FMO DATABASE

FMODB ID: 3J11L

Calculation Name: 1NVP-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NVP

Chain ID: D

ChEMBL ID:

UniProt ID: P52657

Base Structure: X-ray

Registration Date: 2023-09-24

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	97
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-642764.991681
FMO2-HF: Nuclear repulsion	603637.806854
FMO2-HF: Total energy	-39127.184827
FMO2-MP2: Total energy	-39242.382918

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(D:3:TYR)

Summations of interaction energy for fragment #1(D:3:TYR)

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.
-33.483	-28.712	17.435	-9.274	-12.931	-0.055

Interaction energy analysis for fragmet #1(D:3:TYR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.033

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	D	5	LEU	0	-0.009	0.004	2.428	-3.042	0.085	1.172	-1.595	-2.703	0.004
4	D	6	TYR	0	0.012	-0.001	3.497	-0.200	0.541	0.015	-0.103	-0.653	0.000
5	D	7	ARG	1	0.842	0.913	6.305	-1.682	-1.682	0.000	0.000	0.000	0.000
6	D	8	ASN	0	-0.019	0.008	8.643	0.037	0.037	0.000	0.000	0.000	0.000
7	D	9	THR	0	-0.011	-0.018	9.160	-0.106	-0.106	0.000	0.000	0.000	0.000
8	D	10	THR	0	0.053	0.018	11.848	0.047	0.047	0.000	0.000	0.000	0.000
9	D	11	LEU	0	0.003	0.020	12.401	0.030	0.030	0.000	0.000	0.000	0.000
10	D	12	GLY	0	0.014	0.017	11.263	0.049	0.049	0.000	0.000	0.000	0.000
11	D	13	ASN	0	-0.033	-0.027	12.298	0.045	0.045	0.000	0.000	0.000	0.000
12	D	14	SER	0	0.070	0.026	14.800	0.038	0.038	0.000	0.000	0.000	0.000
13	D	15	LEU	0	-0.044	0.001	12.259	0.025	0.025	0.000	0.000	0.000	0.000
14	D	16	GLN	0	-0.019	-0.029	12.193	0.084	0.084	0.000	0.000	0.000	0.000
15	D	17	GLU	-1	-0.858	-0.934	15.860	0.153	0.153	0.000	0.000	0.000	0.000
16	D	18	SER	0	0.004	-0.011	19.131	-0.011	-0.011	0.000	0.000	0.000	0.000
17	D	19	LEU	0	-0.079	-0.042	15.253	0.015	0.015	0.000	0.000	0.000	0.000
18	D	20	ASP	-1	-0.899	-0.961	18.357	0.413	0.413	0.000	0.000	0.000	0.000
19	D	21	GLU	-1	-0.960	-0.977	20.846	0.149	0.149	0.000	0.000	0.000	0.000
20	D	22	LEU	0	-0.035	-0.012	21.308	-0.006	-0.006	0.000	0.000	0.000	0.000
21	D	23	ILE	0	-0.041	-0.021	19.224	0.012	0.012	0.000	0.000	0.000	0.000
22	D	24	GLN	0	-0.046	-0.017	23.715	-0.017	-0.017	0.000	0.000	0.000	0.000
23	D	25	SER	0	-0.036	-0.037	26.516	-0.005	-0.005	0.000	0.000	0.000	0.000
24	D	26	GLN	0	-0.051	-0.035	26.975	-0.011	-0.011	0.000	0.000	0.000	0.000
25	D	27	GLN	0	0.007	0.031	26.036	-0.002	-0.002	0.000	0.000	0.000	0.000
26	D	28	ILE	0	-0.037	-0.007	19.631	0.015	0.015	0.000	0.000	0.000	0.000
27	D	29	THR	0	0.025	0.013	21.707	0.013	0.013	0.000	0.000	0.000	0.000
28	D	30	PRO	0	0.091	0.023	19.159	0.033	0.033	0.000	0.000	0.000	0.000
29	D	31	GLN	0	0.003	0.018	16.263	0.150	0.150	0.000	0.000	0.000	0.000
30	D	32	LEU	0	0.031	0.016	16.592	0.093	0.093	0.000	0.000	0.000	0.000
31	D	33	ALA	0	0.074	0.037	16.416	0.044	0.044	0.000	0.000	0.000	0.000
32	D	34	LEU	0	-0.003	0.000	11.075	0.076	0.076	0.000	0.000	0.000	0.000
33	D	35	GLN	0	-0.025	-0.030	11.928	0.283	0.283	0.000	0.000	0.000	0.000
34	D	36	VAL	0	0.002	0.006	12.202	0.089	0.089	0.000	0.000	0.000	0.000
35	D	37	LEU	0	0.020	0.007	10.344	0.003	0.003	0.000	0.000	0.000	0.000
36	D	38	LEU	0	0.006	0.001	7.322	0.205	0.205	0.000	0.000	0.000	0.000
37	D	39	GLN	0	-0.019	0.001	7.561	0.475	0.475	0.000	0.000	0.000	0.000
38	D	40	PHE	0	0.026	0.009	8.137	-0.187	-0.187	0.000	0.000	0.000	0.000
39	D	41	ASP	-1	-0.725	-0.843	3.653	1.815	2.084	0.003	-0.068	-0.204	0.000
40	D	42	LYS	1	0.866	0.937	4.568	-2.735	-2.628	-0.001	-0.013	-0.093	0.000
41	D	43	ALA	0	0.003	0.010	6.104	-0.535	-0.535	0.000	0.000	0.000	0.000
42	D	44	ILE	0	-0.009	-0.004	5.960	-0.232	-0.232	0.000	0.000	0.000	0.000
43	D	45	ASN	0	-0.017	-0.035	2.530	-5.183	-2.167	1.148	-1.623	-2.541	-0.020
44	D	46	ALA	0	0.023	0.017	5.834	-0.062	-0.062	0.000	0.000	0.000	0.000
45	D	47	ALA	0	-0.017	-0.012	8.875	-0.010	-0.010	0.000	0.000	0.000	0.000
46	D	48	LEU	0	-0.018	0.003	6.862	0.123	0.123	0.000	0.000	0.000	0.000
47	D	49	ALA	0	0.045	0.020	7.646	0.116	0.116	0.000	0.000	0.000	0.000
48	D	50	GLN	0	-0.005	0.002	9.695	-0.007	-0.007	0.000	0.000	0.000	0.000
49	D	51	ARG	1	0.840	0.922	13.011	0.582	0.582	0.000	0.000	0.000	0.000
50	D	52	VAL	0	0.002	0.007	12.674	0.083	0.083	0.000	0.000	0.000	0.000
51	D	53	ARG	1	0.867	0.930	14.101	0.456	0.456	0.000	0.000	0.000	0.000
52	D	54	ASN	0	-0.054	-0.031	16.417	0.036	0.036	0.000	0.000	0.000	0.000
53	D	55	ARG	1	0.905	0.941	16.536	0.537	0.537	0.000	0.000	0.000	0.000
54	D	56	VAL	0	0.036	0.031	17.198	0.065	0.065	0.000	0.000	0.000	0.000
55	D	57	ASN	0	-0.031	-0.014	18.426	-0.093	-0.093	0.000	0.000	0.000	0.000
56	D	58	PHE	0	0.033	0.011	16.259	0.034	0.034	0.000	0.000	0.000	0.000
57	D	59	ARG	1	0.947	0.974	21.531	0.340	0.340	0.000	0.000	0.000	0.000
58	D	60	GLY	0	0.059	0.038	23.817	0.019	0.019	0.000	0.000	0.000	0.000
59	D	61	SER	0	-0.033	-0.004	24.398	-0.012	-0.012	0.000	0.000	0.000	0.000
60	D	62	LEU	0	0.007	-0.011	19.156	-0.013	-0.013	0.000	0.000	0.000	0.000
61	D	63	ASN	0	-0.044	-0.001	22.724	0.026	0.026	0.000	0.000	0.000	0.000
62	D	64	THR	0	0.011	-0.018	20.823	0.020	0.020	0.000	0.000	0.000	0.000
63	D	65	TYR	0	-0.014	-0.010	16.975	-0.038	-0.038	0.000	0.000	0.000	0.000
64	D	66	ARG	1	0.941	0.969	14.135	0.106	0.106	0.000	0.000	0.000	0.000
65	D	67	PHE	0	0.006	0.011	8.807	-0.032	-0.032	0.000	0.000	0.000	0.000
66	D	68	CYS	0	-0.044	-0.035	11.003	0.035	0.035	0.000	0.000	0.000	0.000
67	D	69	ASP	-1	-0.832	-0.898	8.183	0.382	0.382	0.000	0.000	0.000	0.000
68	D	70	ASN	0	-0.035	-0.018	6.086	0.006	0.006	0.000	0.000	0.000	0.000
69	D	71	VAL	0	-0.006	-0.006	5.128	-0.530	-0.530	0.000	0.000	0.000	0.000
70	D	72	TRP	0	0.038	0.019	7.540	0.268	0.268	0.000	0.000	0.000	0.000
71	D	73	THR	0	-0.068	-0.054	10.564	0.136	0.136	0.000	0.000	0.000	0.000
72	D	74	PHE	0	0.000	-0.004	12.288	0.037	0.037	0.000	0.000	0.000	0.000
73	D	75	VAL	0	-0.029	-0.012	16.326	0.030	0.030	0.000	0.000	0.000	0.000
74	D	76	LEU	0	0.004	0.005	18.080	-0.009	-0.009	0.000	0.000	0.000	0.000
75	D	77	ASN	0	0.007	-0.028	21.401	0.028	0.028	0.000	0.000	0.000	0.000
76	D	78	ASP	-1	-0.905	-0.937	24.805	-0.194	-0.194	0.000	0.000	0.000	0.000
77	D	79	VAL	0	-0.064	-0.029	21.170	-0.018	-0.018	0.000	0.000	0.000	0.000
78	D	80	GLU	-1	-0.813	-0.893	24.624	-0.234	-0.234	0.000	0.000	0.000	0.000
79	D	81	PHE	0	-0.001	-0.017	17.224	-0.039	-0.039	0.000	0.000	0.000	0.000
80	D	82	ARG	1	0.743	0.828	22.236	0.327	0.327	0.000	0.000	0.000	0.000
81	D	83	GLU	-1	-0.822	-0.902	19.931	-0.557	-0.557	0.000	0.000	0.000	0.000
82	D	84	VAL	0	0.001	-0.012	23.111	0.027	0.027	0.000	0.000	0.000	0.000
83	D	85	THR	0	-0.025	-0.010	25.704	0.016	0.016	0.000	0.000	0.000	0.000
84	D	86	GLU	-1	-0.800	-0.867	27.169	-0.247	-0.247	0.000	0.000	0.000	0.000
85	D	87	LEU	0	-0.040	-0.015	26.166	-0.024	-0.024	0.000	0.000	0.000	0.000
86	D	88	ILE	0	0.028	0.009	22.040	0.012	0.012	0.000	0.000	0.000	0.000
87	D	89	LYS	1	0.880	0.937	24.364	0.195	0.195	0.000	0.000	0.000	0.000
88	D	90	VAL	0	-0.007	-0.007	21.367	0.007	0.007	0.000	0.000	0.000	0.000
89	D	91	ASP	-1	-0.834	-0.898	24.876	-0.163	-0.163	0.000	0.000	0.000	0.000
90	D	92	LYS	1	0.941	0.964	21.453	0.104	0.104	0.000	0.000	0.000	0.000
91	D	93	VAL	0	-0.002	0.012	16.942	0.003	0.003	0.000	0.000	0.000	0.000
92	D	94	LYS	1	0.933	0.979	13.183	0.079	0.079	0.000	0.000	0.000	0.000
93	D	95	ILE	0	0.014	0.008	12.472	-0.014	-0.014	0.000	0.000	0.000	0.000
94	D	96	VAL	0	-0.017	-0.021	8.038	0.062	0.062	0.000	0.000	0.000	0.000
95	D	97	ALA	0	0.004	0.006	7.453	-0.020	-0.020	0.000	0.000	0.000	0.000
96	D	98	CYS	0	-0.017	0.006	2.865	-1.444	0.642	1.690	-1.002	-2.774	0.008
97	D	99	ASP	-1	-0.905	-0.920	1.678	-24.457	-29.032	13.408	-4.870	-3.963	-0.047

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Interactive mode: IFIE and PIEDA for fragment #1(D:3:TYR)