE0-0.055-0.03936.719-0.249-0.2490.0000.0000.0000.000
75A86THR0-0.065-0.04835.203-0.233-0.2330.0000.0000.0000.000
76A87LEU0-0.002-0.01134.014-0.339-0.3390.0000.0000.0000.000
77A88ASP-1-0.887-0.94934.192-8.129-8.1290.0000.0000.0000.000
78A89CYS0-0.089-0.04233.560-0.110-0.1100.0000.0000.0000.000
79A90PHE0-0.0300.00627.802-0.352-0.3520.0000.0000.0000.000
80A91SER00.0360.01027.330-0.301-0.3010.0000.0000.0000.000
81A92VAL00.0340.00020.7780.0380.0380.0000.0000.0000.000
82A93SER00.0540.02424.108-0.051-0.0510.0000.0000.0000.000
83A94SER0-0.0220.00825.4550.1270.1270.0000.0000.0000.000
84A95ALA00.0310.01624.3660.1510.1510.0000.0000.0000.000
85A96GLU-1-0.912-0.96720.269-14.251-14.2510.0000.0000.0000.000
86A97GLU-1-0.896-0.91623.852-10.018-10.0180.0000.0000.0000.000
87A98ILE00.0220.01627.3690.1150.1150.0000.0000.0000.000
88A99LYS10.8210.87921.46013.02313.0230.0000.0000.0000.000
89A100ARG10.9030.95324.29011.78611.7860.0000.0000.0000.000
90A101LEU00.0080.01626.0030.1180.1180.0000.0000.0000.000
91A102GLU-1-0.829-0.91225.358-11.851-11.8510.0000.0000.0000.000
92A103ARG10.8930.94822.03313.27713.2770.0000.0000.0000.000
93A104VAL0-0.028-0.00526.227-0.028-0.0280.0000.0000.0000.000
94A105THR0-0.029-0.03429.9280.1110.1110.0000.0000.0000.000
95A106ASN0-0.024-0.00127.425-0.088-0.0880.0000.0000.0000.000
96A107HIS00.0150.00429.3320.0400.0400.0000.0000.0000.000
97A108ASP-1-0.743-0.84128.026-10.225-10.2250.0000.0000.0000.000
98A109ILE0-0.003-0.00529.9230.1070.1070.0000.0000.0000.000
99A110LYS10.8600.92133.4348.1518.1510.0000.0000.0000.000
100A111ALA0-0.0020.01229.9080.1240.1240.0000.0000.0000.000
101A112VAL00.0070.00031.2050.0130.0130.0000.0000.0000.000
102A113GLU-1-0.806-0.88533.222-7.695-7.6950.0000.0000.0000.000
103A114TYR00.006-0.01234.3530.2590.2590.0000.0000.0000.000
104A115PHE00.0160.01831.1030.0750.0750.0000.0000.0000.000
105A116ILE0-0.001-0.00134.0990.0830.0830.0000.0000.0000.000
106A117LYS10.7760.86937.3717.6347.6340.0000.0000.0000.000
107A118GLU-1-0.925-0.94835.458-8.248-8.2480.0000.0000.0000.000
108A119ARG10.7600.84332.2769.3229.3220.0000.0000.0000.000
109A120MET0-0.0060.01139.2630.1300.1300.0000.0000.0000.000
110A121ASP-1-0.836-0.90542.744-6.810-6.8100.0000.0000.0000.000
111A122THR00.0470.02740.3930.1550.1550.0000.0000.0000.000
112A123CYS0-0.080-0.01942.2240.0430.0430.0000.0000.0000.000
113A124GLY00.0370.03145.2130.1490.1490.0000.0000.0000.000
114A125LEU0-0.022-0.02644.9210.1420.1420.0000.0000.0000.000
115A126SER00.0230.00746.0520.0270.0270.0000.0000.0000.000
116A127HIS00.0060.01947.151-0.112-0.1120.0000.0000.0000.000
117A128VAL0-0.028-0.01747.9880.0780.0780.0000.0000.0000.000
118A129THR00.041-0.00543.066-0.129-0.1290.0000.0000.0000.000
119A130GLU-1-0.868-0.93844.341-7.338-7.3380.0000.0000.0000.000
120A131PHE0-0.007-0.00946.1840.0800.0800.0000.0000.0000.000
121A132VAL00.0110.00939.825-0.035-0.0350.0000.0000.0000.000
122A133HIS10.7870.87739.2007.7817.7810.0000.0000.0000.000
123A134PHE00.0050.01642.0420.0490.0490.0000.0000.0000.000
124A135GLY00.0300.01945.8310.0510.0510.0000.0000.0000.000
125A136LEU0-0.0220.00841.8300.0310.0310.0000.0000.0000.000
126A137THR0-0.050-0.02340.519-0.174-0.1740.0000.0000.0000.000
127A138SER00.0410.00135.2310.0020.0020.0000.0000.0000.000
128A139GLN00.0190.01435.403-0.334-0.3340.0000.0000.0000.000
129A140ASP-1-0.700-0.81438.209-7.154-7.1540.0000.0000.0000.000
130A141ILE00.0330.03635.4760.0350.0350.0000.0000.0000.000
131A142ASN00.0250.00033.123-0.258-0.2580.0000.0000.0000.000
132A143ASN0-0.020-0.01735.127-0.081-0.0810.0000.0000.0000.000
133A144THR00.0320.00037.5480.1970.1970.0000.0000.0000.000
134A145ALA00.0560.02133.621-0.023-0.0230.0000.0000.0000.000
135A146ILE00.021-0.00431.466-0.089-0.0890.0000.0000.0000.000
136A147PRO00.0110.00333.866-0.092-0.0920.0000.0000.0000.000
137A148MET0-0.0300.01136.1880.0500.0500.0000.0000.0000.000
138A149MET0-0.0600.01128.969-0.011-0.0110.0000.0000.0000.000
139A150ILE0-0.011-0.01032.533-0.151-0.1510.0000.0000.0000.000
140A151ARG10.8260.89433.7847.7147.7140.0000.0000.0000.000
141A152ASP-1-0.756-0.83334.303-8.146-8.1460.0000.0000.0000.000
142A153ALA0-0.0040.02630.687-0.036-0.0360.0000.0000.0000.000
143A154ILE0-0.001-0.01632.502-0.069-0.0690.0000.0000.0000.000
144A155VAL00.0140.00135.0480.0810.0810.0000.0000.0000.000
145A156THR0-0.059-0.05533.464-0.030-0.0300.0000.0000.0000.000
146A157LEU0-0.065-0.03028.622-0.181-0.1810.0000.0000.0000.000
147A158TYR0-0.015-0.02531.9140.0840.0840.0000.0000.0000.000
148A159LEU00.0180.00933.5920.0680.0680.0000.0000.0000.000
149A160PRO00.0340.01935.3170.0800.0800.0000.0000.0000.000
150A161ALA0-0.021-0.00132.1570.0330.0330.0000.0000.0000.000
151A162LEU00.0110.00634.1330.0180.0180.0000.0000.0000.000
152A163ASP-1-0.786-0.87136.524-7.260-7.2600.0000.0000.0000.000
153A164GLY0-0.0020.00736.4050.1540.1540.0000.0000.0000.000
154A165ILE0-0.0190.00134.0680.0720.0720.0000.0000.0000.000
155A166ILE00.0140.00637.5950.1730.1730.0000.0000.0000.000
156A167GLY00.0200.02940.7160.1920.1920.0000.0000.0000.000
157A168SER0-0.037-0.02938.1930.1660.1660.0000.0000.0000.000
158A169LEU00.006-0.00240.0340.1100.1100.0000.0000.0000.000
159A170THR0-0.035-0.04542.2750.1600.1600.0000.0000.0000.000
160A171SER0-0.083-0.04342.6810.1100.1100.0000.0000.0000.000
161A172LYS10.8270.90539.5497.5167.5160.0000.0000.0000.000
162A173LEU0-0.031-0.00445.2630.0540.0540.0000.0000.0000.000
163A174VAL00.0550.02248.1790.0680.0680.0000.0000.0000.000
164A175ASP-1-0.862-0.91846.984-6.288-6.2880.0000.0000.0000.000
165A176TRP0-0.033-0.03841.001-0.019-0.0190.0000.0000.0000.000
166A177ASP-1-0.831-0.89448.574-5.618-5.6180.0000.0000.0000.000
167A178VAL0-0.047-0.02350.4030.0880.0880.0000.0000.0000.000
168A179PRO00.0010.01052.706-0.068-0.0680.0000.0000.0000.000
169A180MET0-0.009-0.01848.428-0.093-0.0930.0000.0000.0000.000
170A181LEU0-0.0110.00852.0830.0960.0960.0000.0000.0000.000
171A182ALA00.0280.02651.136-0.146-0.1460.0000.0000.0000.000
172A183ARG10.8320.89048.2366.1836.1830.0000.0000.0000.000
173A184THR0-0.0110.00449.719-0.058-0.0580.0000.0000.0000.000
174A185HIS00.028-0.00349.401-0.029-0.0290.0000.0000.0000.000
175A186GLY00.0050.00848.014-0.021-0.0210.0000.0000.0000.000
176A187GLN0-0.033-0.01448.7130.0610.0610.0000.0000.0000.000
177A188PRO00.0200.00352.428-0.040-0.0400.0000.0000.0000.000
178A189ALA0-0.030-0.00454.2360.0750.0750.0000.0000.0000.000
179A190SER00.010-0.03555.980-0.025-0.0250.0000.0000.0000.000
180A191PRO0-0.032-0.00555.974-0.099-0.0990.0000.0000.0000.000
181A192THR0-0.007-0.01951.7460.0740.0740.0000.0000.0000.000
182A193ASN0-0.010-0.02852.559-0.070-0.0700.0000.0000.0000.000
183A194LEU00.0250.01245.539-0.074-0.0740.0000.0000.0000.000
184A195ALA00.0220.01647.943-0.133-0.1330.0000.0000.0000.000
185A196LYS10.8920.92848.8235.8555.8550.0000.0000.0000.000
186A197GLU-1-0.804-0.87146.980-6.107-6.1070.0000.0000.0000.000
187A198PHE00.008-0.01041.042-0.137-0.1370.0000.0000.0000.000
188A199VAL0-0.012-0.00545.522-0.095-0.0950.0000.0000.0000.000
189A200VAL0-0.0180.00546.954-0.006-0.0060.0000.0000.0000.000
190A201TRP0-0.016-0.03342.009-0.060-0.0600.0000.0000.0000.000
191A202ILE0-0.0090.00243.762-0.087-0.0870.0000.0000.0000.000
192A203GLU-1-0.800-0.90344.893-6.269-6.2690.0000.0000.0000.000
193A204ARG10.8340.91943.0006.8816.8810.0000.0000.0000.000
194A205LEU0-0.010-0.00839.139-0.080-0.0800.0000.0000.0000.000
195A206ARG10.8760.92242.6766.3896.3890.0000.0000.0000.000
196A207GLU-1-0.805-0.87045.261-6.217-6.2170.0000.0000.0000.000
197A208GLN00.0180.00442.055-0.075-0.0750.0000.0000.0000.000
198A209ARG10.8350.87940.8967.1117.1110.0000.0000.0000.000
199A210ARG10.8630.93042.6046.1706.1700.0000.0000.0000.000
200A211GLN0-0.019-0.03444.854-0.047-0.0470.0000.0000.0000.000
201A212LEU0-0.040-0.01438.029-0.064-0.0640.0000.0000.0000.000
202A213CYS0-0.112-0.05842.122-0.121-0.1210.0000.0000.0000.000
203A214GLU-1-0.895-0.94643.983-6.338-6.3380.0000.0000.0000.000
204A215VAL0-0.055-0.00841.4480.0820.0820.0000.0000.0000.000
205A216PRO0-0.039-0.02443.853-0.046-0.0460.0000.0000.0000.000
206A217THR00.0350.02040.823-0.195-0.1950.0000.0000.0000.000
207A218THR0-0.081-0.03942.0350.1310.1310.0000.0000.0000.000
208A219GLY00.0850.03941.162-0.210-0.2100.0000.0000.0000.000
209A220LYS10.7410.88141.4817.4187.4180.0000.0000.0000.000
210A221PHE00.016-0.01342.232-0.113-0.1130.0000.0000.0000.000
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