FMO DATABASE

FMODB ID: VRGN1

Calculation Name: 4EXW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4EXW

Chain ID: A

ChEMBL ID:

UniProt ID: Q1J1N6

Base Structure: X-ray

Registration Date: 2023-06-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	130
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1087110.137679
FMO2-HF: Nuclear repulsion	1035641.788572
FMO2-HF: Total energy	-51468.349106
FMO2-MP2: Total energy	-51620.405441

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:-5:GLY)

Summations of interaction energy for fragment #1(A:-5:GLY)

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.
0.969	1.92	-0.005	-0.331	-0.614	0

Interaction energy analysis for fragmet #1(A:-5:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.021

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].
3	A	-3	ASP	-1	-0.869	-0.934	3.799	0.049	1.000	-0.005	-0.331	-0.614
4	A	-2	PRO	0	-0.042	-0.026	6.460	0.174	0.174	0.000	0.000	0.000
5	A	-1	PHE	0	-0.033	-0.013	9.481	0.041	0.041	0.000	0.000	0.000
6	A	0	THR	0	-0.001	0.015	10.160	-0.066	-0.066	0.000	0.000	0.000
7	A	1	MET	0	-0.002	-0.004	12.145	-0.014	-0.014	0.000	0.000	0.000
8	A	2	LEU	0	-0.043	-0.015	10.965	-0.038	-0.038	0.000	0.000	0.000
9	A	3	HIS	1	0.845	0.886	15.200	0.234	0.234	0.000	0.000	0.000
10	A	4	ILE	0	0.010	0.025	18.435	-0.022	-0.022	0.000	0.000	0.000
11	A	5	GLU	-1	-0.914	-0.956	20.070	-0.107	-0.107	0.000	0.000	0.000
12	A	6	PHE	0	0.005	-0.015	21.958	-0.003	-0.003	0.000	0.000	0.000
13	A	7	ILE	0	-0.026	-0.009	26.001	0.002	0.002	0.000	0.000	0.000
14	A	8	THR	0	-0.016	-0.012	29.542	0.002	0.002	0.000	0.000	0.000
15	A	9	ASP	-1	-0.835	-0.927	31.452	-0.038	-0.038	0.000	0.000	0.000
16	A	10	LEU	0	-0.062	-0.034	34.422	0.002	0.002	0.000	0.000	0.000
17	A	11	GLY	0	-0.025	-0.005	34.387	0.000	0.000	0.000	0.000	0.000
18	A	12	ALA	0	-0.033	-0.004	33.493	-0.003	-0.003	0.000	0.000	0.000
19	A	13	LYS	1	0.968	0.985	27.751	0.097	0.097	0.000	0.000	0.000
20	A	14	VAL	0	0.002	0.002	27.282	0.001	0.001	0.000	0.000	0.000
21	A	15	THR	0	-0.010	-0.005	22.498	-0.009	-0.009	0.000	0.000	0.000
22	A	16	VAL	0	-0.023	-0.008	21.582	0.009	0.009	0.000	0.000	0.000
23	A	17	ASP	-1	-0.853	-0.907	20.115	-0.137	-0.137	0.000	0.000	0.000
24	A	18	VAL	0	-0.036	-0.025	15.253	0.020	0.020	0.000	0.000	0.000
25	A	19	GLU	-1	-0.865	-0.920	15.096	0.012	0.012	0.000	0.000	0.000
26	A	20	SER	0	0.061	0.019	10.834	-0.018	-0.018	0.000	0.000	0.000
27	A	21	ALA	0	0.033	0.000	8.166	0.022	0.022	0.000	0.000	0.000
28	A	22	ASP	-1	-0.896	-0.950	8.150	0.559	0.559	0.000	0.000	0.000
29	A	23	LYS	1	0.857	0.927	10.670	-0.052	-0.052	0.000	0.000	0.000
30	A	24	LEU	0	-0.003	0.008	13.001	-0.008	-0.008	0.000	0.000	0.000
31	A	25	LEU	0	0.007	-0.018	13.601	0.009	0.009	0.000	0.000	0.000
32	A	26	ASP	-1	-0.888	-0.942	16.003	0.056	0.056	0.000	0.000	0.000
33	A	27	VAL	0	-0.002	0.000	17.958	0.001	0.001	0.000	0.000	0.000
34	A	28	GLN	0	-0.014	-0.023	16.819	-0.013	-0.013	0.000	0.000	0.000
35	A	29	ARG	1	0.848	0.922	17.295	0.004	0.004	0.000	0.000	0.000
36	A	30	GLN	0	-0.020	0.004	22.237	0.007	0.007	0.000	0.000	0.000
37	A	31	TYR	0	0.001	-0.009	23.345	0.004	0.004	0.000	0.000	0.000
38	A	32	GLY	0	0.064	0.046	24.419	-0.001	-0.001	0.000	0.000	0.000
39	A	33	ARG	1	0.827	0.895	24.321	0.013	0.013	0.000	0.000	0.000
40	A	34	LEU	0	-0.037	-0.008	28.236	0.004	0.004	0.000	0.000	0.000
41	A	35	GLY	0	-0.033	-0.003	29.341	0.001	0.001	0.000	0.000	0.000
42	A	36	TRP	0	-0.022	-0.002	26.833	-0.004	-0.004	0.000	0.000	0.000
43	A	37	THR	0	-0.006	-0.006	26.081	0.001	0.001	0.000	0.000	0.000
44	A	38	SER	0	-0.050	-0.033	22.072	-0.007	-0.007	0.000	0.000	0.000
45	A	39	GLY	0	0.009	0.015	23.450	-0.007	-0.007	0.000	0.000	0.000
46	A	40	GLU	-1	-0.943	-0.971	24.602	-0.078	-0.078	0.000	0.000	0.000
47	A	41	VAL	0	-0.042	-0.020	25.517	-0.006	-0.006	0.000	0.000	0.000
48	A	42	PRO	0	-0.013	0.008	24.182	0.001	0.001	0.000	0.000	0.000
49	A	43	VAL	0	0.078	0.024	26.845	0.007	0.007	0.000	0.000	0.000
50	A	44	GLY	0	-0.021	-0.006	29.399	-0.001	-0.001	0.000	0.000	0.000
51	A	45	GLY	0	-0.005	0.002	28.737	0.004	0.004	0.000	0.000	0.000
52	A	46	TYR	0	0.010	-0.011	22.748	-0.002	-0.002	0.000	0.000	0.000
53	A	47	GLN	0	-0.042	-0.023	23.035	0.016	0.016	0.000	0.000	0.000
54	A	48	PHE	0	-0.011	0.001	20.371	-0.011	-0.011	0.000	0.000	0.000
55	A	49	PRO	0	0.014	-0.008	19.437	0.003	0.003	0.000	0.000	0.000
56	A	50	LEU	0	0.015	0.002	22.589	0.003	0.003	0.000	0.000	0.000
57	A	51	GLU	-1	-0.942	-0.975	23.633	0.004	0.004	0.000	0.000	0.000
58	A	52	ASN	0	-0.016	-0.033	20.543	0.000	0.000	0.000	0.000	0.000
59	A	53	GLU	-1	-0.816	-0.895	24.011	-0.016	-0.016	0.000	0.000	0.000
60	A	54	PRO	0	0.011	0.013	27.266	0.000	0.000	0.000	0.000	0.000
61	A	55	ASP	-1	-0.875	-0.943	25.094	0.013	0.013	0.000	0.000	0.000
62	A	56	PHE	0	0.018	0.012	21.517	0.001	0.001	0.000	0.000	0.000
63	A	57	ASP	-1	-0.781	-0.879	22.349	-0.011	-0.011	0.000	0.000	0.000
64	A	58	TRP	0	0.031	-0.003	23.800	-0.011	-0.011	0.000	0.000	0.000
65	A	59	SER	0	-0.058	-0.038	24.527	-0.006	-0.006	0.000	0.000	0.000
66	A	60	LEU	0	-0.011	-0.003	19.037	-0.006	-0.006	0.000	0.000	0.000
67	A	61	ILE	0	-0.043	-0.017	21.998	-0.013	-0.013	0.000	0.000	0.000
68	A	62	GLY	0	0.016	0.015	24.583	0.000	0.000	0.000	0.000	0.000
69	A	63	ALA	0	-0.083	-0.032	27.379	0.002	0.002	0.000	0.000	0.000
70	A	64	ARG	1	0.948	0.962	29.288	0.023	0.023	0.000	0.000	0.000
71	A	65	LYS	1	0.966	0.989	30.830	0.005	0.005	0.000	0.000	0.000
72	A	66	TRP	0	-0.039	-0.034	34.064	0.000	0.000	0.000	0.000	0.000
73	A	67	THR	0	0.040	0.020	37.773	-0.001	-0.001	0.000	0.000	0.000
74	A	68	ASN	0	-0.021	0.003	40.961	0.001	0.001	0.000	0.000	0.000
75	A	69	PRO	0	-0.001	-0.005	43.876	0.001	0.001	0.000	0.000	0.000
76	A	70	GLU	-1	-0.919	-0.959	47.312	-0.012	-0.012	0.000	0.000	0.000
77	A	71	GLY	0	-0.027	-0.008	46.033	0.001	0.001	0.000	0.000	0.000
78	A	72	GLU	-1	-0.976	-0.988	41.778	-0.016	-0.016	0.000	0.000	0.000
79	A	73	GLU	-1	-0.866	-0.929	36.265	-0.010	-0.010	0.000	0.000	0.000
80	A	74	MET	0	-0.065	-0.028	37.737	-0.003	-0.003	0.000	0.000	0.000
81	A	75	ILE	0	-0.012	-0.004	31.260	0.001	0.001	0.000	0.000	0.000
82	A	76	LEU	0	-0.043	-0.026	34.324	-0.002	-0.002	0.000	0.000	0.000
83	A	77	HIS	0	0.011	-0.011	28.237	-0.003	-0.003	0.000	0.000	0.000
84	A	78	ARG	1	0.996	0.994	30.910	0.066	0.066	0.000	0.000	0.000
85	A	79	GLY	0	0.038	0.032	34.443	0.000	0.000	0.000	0.000	0.000
86	A	80	HIS	0	-0.083	-0.033	35.955	-0.001	-0.001	0.000	0.000	0.000
87	A	81	ALA	0	0.051	0.018	36.661	0.000	0.000	0.000	0.000	0.000
88	A	82	TYR	0	-0.065	-0.016	34.025	-0.001	-0.001	0.000	0.000	0.000
89	A	83	ARG	1	1.018	1.012	36.670	0.027	0.027	0.000	0.000	0.000
90	A	84	ARG	1	0.834	0.915	33.200	0.012	0.012	0.000	0.000	0.000
91	A	85	ARG	1	0.900	0.948	35.759	0.032	0.032	0.000	0.000	0.000
92	A	86	GLU	-1	-0.831	-0.918	35.414	-0.015	-0.015	0.000	0.000	0.000
93	A	87	LEU	0	-0.078	-0.052	34.230	-0.002	-0.002	0.000	0.000	0.000
94	A	88	GLU	-1	-0.835	-0.895	35.486	-0.015	-0.015	0.000	0.000	0.000
95	A	89	ALA	0	-0.068	-0.037	35.703	-0.002	-0.002	0.000	0.000	0.000
96	A	99	ALA	0	0.056	0.039	31.954	0.001	0.001	0.000	0.000	0.000
97	A	100	ALA	0	-0.107	-0.077	30.843	-0.003	-0.003	0.000	0.000	0.000
98	A	101	VAL	0	0.027	0.032	30.637	0.003	0.003	0.000	0.000	0.000
99	A	102	LYS	1	0.884	0.952	30.888	0.038	0.038	0.000	0.000	0.000
100	A	103	TYR	0	0.046	0.028	30.523	0.004	0.004	0.000	0.000	0.000
101	A	104	SER	0	-0.052	-0.045	33.214	-0.004	-0.004	0.000	0.000	0.000
102	A	105	ARG	1	0.898	0.962	35.927	0.046	0.046	0.000	0.000	0.000
103	A	106	GLY	0	0.015	0.011	39.093	-0.002	-0.002	0.000	0.000	0.000
104	A	107	ALA	0	0.009	0.013	40.969	-0.001	-0.001	0.000	0.000	0.000
105	A	108	LYS	1	0.824	0.896	39.213	0.044	0.044	0.000	0.000	0.000
106	A	109	ASN	0	0.004	0.004	44.389	-0.001	-0.001	0.000	0.000	0.000
107	A	110	THR	0	0.013	0.000	42.433	-0.001	-0.001	0.000	0.000	0.000
108	A	111	ASP	-1	-0.820	-0.932	38.366	-0.047	-0.047	0.000	0.000	0.000
109	A	112	PRO	0	-0.015	0.029	38.317	0.002	0.002	0.000	0.000	0.000
110	A	113	GLU	-1	-0.937	-0.966	36.365	-0.052	-0.052	0.000	0.000	0.000
111	A	124	GLU	-1	-0.911	-0.946	42.540	-0.031	-0.031	0.000	0.000	0.000
112	A	125	TYR	0	-0.053	-0.051	39.058	0.002	0.002	0.000	0.000	0.000
113	A	126	VAL	0	0.103	0.065	34.729	-0.002	-0.002	0.000	0.000	0.000
114	A	127	THR	0	-0.119	-0.090	31.808	0.002	0.002	0.000	0.000	0.000
115	A	128	LEU	0	0.028	0.032	29.056	-0.003	-0.003	0.000	0.000	0.000
116	A	129	ALA	0	0.015	-0.010	27.057	-0.007	-0.007	0.000	0.000	0.000
117	A	130	ILE	0	-0.043	-0.023	27.453	0.008	0.008	0.000	0.000	0.000
118	A	131	PHE	0	0.008	0.011	24.691	-0.006	-0.006	0.000	0.000	0.000
119	A	132	ARG	1	1.009	0.978	26.044	0.057	0.057	0.000	0.000	0.000
120	A	133	GLY	0	0.021	0.030	25.309	-0.006	-0.006	0.000	0.000	0.000
121	A	134	GLY	0	0.007	0.010	21.658	0.000	0.000	0.000	0.000	0.000
122	A	135	LYS	1	0.996	1.005	14.540	0.063	0.063	0.000	0.000	0.000
123	A	136	ARG	1	0.910	0.953	19.213	-0.032	-0.032	0.000	0.000	0.000
124	A	137	GLN	0	-0.051	-0.028	14.158	-0.023	-0.023	0.000	0.000	0.000
125	A	138	GLU	-1	-0.838	-0.933	16.311	0.047	0.047	0.000	0.000	0.000
126	A	139	ARG	1	0.918	0.971	12.327	0.134	0.134	0.000	0.000	0.000
127	A	140	TYR	0	-0.032	-0.025	16.143	-0.019	-0.019	0.000	0.000	0.000
128	A	141	ALA	0	0.041	0.041	19.119	-0.004	-0.004	0.000	0.000	0.000
129	A	142	VAL	0	-0.026	-0.010	21.063	0.001	0.001	0.000	0.000	0.000
130	A	143	PRO	0	-0.012	0.009	20.778	0.005	0.005	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-5:GLY)