FMO DATABASE

FMODB ID: MN66Z

Calculation Name: 1SMT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1SMT

Chain ID: A

ChEMBL ID:

UniProt ID: P30340

Base Structure: X-ray

Registration Date: 2023-09-20

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	98
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-663942.628754
FMO2-HF: Nuclear repulsion	625570.501754
FMO2-HF: Total energy	-38372.127001
FMO2-MP2: Total energy	-38485.289401

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:24:GLU)

Summations of interaction energy for fragment #1(A:24:GLU)

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.
6.843	8.582	-0.026	-0.813	-0.9	0.001

Interaction energy analysis for fragmet #1(A:24:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.912 / q_NPA : -0.966

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	26	GLN	0	-0.012	-0.004	3.817	-5.178	-3.439	-0.026	-0.813	-0.900	0.001
4	A	27	ALA	0	-0.012	0.006	6.701	-1.023	-1.023	0.000	0.000	0.000	0.000
5	A	28	ILE	0	0.010	0.001	10.240	0.337	0.337	0.000	0.000	0.000	0.000
6	A	29	ALA	0	0.029	0.015	12.897	-0.256	-0.256	0.000	0.000	0.000	0.000
7	A	30	PRO	0	0.037	0.010	14.779	-0.552	-0.552	0.000	0.000	0.000	0.000
8	A	31	GLU	-1	-0.849	-0.937	17.700	15.052	15.052	0.000	0.000	0.000	0.000
9	A	32	VAL	0	-0.019	-0.015	16.637	-0.578	-0.578	0.000	0.000	0.000	0.000
10	A	33	ALA	0	-0.012	-0.008	17.335	-0.410	-0.410	0.000	0.000	0.000	0.000
11	A	34	GLN	0	0.009	0.008	19.087	-0.304	-0.304	0.000	0.000	0.000	0.000
12	A	35	SER	0	0.019	0.005	22.312	-0.609	-0.609	0.000	0.000	0.000	0.000
13	A	36	LEU	0	-0.033	-0.007	19.088	-0.429	-0.429	0.000	0.000	0.000	0.000
14	A	37	ALA	0	0.001	-0.002	22.647	-0.392	-0.392	0.000	0.000	0.000	0.000
15	A	38	GLU	-1	-0.943	-0.980	24.430	9.959	9.959	0.000	0.000	0.000	0.000
16	A	39	PHE	0	-0.035	-0.011	25.236	-0.470	-0.470	0.000	0.000	0.000	0.000
17	A	40	PHE	0	0.019	-0.010	21.974	-0.340	-0.340	0.000	0.000	0.000	0.000
18	A	41	ALA	0	-0.004	0.010	27.529	-0.325	-0.325	0.000	0.000	0.000	0.000
19	A	42	VAL	0	-0.046	-0.016	30.311	-0.416	-0.416	0.000	0.000	0.000	0.000
20	A	43	LEU	0	-0.007	-0.013	28.339	-0.365	-0.365	0.000	0.000	0.000	0.000
21	A	44	ALA	0	-0.022	0.015	31.568	-0.139	-0.139	0.000	0.000	0.000	0.000
22	A	45	ASP	-1	-0.874	-0.955	33.256	7.528	7.528	0.000	0.000	0.000	0.000
23	A	46	PRO	0	0.043	0.004	36.886	0.017	0.017	0.000	0.000	0.000	0.000
24	A	47	ASN	0	-0.001	0.000	38.915	-0.086	-0.086	0.000	0.000	0.000	0.000
25	A	48	ARG	1	0.889	0.953	35.641	-8.273	-8.273	0.000	0.000	0.000	0.000
26	A	49	LEU	0	0.046	0.028	33.125	-0.010	-0.010	0.000	0.000	0.000	0.000
27	A	50	ARG	1	0.954	0.986	36.977	-6.867	-6.867	0.000	0.000	0.000	0.000
28	A	51	LEU	0	-0.002	0.006	40.172	-0.094	-0.094	0.000	0.000	0.000	0.000
29	A	52	LEU	0	-0.015	-0.016	33.538	-0.035	-0.035	0.000	0.000	0.000	0.000
30	A	53	SER	0	-0.040	-0.013	37.182	0.000	0.000	0.000	0.000	0.000	0.000
31	A	54	LEU	0	-0.028	-0.010	38.184	-0.072	-0.072	0.000	0.000	0.000	0.000
32	A	55	LEU	0	-0.017	-0.017	38.246	-0.007	-0.007	0.000	0.000	0.000	0.000
33	A	56	ALA	0	-0.020	0.000	35.184	0.083	0.083	0.000	0.000	0.000	0.000
34	A	57	ARG	1	0.898	0.947	36.650	-7.241	-7.241	0.000	0.000	0.000	0.000
35	A	58	SER	0	-0.006	-0.012	39.464	-0.127	-0.127	0.000	0.000	0.000	0.000
36	A	59	GLU	-1	-0.819	-0.853	41.366	7.106	7.106	0.000	0.000	0.000	0.000
37	A	60	LEU	0	0.006	-0.006	42.289	-0.167	-0.167	0.000	0.000	0.000	0.000
38	A	61	CYS	0	-0.016	0.006	45.200	0.100	0.100	0.000	0.000	0.000	0.000
39	A	62	VAL	0	0.032	-0.002	47.294	0.023	0.023	0.000	0.000	0.000	0.000
40	A	63	GLY	0	0.031	0.016	48.691	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	64	ASP	-1	-0.853	-0.926	48.172	6.128	6.128	0.000	0.000	0.000	0.000
42	A	65	LEU	0	-0.025	-0.021	43.350	0.023	0.023	0.000	0.000	0.000	0.000
43	A	66	ALA	0	-0.029	-0.017	47.278	0.024	0.024	0.000	0.000	0.000	0.000
44	A	67	GLN	0	0.018	0.002	50.091	-0.010	-0.010	0.000	0.000	0.000	0.000
45	A	68	ALA	0	-0.012	0.010	47.168	-0.037	-0.037	0.000	0.000	0.000	0.000
46	A	69	ILE	0	-0.065	-0.028	44.153	0.062	0.062	0.000	0.000	0.000	0.000
47	A	70	GLY	0	0.002	0.018	48.118	-0.027	-0.027	0.000	0.000	0.000	0.000
48	A	71	VAL	0	-0.047	-0.017	48.475	-0.059	-0.059	0.000	0.000	0.000	0.000
49	A	72	SER	0	0.036	0.004	51.741	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	73	GLU	-1	-0.842	-0.942	51.118	5.858	5.858	0.000	0.000	0.000	0.000
51	A	74	SER	0	-0.056	-0.028	50.538	0.152	0.152	0.000	0.000	0.000	0.000
52	A	75	ALA	0	0.035	0.013	49.188	0.095	0.095	0.000	0.000	0.000	0.000
53	A	76	VAL	0	0.036	0.021	45.702	0.159	0.159	0.000	0.000	0.000	0.000
54	A	77	SER	0	-0.008	-0.014	45.669	0.167	0.167	0.000	0.000	0.000	0.000
55	A	78	HIS	0	-0.004	0.009	45.975	0.208	0.208	0.000	0.000	0.000	0.000
56	A	79	GLN	0	0.023	0.006	42.408	0.253	0.253	0.000	0.000	0.000	0.000
57	A	80	LEU	0	0.029	0.013	41.309	0.200	0.200	0.000	0.000	0.000	0.000
58	A	81	ARG	1	0.880	0.950	41.171	-6.410	-6.410	0.000	0.000	0.000	0.000
59	A	82	SER	0	-0.021	-0.018	38.789	0.138	0.138	0.000	0.000	0.000	0.000
60	A	83	LEU	0	0.072	0.026	36.723	0.178	0.178	0.000	0.000	0.000	0.000
61	A	84	ARG	1	0.934	0.985	36.426	-7.137	-7.137	0.000	0.000	0.000	0.000
62	A	85	ASN	0	-0.036	-0.032	36.825	0.171	0.171	0.000	0.000	0.000	0.000
63	A	86	LEU	0	-0.036	0.002	33.116	0.144	0.144	0.000	0.000	0.000	0.000
64	A	87	ARG	1	0.934	0.969	29.894	-9.294	-9.294	0.000	0.000	0.000	0.000
65	A	88	LEU	0	0.066	0.040	30.966	0.196	0.196	0.000	0.000	0.000	0.000
66	A	89	VAL	0	-0.054	-0.014	33.616	-0.045	-0.045	0.000	0.000	0.000	0.000
67	A	90	SER	0	-0.008	-0.001	36.621	0.074	0.074	0.000	0.000	0.000	0.000
68	A	91	TYR	0	-0.052	-0.028	38.472	-0.124	-0.124	0.000	0.000	0.000	0.000
69	A	92	ARG	1	0.828	0.897	41.624	-6.942	-6.942	0.000	0.000	0.000	0.000
70	A	93	LYS	1	0.941	0.966	43.918	-6.568	-6.568	0.000	0.000	0.000	0.000
71	A	94	GLN	0	0.042	0.017	47.245	0.176	0.176	0.000	0.000	0.000	0.000
72	A	95	GLY	0	0.015	0.017	49.647	-0.098	-0.098	0.000	0.000	0.000	0.000
73	A	96	ARG	1	0.926	0.950	53.258	-5.360	-5.360	0.000	0.000	0.000	0.000
74	A	97	HIS	0	0.019	0.019	50.704	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	98	VAL	0	-0.026	-0.011	46.214	0.076	0.076	0.000	0.000	0.000	0.000
76	A	99	TYR	0	0.037	0.013	44.708	-0.087	-0.087	0.000	0.000	0.000	0.000
77	A	100	TYR	0	-0.006	-0.026	41.217	0.117	0.117	0.000	0.000	0.000	0.000
78	A	101	GLN	0	0.065	0.024	37.878	-0.011	-0.011	0.000	0.000	0.000	0.000
79	A	102	LEU	0	0.037	0.022	33.362	0.012	0.012	0.000	0.000	0.000	0.000
80	A	103	GLN	0	-0.035	-0.011	31.493	-0.203	-0.203	0.000	0.000	0.000	0.000
81	A	104	ASP	-1	-0.844	-0.937	28.623	10.460	10.460	0.000	0.000	0.000	0.000
82	A	105	HIS	0	0.047	0.006	27.709	-0.298	-0.298	0.000	0.000	0.000	0.000
83	A	106	HIS	0	0.019	0.021	23.632	0.073	0.073	0.000	0.000	0.000	0.000
84	A	107	ILE	0	-0.010	0.003	26.739	0.054	0.054	0.000	0.000	0.000	0.000
85	A	108	VAL	0	0.003	-0.002	29.262	-0.113	-0.113	0.000	0.000	0.000	0.000
86	A	109	ALA	0	-0.002	-0.009	25.951	-0.079	-0.079	0.000	0.000	0.000	0.000
87	A	110	LEU	0	-0.007	0.003	25.287	0.093	0.093	0.000	0.000	0.000	0.000
88	A	111	TYR	0	-0.016	-0.011	26.524	-0.125	-0.125	0.000	0.000	0.000	0.000
89	A	112	GLN	0	-0.005	-0.017	29.611	-0.152	-0.152	0.000	0.000	0.000	0.000
90	A	113	ASN	0	0.027	0.008	25.127	0.025	0.025	0.000	0.000	0.000	0.000
91	A	114	ALA	0	-0.038	-0.002	27.238	0.086	0.086	0.000	0.000	0.000	0.000
92	A	115	LEU	0	-0.048	-0.029	28.092	-0.140	-0.140	0.000	0.000	0.000	0.000
93	A	116	ASP	-1	-0.856	-0.929	28.640	9.435	9.435	0.000	0.000	0.000	0.000
94	A	117	HIS	0	-0.012	-0.008	25.482	0.069	0.069	0.000	0.000	0.000	0.000
95	A	118	LEU	0	-0.060	-0.043	28.122	-0.147	-0.147	0.000	0.000	0.000	0.000
96	A	119	GLN	0	-0.091	-0.044	31.165	-0.100	-0.100	0.000	0.000	0.000	0.000
97	A	120	GLU	-1	-0.967	-0.965	28.314	9.969	9.969	0.000	0.000	0.000	0.000
98	A	121	CYS	0	-0.101	-0.030	28.300	0.102	0.102	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:24:GLU)