FMO DATABASE

FMODB ID: R9L78

Calculation Name: 5VGL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5VGL

Chain ID: A

ChEMBL ID:

UniProt ID: P59082

Base Structure: X-ray

Registration Date: 2023-06-22

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	154
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1535135.843476
FMO2-HF: Nuclear repulsion	1472872.697158
FMO2-HF: Total energy	-62263.146318
FMO2-MP2: Total energy	-62440.063795

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:15:PRO)

Summations of interaction energy for fragment #1(A:15:PRO)

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.
-6.052	-0.808	2.245	-2.984	-4.504	-0.014

Interaction energy analysis for fragmet #1(A:15:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.032 / q_NPA : -0.037

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	17	ILE	0	-0.005	0.007	3.858	-0.117	1.953	-0.024	-1.128	-0.918	0.001
4	A	18	SER	0	-0.029	-0.018	7.201	-0.144	-0.144	0.000	0.000	0.000	0.000
5	A	19	GLY	0	0.006	0.008	9.964	0.127	0.127	0.000	0.000	0.000	0.000
6	A	20	GLY	0	-0.042	-0.011	12.692	0.006	0.006	0.000	0.000	0.000	0.000
7	A	21	GLY	0	0.038	0.010	11.505	0.081	0.081	0.000	0.000	0.000	0.000
8	A	22	GLY	0	-0.037	-0.021	12.589	-0.076	-0.076	0.000	0.000	0.000	0.000
9	A	23	GLY	0	0.014	0.016	13.603	0.042	0.042	0.000	0.000	0.000	0.000
10	A	24	LYS	1	0.900	0.940	15.435	-0.020	-0.020	0.000	0.000	0.000	0.000
11	A	25	VAL	0	-0.002	0.021	15.845	0.021	0.021	0.000	0.000	0.000	0.000
12	A	26	HIS	0	0.017	0.009	18.912	0.002	0.002	0.000	0.000	0.000	0.000
13	A	27	ALA	0	0.011	0.024	22.277	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	28	LEU	0	-0.030	-0.020	24.875	0.006	0.006	0.000	0.000	0.000	0.000
15	A	29	LEU	0	-0.003	0.007	27.494	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	30	PRO	0	0.009	0.014	31.085	0.004	0.004	0.000	0.000	0.000	0.000
17	A	31	ASN	0	-0.082	-0.067	34.200	0.010	0.010	0.000	0.000	0.000	0.000
18	A	32	THR	0	-0.001	0.000	33.764	0.000	0.000	0.000	0.000	0.000	0.000
19	A	33	LYS	1	0.827	0.914	35.625	0.048	0.048	0.000	0.000	0.000	0.000
20	A	34	PRO	0	0.075	0.027	34.488	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	35	GLU	-1	-0.766	-0.890	34.851	-0.053	-0.053	0.000	0.000	0.000	0.000
22	A	36	GLN	0	-0.017	0.022	36.679	0.000	0.000	0.000	0.000	0.000	0.000
23	A	37	ALA	0	0.092	0.035	31.286	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	38	TRP	0	0.002	0.005	29.776	-0.007	-0.007	0.000	0.000	0.000	0.000
25	A	39	THR	0	-0.082	-0.065	32.908	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	40	LEU	0	-0.022	-0.001	31.552	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	41	LEU	0	0.017	0.013	25.729	-0.006	-0.006	0.000	0.000	0.000	0.000
28	A	42	LYS	1	0.870	0.936	28.823	0.065	0.065	0.000	0.000	0.000	0.000
29	A	43	ASP	-1	-0.807	-0.864	31.300	-0.115	-0.115	0.000	0.000	0.000	0.000
30	A	44	PHE	0	0.027	0.005	24.632	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	45	ILE	0	0.001	-0.008	27.054	-0.015	-0.015	0.000	0.000	0.000	0.000
32	A	46	ASN	0	-0.063	-0.049	28.973	-0.007	-0.007	0.000	0.000	0.000	0.000
33	A	47	LEU	0	0.084	0.036	21.830	0.007	0.007	0.000	0.000	0.000	0.000
34	A	48	HIS	0	0.059	0.027	25.387	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	49	LYS	1	0.792	0.897	26.305	0.121	0.121	0.000	0.000	0.000	0.000
36	A	50	VAL	0	-0.040	-0.030	26.067	0.010	0.010	0.000	0.000	0.000	0.000
37	A	51	MET	0	0.003	0.016	18.388	0.006	0.006	0.000	0.000	0.000	0.000
38	A	52	PRO	0	0.022	-0.004	23.844	-0.012	-0.012	0.000	0.000	0.000	0.000
39	A	53	SER	0	-0.022	-0.030	19.165	-0.009	-0.009	0.000	0.000	0.000	0.000
40	A	54	LEU	0	-0.069	-0.027	19.943	-0.030	-0.030	0.000	0.000	0.000	0.000
41	A	55	SER	0	-0.017	-0.011	22.000	0.019	0.019	0.000	0.000	0.000	0.000
42	A	56	VAL	0	-0.021	-0.015	23.209	0.017	0.017	0.000	0.000	0.000	0.000
43	A	57	CYS	0	-0.064	-0.029	23.435	-0.019	-0.019	0.000	0.000	0.000	0.000
44	A	58	GLU	-1	-0.910	-0.937	25.751	-0.186	-0.186	0.000	0.000	0.000	0.000
45	A	59	LEU	0	-0.031	-0.015	27.416	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	60	VAL	0	-0.022	-0.017	25.786	0.001	0.001	0.000	0.000	0.000	0.000
47	A	61	GLU	-1	-0.830	-0.910	28.736	-0.146	-0.146	0.000	0.000	0.000	0.000
48	A	62	GLY	0	0.007	0.007	30.701	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	63	GLU	-1	-0.880	-0.951	33.442	-0.094	-0.094	0.000	0.000	0.000	0.000
50	A	64	ALA	0	0.019	-0.003	33.716	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	65	ASN	0	-0.023	-0.021	31.579	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	66	VAL	0	0.002	0.019	32.750	0.006	0.006	0.000	0.000	0.000	0.000
53	A	67	VAL	0	0.005	-0.007	30.634	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	68	GLY	0	0.015	0.016	30.269	0.007	0.007	0.000	0.000	0.000	0.000
55	A	69	CYS	0	-0.103	-0.027	30.086	-0.010	-0.010	0.000	0.000	0.000	0.000
56	A	70	VAL	0	0.011	-0.006	24.605	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	71	ARG	1	0.782	0.884	21.767	0.223	0.223	0.000	0.000	0.000	0.000
58	A	72	TYR	0	0.001	0.002	20.316	-0.018	-0.018	0.000	0.000	0.000	0.000
59	A	73	VAL	0	0.001	-0.012	19.315	0.021	0.021	0.000	0.000	0.000	0.000
60	A	74	LYS	1	0.816	0.891	18.685	0.355	0.355	0.000	0.000	0.000	0.000
61	A	75	GLY	0	0.032	0.007	18.160	0.044	0.044	0.000	0.000	0.000	0.000
62	A	76	ILE	0	-0.045	0.003	16.294	-0.048	-0.048	0.000	0.000	0.000	0.000
63	A	77	MET	0	-0.007	0.019	9.464	0.034	0.034	0.000	0.000	0.000	0.000
64	A	78	HIS	1	0.782	0.874	13.615	0.326	0.326	0.000	0.000	0.000	0.000
65	A	79	PRO	0	-0.019	-0.017	12.101	-0.024	-0.024	0.000	0.000	0.000	0.000
66	A	80	ILE	0	0.000	-0.017	8.641	0.045	0.045	0.000	0.000	0.000	0.000
67	A	81	GLU	-1	-0.835	-0.903	12.242	-0.351	-0.351	0.000	0.000	0.000	0.000
68	A	82	GLU	-1	-0.902	-0.938	8.918	-1.180	-1.180	0.000	0.000	0.000	0.000
69	A	83	GLU	-1	-0.846	-0.919	13.183	-0.402	-0.402	0.000	0.000	0.000	0.000
70	A	84	PHE	0	0.008	0.007	12.301	-0.101	-0.101	0.000	0.000	0.000	0.000
71	A	85	TRP	0	-0.004	-0.013	14.393	0.088	0.088	0.000	0.000	0.000	0.000
72	A	86	ALA	0	0.012	0.004	15.698	-0.061	-0.061	0.000	0.000	0.000	0.000
73	A	87	LYS	1	0.829	0.909	18.034	0.309	0.309	0.000	0.000	0.000	0.000
74	A	88	GLU	-1	-0.725	-0.845	18.767	-0.311	-0.311	0.000	0.000	0.000	0.000
75	A	89	LYS	1	0.794	0.884	22.001	0.169	0.169	0.000	0.000	0.000	0.000
76	A	90	LEU	0	-0.011	0.004	24.719	0.001	0.001	0.000	0.000	0.000	0.000
77	A	91	VAL	0	-0.032	-0.026	25.215	0.009	0.009	0.000	0.000	0.000	0.000
78	A	92	ALA	0	-0.010	-0.009	27.913	0.013	0.013	0.000	0.000	0.000	0.000
79	A	93	LEU	0	0.021	0.005	28.765	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	94	ASP	-1	-0.822	-0.880	31.295	-0.045	-0.045	0.000	0.000	0.000	0.000
81	A	95	ASN	0	0.018	-0.015	33.299	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	96	LYS	1	0.935	0.979	35.935	0.032	0.032	0.000	0.000	0.000	0.000
83	A	97	ASN	0	-0.090	-0.075	32.515	0.006	0.006	0.000	0.000	0.000	0.000
84	A	98	MET	0	-0.030	0.006	31.799	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	99	SER	0	0.052	0.024	27.795	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	100	TYR	0	0.005	-0.006	24.585	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	101	SER	0	0.000	-0.014	24.125	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	102	TYR	0	-0.062	-0.048	18.784	0.021	0.021	0.000	0.000	0.000	0.000
89	A	103	ILE	0	0.028	0.020	20.305	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	104	PHE	0	0.013	0.016	13.233	0.012	0.012	0.000	0.000	0.000	0.000
91	A	105	THR	0	-0.057	-0.033	18.986	0.011	0.011	0.000	0.000	0.000	0.000
92	A	106	GLU	-1	-0.822	-0.896	18.584	-0.295	-0.295	0.000	0.000	0.000	0.000
93	A	107	CYS	0	-0.086	-0.011	12.362	0.002	0.002	0.000	0.000	0.000	0.000
94	A	108	PHE	0	0.039	0.010	9.524	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	109	THR	0	0.003	-0.014	7.485	-0.051	-0.051	0.000	0.000	0.000	0.000
96	A	110	GLY	0	0.055	0.028	9.929	0.182	0.182	0.000	0.000	0.000	0.000
97	A	111	TYR	0	-0.051	-0.059	10.174	-0.153	-0.153	0.000	0.000	0.000	0.000
98	A	112	GLU	-1	-0.823	-0.902	12.551	-0.065	-0.065	0.000	0.000	0.000	0.000
99	A	113	ASP	-1	-0.876	-0.957	14.941	-0.128	-0.128	0.000	0.000	0.000	0.000
100	A	114	TYR	0	-0.022	-0.002	13.114	0.018	0.018	0.000	0.000	0.000	0.000
101	A	115	THR	0	-0.001	-0.008	16.498	0.014	0.014	0.000	0.000	0.000	0.000
102	A	116	ALA	0	-0.018	-0.004	17.583	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	117	THR	0	0.004	0.012	19.491	0.011	0.011	0.000	0.000	0.000	0.000
104	A	118	MET	0	-0.007	0.023	20.539	0.000	0.000	0.000	0.000	0.000	0.000
105	A	119	GLN	0	-0.051	-0.044	23.932	0.007	0.007	0.000	0.000	0.000	0.000
106	A	120	ILE	0	-0.020	0.004	26.893	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	121	VAL	0	-0.012	-0.011	29.181	0.005	0.005	0.000	0.000	0.000	0.000
108	A	122	GLU	-1	-0.836	-0.909	31.592	-0.026	-0.026	0.000	0.000	0.000	0.000
109	A	123	GLY	0	0.015	0.022	32.386	0.000	0.000	0.000	0.000	0.000	0.000
110	A	124	PRO	0	0.021	-0.005	31.538	0.004	0.004	0.000	0.000	0.000	0.000
111	A	125	GLU	-1	-0.921	-0.970	34.116	-0.007	-0.007	0.000	0.000	0.000	0.000
112	A	126	HIS	1	0.803	0.884	37.004	0.016	0.016	0.000	0.000	0.000	0.000
113	A	127	LYS	1	0.837	0.933	36.699	0.032	0.032	0.000	0.000	0.000	0.000
114	A	128	GLY	0	0.001	0.012	35.630	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	129	SER	0	-0.026	-0.048	32.228	0.002	0.002	0.000	0.000	0.000	0.000
116	A	130	ARG	1	0.754	0.841	24.212	0.044	0.044	0.000	0.000	0.000	0.000
117	A	131	PHE	0	-0.005	0.007	22.121	0.001	0.001	0.000	0.000	0.000	0.000
118	A	132	ASP	-1	-0.787	-0.871	23.291	-0.050	-0.050	0.000	0.000	0.000	0.000
119	A	133	TRP	0	0.021	0.005	17.722	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	134	SER	0	-0.028	-0.022	18.122	0.011	0.011	0.000	0.000	0.000	0.000
121	A	135	PHE	0	0.023	0.013	11.259	-0.025	-0.025	0.000	0.000	0.000	0.000
122	A	136	GLN	0	-0.019	-0.003	15.920	0.051	0.051	0.000	0.000	0.000	0.000
123	A	137	CYS	0	-0.072	-0.016	12.212	-0.061	-0.061	0.000	0.000	0.000	0.000
124	A	138	LYS	1	0.860	0.917	14.417	0.144	0.144	0.000	0.000	0.000	0.000
125	A	139	TYR	0	-0.082	-0.088	8.032	0.092	0.092	0.000	0.000	0.000	0.000
126	A	140	ILE	0	0.007	-0.001	7.364	0.058	0.058	0.000	0.000	0.000	0.000
127	A	141	GLU	-1	-0.836	-0.877	6.437	-1.516	-1.516	0.000	0.000	0.000	0.000
128	A	142	GLY	0	0.022	0.017	2.896	0.081	0.512	0.126	-0.135	-0.422	0.000
129	A	143	MET	0	-0.007	0.002	2.703	-2.148	-0.375	1.463	-1.211	-2.025	-0.014
130	A	144	THR	0	-0.003	0.003	2.688	-0.742	0.135	0.681	-0.499	-1.058	-0.001
131	A	145	GLU	-1	-0.821	-0.911	4.778	-0.013	0.080	-0.001	-0.011	-0.081	0.000
132	A	146	SER	0	-0.020	-0.003	7.937	-0.069	-0.069	0.000	0.000	0.000	0.000
133	A	147	ALA	0	0.018	0.011	5.234	-0.024	-0.024	0.000	0.000	0.000	0.000
134	A	148	PHE	0	0.058	0.015	7.262	-0.027	-0.027	0.000	0.000	0.000	0.000
135	A	149	THR	0	-0.009	-0.024	8.972	0.067	0.067	0.000	0.000	0.000	0.000
136	A	150	GLU	-1	-0.858	-0.923	10.467	-0.127	-0.127	0.000	0.000	0.000	0.000
137	A	151	ILE	0	-0.031	-0.011	8.398	0.017	0.017	0.000	0.000	0.000	0.000
138	A	152	LEU	0	0.001	0.004	12.328	0.042	0.042	0.000	0.000	0.000	0.000
139	A	153	GLN	0	0.016	-0.005	14.812	0.045	0.045	0.000	0.000	0.000	0.000
140	A	154	HIS	0	-0.058	-0.021	14.211	0.028	0.028	0.000	0.000	0.000	0.000
141	A	155	TRP	0	0.019	-0.004	14.140	0.017	0.017	0.000	0.000	0.000	0.000
142	A	156	ALA	0	0.011	0.002	18.645	0.019	0.019	0.000	0.000	0.000	0.000
143	A	157	THR	0	-0.080	-0.057	20.076	0.028	0.028	0.000	0.000	0.000	0.000
144	A	158	GLU	-1	-0.837	-0.878	20.792	-0.211	-0.211	0.000	0.000	0.000	0.000
145	A	159	ILE	0	0.041	0.017	21.608	0.013	0.013	0.000	0.000	0.000	0.000
146	A	160	GLY	0	-0.009	-0.014	24.586	0.012	0.012	0.000	0.000	0.000	0.000
147	A	161	GLN	0	-0.023	-0.017	25.605	0.008	0.008	0.000	0.000	0.000	0.000
148	A	162	LYS	1	0.806	0.904	27.149	0.122	0.122	0.000	0.000	0.000	0.000
149	A	163	ILE	0	0.020	0.009	27.988	0.006	0.006	0.000	0.000	0.000	0.000
150	A	164	GLU	-1	-0.748	-0.851	30.581	-0.053	-0.053	0.000	0.000	0.000	0.000
151	A	165	GLU	-1	-0.846	-0.890	31.784	-0.099	-0.099	0.000	0.000	0.000	0.000
152	A	166	VAL	0	0.019	0.019	32.389	0.005	0.005	0.000	0.000	0.000	0.000
153	A	167	CYS	0	-0.102	-0.053	33.857	0.005	0.005	0.000	0.000	0.000	0.000
154	A	168	SER	0	-0.134	-0.063	36.355	0.009	0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:15:PRO)