FMO DATABASE

FMODB ID: VRNL1

Calculation Name: 2EHW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2EHW

Chain ID: A

ChEMBL ID:

UniProt ID: Q53WA3

Base Structure: X-ray

Registration Date: 2023-03-13

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	115
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-859613.807667
FMO2-HF: Nuclear repulsion	814244.715424
FMO2-HF: Total energy	-45369.092243
FMO2-MP2: Total energy	-45503.494271

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:3:CYS)

Summations of interaction energy for fragment #1(A:3:CYS)

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.
-13.428	-6.873	7.564	-5.753	-8.363	-0.025

Interaction energy analysis for fragmet #1(A:3:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : -0.008

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

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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	5	GLU	-1	-0.768	-0.875	3.677	-0.591	1.356	0.012	-0.815	-1.144	0.000
4	A	6	LEU	0	-0.032	-0.015	2.433	0.025	1.175	0.686	-0.474	-1.361	0.001
5	A	7	SER	0	-0.017	-0.028	2.898	-0.183	0.637	0.138	-0.366	-0.591	-0.003
6	A	8	ALA	0	0.005	-0.003	5.203	1.043	1.169	-0.001	-0.007	-0.117	0.000
7	A	9	LEU	0	0.006	0.003	7.809	0.431	0.431	0.000	0.000	0.000	0.000
8	A	10	ARG	1	0.807	0.876	7.988	1.475	1.475	0.000	0.000	0.000	0.000
9	A	11	ILE	0	-0.002	0.002	9.044	0.296	0.296	0.000	0.000	0.000	0.000
10	A	12	ALA	0	0.022	0.024	11.351	0.185	0.185	0.000	0.000	0.000	0.000
11	A	13	ILE	0	-0.045	-0.034	12.621	0.133	0.133	0.000	0.000	0.000	0.000
12	A	14	GLY	0	0.026	0.003	13.561	0.086	0.086	0.000	0.000	0.000	0.000
13	A	15	GLU	-1	-0.800	-0.882	14.999	-0.467	-0.467	0.000	0.000	0.000	0.000
14	A	16	LEU	0	-0.098	-0.041	17.280	0.065	0.065	0.000	0.000	0.000	0.000
15	A	17	LEU	0	-0.042	-0.013	16.610	0.045	0.045	0.000	0.000	0.000	0.000
16	A	18	GLU	-1	-0.964	-0.971	19.747	-0.242	-0.242	0.000	0.000	0.000	0.000
17	A	19	LYS	1	0.764	0.889	15.364	0.428	0.428	0.000	0.000	0.000	0.000
18	A	20	GLU	-1	-0.815	-0.898	18.067	-0.315	-0.315	0.000	0.000	0.000	0.000
19	A	21	ALA	0	-0.007	-0.020	16.572	-0.062	-0.062	0.000	0.000	0.000	0.000
20	A	22	HIS	0	-0.035	-0.026	15.269	-0.065	-0.065	0.000	0.000	0.000	0.000
21	A	23	ASP	-1	-0.895	-0.942	14.438	-0.462	-0.462	0.000	0.000	0.000	0.000
22	A	24	LEU	0	-0.065	-0.023	11.114	-0.106	-0.106	0.000	0.000	0.000	0.000
23	A	25	LEU	0	0.020	0.026	11.535	-0.063	-0.063	0.000	0.000	0.000	0.000
24	A	26	HIS	0	0.028	0.005	8.388	-0.062	-0.062	0.000	0.000	0.000	0.000
25	A	27	GLU	-1	-0.785	-0.871	5.763	-1.634	-1.634	0.000	0.000	0.000	0.000
26	A	28	ARG	1	0.776	0.845	7.135	0.667	0.667	0.000	0.000	0.000	0.000
27	A	29	GLU	-1	-0.940	-0.975	10.027	-0.314	-0.314	0.000	0.000	0.000	0.000
28	A	30	GLU	-1	-0.909	-0.930	3.357	-9.021	-7.233	0.126	-0.987	-0.927	-0.008
29	A	31	LEU	0	-0.013	-0.010	7.040	0.566	0.566	0.000	0.000	0.000	0.000
30	A	32	ALA	0	-0.013	-0.004	8.577	0.330	0.330	0.000	0.000	0.000	0.000
31	A	33	PRO	0	-0.039	-0.020	9.737	0.106	0.106	0.000	0.000	0.000	0.000
32	A	34	VAL	0	0.016	0.011	7.396	0.095	0.095	0.000	0.000	0.000	0.000
33	A	35	LEU	0	0.020	0.010	10.498	0.035	0.035	0.000	0.000	0.000	0.000
34	A	36	GLY	0	-0.040	-0.014	12.921	0.002	0.002	0.000	0.000	0.000	0.000
35	A	37	GLN	0	-0.111	-0.069	12.867	0.031	0.031	0.000	0.000	0.000	0.000
36	A	38	ARG	1	0.796	0.893	6.562	-1.060	-1.060	0.000	0.000	0.000	0.000
37	A	39	PRO	0	0.016	-0.004	12.911	-0.119	-0.119	0.000	0.000	0.000	0.000
38	A	40	GLU	-1	-0.746	-0.867	10.808	0.177	0.177	0.000	0.000	0.000	0.000
39	A	41	LEU	0	0.028	0.019	7.368	-0.150	-0.150	0.000	0.000	0.000	0.000
40	A	42	LYS	1	0.835	0.904	11.169	0.053	0.053	0.000	0.000	0.000	0.000
41	A	43	ARG	1	0.789	0.854	14.233	0.025	0.025	0.000	0.000	0.000	0.000
42	A	44	LEU	0	-0.033	-0.014	8.991	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	45	ALA	0	0.032	0.014	11.233	-0.057	-0.057	0.000	0.000	0.000	0.000
44	A	46	GLU	-1	-0.840	-0.903	12.919	-0.258	-0.258	0.000	0.000	0.000	0.000
45	A	47	ALA	0	-0.017	0.016	16.418	0.058	0.058	0.000	0.000	0.000	0.000
46	A	48	LYS	1	0.858	0.910	17.417	0.394	0.394	0.000	0.000	0.000	0.000
47	A	49	THR	0	0.002	0.003	20.395	0.016	0.016	0.000	0.000	0.000	0.000
48	A	50	LEU	0	0.083	0.044	18.454	-0.017	-0.017	0.000	0.000	0.000	0.000
49	A	51	PRO	0	0.019	0.005	19.113	-0.014	-0.014	0.000	0.000	0.000	0.000
50	A	52	ALA	0	-0.002	0.004	19.993	0.009	0.009	0.000	0.000	0.000	0.000
51	A	53	LEU	0	-0.004	0.005	13.377	0.003	0.003	0.000	0.000	0.000	0.000
52	A	54	GLU	-1	-0.800	-0.916	15.056	-0.278	-0.278	0.000	0.000	0.000	0.000
53	A	55	GLU	-1	-0.894	-0.931	16.289	-0.111	-0.111	0.000	0.000	0.000	0.000
54	A	56	ALA	0	0.022	0.016	14.263	0.026	0.026	0.000	0.000	0.000	0.000
55	A	57	LEU	0	0.004	0.009	9.679	0.002	0.002	0.000	0.000	0.000	0.000
56	A	58	ARG	1	0.847	0.913	11.688	0.204	0.204	0.000	0.000	0.000	0.000
57	A	59	GLU	-1	-0.837	-0.877	14.132	-0.011	-0.011	0.000	0.000	0.000	0.000
58	A	60	ALA	0	-0.023	-0.021	8.679	0.088	0.088	0.000	0.000	0.000	0.000
59	A	61	LEU	0	-0.011	-0.016	9.371	0.174	0.174	0.000	0.000	0.000	0.000
60	A	62	LEU	0	-0.002	0.020	10.681	0.090	0.090	0.000	0.000	0.000	0.000
61	A	63	HIS	0	0.021	0.012	10.350	0.193	0.193	0.000	0.000	0.000	0.000
62	A	64	LEU	0	-0.015	-0.001	5.583	0.174	0.174	0.000	0.000	0.000	0.000
63	A	65	GLU	-1	-0.906	-0.961	8.906	0.312	0.312	0.000	0.000	0.000	0.000
64	A	66	GLU	-1	-0.958	-0.985	12.191	0.377	0.377	0.000	0.000	0.000	0.000
65	A	67	ARG	1	0.801	0.877	9.003	-1.215	-1.215	0.000	0.000	0.000	0.000
66	A	68	ALA	0	0.007	-0.004	10.637	-0.019	-0.019	0.000	0.000	0.000	0.000
67	A	69	ALA	0	-0.039	-0.016	12.126	-0.082	-0.082	0.000	0.000	0.000	0.000
68	A	70	GLN	0	-0.056	-0.033	14.350	0.029	0.029	0.000	0.000	0.000	0.000
69	A	71	GLU	-1	-0.827	-0.864	11.035	1.017	1.017	0.000	0.000	0.000	0.000
70	A	72	PRO	0	-0.020	-0.014	13.990	0.013	0.013	0.000	0.000	0.000	0.000
71	A	73	GLU	-1	-0.895	-0.955	15.921	0.357	0.357	0.000	0.000	0.000	0.000
72	A	74	GLU	-1	-0.889	-0.927	9.808	0.635	0.635	0.000	0.000	0.000	0.000
73	A	75	PRO	0	-0.026	-0.021	11.718	0.028	0.028	0.000	0.000	0.000	0.000
74	A	76	TYR	0	-0.006	-0.004	2.028	-5.330	-5.329	4.242	-1.803	-2.440	-0.009
75	A	77	TRP	0	0.020	-0.010	5.192	0.213	0.213	0.000	0.000	0.000	0.000
76	A	78	ARG	1	0.887	0.945	8.020	-0.481	-0.481	0.000	0.000	0.000	0.000
77	A	79	GLY	0	-0.021	-0.001	8.792	-0.102	-0.102	0.000	0.000	0.000	0.000
78	A	80	LEU	0	-0.050	-0.024	2.379	-1.213	-0.490	2.361	-1.301	-1.783	-0.006
79	A	81	LEU	0	0.019	0.011	5.919	-0.274	-0.274	0.000	0.000	0.000	0.000
80	A	82	LEU	0	0.043	0.032	8.726	-0.155	-0.155	0.000	0.000	0.000	0.000
81	A	83	ALA	0	-0.031	-0.017	6.601	-0.055	-0.055	0.000	0.000	0.000	0.000
82	A	84	VAL	0	0.008	-0.010	5.549	-0.191	-0.191	0.000	0.000	0.000	0.000
83	A	85	GLU	-1	-0.895	-0.953	8.238	-0.045	-0.045	0.000	0.000	0.000	0.000
84	A	86	ALA	0	-0.034	-0.009	11.284	0.013	0.013	0.000	0.000	0.000	0.000
85	A	87	MET	0	-0.071	-0.039	8.631	0.068	0.068	0.000	0.000	0.000	0.000
86	A	88	GLU	-1	-0.764	-0.862	11.494	-0.216	-0.216	0.000	0.000	0.000	0.000
87	A	89	GLY	0	0.035	0.013	13.625	0.045	0.045	0.000	0.000	0.000	0.000
88	A	90	ARG	1	0.903	0.937	13.039	0.471	0.471	0.000	0.000	0.000	0.000
89	A	91	LEU	0	-0.005	0.016	14.186	0.021	0.021	0.000	0.000	0.000	0.000
90	A	92	LYS	1	0.839	0.894	16.212	0.251	0.251	0.000	0.000	0.000	0.000
91	A	93	ALA	0	-0.039	-0.009	18.961	0.028	0.028	0.000	0.000	0.000	0.000
92	A	94	LEU	0	0.001	0.001	17.755	0.017	0.017	0.000	0.000	0.000	0.000
93	A	95	ARG	1	0.871	0.915	20.343	0.208	0.208	0.000	0.000	0.000	0.000
94	A	96	ALA	0	-0.022	-0.008	22.230	0.020	0.020	0.000	0.000	0.000	0.000
95	A	97	GLU	-1	-0.926	-0.958	23.595	-0.163	-0.163	0.000	0.000	0.000	0.000
96	A	98	ALA	0	-0.035	-0.018	24.358	0.013	0.013	0.000	0.000	0.000	0.000
97	A	99	GLU	-1	-0.922	-0.958	26.156	-0.124	-0.124	0.000	0.000	0.000	0.000
98	A	100	ALA	0	0.022	0.011	28.187	0.013	0.013	0.000	0.000	0.000	0.000
99	A	101	LEU	0	0.020	0.011	28.888	0.010	0.010	0.000	0.000	0.000	0.000
100	A	102	TYR	0	-0.061	-0.033	30.269	0.009	0.009	0.000	0.000	0.000	0.000
101	A	103	GLN	0	-0.049	-0.034	31.614	0.014	0.014	0.000	0.000	0.000	0.000
102	A	104	ASP	-1	-0.891	-0.953	33.904	-0.098	-0.098	0.000	0.000	0.000	0.000
103	A	105	LEU	0	-0.073	-0.032	33.169	0.007	0.007	0.000	0.000	0.000	0.000
104	A	106	ASP	-1	-0.929	-0.948	36.678	-0.074	-0.074	0.000	0.000	0.000	0.000
105	A	107	ALA	0	0.027	0.012	38.604	0.006	0.006	0.000	0.000	0.000	0.000
106	A	108	LEU	0	-0.036	-0.018	38.733	0.006	0.006	0.000	0.000	0.000	0.000
107	A	109	HIS	0	-0.004	0.000	40.923	0.005	0.005	0.000	0.000	0.000	0.000
108	A	110	GLY	0	0.078	0.034	42.899	0.004	0.004	0.000	0.000	0.000	0.000
109	A	111	ARG	1	0.863	0.939	43.824	0.065	0.065	0.000	0.000	0.000	0.000
110	A	112	LEU	0	0.033	0.000	43.104	0.004	0.004	0.000	0.000	0.000	0.000
111	A	113	HIS	0	0.010	0.009	46.700	0.002	0.002	0.000	0.000	0.000	0.000
112	A	114	ARG	1	0.855	0.907	45.415	0.062	0.062	0.000	0.000	0.000	0.000
113	A	115	LEU	0	-0.075	-0.025	47.113	0.002	0.002	0.000	0.000	0.000	0.000
114	A	116	PHE	0	-0.046	-0.013	48.083	0.001	0.001	0.000	0.000	0.000	0.000
115	A	117	PRO	0	-0.004	0.014	52.576	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:CYS)