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: N674Q

Calculation Name: 4R6D-A-Xray547

Preferred Name:

Target Type:

Ligand Name: [(4z)-2-[(1s)-1-aminoethyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1h-imidazol-1-yl]acetic acid | copper (ii) ion

Ligand 3-letter code: PIA | CU

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4R6D

Chain ID: A

ChEMBL ID:

UniProt ID: Q9U6Y3

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 214
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2722972.432679
FMO2-HF: Nuclear repulsion 2637093.269444
FMO2-HF: Total energy -85879.163235
FMO2-MP2: Total energy -86131.468813


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:2:GLY)


Summations of interaction energy for fragment #1(A:2:GLY)
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.
-29.322-27.525-0.007-0.797-0.992-0.004
Interaction energy analysis for fragmet #1(A:2:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.884 / q_NPA : 0.927
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].
3A4ILE00.0490.0443.7805.2586.678-0.005-0.686-0.728-0.004
4A5LYS10.8910.9323.65255.21655.534-0.001-0.109-0.2080.000
33A34TYR0-0.063-0.0394.6071.2821.341-0.001-0.002-0.0560.000
5A6PRO00.018-0.0136.2362.6282.6280.0000.0000.0000.000
6A7ASP-1-0.837-0.9019.188-20.492-20.4920.0000.0000.0000.000
7A8MET0-0.0330.0258.833-4.655-4.6550.0000.0000.0000.000
8A9LYS10.9140.94511.86222.00322.0030.0000.0000.0000.000
9A10ILE0-0.032-0.00914.747-0.978-0.9780.0000.0000.0000.000
10A11LYS10.8930.94917.56517.46617.4660.0000.0000.0000.000
11A12LEU0-0.046-0.00720.092-0.422-0.4220.0000.0000.0000.000
12A13LYS10.8970.94722.73811.05411.0540.0000.0000.0000.000
13A14MET0-0.0110.00725.795-0.113-0.1130.0000.0000.0000.000
14A15GLU-1-0.875-0.92128.218-9.836-9.8360.0000.0000.0000.000
15A16GLY00.0330.00731.435-0.162-0.1620.0000.0000.0000.000
16A17ASN0-0.091-0.05333.7920.3660.3660.0000.0000.0000.000
17A18VAL00.0530.02836.355-0.122-0.1220.0000.0000.0000.000
18A19ASN0-0.039-0.04738.9590.0620.0620.0000.0000.0000.000
19A20GLY00.0030.01841.5830.2130.2130.0000.0000.0000.000
20A21TYR0-0.021-0.00841.1490.0300.0300.0000.0000.0000.000
21A22ALA00.006-0.00438.432-0.200-0.2000.0000.0000.0000.000
22A23PHE0-0.031-0.01732.6990.1270.1270.0000.0000.0000.000
23A24VAL00.0250.01931.440-0.217-0.2170.0000.0000.0000.000
24A25ILE0-0.021-0.00728.5630.2140.2140.0000.0000.0000.000
25A26GLU-1-0.878-0.95027.191-11.259-11.2590.0000.0000.0000.000
26A27GLY00.023-0.00325.1420.3580.3580.0000.0000.0000.000
27A28GLU-1-0.904-0.92721.893-14.037-14.0370.0000.0000.0000.000
28A29GLY00.0810.04020.4070.5940.5940.0000.0000.0000.000
29A30GLU-1-0.918-0.94816.427-18.427-18.4270.0000.0000.0000.000
30A31GLY00.0490.01515.1741.1361.1360.0000.0000.0000.000
31A32LYS10.8820.94512.79518.64118.6410.0000.0000.0000.000
32A33PRO0-0.033-0.0219.1530.9510.9510.0000.0000.0000.000
34A35ASP-1-0.884-0.95211.354-19.477-19.4770.0000.0000.0000.000
35A36GLY0-0.034-0.01114.3041.2331.2330.0000.0000.0000.000
36A37THR0-0.015-0.00215.9800.9050.9050.0000.0000.0000.000
37A38ASN0-0.050-0.04016.319-1.014-1.0140.0000.0000.0000.000
38A39THR0-0.023-0.01518.3900.9660.9660.0000.0000.0000.000
39A40ILE00.0180.00220.547-0.665-0.6650.0000.0000.0000.000
40A41ASN0-0.0100.00623.0240.9150.9150.0000.0000.0000.000
41A42LEU0-0.008-0.00425.527-0.261-0.2610.0000.0000.0000.000
42A43GLU-1-0.861-0.94028.265-9.720-9.7200.0000.0000.0000.000
43A44VAL0-0.030-0.01331.242-0.169-0.1690.0000.0000.0000.000
44A45LYS10.8080.91230.49210.56510.5650.0000.0000.0000.000
45A46GLU-1-0.914-0.96134.568-8.568-8.5680.0000.0000.0000.000
46A47GLY00.0290.00136.687-0.147-0.1470.0000.0000.0000.000
47A48ALA0-0.0290.01338.0180.0360.0360.0000.0000.0000.000
48A49PRO0-0.046-0.02339.6610.1610.1610.0000.0000.0000.000
49A50LEU00.0630.02735.0920.1210.1210.0000.0000.0000.000
50A51PRO0-0.044-0.01939.7630.0700.0700.0000.0000.0000.000
51A52PHE00.019-0.00735.7370.1800.1800.0000.0000.0000.000
52A53SER0-0.048-0.04437.268-0.184-0.1840.0000.0000.0000.000
53A54TYR00.1150.03730.296-0.164-0.1640.0000.0000.0000.000
54A55ASP-1-0.743-0.83532.624-9.344-9.3440.0000.0000.0000.000
55A56ILE0-0.074-0.03931.903-0.260-0.2600.0000.0000.0000.000
56A57LEU0-0.017-0.01030.375-0.104-0.1040.0000.0000.0000.000
57A58THR00.0330.02528.059-0.409-0.4090.0000.0000.0000.000
58A59THR0-0.026-0.01426.236-0.492-0.4920.0000.0000.0000.000
59A60ALA0-0.018-0.01325.958-0.209-0.2090.0000.0000.0000.000
60A61PHE00.0500.01422.870-0.087-0.0870.0000.0000.0000.000
61A62TYR0-0.0110.00720.266-0.827-0.8270.0000.0000.0000.000
62A65ASN00.0770.04313.811-0.304-0.3040.0000.0000.0000.000
63A66ARG10.8100.86916.24915.18215.1820.0000.0000.0000.000
64A67ALA00.0160.02210.952-0.787-0.7870.0000.0000.0000.000
65A68PHE0-0.035-0.00711.774-2.049-2.0490.0000.0000.0000.000
66A69THR0-0.009-0.00513.4822.0742.0740.0000.0000.0000.000
67A70LYS10.9350.99213.47615.90015.9000.0000.0000.0000.000
68A71TYR0-0.046-0.06813.0280.7180.7180.0000.0000.0000.000
69A72PRO0-0.0010.01013.943-1.121-1.1210.0000.0000.0000.000
70A73ASP-1-0.916-0.95313.360-22.164-22.1640.0000.0000.0000.000
71A74ASP-1-0.937-0.96914.399-16.018-16.0180.0000.0000.0000.000
72A75ILE0-0.0250.00316.3870.5980.5980.0000.0000.0000.000
73A76PRO0-0.044-0.03213.950-1.214-1.2140.0000.0000.0000.000
74A77ASN00.0540.03410.7580.4190.4190.0000.0000.0000.000
75A78TYR00.0300.01311.733-1.613-1.6130.0000.0000.0000.000
76A79PHE00.0470.02613.019-0.581-0.5810.0000.0000.0000.000
77A80LYS10.8270.9137.42426.15926.1590.0000.0000.0000.000
78A81GLN0-0.044-0.0348.094-2.688-2.6880.0000.0000.0000.000
79A82SER0-0.029-0.0209.6880.1240.1240.0000.0000.0000.000
80A83PHE00.0010.0357.9620.7790.7790.0000.0000.0000.000
81A84PRO0-0.037-0.0386.896-2.556-2.5560.0000.0000.0000.000
82A85GLU-1-0.799-0.8859.149-24.421-24.4210.0000.0000.0000.000
83A86GLY00.0300.01912.0551.3421.3420.0000.0000.0000.000
84A87TYR0-0.083-0.07413.4631.1151.1150.0000.0000.0000.000
85A88SER00.0030.01616.5840.5130.5130.0000.0000.0000.000
86A89TRP00.011-0.00619.5850.1420.1420.0000.0000.0000.000
87A90GLU-1-0.849-0.90122.397-10.545-10.5450.0000.0000.0000.000
88A91ARG00.005-0.00423.8190.1310.1310.0000.0000.0000.000
89A92THR0-0.062-0.02628.3350.4070.4070.0000.0000.0000.000
90A93MET00.0090.01230.695-0.206-0.2060.0000.0000.0000.000
91A94THR0-0.003-0.00833.2830.1980.1980.0000.0000.0000.000
92A95PHE00.0400.00434.772-0.057-0.0570.0000.0000.0000.000
93A96GLU-1-0.801-0.88439.072-7.187-7.1870.0000.0000.0000.000
94A97ASP-1-0.872-0.94542.242-7.169-7.1690.0000.0000.0000.000
95A98LYS10.9070.93742.7896.7576.7570.0000.0000.0000.000
96A99GLY00.0420.04541.050-0.004-0.0040.0000.0000.0000.000
97A100ILE0-0.075-0.03436.089-0.122-0.1220.0000.0000.0000.000
98A101VAL00.0580.02032.0450.0970.0970.0000.0000.0000.000
99A102LYS10.9010.95932.2598.7058.7050.0000.0000.0000.000
100A103VAL00.0200.00727.1420.1000.1000.0000.0000.0000.000
101A104LYS10.9270.97525.99710.86710.8670.0000.0000.0000.000
102A105SER00.0330.01221.3320.2460.2460.0000.0000.0000.000
103A106ASP-1-0.851-0.89319.410-16.091-16.0910.0000.0000.0000.000
104A107ILE0-0.031-0.00715.008-0.009-0.0090.0000.0000.0000.000
105A108SER00.0350.01014.765-0.980-0.9800.0000.0000.0000.000
106A109LEU0-0.039-0.0388.476-0.885-0.8850.0000.0000.0000.000
107A110GLU-1-0.843-0.91113.133-17.018-17.0180.0000.0000.0000.000
108A111GLU-1-0.919-0.97011.310-25.093-25.0930.0000.0000.0000.000
109A112ASP-1-0.914-0.9539.979-27.052-27.0520.0000.0000.0000.000
110A113SER0-0.032-0.02311.2381.0331.0330.0000.0000.0000.000
111A114PHE0-0.027-0.0239.979-0.595-0.5950.0000.0000.0000.000
112A115ILE0-0.0050.00214.4291.1511.1510.0000.0000.0000.000
113A116TYR00.002-0.01516.271-0.850-0.8500.0000.0000.0000.000
114A117GLU-1-0.840-0.88620.379-12.137-12.1370.0000.0000.0000.000
115A118ILE0-0.011-0.01123.1400.0650.0650.0000.0000.0000.000
116A119TYR0-0.060-0.06525.7100.6120.6120.0000.0000.0000.000
117A120LEU0-0.014-0.00829.200-0.090-0.0900.0000.0000.0000.000
118A121LYS10.8450.91031.4818.3348.3340.0000.0000.0000.000
119A122GLY00.0290.01235.065-0.112-0.1120.0000.0000.0000.000
120A123GLU-1-0.868-0.93437.191-7.782-7.7820.0000.0000.0000.000
121A124ASN0-0.005-0.01540.7100.0450.0450.0000.0000.0000.000
122A125PHE00.0570.04937.4030.1020.1020.0000.0000.0000.000
123A126PRO00.0130.01843.4360.1270.1270.0000.0000.0000.000
124A127PRO00.0220.01746.187-0.095-0.0950.0000.0000.0000.000
125A128ASN0-0.009-0.01347.985-0.063-0.0630.0000.0000.0000.000
126A129GLY00.0490.03145.6760.0540.0540.0000.0000.0000.000
127A130PRO0-0.0010.00742.657-0.031-0.0310.0000.0000.0000.000
128A131VAL00.0350.02238.704-0.090-0.0900.0000.0000.0000.000
129A132MET0-0.021-0.00341.077-0.179-0.1790.0000.0000.0000.000
130A133GLN0-0.041-0.03243.5850.0460.0460.0000.0000.0000.000
131A134LYS10.7980.90640.4457.8157.8150.0000.0000.0000.000
132A135LYS10.9100.96642.4966.8816.8810.0000.0000.0000.000
133A136THR0-0.031-0.02837.5450.1080.1080.0000.0000.0000.000
134A137THR0-0.026-0.01237.7100.0910.0910.0000.0000.0000.000
135A138GLY00.0550.03733.521-0.107-0.1070.0000.0000.0000.000
136A139TRP0-0.044-0.05130.6560.2720.2720.0000.0000.0000.000
137A140ASP-1-0.820-0.89832.569-9.141-9.1410.0000.0000.0000.000
138A141ALA0-0.041-0.02029.311-0.349-0.3490.0000.0000.0000.000
139A142SER0-0.043-0.02028.0130.1850.1850.0000.0000.0000.000
140A143THR00.003-0.02226.435-0.245-0.2450.0000.0000.0000.000
141A144GLU-1-0.805-0.87822.854-12.744-12.7440.0000.0000.0000.000
142A145ARG10.8830.94524.71110.29510.2950.0000.0000.0000.000
143A146MET00.0010.01919.7850.2290.2290.0000.0000.0000.000
144A147TYR0-0.087-0.08823.6550.2790.2790.0000.0000.0000.000
145A148VAL00.0530.04221.911-0.067-0.0670.0000.0000.0000.000
146A149ARG10.8480.91324.49510.83110.8310.0000.0000.0000.000
147A150ASP-1-0.828-0.91726.245-10.612-10.6120.0000.0000.0000.000
148A151GLY0-0.0010.00824.286-0.070-0.0700.0000.0000.0000.000
149A152VAL0-0.048-0.00821.736-0.675-0.6750.0000.0000.0000.000
150A153LEU00.0170.01118.4520.3340.3340.0000.0000.0000.000
151A154LYS10.8560.92721.90110.92110.9210.0000.0000.0000.000
152A155GLY00.0670.03024.293-0.270-0.2700.0000.0000.0000.000
153A156ASP-1-0.874-0.89725.219-9.871-9.8710.0000.0000.0000.000
154A157VAL00.0250.00627.079-0.125-0.1250.0000.0000.0000.000
155A158LYS10.9320.97729.8118.8848.8840.0000.0000.0000.000
156A159HIS00.0380.02828.7170.2890.2890.0000.0000.0000.000
157A160LYS10.8390.91333.0369.0849.0840.0000.0000.0000.000
158A161LEU00.0100.02534.568-0.199-0.1990.0000.0000.0000.000
159A162LEU0-0.021-0.01535.3880.3240.3240.0000.0000.0000.000
160A163LEU0-0.015-0.01138.242-0.009-0.0090.0000.0000.0000.000
161A164GLU-1-0.910-0.96241.728-7.144-7.1440.0000.0000.0000.000
162A165GLY0-0.045-0.01643.5500.1520.1520.0000.0000.0000.000
163A166GLY0-0.015-0.01944.3760.0850.0850.0000.0000.0000.000
164A167GLY0-0.0080.00943.4490.0680.0680.0000.0000.0000.000
165A168TYR0-0.013-0.02538.918-0.187-0.1870.0000.0000.0000.000
166A169TYR0-0.040-0.01139.7480.2480.2480.0000.0000.0000.000
167A170ARG10.8240.88838.0107.2177.2170.0000.0000.0000.000
168A171VAL0-0.020-0.01834.1480.1410.1410.0000.0000.0000.000
169A172ASP-1-0.912-0.94234.025-8.893-8.8930.0000.0000.0000.000
170A173PHE0-0.015-0.01527.9070.0980.0980.0000.0000.0000.000
171A174LYS10.8570.92129.5349.5889.5880.0000.0000.0000.000
172A175THR00.0370.03723.8070.2630.2630.0000.0000.0000.000
173A176ILE0-0.057-0.03024.4100.0290.0290.0000.0000.0000.000
174A177TYR0-0.018-0.05119.248-0.394-0.3940.0000.0000.0000.000
175A178ARG10.8310.88120.28612.11712.1170.0000.0000.0000.000
176A179ALA00.0360.01015.017-0.391-0.3910.0000.0000.0000.000
177A180LYS10.8020.88515.74517.75417.7540.0000.0000.0000.000
178A181LYS10.7820.8899.07327.92627.9260.0000.0000.0000.000
179A182ALA0-0.0080.00316.1560.1680.1680.0000.0000.0000.000
180A183VAL0-0.0030.00012.478-1.298-1.2980.0000.0000.0000.000
181A184LYS10.9320.97313.81618.17318.1730.0000.0000.0000.000
182A185LEU00.0190.00315.615-0.635-0.6350.0000.0000.0000.000
183A186PRO0-0.038-0.01017.1870.0500.0500.0000.0000.0000.000
184A187ASP-1-0.851-0.92019.213-12.572-12.5720.0000.0000.0000.000
185A188TYR0-0.082-0.05522.094-0.203-0.2030.0000.0000.0000.000
186A189HIS00.0150.02319.461-0.567-0.5670.0000.0000.0000.000
187A190PHE0-0.044-0.02823.1050.5690.5690.0000.0000.0000.000
188A191VAL00.0330.01419.619-0.764-0.7640.0000.0000.0000.000
189A192ASP-1-0.798-0.84222.182-11.216-11.2160.0000.0000.0000.000
190A193HIS0-0.034-0.03721.940-0.641-0.6410.0000.0000.0000.000
191A194ARG10.8830.94424.26611.35011.3500.0000.0000.0000.000
192A195ILE0-0.005-0.00324.757-0.523-0.5230.0000.0000.0000.000
193A196GLU-1-0.896-0.95226.627-10.481-10.4810.0000.0000.0000.000
194A197CYS-1-0.823-0.89327.814-10.575-10.5750.0000.0000.0000.000
195A198LEU0-0.018-0.00628.7240.2010.2010.0000.0000.0000.000
196A199ASN0-0.047-0.03231.5790.2230.2230.0000.0000.0000.000
197A200HIS10.8680.92033.4929.1409.1400.0000.0000.0000.000
198A201ASP-1-0.770-0.87036.440-7.413-7.4130.0000.0000.0000.000
199A202LYS10.9010.93938.5697.1397.1390.0000.0000.0000.000
200A203ASP-1-0.883-0.93838.953-8.188-8.1880.0000.0000.0000.000
201A204HIS0-0.033-0.02134.898-0.154-0.1540.0000.0000.0000.000
202A205ASN0-0.004-0.01935.088-0.275-0.2750.0000.0000.0000.000
203A206LYS10.8800.94032.7799.3429.3420.0000.0000.0000.000
204A207VAL0-0.033-0.00930.2400.2750.2750.0000.0000.0000.000
205A208THR00.0180.01226.239-0.114-0.1140.0000.0000.0000.000
206A209VAL0-0.021-0.00925.0260.3260.3260.0000.0000.0000.000
207A210TYR00.0170.01322.893-0.499-0.4990.0000.0000.0000.000
208A211GLU-1-0.741-0.84120.519-14.139-14.1390.0000.0000.0000.000
209A212SER0-0.044-0.01820.338-0.983-0.9830.0000.0000.0000.000
210A213ALA00.0190.01018.7100.7180.7180.0000.0000.0000.000
211A214VAL0-0.005-0.01818.141-1.196-1.1960.0000.0000.0000.000
212A215ALA0-0.0100.00217.5090.7880.7880.0000.0000.0000.000
213A216ARG10.7840.86619.44011.60611.6060.0000.0000.0000.000
214A217ASN-1-0.827-0.92421.550-11.883-11.8830.0000.0000.0000.000