FMO DATABASE

FMODB ID: MV58Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1509286.705071
FMO2-HF: Nuclear repulsion	1445080.306253
FMO2-HF: Total energy	-64206.398818
FMO2-MP2: Total energy	-64393.000924

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.
-0.858	1.7	0.029	-1.057	-1.529	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 : 0.040 / 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	0.041	0.031	3.876	0.093	2.617	0.030	-1.051	-1.503	0.004
4	A	4	LEU	0	-0.033	-0.035	5.474	-0.938	-0.904	-0.001	-0.006	-0.026	0.000
5	A	5	ASN	0	0.060	0.026	8.574	-0.277	-0.277	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.002	0.031	9.653	0.174	0.174	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.020	-0.007	12.265	-0.034	-0.034	0.000	0.000	0.000	0.000
8	A	8	ILE	0	-0.018	-0.001	14.031	-0.014	-0.014	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.028	0.016	17.360	-0.005	-0.005	0.000	0.000	0.000	0.000
10	A	10	VAL	0	-0.013	-0.005	19.452	-0.011	-0.011	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.783	-0.875	23.022	0.075	0.075	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.869	-0.943	26.304	0.063	0.063	0.000	0.000	0.000	0.000
13	A	13	ILE	0	0.055	0.033	21.830	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.802	-0.890	25.715	0.079	0.079	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.818	0.895	28.859	-0.059	-0.059	0.000	0.000	0.000	0.000
16	A	16	SER	0	0.014	-0.011	24.967	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.773	0.866	24.868	-0.088	-0.088	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.797	0.889	26.503	-0.043	-0.043	0.000	0.000	0.000	0.000
19	A	19	PHE	0	-0.002	0.010	26.786	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	20	TYR	0	0.014	-0.037	22.304	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	21	TYR	0	-0.016	0.010	26.584	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.829	-0.907	28.901	0.032	0.032	0.000	0.000	0.000	0.000
23	A	23	VAL	0	-0.021	-0.004	29.369	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.018	-0.015	24.195	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	25	GLY	0	-0.011	0.015	27.854	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.056	-0.011	21.194	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.828	0.887	25.057	-0.034	-0.034	0.000	0.000	0.000	0.000
28	A	28	VAL	0	-0.010	-0.012	22.789	0.007	0.007	0.000	0.000	0.000	0.000
29	A	29	ILE	0	-0.054	-0.031	17.743	-0.014	-0.014	0.000	0.000	0.000	0.000
30	A	30	CYS	0	-0.040	-0.019	18.905	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.820	-0.913	20.942	0.115	0.115	0.000	0.000	0.000	0.000
32	A	32	PHE	0	-0.045	-0.014	16.890	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	33	GLY	0	-0.019	0.010	22.126	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.884	-0.963	20.311	0.155	0.155	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.044	-0.023	15.295	0.009	0.009	0.000	0.000	0.000	0.000
36	A	36	VAL	0	0.011	-0.002	19.444	-0.007	-0.007	0.000	0.000	0.000	0.000
37	A	37	VAL	0	-0.017	0.014	16.058	0.008	0.008	0.000	0.000	0.000	0.000
38	A	38	LEU	0	0.056	0.012	18.515	-0.025	-0.025	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.784	-0.892	18.482	0.061	0.061	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.033	0.014	17.172	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	41	ASN	0	-0.116	-0.058	12.384	-0.015	-0.015	0.000	0.000	0.000	0.000
42	A	42	ILE	0	0.046	0.023	13.962	0.069	0.069	0.000	0.000	0.000	0.000
43	A	43	SER	0	0.006	-0.002	14.365	-0.023	-0.023	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.010	0.012	16.371	0.002	0.002	0.000	0.000	0.000	0.000
45	A	45	GLN	0	-0.018	-0.003	16.585	0.025	0.025	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.758	-0.869	19.053	0.088	0.088	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.823	0.904	21.170	-0.063	-0.063	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.760	0.855	22.451	-0.081	-0.081	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.031	0.020	19.683	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	50	TRP	0	0.023	-0.002	12.606	0.013	0.013	0.000	0.000	0.000	0.000
51	A	51	LEU	0	-0.064	-0.037	18.803	0.002	0.002	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.959	-0.964	21.124	0.112	0.112	0.000	0.000	0.000	0.000
53	A	53	PHE	0	-0.021	-0.016	15.876	0.004	0.004	0.000	0.000	0.000	0.000
54	A	54	ILE	0	-0.052	-0.014	14.340	0.007	0.007	0.000	0.000	0.000	0.000
55	A	55	ASN	0	-0.074	-0.037	16.826	-0.011	-0.011	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.819	0.911	18.975	-0.076	-0.076	0.000	0.000	0.000	0.000
57	A	57	SER	0	0.004	-0.017	21.840	0.000	0.000	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.779	-0.920	24.332	0.069	0.069	0.000	0.000	0.000	0.000
59	A	59	SER	0	-0.093	-0.043	26.241	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.794	-0.861	22.441	0.058	0.058	0.000	0.000	0.000	0.000
61	A	61	VAL	0	0.017	0.032	20.352	0.002	0.002	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.788	0.874	22.131	-0.060	-0.060	0.000	0.000	0.000	0.000
63	A	63	PHE	0	0.025	0.015	22.171	0.008	0.008	0.000	0.000	0.000	0.000
64	A	64	ASN	0	0.036	0.017	24.503	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	65	GLY	0	-0.010	0.014	23.159	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	66	ASN	0	-0.027	-0.012	23.582	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	67	ASP	-1	-0.925	-0.953	18.579	0.067	0.067	0.000	0.000	0.000	0.000
68	A	68	ALA	0	-0.013	-0.008	16.921	0.001	0.001	0.000	0.000	0.000	0.000
69	A	69	GLH	0	-0.043	-0.051	18.313	-0.010	-0.010	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.030	-0.003	16.797	0.019	0.019	0.000	0.000	0.000	0.000
71	A	71	TYR	0	-0.094	-0.074	18.618	-0.014	-0.014	0.000	0.000	0.000	0.000
72	A	72	PHE	0	0.003	-0.003	19.609	0.009	0.009	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.763	-0.866	22.284	-0.054	-0.054	0.000	0.000	0.000	0.000
74	A	74	GLU	-1	-0.833	-0.907	24.599	0.000	0.000	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.846	-0.900	27.888	-0.036	-0.036	0.000	0.000	0.000	0.000
76	A	76	ASN	0	-0.120	-0.070	30.455	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	77	PHE	0	0.016	0.017	30.192	0.003	0.003	0.000	0.000	0.000	0.000
78	A	78	ASP	-1	-0.777	-0.854	32.402	-0.011	-0.011	0.000	0.000	0.000	0.000
79	A	79	THR	0	0.014	0.000	35.424	0.003	0.003	0.000	0.000	0.000	0.000
80	A	80	PHE	0	0.003	0.008	29.137	0.003	0.003	0.000	0.000	0.000	0.000
81	A	81	VAL	0	0.011	-0.004	33.177	0.003	0.003	0.000	0.000	0.000	0.000
82	A	82	GLU	-1	-0.929	-0.964	35.017	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	83	ARG	1	0.862	0.936	32.990	-0.019	-0.019	0.000	0.000	0.000	0.000
84	A	84	LEU	0	0.015	0.011	31.620	0.002	0.002	0.000	0.000	0.000	0.000
85	A	85	SER	0	-0.086	-0.047	35.464	0.001	0.001	0.000	0.000	0.000	0.000
86	A	86	THR	0	-0.107	-0.066	38.752	0.000	0.000	0.000	0.000	0.000	0.000
87	A	87	MET	0	-0.076	-0.024	33.990	0.001	0.001	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.869	0.907	37.685	-0.025	-0.025	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.894	-0.944	36.180	0.027	0.027	0.000	0.000	0.000	0.000
90	A	90	ILE	0	0.002	0.017	31.915	0.004	0.004	0.000	0.000	0.000	0.000
91	A	91	ASP	-1	-0.909	-0.946	31.147	0.027	0.027	0.000	0.000	0.000	0.000
92	A	92	TYR	0	-0.016	-0.023	30.985	0.002	0.002	0.000	0.000	0.000	0.000
93	A	93	VAL	0	-0.004	0.014	27.308	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	94	HIS	0	-0.046	-0.029	29.428	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	95	LEU	0	0.017	0.007	33.235	0.001	0.001	0.000	0.000	0.000	0.000
96	A	96	ALA	0	0.026	0.026	33.308	0.000	0.000	0.000	0.000	0.000	0.000
97	A	97	ILE	0	-0.052	-0.016	28.491	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.896	-0.954	31.839	-0.029	-0.029	0.000	0.000	0.000	0.000
99	A	99	HIS	1	0.789	0.896	24.368	0.025	0.025	0.000	0.000	0.000	0.000
100	A	100	ARG	1	0.831	0.875	28.555	0.058	0.058	0.000	0.000	0.000	0.000
101	A	101	TRP	0	0.050	0.020	23.422	0.001	0.001	0.000	0.000	0.000	0.000
102	A	102	GLY	0	0.049	0.011	29.411	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	103	GLN	0	-0.040	-0.010	24.361	0.000	0.000	0.000	0.000	0.000	0.000
104	A	104	ARG	1	0.742	0.817	29.615	0.021	0.021	0.000	0.000	0.000	0.000
105	A	105	ALA	0	0.001	-0.004	27.665	0.000	0.000	0.000	0.000	0.000	0.000
106	A	106	ILE	0	-0.013	-0.006	29.125	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.830	0.878	24.571	-0.002	-0.002	0.000	0.000	0.000	0.000
108	A	108	PHE	0	-0.008	-0.005	27.513	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	109	TYR	0	-0.023	-0.023	25.873	0.004	0.004	0.000	0.000	0.000	0.000
110	A	110	ASP	-1	-0.759	-0.862	23.181	0.085	0.085	0.000	0.000	0.000	0.000
111	A	111	LEU	0	-0.018	-0.031	26.745	-0.004	-0.004	0.000	0.000	0.000	0.000
112	A	112	ASP	-1	-0.821	-0.878	23.835	0.082	0.082	0.000	0.000	0.000	0.000
113	A	113	GLY	0	0.009	0.003	24.178	0.004	0.004	0.000	0.000	0.000	0.000
114	A	114	HIS	1	0.807	0.890	20.444	-0.104	-0.104	0.000	0.000	0.000	0.000
115	A	115	ILE	0	0.015	0.016	22.610	-0.005	-0.005	0.000	0.000	0.000	0.000
116	A	116	ILE	0	0.015	0.017	21.888	0.012	0.012	0.000	0.000	0.000	0.000
117	A	117	GLU	-1	-0.797	-0.862	22.938	-0.011	-0.011	0.000	0.000	0.000	0.000
118	A	118	VAL	0	0.009	-0.001	23.701	0.004	0.004	0.000	0.000	0.000	0.000
119	A	119	GLY	0	0.042	0.007	26.010	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	120	GLU	-1	-0.702	-0.790	27.488	-0.026	-0.026	0.000	0.000	0.000	0.000
121	A	121	THR	0	0.010	-0.001	25.633	-0.003	-0.003	0.000	0.000	0.000	0.000
122	A	122	MET	0	0.006	0.004	23.150	0.000	0.000	0.000	0.000	0.000	0.000
123	A	123	SER	0	0.035	0.017	26.367	0.000	0.000	0.000	0.000	0.000	0.000
124	A	124	SER	0	-0.027	-0.016	28.274	0.001	0.001	0.000	0.000	0.000	0.000
125	A	125	VAL	0	-0.034	-0.011	28.927	0.001	0.001	0.000	0.000	0.000	0.000
126	A	126	CYS	0	-0.027	-0.020	28.346	-0.002	-0.002	0.000	0.000	0.000	0.000
127	A	127	ARG	1	0.863	0.934	30.728	0.058	0.058	0.000	0.000	0.000	0.000
128	A	128	ARG	1	0.873	0.904	32.949	0.033	0.033	0.000	0.000	0.000	0.000
129	A	129	PHE	0	-0.012	-0.014	32.266	0.002	0.002	0.000	0.000	0.000	0.000
130	A	130	LEU	0	-0.005	0.012	33.775	0.000	0.000	0.000	0.000	0.000	0.000
131	A	131	ASP	-1	-0.919	-0.955	37.358	-0.038	-0.038	0.000	0.000	0.000	0.000
132	A	132	SER	0	-0.153	-0.085	39.189	0.002	0.002	0.000	0.000	0.000	0.000
133	A	133	GLY	0	-0.016	-0.014	40.729	0.002	0.002	0.000	0.000	0.000	0.000
134	A	134	LEU	0	-0.068	-0.015	36.774	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	135	SER	0	-0.011	-0.045	37.660	-0.001	-0.001	0.000	0.000	0.000	0.000
136	A	136	ILE	0	0.088	0.028	31.430	0.000	0.000	0.000	0.000	0.000	0.000
137	A	137	ASP	-1	-0.838	-0.903	33.023	-0.073	-0.073	0.000	0.000	0.000	0.000
138	A	138	GLU	-1	-0.968	-0.979	34.067	-0.051	-0.051	0.000	0.000	0.000	0.000
139	A	139	VAL	0	0.016	0.007	31.450	0.001	0.001	0.000	0.000	0.000	0.000
140	A	140	ALA	0	-0.008	-0.011	29.846	-0.001	-0.001	0.000	0.000	0.000	0.000
141	A	141	LYS	1	0.878	0.940	30.059	0.064	0.064	0.000	0.000	0.000	0.000
142	A	142	ARG	1	0.814	0.910	32.324	0.047	0.047	0.000	0.000	0.000	0.000
143	A	143	MET	0	-0.047	-0.017	27.617	0.004	0.004	0.000	0.000	0.000	0.000
144	A	144	ASP	-1	-0.833	-0.863	26.833	-0.071	-0.071	0.000	0.000	0.000	0.000
145	A	145	VAL	0	-0.009	0.007	23.837	-0.010	-0.010	0.000	0.000	0.000	0.000
146	A	146	THR	0	-0.033	-0.052	24.912	0.007	0.007	0.000	0.000	0.000	0.000
147	A	147	VAL	0	0.014	-0.008	27.030	0.002	0.002	0.000	0.000	0.000	0.000
148	A	148	GLU	-1	-0.839	-0.892	24.739	-0.154	-0.154	0.000	0.000	0.000	0.000
149	A	149	TYR	0	-0.008	0.008	20.566	0.000	0.000	0.000	0.000	0.000	0.000
150	A	150	ILE	0	0.053	0.034	24.240	0.004	0.004	0.000	0.000	0.000	0.000
151	A	151	GLU	-1	-0.921	-0.976	27.474	-0.095	-0.095	0.000	0.000	0.000	0.000
152	A	152	SER	0	-0.077	-0.043	23.005	-0.001	-0.001	0.000	0.000	0.000	0.000
153	A	153	VAL	0	0.009	0.000	23.009	0.003	0.003	0.000	0.000	0.000	0.000
154	A	154	LEU	0	-0.027	-0.021	25.418	0.011	0.011	0.000	0.000	0.000	0.000
155	A	155	GLU	-1	-0.978	-0.972	27.136	-0.091	-0.091	0.000	0.000	0.000	0.000
156	A	156	LEU	0	-0.067	-0.016	22.757	0.004	0.004	0.000	0.000	0.000	0.000

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