FMO DATABASE

FMODB ID: JQ559

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

Total energy (hartree)

FMO2-HF: Electronic energy	-642767.034236
FMO2-HF: Nuclear repulsion	603640.212584
FMO2-HF: Total energy	-39126.821652
FMO2-MP2: Total energy	-39242.094235

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.
-30.503	-25.265	15.712	-9.277	-11.674	-0.035

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 : 0.005 / 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

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	-0.005	-0.025	2.163	-3.854	0.472	2.659	-3.120	-3.864	0.009
4	D	6	TYR	0	-0.007	-0.013	3.639	-0.025	0.550	0.023	-0.032	-0.567	0.000
5	D	7	ARG	1	0.867	0.913	6.675	-1.281	-1.281	0.000	0.000	0.000	0.000
6	D	8	ASN	0	-0.022	0.009	8.839	0.088	0.088	0.000	0.000	0.000	0.000
7	D	9	THR	0	-0.011	-0.011	9.484	-0.065	-0.065	0.000	0.000	0.000	0.000
8	D	10	THR	0	0.075	0.030	12.240	0.041	0.041	0.000	0.000	0.000	0.000
9	D	11	LEU	0	-0.007	0.001	12.195	0.036	0.036	0.000	0.000	0.000	0.000
10	D	12	GLY	0	0.005	0.008	11.410	0.052	0.052	0.000	0.000	0.000	0.000
11	D	13	ASN	0	-0.003	-0.008	12.344	0.042	0.042	0.000	0.000	0.000	0.000
12	D	14	SER	0	0.044	0.025	14.967	0.034	0.034	0.000	0.000	0.000	0.000
13	D	15	LEU	0	-0.041	-0.003	12.351	0.034	0.034	0.000	0.000	0.000	0.000
14	D	16	GLN	0	-0.003	-0.026	12.125	0.045	0.045	0.000	0.000	0.000	0.000
15	D	17	GLU	-1	-0.870	-0.928	15.952	0.087	0.087	0.000	0.000	0.000	0.000
16	D	18	SER	0	0.000	-0.014	19.264	-0.002	-0.002	0.000	0.000	0.000	0.000
17	D	19	LEU	0	-0.083	-0.052	15.161	0.019	0.019	0.000	0.000	0.000	0.000
18	D	20	ASP	-1	-0.879	-0.949	18.850	0.318	0.318	0.000	0.000	0.000	0.000
19	D	21	GLU	-1	-0.944	-0.953	20.964	0.115	0.115	0.000	0.000	0.000	0.000
20	D	22	LEU	0	-0.018	-0.001	21.459	0.002	0.002	0.000	0.000	0.000	0.000
21	D	23	ILE	0	-0.041	-0.015	19.056	0.016	0.016	0.000	0.000	0.000	0.000
22	D	24	GLN	0	-0.048	-0.017	23.591	-0.008	-0.008	0.000	0.000	0.000	0.000
23	D	25	SER	0	-0.088	-0.060	26.285	-0.002	-0.002	0.000	0.000	0.000	0.000
24	D	26	GLN	0	-0.042	-0.042	27.012	-0.011	-0.011	0.000	0.000	0.000	0.000
25	D	27	GLN	0	-0.007	0.020	26.114	-0.003	-0.003	0.000	0.000	0.000	0.000
26	D	28	ILE	0	-0.035	-0.005	19.783	0.013	0.013	0.000	0.000	0.000	0.000
27	D	29	THR	0	0.023	0.010	21.939	0.011	0.011	0.000	0.000	0.000	0.000
28	D	30	PRO	0	0.103	0.029	19.326	0.025	0.025	0.000	0.000	0.000	0.000
29	D	31	GLN	0	0.001	0.013	16.616	0.124	0.124	0.000	0.000	0.000	0.000
30	D	32	LEU	0	0.033	0.019	16.705	0.088	0.088	0.000	0.000	0.000	0.000
31	D	33	ALA	0	0.093	0.045	16.514	0.036	0.036	0.000	0.000	0.000	0.000
32	D	34	LEU	0	-0.017	-0.013	11.089	0.054	0.054	0.000	0.000	0.000	0.000
33	D	35	GLN	0	-0.031	-0.035	12.020	0.246	0.246	0.000	0.000	0.000	0.000
34	D	36	VAL	0	-0.002	0.008	12.483	0.065	0.065	0.000	0.000	0.000	0.000
35	D	37	LEU	0	0.007	0.005	10.194	-0.008	-0.008	0.000	0.000	0.000	0.000
36	D	38	LEU	0	-0.006	0.002	7.471	0.143	0.143	0.000	0.000	0.000	0.000
37	D	39	GLN	0	-0.010	-0.001	7.648	0.326	0.326	0.000	0.000	0.000	0.000
38	D	40	PHE	0	0.032	0.008	8.381	-0.184	-0.184	0.000	0.000	0.000	0.000
39	D	41	ASP	-1	-0.733	-0.840	3.679	1.274	1.492	0.001	-0.041	-0.178	0.000
40	D	42	LYS	1	0.899	0.952	5.132	-2.310	-2.230	-0.001	-0.004	-0.076	0.000
41	D	43	ALA	0	-0.001	0.002	6.394	-0.421	-0.421	0.000	0.000	0.000	0.000
42	D	44	ILE	0	-0.016	-0.006	6.281	-0.158	-0.158	0.000	0.000	0.000	0.000
43	D	45	ASN	0	-0.036	-0.042	2.786	-3.566	-1.272	0.224	-1.060	-1.458	-0.009
44	D	46	ALA	0	0.005	0.008	6.315	-0.051	-0.051	0.000	0.000	0.000	0.000
45	D	47	ALA	0	-0.023	-0.017	9.211	0.006	0.006	0.000	0.000	0.000	0.000
46	D	48	LEU	0	-0.042	-0.022	7.209	0.083	0.083	0.000	0.000	0.000	0.000
47	D	49	ALA	0	0.018	0.022	8.076	0.044	0.044	0.000	0.000	0.000	0.000
48	D	50	GLN	0	-0.003	0.007	10.043	0.019	0.019	0.000	0.000	0.000	0.000
49	D	51	ARG	1	0.940	0.977	13.196	0.482	0.482	0.000	0.000	0.000	0.000
50	D	52	VAL	0	-0.034	-0.013	13.383	0.067	0.067	0.000	0.000	0.000	0.000
51	D	53	ARG	1	0.898	0.944	14.567	0.429	0.429	0.000	0.000	0.000	0.000
52	D	54	ASN	0	-0.035	-0.018	16.687	0.011	0.011	0.000	0.000	0.000	0.000
53	D	55	ARG	1	0.923	0.953	16.859	0.492	0.492	0.000	0.000	0.000	0.000
54	D	56	VAL	0	0.023	0.015	17.775	0.053	0.053	0.000	0.000	0.000	0.000
55	D	57	ASN	0	-0.056	-0.032	19.254	-0.073	-0.073	0.000	0.000	0.000	0.000
56	D	58	PHE	0	0.052	0.032	16.389	0.035	0.035	0.000	0.000	0.000	0.000
57	D	59	ARG	1	0.955	0.983	21.667	0.318	0.318	0.000	0.000	0.000	0.000
58	D	60	GLY	0	0.080	0.038	23.890	0.015	0.015	0.000	0.000	0.000	0.000
59	D	61	SER	0	-0.023	0.013	24.799	-0.008	-0.008	0.000	0.000	0.000	0.000
60	D	62	LEU	0	-0.010	-0.014	19.151	-0.006	-0.006	0.000	0.000	0.000	0.000
61	D	63	ASN	0	-0.043	-0.007	22.407	0.025	0.025	0.000	0.000	0.000	0.000
62	D	64	THR	0	0.007	-0.014	20.223	0.017	0.017	0.000	0.000	0.000	0.000
63	D	65	TYR	0	0.000	-0.005	17.057	-0.043	-0.043	0.000	0.000	0.000	0.000
64	D	66	ARG	1	0.953	0.975	14.045	0.197	0.197	0.000	0.000	0.000	0.000
65	D	67	PHE	0	0.003	0.010	9.384	-0.040	-0.040	0.000	0.000	0.000	0.000
66	D	68	CYS	0	-0.029	-0.026	11.077	0.067	0.067	0.000	0.000	0.000	0.000
67	D	69	ASP	-1	-0.840	-0.903	8.200	0.177	0.177	0.000	0.000	0.000	0.000
68	D	70	ASN	0	-0.053	-0.031	6.151	-0.126	-0.126	0.000	0.000	0.000	0.000
69	D	71	VAL	0	0.002	0.002	5.354	-0.527	-0.527	0.000	0.000	0.000	0.000
70	D	72	TRP	0	0.019	0.012	7.700	0.326	0.326	0.000	0.000	0.000	0.000
71	D	73	THR	0	-0.066	-0.038	10.738	0.051	0.051	0.000	0.000	0.000	0.000
72	D	74	PHE	0	-0.015	-0.014	12.656	0.065	0.065	0.000	0.000	0.000	0.000
73	D	75	VAL	0	-0.010	-0.014	16.139	0.027	0.027	0.000	0.000	0.000	0.000
74	D	76	LEU	0	-0.018	-0.001	18.093	0.007	0.007	0.000	0.000	0.000	0.000
75	D	77	ASN	0	0.013	-0.020	21.253	0.020	0.020	0.000	0.000	0.000	0.000
76	D	78	ASP	-1	-0.909	-0.954	24.625	-0.205	-0.205	0.000	0.000	0.000	0.000
77	D	79	VAL	0	-0.076	-0.032	20.868	-0.017	-0.017	0.000	0.000	0.000	0.000
78	D	80	GLU	-1	-0.810	-0.912	24.280	-0.229	-0.229	0.000	0.000	0.000	0.000
79	D	81	PHE	0	-0.040	-0.028	17.455	-0.029	-0.029	0.000	0.000	0.000	0.000
80	D	82	ARG	1	0.755	0.833	22.650	0.307	0.307	0.000	0.000	0.000	0.000
81	D	83	GLU	-1	-0.833	-0.910	20.709	-0.502	-0.502	0.000	0.000	0.000	0.000
82	D	84	VAL	0	0.016	-0.011	23.695	0.028	0.028	0.000	0.000	0.000	0.000
83	D	85	THR	0	-0.051	0.004	26.373	0.016	0.016	0.000	0.000	0.000	0.000
84	D	86	GLU	-1	-0.822	-0.909	28.183	-0.244	-0.244	0.000	0.000	0.000	0.000
85	D	87	LEU	0	-0.041	-0.021	26.338	-0.020	-0.020	0.000	0.000	0.000	0.000
86	D	88	ILE	0	0.072	0.052	22.163	0.011	0.011	0.000	0.000	0.000	0.000
87	D	89	LYS	1	0.854	0.933	24.829	0.192	0.192	0.000	0.000	0.000	0.000
88	D	90	VAL	0	-0.009	-0.005	21.398	0.010	0.010	0.000	0.000	0.000	0.000
89	D	91	ASP	-1	-0.810	-0.889	24.855	-0.176	-0.176	0.000	0.000	0.000	0.000
90	D	92	LYS	1	0.931	0.959	21.113	0.141	0.141	0.000	0.000	0.000	0.000
91	D	93	VAL	0	0.002	0.013	16.850	0.002	0.002	0.000	0.000	0.000	0.000
92	D	94	LYS	1	0.940	0.981	13.235	0.179	0.179	0.000	0.000	0.000	0.000
93	D	95	ILE	0	-0.003	-0.003	12.133	-0.010	-0.010	0.000	0.000	0.000	0.000
94	D	96	VAL	0	0.003	0.005	7.615	0.019	0.019	0.000	0.000	0.000	0.000
95	D	97	ALA	0	-0.007	-0.010	7.720	-0.013	-0.013	0.000	0.000	0.000	0.000
96	D	98	CYS	0	0.000	0.010	2.890	-1.451	0.301	1.028	-0.774	-2.007	0.007
97	D	99	ASP	-1	-0.901	-0.928	1.695	-22.107	-26.114	11.778	-4.246	-3.524	-0.042

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