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: 5GG1Z

Calculation Name: 6DEJ-B-Xray547

Preferred Name:

Target Type:

Ligand Name: 4-[(4z)-1-(carboxymethyl)-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1h-imidazol-2-yl]-4-iminobutanoic acid | dodecaethylene glycol | sulfate ion | chloride ion

Ligand 3-letter code: CRU | 12P | SO4 | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6DEJ

Chain ID: B

ChEMBL ID:

UniProt ID: Q95W85

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 224
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2824217.48364
FMO2-HF: Nuclear repulsion 2733139.348173
FMO2-HF: Total energy -91078.135466
FMO2-MP2: Total energy -91336.522563


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:2:MET)


Summations of interaction energy for fragment #1(B:2: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.
-28.488-18.34512.808-7.657-15.293-0.079
Interaction energy analysis for fragmet #1(B:2:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.828 / q_NPA : 0.919
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].
3B4GLY00.0340.0243.8548.10511.083-0.029-1.551-1.398-0.003
5B6LEU00.0280.0264.6101.6991.888-0.001-0.017-0.1710.000
6B7LYS10.8520.9072.44923.51525.7880.965-1.548-1.690-0.014
7B8GLU-1-0.872-0.9532.391-54.226-52.1493.125-1.521-3.681-0.020
8B9SER0-0.042-0.0064.5445.9176.030-0.001-0.020-0.0930.000
33B34ASN00.0450.0334.365-4.968-4.857-0.001-0.005-0.1050.000
35B36PHE00.020-0.0192.540-9.622-7.3408.751-2.979-8.053-0.042
36B37ALA00.0060.0064.5242.4602.580-0.001-0.016-0.1020.000
4B5LEU00.0170.0065.770-0.676-0.6760.0000.0000.0000.000
9B10MET0-0.0180.0296.537-3.085-3.0850.0000.0000.0000.000
10B11ARG10.9580.9749.04821.12121.1210.0000.0000.0000.000
11B12ILE00.0090.00712.782-0.724-0.7240.0000.0000.0000.000
12B13LYS10.8570.93715.38213.46413.4640.0000.0000.0000.000
13B14MET0-0.0230.01018.918-0.185-0.1850.0000.0000.0000.000
14B15TYR00.0310.01421.1880.5380.5380.0000.0000.0000.000
15B16MET0-0.008-0.00424.679-0.028-0.0280.0000.0000.0000.000
16B17GLU-1-0.794-0.87026.940-9.103-9.1030.0000.0000.0000.000
17B18GLY00.0280.00230.701-0.200-0.2000.0000.0000.0000.000
18B19THR0-0.028-0.00633.3100.1960.1960.0000.0000.0000.000
19B20VAL00.0080.01334.284-0.111-0.1110.0000.0000.0000.000
20B21ASN0-0.012-0.03037.2950.0400.0400.0000.0000.0000.000
21B22GLY0-0.0030.01040.5790.1620.1620.0000.0000.0000.000
22B23HIS0-0.027-0.01139.1670.1660.1660.0000.0000.0000.000
23B24TYR0-0.040-0.04534.221-0.190-0.1900.0000.0000.0000.000
24B25PHE00.004-0.00529.9220.0520.0520.0000.0000.0000.000
25B26LYS10.9280.97130.3669.2539.2530.0000.0000.0000.000
26B27CYS0-0.054-0.01627.8580.0250.0250.0000.0000.0000.000
27B28GLU-1-0.861-0.92525.168-11.612-11.6120.0000.0000.0000.000
28B29GLY0-0.006-0.01622.2470.2320.2320.0000.0000.0000.000
29B30GLU-1-0.881-0.93219.564-14.001-14.0010.0000.0000.0000.000
30B31GLY0-0.010-0.02416.9330.4550.4550.0000.0000.0000.000
31B32ASP-1-0.893-0.93013.092-18.987-18.9870.0000.0000.0000.000
32B33GLY00.0800.03311.1731.2271.2270.0000.0000.0000.000
34B35PRO0-0.015-0.0065.2471.1271.1270.0000.0000.0000.000
37B38GLY0-0.0110.0246.4262.6242.6240.0000.0000.0000.000
38B39THR0-0.005-0.0129.3551.7451.7450.0000.0000.0000.000
39B40GLN00.027-0.00410.835-2.186-2.1860.0000.0000.0000.000
40B41SER0-0.041-0.01513.6021.4921.4920.0000.0000.0000.000
41B42MET00.0140.00216.833-0.351-0.3510.0000.0000.0000.000
42B43ARG10.8090.91817.44016.06616.0660.0000.0000.0000.000
43B44ILE0-0.007-0.01422.790-0.213-0.2130.0000.0000.0000.000
44B45HIS00.0250.01325.3750.6080.6080.0000.0000.0000.000
45B46VAL0-0.019-0.02328.658-0.212-0.2120.0000.0000.0000.000
46B47THR0-0.004-0.00829.7500.2350.2350.0000.0000.0000.000
47B48GLU-1-0.901-0.95032.431-8.210-8.2100.0000.0000.0000.000
48B49GLY00.012-0.00134.727-0.168-0.1680.0000.0000.0000.000
49B50ALA0-0.0150.01635.036-0.032-0.0320.0000.0000.0000.000
50B51PRO0-0.050-0.02536.8630.1740.1740.0000.0000.0000.000
51B52LEU00.0140.00032.2020.0870.0870.0000.0000.0000.000
52B53PRO0-0.039-0.00836.8470.0330.0330.0000.0000.0000.000
53B54PHE00.001-0.02832.8930.1050.1050.0000.0000.0000.000
54B55ALA00.0110.01733.701-0.169-0.1690.0000.0000.0000.000
55B56PHE00.0460.00526.043-0.148-0.1480.0000.0000.0000.000
56B57ASP-1-0.773-0.86628.768-10.235-10.2350.0000.0000.0000.000
57B58ILE0-0.004-0.01028.363-0.352-0.3520.0000.0000.0000.000
58B59LEU0-0.0030.00327.881-0.185-0.1850.0000.0000.0000.000
59B60ALA00.0170.02624.426-0.464-0.4640.0000.0000.0000.000
60B61PRO00.0250.01222.824-0.658-0.6580.0000.0000.0000.000
61B62CYS0-0.069-0.02122.723-0.296-0.2960.0000.0000.0000.000
62B63CYS0-0.045-0.03521.037-0.294-0.2940.0000.0000.0000.000
63B64TYR00.0220.00617.033-0.909-0.9090.0000.0000.0000.000
64B67SER00.0770.04213.739-0.365-0.3650.0000.0000.0000.000
65B68LYS10.8570.96713.63115.75715.7570.0000.0000.0000.000
66B69THR00.000-0.0059.252-0.441-0.4410.0000.0000.0000.000
67B70PHE0-0.059-0.0329.035-3.532-3.5320.0000.0000.0000.000
68B71VAL00.0390.04410.2910.8040.8040.0000.0000.0000.000
69B72HIS0-0.043-0.0366.726-0.377-0.3770.0000.0000.0000.000
70B73HIS0-0.015-0.0188.9453.7393.7390.0000.0000.0000.000
71B74THR0-0.017-0.0199.476-1.123-1.1230.0000.0000.0000.000
72B75ALA00.000-0.02012.0550.5070.5070.0000.0000.0000.000
73B76GLU-1-0.888-0.93911.511-22.774-22.7740.0000.0000.0000.000
74B77ILE0-0.075-0.01313.4510.7040.7040.0000.0000.0000.000
75B78PRO0-0.017-0.01012.334-1.523-1.5230.0000.0000.0000.000
76B79ASP-1-0.748-0.8649.201-26.059-26.0590.0000.0000.0000.000
77B80PHE00.008-0.00511.376-0.835-0.8350.0000.0000.0000.000
78B81PHE00.0010.01412.0340.5250.5250.0000.0000.0000.000
79B82LYS10.8170.8945.52232.14832.1480.0000.0000.0000.000
80B83GLN0-0.004-0.0099.208-0.452-0.4520.0000.0000.0000.000
81B84SER0-0.0190.00411.2891.3381.3380.0000.0000.0000.000
82B85PHE0-0.0360.0229.8281.0861.0860.0000.0000.0000.000
83B86PRO0-0.021-0.02211.573-1.153-1.1530.0000.0000.0000.000
84B87GLU-1-0.830-0.93013.093-18.224-18.2240.0000.0000.0000.000
85B88GLY00.0210.01914.7210.7280.7280.0000.0000.0000.000
86B89PHE0-0.050-0.04013.7590.3160.3160.0000.0000.0000.000
87B90THR0-0.0020.00518.2390.3400.3400.0000.0000.0000.000
88B91TRP0-0.047-0.02819.8250.0240.0240.0000.0000.0000.000
89B92GLU-1-0.799-0.88122.755-10.498-10.4980.0000.0000.0000.000
90B93ARG10.8640.90521.73912.33412.3340.0000.0000.0000.000
91B94THR00.0300.03027.4840.3490.3490.0000.0000.0000.000
92B95THR0-0.032-0.02229.148-0.366-0.3660.0000.0000.0000.000
93B96THR00.0220.01331.3730.1630.1630.0000.0000.0000.000
94B97TYR00.030-0.01431.059-0.270-0.2700.0000.0000.0000.000
95B98GLU-1-0.842-0.91935.983-8.048-8.0480.0000.0000.0000.000
96B99ASP-1-0.898-0.96238.817-7.699-7.6990.0000.0000.0000.000
97B100GLY00.0050.00340.0810.1980.1980.0000.0000.0000.000
98B101GLY0-0.0190.00037.8250.0060.0060.0000.0000.0000.000
99B102ILE0-0.032-0.01635.368-0.159-0.1590.0000.0000.0000.000
100B103LEU0-0.005-0.00829.7250.1070.1070.0000.0000.0000.000
101B104THR0-0.048-0.02631.277-0.129-0.1290.0000.0000.0000.000
102B105ALA00.0240.00026.9850.0240.0240.0000.0000.0000.000
103B106HIS0-0.0040.01026.8510.1460.1460.0000.0000.0000.000
104B107GLN00.0100.01418.580-0.039-0.0390.0000.0000.0000.000
105B108ASP-1-0.793-0.86121.013-14.589-14.5890.0000.0000.0000.000
106B109THR00.004-0.01015.176-0.387-0.3870.0000.0000.0000.000
107B110SER0-0.010-0.02716.952-0.186-0.1860.0000.0000.0000.000
108B111LEU0-0.038-0.02610.563-0.826-0.8260.0000.0000.0000.000
109B112GLU-1-0.900-0.94614.694-14.554-14.5540.0000.0000.0000.000
110B113GLY00.0050.00213.413-0.051-0.0510.0000.0000.0000.000
111B114ASN0-0.072-0.0618.428-0.254-0.2540.0000.0000.0000.000
112B115CYS0-0.0080.00311.137-0.612-0.6120.0000.0000.0000.000
113B116LEU0-0.0040.0129.9680.1540.1540.0000.0000.0000.000
114B117ILE0-0.004-0.00213.8350.8510.8510.0000.0000.0000.000
115B118TYR0-0.022-0.03814.381-0.275-0.2750.0000.0000.0000.000
116B119LYS10.9660.98519.76613.51313.5130.0000.0000.0000.000
117B120VAL00.0140.00122.878-0.025-0.0250.0000.0000.0000.000
118B121LYS10.8470.91525.4589.7409.7400.0000.0000.0000.000
119B122VAL00.007-0.00628.455-0.088-0.0880.0000.0000.0000.000
120B123HIS0-0.027-0.01131.0030.3620.3620.0000.0000.0000.000
121B124GLY00.0410.02134.393-0.142-0.1420.0000.0000.0000.000
122B125THR00.0070.00235.8360.2190.2190.0000.0000.0000.000
123B126ASN00.0130.00039.009-0.051-0.0510.0000.0000.0000.000
124B127PHE00.0370.03734.3520.0430.0430.0000.0000.0000.000
125B128PRO00.0340.02940.4420.1380.1380.0000.0000.0000.000
126B129ALA00.0240.01042.863-0.110-0.1100.0000.0000.0000.000
127B130ASP-1-0.906-0.97844.783-6.527-6.5270.0000.0000.0000.000
128B131GLY00.0190.02041.815-0.004-0.0040.0000.0000.0000.000
129B132PRO0-0.004-0.01837.620-0.035-0.0350.0000.0000.0000.000
130B133VAL00.0310.02335.122-0.069-0.0690.0000.0000.0000.000
131B134MET00.0050.01437.421-0.159-0.1590.0000.0000.0000.000
132B135LYS10.8700.96440.4256.7936.7930.0000.0000.0000.000
133B136ASN0-0.069-0.04636.102-0.112-0.1120.0000.0000.0000.000
134B137LYS10.8980.94638.3147.2577.2570.0000.0000.0000.000
135B138SER0-0.035-0.03033.1600.1220.1220.0000.0000.0000.000
136B139GLY0-0.037-0.01932.5900.0230.0230.0000.0000.0000.000
137B140GLY0-0.0110.00028.508-0.197-0.1970.0000.0000.0000.000
138B141TRP0-0.036-0.03325.5220.3240.3240.0000.0000.0000.000
139B142GLU-1-0.821-0.89426.761-10.048-10.0480.0000.0000.0000.000
140B143PRO0-0.092-0.04722.228-0.314-0.3140.0000.0000.0000.000
141B144SER00.0110.00022.2890.2750.2750.0000.0000.0000.000
142B145THR00.010-0.02021.629-0.474-0.4740.0000.0000.0000.000
143B146GLU-1-0.793-0.84419.884-13.923-13.9230.0000.0000.0000.000
144B147VAL00.0310.01021.745-0.479-0.4790.0000.0000.0000.000
145B148VAL0-0.041-0.02618.5350.0630.0630.0000.0000.0000.000
146B149TYR00.001-0.00321.751-0.176-0.1760.0000.0000.0000.000
147B150PRO0-0.0160.01021.813-0.009-0.0090.0000.0000.0000.000
148B151GLU-1-0.890-0.96223.329-9.827-9.8270.0000.0000.0000.000
149B152ASN0-0.022-0.01926.3510.1280.1280.0000.0000.0000.000
150B153GLY00.0150.00522.948-0.377-0.3770.0000.0000.0000.000
151B154VAL0-0.035-0.01122.255-0.517-0.5170.0000.0000.0000.000
152B155LEU0-0.0110.00117.553-0.055-0.0550.0000.0000.0000.000
153B156CYS0-0.0080.00521.6340.1420.1420.0000.0000.0000.000
154B157GLY00.0300.01222.899-0.510-0.5100.0000.0000.0000.000
155B158ARG10.8790.94423.76611.18711.1870.0000.0000.0000.000
156B159ASN00.0380.00423.130-0.064-0.0640.0000.0000.0000.000
157B160VAL00.0170.03026.3580.2860.2860.0000.0000.0000.000
158B161MET0-0.0260.01424.459-0.429-0.4290.0000.0000.0000.000
159B162ALA00.0450.01728.5810.3600.3600.0000.0000.0000.000
160B163LEU0-0.033-0.01329.694-0.270-0.2700.0000.0000.0000.000
161B164LYS10.8810.94428.27310.44410.4440.0000.0000.0000.000
162B165VAL00.001-0.02133.165-0.003-0.0030.0000.0000.0000.000
163B166GLY0-0.0150.00136.7700.2200.2200.0000.0000.0000.000
164B167ASP-1-0.840-0.89936.511-7.484-7.4840.0000.0000.0000.000
165B168ARG10.8280.89738.0547.3127.3120.0000.0000.0000.000
166B169HIS0-0.022-0.03031.9870.0060.0060.0000.0000.0000.000
167B170LEU0-0.047-0.00135.0980.2150.2150.0000.0000.0000.000
168B171ILE00.0260.01532.804-0.342-0.3420.0000.0000.0000.000
169B172CYS0-0.053-0.01630.8870.0890.0890.0000.0000.0000.000
170B173HIS0-0.018-0.01330.717-0.488-0.4880.0000.0000.0000.000
171B174HIS0-0.039-0.03124.474-0.252-0.2520.0000.0000.0000.000
172B175TYR00.0200.00028.131-0.151-0.1510.0000.0000.0000.000
173B176THR00.0000.00622.6210.1980.1980.0000.0000.0000.000
174B177SER0-0.044-0.02024.3560.2350.2350.0000.0000.0000.000
175B178TYR0-0.014-0.05319.264-0.223-0.2230.0000.0000.0000.000
176B179ARG10.8910.92421.23811.57211.5720.0000.0000.0000.000
177B180SER00.035-0.00116.655-0.136-0.1360.0000.0000.0000.000
178B181LYS10.7890.87618.48116.25416.2540.0000.0000.0000.000
179B182LYS10.8040.92012.69922.06222.0620.0000.0000.0000.000
180B183ALA0-0.022-0.01418.3970.6410.6410.0000.0000.0000.000
181B184VAL00.0670.01319.835-0.529-0.5290.0000.0000.0000.000
182B185ARG10.9380.96420.96212.88712.8870.0000.0000.0000.000
183B186ALA0-0.032-0.00916.7240.0160.0160.0000.0000.0000.000
184B187LEU0-0.0290.00115.674-1.221-1.2210.0000.0000.0000.000
185B188THR00.0160.01214.8201.1521.1520.0000.0000.0000.000
186B189MET0-0.021-0.00815.863-1.083-1.0830.0000.0000.0000.000
187B190PRO0-0.0110.00616.1360.2100.2100.0000.0000.0000.000
188B191GLY00.0750.03017.9680.7350.7350.0000.0000.0000.000
189B192PHE0-0.014-0.01220.599-0.455-0.4550.0000.0000.0000.000
190B193HIS10.8440.92716.28016.01016.0100.0000.0000.0000.000
191B194PHE00.0450.02619.8070.4560.4560.0000.0000.0000.000
192B195THR0-0.064-0.04615.670-1.355-1.3550.0000.0000.0000.000
193B196ASP-1-0.766-0.82617.368-13.224-13.2240.0000.0000.0000.000
194B197TYR0-0.043-0.05616.934-1.317-1.3170.0000.0000.0000.000
195B198ARG10.9410.96418.02513.55713.5570.0000.0000.0000.000
196B199LEU00.0200.03018.845-0.497-0.4970.0000.0000.0000.000
197B200GLN0-0.035-0.02920.9680.2940.2940.0000.0000.0000.000
198B201MET00.0370.02522.511-0.243-0.2430.0000.0000.0000.000
199B202LEU0-0.028-0.01020.8100.3030.3030.0000.0000.0000.000
200B203ARG10.8350.89025.16611.74111.7410.0000.0000.0000.000
201B204LYS10.9901.01028.0798.7998.7990.0000.0000.0000.000
202B205LYS10.9230.96130.90710.01310.0130.0000.0000.0000.000
203B206LYS10.8710.91033.8258.1688.1680.0000.0000.0000.000
204B207ASP-1-0.834-0.89534.379-8.444-8.4440.0000.0000.0000.000
205B208GLU-1-0.816-0.89033.330-8.621-8.6210.0000.0000.0000.000
206B209TYR0-0.076-0.06326.124-0.275-0.2750.0000.0000.0000.000
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208B211GLU-1-0.819-0.87023.631-12.180-12.1800.0000.0000.0000.000
209B212LEU00.003-0.00621.3830.4010.4010.0000.0000.0000.000
210B213TYR00.010-0.00714.495-0.761-0.7610.0000.0000.0000.000
211B214GLU-1-0.886-0.95116.320-15.371-15.3710.0000.0000.0000.000
212B215ALA0-0.0040.00113.768-1.141-1.1410.0000.0000.0000.000
213B216SER00.0150.00913.0940.8240.8240.0000.0000.0000.000
214B217VAL00.0050.00812.245-1.744-1.7440.0000.0000.0000.000
215B218ALA0-0.026-0.00112.8421.3471.3470.0000.0000.0000.000
216B219ARG10.8060.88613.91812.93112.9310.0000.0000.0000.000
217B220TYR00.0660.01916.6640.6790.6790.0000.0000.0000.000
218B221SER00.020-0.00220.118-0.074-0.0740.0000.0000.0000.000
219B222ASP-1-0.839-0.90620.768-13.402-13.4020.0000.0000.0000.000
220B223LEU0-0.067-0.02623.2650.2990.2990.0000.0000.0000.000
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222B225GLU-1-0.928-0.96128.061-10.199-10.1990.0000.0000.0000.000
223B226LYS10.7860.86929.8648.2438.2430.0000.0000.0000.000
224B227ALA-1-0.828-0.88833.587-8.289-8.2890.0000.0000.0000.000