FMO DATABASE

FMODB ID: 17VNZ

Calculation Name: 1SMX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1SMX

Chain ID: A

ChEMBL ID:

UniProt ID: P21513

Base Structure: X-ray

Registration Date: 2023-06-26

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	87
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-569642.903474
FMO2-HF: Nuclear repulsion	536601.983557
FMO2-HF: Total energy	-33040.919917
FMO2-MP2: Total energy	-33140.019229

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:39:ALA)

Summations of interaction energy for fragment #1(A:39: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.
-1.916	0.566	-0.007	-1.166	-1.31	-0.002

Interaction energy analysis for fragmet #1(A:39:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : -0.019

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	41	ILE	0	0.012	0.010	3.235	-0.505	1.885	-0.006	-1.152	-1.233	-0.002
4	A	42	TYR	0	0.003	0.011	4.823	-0.523	-0.431	-0.001	-0.014	-0.077	0.000
5	A	43	LYS	1	0.953	0.977	7.586	0.550	0.550	0.000	0.000	0.000	0.000
6	A	44	GLY	0	0.024	0.009	10.918	-0.052	-0.052	0.000	0.000	0.000	0.000
7	A	45	LYS	1	0.896	0.944	13.404	0.344	0.344	0.000	0.000	0.000	0.000
8	A	46	ILE	0	-0.016	-0.012	16.946	-0.013	-0.013	0.000	0.000	0.000	0.000
9	A	47	THR	0	-0.036	-0.021	19.340	0.024	0.024	0.000	0.000	0.000	0.000
10	A	48	ARG	1	0.946	0.962	21.932	0.181	0.181	0.000	0.000	0.000	0.000
11	A	49	ILE	0	-0.053	-0.012	23.676	-0.008	-0.008	0.000	0.000	0.000	0.000
12	A	50	GLU	-1	-0.845	-0.924	25.759	-0.136	-0.136	0.000	0.000	0.000	0.000
13	A	51	PRO	0	0.008	-0.014	27.899	0.002	0.002	0.000	0.000	0.000	0.000
14	A	52	SER	0	-0.043	-0.014	30.080	0.003	0.003	0.000	0.000	0.000	0.000
15	A	53	LEU	0	0.000	0.000	26.973	0.004	0.004	0.000	0.000	0.000	0.000
16	A	54	GLU	-1	-0.975	-0.976	26.956	-0.082	-0.082	0.000	0.000	0.000	0.000
17	A	55	ALA	0	0.010	0.002	22.903	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	56	ALA	0	0.011	0.003	20.981	0.012	0.012	0.000	0.000	0.000	0.000
19	A	57	PHE	0	-0.026	-0.007	20.083	-0.014	-0.014	0.000	0.000	0.000	0.000
20	A	58	VAL	0	-0.004	-0.002	14.650	0.015	0.015	0.000	0.000	0.000	0.000
21	A	59	ASP	-1	-0.850	-0.917	15.085	-0.561	-0.561	0.000	0.000	0.000	0.000
22	A	60	TYR	0	-0.014	-0.033	9.277	0.048	0.048	0.000	0.000	0.000	0.000
23	A	61	GLY	0	0.016	0.015	10.105	-0.192	-0.192	0.000	0.000	0.000	0.000
24	A	62	ALA	0	-0.033	0.004	11.321	-0.034	-0.034	0.000	0.000	0.000	0.000
25	A	63	GLU	-1	-0.906	-0.959	12.634	-0.380	-0.380	0.000	0.000	0.000	0.000
26	A	64	ARG	1	0.818	0.923	15.858	0.428	0.428	0.000	0.000	0.000	0.000
27	A	65	HIS	0	0.034	0.016	15.421	-0.040	-0.040	0.000	0.000	0.000	0.000
28	A	66	GLY	0	0.015	0.001	15.238	0.012	0.012	0.000	0.000	0.000	0.000
29	A	67	PHE	0	-0.071	-0.037	16.163	0.050	0.050	0.000	0.000	0.000	0.000
30	A	68	LEU	0	0.039	0.022	16.103	-0.015	-0.015	0.000	0.000	0.000	0.000
31	A	69	PRO	0	0.001	-0.008	18.670	0.028	0.028	0.000	0.000	0.000	0.000
32	A	70	LEU	0	0.076	0.020	20.911	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	71	LYS	1	0.887	0.933	21.843	0.104	0.104	0.000	0.000	0.000	0.000
34	A	72	GLU	-1	-0.861	-0.904	17.511	-0.087	-0.087	0.000	0.000	0.000	0.000
35	A	73	ILE	0	-0.028	0.023	17.839	-0.025	-0.025	0.000	0.000	0.000	0.000
36	A	74	ALA	0	0.026	0.023	18.154	0.022	0.022	0.000	0.000	0.000	0.000
37	A	75	ARG	1	0.963	0.948	20.058	0.037	0.037	0.000	0.000	0.000	0.000
38	A	76	GLU	-1	-0.875	-0.929	18.214	-0.049	-0.049	0.000	0.000	0.000	0.000
39	A	77	TYR	0	-0.009	-0.010	14.915	-0.021	-0.021	0.000	0.000	0.000	0.000
40	A	78	PHE	0	-0.089	-0.039	21.619	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	79	PRO	0	-0.008	0.007	25.256	0.006	0.006	0.000	0.000	0.000	0.000
42	A	80	ALA	0	0.007	0.003	27.818	0.006	0.006	0.000	0.000	0.000	0.000
43	A	81	ASN	0	-0.025	-0.007	29.467	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	82	TYR	0	-0.012	-0.025	29.067	0.004	0.004	0.000	0.000	0.000	0.000
45	A	83	SER	0	0.006	0.001	32.587	0.006	0.006	0.000	0.000	0.000	0.000
46	A	84	ALA	0	-0.002	0.002	33.142	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	85	HIS	0	-0.013	-0.004	33.885	0.000	0.000	0.000	0.000	0.000	0.000
48	A	86	GLY	0	0.001	0.001	34.363	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	87	ARG	1	0.935	0.962	29.171	0.059	0.059	0.000	0.000	0.000	0.000
50	A	88	PRO	0	0.006	0.019	28.663	0.002	0.002	0.000	0.000	0.000	0.000
51	A	89	ASN	0	0.099	0.042	30.214	-0.011	-0.011	0.000	0.000	0.000	0.000
52	A	90	ILE	0	0.044	0.026	23.071	0.001	0.001	0.000	0.000	0.000	0.000
53	A	91	LYS	1	0.926	0.949	26.754	0.121	0.121	0.000	0.000	0.000	0.000
54	A	92	ASP	-1	-0.917	-0.933	29.119	-0.080	-0.080	0.000	0.000	0.000	0.000
55	A	93	VAL	0	-0.086	-0.037	23.687	0.007	0.007	0.000	0.000	0.000	0.000
56	A	94	LEU	0	0.024	0.015	20.722	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	95	ARG	1	0.949	0.967	23.685	0.124	0.124	0.000	0.000	0.000	0.000
58	A	96	GLU	-1	-0.921	-0.971	23.224	-0.185	-0.185	0.000	0.000	0.000	0.000
59	A	97	GLY	0	-0.035	-0.010	21.761	0.013	0.013	0.000	0.000	0.000	0.000
60	A	98	GLN	0	0.046	0.023	19.772	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	99	GLU	-1	-0.955	-0.981	15.321	-0.340	-0.340	0.000	0.000	0.000	0.000
62	A	100	VAL	0	-0.027	-0.009	14.732	0.044	0.044	0.000	0.000	0.000	0.000
63	A	101	ILE	0	-0.009	-0.001	9.739	-0.074	-0.074	0.000	0.000	0.000	0.000
64	A	102	VAL	0	-0.020	-0.014	10.158	0.074	0.074	0.000	0.000	0.000	0.000
65	A	103	GLN	0	0.064	0.033	8.006	-0.189	-0.189	0.000	0.000	0.000	0.000
66	A	104	ILE	0	-0.017	-0.017	7.500	0.224	0.224	0.000	0.000	0.000	0.000
67	A	105	ASP	-1	-0.932	-0.956	9.976	-0.014	-0.014	0.000	0.000	0.000	0.000
68	A	106	LYS	1	0.884	0.929	12.790	0.177	0.177	0.000	0.000	0.000	0.000
69	A	107	GLU	-1	-0.880	-0.950	8.132	-0.988	-0.988	0.000	0.000	0.000	0.000
70	A	108	GLU	-1	-0.905	-0.955	12.142	-0.493	-0.493	0.000	0.000	0.000	0.000
71	A	109	ARG	1	0.935	0.973	14.390	0.202	0.202	0.000	0.000	0.000	0.000
72	A	110	GLY	0	0.003	0.004	17.247	0.025	0.025	0.000	0.000	0.000	0.000
73	A	111	ASN	0	0.004	-0.011	19.840	-0.034	-0.034	0.000	0.000	0.000	0.000
74	A	112	LYS	1	0.914	0.971	19.383	0.204	0.204	0.000	0.000	0.000	0.000
75	A	113	GLY	0	0.091	0.037	16.897	-0.027	-0.027	0.000	0.000	0.000	0.000
76	A	114	ALA	0	0.010	0.018	12.540	0.048	0.048	0.000	0.000	0.000	0.000
77	A	115	ALA	0	-0.050	-0.023	14.475	0.036	0.036	0.000	0.000	0.000	0.000
78	A	116	LEU	0	0.011	0.000	11.749	-0.046	-0.046	0.000	0.000	0.000	0.000
79	A	117	THR	0	0.009	-0.019	12.806	0.080	0.080	0.000	0.000	0.000	0.000
80	A	118	THR	0	-0.030	-0.040	12.806	-0.063	-0.063	0.000	0.000	0.000	0.000
81	A	119	PHE	0	-0.033	-0.001	14.244	0.028	0.028	0.000	0.000	0.000	0.000
82	A	120	ILE	0	-0.022	0.001	8.746	-0.010	-0.010	0.000	0.000	0.000	0.000
83	A	121	SER	0	-0.023	-0.018	9.048	0.070	0.070	0.000	0.000	0.000	0.000
84	A	122	LEU	0	0.012	0.007	9.115	0.113	0.113	0.000	0.000	0.000	0.000
85	A	123	ALA	0	0.014	0.009	10.958	-0.058	-0.058	0.000	0.000	0.000	0.000
86	A	124	GLY	0	-0.013	-0.011	12.922	-0.022	-0.022	0.000	0.000	0.000	0.000
87	A	125	SER	0	-0.032	-0.007	14.627	-0.053	-0.053	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:39:ALA)