FMO DATABASE

FMODB ID: 5J29Z

Calculation Name: 2NWV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NWV

Chain ID: A

ChEMBL ID:

UniProt ID: Q3M7V9

Base Structure: X-ray

Registration Date: 2023-09-21

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	112
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-955771.024833
FMO2-HF: Nuclear repulsion	909532.267879
FMO2-HF: Total energy	-46238.756954
FMO2-MP2: Total energy	-46375.509155

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(A:2:ASP)

Summations of interaction energy for fragment #1(A:2:ASP)

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.
-5.833	-11.377	20.94	-3.27	-12.125	0.121

Interaction energy analysis for fragmet #1(A:2:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.844 / q_NPA : -0.927

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	A	4	VAL	0	0.044	0.022	2.924	5.713	0.824	1.874	5.484	-2.470	0.008
4	A	5	ALA	0	-0.009	-0.004	2.054	-25.724	-24.470	8.064	-4.419	-4.899	0.062
5	A	6	GLU	-1	-0.820	-0.902	1.813	14.770	12.245	10.982	-4.035	-4.421	0.048
6	A	7	TYR	0	-0.004	-0.046	3.848	-13.917	-13.301	0.020	-0.300	-0.335	0.003
7	A	8	ARG	1	0.849	0.902	5.692	-44.347	-44.347	0.000	0.000	0.000	0.000
8	A	9	LYS	1	0.797	0.887	6.583	-46.633	-46.633	0.000	0.000	0.000	0.000
9	A	10	LEU	0	0.020	0.014	7.803	-4.605	-4.605	0.000	0.000	0.000	0.000
10	A	11	ILE	0	0.014	0.003	9.668	-3.511	-3.511	0.000	0.000	0.000	0.000
11	A	12	LYS	1	0.787	0.880	10.572	-30.586	-30.586	0.000	0.000	0.000	0.000
12	A	13	GLN	0	-0.072	-0.018	12.247	-0.110	-0.110	0.000	0.000	0.000	0.000
13	A	14	VAL	0	0.047	0.027	13.720	-1.741	-1.741	0.000	0.000	0.000	0.000
14	A	15	LEU	0	0.003	-0.002	15.604	-1.458	-1.458	0.000	0.000	0.000	0.000
15	A	16	THR	0	-0.029	-0.034	16.545	-1.355	-1.355	0.000	0.000	0.000	0.000
16	A	17	GLU	-1	-0.895	-0.940	17.013	17.145	17.145	0.000	0.000	0.000	0.000
17	A	18	TYR	0	-0.038	-0.053	19.545	-0.705	-0.705	0.000	0.000	0.000	0.000
18	A	19	ASP	-1	-0.827	-0.864	21.492	12.128	12.128	0.000	0.000	0.000	0.000
19	A	20	ASN	0	-0.028	-0.022	22.117	-1.148	-1.148	0.000	0.000	0.000	0.000
20	A	21	LEU	0	0.008	0.005	22.324	-0.619	-0.619	0.000	0.000	0.000	0.000
21	A	22	SER	0	-0.044	-0.037	25.492	-0.687	-0.687	0.000	0.000	0.000	0.000
22	A	23	ARG	1	0.795	0.892	27.450	-11.349	-11.349	0.000	0.000	0.000	0.000
23	A	24	GLN	0	-0.053	-0.025	28.526	-0.046	-0.046	0.000	0.000	0.000	0.000
24	A	25	SER	0	-0.027	-0.012	30.852	-0.147	-0.147	0.000	0.000	0.000	0.000
25	A	26	PRO	0	-0.050	-0.021	32.435	-0.223	-0.223	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.884	-0.912	33.851	8.427	8.427	0.000	0.000	0.000	0.000
27	A	28	THR	0	-0.043	-0.052	34.387	0.134	0.134	0.000	0.000	0.000	0.000
28	A	29	ASN	0	-0.032	-0.026	30.383	0.122	0.122	0.000	0.000	0.000	0.000
29	A	30	TYR	0	0.003	-0.001	32.274	-0.287	-0.287	0.000	0.000	0.000	0.000
30	A	31	GLU	-1	-0.891	-0.928	31.373	10.445	10.445	0.000	0.000	0.000	0.000
31	A	32	THR	0	-0.048	-0.060	26.273	-0.190	-0.190	0.000	0.000	0.000	0.000
32	A	33	CYS	0	-0.083	-0.043	25.145	-0.164	-0.164	0.000	0.000	0.000	0.000
33	A	34	LEU	0	0.032	0.028	19.277	0.197	0.197	0.000	0.000	0.000	0.000
34	A	35	VAL	0	-0.035	-0.016	19.889	-0.348	-0.348	0.000	0.000	0.000	0.000
35	A	36	PHE	0	0.040	0.011	14.619	0.928	0.928	0.000	0.000	0.000	0.000
36	A	37	ASP	-1	-0.767	-0.852	15.414	18.233	18.233	0.000	0.000	0.000	0.000
37	A	38	GLU	-1	-0.786	-0.888	10.027	30.255	30.255	0.000	0.000	0.000	0.000
38	A	39	ASN	0	-0.087	-0.039	11.681	1.777	1.777	0.000	0.000	0.000	0.000
39	A	40	HIS	1	0.783	0.853	14.447	-17.453	-17.453	0.000	0.000	0.000	0.000
40	A	41	ASP	-1	-0.766	-0.819	9.848	31.814	31.814	0.000	0.000	0.000	0.000
41	A	42	ASN	0	-0.041	-0.019	12.868	-0.800	-0.800	0.000	0.000	0.000	0.000
42	A	43	TYR	0	0.009	-0.032	10.472	0.269	0.269	0.000	0.000	0.000	0.000
43	A	44	LEU	0	0.010	0.003	15.975	-0.481	-0.481	0.000	0.000	0.000	0.000
44	A	45	TRP	0	0.012	0.000	19.475	0.407	0.407	0.000	0.000	0.000	0.000
45	A	46	LEU	0	-0.026	-0.008	21.855	-0.463	-0.463	0.000	0.000	0.000	0.000
46	A	47	ALA	0	0.099	0.064	25.527	-0.047	-0.047	0.000	0.000	0.000	0.000
47	A	48	VAL	0	-0.050	-0.046	28.433	-0.063	-0.063	0.000	0.000	0.000	0.000
48	A	49	ASP	-1	-0.718	-0.828	31.332	8.941	8.941	0.000	0.000	0.000	0.000
49	A	50	TRP	0	-0.066	-0.043	34.715	-0.103	-0.103	0.000	0.000	0.000	0.000
50	A	51	GLN	0	0.075	0.059	38.556	0.043	0.043	0.000	0.000	0.000	0.000
51	A	52	GLY	0	0.002	-0.006	40.589	-0.218	-0.218	0.000	0.000	0.000	0.000
52	A	53	SER	0	-0.006	-0.028	42.393	0.090	0.090	0.000	0.000	0.000	0.000
53	A	54	LYS	1	0.935	0.984	39.169	-8.033	-8.033	0.000	0.000	0.000	0.000
54	A	55	ARG	1	0.830	0.905	33.825	-9.127	-9.127	0.000	0.000	0.000	0.000
55	A	56	ILE	0	-0.037	-0.014	33.467	-0.093	-0.093	0.000	0.000	0.000	0.000
56	A	57	LYS	1	0.853	0.931	27.882	-10.928	-10.928	0.000	0.000	0.000	0.000
57	A	58	TYR	0	-0.009	-0.010	28.783	-0.345	-0.345	0.000	0.000	0.000	0.000
58	A	59	THR	0	-0.030	-0.019	23.619	0.104	0.104	0.000	0.000	0.000	0.000
59	A	60	TYR	0	0.029	0.023	24.263	-0.505	-0.505	0.000	0.000	0.000	0.000
60	A	61	VAL	0	0.016	0.002	18.672	0.089	0.089	0.000	0.000	0.000	0.000
61	A	62	HIS	0	-0.089	-0.049	18.478	-0.491	-0.491	0.000	0.000	0.000	0.000
62	A	63	ILE	0	0.013	0.008	13.476	-0.051	-0.051	0.000	0.000	0.000	0.000
63	A	64	ARG	1	0.900	0.949	14.232	-18.826	-18.826	0.000	0.000	0.000	0.000
64	A	65	ILE	0	0.001	0.023	7.357	-0.137	-0.137	0.000	0.000	0.000	0.000
65	A	66	LYS	1	0.729	0.849	11.442	-17.959	-17.959	0.000	0.000	0.000	0.000
66	A	67	ASN	0	-0.063	-0.043	13.433	0.024	0.024	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.898	-0.950	8.721	31.701	31.701	0.000	0.000	0.000	0.000
68	A	69	LYS	1	0.781	0.922	9.087	-19.027	-19.027	0.000	0.000	0.000	0.000
69	A	70	ILE	0	0.039	0.013	9.139	-0.413	-0.413	0.000	0.000	0.000	0.000
70	A	71	TYR	0	-0.027	-0.023	12.133	-2.571	-2.571	0.000	0.000	0.000	0.000
71	A	72	ILE	0	0.047	0.015	15.715	0.362	0.362	0.000	0.000	0.000	0.000
72	A	73	GLU	-1	-0.800	-0.900	17.908	15.685	15.685	0.000	0.000	0.000	0.000
73	A	74	GLU	-1	-0.842	-0.906	20.423	11.360	11.360	0.000	0.000	0.000	0.000
74	A	75	ASP	-1	-0.782	-0.883	21.157	15.405	15.405	0.000	0.000	0.000	0.000
75	A	76	TYR	0	-0.097	-0.052	23.154	-0.625	-0.625	0.000	0.000	0.000	0.000
76	A	77	THR	0	-0.056	-0.050	22.186	-0.282	-0.282	0.000	0.000	0.000	0.000
77	A	78	GLU	-1	-0.950	-0.963	25.081	10.302	10.302	0.000	0.000	0.000	0.000
78	A	79	GLU	-1	-0.864	-0.917	22.612	13.357	13.357	0.000	0.000	0.000	0.000
79	A	80	GLY	0	0.027	0.042	22.478	0.239	0.239	0.000	0.000	0.000	0.000
80	A	81	ILE	0	0.027	-0.008	16.161	0.585	0.585	0.000	0.000	0.000	0.000
81	A	82	ALA	0	-0.013	-0.015	16.982	1.060	1.060	0.000	0.000	0.000	0.000
82	A	83	THR	0	-0.041	-0.038	17.328	0.690	0.690	0.000	0.000	0.000	0.000
83	A	84	GLU	-1	-0.820	-0.890	16.389	17.139	17.139	0.000	0.000	0.000	0.000
84	A	85	LEU	0	-0.001	-0.014	11.633	1.147	1.147	0.000	0.000	0.000	0.000
85	A	86	MET	0	-0.032	-0.002	13.134	0.932	0.932	0.000	0.000	0.000	0.000
86	A	87	ARG	1	0.791	0.896	15.133	-14.917	-14.917	0.000	0.000	0.000	0.000
87	A	88	LEU	0	-0.026	-0.011	12.139	0.079	0.079	0.000	0.000	0.000	0.000
88	A	89	GLY	0	-0.016	0.002	11.241	1.873	1.873	0.000	0.000	0.000	0.000
89	A	90	VAL	0	-0.053	-0.022	8.921	1.396	1.396	0.000	0.000	0.000	0.000
90	A	91	THR	0	0.012	0.000	9.766	-2.738	-2.738	0.000	0.000	0.000	0.000
91	A	92	ASN	0	0.067	0.008	12.348	1.226	1.226	0.000	0.000	0.000	0.000
92	A	93	ASN	0	-0.063	-0.035	11.229	-1.712	-1.712	0.000	0.000	0.000	0.000
93	A	94	ASP	-1	-0.789	-0.883	8.249	28.557	28.557	0.000	0.000	0.000	0.000
94	A	95	ILE	0	0.018	0.025	11.790	1.293	1.293	0.000	0.000	0.000	0.000
95	A	96	VAL	0	-0.038	-0.015	14.713	-1.098	-1.098	0.000	0.000	0.000	0.000
96	A	97	LEU	0	0.044	0.029	17.434	0.252	0.252	0.000	0.000	0.000	0.000
97	A	98	ALA	0	-0.034	-0.027	19.141	-0.795	-0.795	0.000	0.000	0.000	0.000
98	A	99	PHE	0	0.061	0.035	21.053	-0.584	-0.584	0.000	0.000	0.000	0.000
99	A	100	HIS	0	-0.023	-0.002	23.845	-0.457	-0.457	0.000	0.000	0.000	0.000
100	A	101	PRO	0	0.032	0.010	25.022	0.421	0.421	0.000	0.000	0.000	0.000
101	A	102	PRO	0	0.009	-0.008	24.665	0.120	0.120	0.000	0.000	0.000	0.000
102	A	103	ASP	-1	-0.911	-0.950	25.699	10.636	10.636	0.000	0.000	0.000	0.000
103	A	104	VAL	0	0.012	-0.002	27.944	-0.237	-0.237	0.000	0.000	0.000	0.000
104	A	105	ARG	1	0.883	0.959	21.553	-13.970	-13.970	0.000	0.000	0.000	0.000
105	A	106	LYS	1	0.855	0.936	24.123	-10.343	-10.343	0.000	0.000	0.000	0.000
106	A	107	PHE	0	-0.060	-0.032	25.338	-0.285	-0.285	0.000	0.000	0.000	0.000
107	A	108	THR	0	-0.017	-0.009	23.402	-0.079	-0.079	0.000	0.000	0.000	0.000
108	A	109	ASP	-1	-0.892	-0.935	21.860	12.648	12.648	0.000	0.000	0.000	0.000
109	A	110	PHE	0	0.007	-0.011	17.707	0.830	0.830	0.000	0.000	0.000	0.000
110	A	111	ALA	0	0.007	0.025	16.079	-0.630	-0.630	0.000	0.000	0.000	0.000
111	A	112	THR	0	0.006	-0.015	18.056	-0.337	-0.337	0.000	0.000	0.000	0.000
112	A	113	ALA	0	0.018	0.025	15.283	-0.060	-0.060	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ASP)