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

tag_button

FMODB ID: 4YR2N

Calculation Name: 1J2Q-H-Xray547

Preferred Name:

Target Type:

Ligand Name: 2-acetylamino-4-methyl-pentanoic acid [1-(1-formyl-pentylcarbamoyl)-3-methyl-butyl]-amide

Ligand 3-letter code: CIB

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1J2Q

Chain ID: H

ChEMBL ID:

UniProt ID: O29760

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 202
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2242410.091368
FMO2-HF: Nuclear repulsion 2164923.804301
FMO2-HF: Total energy -77486.287067
FMO2-MP2: Total energy -77712.534187


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:THR)


Summations of interaction energy for fragment #1(A:1:THR)
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.
-150.397-143.22937.454-19.705-24.911-0.169
Interaction energy analysis for fragmet #1(A:1:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.724 / q_NPA : 0.859
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].
3A3THR00.008-0.0082.7651.5363.6790.254-0.755-1.643-0.005
4A4VAL00.0220.0064.9740.3170.309-0.001-0.0030.0130.000
16A16THR00.003-0.0164.392-2.476-2.434-0.001-0.008-0.0320.000
17A17GLU-1-0.743-0.8282.111-77.509-76.2957.060-4.389-3.884-0.047
18A18LYS10.8030.9004.91424.43524.537-0.001-0.004-0.0960.000
19A19ARG10.7810.8874.34243.19943.321-0.001-0.013-0.1070.000
20A20ALA0-0.016-0.0074.031-5.441-5.0630.002-0.054-0.3260.000
33A33LYS10.7980.8771.95851.99650.6127.836-2.493-3.9590.026
46A46ALA0-0.003-0.0062.482-7.363-7.1211.969-0.616-1.595-0.002
47A47GLY00.0260.0243.1785.4755.1020.0190.587-0.233-0.001
48A48SER0-0.043-0.0374.984-2.557-2.505-0.0010.000-0.0500.000
129A127THR00.0180.0013.8661.4701.6240.000-0.022-0.1320.000
130A128GLY00.0090.0002.607-7.903-7.2530.304-0.404-0.550-0.001
131A129SER0-0.042-0.0411.954-8.906-8.9685.967-2.820-3.086-0.036
132A130GLY00.011-0.0033.5009.97010.3870.000-0.143-0.2740.000
133A131SER0-0.039-0.0225.2438.7488.865-0.001-0.006-0.1100.000
168A166ASP-1-0.694-0.7922.689-94.042-91.1720.417-1.973-1.313-0.021
169A167SER00.0330.0175.185-4.562-4.535-0.001-0.001-0.0240.000
170A168ALA0-0.0050.0062.9983.9744.6740.144-0.333-0.512-0.001
171A169SER0-0.074-0.0701.989-45.835-46.18913.410-6.277-6.779-0.080
172A170GLY0-0.010-0.0243.08411.56111.6800.0790.022-0.219-0.001
5A5GLY00.0060.0018.6220.4620.4620.0000.0000.0000.000
6A6LEU0-0.0020.00111.642-0.036-0.0360.0000.0000.0000.000
7A7VAL0-0.0240.00415.2560.2520.2520.0000.0000.0000.000
8A8CYS0-0.0150.00818.724-0.068-0.0680.0000.0000.0000.000
9A9LYS10.9210.96221.66511.26911.2690.0000.0000.0000.000
10A10ASP-1-0.806-0.90624.073-11.979-11.9790.0000.0000.0000.000
11A11GLY0-0.013-0.02122.0370.1810.1810.0000.0000.0000.000
12A12VAL0-0.050-0.00716.045-0.188-0.1880.0000.0000.0000.000
13A13VAL00.0120.01714.0790.0970.0970.0000.0000.0000.000
14A14MET0-0.026-0.00510.494-1.198-1.1980.0000.0000.0000.000
15A15ALA0-0.0080.0089.3190.9810.9810.0000.0000.0000.000
21A21THR0-0.019-0.0234.9011.5561.5560.0000.0000.0000.000
22A22MET00.0110.0146.8500.4040.4040.0000.0000.0000.000
23A23GLY00.0210.0129.1832.5132.5130.0000.0000.0000.000
24A24ASN00.012-0.0148.436-4.813-4.8130.0000.0000.0000.000
25A25PHE0-0.0060.01910.5880.2720.2720.0000.0000.0000.000
26A26ILE0-0.001-0.0128.114-2.146-2.1460.0000.0000.0000.000
27A27ALA00.0060.0099.1662.3632.3630.0000.0000.0000.000
28A28SER0-0.025-0.0258.7462.0422.0420.0000.0000.0000.000
29A29LYS10.9500.9798.74420.56120.5610.0000.0000.0000.000
30A30ALA00.0560.02810.355-0.073-0.0730.0000.0000.0000.000
31A31ALA0-0.031-0.0076.4221.6011.6010.0000.0000.0000.000
32A32LYS10.9480.9767.78118.23718.2370.0000.0000.0000.000
34A34ILE00.0520.0426.396-0.442-0.4420.0000.0000.0000.000
35A35TYR0-0.072-0.0578.3862.7202.7200.0000.0000.0000.000
36A36GLN00.0210.03312.507-0.120-0.1200.0000.0000.0000.000
37A37ILE0-0.080-0.05014.0610.1570.1570.0000.0000.0000.000
38A38ALA00.0620.02317.5220.6800.6800.0000.0000.0000.000
39A39ASP-1-0.842-0.92320.188-11.742-11.7420.0000.0000.0000.000
40A40ARG10.8020.89920.98111.59211.5920.0000.0000.0000.000
41A41MET00.0020.02316.979-0.328-0.3280.0000.0000.0000.000
42A42ALA00.0290.01413.1960.0160.0160.0000.0000.0000.000
43A43MET00.0210.0189.9910.4150.4150.0000.0000.0000.000
44A44THR0-0.035-0.0076.582-2.146-2.1460.0000.0000.0000.000
45A45THR0-0.005-0.0195.0682.2262.2260.0000.0000.0000.000
49A49VAL00.0340.0055.6770.7720.7720.0000.0000.0000.000
50A50GLY00.0120.0117.7931.4961.4960.0000.0000.0000.000
51A51ASP-1-0.782-0.88110.487-20.233-20.2330.0000.0000.0000.000
52A52ALA00.0320.0187.4081.1611.1610.0000.0000.0000.000
53A53GLN0-0.034-0.0229.4422.4142.4140.0000.0000.0000.000
54A54PHE0-0.080-0.04511.9481.3351.3350.0000.0000.0000.000
55A55LEU00.0760.03212.3920.9320.9320.0000.0000.0000.000
56A56ALA00.0070.01011.4520.8850.8850.0000.0000.0000.000
57A57ARG10.8790.95213.49017.43217.4320.0000.0000.0000.000
58A58ILE00.0220.02216.9670.7080.7080.0000.0000.0000.000
59A59ILE00.0390.01414.6510.6270.6270.0000.0000.0000.000
60A60LYS10.9090.95515.27116.29416.2940.0000.0000.0000.000
61A61ILE0-0.036-0.01018.7910.6400.6400.0000.0000.0000.000
62A62GLU-1-0.902-0.96421.195-11.923-11.9230.0000.0000.0000.000
63A63ALA0-0.001-0.00120.3570.5020.5020.0000.0000.0000.000
64A64ASN00.014-0.00122.2860.4060.4060.0000.0000.0000.000
65A65LEU0-0.021-0.00824.5410.5110.5110.0000.0000.0000.000
66A66TYR0-0.034-0.01925.5810.4810.4810.0000.0000.0000.000
67A67GLU-1-0.876-0.95126.647-10.131-10.1310.0000.0000.0000.000
68A68ILE0-0.031-0.02527.6220.3680.3680.0000.0000.0000.000
69A69ARG10.8780.94028.7759.8559.8550.0000.0000.0000.000
70A70ARG10.8910.95529.7669.7159.7150.0000.0000.0000.000
71A71GLU-1-0.917-0.93932.599-7.877-7.8770.0000.0000.0000.000
72A72ARG10.9250.96030.6179.0419.0410.0000.0000.0000.000
73A73LYS10.9290.97125.45010.49010.4900.0000.0000.0000.000
74A74PRO0-0.052-0.01322.7550.2170.2170.0000.0000.0000.000
75A75THR00.009-0.00923.581-0.319-0.3190.0000.0000.0000.000
76A76VAL00.035-0.00918.810-0.241-0.2410.0000.0000.0000.000
77A77ARG10.8780.93619.88011.24411.2440.0000.0000.0000.000
78A78ALA0-0.033-0.00122.204-0.049-0.0490.0000.0000.0000.000
79A79ILE00.0200.00517.349-0.069-0.0690.0000.0000.0000.000
80A80ALA00.0480.04617.410-0.480-0.4800.0000.0000.0000.000
81A81THR0-0.016-0.00718.433-0.199-0.1990.0000.0000.0000.000
82A82LEU0-0.057-0.02220.7240.0630.0630.0000.0000.0000.000
83A83THR0-0.012-0.02814.369-0.222-0.2220.0000.0000.0000.000
84A84SER0-0.009-0.02317.517-0.569-0.5690.0000.0000.0000.000
85A85ASN0-0.021-0.01618.625-0.024-0.0240.0000.0000.0000.000
86A86LEU0-0.0170.00617.2100.1730.1730.0000.0000.0000.000
87A87LEU00.0050.00113.5830.1290.1290.0000.0000.0000.000
88A88ASN0-0.051-0.02417.5060.7400.7400.0000.0000.0000.000
89A89SER0-0.072-0.04620.6310.4410.4410.0000.0000.0000.000
90A90TYR00.0090.00118.9120.4690.4690.0000.0000.0000.000
91A91ARG10.9540.98219.54711.95311.9530.0000.0000.0000.000
92A92TYR0-0.054-0.03020.6300.0180.0180.0000.0000.0000.000
93A93PHE0-0.080-0.03919.5180.2050.2050.0000.0000.0000.000
94A94PRO00.0140.03015.6660.0470.0470.0000.0000.0000.000
95A95TYR00.0420.01413.011-0.428-0.4280.0000.0000.0000.000
96A96LEU00.0110.00410.224-0.803-0.8030.0000.0000.0000.000
97A97VAL0-0.069-0.0516.980-3.376-3.3760.0000.0000.0000.000
98A98GLN00.0210.0146.3293.0233.0230.0000.0000.0000.000
99A99LEU0-0.054-0.0396.708-2.602-2.6020.0000.0000.0000.000
100A100LEU00.0200.0258.1250.2640.2640.0000.0000.0000.000
101A101ILE00.0190.00710.265-0.169-0.1690.0000.0000.0000.000
102A102GLY00.0640.01513.6740.3670.3670.0000.0000.0000.000
103A103GLY0-0.032-0.01616.072-0.273-0.2730.0000.0000.0000.000
104A104ILE0-0.007-0.00118.7290.1640.1640.0000.0000.0000.000
105A105ASP-1-0.788-0.87522.546-11.855-11.8550.0000.0000.0000.000
106A106SER0-0.010-0.01025.4240.1810.1810.0000.0000.0000.000
107A106GLU-1-0.892-0.92125.665-10.675-10.6750.0000.0000.0000.000
108A107GLY00.0010.01526.1360.0310.0310.0000.0000.0000.000
109A108LYS10.8650.92421.67511.41311.4130.0000.0000.0000.000
110A109SER00.0090.01019.641-0.003-0.0030.0000.0000.0000.000
111A110ILE0-0.006-0.01012.833-0.462-0.4620.0000.0000.0000.000
112A111TYR0-0.016-0.01814.8550.6810.6810.0000.0000.0000.000
113A112SER00.0150.02211.019-1.672-1.6720.0000.0000.0000.000
114A113ILE0-0.031-0.02311.4461.4171.4170.0000.0000.0000.000
115A114ASP-1-0.762-0.86211.286-20.164-20.1640.0000.0000.0000.000
116A115PRO0-0.018-0.03211.3121.0871.0870.0000.0000.0000.000
117A116ILE0-0.045-0.02513.6561.0861.0860.0000.0000.0000.000
118A117GLY0-0.0110.00015.9541.1041.1040.0000.0000.0000.000
119A118GLY0-0.023-0.01016.7590.8580.8580.0000.0000.0000.000
120A119ALA0-0.026-0.01215.471-1.153-1.1530.0000.0000.0000.000
121A120ILE0-0.013-0.00415.4841.0101.0100.0000.0000.0000.000
122A121GLU-1-0.874-0.92916.355-13.105-13.1050.0000.0000.0000.000
123A121GLU-1-0.871-0.97113.811-18.832-18.8320.0000.0000.0000.000
124A121LYS10.8910.93417.26012.55112.5510.0000.0000.0000.000
125A122ASP-1-0.850-0.91618.163-14.711-14.7110.0000.0000.0000.000
126A123ILE0-0.041-0.02713.896-0.852-0.8520.0000.0000.0000.000
127A124VAL00.0310.0269.687-0.350-0.3500.0000.0000.0000.000
128A125ALA0-0.0130.0027.741-1.274-1.2740.0000.0000.0000.000
134A132LEU00.0460.0207.3903.6833.6830.0000.0000.0000.000
135A133THR0-0.041-0.0189.0863.1863.1860.0000.0000.0000.000
136A134ALA0-0.017-0.0078.9441.9901.9900.0000.0000.0000.000
137A135TYR00.0930.03110.0052.0372.0370.0000.0000.0000.000
138A136GLY00.0140.02112.9231.5681.5680.0000.0000.0000.000
139A137VAL0-0.043-0.02113.4711.1961.1960.0000.0000.0000.000
140A138LEU0-0.017-0.02811.1570.8550.8550.0000.0000.0000.000
141A139GLU-1-0.929-0.97515.555-16.146-16.1460.0000.0000.0000.000
142A140ASP-1-0.973-0.97018.174-14.203-14.2030.0000.0000.0000.000
143A141ARG10.8640.92318.98315.79315.7930.0000.0000.0000.000
144A142PHE00.0200.02318.3770.2840.2840.0000.0000.0000.000
145A143THR00.0000.00620.3950.5720.5720.0000.0000.0000.000
146A144PRO00.0240.01522.928-0.321-0.3210.0000.0000.0000.000
147A145GLU-1-0.907-0.96624.236-10.990-10.9900.0000.0000.0000.000
148A146ILE0-0.0330.00919.7060.2090.2090.0000.0000.0000.000
149A147GLY00.008-0.01223.7560.1470.1470.0000.0000.0000.000
150A148VAL0-0.007-0.03320.281-0.663-0.6630.0000.0000.0000.000
151A149ASP-1-0.820-0.92319.754-13.483-13.4830.0000.0000.0000.000
152A150GLU-1-0.889-0.93820.669-12.949-12.9490.0000.0000.0000.000
153A151ALA00.0350.01717.886-0.763-0.7630.0000.0000.0000.000
154A152VAL00.000-0.00115.691-1.455-1.4550.0000.0000.0000.000
155A153GLU-1-0.878-0.92715.555-15.447-15.4470.0000.0000.0000.000
156A154LEU0-0.027-0.01815.924-0.997-0.9970.0000.0000.0000.000
157A155ALA00.0270.01012.001-1.392-1.3920.0000.0000.0000.000
158A156VAL00.012-0.00711.578-2.601-2.6010.0000.0000.0000.000
159A157ARG10.8890.96012.41714.77614.7760.0000.0000.0000.000
160A158ALA00.0260.02711.706-0.564-0.5640.0000.0000.0000.000
161A159ILE00.0000.0036.615-2.597-2.5970.0000.0000.0000.000
162A160TYR00.0390.0008.589-2.015-2.0150.0000.0000.0000.000
163A161SER0-0.043-0.03511.1111.3231.3230.0000.0000.0000.000
164A162ALA00.0160.0056.4690.1730.1730.0000.0000.0000.000
165A163MET0-0.0160.0026.584-2.497-2.4970.0000.0000.0000.000
166A164LYS10.8720.9717.57223.18523.1850.0000.0000.0000.000
167A165ARG10.8390.9148.60826.20426.2040.0000.0000.0000.000
173A171ASP-1-0.814-0.9016.521-32.310-32.3100.0000.0000.0000.000
174A172GLY00.0430.0308.4623.0183.0180.0000.0000.0000.000
175A173ILE0-0.026-0.0268.257-3.860-3.8600.0000.0000.0000.000
176A174ASP-1-0.823-0.8728.844-21.753-21.7530.0000.0000.0000.000
177A175VAL00.019-0.0179.880-1.744-1.7440.0000.0000.0000.000
178A176VAL0-0.017-0.01412.5291.0251.0250.0000.0000.0000.000
179A177LYS10.9090.96214.53212.71512.7150.0000.0000.0000.000
180A178ILE0-0.037-0.02116.4190.3700.3700.0000.0000.0000.000
181A179THR0-0.0100.00619.814-0.067-0.0670.0000.0000.0000.000
182A180GLU-1-0.902-0.96423.349-10.366-10.3660.0000.0000.0000.000
183A181ASP-1-0.832-0.91225.894-10.329-10.3290.0000.0000.0000.000
184A182GLU-1-0.982-1.00022.739-11.937-11.9370.0000.0000.0000.000
185A183PHE0-0.025-0.02215.667-0.510-0.5100.0000.0000.0000.000
186A184TYR0-0.047-0.04319.4230.2060.2060.0000.0000.0000.000
187A185GLN0-0.020-0.02712.960-0.467-0.4670.0000.0000.0000.000
188A186TYR0-0.004-0.00616.1100.1810.1810.0000.0000.0000.000
189A187SER00.0100.01416.9500.4000.4000.0000.0000.0000.000
190A188PRO0-0.024-0.01815.954-0.526-0.5260.0000.0000.0000.000
191A188GLU-1-0.877-0.94116.931-14.458-14.4580.0000.0000.0000.000
192A188GLU-1-0.803-0.87519.419-13.523-13.5230.0000.0000.0000.000
193A189VAL0-0.041-0.02613.280-0.137-0.1370.0000.0000.0000.000
194A190GLU-1-0.920-0.96116.746-17.801-17.8010.0000.0000.0000.000
195A191GLN0-0.029-0.02217.9760.2310.2310.0000.0000.0000.000
196A192ILE0-0.031-0.01117.4130.4890.4890.0000.0000.0000.000
197A193LEU0-0.038-0.01213.683-0.176-0.1760.0000.0000.0000.000
198A194ALA00.0620.03917.2990.1760.1760.0000.0000.0000.000
199A195LYS10.8300.92320.56514.17214.1720.0000.0000.0000.000
200A196PHE0-0.112-0.04715.7780.1710.1710.0000.0000.0000.000
201A197ARG10.8210.88618.11715.26415.2640.0000.0000.0000.000
202A198LYS00.1290.08616.063-0.260-0.2600.0000.0000.0000.000