FMO DATABASE

FMODB ID: 43R5N

Calculation Name: 1NVP-D-Xray319

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	99
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-648976.679163
FMO2-HF: Nuclear repulsion	609679.459766
FMO2-HF: Total energy	-39297.219397
FMO2-MP2: Total energy	-39413.133176

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:2:ACE )

Summations of interaction energy for fragment #1(D:2:ACE )

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.
-0.292	0.548	-0.003	-0.398	-0.439	0

Interaction energy analysis for fragmet #1(D:2:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.017

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].
3	D	4	GLN	0	-0.054	-0.002	3.852	1.111	1.954	-0.005	-0.354	-0.484
4	D	5	LEU	0	0.004	-0.028	6.591	0.256	0.256	0.000	0.000	0.000
5	D	6	TYR	0	-0.008	-0.014	6.427	0.256	0.256	0.000	0.000	0.000
6	D	7	ARG	1	0.857	0.917	7.583	0.292	0.292	0.000	0.000	0.000
7	D	8	ASN	0	-0.016	0.011	11.804	0.065	0.065	0.000	0.000	0.000
8	D	9	THR	0	-0.011	-0.018	13.218	0.011	0.011	0.000	0.000	0.000
9	D	10	THR	0	0.073	0.029	15.883	0.008	0.008	0.000	0.000	0.000
10	D	11	LEU	0	-0.016	-0.003	13.677	0.009	0.009	0.000	0.000	0.000
11	D	12	GLY	0	0.012	0.010	13.817	0.020	0.020	0.000	0.000	0.000
12	D	13	ASN	0	0.028	0.006	14.564	-0.003	-0.003	0.000	0.000	0.000
13	D	14	SER	0	0.035	0.024	17.553	0.018	0.018	0.000	0.000	0.000
14	D	15	LEU	0	-0.037	0.003	13.432	0.016	0.016	0.000	0.000	0.000
15	D	16	GLN	0	-0.026	-0.041	14.686	-0.022	-0.022	0.000	0.000	0.000
16	D	17	GLU	-1	-0.862	-0.920	17.464	-0.051	-0.051	0.000	0.000	0.000
17	D	18	SER	0	0.001	-0.017	20.303	0.009	0.009	0.000	0.000	0.000
18	D	19	LEU	0	-0.087	-0.050	15.570	0.009	0.009	0.000	0.000	0.000
19	D	20	ASP	-1	-0.867	-0.952	20.118	-0.045	-0.045	0.000	0.000	0.000
20	D	21	GLU	-1	-0.944	-0.952	22.089	-0.001	-0.001	0.000	0.000	0.000
21	D	22	LEU	0	-0.009	0.003	21.923	0.004	0.004	0.000	0.000	0.000
22	D	23	ILE	0	-0.053	-0.018	19.592	0.004	0.004	0.000	0.000	0.000
23	D	24	GLN	0	-0.059	-0.022	24.031	0.001	0.001	0.000	0.000	0.000
24	D	25	SER	0	-0.080	-0.044	27.120	0.001	0.001	0.000	0.000	0.000
25	D	26	GLN	0	-0.034	-0.035	27.140	0.006	0.006	0.000	0.000	0.000
26	D	27	GLN	0	-0.006	0.006	26.446	0.002	0.002	0.000	0.000	0.000
27	D	28	ILE	0	-0.049	-0.008	19.894	0.012	0.012	0.000	0.000	0.000
28	D	29	THR	0	0.019	0.009	21.252	-0.007	-0.007	0.000	0.000	0.000
29	D	30	PRO	0	0.098	0.026	19.615	0.007	0.007	0.000	0.000	0.000
30	D	31	GLN	0	0.000	0.005	15.900	0.021	0.021	0.000	0.000	0.000
31	D	32	LEU	0	0.034	0.017	15.990	0.022	0.022	0.000	0.000	0.000
32	D	33	ALA	0	0.089	0.043	16.080	0.023	0.023	0.000	0.000	0.000
33	D	34	LEU	0	-0.014	-0.013	11.299	0.002	0.002	0.000	0.000	0.000
34	D	35	GLN	0	-0.012	-0.022	11.619	0.076	0.076	0.000	0.000	0.000
35	D	36	VAL	0	0.003	0.015	11.809	0.073	0.073	0.000	0.000	0.000
36	D	37	LEU	0	0.006	0.001	10.721	0.036	0.036	0.000	0.000	0.000
37	D	38	LEU	0	-0.024	-0.005	6.782	0.034	0.034	0.000	0.000	0.000
38	D	39	GLN	0	-0.032	-0.011	7.171	0.290	0.290	0.000	0.000	0.000
39	D	40	PHE	0	0.018	-0.002	9.318	0.101	0.101	0.000	0.000	0.000
40	D	41	ASP	-1	-0.731	-0.837	4.591	-0.170	-0.173	0.000	-0.005	0.008
41	D	42	LYS	1	0.933	0.977	5.008	-1.112	-1.112	0.000	0.000	0.000
42	D	43	ALA	0	0.005	0.005	6.180	-0.115	-0.115	0.000	0.000	0.000
43	D	44	ILE	0	-0.007	0.000	7.735	-0.066	-0.066	0.000	0.000	0.000
44	D	45	ASN	0	-0.041	-0.051	4.325	-0.423	-0.423	0.002	-0.039	0.037
45	D	46	ALA	0	-0.002	0.005	6.650	-0.077	-0.077	0.000	0.000	0.000
46	D	47	ALA	0	-0.024	-0.018	8.661	-0.098	-0.098	0.000	0.000	0.000
47	D	48	LEU	0	-0.039	-0.020	9.211	-0.041	-0.041	0.000	0.000	0.000
48	D	49	ALA	0	0.018	0.023	9.366	-0.027	-0.027	0.000	0.000	0.000
49	D	50	GLN	0	-0.007	0.004	11.285	-0.009	-0.009	0.000	0.000	0.000
50	D	51	ARG	1	0.936	0.976	13.776	-0.108	-0.108	0.000	0.000	0.000
51	D	52	VAL	0	-0.022	-0.008	15.130	-0.011	-0.011	0.000	0.000	0.000
52	D	53	ARG	1	0.892	0.941	16.266	-0.070	-0.070	0.000	0.000	0.000
53	D	54	ASN	0	-0.037	-0.011	18.686	0.003	0.003	0.000	0.000	0.000
54	D	55	ARG	1	0.952	0.970	19.613	0.046	0.046	0.000	0.000	0.000
55	D	56	VAL	0	0.026	0.016	21.012	0.005	0.005	0.000	0.000	0.000
56	D	57	ASN	0	-0.076	-0.040	22.807	-0.010	-0.010	0.000	0.000	0.000
57	D	58	PHE	0	0.044	0.023	21.062	0.003	0.003	0.000	0.000	0.000
58	D	59	ARG	1	0.960	0.984	25.853	0.066	0.066	0.000	0.000	0.000
59	D	60	GLY	0	0.083	0.040	28.517	0.002	0.002	0.000	0.000	0.000
60	D	61	SER	0	-0.033	0.011	29.723	-0.001	-0.001	0.000	0.000	0.000
61	D	62	LEU	0	-0.001	-0.011	24.582	-0.006	-0.006	0.000	0.000	0.000
62	D	63	ASN	0	-0.061	-0.022	27.751	0.002	0.002	0.000	0.000	0.000
63	D	64	THR	0	-0.002	-0.016	25.645	-0.004	-0.004	0.000	0.000	0.000
64	D	65	TYR	0	0.023	-0.003	22.940	-0.007	-0.007	0.000	0.000	0.000
65	D	66	ARG	1	0.952	0.974	20.132	0.228	0.228	0.000	0.000	0.000
66	D	67	PHE	0	0.010	0.017	15.791	-0.018	-0.018	0.000	0.000	0.000
67	D	68	CYS	0	0.002	-0.009	17.365	0.046	0.046	0.000	0.000	0.000
68	D	69	ASP	-1	-0.888	-0.927	13.364	-0.441	-0.441	0.000	0.000	0.000
69	D	70	ASN	0	-0.053	-0.039	12.346	-0.057	-0.057	0.000	0.000	0.000
70	D	71	VAL	0	0.009	0.011	11.337	-0.066	-0.066	0.000	0.000	0.000
71	D	72	TRP	0	0.011	0.007	13.934	0.088	0.088	0.000	0.000	0.000
72	D	73	THR	0	-0.059	-0.034	16.145	-0.028	-0.028	0.000	0.000	0.000
73	D	74	PHE	0	-0.009	-0.011	18.587	0.028	0.028	0.000	0.000	0.000
74	D	75	VAL	0	-0.030	-0.020	21.625	-0.006	-0.006	0.000	0.000	0.000
75	D	76	LEU	0	-0.018	-0.001	23.429	0.008	0.008	0.000	0.000	0.000
76	D	77	ASN	0	0.014	-0.002	26.488	-0.003	-0.003	0.000	0.000	0.000
77	D	78	ASP	-1	-0.888	-0.945	29.865	-0.072	-0.072	0.000	0.000	0.000
78	D	79	VAL	0	-0.078	-0.035	25.632	-0.001	-0.001	0.000	0.000	0.000
79	D	80	GLU	-1	-0.902	-0.978	28.818	-0.051	-0.051	0.000	0.000	0.000
80	D	81	PHE	0	-0.041	-0.029	21.896	-0.004	-0.004	0.000	0.000	0.000
81	D	82	ARG	1	0.906	0.946	26.160	0.056	0.056	0.000	0.000	0.000
82	D	83	GLU	-1	-0.819	-0.909	23.450	-0.049	-0.049	0.000	0.000	0.000
83	D	84	VAL	0	0.009	-0.016	26.749	0.004	0.004	0.000	0.000	0.000
84	D	85	THR	0	-0.050	0.005	29.134	0.002	0.002	0.000	0.000	0.000
85	D	86	GLU	-1	-0.895	-0.957	31.023	-0.040	-0.040	0.000	0.000	0.000
86	D	87	LEU	0	-0.041	-0.047	29.636	-0.004	-0.004	0.000	0.000	0.000
87	D	88	ILE	0	0.048	0.054	25.390	0.002	0.002	0.000	0.000	0.000
88	D	89	LYS	1	0.868	0.947	28.936	0.045	0.045	0.000	0.000	0.000
89	D	90	VAL	0	-0.009	0.004	26.286	0.001	0.001	0.000	0.000	0.000
90	D	91	ASP	-1	-0.798	-0.886	29.597	-0.070	-0.070	0.000	0.000	0.000
91	D	92	LYS	1	0.922	0.943	26.539	0.106	0.106	0.000	0.000	0.000
92	D	93	VAL	0	0.002	0.018	21.894	0.000	0.000	0.000	0.000	0.000
93	D	94	LYS	1	0.944	0.975	19.411	0.217	0.217	0.000	0.000	0.000
94	D	95	ILE	0	0.002	0.003	17.068	-0.005	-0.005	0.000	0.000	0.000
95	D	96	VAL	0	0.003	0.006	13.158	0.008	0.008	0.000	0.000	0.000
96	D	97	ALA	0	-0.012	-0.012	12.655	-0.014	-0.014	0.000	0.000	0.000
97	D	98	CYS	0	-0.011	-0.001	8.408	-0.045	-0.045	0.000	0.000	0.000
98	D	99	ASP	-1	-0.889	-0.950	10.160	-0.405	-0.405	0.000	0.000	0.000
99	D	100	NME	0	-0.032	0.002	8.759	-0.190	-0.190	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:2:ACE )