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: N6JNQ

Calculation Name: 5LTP-B-Xray547

Preferred Name:

Target Type:

Ligand Name: {(4z)-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1h-imidazol-1-yl}acetic acid | citrate anion | chloride ion

Ligand 3-letter code: CR2 | FLC | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5LTP

Chain ID: B

ChEMBL ID:

UniProt ID: A0A1S4

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 226
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2872664.438261
FMO2-HF: Nuclear repulsion 2781580.512193
FMO2-HF: Total energy -91083.926068
FMO2-MP2: Total energy -91346.007337


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:-3:GLU)


Summations of interaction energy for fragment #1(B:-3:GLU)
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.
-10.28-8.097-0.011-0.928-1.243-0.001
Interaction energy analysis for fragmet #1(B:-3:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.133 / q_NPA : -0.073
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].
3B-1ASN0-0.031-0.0143.845-4.066-1.998-0.010-0.921-1.137-0.001
4B0MET0-0.028-0.0115.2433.6043.719-0.001-0.007-0.1060.000
5B1ALA00.0040.0139.021-0.163-0.1630.0000.0000.0000.000
6B2SER0-0.082-0.04311.4850.3500.3500.0000.0000.0000.000
7B3LEU00.0430.01414.9560.1570.1570.0000.0000.0000.000
8B4PRO0-0.040-0.01015.735-0.119-0.1190.0000.0000.0000.000
9B5ALA0-0.008-0.00917.3350.0850.0850.0000.0000.0000.000
10B6THR0-0.0010.00718.3060.1540.1540.0000.0000.0000.000
11B7HIS0-0.0180.02716.042-0.247-0.2470.0000.0000.0000.000
12B8GLU-1-0.795-0.86414.4910.9340.9340.0000.0000.0000.000
13B9LEU0-0.024-0.00615.2480.2390.2390.0000.0000.0000.000
14B10HIS10.7840.86614.759-3.471-3.4710.0000.0000.0000.000
15B11ILE0-0.013-0.01316.3350.3130.3130.0000.0000.0000.000
16B12PHE00.0020.00514.679-0.233-0.2330.0000.0000.0000.000
17B13GLY00.0480.01919.8300.1790.1790.0000.0000.0000.000
18B14SER0-0.0310.00221.872-0.110-0.1100.0000.0000.0000.000
19B15ILE0-0.0050.00425.4630.0290.0290.0000.0000.0000.000
20B16ASN0-0.027-0.04128.467-0.023-0.0230.0000.0000.0000.000
21B17GLY0-0.019-0.00328.418-0.041-0.0410.0000.0000.0000.000
22B18VAL00.0160.01429.3350.0230.0230.0000.0000.0000.000
23B19ASP-1-0.903-0.95725.3441.7881.7880.0000.0000.0000.000
24B20PHE0-0.048-0.04122.632-0.117-0.1170.0000.0000.0000.000
25B21ASP-1-0.787-0.86820.2252.4352.4350.0000.0000.0000.000
26B22MET0-0.0140.00321.596-0.199-0.1990.0000.0000.0000.000
27B23VAL00.0310.01418.6710.2460.2460.0000.0000.0000.000
28B24GLY0-0.0070.00019.679-0.173-0.1730.0000.0000.0000.000
29B25GLN00.0210.00117.165-0.027-0.0270.0000.0000.0000.000
30B26GLY00.0470.00920.1210.0230.0230.0000.0000.0000.000
31B27THR0-0.054-0.01520.825-0.135-0.1350.0000.0000.0000.000
32B28GLY00.0820.02322.4080.1350.1350.0000.0000.0000.000
33B29ASN0-0.013-0.00722.904-0.226-0.2260.0000.0000.0000.000
34B30PRO0-0.005-0.00120.3700.0800.0800.0000.0000.0000.000
35B31ASN0-0.023-0.01922.381-0.078-0.0780.0000.0000.0000.000
36B32ASP-1-0.868-0.92925.857-0.200-0.2000.0000.0000.0000.000
37B33GLY00.0110.00723.7210.0630.0630.0000.0000.0000.000
38B34TYR0-0.146-0.09224.7930.1320.1320.0000.0000.0000.000
39B35GLU-1-0.823-0.92420.9970.4500.4500.0000.0000.0000.000
40B36GLU-1-0.817-0.88824.0430.1840.1840.0000.0000.0000.000
41B37LEU0-0.031-0.02120.528-0.004-0.0040.0000.0000.0000.000
42B38ASN0-0.047-0.03123.8940.0470.0470.0000.0000.0000.000
43B39LEU0-0.011-0.00520.9900.0930.0930.0000.0000.0000.000
44B40LYS10.8660.92324.393-0.688-0.6880.0000.0000.0000.000
45B41SER0-0.020-0.02324.7240.1730.1730.0000.0000.0000.000
46B42THR0-0.046-0.05422.420-0.115-0.1150.0000.0000.0000.000
47B43LYS10.9050.95524.698-1.556-1.5560.0000.0000.0000.000
48B44GLY00.0240.03028.206-0.048-0.0480.0000.0000.0000.000
49B45ASP-1-0.811-0.89530.8410.7110.7110.0000.0000.0000.000
50B46LEU0-0.002-0.00127.8010.0480.0480.0000.0000.0000.000
51B47GLN0-0.073-0.04431.789-0.090-0.0900.0000.0000.0000.000
52B48PHE0-0.006-0.00627.3580.0010.0010.0000.0000.0000.000
53B49SER00.0220.00632.6210.0030.0030.0000.0000.0000.000
54B50PRO00.0020.00529.9990.0530.0530.0000.0000.0000.000
55B51TRP00.0390.03029.4370.0230.0230.0000.0000.0000.000
56B52ILE0-0.0040.00628.1630.0530.0530.0000.0000.0000.000
57B53LEU0-0.013-0.01524.3560.1090.1090.0000.0000.0000.000
58B54VAL0-0.0040.02924.8540.0420.0420.0000.0000.0000.000
59B55PRO0-0.043-0.00126.160-0.008-0.0080.0000.0000.0000.000
60B56HIS00.030-0.01621.3620.1000.1000.0000.0000.0000.000
61B57ILE0-0.0220.02120.4070.1670.1670.0000.0000.0000.000
62B59TYR-1-0.839-0.91520.5700.6600.6600.0000.0000.0000.000
63B61PHE0-0.011-0.02313.7970.3040.3040.0000.0000.0000.000
64B62HIS00.006-0.00617.779-0.211-0.2110.0000.0000.0000.000
65B63GLN00.0590.01911.982-0.149-0.1490.0000.0000.0000.000
66B64TYR0-0.027-0.03716.593-0.351-0.3510.0000.0000.0000.000
67B65LEU0-0.059-0.02120.023-0.043-0.0430.0000.0000.0000.000
68B66PRO00.0270.04821.430-0.070-0.0700.0000.0000.0000.000
69B67TYR0-0.048-0.07122.8140.1590.1590.0000.0000.0000.000
70B68PRO0-0.061-0.03825.622-0.040-0.0400.0000.0000.0000.000
71B69ASP-1-0.863-0.92128.412-0.422-0.4220.0000.0000.0000.000
72B70GLY0-0.008-0.00425.560-0.088-0.0880.0000.0000.0000.000
73B71MET0-0.0030.01218.5410.0410.0410.0000.0000.0000.000
74B72SER00.0010.01219.6510.0400.0400.0000.0000.0000.000
75B73PRO00.004-0.00817.941-0.181-0.1810.0000.0000.0000.000
76B74PHE0-0.024-0.01715.215-0.141-0.1410.0000.0000.0000.000
77B75GLN00.0470.02314.537-0.181-0.1810.0000.0000.0000.000
78B76ALA00.0010.00115.248-0.370-0.3700.0000.0000.0000.000
79B77ALA00.0050.00811.625-0.486-0.4860.0000.0000.0000.000
80B78MET0-0.0220.01310.511-0.132-0.1320.0000.0000.0000.000
81B79VAL0-0.017-0.01211.237-0.904-0.9040.0000.0000.0000.000
82B80ASP-1-0.779-0.87211.547-4.575-4.5750.0000.0000.0000.000
83B81GLY00.0220.0167.986-1.190-1.1900.0000.0000.0000.000
84B82SER0-0.141-0.0916.8980.3170.3170.0000.0000.0000.000
85B83GLY00.0290.0177.8941.7121.7120.0000.0000.0000.000
86B84TYR0-0.023-0.0228.9060.0110.0110.0000.0000.0000.000
87B85GLN0-0.017-0.0036.893-0.152-0.1520.0000.0000.0000.000
88B86VAL0-0.015-0.00911.376-0.771-0.7710.0000.0000.0000.000
89B87HIS0-0.008-0.00514.8160.2380.2380.0000.0000.0000.000
90B88ARG10.8620.92617.428-1.682-1.6820.0000.0000.0000.000
91B89THR00.0110.01321.0000.0580.0580.0000.0000.0000.000
92B90MET0-0.026-0.01124.202-0.074-0.0740.0000.0000.0000.000
93B91GLN0-0.0070.01427.4040.1040.1040.0000.0000.0000.000
94B92PHE00.004-0.02129.419-0.052-0.0520.0000.0000.0000.000
95B93GLU-1-0.849-0.92333.9630.5290.5290.0000.0000.0000.000
96B94ASP-1-0.804-0.87936.0570.7400.7400.0000.0000.0000.000
97B95GLY00.015-0.01436.3710.0130.0130.0000.0000.0000.000
98B96ALA0-0.0430.00332.4540.0500.0500.0000.0000.0000.000
99B97SER0-0.002-0.00228.5940.0130.0130.0000.0000.0000.000
100B98LEU0-0.012-0.01124.0440.0350.0350.0000.0000.0000.000
101B99THR0-0.030-0.01920.246-0.035-0.0350.0000.0000.0000.000
102B100VAL00.0110.00218.0160.0280.0280.0000.0000.0000.000
103B101ASN0-0.0210.00714.390-0.192-0.1920.0000.0000.0000.000
104B102TYR00.029-0.01813.5710.0870.0870.0000.0000.0000.000
105B103ARG10.8510.9207.900-6.578-6.5780.0000.0000.0000.000
106B104TYR00.0090.0118.595-0.607-0.6070.0000.0000.0000.000
107B105THR00.0000.0124.9661.0991.0990.0000.0000.0000.000
108B106TYR00.0400.0046.9280.5720.5720.0000.0000.0000.000
109B107GLU-1-0.902-0.9448.093-4.192-4.1920.0000.0000.0000.000
110B108GLY00.0340.02510.5710.7310.7310.0000.0000.0000.000
111B109SER00.0220.00413.3630.0580.0580.0000.0000.0000.000
112B110HIS10.8350.89013.2510.6090.6090.0000.0000.0000.000
113B111ILE00.010-0.00411.299-0.326-0.3260.0000.0000.0000.000
114B112LYS10.9070.93810.075-1.039-1.0390.0000.0000.0000.000
115B113GLY0-0.010-0.00910.3380.6340.6340.0000.0000.0000.000
116B114GLU-1-0.821-0.88510.6034.1594.1590.0000.0000.0000.000
117B115ALA0-0.005-0.01612.9330.2320.2320.0000.0000.0000.000
118B116GLN00.0100.02015.6320.1040.1040.0000.0000.0000.000
119B117VAL0-0.009-0.01817.174-0.080-0.0800.0000.0000.0000.000
120B118LYS10.9340.96520.815-1.910-1.9100.0000.0000.0000.000
121B119GLY00.0190.01823.548-0.042-0.0420.0000.0000.0000.000
122B120THR0-0.051-0.02827.134-0.010-0.0100.0000.0000.0000.000
123B121GLY00.0790.03030.278-0.023-0.0230.0000.0000.0000.000
124B122PHE00.0110.01129.552-0.044-0.0440.0000.0000.0000.000
125B123PRO00.0310.02435.0000.0110.0110.0000.0000.0000.000
126B124ALA0-0.007-0.00738.1500.0090.0090.0000.0000.0000.000
127B125ASP-1-0.874-0.94139.4410.5900.5900.0000.0000.0000.000
128B126GLY00.0300.01839.117-0.028-0.0280.0000.0000.0000.000
129B127PRO0-0.038-0.02737.6150.0090.0090.0000.0000.0000.000
130B128VAL00.0190.00932.181-0.008-0.0080.0000.0000.0000.000
131B129MET00.0050.01132.4230.0260.0260.0000.0000.0000.000
132B130THR0-0.0070.00636.499-0.014-0.0140.0000.0000.0000.000
133B131ASN0-0.041-0.02235.825-0.008-0.0080.0000.0000.0000.000
134B132SER00.0150.01737.802-0.041-0.0410.0000.0000.0000.000
135B133LEU0-0.063-0.02933.558-0.036-0.0360.0000.0000.0000.000
136B134THR0-0.054-0.03537.290-0.009-0.0090.0000.0000.0000.000
137B135ALA00.0270.01136.070-0.017-0.0170.0000.0000.0000.000
138B136ALA00.0060.01132.4640.0260.0260.0000.0000.0000.000
139B137ASP-1-0.833-0.88334.4430.3610.3610.0000.0000.0000.000
140B138TRP0-0.025-0.00733.2050.0240.0240.0000.0000.0000.000
141B139CYS0-0.046-0.02130.4350.0140.0140.0000.0000.0000.000
142B140ARG10.9360.98331.229-0.287-0.2870.0000.0000.0000.000
143B141SER0-0.013-0.00726.6860.0350.0350.0000.0000.0000.000
144B142LYS10.9590.98928.705-0.414-0.4140.0000.0000.0000.000
145B143LYS0-0.0040.01822.3200.1220.1220.0000.0000.0000.000
146B144THR00.007-0.00825.323-0.064-0.0640.0000.0000.0000.000
147B145TYR00.0450.02521.6740.0960.0960.0000.0000.0000.000
148B146PRO0-0.031-0.00922.901-0.067-0.0670.0000.0000.0000.000
149B147ASN00.0100.00620.185-0.006-0.0060.0000.0000.0000.000
150B148ASP-1-0.813-0.91919.479-0.042-0.0420.0000.0000.0000.000
151B149LYS10.9470.99213.995-0.376-0.3760.0000.0000.0000.000
152B150THR0-0.015-0.01016.5320.3660.3660.0000.0000.0000.000
153B151ILE00.0090.00418.884-0.188-0.1880.0000.0000.0000.000
154B152ILE0-0.039-0.01520.4860.2200.2200.0000.0000.0000.000
155B153SER00.0350.01522.717-0.166-0.1660.0000.0000.0000.000
156B154THR0-0.043-0.02524.3510.0980.0980.0000.0000.0000.000
157B155PHE00.0240.00124.883-0.090-0.0900.0000.0000.0000.000
158B156LYS10.9550.98229.949-0.410-0.4100.0000.0000.0000.000
159B157TRP00.0570.01329.389-0.029-0.0290.0000.0000.0000.000
160B158SER0-0.035-0.04132.8290.0130.0130.0000.0000.0000.000
161B159TYR00.015-0.00829.6890.0000.0000.0000.0000.0000.000
162B160THR00.0030.00736.431-0.026-0.0260.0000.0000.0000.000
163B161THR0-0.017-0.01939.2490.0200.0200.0000.0000.0000.000
164B162GLY00.0370.00941.135-0.027-0.0270.0000.0000.0000.000
165B163ASN0-0.039-0.01243.586-0.029-0.0290.0000.0000.0000.000
166B164GLY00.0400.02544.978-0.021-0.0210.0000.0000.0000.000
167B165LYS10.9270.96943.778-0.464-0.4640.0000.0000.0000.000
168B166ARG10.8240.91639.967-0.363-0.3630.0000.0000.0000.000
169B167TYR0-0.050-0.03634.3900.0040.0040.0000.0000.0000.000
170B168ARG10.9370.94736.353-0.431-0.4310.0000.0000.0000.000
171B169SER00.0080.00231.6460.0470.0470.0000.0000.0000.000
172B170THR0-0.070-0.03831.577-0.043-0.0430.0000.0000.0000.000
173B171ALA00.0520.03126.1390.0780.0780.0000.0000.0000.000
174B172ARG10.9610.97924.251-1.128-1.1280.0000.0000.0000.000
175B173THR00.0000.00919.6740.1560.1560.0000.0000.0000.000
176B174THR0-0.019-0.00718.153-0.251-0.2510.0000.0000.0000.000
177B175TYR00.002-0.00115.9060.2700.2700.0000.0000.0000.000
178B176THR0-0.001-0.00513.392-0.292-0.2920.0000.0000.0000.000
179B177PHE00.013-0.00412.1450.6140.6140.0000.0000.0000.000
180B178ALA00.0320.0258.8210.1520.1520.0000.0000.0000.000
181B179LYS10.8540.90910.3794.2294.2290.0000.0000.0000.000
182B180PRO0-0.048-0.02312.8850.2650.2650.0000.0000.0000.000
183B181MET0-0.0140.00916.659-0.282-0.2820.0000.0000.0000.000
184B182ALA00.0240.01218.3350.0120.0120.0000.0000.0000.000
185B183ALA00.022-0.00921.0480.1390.1390.0000.0000.0000.000
186B184ASN0-0.016-0.00324.3960.1110.1110.0000.0000.0000.000
187B185TYR00.041-0.00319.8500.0520.0520.0000.0000.0000.000
188B186LEU0-0.017-0.00122.0870.0860.0860.0000.0000.0000.000
189B187LYS10.9410.97425.7820.4430.4430.0000.0000.0000.000
190B188ASN0-0.027-0.00327.8440.0330.0330.0000.0000.0000.000
191B189GLN0-0.025-0.00326.9160.1120.1120.0000.0000.0000.000
192B190PRO00.0110.00029.2860.0060.0060.0000.0000.0000.000
193B191MET00.0120.01825.938-0.050-0.0500.0000.0000.0000.000
194B192TYR0-0.108-0.08027.8140.1200.1200.0000.0000.0000.000
195B193VAL0-0.006-0.01524.984-0.055-0.0550.0000.0000.0000.000
196B194PHE0-0.034-0.00228.3810.0680.0680.0000.0000.0000.000
197B195ARG10.8840.92723.239-0.484-0.4840.0000.0000.0000.000
198B196LYS10.9550.98129.616-0.114-0.1140.0000.0000.0000.000
199B197THR00.0150.00327.594-0.021-0.0210.0000.0000.0000.000
200B198GLU-1-0.886-0.94230.3080.2350.2350.0000.0000.0000.000
201B199LEU0-0.0060.00528.8410.0240.0240.0000.0000.0000.000
202B200LYS10.8530.92931.723-0.354-0.3540.0000.0000.0000.000
203B201HIS0-0.013-0.01631.9410.0200.0200.0000.0000.0000.000
204B202SER00.0510.03833.184-0.023-0.0230.0000.0000.0000.000
205B203LYS10.8990.92533.852-0.597-0.5970.0000.0000.0000.000
206B204THR0-0.0050.00431.1700.0430.0430.0000.0000.0000.000
207B205GLU-1-0.821-0.90028.9910.6060.6060.0000.0000.0000.000
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