FMO DATABASE

FMODB ID: R98K8

Calculation Name: 1SPP-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1SPP

Chain ID: B

ChEMBL ID:

UniProt ID: P35495

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	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	110
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-876726.98791
FMO2-HF: Nuclear repulsion	832914.633539
FMO2-HF: Total energy	-43812.354371
FMO2-MP2: Total energy	-43936.559994

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(B:1:ALA)

Summations of interaction energy for fragment #1(B:1: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.
-7.146	-1.473	3.891	-4.052	-5.511	-0.014

Interaction energy analysis for fragmet #1(B:1:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.074 / q_NPA : 0.036

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	B	3	ILE	0	0.038	0.022	3.427	-2.082	0.972	0.007	-1.512	-1.549	0.007
4	B	4	ASN	0	-0.060	-0.049	5.800	0.495	0.495	0.000	0.000	0.000	0.000
5	B	5	GLY	0	0.068	0.014	9.125	0.012	0.012	0.000	0.000	0.000	0.000
6	B	6	PRO	0	-0.038	-0.029	11.659	0.001	0.001	0.000	0.000	0.000	0.000
7	B	7	ASP	-1	-0.804	-0.885	10.513	-0.549	-0.549	0.000	0.000	0.000	0.000
8	B	8	GLU	-1	-0.821	-0.907	8.608	-1.219	-1.219	0.000	0.000	0.000	0.000
9	B	9	CYS	0	-0.144	-0.029	11.652	-0.012	-0.012	0.000	0.000	0.000	0.000
10	B	10	GLY	0	-0.022	-0.019	15.042	0.035	0.035	0.000	0.000	0.000	0.000
11	B	11	ARG	1	0.857	0.942	10.775	0.855	0.855	0.000	0.000	0.000	0.000
12	B	12	VAL	0	-0.006	-0.018	11.950	-0.021	-0.021	0.000	0.000	0.000	0.000
13	B	13	ILE	0	-0.027	-0.008	5.685	-0.024	-0.024	0.000	0.000	0.000	0.000
14	B	14	LYS	1	0.943	0.953	7.388	0.634	0.634	0.000	0.000	0.000	0.000
15	B	15	ASP	-1	-0.875	-0.924	2.660	-7.209	-4.626	0.517	-1.646	-1.454	-0.020
16	B	16	THR	0	0.043	0.004	5.171	-0.030	-0.017	-0.001	-0.001	-0.010	0.000
17	B	17	SER	0	-0.013	-0.024	4.442	-0.575	-0.464	-0.001	-0.040	-0.070	0.000
18	B	18	GLY	0	0.009	0.018	2.124	-1.815	-0.664	3.284	-2.544	-1.891	0.000
19	B	19	SER	0	-0.045	-0.023	2.699	3.932	2.560	0.086	1.719	-0.433	-0.001
20	B	20	ILE	0	0.016	0.027	5.365	-0.829	-0.829	0.000	0.000	0.000	0.000
21	B	21	SER	0	-0.014	-0.001	7.968	0.364	0.364	0.000	0.000	0.000	0.000
22	B	22	ASN	0	0.009	-0.002	10.768	-0.074	-0.074	0.000	0.000	0.000	0.000
23	B	23	THR	0	-0.020	-0.019	13.529	0.027	0.027	0.000	0.000	0.000	0.000
24	B	24	ASP	-1	-0.842	-0.930	15.746	-0.249	-0.249	0.000	0.000	0.000	0.000
25	B	25	ARG	1	0.877	0.911	13.452	0.485	0.485	0.000	0.000	0.000	0.000
26	B	26	GLN	0	0.018	0.018	14.770	0.003	0.003	0.000	0.000	0.000	0.000
27	B	27	LYS	1	0.921	0.958	16.601	0.497	0.497	0.000	0.000	0.000	0.000
28	B	28	ASN	0	-0.019	-0.024	20.636	-0.010	-0.010	0.000	0.000	0.000	0.000
29	B	29	LEU	0	0.014	0.015	21.436	0.011	0.011	0.000	0.000	0.000	0.000
30	B	31	THR	0	-0.001	-0.002	16.546	0.041	0.041	0.000	0.000	0.000	0.000
31	B	32	TRP	0	0.025	0.031	11.160	-0.033	-0.033	0.000	0.000	0.000	0.000
32	B	33	THR	0	-0.011	-0.003	12.940	0.069	0.069	0.000	0.000	0.000	0.000
33	B	34	ILE	0	0.014	0.015	8.691	-0.109	-0.109	0.000	0.000	0.000	0.000
34	B	35	LEU	0	-0.018	-0.019	10.611	0.157	0.157	0.000	0.000	0.000	0.000
35	B	36	MET	0	-0.036	0.005	7.784	0.026	0.026	0.000	0.000	0.000	0.000
36	B	37	LYS	1	0.862	0.918	12.419	-0.128	-0.128	0.000	0.000	0.000	0.000
37	B	38	PRO	0	0.041	-0.001	14.962	-0.006	-0.006	0.000	0.000	0.000	0.000
38	B	39	ASP	-1	-0.814	-0.881	17.350	0.067	0.067	0.000	0.000	0.000	0.000
39	B	40	GLN	0	-0.043	-0.032	11.964	-0.005	-0.005	0.000	0.000	0.000	0.000
40	B	41	LYS	1	0.942	0.996	15.708	0.041	0.041	0.000	0.000	0.000	0.000
41	B	42	VAL	0	0.019	0.005	10.706	0.031	0.031	0.000	0.000	0.000	0.000
42	B	43	ARG	1	0.927	0.969	11.933	0.031	0.031	0.000	0.000	0.000	0.000
43	B	44	MET	0	-0.025	-0.005	11.052	-0.065	-0.065	0.000	0.000	0.000	0.000
44	B	45	ALA	0	0.025	0.005	11.817	0.084	0.084	0.000	0.000	0.000	0.000
45	B	46	ILE	0	0.009	0.011	12.382	-0.095	-0.095	0.000	0.000	0.000	0.000
46	B	47	PRO	0	-0.053	-0.015	13.289	0.047	0.047	0.000	0.000	0.000	0.000
47	B	48	TYR	0	0.022	-0.013	16.303	0.033	0.033	0.000	0.000	0.000	0.000
48	B	49	LEU	0	-0.035	0.000	17.770	-0.034	-0.034	0.000	0.000	0.000	0.000
49	B	50	ASN	0	0.013	0.008	19.942	0.034	0.034	0.000	0.000	0.000	0.000
50	B	51	LEU	0	-0.024	-0.003	19.610	-0.008	-0.008	0.000	0.000	0.000	0.000
51	B	52	ALA	0	0.015	0.023	23.557	0.018	0.018	0.000	0.000	0.000	0.000
52	B	53	CYS	0	0.050	-0.024	22.922	-0.020	-0.020	0.000	0.000	0.000	0.000
53	B	54	GLY	0	0.003	0.017	28.210	0.009	0.009	0.000	0.000	0.000	0.000
54	B	55	LYS	1	0.872	0.947	25.411	0.191	0.191	0.000	0.000	0.000	0.000
55	B	56	GLU	-1	-0.766	-0.841	22.359	-0.254	-0.254	0.000	0.000	0.000	0.000
56	B	57	TYR	0	-0.003	-0.004	23.097	0.015	0.015	0.000	0.000	0.000	0.000
57	B	58	VAL	0	0.001	0.006	17.040	-0.028	-0.028	0.000	0.000	0.000	0.000
58	B	59	GLU	-1	-0.803	-0.866	19.565	-0.183	-0.183	0.000	0.000	0.000	0.000
59	B	60	VAL	0	0.021	0.018	16.261	-0.048	-0.048	0.000	0.000	0.000	0.000
60	B	61	PHE	0	-0.012	-0.013	18.248	0.036	0.036	0.000	0.000	0.000	0.000
61	B	62	ASP	-1	-0.754	-0.849	18.263	-0.217	-0.217	0.000	0.000	0.000	0.000
62	B	63	GLY	0	0.057	0.025	18.372	0.028	0.028	0.000	0.000	0.000	0.000
63	B	64	LEU	0	0.015	0.011	18.101	-0.044	-0.044	0.000	0.000	0.000	0.000
64	B	65	LEU	0	0.010	-0.007	19.834	0.012	0.012	0.000	0.000	0.000	0.000
65	B	66	SER	0	-0.034	-0.002	21.582	0.008	0.008	0.000	0.000	0.000	0.000
66	B	67	GLY	0	-0.025	0.006	22.723	0.021	0.021	0.000	0.000	0.000	0.000
67	B	68	PRO	0	0.022	-0.003	23.691	-0.005	-0.005	0.000	0.000	0.000	0.000
68	B	69	SER	0	-0.016	-0.014	22.893	-0.019	-0.019	0.000	0.000	0.000	0.000
69	B	70	TYR	0	-0.033	-0.040	18.952	0.012	0.012	0.000	0.000	0.000	0.000
70	B	71	GLY	0	0.018	0.018	23.139	0.015	0.015	0.000	0.000	0.000	0.000
71	B	72	LYS	1	0.798	0.876	22.733	0.172	0.172	0.000	0.000	0.000	0.000
72	B	73	LEU	0	0.004	0.001	20.311	0.017	0.017	0.000	0.000	0.000	0.000
73	B	75	ALA	0	0.023	0.009	23.181	-0.003	-0.003	0.000	0.000	0.000	0.000
74	B	76	GLY	0	0.041	0.018	22.497	0.002	0.002	0.000	0.000	0.000	0.000
75	B	77	ALA	0	0.001	0.001	20.462	-0.011	-0.011	0.000	0.000	0.000	0.000
76	B	78	ALA	0	-0.028	-0.006	18.107	0.008	0.008	0.000	0.000	0.000	0.000
77	B	79	ILE	0	0.018	0.030	17.917	0.012	0.012	0.000	0.000	0.000	0.000
78	B	80	VAL	0	-0.005	-0.009	16.060	-0.030	-0.030	0.000	0.000	0.000	0.000
79	B	81	PHE	0	0.012	0.000	16.055	0.007	0.007	0.000	0.000	0.000	0.000
80	B	82	LEU	0	-0.022	-0.014	15.833	-0.003	-0.003	0.000	0.000	0.000	0.000
81	B	83	SER	0	0.006	0.027	16.422	0.003	0.003	0.000	0.000	0.000	0.000
82	B	84	THR	0	-0.088	-0.111	18.186	0.033	0.033	0.000	0.000	0.000	0.000
83	B	85	ALA	0	0.030	0.012	19.511	0.023	0.023	0.000	0.000	0.000	0.000
84	B	86	ASN	0	-0.024	0.001	15.645	-0.011	-0.011	0.000	0.000	0.000	0.000
85	B	87	THR	0	-0.021	-0.011	14.664	-0.036	-0.036	0.000	0.000	0.000	0.000
86	B	88	MET	0	0.012	0.009	13.414	0.020	0.020	0.000	0.000	0.000	0.000
87	B	89	THR	0	-0.033	-0.013	13.926	-0.108	-0.108	0.000	0.000	0.000	0.000
88	B	90	ILE	0	0.016	0.021	11.729	0.052	0.052	0.000	0.000	0.000	0.000
89	B	91	LYS	1	0.930	0.966	15.630	0.224	0.224	0.000	0.000	0.000	0.000
90	B	92	TYR	0	-0.018	-0.036	17.286	0.029	0.029	0.000	0.000	0.000	0.000
91	B	93	ASN	0	-0.008	-0.022	18.974	0.000	0.000	0.000	0.000	0.000	0.000
92	B	94	ARG	1	0.825	0.903	21.599	0.278	0.278	0.000	0.000	0.000	0.000
93	B	95	ILE	0	0.008	0.006	24.978	0.001	0.001	0.000	0.000	0.000	0.000
94	B	96	SER	0	-0.025	-0.018	28.727	0.011	0.011	0.000	0.000	0.000	0.000
95	B	97	GLY	0	0.059	0.011	27.898	-0.004	-0.004	0.000	0.000	0.000	0.000
96	B	98	ASN	0	-0.047	-0.024	25.837	-0.003	-0.003	0.000	0.000	0.000	0.000
97	B	99	SER	0	0.041	0.026	23.535	-0.014	-0.014	0.000	0.000	0.000	0.000
98	B	100	SER	0	-0.109	-0.043	18.905	0.000	0.000	0.000	0.000	0.000	0.000
99	B	101	SER	0	0.033	0.009	21.156	0.022	0.022	0.000	0.000	0.000	0.000
100	B	102	PRO	0	-0.026	-0.005	16.828	-0.044	-0.044	0.000	0.000	0.000	0.000
101	B	103	PHE	0	0.033	-0.004	14.256	0.027	0.027	0.000	0.000	0.000	0.000
102	B	104	LEU	0	0.009	0.006	9.301	-0.092	-0.092	0.000	0.000	0.000	0.000
103	B	105	ILE	0	0.024	0.013	9.712	0.129	0.129	0.000	0.000	0.000	0.000
104	B	106	TYR	0	0.012	0.005	7.643	-0.332	-0.332	0.000	0.000	0.000	0.000
105	B	107	PHE	0	0.005	-0.009	4.074	0.041	0.174	-0.001	-0.028	-0.104	0.000
106	B	108	TYR	0	0.026	-0.003	6.633	0.064	0.064	0.000	0.000	0.000	0.000
107	B	109	GLY	0	0.030	0.035	8.549	-0.096	-0.096	0.000	0.000	0.000	0.000
108	B	110	SER	0	-0.030	-0.023	11.206	0.102	0.102	0.000	0.000	0.000	0.000
109	B	111	SER	0	-0.040	-0.017	14.624	-0.034	-0.034	0.000	0.000	0.000	0.000
110	B	112	PRO	0	0.021	0.022	17.073	0.020	0.020	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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