FMO DATABASE

FMODB ID: R9638

Calculation Name: 5MIX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5MIX

Chain ID: A

ChEMBL ID:

UniProt ID: Q01151

Base Structure: X-ray

Registration Date: 2023-09-19

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	OptAll
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	76
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-462652.495181
FMO2-HF: Nuclear repulsion	432510.346973
FMO2-HF: Total energy	-30142.148208
FMO2-MP2: Total energy	-30230.106843

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:19:GLY)

Summations of interaction energy for fragment #1(A:19:GLY)

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.
-0.934	-0.054	-0.004	-0.388	-0.487	0.001

Interaction energy analysis for fragmet #1(A:19:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.041 / q_NPA : 0.007

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	21	PRO	0	0.029	0.029	3.860	-0.682	0.198	-0.004	-0.388	-0.487	0.001
4	A	22	GLU	-1	-0.805	-0.900	6.341	0.306	0.306	0.000	0.000	0.000	0.000
5	A	23	VAL	0	0.005	0.012	8.997	-0.040	-0.040	0.000	0.000	0.000	0.000
6	A	24	LYS	1	0.883	0.932	10.576	0.460	0.460	0.000	0.000	0.000	0.000
7	A	25	VAL	0	0.046	0.031	15.011	-0.013	-0.013	0.000	0.000	0.000	0.000
8	A	26	ALA	0	0.055	0.041	18.749	0.015	0.015	0.000	0.000	0.000	0.000
9	A	27	SER	0	0.037	-0.013	22.010	0.007	0.007	0.000	0.000	0.000	0.000
10	A	28	SER	0	-0.093	-0.052	23.799	-0.003	-0.003	0.000	0.000	0.000	0.000
11	A	29	GLU	-1	-0.857	-0.910	23.443	-0.095	-0.095	0.000	0.000	0.000	0.000
12	A	30	ASP	-1	-0.803	-0.894	23.829	-0.064	-0.064	0.000	0.000	0.000	0.000
13	A	31	VAL	0	-0.029	-0.015	17.773	-0.017	-0.017	0.000	0.000	0.000	0.000
14	A	32	ASP	-1	-0.804	-0.902	19.548	-0.101	-0.101	0.000	0.000	0.000	0.000
15	A	33	LEU	0	-0.008	0.004	13.856	-0.042	-0.042	0.000	0.000	0.000	0.000
16	A	34	PRO	0	0.036	0.025	12.664	0.029	0.029	0.000	0.000	0.000	0.000
17	A	35	CYS	0	0.021	0.059	13.293	-0.046	-0.046	0.000	0.000	0.000	0.000
18	A	36	THR	0	-0.018	-0.048	9.194	0.028	0.028	0.000	0.000	0.000	0.000
19	A	37	ALA	0	0.009	0.008	10.868	-0.050	-0.050	0.000	0.000	0.000	0.000
20	A	38	PRO	0	-0.010	-0.003	11.571	-0.022	-0.022	0.000	0.000	0.000	0.000
21	A	39	TRP	0	-0.041	-0.028	14.019	0.026	0.026	0.000	0.000	0.000	0.000
22	A	40	ASP	-1	-0.788	-0.893	17.670	-0.105	-0.105	0.000	0.000	0.000	0.000
23	A	41	PRO	0	-0.051	-0.037	20.487	0.004	0.004	0.000	0.000	0.000	0.000
24	A	42	GLN	0	-0.017	-0.017	22.570	0.001	0.001	0.000	0.000	0.000	0.000
25	A	43	VAL	0	-0.017	0.011	23.391	0.011	0.011	0.000	0.000	0.000	0.000
26	A	44	PRO	0	-0.033	-0.009	24.071	-0.008	-0.008	0.000	0.000	0.000	0.000
27	A	45	TYR	0	0.004	-0.007	21.069	0.004	0.004	0.000	0.000	0.000	0.000
28	A	46	THR	0	-0.007	0.003	23.950	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	47	VAL	0	-0.014	-0.022	19.589	0.000	0.000	0.000	0.000	0.000	0.000
30	A	48	SER	0	-0.036	-0.008	20.395	0.015	0.015	0.000	0.000	0.000	0.000
31	A	49	TRP	0	-0.018	-0.032	14.191	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	50	VAL	0	-0.007	0.005	16.374	0.011	0.011	0.000	0.000	0.000	0.000
33	A	51	LYS	1	0.883	0.953	16.142	-0.117	-0.117	0.000	0.000	0.000	0.000
34	A	52	LEU	0	-0.076	-0.048	11.474	0.021	0.021	0.000	0.000	0.000	0.000
35	A	53	LEU	0	-0.019	-0.012	15.319	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	54	GLU	-1	-0.935	-0.955	16.653	0.267	0.267	0.000	0.000	0.000	0.000
37	A	87	GLU	-1	-0.879	-0.929	21.329	-0.195	-0.195	0.000	0.000	0.000	0.000
38	A	88	ARG	1	0.841	0.900	14.064	0.361	0.361	0.000	0.000	0.000	0.000
39	A	89	PRO	0	0.030	0.026	20.668	0.006	0.006	0.000	0.000	0.000	0.000
40	A	90	TYR	0	0.014	-0.015	18.823	-0.014	-0.014	0.000	0.000	0.000	0.000
41	A	91	SER	0	-0.011	-0.006	17.945	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	92	LEU	0	-0.029	0.004	17.955	0.024	0.024	0.000	0.000	0.000	0.000
43	A	93	LYS	1	0.835	0.913	19.631	0.092	0.092	0.000	0.000	0.000	0.000
44	A	94	ILE	0	-0.066	-0.031	18.475	0.020	0.020	0.000	0.000	0.000	0.000
45	A	95	ARG	1	0.903	0.923	22.420	0.049	0.049	0.000	0.000	0.000	0.000
46	A	96	ASN	0	-0.044	-0.016	25.216	0.006	0.006	0.000	0.000	0.000	0.000
47	A	97	THR	0	-0.034	-0.004	20.626	0.010	0.010	0.000	0.000	0.000	0.000
48	A	98	THR	0	0.048	0.005	22.484	0.004	0.004	0.000	0.000	0.000	0.000
49	A	99	SER	0	0.058	0.024	20.424	0.003	0.003	0.000	0.000	0.000	0.000
50	A	100	SER	0	0.065	0.030	19.548	0.011	0.011	0.000	0.000	0.000	0.000
51	A	101	ASN	0	0.009	0.014	19.660	0.016	0.016	0.000	0.000	0.000	0.000
52	A	102	SER	0	0.035	0.035	15.470	-0.017	-0.017	0.000	0.000	0.000	0.000
53	A	103	GLY	0	-0.006	0.000	13.425	0.034	0.034	0.000	0.000	0.000	0.000
54	A	104	THR	0	0.001	-0.003	9.166	-0.092	-0.092	0.000	0.000	0.000	0.000
55	A	105	TYR	0	-0.015	-0.026	11.552	0.004	0.004	0.000	0.000	0.000	0.000
56	A	106	ARG	1	0.887	0.934	11.567	-0.172	-0.172	0.000	0.000	0.000	0.000
57	A	108	THR	0	-0.040	-0.060	14.684	0.048	0.048	0.000	0.000	0.000	0.000
58	A	109	LEU	0	0.023	0.028	17.244	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	110	GLN	0	0.047	0.024	19.521	0.012	0.012	0.000	0.000	0.000	0.000
60	A	111	ASP	-1	-0.809	-0.897	22.663	-0.027	-0.027	0.000	0.000	0.000	0.000
61	A	112	PRO	0	0.021	0.010	24.741	0.008	0.008	0.000	0.000	0.000	0.000
62	A	113	ASP	-1	-0.805	-0.870	27.750	0.007	0.007	0.000	0.000	0.000	0.000
63	A	114	GLY	0	-0.028	-0.012	27.167	0.005	0.005	0.000	0.000	0.000	0.000
64	A	115	GLN	0	-0.094	-0.057	26.845	0.013	0.013	0.000	0.000	0.000	0.000
65	A	116	ARG	1	0.771	0.859	21.893	0.006	0.006	0.000	0.000	0.000	0.000
66	A	117	ASN	0	-0.022	-0.017	19.191	0.005	0.005	0.000	0.000	0.000	0.000
67	A	118	LEU	0	0.022	0.032	15.429	0.006	0.006	0.000	0.000	0.000	0.000
68	A	119	SER	0	-0.050	-0.030	13.255	0.023	0.023	0.000	0.000	0.000	0.000
69	A	120	GLY	0	0.050	0.025	9.902	-0.035	-0.035	0.000	0.000	0.000	0.000
70	A	121	LYS	1	0.931	0.963	7.355	-0.764	-0.764	0.000	0.000	0.000	0.000
71	A	122	VAL	0	0.045	0.038	8.348	-0.348	-0.348	0.000	0.000	0.000	0.000
72	A	123	ILE	0	-0.021	-0.008	6.126	0.268	0.268	0.000	0.000	0.000	0.000
73	A	124	LEU	0	0.016	0.023	9.961	-0.132	-0.132	0.000	0.000	0.000	0.000
74	A	125	ARG	1	0.827	0.876	8.359	0.059	0.059	0.000	0.000	0.000	0.000
75	A	126	VAL	0	0.024	0.022	14.609	-0.035	-0.035	0.000	0.000	0.000	0.000
76	A	127	THR	0	-0.048	-0.019	17.330	0.015	0.015	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:19:GLY)