FMO DATABASE

FMODB ID: 17NVZ

Calculation Name: 1SFP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1SFP

Chain ID: A

ChEMBL ID:

UniProt ID: P29392

Base Structure: X-ray

Registration Date: 2023-06-22

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	109
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-894142.434153
FMO2-HF: Nuclear repulsion	849364.315729
FMO2-HF: Total energy	-44778.118423
FMO2-MP2: Total energy	-44905.23114

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:4:LEU)

Summations of interaction energy for fragment #1(A:4:LEU)

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.
-6.548	-0.363	4.913	-3.037	-8.06	-0.02

Interaction energy analysis for fragmet #1(A:4:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / q_NPA : -0.014

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	6	ARG	1	0.859	0.896	3.483	-0.106	1.319	0.026	-0.644	-0.806	0.000
4	A	7	ASN	0	-0.020	-0.013	5.724	0.534	0.534	0.000	0.000	0.000	0.000
5	A	8	THR	0	0.081	0.037	8.891	-0.013	-0.013	0.000	0.000	0.000	0.000
6	A	9	ASN	0	0.005	0.004	12.156	0.093	0.093	0.000	0.000	0.000	0.000
7	A	10	CYS	0	-0.135	-0.043	14.433	-0.012	-0.012	0.000	0.000	0.000	0.000
8	A	11	GLY	0	0.009	-0.013	15.349	0.045	0.045	0.000	0.000	0.000	0.000
9	A	12	GLY	0	-0.026	-0.013	14.977	-0.003	-0.003	0.000	0.000	0.000	0.000
10	A	13	ILE	0	-0.022	-0.006	15.255	-0.015	-0.015	0.000	0.000	0.000	0.000
11	A	14	LEU	0	-0.049	-0.020	8.999	0.017	0.017	0.000	0.000	0.000	0.000
12	A	15	LYS	1	0.920	0.931	10.992	0.194	0.194	0.000	0.000	0.000	0.000
13	A	16	GLU	-1	-0.913	-0.932	5.792	-0.225	-0.225	0.000	0.000	0.000	0.000
14	A	17	GLU	-1	-0.777	-0.890	6.814	-0.244	-0.244	0.000	0.000	0.000	0.000
15	A	18	SER	0	0.016	0.007	2.683	-1.468	-0.064	0.651	-0.734	-1.321	-0.003
16	A	19	GLY	0	0.006	0.003	2.180	-1.682	-0.456	2.260	-1.459	-2.027	-0.010
17	A	20	VAL	0	-0.030	-0.006	2.456	-0.690	-0.154	1.756	0.136	-2.427	-0.007
18	A	21	ILE	0	-0.009	0.005	4.777	0.008	0.031	-0.001	-0.009	-0.014	0.000
19	A	22	ALA	0	0.004	-0.008	8.514	0.027	0.027	0.000	0.000	0.000	0.000
20	A	23	THR	0	-0.015	-0.015	10.599	0.014	0.014	0.000	0.000	0.000	0.000
21	A	24	TYR	0	-0.023	0.013	14.279	0.016	0.016	0.000	0.000	0.000	0.000
22	A	25	TYR	0	0.004	-0.010	15.751	0.013	0.013	0.000	0.000	0.000	0.000
23	A	26	GLY	0	-0.010	-0.001	19.226	0.023	0.023	0.000	0.000	0.000	0.000
24	A	27	PRO	0	0.016	-0.007	21.729	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	28	LYS	1	0.861	0.933	20.132	0.198	0.198	0.000	0.000	0.000	0.000
26	A	29	THR	0	0.065	0.033	22.936	-0.011	-0.011	0.000	0.000	0.000	0.000
27	A	30	ASN	0	0.009	0.010	22.162	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	32	VAL	0	0.046	0.009	17.717	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	33	TRP	0	0.026	0.013	12.512	0.016	0.016	0.000	0.000	0.000	0.000
30	A	34	THR	0	-0.013	-0.013	14.346	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	35	ILE	0	0.010	0.014	9.719	0.006	0.006	0.000	0.000	0.000	0.000
32	A	36	GLN	0	0.018	0.008	12.743	0.063	0.063	0.000	0.000	0.000	0.000
33	A	37	MET	0	-0.007	0.018	8.267	0.014	0.014	0.000	0.000	0.000	0.000
34	A	38	PRO	0	0.013	0.000	13.289	0.026	0.026	0.000	0.000	0.000	0.000
35	A	39	PRO	0	0.007	-0.013	16.484	-0.012	-0.012	0.000	0.000	0.000	0.000
36	A	40	GLU	-1	-0.938	-0.949	19.362	-0.070	-0.070	0.000	0.000	0.000	0.000
37	A	41	TYR	0	-0.033	0.006	13.725	0.006	0.006	0.000	0.000	0.000	0.000
38	A	42	HIS	0	-0.052	-0.033	14.819	0.021	0.021	0.000	0.000	0.000	0.000
39	A	43	VAL	0	-0.004	-0.007	10.446	-0.033	-0.033	0.000	0.000	0.000	0.000
40	A	44	ARG	1	0.771	0.862	9.109	0.366	0.366	0.000	0.000	0.000	0.000
41	A	45	VAL	0	-0.010	-0.017	8.580	-0.126	-0.126	0.000	0.000	0.000	0.000
42	A	46	SER	0	-0.019	-0.029	7.681	0.062	0.062	0.000	0.000	0.000	0.000
43	A	47	ILE	0	-0.042	-0.025	8.365	-0.069	-0.069	0.000	0.000	0.000	0.000
44	A	48	GLN	0	0.014	0.007	9.045	0.072	0.072	0.000	0.000	0.000	0.000
45	A	49	TYR	0	0.028	0.002	11.401	0.044	0.044	0.000	0.000	0.000	0.000
46	A	50	LEU	0	-0.035	-0.005	13.245	-0.041	-0.041	0.000	0.000	0.000	0.000
47	A	51	GLN	0	-0.012	-0.020	15.942	0.018	0.018	0.000	0.000	0.000	0.000
48	A	52	LEU	0	-0.036	0.007	17.269	0.000	0.000	0.000	0.000	0.000	0.000
49	A	53	ASN	0	0.047	0.011	20.463	0.018	0.018	0.000	0.000	0.000	0.000
50	A	54	CYS	0	0.006	-0.030	20.195	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	55	ASN	0	-0.054	-0.019	25.177	0.007	0.007	0.000	0.000	0.000	0.000
52	A	56	LYS	1	0.945	0.973	26.545	0.111	0.111	0.000	0.000	0.000	0.000
53	A	57	GLU	-1	-0.730	-0.792	20.933	-0.205	-0.205	0.000	0.000	0.000	0.000
54	A	58	SER	0	-0.062	-0.023	21.334	0.007	0.007	0.000	0.000	0.000	0.000
55	A	59	LEU	0	0.036	0.014	13.757	-0.011	-0.011	0.000	0.000	0.000	0.000
56	A	60	GLU	-1	-0.828	-0.893	17.650	-0.163	-0.163	0.000	0.000	0.000	0.000
57	A	61	ILE	0	0.029	0.022	13.746	-0.030	-0.030	0.000	0.000	0.000	0.000
58	A	62	ILE	0	-0.036	-0.021	17.209	0.029	0.029	0.000	0.000	0.000	0.000
59	A	63	ASP	-1	-0.738	-0.836	17.772	-0.220	-0.220	0.000	0.000	0.000	0.000
60	A	64	GLY	0	0.052	0.022	18.584	0.020	0.020	0.000	0.000	0.000	0.000
61	A	65	LEU	0	0.000	0.020	18.896	-0.023	-0.023	0.000	0.000	0.000	0.000
62	A	66	PRO	0	-0.001	-0.008	20.349	0.006	0.006	0.000	0.000	0.000	0.000
63	A	67	GLY	0	0.001	0.009	22.704	0.012	0.012	0.000	0.000	0.000	0.000
64	A	68	SER	0	-0.043	-0.018	21.972	0.013	0.013	0.000	0.000	0.000	0.000
65	A	69	PRO	0	0.019	0.000	23.442	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	70	VAL	0	-0.014	-0.001	21.596	-0.015	-0.015	0.000	0.000	0.000	0.000
67	A	71	LEU	0	0.002	0.007	17.163	0.010	0.010	0.000	0.000	0.000	0.000
68	A	72	GLY	0	0.012	0.002	20.154	0.006	0.006	0.000	0.000	0.000	0.000
69	A	73	LYS	1	0.843	0.916	20.009	0.160	0.160	0.000	0.000	0.000	0.000
70	A	74	ILE	0	0.002	0.004	15.879	0.014	0.014	0.000	0.000	0.000	0.000
71	A	76	GLU	-1	-0.854	-0.916	19.861	-0.157	-0.157	0.000	0.000	0.000	0.000
72	A	77	GLY	0	0.026	0.012	18.940	0.009	0.009	0.000	0.000	0.000	0.000
73	A	78	SER	0	-0.042	-0.031	15.522	-0.012	-0.012	0.000	0.000	0.000	0.000
74	A	79	LEU	0	-0.028	-0.018	13.774	0.010	0.010	0.000	0.000	0.000	0.000
75	A	80	MET	0	-0.016	0.019	14.267	0.015	0.015	0.000	0.000	0.000	0.000
76	A	81	ASP	-1	-0.798	-0.881	11.114	-0.407	-0.407	0.000	0.000	0.000	0.000
77	A	82	TYR	0	0.002	0.005	12.544	0.040	0.040	0.000	0.000	0.000	0.000
78	A	83	ARG	1	0.844	0.921	12.777	0.155	0.155	0.000	0.000	0.000	0.000
79	A	84	SER	0	0.007	-0.010	14.907	0.012	0.012	0.000	0.000	0.000	0.000
80	A	85	SER	0	-0.049	-0.062	16.888	0.011	0.011	0.000	0.000	0.000	0.000
81	A	86	GLY	0	0.033	0.013	19.100	0.018	0.018	0.000	0.000	0.000	0.000
82	A	87	SER	0	-0.005	0.007	16.295	-0.028	-0.028	0.000	0.000	0.000	0.000
83	A	88	ILE	0	-0.082	-0.050	15.782	-0.017	-0.017	0.000	0.000	0.000	0.000
84	A	89	MET	0	0.005	0.023	13.183	0.026	0.026	0.000	0.000	0.000	0.000
85	A	90	THR	0	-0.046	-0.033	14.464	-0.032	-0.032	0.000	0.000	0.000	0.000
86	A	91	VAL	0	0.020	0.026	11.476	0.017	0.017	0.000	0.000	0.000	0.000
87	A	92	LYS	1	0.849	0.903	14.869	0.197	0.197	0.000	0.000	0.000	0.000
88	A	93	TYR	0	-0.012	-0.028	16.698	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	94	ILE	0	-0.027	-0.021	18.556	0.012	0.012	0.000	0.000	0.000	0.000
90	A	95	ARG	1	0.817	0.916	21.941	0.157	0.157	0.000	0.000	0.000	0.000
91	A	96	GLU	-1	-0.844	-0.927	24.395	-0.108	-0.108	0.000	0.000	0.000	0.000
92	A	97	PRO	0	-0.034	-0.034	27.073	-0.006	-0.006	0.000	0.000	0.000	0.000
93	A	98	GLU	-1	-0.944	-0.971	28.322	-0.089	-0.089	0.000	0.000	0.000	0.000
94	A	99	HIS	0	-0.047	-0.019	23.400	0.013	0.013	0.000	0.000	0.000	0.000
95	A	100	PRO	0	-0.025	-0.008	23.731	-0.010	-0.010	0.000	0.000	0.000	0.000
96	A	101	ALA	0	0.010	-0.001	19.106	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	102	SER	0	0.006	-0.036	19.202	0.003	0.003	0.000	0.000	0.000	0.000
98	A	103	PHE	0	-0.044	-0.013	10.970	-0.020	-0.020	0.000	0.000	0.000	0.000
99	A	104	TYR	0	-0.001	-0.007	12.728	0.010	0.010	0.000	0.000	0.000	0.000
100	A	105	GLU	-1	-0.822	-0.895	6.546	-0.948	-0.948	0.000	0.000	0.000	0.000
101	A	106	VAL	0	-0.024	-0.012	8.440	0.079	0.079	0.000	0.000	0.000	0.000
102	A	107	LEU	0	0.022	0.020	2.875	-0.710	-0.190	0.118	-0.106	-0.533	0.001
103	A	108	TYR	0	-0.019	-0.014	4.099	0.074	0.222	-0.001	-0.014	-0.132	0.000
104	A	109	PHE	0	0.019	-0.003	3.154	-1.535	-0.632	0.104	-0.207	-0.800	-0.001
105	A	110	GLN	0	-0.051	-0.023	6.820	0.148	0.148	0.000	0.000	0.000	0.000
106	A	111	ASP	-1	-0.834	-0.873	9.366	-0.272	-0.272	0.000	0.000	0.000	0.000
107	A	112	PRO	0	0.002	-0.010	11.972	0.025	0.025	0.000	0.000	0.000	0.000
108	A	113	GLN	0	0.004	-0.034	5.507	-0.078	-0.078	0.000	0.000	0.000	0.000
109	A	114	ALA	0	-0.057	-0.032	9.790	0.055	0.055	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:LEU)