FMO DATABASE

FMODB ID: 49V9N

Calculation Name: 1NYS-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NYS

Chain ID: B

ChEMBL ID:

UniProt ID: P38444

Base Structure: X-ray

Registration Date: 2023-09-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	83
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-547844.01222
FMO2-HF: Nuclear repulsion	510383.881254
FMO2-HF: Total energy	-37460.130966
FMO2-MP2: Total energy	-37559.849442

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:2:LEU)

Summations of interaction energy for fragment #1(B:2: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.
-5.656	0.95	4.486	-3.572	-7.519	-0.006

Interaction energy analysis for fragmet #1(B:2:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.023 / 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

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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	B	4	CYS	0	-0.063	0.008	3.181	-0.977	2.484	0.093	-1.518	-2.036	-0.004
4	B	5	ASP	-1	-0.782	-0.877	5.579	0.166	0.314	-0.001	-0.006	-0.141	0.000
5	B	6	GLY	0	-0.042	-0.027	8.430	-0.050	-0.050	0.000	0.000	0.000	0.000
6	B	7	LYS	1	0.849	0.907	9.133	-0.845	-0.845	0.000	0.000	0.000	0.000
7	B	8	VAL	0	0.039	0.025	8.292	0.352	0.352	0.000	0.000	0.000	0.000
8	B	9	ASN	0	-0.034	-0.007	8.214	-0.231	-0.231	0.000	0.000	0.000	0.000
9	B	10	ILE	0	0.019	0.015	4.978	-0.173	-0.173	0.000	0.000	0.000	0.000
10	B	11	CYS	0	-0.013	0.026	5.358	0.683	0.683	0.000	0.000	0.000	0.000
11	B	13	LYS	1	0.899	0.936	3.160	-0.903	0.069	0.050	-0.258	-0.764	0.001
12	B	14	LYS	1	0.840	0.915	4.708	-0.762	-0.734	-0.001	-0.009	-0.017	0.000
13	B	15	GLN	0	-0.022	-0.007	7.176	-0.142	-0.142	0.000	0.000	0.000	0.000
14	B	16	PHE	0	-0.009	-0.011	10.015	0.017	0.017	0.000	0.000	0.000	0.000
15	B	17	PHE	0	-0.026	-0.011	13.757	-0.010	-0.010	0.000	0.000	0.000	0.000
16	B	18	VAL	0	0.002	0.011	16.772	0.009	0.009	0.000	0.000	0.000	0.000
17	B	19	SER	0	-0.020	-0.038	20.015	-0.009	-0.009	0.000	0.000	0.000	0.000
18	B	20	PHE	0	0.085	0.012	21.507	0.009	0.009	0.000	0.000	0.000	0.000
19	B	21	LYS	1	0.847	0.921	25.219	-0.035	-0.035	0.000	0.000	0.000	0.000
20	B	22	ASP	-1	-0.873	-0.897	24.597	0.045	0.045	0.000	0.000	0.000	0.000
21	B	23	ILE	0	-0.018	-0.012	21.925	0.009	0.009	0.000	0.000	0.000	0.000
22	B	24	GLY	0	0.012	0.027	26.471	0.001	0.001	0.000	0.000	0.000	0.000
23	B	25	TRP	0	-0.009	-0.025	23.100	0.000	0.000	0.000	0.000	0.000	0.000
24	B	26	ASN	0	-0.037	-0.022	28.555	0.000	0.000	0.000	0.000	0.000	0.000
25	B	27	ASP	-1	-0.879	-0.928	29.554	0.022	0.022	0.000	0.000	0.000	0.000
26	B	28	TRP	0	-0.027	-0.009	26.426	-0.003	-0.003	0.000	0.000	0.000	0.000
27	B	29	ILE	0	-0.046	-0.023	24.572	-0.003	-0.003	0.000	0.000	0.000	0.000
28	B	30	ILE	0	0.007	0.013	28.447	-0.001	-0.001	0.000	0.000	0.000	0.000
29	B	31	ALA	0	-0.028	-0.008	26.678	-0.004	-0.004	0.000	0.000	0.000	0.000
30	B	32	PRO	0	0.013	0.002	21.181	0.001	0.001	0.000	0.000	0.000	0.000
31	B	33	SER	0	0.047	0.009	24.254	0.005	0.005	0.000	0.000	0.000	0.000
32	B	34	GLY	0	0.008	-0.002	21.781	0.007	0.007	0.000	0.000	0.000	0.000
33	B	35	TYR	0	-0.017	-0.003	16.634	-0.006	-0.006	0.000	0.000	0.000	0.000
34	B	36	HIS	0	0.034	0.009	12.831	0.002	0.002	0.000	0.000	0.000	0.000
35	B	37	ALA	0	0.010	0.030	13.358	0.020	0.020	0.000	0.000	0.000	0.000
36	B	38	ASN	0	-0.012	-0.030	8.832	-0.016	-0.016	0.000	0.000	0.000	0.000
37	B	39	TYR	0	-0.022	-0.009	9.433	0.037	0.037	0.000	0.000	0.000	0.000
38	B	40	CYS	0	-0.057	0.002	1.980	-1.804	-1.519	2.144	-0.731	-1.698	0.004
39	B	41	GLU	-1	-0.848	-0.930	7.265	0.551	0.551	0.000	0.000	0.000	0.000
40	B	42	GLY	0	0.022	-0.007	7.333	0.331	0.331	0.000	0.000	0.000	0.000
41	B	43	GLU	-1	-0.911	-0.962	9.052	0.507	0.507	0.000	0.000	0.000	0.000
42	B	44	CYS	0	-0.045	-0.021	5.243	0.237	0.289	-0.002	-0.003	-0.047	0.000
43	B	45	PRO	0	0.015	0.015	10.058	-0.038	-0.038	0.000	0.000	0.000	0.000
44	B	46	SER	0	-0.008	-0.012	13.079	0.003	0.003	0.000	0.000	0.000	0.000
45	B	47	HIS	0	-0.017	0.008	14.934	-0.024	-0.024	0.000	0.000	0.000	0.000
46	B	48	ILE	0	0.004	0.003	17.221	-0.005	-0.005	0.000	0.000	0.000	0.000
47	B	77	LEU	0	0.044	0.029	19.265	-0.004	-0.004	0.000	0.000	0.000	0.000
48	B	78	LYS	1	0.899	0.920	17.204	-0.244	-0.244	0.000	0.000	0.000	0.000
49	B	79	SER	0	0.021	-0.007	11.997	0.005	0.005	0.000	0.000	0.000	0.000
50	B	80	CYS	0	-0.032	-0.017	12.366	-0.014	-0.014	0.000	0.000	0.000	0.000
51	B	82	VAL	0	-0.010	-0.002	8.020	-0.079	-0.079	0.000	0.000	0.000	0.000
52	B	83	PRO	0	0.059	-0.005	6.988	0.153	0.153	0.000	0.000	0.000	0.000
53	B	84	THR	0	-0.042	-0.009	4.998	-0.039	-0.039	0.000	0.000	0.000	0.000
54	B	85	LYS	1	0.804	0.885	5.772	-0.274	-0.274	0.000	0.000	0.000	0.000
55	B	86	LEU	0	-0.008	0.010	8.052	0.060	0.060	0.000	0.000	0.000	0.000
56	B	87	ARG	1	0.851	0.906	10.826	0.003	0.003	0.000	0.000	0.000	0.000
57	B	88	PRO	0	-0.020	-0.018	12.846	0.006	0.006	0.000	0.000	0.000	0.000
58	B	89	MET	0	-0.036	-0.004	16.019	-0.013	-0.013	0.000	0.000	0.000	0.000
59	B	90	SER	0	-0.045	-0.040	18.397	0.002	0.002	0.000	0.000	0.000	0.000
60	B	91	MET	0	-0.041	-0.015	21.982	0.002	0.002	0.000	0.000	0.000	0.000
61	B	92	LEU	0	-0.017	-0.018	24.541	-0.003	-0.003	0.000	0.000	0.000	0.000
62	B	93	TYR	0	-0.034	-0.021	26.790	0.002	0.002	0.000	0.000	0.000	0.000
63	B	94	TYR	0	0.047	0.029	30.117	-0.003	-0.003	0.000	0.000	0.000	0.000
64	B	95	ASP	-1	-0.830	-0.918	32.165	0.019	0.019	0.000	0.000	0.000	0.000
65	B	96	ASP	-1	-0.912	-0.964	34.111	0.023	0.023	0.000	0.000	0.000	0.000
66	B	97	GLY	0	0.034	0.026	37.073	-0.001	-0.001	0.000	0.000	0.000	0.000
67	B	98	GLN	0	-0.104	-0.057	37.734	-0.002	-0.002	0.000	0.000	0.000	0.000
68	B	99	ASN	0	-0.074	-0.031	36.030	-0.003	-0.003	0.000	0.000	0.000	0.000
69	B	100	ILE	0	-0.021	-0.018	32.947	0.001	0.001	0.000	0.000	0.000	0.000
70	B	101	ILE	0	-0.016	0.004	29.798	-0.002	-0.002	0.000	0.000	0.000	0.000
71	B	102	LYS	1	0.869	0.926	24.503	0.016	0.016	0.000	0.000	0.000	0.000
72	B	103	LYS	1	0.946	0.969	25.059	-0.026	-0.026	0.000	0.000	0.000	0.000
73	B	104	ASP	-1	-0.794	-0.867	21.363	-0.013	-0.013	0.000	0.000	0.000	0.000
74	B	105	ILE	0	0.009	0.017	20.362	0.004	0.004	0.000	0.000	0.000	0.000
75	B	106	GLN	0	0.022	-0.021	18.217	0.004	0.004	0.000	0.000	0.000	0.000
76	B	107	ASN	0	-0.031	-0.028	14.473	0.005	0.005	0.000	0.000	0.000	0.000
77	B	108	MET	0	0.026	0.028	14.963	0.023	0.023	0.000	0.000	0.000	0.000
78	B	109	ILE	0	-0.021	0.007	10.735	-0.007	-0.007	0.000	0.000	0.000	0.000
79	B	110	VAL	0	0.031	0.022	6.990	0.010	0.010	0.000	0.000	0.000	0.000
80	B	111	GLU	-1	-0.813	-0.894	6.910	-0.149	-0.149	0.000	0.000	0.000	0.000
81	B	112	GLU	-1	-0.797	-0.893	2.362	-0.857	-0.267	1.754	-0.468	-1.877	-0.001
82	B	114	GLY	0	0.049	0.014	2.881	-1.123	-0.053	0.449	-0.579	-0.939	-0.006
83	B	116	SER	0	-0.002	0.014	8.592	-0.111	-0.111	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:2:LEU)