FMO DATABASE

FMODB ID: M384Z

Calculation Name: 2DGC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2DGC

Chain ID: A

ChEMBL ID:

UniProt ID: P03069

Base Structure: X-ray

Registration Date: 2023-03-13

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	49
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-205736.270954
FMO2-HF: Nuclear repulsion	185334.827989
FMO2-HF: Total energy	-20401.442965
FMO2-MP2: Total energy	-20461.63614

3D Structure

Snapshot

Ligand structure

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/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:229:ALA)

Summations of interaction energy for fragment #1(A:229:ALA)

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.
-20.483	-14.906	3.735	-3.819	-5.49	0.03

Interaction energy analysis for fragmet #1(A:229:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.079 / q_NPA : 0.017

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

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Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

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].
3	A	231	LYS	1	1.011	1.006	3.188	-4.546	-1.929	0.057	-1.267	-1.406	0.002
4	A	232	ARG	1	0.941	0.970	2.103	-16.690	-13.985	3.678	-2.487	-3.895	0.028
5	A	233	ALA	0	0.063	0.048	4.285	-0.038	0.217	0.000	-0.065	-0.189	0.000
6	A	234	ARG	1	1.002	0.995	5.753	1.007	1.007	0.000	0.000	0.000	0.000
7	A	235	ASN	0	0.015	0.008	7.671	-0.036	-0.036	0.000	0.000	0.000	0.000
8	A	236	THR	0	-0.016	-0.015	7.611	0.118	0.118	0.000	0.000	0.000	0.000
9	A	237	GLU	-1	-0.797	-0.877	10.057	-0.262	-0.262	0.000	0.000	0.000	0.000
10	A	238	ALA	0	-0.048	-0.021	12.059	0.021	0.021	0.000	0.000	0.000	0.000
11	A	239	ALA	0	0.008	0.002	12.945	0.007	0.007	0.000	0.000	0.000	0.000
12	A	240	ARG	1	0.863	0.907	12.141	0.124	0.124	0.000	0.000	0.000	0.000
13	A	241	ARG	1	1.001	0.992	14.316	0.174	0.174	0.000	0.000	0.000	0.000
14	A	242	SER	0	-0.007	-0.002	17.641	0.001	0.001	0.000	0.000	0.000	0.000
15	A	243	ARG	1	0.931	0.953	14.318	-0.185	-0.185	0.000	0.000	0.000	0.000
16	A	244	ALA	0	0.063	0.041	20.578	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	245	ARG	1	0.963	0.975	19.116	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	246	LYS	1	0.910	0.948	19.563	-0.138	-0.138	0.000	0.000	0.000	0.000
19	A	247	LEU	0	0.050	0.036	24.914	0.000	0.000	0.000	0.000	0.000	0.000
20	A	248	GLN	0	-0.018	-0.010	26.877	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	249	ARG	1	0.933	0.968	23.464	-0.061	-0.061	0.000	0.000	0.000	0.000
22	A	250	MET	0	0.000	0.022	29.421	0.001	0.001	0.000	0.000	0.000	0.000
23	A	251	LYS	1	1.015	1.007	29.336	-0.012	-0.012	0.000	0.000	0.000	0.000
24	A	252	GLN	0	0.004	0.015	32.420	0.002	0.002	0.000	0.000	0.000	0.000
25	A	253	LEU	0	-0.042	-0.030	33.676	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	254	GLU	-1	-0.909	-0.977	34.174	0.040	0.040	0.000	0.000	0.000	0.000
27	A	255	ASP	-1	-0.837	-0.906	37.286	0.010	0.010	0.000	0.000	0.000	0.000
28	A	256	LYS	1	0.877	0.942	38.713	-0.019	-0.019	0.000	0.000	0.000	0.000
29	A	257	VAL	0	-0.014	-0.005	39.604	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	258	GLU	-1	-0.915	-0.950	41.826	0.014	0.014	0.000	0.000	0.000	0.000
31	A	259	GLU	-1	-0.910	-0.965	43.251	0.009	0.009	0.000	0.000	0.000	0.000
32	A	260	LEU	0	-0.008	-0.019	43.133	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	261	LEU	0	0.009	0.012	45.161	0.000	0.000	0.000	0.000	0.000	0.000
34	A	262	SER	0	-0.046	-0.018	47.981	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	263	LYS	1	0.909	0.954	47.370	-0.009	-0.009	0.000	0.000	0.000	0.000
36	A	264	ASN	0	-0.014	-0.011	50.232	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	265	TYR	0	0.010	0.012	51.952	0.000	0.000	0.000	0.000	0.000	0.000
38	A	266	HIS	0	0.026	0.003	53.342	0.000	0.000	0.000	0.000	0.000	0.000
39	A	267	LEU	0	-0.003	0.001	53.323	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	268	GLU	-1	-0.915	-0.947	56.056	0.017	0.017	0.000	0.000	0.000	0.000
41	A	269	ASN	0	-0.040	-0.026	57.871	0.000	0.000	0.000	0.000	0.000	0.000
42	A	270	GLU	-1	-0.980	-0.992	59.359	0.006	0.006	0.000	0.000	0.000	0.000
43	A	271	VAL	0	0.008	0.002	59.803	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	272	ALA	0	0.009	0.010	62.149	0.000	0.000	0.000	0.000	0.000	0.000
45	A	273	ARG	1	0.911	0.958	64.177	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	274	LEU	0	-0.006	-0.022	63.290	0.000	0.000	0.000	0.000	0.000	0.000
47	A	275	LYS	1	0.905	0.963	64.288	-0.012	-0.012	0.000	0.000	0.000	0.000
48	A	276	LYS	1	0.915	0.978	67.840	-0.008	-0.008	0.000	0.000	0.000	0.000
49	A	277	LEU	0	-0.009	0.003	69.920	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:229:ALA)