FMO DATABASE

FMODB ID: Z6KMN

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	OptHSide
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	-463293.083095
FMO2-HF: Nuclear repulsion	433151.068592
FMO2-HF: Total energy	-30142.014503
FMO2-MP2: Total energy	-30229.959563

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.
-1.29	-0.312	-0.009	-0.441	-0.529	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 : 0.032 / 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

Sort

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	0.032	0.029	3.810	-0.901	0.077	-0.009	-0.441	-0.529	0.001
4	A	22	GLU	-1	-0.793	-0.894	6.301	0.078	0.078	0.000	0.000	0.000	0.000
5	A	23	VAL	0	0.005	0.007	8.983	-0.014	-0.014	0.000	0.000	0.000	0.000
6	A	24	LYS	1	0.893	0.947	10.935	0.441	0.441	0.000	0.000	0.000	0.000
7	A	25	VAL	0	0.037	0.022	15.030	-0.007	-0.007	0.000	0.000	0.000	0.000
8	A	26	ALA	0	0.032	0.033	18.697	0.013	0.013	0.000	0.000	0.000	0.000
9	A	27	SER	0	0.039	-0.017	21.897	0.008	0.008	0.000	0.000	0.000	0.000
10	A	28	SER	0	-0.114	-0.060	23.624	0.000	0.000	0.000	0.000	0.000	0.000
11	A	29	GLU	-1	-0.865	-0.911	23.323	-0.086	-0.086	0.000	0.000	0.000	0.000
12	A	30	ASP	-1	-0.802	-0.898	23.577	-0.056	-0.056	0.000	0.000	0.000	0.000
13	A	31	VAL	0	-0.029	-0.021	17.615	-0.016	-0.016	0.000	0.000	0.000	0.000
14	A	32	ASP	-1	-0.824	-0.904	20.030	-0.080	-0.080	0.000	0.000	0.000	0.000
15	A	33	LEU	0	-0.007	-0.007	13.861	-0.036	-0.036	0.000	0.000	0.000	0.000
16	A	34	PRO	0	0.036	0.025	12.627	0.027	0.027	0.000	0.000	0.000	0.000
17	A	35	CYS	0	0.002	0.031	13.555	-0.029	-0.029	0.000	0.000	0.000	0.000
18	A	36	THR	0	-0.035	-0.038	9.346	0.023	0.023	0.000	0.000	0.000	0.000
19	A	37	ALA	0	0.010	0.004	11.013	-0.024	-0.024	0.000	0.000	0.000	0.000
20	A	38	PRO	0	-0.015	-0.007	11.897	-0.031	-0.031	0.000	0.000	0.000	0.000
21	A	39	TRP	0	-0.049	-0.025	14.046	0.019	0.019	0.000	0.000	0.000	0.000
22	A	40	ASP	-1	-0.795	-0.894	17.737	-0.070	-0.070	0.000	0.000	0.000	0.000
23	A	41	PRO	0	-0.035	-0.032	20.251	0.006	0.006	0.000	0.000	0.000	0.000
24	A	42	GLN	0	-0.013	-0.007	22.639	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	43	VAL	0	-0.026	-0.001	23.666	0.009	0.009	0.000	0.000	0.000	0.000
26	A	44	PRO	0	-0.045	-0.008	24.354	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	45	TYR	0	0.042	0.001	21.286	0.004	0.004	0.000	0.000	0.000	0.000
28	A	46	THR	0	-0.006	0.007	24.306	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	47	VAL	0	0.004	-0.005	19.590	0.005	0.005	0.000	0.000	0.000	0.000
30	A	48	SER	0	-0.036	-0.006	20.717	0.009	0.009	0.000	0.000	0.000	0.000
31	A	49	TRP	0	-0.018	-0.019	14.322	0.019	0.019	0.000	0.000	0.000	0.000
32	A	50	VAL	0	-0.007	0.001	16.814	0.006	0.006	0.000	0.000	0.000	0.000
33	A	51	LYS	1	0.891	0.949	16.284	-0.088	-0.088	0.000	0.000	0.000	0.000
34	A	52	LEU	0	-0.076	-0.047	11.834	0.017	0.017	0.000	0.000	0.000	0.000
35	A	53	LEU	0	-0.010	-0.007	15.092	0.008	0.008	0.000	0.000	0.000	0.000
36	A	54	GLU	-1	-0.947	-0.958	16.611	0.218	0.218	0.000	0.000	0.000	0.000
37	A	87	GLU	-1	-0.940	-0.983	21.384	-0.158	-0.158	0.000	0.000	0.000	0.000
38	A	88	ARG	1	0.930	0.970	13.860	0.277	0.277	0.000	0.000	0.000	0.000
39	A	89	PRO	0	-0.012	-0.004	20.704	0.005	0.005	0.000	0.000	0.000	0.000
40	A	90	TYR	0	0.030	-0.008	18.962	-0.009	-0.009	0.000	0.000	0.000	0.000
41	A	91	SER	0	0.005	0.009	18.303	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	92	LEU	0	-0.025	0.001	18.377	0.020	0.020	0.000	0.000	0.000	0.000
43	A	93	LYS	1	0.841	0.924	20.046	0.072	0.072	0.000	0.000	0.000	0.000
44	A	94	ILE	0	-0.050	-0.025	18.688	0.017	0.017	0.000	0.000	0.000	0.000
45	A	95	ARG	1	0.903	0.929	22.715	0.037	0.037	0.000	0.000	0.000	0.000
46	A	96	ASN	0	-0.045	-0.015	25.572	0.004	0.004	0.000	0.000	0.000	0.000
47	A	97	THR	0	-0.022	-0.008	20.517	0.008	0.008	0.000	0.000	0.000	0.000
48	A	98	THR	0	0.057	0.023	22.614	0.003	0.003	0.000	0.000	0.000	0.000
49	A	99	SER	0	0.061	0.021	20.443	0.001	0.001	0.000	0.000	0.000	0.000
50	A	100	SER	0	0.048	0.017	19.629	0.008	0.008	0.000	0.000	0.000	0.000
51	A	101	ASN	0	-0.002	0.004	19.563	0.013	0.013	0.000	0.000	0.000	0.000
52	A	102	SER	0	0.041	0.044	15.318	-0.011	-0.011	0.000	0.000	0.000	0.000
53	A	103	GLY	0	-0.002	0.005	13.449	0.032	0.032	0.000	0.000	0.000	0.000
54	A	104	THR	0	0.006	0.001	9.341	-0.083	-0.083	0.000	0.000	0.000	0.000
55	A	105	TYR	0	-0.019	-0.026	11.743	0.018	0.018	0.000	0.000	0.000	0.000
56	A	106	ARG	1	0.924	0.960	12.095	-0.214	-0.214	0.000	0.000	0.000	0.000
57	A	108	THR	0	-0.019	-0.046	15.127	0.038	0.038	0.000	0.000	0.000	0.000
58	A	109	LEU	0	0.007	0.007	17.480	-0.010	-0.010	0.000	0.000	0.000	0.000
59	A	110	GLN	0	0.032	0.005	19.803	0.015	0.015	0.000	0.000	0.000	0.000
60	A	111	ASP	-1	-0.813	-0.910	22.958	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	112	PRO	0	0.006	0.002	24.895	0.006	0.006	0.000	0.000	0.000	0.000
62	A	113	ASP	-1	-0.804	-0.877	27.883	0.026	0.026	0.000	0.000	0.000	0.000
63	A	114	GLY	0	-0.010	0.007	27.250	0.003	0.003	0.000	0.000	0.000	0.000
64	A	115	GLN	0	-0.112	-0.062	27.032	0.011	0.011	0.000	0.000	0.000	0.000
65	A	116	ARG	1	0.776	0.863	22.051	-0.016	-0.016	0.000	0.000	0.000	0.000
66	A	117	ASN	0	-0.022	-0.006	19.171	0.005	0.005	0.000	0.000	0.000	0.000
67	A	118	LEU	0	0.040	0.032	15.767	0.011	0.011	0.000	0.000	0.000	0.000
68	A	119	SER	0	-0.058	-0.028	13.915	0.015	0.015	0.000	0.000	0.000	0.000
69	A	120	GLY	0	0.044	0.027	10.294	0.005	0.005	0.000	0.000	0.000	0.000
70	A	121	LYS	1	0.923	0.956	8.026	-0.909	-0.909	0.000	0.000	0.000	0.000
71	A	122	VAL	0	0.042	0.031	8.481	-0.253	-0.253	0.000	0.000	0.000	0.000
72	A	123	ILE	0	-0.026	-0.006	5.905	0.215	0.215	0.000	0.000	0.000	0.000
73	A	124	LEU	0	0.016	0.018	9.751	-0.124	-0.124	0.000	0.000	0.000	0.000
74	A	125	ARG	1	0.815	0.864	8.155	0.191	0.191	0.000	0.000	0.000	0.000
75	A	126	VAL	0	0.025	0.018	14.345	-0.028	-0.028	0.000	0.000	0.000	0.000
76	A	127	THR	0	-0.019	0.001	17.312	0.011	0.011	0.000	0.000	0.000	0.000

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