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: 1V3RZ

Calculation Name: 2C9I-A-Xray547

Preferred Name:

Target Type:

Ligand Name: [2-(3-carbamoyl-1-imino-propyl)-4-(4-hydroxy-benzylidene)-5-oxo-4,5-dihydro-imidazol-1-yl]-acetic acid

Ligand 3-letter code: CRQ

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2C9I

Chain ID: A

ChEMBL ID:

UniProt ID: Q9GPI6

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 -2775321.882901
FMO2-HF: Nuclear repulsion 2685707.992613
FMO2-HF: Total energy -89613.890288
FMO2-MP2: Total energy -89870.771928


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.
-51.96-41.4186.559-6.138-10.965-0.068
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 : 0.797 / q_NPA : 0.900
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].
3A3PRO00.0500.0153.631-1.1340.370-0.003-0.640-0.8610.000
5A5ILE00.0140.0134.1913.0653.325-0.001-0.032-0.2270.000
6A6LYS10.9460.9742.83412.38914.2850.677-1.068-1.507-0.010
7A7GLU-1-0.859-0.9452.556-44.372-41.7271.561-1.504-2.702-0.022
8A8THR0-0.039-0.0173.9523.6623.7570.004-0.010-0.0890.000
35A35TYR0-0.037-0.0442.517-13.942-9.8004.321-2.884-5.579-0.036
4A4SER0-0.037-0.0196.1304.2684.2680.0000.0000.0000.000
9A9MET0-0.052-0.0057.020-1.787-1.7870.0000.0000.0000.000
10A10ARG10.8800.9279.53521.67421.6740.0000.0000.0000.000
11A11VAL00.0150.01513.395-0.783-0.7830.0000.0000.0000.000
12A12GLN0-0.017-0.01316.1420.9490.9490.0000.0000.0000.000
13A13LEU00.0090.01719.494-0.159-0.1590.0000.0000.0000.000
14A14SER0-0.047-0.02721.7700.5940.5940.0000.0000.0000.000
15A15MET00.0130.01025.431-0.151-0.1510.0000.0000.0000.000
16A16GLU-1-0.916-0.95427.943-9.221-9.2210.0000.0000.0000.000
17A17GLY00.0480.00931.665-0.224-0.2240.0000.0000.0000.000
18A18SER0-0.057-0.01834.2410.3060.3060.0000.0000.0000.000
19A19VAL00.0320.01535.457-0.172-0.1720.0000.0000.0000.000
20A20ASN0-0.034-0.02538.3660.0540.0540.0000.0000.0000.000
21A21TYR0-0.026-0.01942.1150.1500.1500.0000.0000.0000.000
22A22HIS0-0.0340.00238.5810.1790.1790.0000.0000.0000.000
23A23ALA00.010-0.00838.283-0.238-0.2380.0000.0000.0000.000
24A24PHE0-0.022-0.02931.1390.1270.1270.0000.0000.0000.000
25A25LYS10.8420.91831.7648.6818.6810.0000.0000.0000.000
26A26CYS0-0.0280.00228.3520.2530.2530.0000.0000.0000.000
27A27THR0-0.023-0.00725.592-0.240-0.2400.0000.0000.0000.000
28A28GLY00.0420.02222.7120.2330.2330.0000.0000.0000.000
29A29LYS10.9490.98120.17612.20812.2080.0000.0000.0000.000
30A30GLY00.0240.01217.7800.4930.4930.0000.0000.0000.000
31A31GLU-1-0.964-0.98012.848-16.532-16.5320.0000.0000.0000.000
32A32GLY00.1140.04911.5870.8320.8320.0000.0000.0000.000
33A33LYS10.8200.9077.92021.97421.9740.0000.0000.0000.000
34A34PRO0-0.018-0.0145.8900.1130.1130.0000.0000.0000.000
36A36GLU-1-0.856-0.9276.641-22.770-22.7700.0000.0000.0000.000
37A37GLY0-0.0310.0069.9541.4501.4500.0000.0000.0000.000
38A38THR00.0260.01311.5471.3701.3700.0000.0000.0000.000
39A39GLN00.0280.00012.293-1.753-1.7530.0000.0000.0000.000
40A40SER00.0030.01514.8090.9350.9350.0000.0000.0000.000
41A41LEU0-0.019-0.00917.413-0.520-0.5200.0000.0000.0000.000
42A42ASN0-0.011-0.00120.1520.8670.8670.0000.0000.0000.000
43A43ILE0-0.015-0.01123.182-0.117-0.1170.0000.0000.0000.000
44A44THR0-0.016-0.00725.6200.4350.4350.0000.0000.0000.000
45A45ILE00.0320.00128.907-0.196-0.1960.0000.0000.0000.000
46A46THR0-0.038-0.02030.3280.1320.1320.0000.0000.0000.000
47A47GLU-1-0.866-0.92833.159-8.262-8.2620.0000.0000.0000.000
48A48GLY00.0650.03335.508-0.172-0.1720.0000.0000.0000.000
49A49GLY0-0.019-0.00237.8230.1360.1360.0000.0000.0000.000
50A50PRO00.015-0.00336.982-0.211-0.2110.0000.0000.0000.000
51A51LEU00.0210.03433.7570.1710.1710.0000.0000.0000.000
52A52PRO0-0.0070.01137.9840.0600.0600.0000.0000.0000.000
53A53PHE00.0350.00934.2140.1360.1360.0000.0000.0000.000
54A54ALA00.014-0.00235.529-0.094-0.0940.0000.0000.0000.000
55A55PHE00.0390.00527.489-0.094-0.0940.0000.0000.0000.000
56A56ASP-1-0.693-0.81330.383-9.854-9.8540.0000.0000.0000.000
57A57ILE0-0.017-0.00330.069-0.338-0.3380.0000.0000.0000.000
58A58LEU0-0.029-0.00729.055-0.146-0.1460.0000.0000.0000.000
59A59SER0-0.021-0.00826.003-0.264-0.2640.0000.0000.0000.000
60A60HIS00.1010.03424.404-0.950-0.9500.0000.0000.0000.000
61A61ALA0-0.067-0.02423.994-0.473-0.4730.0000.0000.0000.000
62A62PHE0-0.006-0.03222.854-0.079-0.0790.0000.0000.0000.000
63A63TYR0-0.042-0.04718.084-0.978-0.9780.0000.0000.0000.000
64A66ILE00.010-0.00714.304-0.200-0.2000.0000.0000.0000.000
65A67LYS10.9120.98214.77514.86814.8680.0000.0000.0000.000
66A68VAL00.0140.0059.811-1.254-1.2540.0000.0000.0000.000
67A69PHE0-0.093-0.0299.737-3.673-3.6730.0000.0000.0000.000
68A70ALA00.0570.04511.0211.4931.4930.0000.0000.0000.000
69A71LYS10.8970.9529.63618.59618.5960.0000.0000.0000.000
70A72TYR00.0380.0078.4272.0742.0740.0000.0000.0000.000
71A73PRO0-0.0220.0038.726-3.322-3.3220.0000.0000.0000.000
72A74LYS10.9150.9247.03632.47532.4750.0000.0000.0000.000
73A75GLU-1-0.912-0.9448.743-21.001-21.0010.0000.0000.0000.000
74A76ILE00.0030.02011.0841.2231.2230.0000.0000.0000.000
75A77PRO0-0.044-0.0199.907-2.550-2.5500.0000.0000.0000.000
76A78ASP-1-0.755-0.8707.854-29.856-29.8560.0000.0000.0000.000
77A79PHE00.0530.0249.889-1.226-1.2260.0000.0000.0000.000
78A80PHE00.0220.02811.5310.1910.1910.0000.0000.0000.000
79A81LYS10.7720.8735.19034.48034.4800.0000.0000.0000.000
80A82GLN0-0.085-0.0518.604-1.086-1.0860.0000.0000.0000.000
81A83SER0-0.008-0.01610.0401.4291.4290.0000.0000.0000.000
82A84LEU0-0.0040.00410.2631.1581.1580.0000.0000.0000.000
83A85PRO0-0.025-0.0119.7301.7451.7450.0000.0000.0000.000
84A86GLY0-0.058-0.01712.5331.3001.3000.0000.0000.0000.000
85A87GLY0-0.010-0.00115.2731.5511.5510.0000.0000.0000.000
86A88PHE0-0.053-0.04614.070-0.275-0.2750.0000.0000.0000.000
87A89SER00.0350.01518.5800.1770.1770.0000.0000.0000.000
88A90TRP0-0.024-0.00119.8790.0080.0080.0000.0000.0000.000
89A91GLU-1-0.866-0.90122.814-10.663-10.6630.0000.0000.0000.000
90A92ARG10.8480.89922.42412.66312.6630.0000.0000.0000.000
91A93VAL00.0130.01927.8630.3190.3190.0000.0000.0000.000
92A94SER00.010-0.00229.883-0.407-0.4070.0000.0000.0000.000
93A95THR0-0.005-0.00331.7620.2630.2630.0000.0000.0000.000
94A96TYR00.022-0.01032.710-0.199-0.1990.0000.0000.0000.000
95A97GLU-1-0.849-0.91836.936-7.957-7.9570.0000.0000.0000.000
96A98ASP-1-0.895-0.96139.608-7.636-7.6360.0000.0000.0000.000
97A99GLY0-0.019-0.01140.9120.2040.2040.0000.0000.0000.000
98A100GLY0-0.018-0.01039.1220.0260.0260.0000.0000.0000.000
99A101VAL0-0.0160.00035.850-0.186-0.1860.0000.0000.0000.000
100A102LEU0-0.015-0.01030.7600.1430.1430.0000.0000.0000.000
101A103SER00.0120.00931.976-0.266-0.2660.0000.0000.0000.000
102A104ALA0-0.025-0.02227.9470.0850.0850.0000.0000.0000.000
103A105THR0-0.050-0.04927.148-0.250-0.2500.0000.0000.0000.000
104A106GLN00.0350.01719.890-0.087-0.0870.0000.0000.0000.000
105A107GLU-1-0.981-0.98121.321-13.512-13.5120.0000.0000.0000.000
106A108THR00.029-0.00315.828-0.124-0.1240.0000.0000.0000.000
107A109SER0-0.021-0.01816.247-0.362-0.3620.0000.0000.0000.000
108A110LEU00.0110.0109.730-0.181-0.1810.0000.0000.0000.000
109A111GLN0-0.007-0.00614.2030.8350.8350.0000.0000.0000.000
110A112GLY00.0130.00812.8190.3350.3350.0000.0000.0000.000
111A113ASP-1-0.845-0.9219.575-22.725-22.7250.0000.0000.0000.000
112A114CYS0-0.042-0.00410.879-0.134-0.1340.0000.0000.0000.000
113A115ILE00.0400.01910.701-0.093-0.0930.0000.0000.0000.000
114A116ILE0-0.020-0.01514.5420.9880.9880.0000.0000.0000.000
115A117CYS0-0.004-0.00918.302-0.577-0.5770.0000.0000.0000.000
116A118LYS10.9390.98120.71013.16613.1660.0000.0000.0000.000
117A119VAL00.0210.01023.784-0.248-0.2480.0000.0000.0000.000
118A120LYS10.9360.97526.33610.95910.9590.0000.0000.0000.000
119A121VAL00.011-0.00229.566-0.178-0.1780.0000.0000.0000.000
120A122LEU00.000-0.00432.0190.2870.2870.0000.0000.0000.000
121A123GLY00.0240.01635.316-0.136-0.1360.0000.0000.0000.000
122A124THR0-0.019-0.03036.9660.1590.1590.0000.0000.0000.000
123A125ASN00.0110.00040.058-0.178-0.1780.0000.0000.0000.000
124A126PHE00.0700.06035.7230.0850.0850.0000.0000.0000.000
125A127PRO00.0220.02441.8800.1780.1780.0000.0000.0000.000
126A128ALA00.0140.00744.587-0.073-0.0730.0000.0000.0000.000
127A129ASN0-0.008-0.01146.469-0.029-0.0290.0000.0000.0000.000
128A130GLY00.0550.03843.8630.0360.0360.0000.0000.0000.000
129A131PRO00.0220.01340.2680.0160.0160.0000.0000.0000.000
130A132VAL00.0560.03037.109-0.073-0.0730.0000.0000.0000.000
131A133MET0-0.031-0.01339.321-0.142-0.1420.0000.0000.0000.000
132A134GLN0-0.073-0.04042.0810.1320.1320.0000.0000.0000.000
133A135LYS10.8060.90538.6707.7497.7490.0000.0000.0000.000
134A136LYS10.9270.96840.2186.9756.9750.0000.0000.0000.000
135A137THR0-0.022-0.02835.0210.0970.0970.0000.0000.0000.000
136A138CYS0-0.024-0.01034.7950.1020.1020.0000.0000.0000.000
137A139GLY0-0.033-0.00730.640-0.205-0.2050.0000.0000.0000.000
138A140TRP0-0.039-0.04727.8360.2600.2600.0000.0000.0000.000
139A141GLU-1-0.791-0.87628.836-9.903-9.9030.0000.0000.0000.000
140A142PRO0-0.106-0.04725.154-0.373-0.3730.0000.0000.0000.000
141A143SER0-0.039-0.04424.4970.2720.2720.0000.0000.0000.000
142A144THR0-0.065-0.04822.166-0.489-0.4890.0000.0000.0000.000
143A145GLU-1-0.817-0.90121.202-13.752-13.7520.0000.0000.0000.000
144A146THR0-0.015-0.02321.351-0.563-0.5630.0000.0000.0000.000
145A147VAL0-0.019-0.01117.0690.2460.2460.0000.0000.0000.000
146A148ILE00.013-0.00620.423-0.008-0.0080.0000.0000.0000.000
147A149PRO00.0030.01619.792-0.085-0.0850.0000.0000.0000.000
148A150ARG10.9360.95021.34011.91811.9180.0000.0000.0000.000
149A151ASP-1-0.880-0.94123.549-11.967-11.9670.0000.0000.0000.000
150A152GLY0-0.029-0.00721.3240.0510.0510.0000.0000.0000.000
151A153GLY0-0.036-0.02319.994-0.780-0.7800.0000.0000.0000.000
152A154LEU0-0.023-0.01216.774-0.346-0.3460.0000.0000.0000.000
153A155LEU0-0.034-0.01520.7900.6190.6190.0000.0000.0000.000
154A156LEU0-0.028-0.00118.663-0.331-0.3310.0000.0000.0000.000
155A157ARG10.8600.92123.04511.08211.0820.0000.0000.0000.000
156A158ASP-1-0.734-0.84724.971-12.441-12.4410.0000.0000.0000.000
157A159THR0-0.056-0.03526.9330.4690.4690.0000.0000.0000.000
158A160PRO0-0.0020.02827.5790.2000.2000.0000.0000.0000.000
159A161ALA00.0630.01929.5860.3110.3110.0000.0000.0000.000
160A162LEU0-0.062-0.02731.787-0.239-0.2390.0000.0000.0000.000
161A163MET00.0190.01131.2130.3560.3560.0000.0000.0000.000
162A164LEU0-0.017-0.00735.4560.0010.0010.0000.0000.0000.000
163A165ALA0-0.021-0.02938.8740.0290.0290.0000.0000.0000.000
164A166ASP-1-0.943-0.96840.950-7.260-7.2600.0000.0000.0000.000
165A167GLY0-0.033-0.01140.3110.1260.1260.0000.0000.0000.000
166A168GLY0-0.0200.00540.401-0.067-0.0670.0000.0000.0000.000
167A169HIS0-0.059-0.06734.857-0.019-0.0190.0000.0000.0000.000
168A170LEU0-0.048-0.01036.9940.2220.2220.0000.0000.0000.000
169A171SER00.000-0.00834.397-0.372-0.3720.0000.0000.0000.000
170A172CYS0-0.065-0.02831.6920.1190.1190.0000.0000.0000.000
171A173PHE00.0040.01231.536-0.197-0.1970.0000.0000.0000.000
172A174MET0-0.038-0.01324.8720.1690.1690.0000.0000.0000.000
173A175GLU-1-0.879-0.93427.800-10.092-10.0920.0000.0000.0000.000
174A176THR00.0120.02122.6370.3690.3690.0000.0000.0000.000
175A177THR0-0.014-0.00324.209-0.288-0.2880.0000.0000.0000.000
176A178TYR-1-0.765-0.86518.923-15.846-15.8460.0000.0000.0000.000
177A179LYS10.9420.95921.36313.59813.5980.0000.0000.0000.000
178A180SER00.0680.04016.1630.0030.0030.0000.0000.0000.000
179A181LYS10.8820.94518.62316.05516.0550.0000.0000.0000.000
180A182LYS10.8880.94116.41718.83018.8300.0000.0000.0000.000
181A183GLU-1-0.902-0.94317.790-16.466-16.4660.0000.0000.0000.000
182A184VAL0-0.033-0.01513.542-1.241-1.2410.0000.0000.0000.000
183A185LYS10.9380.96211.95023.10323.1030.0000.0000.0000.000
184A186LEU00.0210.01713.570-1.377-1.3770.0000.0000.0000.000
185A187PRO0-0.039-0.00314.140-0.017-0.0170.0000.0000.0000.000
186A188GLU-1-0.885-0.94415.780-14.600-14.6000.0000.0000.0000.000
187A189LEU0-0.034-0.01418.435-0.557-0.5570.0000.0000.0000.000
188A190HIS0-0.032-0.01315.802-0.991-0.9910.0000.0000.0000.000
189A191PHE0-0.0020.01019.0770.5470.5470.0000.0000.0000.000
190A192HIS00.009-0.01014.834-0.591-0.5910.0000.0000.0000.000
191A193HIS00.0060.00418.1781.2741.2740.0000.0000.0000.000
192A194LEU0-0.023-0.01218.788-1.103-1.1030.0000.0000.0000.000
193A195ARG10.9040.94020.55412.75912.7590.0000.0000.0000.000
194A196MET0-0.0010.02121.094-0.622-0.6220.0000.0000.0000.000
195A197GLU-1-0.843-0.91222.986-11.470-11.4700.0000.0000.0000.000
196A198LYS10.8330.89224.0709.6079.6070.0000.0000.0000.000
197A199LEU0-0.038-0.00421.9980.2320.2320.0000.0000.0000.000
198A200ASN0-0.018-0.01925.9600.6880.6880.0000.0000.0000.000
199A201ILE0-0.004-0.01628.548-0.236-0.2360.0000.0000.0000.000
200A202SER0-0.031-0.02231.2940.0700.0700.0000.0000.0000.000
201A203ASP-1-0.873-0.93733.725-7.910-7.9100.0000.0000.0000.000
202A204ASP-1-0.813-0.88935.703-8.149-8.1490.0000.0000.0000.000
203A205TRP0-0.041-0.03534.9780.1240.1240.0000.0000.0000.000
204A206LYS10.8220.91633.5437.9257.9250.0000.0000.0000.000
205A207THR0-0.012-0.00328.499-0.308-0.3080.0000.0000.0000.000
206A208VAL0-0.003-0.00727.2880.2130.2130.0000.0000.0000.000
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