FMO DATABASE

FMODB ID: 72V2K

Calculation Name: 1NYU-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NYU

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-550834.983914
FMO2-HF: Nuclear repulsion	513375.879379
FMO2-HF: Total energy	-37459.104535
FMO2-MP2: Total energy	-37558.974033

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.
-3.865	2.993	2.689	-3.271	-6.278	-0.015

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 : 0.005 / q_NPA : 0.012

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	-0.055	-0.002	2.515	-5.808	-0.860	2.203	-2.933	-4.218	-0.015
4	B	5	ASP	-1	-0.837	-0.932	4.855	-0.924	-0.772	-0.001	-0.009	-0.142	0.000
5	B	6	GLY	0	-0.014	0.002	7.483	-0.038	-0.038	0.000	0.000	0.000	0.000
6	B	7	LYS	1	0.706	0.836	7.894	0.726	0.726	0.000	0.000	0.000	0.000
7	B	8	VAL	0	0.137	0.062	5.822	0.153	0.153	0.000	0.000	0.000	0.000
8	B	9	ASN	0	0.012	0.062	8.289	0.146	0.146	0.000	0.000	0.000	0.000
9	B	10	ILE	0	-0.089	-0.110	2.744	-0.623	0.022	0.489	-0.179	-0.956	0.000
10	B	11	CYS	0	-0.071	0.079	4.295	-0.394	-0.186	-0.002	-0.025	-0.181	0.000
11	B	13	LYS	1	0.819	0.879	3.757	3.060	3.488	0.004	-0.048	-0.385	0.000
12	B	14	LYS	1	0.814	0.889	6.189	1.411	1.411	0.000	0.000	0.000	0.000
13	B	15	GLN	0	-0.033	-0.027	7.798	0.240	0.240	0.000	0.000	0.000	0.000
14	B	16	PHE	0	0.012	0.014	11.039	0.088	0.088	0.000	0.000	0.000	0.000
15	B	17	PHE	0	0.008	0.008	14.728	0.023	0.023	0.000	0.000	0.000	0.000
16	B	18	VAL	0	-0.012	-0.004	17.414	0.014	0.014	0.000	0.000	0.000	0.000
17	B	19	SER	0	0.037	0.034	20.726	0.021	0.021	0.000	0.000	0.000	0.000
18	B	20	PHE	0	0.075	0.005	22.982	-0.007	-0.007	0.000	0.000	0.000	0.000
19	B	21	LYS	1	0.859	0.930	26.019	0.159	0.159	0.000	0.000	0.000	0.000
20	B	22	ASP	-1	-0.897	-0.964	25.439	-0.235	-0.235	0.000	0.000	0.000	0.000
21	B	23	ILE	0	-0.065	-0.032	23.758	-0.008	-0.008	0.000	0.000	0.000	0.000
22	B	24	GLY	0	-0.004	0.009	27.447	0.009	0.009	0.000	0.000	0.000	0.000
23	B	25	TRP	0	-0.007	-0.021	24.967	0.005	0.005	0.000	0.000	0.000	0.000
24	B	26	ASN	0	-0.067	-0.025	29.437	-0.002	-0.002	0.000	0.000	0.000	0.000
25	B	27	ASP	-1	-0.865	-0.926	30.266	-0.118	-0.118	0.000	0.000	0.000	0.000
26	B	28	TRP	0	0.013	0.017	28.088	0.008	0.008	0.000	0.000	0.000	0.000
27	B	29	ILE	0	-0.015	-0.012	26.234	0.006	0.006	0.000	0.000	0.000	0.000
28	B	30	ILE	0	-0.022	0.013	30.008	-0.002	-0.002	0.000	0.000	0.000	0.000
29	B	31	ALA	0	-0.021	-0.003	26.874	-0.004	-0.004	0.000	0.000	0.000	0.000
30	B	32	PRO	0	-0.006	-0.011	21.844	0.008	0.008	0.000	0.000	0.000	0.000
31	B	33	SER	0	0.052	0.002	24.500	0.003	0.003	0.000	0.000	0.000	0.000
32	B	34	GLY	0	0.014	0.010	22.409	0.000	0.000	0.000	0.000	0.000	0.000
33	B	35	TYR	0	-0.016	-0.004	17.257	0.004	0.004	0.000	0.000	0.000	0.000
34	B	36	HIS	0	-0.008	-0.010	13.463	-0.052	-0.052	0.000	0.000	0.000	0.000
35	B	37	ALA	0	-0.017	0.017	14.848	0.004	0.004	0.000	0.000	0.000	0.000
36	B	38	ASN	0	0.023	-0.011	9.680	-0.011	-0.011	0.000	0.000	0.000	0.000
37	B	39	TYR	0	-0.001	-0.008	11.390	0.100	0.100	0.000	0.000	0.000	0.000
38	B	40	CYS	0	-0.063	0.009	3.799	0.327	0.487	-0.002	-0.024	-0.134	0.000
39	B	41	GLU	-1	-0.835	-0.940	7.906	-0.796	-0.796	0.000	0.000	0.000	0.000
40	B	42	GLY	0	0.127	0.038	7.075	-0.412	-0.412	0.000	0.000	0.000	0.000
41	B	43	GLU	-1	-0.854	-0.943	7.627	-0.444	-0.444	0.000	0.000	0.000	0.000
42	B	44	CYS	0	-0.107	-0.051	6.786	-0.336	-0.336	0.000	0.000	0.000	0.000
43	B	45	PRO	0	0.012	0.005	7.939	0.010	0.010	0.000	0.000	0.000	0.000
44	B	46	SER	0	0.010	-0.021	11.129	-0.035	-0.035	0.000	0.000	0.000	0.000
45	B	47	HIS	0	0.021	0.022	14.701	-0.018	-0.018	0.000	0.000	0.000	0.000
46	B	48	ILE	0	-0.028	0.044	14.043	-0.016	-0.016	0.000	0.000	0.000	0.000
47	B	77	LEU	0	-0.014	-0.014	18.428	-0.003	-0.003	0.000	0.000	0.000	0.000
48	B	78	LYS	1	0.943	0.944	13.462	0.181	0.181	0.000	0.000	0.000	0.000
49	B	79	SER	0	0.037	0.021	11.421	-0.018	-0.018	0.000	0.000	0.000	0.000
50	B	80	CYS	0	-0.030	-0.032	11.807	-0.017	-0.017	0.000	0.000	0.000	0.000
51	B	82	VAL	0	-0.009	-0.018	9.154	0.013	0.013	0.000	0.000	0.000	0.000
52	B	83	PRO	0	0.053	0.001	8.521	-0.095	-0.095	0.000	0.000	0.000	0.000
53	B	84	THR	0	-0.053	-0.029	7.067	0.229	0.229	0.000	0.000	0.000	0.000
54	B	85	LYS	1	0.795	0.884	8.355	-0.165	-0.165	0.000	0.000	0.000	0.000
55	B	86	LEU	0	-0.026	-0.003	9.925	-0.180	-0.180	0.000	0.000	0.000	0.000
56	B	87	ARG	1	0.926	0.955	10.056	0.484	0.484	0.000	0.000	0.000	0.000
57	B	88	PRO	0	-0.004	-0.011	14.196	-0.042	-0.042	0.000	0.000	0.000	0.000
58	B	89	MET	0	0.000	0.005	17.236	-0.021	-0.021	0.000	0.000	0.000	0.000
59	B	90	SER	0	-0.064	-0.044	19.212	0.017	0.017	0.000	0.000	0.000	0.000
60	B	91	MET	0	-0.031	-0.022	22.551	-0.022	-0.022	0.000	0.000	0.000	0.000
61	B	92	LEU	0	0.004	0.001	25.402	0.015	0.015	0.000	0.000	0.000	0.000
62	B	93	TYR	0	-0.012	-0.012	27.874	-0.009	-0.009	0.000	0.000	0.000	0.000
63	B	94	TYR	0	0.028	0.021	31.020	0.010	0.010	0.000	0.000	0.000	0.000
64	B	95	ASP	-1	-0.844	-0.914	33.653	-0.071	-0.071	0.000	0.000	0.000	0.000
65	B	96	ASP	-1	-0.875	-0.969	35.229	-0.084	-0.084	0.000	0.000	0.000	0.000
66	B	97	GLY	0	-0.068	-0.022	37.953	0.002	0.002	0.000	0.000	0.000	0.000
67	B	98	GLN	0	-0.066	-0.038	38.700	0.002	0.002	0.000	0.000	0.000	0.000
68	B	99	ASN	0	-0.052	-0.025	37.621	0.005	0.005	0.000	0.000	0.000	0.000
69	B	100	ILE	0	-0.007	0.010	33.926	-0.005	-0.005	0.000	0.000	0.000	0.000
70	B	101	ILE	0	-0.009	-0.002	30.772	0.006	0.006	0.000	0.000	0.000	0.000
71	B	102	LYS	1	0.868	0.928	25.683	0.061	0.061	0.000	0.000	0.000	0.000
72	B	103	LYS	1	0.886	0.942	24.965	0.095	0.095	0.000	0.000	0.000	0.000
73	B	104	ASP	-1	-0.793	-0.865	22.330	-0.084	-0.084	0.000	0.000	0.000	0.000
74	B	105	ILE	0	-0.026	-0.021	21.493	0.014	0.014	0.000	0.000	0.000	0.000
75	B	106	GLN	0	0.040	0.019	19.554	-0.019	-0.019	0.000	0.000	0.000	0.000
76	B	107	ASN	0	-0.039	-0.030	16.361	-0.007	-0.007	0.000	0.000	0.000	0.000
77	B	108	MET	0	0.070	0.031	17.062	-0.007	-0.007	0.000	0.000	0.000	0.000
78	B	109	ILE	0	-0.056	-0.007	11.816	-0.039	-0.039	0.000	0.000	0.000	0.000
79	B	110	VAL	0	0.025	0.010	8.679	0.057	0.057	0.000	0.000	0.000	0.000
80	B	111	GLU	-1	-0.831	-0.885	7.548	-0.330	-0.330	0.000	0.000	0.000	0.000
81	B	112	GLU	-1	-0.785	-0.896	4.041	0.072	0.218	-0.001	-0.014	-0.131	0.000
82	B	114	GLY	0	0.069	0.037	4.169	-0.300	-0.129	-0.001	-0.039	-0.131	0.000
83	B	116	SER	0	0.035	0.026	9.275	0.148	0.148	0.000	0.000	0.000	0.000

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