FMO DATABASE

FMODB ID: 94372

Calculation Name: 4NVS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4NVS

Chain ID: A

ChEMBL ID:

UniProt ID: Q18CP6

Base Structure: X-ray

Registration Date: 2023-09-20

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	156
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1507033.208065
FMO2-HF: Nuclear repulsion	1442827.315541
FMO2-HF: Total energy	-64205.892524
FMO2-MP2: Total energy	-64392.496631

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:1:MET)

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

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.
-0.605	2.079	0.055	-1.092	-1.646	0.004

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.042 / q_NPA : 0.024

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	3	PHE	0	0.014	0.023	3.856	0.372	3.014	0.056	-1.084	-1.614	0.004
4	A	4	LEU	0	-0.044	-0.033	5.428	-0.859	-0.817	-0.001	-0.008	-0.032	0.000
5	A	5	ASN	0	0.058	0.018	8.402	-0.288	-0.288	0.000	0.000	0.000	0.000
6	A	6	VAL	0	0.007	0.038	9.906	0.141	0.141	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.018	-0.001	12.348	-0.042	-0.042	0.000	0.000	0.000	0.000
8	A	8	ILE	0	-0.010	-0.005	14.335	-0.009	-0.009	0.000	0.000	0.000	0.000
9	A	9	VAL	0	-0.001	0.000	17.569	-0.004	-0.004	0.000	0.000	0.000	0.000
10	A	10	VAL	0	-0.015	0.001	19.792	-0.012	-0.012	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.831	-0.922	23.366	0.077	0.077	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.871	-0.945	26.583	0.060	0.060	0.000	0.000	0.000	0.000
13	A	13	ILE	0	0.046	0.024	22.137	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.811	-0.902	26.005	0.067	0.067	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.830	0.912	29.198	-0.057	-0.057	0.000	0.000	0.000	0.000
16	A	16	SER	0	0.055	0.025	25.055	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.818	0.919	25.332	-0.079	-0.079	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.840	0.903	26.844	-0.038	-0.038	0.000	0.000	0.000	0.000
19	A	19	PHE	0	0.010	0.026	26.847	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	20	TYR	0	-0.008	-0.059	22.395	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	21	TYR	0	-0.030	0.001	26.680	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.868	-0.915	28.949	0.025	0.025	0.000	0.000	0.000	0.000
23	A	23	VAL	0	-0.027	-0.008	29.365	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.007	-0.006	24.063	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	25	GLY	0	0.001	0.028	27.712	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.030	-0.017	21.255	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.815	0.898	25.193	-0.012	-0.012	0.000	0.000	0.000	0.000
28	A	28	VAL	0	-0.020	-0.014	22.966	0.005	0.005	0.000	0.000	0.000	0.000
29	A	29	ILE	0	-0.048	-0.029	17.956	-0.014	-0.014	0.000	0.000	0.000	0.000
30	A	30	CYS	0	-0.033	-0.022	19.032	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.838	-0.921	21.156	0.104	0.104	0.000	0.000	0.000	0.000
32	A	32	PHE	0	-0.020	-0.001	16.803	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	33	GLY	0	-0.032	-0.001	22.048	0.000	0.000	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.922	-0.982	21.007	0.149	0.149	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.034	-0.024	15.772	0.010	0.010	0.000	0.000	0.000	0.000
36	A	36	VAL	0	0.005	0.011	19.952	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	37	VAL	0	0.015	0.010	16.113	0.012	0.012	0.000	0.000	0.000	0.000
38	A	38	LEU	0	0.030	0.001	18.846	-0.025	-0.025	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.781	-0.896	18.682	0.030	0.030	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.019	0.009	17.279	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	41	ASN	0	-0.110	-0.050	12.213	-0.020	-0.020	0.000	0.000	0.000	0.000
42	A	42	ILE	0	0.038	0.028	13.969	0.066	0.066	0.000	0.000	0.000	0.000
43	A	43	SER	0	-0.010	-0.009	14.628	-0.016	-0.016	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.024	-0.007	16.734	0.003	0.003	0.000	0.000	0.000	0.000
45	A	45	GLN	0	-0.025	-0.006	17.157	0.023	0.023	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.740	-0.850	19.426	0.087	0.087	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.872	0.934	21.624	-0.064	-0.064	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.806	0.875	22.568	-0.077	-0.077	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.030	0.015	19.791	0.001	0.001	0.000	0.000	0.000	0.000
50	A	50	TRP	0	0.039	0.007	12.926	0.013	0.013	0.000	0.000	0.000	0.000
51	A	51	LEU	0	-0.082	-0.043	19.041	0.004	0.004	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.974	-0.980	21.093	0.114	0.114	0.000	0.000	0.000	0.000
53	A	53	PHE	0	-0.037	-0.021	16.000	0.006	0.006	0.000	0.000	0.000	0.000
54	A	54	ILE	0	-0.041	-0.012	14.406	0.006	0.006	0.000	0.000	0.000	0.000
55	A	55	ASN	0	-0.072	-0.030	16.880	-0.012	-0.012	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.842	0.933	18.952	-0.086	-0.086	0.000	0.000	0.000	0.000
57	A	57	SER	0	-0.004	-0.019	22.022	0.000	0.000	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.783	-0.917	24.751	0.071	0.071	0.000	0.000	0.000	0.000
59	A	59	SER	0	-0.072	-0.022	26.347	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.857	-0.923	22.500	0.066	0.066	0.000	0.000	0.000	0.000
61	A	61	VAL	0	0.006	0.019	20.598	0.005	0.005	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.861	0.932	22.594	-0.058	-0.058	0.000	0.000	0.000	0.000
63	A	63	PHE	0	0.034	0.017	22.525	0.007	0.007	0.000	0.000	0.000	0.000
64	A	64	ASN	0	0.032	0.006	24.631	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	65	GLY	0	-0.020	0.007	23.366	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	66	ASN	0	-0.022	-0.004	24.036	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	67	ASP	-1	-0.919	-0.949	18.702	0.075	0.075	0.000	0.000	0.000	0.000
68	A	68	ALA	0	-0.022	-0.009	17.091	0.007	0.007	0.000	0.000	0.000	0.000
69	A	69	GLH	0	-0.040	-0.057	18.110	-0.012	-0.012	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.044	-0.004	16.669	0.014	0.014	0.000	0.000	0.000	0.000
71	A	71	TYR	0	-0.083	-0.071	18.304	-0.010	-0.010	0.000	0.000	0.000	0.000
72	A	72	PHE	0	0.007	-0.010	19.351	0.002	0.002	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.790	-0.867	22.078	-0.068	-0.068	0.000	0.000	0.000	0.000
74	A	74	GLU	-1	-0.840	-0.923	24.348	-0.013	-0.013	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.879	-0.939	27.635	-0.047	-0.047	0.000	0.000	0.000	0.000
76	A	76	ASN	0	-0.127	-0.057	30.009	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	77	PHE	0	0.033	0.007	29.865	0.004	0.004	0.000	0.000	0.000	0.000
78	A	78	ASP	-1	-0.775	-0.859	32.274	-0.016	-0.016	0.000	0.000	0.000	0.000
79	A	79	THR	0	0.012	0.012	35.081	0.003	0.003	0.000	0.000	0.000	0.000
80	A	80	PHE	0	0.020	0.011	29.237	0.003	0.003	0.000	0.000	0.000	0.000
81	A	81	VAL	0	0.019	-0.006	32.833	0.004	0.004	0.000	0.000	0.000	0.000
82	A	82	GLU	-1	-0.934	-0.972	34.805	-0.007	-0.007	0.000	0.000	0.000	0.000
83	A	83	ARG	1	0.828	0.913	33.115	-0.011	-0.011	0.000	0.000	0.000	0.000
84	A	84	LEU	0	0.009	-0.002	31.629	0.003	0.003	0.000	0.000	0.000	0.000
85	A	85	SER	0	-0.085	-0.029	35.505	0.002	0.002	0.000	0.000	0.000	0.000
86	A	86	THR	0	-0.091	-0.048	38.604	0.001	0.001	0.000	0.000	0.000	0.000
87	A	87	MET	0	-0.072	-0.023	34.022	0.001	0.001	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.927	0.950	38.277	-0.019	-0.019	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.943	-0.983	36.399	0.027	0.027	0.000	0.000	0.000	0.000
90	A	90	ILE	0	-0.027	0.013	32.316	0.003	0.003	0.000	0.000	0.000	0.000
91	A	91	ASP	-1	-0.908	-0.952	31.425	0.025	0.025	0.000	0.000	0.000	0.000
92	A	92	TYR	0	-0.014	-0.019	31.072	0.002	0.002	0.000	0.000	0.000	0.000
93	A	93	VAL	0	-0.008	0.007	27.239	0.000	0.000	0.000	0.000	0.000	0.000
94	A	94	HIS	0	-0.039	-0.036	29.347	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	95	LEU	0	0.010	0.008	33.147	0.001	0.001	0.000	0.000	0.000	0.000
96	A	96	ALA	0	0.016	0.019	32.925	0.000	0.000	0.000	0.000	0.000	0.000
97	A	97	ILE	0	-0.029	-0.002	28.371	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.899	-0.964	31.977	-0.032	-0.032	0.000	0.000	0.000	0.000
99	A	99	HIS	1	0.769	0.889	24.671	0.029	0.029	0.000	0.000	0.000	0.000
100	A	100	ARG	1	0.851	0.884	28.799	0.058	0.058	0.000	0.000	0.000	0.000
101	A	101	TRP	0	0.026	-0.002	23.713	0.001	0.001	0.000	0.000	0.000	0.000
102	A	102	GLY	0	0.057	0.019	29.532	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	103	GLN	0	-0.042	-0.010	24.339	0.000	0.000	0.000	0.000	0.000	0.000
104	A	104	ARG	1	0.758	0.839	29.729	0.026	0.026	0.000	0.000	0.000	0.000
105	A	105	ALA	0	0.014	0.002	27.280	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	106	ILE	0	-0.028	-0.005	28.861	0.000	0.000	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.830	0.882	24.501	0.001	0.001	0.000	0.000	0.000	0.000
108	A	108	PHE	0	-0.004	0.002	27.446	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	109	TYR	0	-0.029	-0.031	26.191	0.003	0.003	0.000	0.000	0.000	0.000
110	A	110	ASP	-1	-0.776	-0.871	23.476	0.081	0.081	0.000	0.000	0.000	0.000
111	A	111	LEU	0	-0.005	-0.025	26.811	-0.004	-0.004	0.000	0.000	0.000	0.000
112	A	112	ASP	-1	-0.843	-0.920	24.196	0.078	0.078	0.000	0.000	0.000	0.000
113	A	113	GLY	0	0.022	0.008	24.739	0.005	0.005	0.000	0.000	0.000	0.000
114	A	114	HIS	1	0.799	0.889	20.551	-0.103	-0.103	0.000	0.000	0.000	0.000
115	A	115	ILE	0	0.015	0.017	22.490	-0.007	-0.007	0.000	0.000	0.000	0.000
116	A	116	ILE	0	0.012	0.017	21.906	0.010	0.010	0.000	0.000	0.000	0.000
117	A	117	GLU	-1	-0.776	-0.855	22.912	-0.016	-0.016	0.000	0.000	0.000	0.000
118	A	118	VAL	0	0.016	0.013	23.552	0.002	0.002	0.000	0.000	0.000	0.000
119	A	119	GLY	0	0.034	-0.007	25.426	0.000	0.000	0.000	0.000	0.000	0.000
120	A	120	GLU	-1	-0.719	-0.801	27.020	-0.033	-0.033	0.000	0.000	0.000	0.000
121	A	121	THR	0	0.060	0.042	25.450	-0.003	-0.003	0.000	0.000	0.000	0.000
122	A	122	MET	0	0.023	0.010	23.111	0.003	0.003	0.000	0.000	0.000	0.000
123	A	123	SER	0	0.020	0.004	26.126	0.002	0.002	0.000	0.000	0.000	0.000
124	A	124	SER	0	-0.024	-0.013	28.120	0.003	0.003	0.000	0.000	0.000	0.000
125	A	125	VAL	0	-0.027	-0.003	28.919	0.003	0.003	0.000	0.000	0.000	0.000
126	A	126	CYS	0	-0.031	-0.022	28.305	-0.001	-0.001	0.000	0.000	0.000	0.000
127	A	127	ARG	1	0.912	0.943	30.823	0.069	0.069	0.000	0.000	0.000	0.000
128	A	128	ARG	1	0.860	0.911	32.789	0.039	0.039	0.000	0.000	0.000	0.000
129	A	129	PHE	0	-0.043	-0.038	32.048	0.003	0.003	0.000	0.000	0.000	0.000
130	A	130	LEU	0	-0.031	-0.016	33.405	0.000	0.000	0.000	0.000	0.000	0.000
131	A	131	ASP	-1	-0.910	-0.931	37.056	-0.043	-0.043	0.000	0.000	0.000	0.000
132	A	132	SER	0	-0.166	-0.079	39.347	0.003	0.003	0.000	0.000	0.000	0.000
133	A	133	GLY	0	-0.005	-0.017	40.971	0.002	0.002	0.000	0.000	0.000	0.000
134	A	134	LEU	0	-0.070	-0.009	36.786	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	135	SER	0	0.000	-0.013	38.020	-0.002	-0.002	0.000	0.000	0.000	0.000
136	A	136	ILE	0	0.108	0.031	31.537	0.000	0.000	0.000	0.000	0.000	0.000
137	A	137	ASP	-1	-0.886	-0.944	33.267	-0.074	-0.074	0.000	0.000	0.000	0.000
138	A	138	GLU	-1	-0.953	-0.971	34.066	-0.052	-0.052	0.000	0.000	0.000	0.000
139	A	139	VAL	0	0.022	0.010	31.438	0.000	0.000	0.000	0.000	0.000	0.000
140	A	140	ALA	0	0.006	-0.002	29.682	-0.001	-0.001	0.000	0.000	0.000	0.000
141	A	141	LYS	1	0.905	0.960	29.845	0.065	0.065	0.000	0.000	0.000	0.000
142	A	142	ARG	1	0.818	0.907	32.147	0.050	0.050	0.000	0.000	0.000	0.000
143	A	143	MET	0	-0.055	-0.024	27.509	0.004	0.004	0.000	0.000	0.000	0.000
144	A	144	ASP	-1	-0.847	-0.867	27.022	-0.072	-0.072	0.000	0.000	0.000	0.000
145	A	145	VAL	0	-0.014	-0.007	23.873	-0.010	-0.010	0.000	0.000	0.000	0.000
146	A	146	THR	0	-0.024	-0.049	24.372	0.007	0.007	0.000	0.000	0.000	0.000
147	A	147	VAL	0	0.033	-0.006	26.775	0.000	0.000	0.000	0.000	0.000	0.000
148	A	148	GLU	-1	-0.865	-0.901	24.275	-0.164	-0.164	0.000	0.000	0.000	0.000
149	A	149	TYR	0	-0.002	0.006	20.636	0.001	0.001	0.000	0.000	0.000	0.000
150	A	150	ILE	0	0.044	0.023	24.141	0.001	0.001	0.000	0.000	0.000	0.000
151	A	151	GLU	-1	-0.935	-0.973	27.200	-0.099	-0.099	0.000	0.000	0.000	0.000
152	A	152	SER	0	-0.072	-0.030	22.723	-0.003	-0.003	0.000	0.000	0.000	0.000
153	A	153	VAL	0	0.010	0.002	22.929	0.006	0.006	0.000	0.000	0.000	0.000
154	A	154	LEU	0	-0.014	-0.015	25.127	0.010	0.010	0.000	0.000	0.000	0.000
155	A	155	GLU	-1	-1.010	-0.984	26.971	-0.099	-0.099	0.000	0.000	0.000	0.000
156	A	156	LEU	0	-0.053	-0.016	22.707	-0.002	-0.002	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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