FMO DATABASE

FMODB ID: 6N41Z

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	OptH
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	-1533582.519841
FMO2-HF: Nuclear repulsion	1471319.995485
FMO2-HF: Total energy	-62262.524356
FMO2-MP2: Total energy	-62439.357824

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.
-7.481	-1.781	3.053	-3.484	-5.269	-0.018

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 : -0.003 / q_NPA : -0.026

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	-0.018	0.012	3.777	-0.444	2.230	-0.034	-1.430	-1.210	0.002
4	A	18	SER	0	-0.022	-0.024	7.119	-0.152	-0.152	0.000	0.000	0.000	0.000
5	A	19	GLY	0	-0.006	-0.004	9.530	0.139	0.139	0.000	0.000	0.000	0.000
6	A	20	GLY	0	-0.048	-0.013	12.468	0.054	0.054	0.000	0.000	0.000	0.000
7	A	21	GLY	0	0.023	0.005	11.401	0.065	0.065	0.000	0.000	0.000	0.000
8	A	22	GLY	0	-0.040	-0.027	12.453	-0.059	-0.059	0.000	0.000	0.000	0.000
9	A	23	GLY	0	0.009	0.018	13.484	0.053	0.053	0.000	0.000	0.000	0.000
10	A	24	LYS	1	0.897	0.941	15.058	-0.014	-0.014	0.000	0.000	0.000	0.000
11	A	25	VAL	0	0.005	0.018	16.129	0.025	0.025	0.000	0.000	0.000	0.000
12	A	26	HIS	0	-0.014	-0.013	19.029	-0.006	-0.006	0.000	0.000	0.000	0.000
13	A	27	ALA	0	0.023	0.029	22.263	0.003	0.003	0.000	0.000	0.000	0.000
14	A	28	LEU	0	-0.040	-0.034	24.784	0.003	0.003	0.000	0.000	0.000	0.000
15	A	29	LEU	0	0.003	0.016	28.055	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	30	PRO	0	-0.041	-0.019	31.218	0.004	0.004	0.000	0.000	0.000	0.000
17	A	31	ASN	0	-0.030	-0.035	34.245	0.008	0.008	0.000	0.000	0.000	0.000
18	A	32	THR	0	0.015	-0.005	33.884	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	33	LYS	1	0.906	0.969	35.498	0.047	0.047	0.000	0.000	0.000	0.000
20	A	34	PRO	0	0.090	0.035	34.334	-0.005	-0.005	0.000	0.000	0.000	0.000
21	A	35	GLU	-1	-0.836	-0.941	34.915	-0.059	-0.059	0.000	0.000	0.000	0.000
22	A	36	GLN	0	-0.030	-0.006	36.787	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	37	ALA	0	0.077	0.035	31.401	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	38	TRP	0	-0.003	0.003	29.574	-0.009	-0.009	0.000	0.000	0.000	0.000
25	A	39	THR	0	-0.068	-0.035	33.177	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	40	LEU	0	-0.022	-0.010	31.761	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	41	LEU	0	0.017	0.005	25.741	-0.007	-0.007	0.000	0.000	0.000	0.000
28	A	42	LYS	1	0.881	0.948	28.883	0.082	0.082	0.000	0.000	0.000	0.000
29	A	43	ASP	-1	-0.876	-0.919	31.269	-0.133	-0.133	0.000	0.000	0.000	0.000
30	A	44	PHE	0	0.023	0.010	24.230	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	45	ILE	0	-0.013	-0.017	27.004	-0.016	-0.016	0.000	0.000	0.000	0.000
32	A	46	ASN	0	-0.062	-0.049	28.999	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	47	LEU	0	0.085	0.043	22.007	0.008	0.008	0.000	0.000	0.000	0.000
34	A	48	HIS	0	0.065	0.028	25.561	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	49	LYS	1	0.870	0.941	26.513	0.130	0.130	0.000	0.000	0.000	0.000
36	A	50	VAL	0	-0.032	-0.025	26.509	0.011	0.011	0.000	0.000	0.000	0.000
37	A	51	MET	0	0.014	0.020	18.761	0.006	0.006	0.000	0.000	0.000	0.000
38	A	52	PRO	0	0.004	-0.007	24.439	-0.011	-0.011	0.000	0.000	0.000	0.000
39	A	53	SER	0	-0.020	-0.009	19.423	-0.007	-0.007	0.000	0.000	0.000	0.000
40	A	54	LEU	0	-0.047	-0.021	19.942	-0.034	-0.034	0.000	0.000	0.000	0.000
41	A	55	SER	0	-0.034	-0.019	22.169	0.018	0.018	0.000	0.000	0.000	0.000
42	A	56	VAL	0	-0.033	-0.017	23.108	0.018	0.018	0.000	0.000	0.000	0.000
43	A	57	CYS	0	-0.041	-0.021	23.339	-0.022	-0.022	0.000	0.000	0.000	0.000
44	A	58	GLU	-1	-0.944	-0.948	25.616	-0.201	-0.201	0.000	0.000	0.000	0.000
45	A	59	LEU	0	-0.023	-0.016	27.074	-0.013	-0.013	0.000	0.000	0.000	0.000
46	A	60	VAL	0	-0.025	-0.020	25.612	0.000	0.000	0.000	0.000	0.000	0.000
47	A	61	GLU	-1	-0.942	-0.972	28.704	-0.187	-0.187	0.000	0.000	0.000	0.000
48	A	62	GLY	0	-0.003	0.004	30.527	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	63	GLU	-1	-0.919	-0.963	33.086	-0.110	-0.110	0.000	0.000	0.000	0.000
50	A	64	ALA	0	0.035	0.001	33.038	-0.006	-0.006	0.000	0.000	0.000	0.000
51	A	65	ASN	0	-0.024	-0.023	31.354	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	66	VAL	0	-0.001	0.016	32.599	0.008	0.008	0.000	0.000	0.000	0.000
53	A	67	VAL	0	-0.013	-0.014	30.239	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	68	GLY	0	-0.035	-0.024	29.683	0.007	0.007	0.000	0.000	0.000	0.000
55	A	69	CYS	0	-0.084	-0.012	29.592	-0.011	-0.011	0.000	0.000	0.000	0.000
56	A	70	VAL	0	0.038	0.008	24.268	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	71	ARG	1	0.803	0.903	21.512	0.263	0.263	0.000	0.000	0.000	0.000
58	A	72	TYR	0	-0.016	-0.007	20.528	-0.019	-0.019	0.000	0.000	0.000	0.000
59	A	73	VAL	0	0.014	-0.006	18.970	0.026	0.026	0.000	0.000	0.000	0.000
60	A	74	LYS	1	0.960	0.980	18.769	0.320	0.320	0.000	0.000	0.000	0.000
61	A	75	GLY	0	0.040	0.010	17.848	0.050	0.050	0.000	0.000	0.000	0.000
62	A	76	ILE	0	-0.048	0.011	16.125	-0.050	-0.050	0.000	0.000	0.000	0.000
63	A	77	MET	0	-0.011	0.013	9.709	0.033	0.033	0.000	0.000	0.000	0.000
64	A	78	HIS	1	0.787	0.875	14.044	0.291	0.291	0.000	0.000	0.000	0.000
65	A	79	PRO	0	-0.009	-0.020	12.694	-0.013	-0.013	0.000	0.000	0.000	0.000
66	A	80	ILE	0	0.001	-0.021	8.788	0.056	0.056	0.000	0.000	0.000	0.000
67	A	81	GLU	-1	-0.847	-0.893	12.054	-0.305	-0.305	0.000	0.000	0.000	0.000
68	A	82	GLU	-1	-0.922	-0.956	8.893	-1.033	-1.033	0.000	0.000	0.000	0.000
69	A	83	GLU	-1	-0.929	-0.982	13.074	-0.439	-0.439	0.000	0.000	0.000	0.000
70	A	84	PHE	0	-0.012	0.002	12.240	-0.107	-0.107	0.000	0.000	0.000	0.000
71	A	85	TRP	0	-0.003	-0.012	14.176	0.092	0.092	0.000	0.000	0.000	0.000
72	A	86	ALA	0	0.023	0.011	15.445	-0.072	-0.072	0.000	0.000	0.000	0.000
73	A	87	LYS	1	0.922	0.979	17.712	0.346	0.346	0.000	0.000	0.000	0.000
74	A	88	GLU	-1	-0.775	-0.904	18.348	-0.383	-0.383	0.000	0.000	0.000	0.000
75	A	89	LYS	1	0.940	0.982	21.604	0.213	0.213	0.000	0.000	0.000	0.000
76	A	90	LEU	0	0.001	0.010	24.295	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	91	VAL	0	-0.030	-0.024	24.808	0.011	0.011	0.000	0.000	0.000	0.000
78	A	92	ALA	0	-0.009	-0.011	27.420	0.015	0.015	0.000	0.000	0.000	0.000
79	A	93	LEU	0	0.018	0.005	28.598	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	94	ASP	-1	-0.840	-0.907	31.187	-0.068	-0.068	0.000	0.000	0.000	0.000
81	A	95	ASN	0	0.046	-0.014	33.321	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	96	LYS	1	0.926	0.985	35.673	0.050	0.050	0.000	0.000	0.000	0.000
83	A	97	ASN	0	-0.080	-0.055	32.371	0.008	0.008	0.000	0.000	0.000	0.000
84	A	98	MET	0	-0.036	0.009	32.038	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	99	SER	0	0.047	0.025	27.971	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	100	TYR	0	0.013	0.002	24.068	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	101	SER	0	0.019	0.028	23.971	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	102	TYR	0	0.012	-0.001	18.600	0.026	0.026	0.000	0.000	0.000	0.000
89	A	103	ILE	0	0.011	0.013	19.836	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	104	PHE	0	0.006	0.010	12.828	0.014	0.014	0.000	0.000	0.000	0.000
91	A	105	THR	0	-0.060	-0.040	18.462	0.011	0.011	0.000	0.000	0.000	0.000
92	A	106	GLU	-1	-0.939	-0.981	18.236	-0.387	-0.387	0.000	0.000	0.000	0.000
93	A	107	CYS	0	-0.069	-0.013	12.537	-0.009	-0.009	0.000	0.000	0.000	0.000
94	A	108	PHE	0	0.037	0.022	9.189	-0.013	-0.013	0.000	0.000	0.000	0.000
95	A	109	THR	0	-0.003	-0.014	7.400	-0.050	-0.050	0.000	0.000	0.000	0.000
96	A	110	GLY	0	0.051	0.022	9.925	0.222	0.222	0.000	0.000	0.000	0.000
97	A	111	TYR	0	-0.049	-0.041	10.034	-0.153	-0.153	0.000	0.000	0.000	0.000
98	A	112	GLU	-1	-0.897	-0.956	12.333	-0.257	-0.257	0.000	0.000	0.000	0.000
99	A	113	ASP	-1	-0.908	-0.962	15.024	-0.271	-0.271	0.000	0.000	0.000	0.000
100	A	114	TYR	0	-0.003	0.005	12.933	0.013	0.013	0.000	0.000	0.000	0.000
101	A	115	THR	0	-0.007	-0.020	16.231	0.029	0.029	0.000	0.000	0.000	0.000
102	A	116	ALA	0	-0.010	0.004	17.736	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	117	THR	0	-0.019	-0.033	19.445	0.014	0.014	0.000	0.000	0.000	0.000
104	A	118	MET	0	-0.045	-0.004	20.866	0.005	0.005	0.000	0.000	0.000	0.000
105	A	119	GLN	0	-0.028	-0.032	24.185	0.006	0.006	0.000	0.000	0.000	0.000
106	A	120	ILE	0	-0.034	0.003	27.104	0.000	0.000	0.000	0.000	0.000	0.000
107	A	121	VAL	0	0.000	-0.001	29.142	0.004	0.004	0.000	0.000	0.000	0.000
108	A	122	GLU	-1	-0.844	-0.927	31.534	-0.033	-0.033	0.000	0.000	0.000	0.000
109	A	123	GLY	0	0.021	0.018	32.170	0.001	0.001	0.000	0.000	0.000	0.000
110	A	124	PRO	0	-0.001	-0.011	31.244	0.004	0.004	0.000	0.000	0.000	0.000
111	A	125	GLU	-1	-0.926	-0.976	33.893	-0.006	-0.006	0.000	0.000	0.000	0.000
112	A	126	HIS	1	0.773	0.881	36.692	0.022	0.022	0.000	0.000	0.000	0.000
113	A	127	LYS	1	0.913	0.981	36.382	0.026	0.026	0.000	0.000	0.000	0.000
114	A	128	GLY	0	-0.014	0.009	35.212	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	129	SER	0	-0.008	-0.030	32.059	0.001	0.001	0.000	0.000	0.000	0.000
116	A	130	ARG	1	0.831	0.906	24.692	0.048	0.048	0.000	0.000	0.000	0.000
117	A	131	PHE	0	-0.026	-0.002	22.521	0.000	0.000	0.000	0.000	0.000	0.000
118	A	132	ASP	-1	-0.798	-0.887	23.435	-0.067	-0.067	0.000	0.000	0.000	0.000
119	A	133	TRP	0	0.024	-0.003	17.981	-0.005	-0.005	0.000	0.000	0.000	0.000
120	A	134	SER	0	-0.038	-0.024	18.225	0.011	0.011	0.000	0.000	0.000	0.000
121	A	135	PHE	0	0.008	0.010	11.086	-0.025	-0.025	0.000	0.000	0.000	0.000
122	A	136	GLN	0	0.026	0.015	15.816	0.053	0.053	0.000	0.000	0.000	0.000
123	A	137	CYS	0	-0.064	-0.014	12.138	-0.069	-0.069	0.000	0.000	0.000	0.000
124	A	138	LYS	1	0.947	0.986	14.160	0.289	0.289	0.000	0.000	0.000	0.000
125	A	139	TYR	0	-0.015	-0.031	7.738	-0.031	-0.031	0.000	0.000	0.000	0.000
126	A	140	ILE	0	0.019	0.010	6.693	0.144	0.144	0.000	0.000	0.000	0.000
127	A	141	GLU	-1	-0.910	-0.947	6.357	-2.294	-2.294	0.000	0.000	0.000	0.000
128	A	142	GLY	0	0.042	0.014	2.878	-0.056	0.572	0.166	-0.193	-0.602	-0.001
129	A	143	MET	0	-0.013	-0.005	2.608	-2.372	-0.478	1.459	-1.356	-1.997	-0.019
130	A	144	THR	0	0.000	0.007	2.204	-0.364	0.056	1.462	-0.486	-1.396	0.000
131	A	145	GLU	-1	-0.807	-0.907	4.433	-0.162	-0.078	0.000	-0.019	-0.064	0.000
132	A	146	SER	0	-0.026	-0.018	7.638	-0.050	-0.050	0.000	0.000	0.000	0.000
133	A	147	ALA	0	0.022	0.013	5.327	-0.048	-0.048	0.000	0.000	0.000	0.000
134	A	148	PHE	0	0.045	0.007	7.222	-0.061	-0.061	0.000	0.000	0.000	0.000
135	A	149	THR	0	0.006	-0.012	9.101	0.047	0.047	0.000	0.000	0.000	0.000
136	A	150	GLU	-1	-0.875	-0.940	10.624	-0.051	-0.051	0.000	0.000	0.000	0.000
137	A	151	ILE	0	-0.009	-0.003	8.955	0.008	0.008	0.000	0.000	0.000	0.000
138	A	152	LEU	0	-0.009	-0.004	12.577	0.037	0.037	0.000	0.000	0.000	0.000
139	A	153	GLN	0	-0.023	-0.006	14.856	0.046	0.046	0.000	0.000	0.000	0.000
140	A	154	HIS	0	-0.069	-0.032	14.549	0.015	0.015	0.000	0.000	0.000	0.000
141	A	155	TRP	0	0.015	-0.002	14.507	0.013	0.013	0.000	0.000	0.000	0.000
142	A	156	ALA	0	0.015	0.003	18.903	0.018	0.018	0.000	0.000	0.000	0.000
143	A	157	THR	0	-0.037	-0.031	20.620	0.018	0.018	0.000	0.000	0.000	0.000
144	A	158	GLU	-1	-0.849	-0.890	21.789	-0.191	-0.191	0.000	0.000	0.000	0.000
145	A	159	ILE	0	0.030	0.003	21.902	0.010	0.010	0.000	0.000	0.000	0.000
146	A	160	GLY	0	-0.017	-0.009	24.911	0.011	0.011	0.000	0.000	0.000	0.000
147	A	161	GLN	0	-0.017	-0.017	26.259	0.005	0.005	0.000	0.000	0.000	0.000
148	A	162	LYS	1	0.855	0.934	27.624	0.124	0.124	0.000	0.000	0.000	0.000
149	A	163	ILE	0	-0.001	-0.008	28.221	0.006	0.006	0.000	0.000	0.000	0.000
150	A	164	GLU	-1	-0.798	-0.888	30.933	-0.053	-0.053	0.000	0.000	0.000	0.000
151	A	165	GLU	-1	-0.883	-0.911	32.029	-0.096	-0.096	0.000	0.000	0.000	0.000
152	A	166	VAL	0	-0.043	-0.022	32.628	0.004	0.004	0.000	0.000	0.000	0.000
153	A	167	CYS	0	-0.087	-0.034	34.537	0.004	0.004	0.000	0.000	0.000	0.000
154	A	168	SER	0	-0.085	-0.031	36.894	0.008	0.008	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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