FMO DATABASE

FMODB ID: 6NKJZ

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	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	77
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-463213.258576
FMO2-HF: Nuclear repulsion	433071.805945
FMO2-HF: Total energy	-30141.452631
FMO2-MP2: Total energy	-30229.466588

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.
0.8	1.749	-0.009	-0.413	-0.528	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 : 0.023 / q_NPA : 0.001

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	0.035	0.030	3.810	0.917	1.866	-0.009	-0.413	-0.528	0.001
4	A	22	GLU	-1	-0.773	-0.859	6.262	1.722	1.722	0.000	0.000	0.000	0.000
5	A	23	VAL	0	0.028	0.022	9.090	-0.121	-0.121	0.000	0.000	0.000	0.000
6	A	24	LYS	1	0.918	0.953	12.314	-0.370	-0.370	0.000	0.000	0.000	0.000
7	A	25	VAL	0	0.046	0.030	15.328	-0.033	-0.033	0.000	0.000	0.000	0.000
8	A	26	ALA	0	0.011	0.019	18.999	0.022	0.022	0.000	0.000	0.000	0.000
9	A	27	SER	0	0.031	-0.049	22.337	-0.003	-0.003	0.000	0.000	0.000	0.000
10	A	28	SER	0	-0.122	-0.065	24.319	-0.010	-0.010	0.000	0.000	0.000	0.000
11	A	29	GLU	-1	-0.877	-0.920	23.606	0.030	0.030	0.000	0.000	0.000	0.000
12	A	30	ASP	-1	-0.856	-0.911	23.939	0.030	0.030	0.000	0.000	0.000	0.000
13	A	31	VAL	0	-0.040	-0.025	17.682	0.002	0.002	0.000	0.000	0.000	0.000
14	A	32	ASP	-1	-0.872	-0.937	20.030	-0.029	-0.029	0.000	0.000	0.000	0.000
15	A	33	LEU	0	-0.049	-0.032	14.142	-0.009	-0.009	0.000	0.000	0.000	0.000
16	A	34	PRO	0	-0.010	0.000	12.649	-0.008	-0.008	0.000	0.000	0.000	0.000
17	A	35	CYS	-1	-0.757	-0.890	13.555	-0.262	-0.262	0.000	0.000	0.000	0.000
18	A	36	THR	0	-0.092	-0.068	9.294	-0.011	-0.011	0.000	0.000	0.000	0.000
19	A	37	ALA	0	0.091	0.033	11.040	-0.123	-0.123	0.000	0.000	0.000	0.000
20	A	38	PRO	0	-0.054	-0.028	11.935	0.019	0.019	0.000	0.000	0.000	0.000
21	A	39	TRP	0	-0.051	-0.025	14.068	0.030	0.030	0.000	0.000	0.000	0.000
22	A	40	ASP	-1	-0.823	-0.917	17.760	-0.167	-0.167	0.000	0.000	0.000	0.000
23	A	41	PRO	0	-0.044	-0.030	20.322	0.012	0.012	0.000	0.000	0.000	0.000
24	A	42	GLN	0	-0.018	-0.016	22.653	0.007	0.007	0.000	0.000	0.000	0.000
25	A	43	VAL	0	-0.030	-0.002	23.695	0.013	0.013	0.000	0.000	0.000	0.000
26	A	44	PRO	0	-0.056	-0.013	24.380	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	45	TYR	0	0.058	0.017	21.254	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	46	THR	0	-0.041	-0.009	24.341	0.009	0.009	0.000	0.000	0.000	0.000
29	A	47	VAL	0	0.037	0.017	19.634	-0.009	-0.009	0.000	0.000	0.000	0.000
30	A	48	SER	0	-0.065	-0.024	20.723	0.018	0.018	0.000	0.000	0.000	0.000
31	A	49	TRP	0	0.007	0.006	14.517	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	50	VAL	0	-0.038	-0.018	16.264	0.015	0.015	0.000	0.000	0.000	0.000
33	A	51	LYS	1	0.896	0.961	16.112	-0.175	-0.175	0.000	0.000	0.000	0.000
34	A	52	LEU	0	-0.073	-0.046	11.314	-0.019	-0.019	0.000	0.000	0.000	0.000
35	A	53	LEU	0	-0.019	-0.013	14.922	0.045	0.045	0.000	0.000	0.000	0.000
36	A	54	GLU	-1	-0.957	-0.963	15.937	0.150	0.150	0.000	0.000	0.000	0.000
37	A	87	GLU	-1	-0.951	-0.987	21.424	-0.103	-0.103	0.000	0.000	0.000	0.000
38	A	88	ARG	1	0.903	0.955	13.472	0.273	0.273	0.000	0.000	0.000	0.000
39	A	89	PRO	0	-0.018	-0.002	20.593	0.011	0.011	0.000	0.000	0.000	0.000
40	A	90	TYR	0	0.054	0.007	18.881	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	91	SER	0	0.043	0.025	18.304	-0.014	-0.014	0.000	0.000	0.000	0.000
42	A	92	LEU	0	-0.031	0.002	18.503	0.013	0.013	0.000	0.000	0.000	0.000
43	A	93	LYS	1	0.920	0.968	20.046	0.020	0.020	0.000	0.000	0.000	0.000
44	A	94	ILE	0	-0.045	-0.023	18.938	0.007	0.007	0.000	0.000	0.000	0.000
45	A	95	ARG	1	0.935	0.954	22.852	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	96	ASN	0	-0.031	-0.016	25.978	0.005	0.005	0.000	0.000	0.000	0.000
47	A	97	THR	0	-0.013	-0.015	21.091	0.011	0.011	0.000	0.000	0.000	0.000
48	A	98	THR	0	0.042	0.017	23.233	0.004	0.004	0.000	0.000	0.000	0.000
49	A	99	SER	0	0.055	0.016	21.210	0.016	0.016	0.000	0.000	0.000	0.000
50	A	100	SER	0	0.038	0.011	20.339	0.026	0.026	0.000	0.000	0.000	0.000
51	A	101	ASN	0	-0.018	-0.005	19.999	0.001	0.001	0.000	0.000	0.000	0.000
52	A	102	SER	0	0.039	0.048	16.077	0.002	0.002	0.000	0.000	0.000	0.000
53	A	103	GLY	0	-0.003	-0.002	13.999	-0.020	-0.020	0.000	0.000	0.000	0.000
54	A	104	THR	0	0.013	0.002	9.323	0.056	0.056	0.000	0.000	0.000	0.000
55	A	105	TYR	0	-0.035	-0.039	11.885	-0.053	-0.053	0.000	0.000	0.000	0.000
56	A	106	ARG	1	0.895	0.942	11.883	0.051	0.051	0.000	0.000	0.000	0.000
57	A	107	CYS	-1	-0.878	-0.880	13.641	-0.225	-0.225	0.000	0.000	0.000	0.000
58	A	108	THR	0	-0.036	-0.053	15.174	-0.038	-0.038	0.000	0.000	0.000	0.000
59	A	109	LEU	0	0.036	0.010	17.511	0.029	0.029	0.000	0.000	0.000	0.000
60	A	110	GLN	0	-0.011	-0.022	19.844	-0.013	-0.013	0.000	0.000	0.000	0.000
61	A	111	ASP	-1	-0.846	-0.939	23.002	-0.115	-0.115	0.000	0.000	0.000	0.000
62	A	112	PRO	0	0.005	0.000	24.934	0.009	0.009	0.000	0.000	0.000	0.000
63	A	113	ASP	-1	-0.845	-0.914	27.841	-0.090	-0.090	0.000	0.000	0.000	0.000
64	A	114	GLY	0	-0.014	0.004	27.362	0.006	0.006	0.000	0.000	0.000	0.000
65	A	115	GLN	0	-0.121	-0.063	27.075	0.002	0.002	0.000	0.000	0.000	0.000
66	A	116	ARG	1	0.847	0.923	22.027	0.111	0.111	0.000	0.000	0.000	0.000
67	A	117	ASN	0	-0.035	-0.012	19.321	-0.008	-0.008	0.000	0.000	0.000	0.000
68	A	118	LEU	0	0.024	0.021	15.798	-0.017	-0.017	0.000	0.000	0.000	0.000
69	A	119	SER	0	-0.043	-0.016	13.923	0.020	0.020	0.000	0.000	0.000	0.000
70	A	120	GLY	0	0.048	0.030	10.340	-0.092	-0.092	0.000	0.000	0.000	0.000
71	A	121	LYS	1	0.908	0.957	7.740	0.423	0.423	0.000	0.000	0.000	0.000
72	A	122	VAL	0	0.060	0.037	8.481	-0.239	-0.239	0.000	0.000	0.000	0.000
73	A	123	ILE	0	-0.039	-0.009	6.554	0.127	0.127	0.000	0.000	0.000	0.000
74	A	124	LEU	0	0.020	0.018	10.241	-0.083	-0.083	0.000	0.000	0.000	0.000
75	A	125	ARG	1	0.725	0.797	9.046	-0.949	-0.949	0.000	0.000	0.000	0.000
76	A	126	VAL	0	0.048	0.029	15.129	-0.031	-0.031	0.000	0.000	0.000	0.000
77	A	127	THR	0	-0.034	0.022	18.341	-0.003	-0.003	0.000	0.000	0.000	0.000

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