FMO DATABASE

FMODB ID: Z6VGN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-876285.671833
FMO2-HF: Nuclear repulsion	832473.948109
FMO2-HF: Total energy	-43811.723724
FMO2-MP2: Total energy	-43935.951328

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.
-4.841	0.143	2.623	-3.154	-4.451	-0.009

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 : 0.089 / q_NPA : 0.037

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	0.036	0.030	3.336	-1.482	1.007	0.000	-1.225	-1.263	0.004
4	B	4	ASN	0	-0.017	-0.016	5.607	0.662	0.662	0.000	0.000	0.000	0.000
5	B	5	GLY	0	0.071	0.016	8.926	0.010	0.010	0.000	0.000	0.000	0.000
6	B	6	PRO	0	-0.059	-0.045	11.470	-0.003	-0.003	0.000	0.000	0.000	0.000
7	B	7	ASP	-1	-0.844	-0.920	10.286	-0.657	-0.657	0.000	0.000	0.000	0.000
8	B	8	GLU	-1	-0.870	-0.952	8.686	-1.501	-1.501	0.000	0.000	0.000	0.000
9	B	9	CYS	0	-0.168	-0.038	11.515	-0.009	-0.009	0.000	0.000	0.000	0.000
10	B	10	GLY	0	-0.030	-0.024	14.913	0.032	0.032	0.000	0.000	0.000	0.000
11	B	11	ARG	1	0.891	0.966	10.967	0.934	0.934	0.000	0.000	0.000	0.000
12	B	12	VAL	0	0.007	-0.007	11.984	-0.009	-0.009	0.000	0.000	0.000	0.000
13	B	13	ILE	0	-0.023	-0.008	5.697	-0.059	-0.059	0.000	0.000	0.000	0.000
14	B	14	LYS	1	0.954	0.956	7.567	0.755	0.755	0.000	0.000	0.000	0.000
15	B	15	ASP	-1	-0.900	-0.930	2.914	-7.046	-5.134	0.238	-1.114	-1.036	-0.012
16	B	16	THR	0	0.014	-0.013	5.200	0.296	0.306	-0.001	-0.001	-0.008	0.000
17	B	17	SER	0	-0.037	-0.028	4.767	-0.362	-0.285	-0.001	-0.024	-0.051	0.000
18	B	18	GLY	0	0.060	0.039	2.180	1.085	2.170	2.335	-1.743	-1.677	-0.001
19	B	19	SER	0	-0.058	-0.031	2.885	2.291	1.681	0.054	0.982	-0.426	0.000
20	B	20	ILE	0	0.044	0.040	5.191	-0.986	-1.075	-0.001	-0.011	0.102	0.000
21	B	21	SER	0	-0.043	-0.018	7.779	0.411	0.411	0.000	0.000	0.000	0.000
22	B	22	ASN	0	0.001	-0.011	10.672	-0.101	-0.101	0.000	0.000	0.000	0.000
23	B	23	THR	0	-0.026	-0.017	13.221	0.021	0.021	0.000	0.000	0.000	0.000
24	B	24	ASP	-1	-0.851	-0.931	15.671	-0.240	-0.240	0.000	0.000	0.000	0.000
25	B	25	ARG	1	0.925	0.937	13.739	0.513	0.513	0.000	0.000	0.000	0.000
26	B	26	GLN	0	0.008	0.017	14.674	-0.005	-0.005	0.000	0.000	0.000	0.000
27	B	27	LYS	1	0.909	0.964	16.775	0.520	0.520	0.000	0.000	0.000	0.000
28	B	28	ASN	0	-0.021	-0.032	20.453	-0.007	-0.007	0.000	0.000	0.000	0.000
29	B	29	LEU	0	0.036	0.029	20.862	0.015	0.015	0.000	0.000	0.000	0.000
30	B	31	THR	0	0.016	0.006	16.306	0.049	0.049	0.000	0.000	0.000	0.000
31	B	32	TRP	0	0.020	0.025	10.872	-0.031	-0.031	0.000	0.000	0.000	0.000
32	B	33	THR	0	-0.010	0.015	12.784	0.077	0.077	0.000	0.000	0.000	0.000
33	B	34	ILE	0	0.033	0.015	8.547	-0.129	-0.129	0.000	0.000	0.000	0.000
34	B	35	LEU	0	-0.021	-0.024	10.554	0.163	0.163	0.000	0.000	0.000	0.000
35	B	36	MET	0	-0.024	0.007	8.010	0.000	0.000	0.000	0.000	0.000	0.000
36	B	37	LYS	1	0.972	1.000	12.403	-0.261	-0.261	0.000	0.000	0.000	0.000
37	B	38	PRO	0	0.028	-0.008	14.954	0.005	0.005	0.000	0.000	0.000	0.000
38	B	39	ASP	-1	-0.876	-0.928	17.739	0.083	0.083	0.000	0.000	0.000	0.000
39	B	40	GLN	0	-0.060	-0.045	12.359	-0.026	-0.026	0.000	0.000	0.000	0.000
40	B	41	LYS	1	0.927	0.985	15.834	-0.027	-0.027	0.000	0.000	0.000	0.000
41	B	42	VAL	0	0.021	0.006	10.781	0.052	0.052	0.000	0.000	0.000	0.000
42	B	43	ARG	1	0.918	0.964	12.057	-0.103	-0.103	0.000	0.000	0.000	0.000
43	B	44	MET	0	-0.013	0.000	11.178	-0.017	-0.017	0.000	0.000	0.000	0.000
44	B	45	ALA	0	0.016	-0.001	11.906	0.059	0.059	0.000	0.000	0.000	0.000
45	B	46	ILE	0	-0.014	0.008	12.456	-0.071	-0.071	0.000	0.000	0.000	0.000
46	B	47	PRO	0	-0.038	-0.017	13.490	0.036	0.036	0.000	0.000	0.000	0.000
47	B	48	TYR	0	0.018	-0.011	16.413	0.021	0.021	0.000	0.000	0.000	0.000
48	B	49	LEU	0	-0.030	0.000	17.832	-0.035	-0.035	0.000	0.000	0.000	0.000
49	B	50	ASN	0	0.013	0.009	19.921	0.023	0.023	0.000	0.000	0.000	0.000
50	B	51	LEU	0	-0.029	-0.002	19.498	-0.011	-0.011	0.000	0.000	0.000	0.000
51	B	52	ALA	0	0.033	0.021	23.443	0.018	0.018	0.000	0.000	0.000	0.000
52	B	53	CYS	0	0.050	-0.027	22.809	-0.023	-0.023	0.000	0.000	0.000	0.000
53	B	54	GLY	0	-0.012	0.011	28.080	0.008	0.008	0.000	0.000	0.000	0.000
54	B	55	LYS	1	0.909	0.980	25.175	0.180	0.180	0.000	0.000	0.000	0.000
55	B	56	GLU	-1	-0.777	-0.869	22.283	-0.240	-0.240	0.000	0.000	0.000	0.000
56	B	57	TYR	0	-0.012	-0.016	22.786	0.016	0.016	0.000	0.000	0.000	0.000
57	B	58	VAL	0	0.002	0.010	16.877	-0.031	-0.031	0.000	0.000	0.000	0.000
58	B	59	GLU	-1	-0.839	-0.891	19.401	-0.169	-0.169	0.000	0.000	0.000	0.000
59	B	60	VAL	0	0.008	0.015	16.232	-0.048	-0.048	0.000	0.000	0.000	0.000
60	B	61	PHE	0	-0.011	-0.011	18.121	0.031	0.031	0.000	0.000	0.000	0.000
61	B	62	ASP	-1	-0.776	-0.861	18.158	-0.172	-0.172	0.000	0.000	0.000	0.000
62	B	63	GLY	0	0.062	0.002	18.281	0.022	0.022	0.000	0.000	0.000	0.000
63	B	64	LEU	0	0.013	0.007	17.870	-0.044	-0.044	0.000	0.000	0.000	0.000
64	B	65	LEU	0	0.014	-0.009	19.606	0.017	0.017	0.000	0.000	0.000	0.000
65	B	66	SER	0	-0.037	-0.001	21.368	0.009	0.009	0.000	0.000	0.000	0.000
66	B	67	GLY	0	-0.029	0.006	22.593	0.021	0.021	0.000	0.000	0.000	0.000
67	B	68	PRO	0	0.023	0.000	23.553	-0.004	-0.004	0.000	0.000	0.000	0.000
68	B	69	SER	0	-0.029	-0.039	22.799	-0.012	-0.012	0.000	0.000	0.000	0.000
69	B	70	TYR	0	-0.021	-0.024	18.616	0.012	0.012	0.000	0.000	0.000	0.000
70	B	71	GLY	0	0.021	0.019	23.086	0.015	0.015	0.000	0.000	0.000	0.000
71	B	72	LYS	1	0.867	0.931	22.640	0.153	0.153	0.000	0.000	0.000	0.000
72	B	73	LEU	0	0.001	-0.003	20.182	0.018	0.018	0.000	0.000	0.000	0.000
73	B	75	ALA	0	0.027	0.013	23.144	-0.003	-0.003	0.000	0.000	0.000	0.000
74	B	76	GLY	0	0.031	0.013	22.548	0.002	0.002	0.000	0.000	0.000	0.000
75	B	77	ALA	0	0.007	0.004	20.557	-0.009	-0.009	0.000	0.000	0.000	0.000
76	B	78	ALA	0	-0.031	-0.009	18.268	0.006	0.006	0.000	0.000	0.000	0.000
77	B	79	ILE	0	0.014	0.032	17.910	0.008	0.008	0.000	0.000	0.000	0.000
78	B	80	VAL	0	0.001	-0.008	16.448	-0.013	-0.013	0.000	0.000	0.000	0.000
79	B	81	PHE	0	0.007	-0.004	16.092	-0.007	-0.007	0.000	0.000	0.000	0.000
80	B	82	LEU	0	-0.039	-0.024	15.929	0.016	0.016	0.000	0.000	0.000	0.000
81	B	83	SER	0	0.003	0.015	16.509	0.000	0.000	0.000	0.000	0.000	0.000
82	B	84	THR	0	-0.069	-0.093	18.215	0.034	0.034	0.000	0.000	0.000	0.000
83	B	85	ALA	0	0.047	0.023	19.519	0.020	0.020	0.000	0.000	0.000	0.000
84	B	86	ASN	0	-0.027	-0.004	15.479	-0.001	-0.001	0.000	0.000	0.000	0.000
85	B	87	THR	0	-0.049	0.001	14.615	-0.048	-0.048	0.000	0.000	0.000	0.000
86	B	88	MET	0	0.023	0.008	13.318	0.037	0.037	0.000	0.000	0.000	0.000
87	B	89	THR	0	-0.037	-0.017	13.773	-0.113	-0.113	0.000	0.000	0.000	0.000
88	B	90	ILE	0	-0.002	0.015	11.629	0.056	0.056	0.000	0.000	0.000	0.000
89	B	91	LYS	1	0.962	0.977	15.448	0.213	0.213	0.000	0.000	0.000	0.000
90	B	92	TYR	0	-0.027	-0.015	17.090	0.035	0.035	0.000	0.000	0.000	0.000
91	B	93	ASN	0	0.000	-0.026	18.739	-0.015	-0.015	0.000	0.000	0.000	0.000
92	B	94	ARG	1	0.846	0.921	21.634	0.278	0.278	0.000	0.000	0.000	0.000
93	B	95	ILE	0	0.026	0.019	24.728	-0.001	-0.001	0.000	0.000	0.000	0.000
94	B	96	SER	0	-0.041	-0.024	28.473	0.012	0.012	0.000	0.000	0.000	0.000
95	B	97	GLY	0	0.056	0.006	27.676	-0.002	-0.002	0.000	0.000	0.000	0.000
96	B	98	ASN	0	-0.047	-0.022	25.560	-0.004	-0.004	0.000	0.000	0.000	0.000
97	B	99	SER	0	0.041	0.028	23.370	-0.015	-0.015	0.000	0.000	0.000	0.000
98	B	100	SER	0	-0.079	-0.036	19.495	-0.008	-0.008	0.000	0.000	0.000	0.000
99	B	101	SER	0	0.004	-0.015	20.997	0.018	0.018	0.000	0.000	0.000	0.000
100	B	102	PRO	0	-0.034	-0.002	16.834	-0.045	-0.045	0.000	0.000	0.000	0.000
101	B	103	PHE	0	0.037	0.000	14.230	0.029	0.029	0.000	0.000	0.000	0.000
102	B	104	LEU	0	0.007	-0.003	9.231	-0.103	-0.103	0.000	0.000	0.000	0.000
103	B	105	ILE	0	0.026	0.025	9.459	0.127	0.127	0.000	0.000	0.000	0.000
104	B	106	TYR	0	0.008	0.000	7.745	-0.290	-0.290	0.000	0.000	0.000	0.000
105	B	107	PHE	0	0.004	-0.013	4.215	0.037	0.147	-0.001	-0.018	-0.092	0.000
106	B	108	TYR	0	0.032	-0.003	6.840	0.281	0.281	0.000	0.000	0.000	0.000
107	B	109	GLY	0	0.029	0.035	8.758	-0.170	-0.170	0.000	0.000	0.000	0.000
108	B	110	SER	0	-0.038	-0.030	11.385	0.111	0.111	0.000	0.000	0.000	0.000
109	B	111	SER	0	-0.052	-0.022	14.838	-0.049	-0.049	0.000	0.000	0.000	0.000
110	B	112	PRO	0	0.023	0.027	17.283	0.023	0.023	0.000	0.000	0.000	0.000

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