FMO DATABASE

FMODB ID: V5NR1

Calculation Name: 1VHX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VHX

Chain ID: A

ChEMBL ID:

UniProt ID: O34634

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:

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	140
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1204586.29798
FMO2-HF: Nuclear repulsion	1150162.691744
FMO2-HF: Total energy	-54423.606236
FMO2-MP2: Total energy	-54580.84811

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:0:SER)

Summations of interaction energy for fragment #1(A:0:SER)

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.
-28.39	-31.65	25.819	-13.664	-8.893	-0.05

Interaction energy analysis for fragmet #1(A:0:SER)

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 : -0.047

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	2	ARG	1	0.834	0.910	2.546	-1.538	3.819	0.394	-2.891	-2.860	0.021
4	A	3	ILE	0	0.048	0.019	5.820	-0.445	-0.445	0.000	0.000	0.000	0.000
5	A	4	LEU	0	0.001	0.000	9.447	0.024	0.024	0.000	0.000	0.000	0.000
6	A	5	GLY	0	0.016	0.009	11.856	0.031	0.031	0.000	0.000	0.000	0.000
7	A	6	LEU	0	-0.039	-0.040	14.982	-0.022	-0.022	0.000	0.000	0.000	0.000
8	A	7	ASP	-1	-0.893	-0.961	18.274	-0.052	-0.052	0.000	0.000	0.000	0.000
9	A	8	LEU	0	0.011	0.012	21.895	-0.006	-0.006	0.000	0.000	0.000	0.000
10	A	9	GLY	0	0.022	0.013	24.623	0.007	0.007	0.000	0.000	0.000	0.000
11	A	10	THR	0	-0.051	-0.040	27.790	-0.002	-0.002	0.000	0.000	0.000	0.000
12	A	11	LYS	1	0.926	0.953	29.801	0.050	0.050	0.000	0.000	0.000	0.000
13	A	12	THR	0	-0.022	-0.019	25.161	0.000	0.000	0.000	0.000	0.000	0.000
14	A	13	LEU	0	0.041	0.037	19.506	0.006	0.006	0.000	0.000	0.000	0.000
15	A	14	GLY	0	-0.050	-0.014	20.655	-0.009	-0.009	0.000	0.000	0.000	0.000
16	A	15	VAL	0	0.027	0.002	14.439	0.004	0.004	0.000	0.000	0.000	0.000
17	A	16	ALA	0	-0.003	-0.003	14.261	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	17	LEU	0	0.052	0.025	7.364	-0.015	-0.015	0.000	0.000	0.000	0.000
19	A	18	SER	0	0.034	0.047	6.470	-0.164	-0.164	0.000	0.000	0.000	0.000
20	A	19	ASP	-1	-0.783	-0.889	6.983	0.163	0.163	0.000	0.000	0.000	0.000
21	A	20	GLU	-1	-0.846	-0.891	1.593	-25.933	-35.520	25.418	-10.424	-5.406	-0.070
22	A	21	MET	0	-0.057	-0.032	4.099	0.370	0.537	-0.001	-0.015	-0.152	0.000
23	A	22	GLY	0	0.000	0.025	7.117	0.033	0.033	0.000	0.000	0.000	0.000
24	A	23	TRP	0	-0.037	-0.012	8.524	-0.127	-0.127	0.000	0.000	0.000	0.000
25	A	24	THR	0	-0.060	-0.034	10.845	-0.047	-0.047	0.000	0.000	0.000	0.000
26	A	25	ALA	0	0.023	0.015	10.710	0.047	0.047	0.000	0.000	0.000	0.000
27	A	26	GLN	0	-0.023	-0.017	8.618	-0.015	-0.015	0.000	0.000	0.000	0.000
28	A	27	GLY	0	-0.030	-0.035	12.957	0.003	0.003	0.000	0.000	0.000	0.000
29	A	28	ILE	0	-0.025	0.002	11.123	-0.021	-0.021	0.000	0.000	0.000	0.000
30	A	29	GLU	-1	-0.799	-0.899	15.152	-0.161	-0.161	0.000	0.000	0.000	0.000
31	A	30	THR	0	-0.104	-0.056	18.629	0.010	0.010	0.000	0.000	0.000	0.000
32	A	31	ILE	0	0.027	0.031	18.122	0.005	0.005	0.000	0.000	0.000	0.000
33	A	32	LYS	1	0.890	0.945	22.326	0.083	0.083	0.000	0.000	0.000	0.000
34	A	33	ILE	0	0.032	0.031	24.311	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	34	ASN	0	-0.094	-0.078	27.172	0.009	0.009	0.000	0.000	0.000	0.000
36	A	35	GLU	-1	-0.697	-0.806	30.227	-0.049	-0.049	0.000	0.000	0.000	0.000
37	A	36	ALA	0	-0.050	-0.002	31.797	0.001	0.001	0.000	0.000	0.000	0.000
38	A	37	GLU	-1	-0.904	-0.950	32.477	-0.040	-0.040	0.000	0.000	0.000	0.000
39	A	38	GLY	0	-0.067	-0.028	31.259	0.000	0.000	0.000	0.000	0.000	0.000
40	A	39	ASP	-1	-0.944	-0.988	26.486	-0.082	-0.082	0.000	0.000	0.000	0.000
41	A	40	TYR	0	0.054	0.013	24.878	0.002	0.002	0.000	0.000	0.000	0.000
42	A	41	GLY	0	0.028	0.007	22.610	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	42	LEU	0	0.017	0.000	20.257	-0.013	-0.013	0.000	0.000	0.000	0.000
44	A	43	SER	0	0.017	0.001	19.244	-0.015	-0.015	0.000	0.000	0.000	0.000
45	A	44	ARG	1	0.874	0.941	17.268	0.165	0.165	0.000	0.000	0.000	0.000
46	A	45	LEU	0	0.016	0.009	14.964	-0.020	-0.020	0.000	0.000	0.000	0.000
47	A	46	SER	0	0.049	0.030	14.573	-0.044	-0.044	0.000	0.000	0.000	0.000
48	A	47	GLU	-1	-0.978	-0.974	13.912	-0.176	-0.176	0.000	0.000	0.000	0.000
49	A	48	LEU	0	-0.081	-0.058	13.322	-0.035	-0.035	0.000	0.000	0.000	0.000
50	A	49	ILE	0	-0.004	-0.004	9.848	-0.057	-0.057	0.000	0.000	0.000	0.000
51	A	50	LYS	1	0.919	0.976	9.046	0.033	0.033	0.000	0.000	0.000	0.000
52	A	51	ASP	-1	-0.938	-0.965	7.889	-0.309	-0.309	0.000	0.000	0.000	0.000
53	A	52	TYR	0	-0.062	-0.031	4.547	-0.255	-0.087	-0.001	-0.014	-0.153	0.000
54	A	53	THR	0	-0.010	-0.002	3.173	0.252	0.959	0.010	-0.308	-0.408	-0.001
55	A	54	ILE	0	-0.014	-0.006	5.289	-0.257	-0.329	-0.001	-0.012	0.086	0.000
56	A	55	ASP	-1	-0.863	-0.938	8.058	-0.114	-0.114	0.000	0.000	0.000	0.000
57	A	56	LYS	1	0.918	0.948	9.848	0.102	0.102	0.000	0.000	0.000	0.000
58	A	57	ILE	0	0.018	0.020	12.090	-0.014	-0.014	0.000	0.000	0.000	0.000
59	A	58	VAL	0	-0.023	-0.001	14.484	0.020	0.020	0.000	0.000	0.000	0.000
60	A	59	LEU	0	-0.037	-0.021	16.768	-0.011	-0.011	0.000	0.000	0.000	0.000
61	A	60	GLY	0	0.004	0.003	20.051	0.009	0.009	0.000	0.000	0.000	0.000
62	A	61	PHE	0	-0.052	-0.021	22.567	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	62	PRO	0	-0.021	-0.010	25.721	0.003	0.003	0.000	0.000	0.000	0.000
64	A	63	LYS	1	0.935	0.973	29.126	0.023	0.023	0.000	0.000	0.000	0.000
65	A	64	ASN	0	0.016	0.010	31.129	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	65	MET	0	-0.027	-0.009	33.881	0.001	0.001	0.000	0.000	0.000	0.000
67	A	66	ASN	0	-0.022	-0.033	37.079	0.001	0.001	0.000	0.000	0.000	0.000
68	A	67	GLY	0	0.038	0.020	36.170	0.001	0.001	0.000	0.000	0.000	0.000
69	A	68	THR	0	-0.013	0.009	36.819	0.000	0.000	0.000	0.000	0.000	0.000
70	A	69	VAL	0	0.030	0.025	32.349	0.000	0.000	0.000	0.000	0.000	0.000
71	A	70	GLY	0	0.005	0.007	34.403	0.001	0.001	0.000	0.000	0.000	0.000
72	A	71	PRO	0	0.064	0.010	34.315	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	72	ARG	1	0.833	0.879	29.282	0.047	0.047	0.000	0.000	0.000	0.000
74	A	73	GLY	0	0.050	0.019	29.718	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	74	GLU	-1	-0.901	-0.936	29.851	-0.035	-0.035	0.000	0.000	0.000	0.000
76	A	75	ALA	0	0.015	0.001	29.858	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	76	SER	0	-0.010	-0.015	25.943	-0.006	-0.006	0.000	0.000	0.000	0.000
78	A	77	GLN	0	0.004	-0.003	25.573	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	78	THR	0	-0.050	-0.020	26.567	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	79	PHE	0	0.011	0.006	21.125	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	80	ALA	0	0.055	0.008	21.921	-0.008	-0.008	0.000	0.000	0.000	0.000
82	A	81	LYS	1	0.986	1.006	21.832	0.032	0.032	0.000	0.000	0.000	0.000
83	A	82	VAL	0	0.012	0.015	22.282	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	83	LEU	0	-0.010	0.007	17.876	-0.009	-0.009	0.000	0.000	0.000	0.000
85	A	84	GLU	-1	-0.942	-0.974	18.293	-0.076	-0.076	0.000	0.000	0.000	0.000
86	A	85	THR	0	-0.086	-0.049	19.135	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	86	THR	0	-0.084	-0.035	17.736	0.006	0.006	0.000	0.000	0.000	0.000
88	A	87	TYR	0	-0.058	-0.066	13.939	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	88	ASN	0	-0.056	-0.015	14.607	-0.017	-0.017	0.000	0.000	0.000	0.000
90	A	89	VAL	0	-0.013	0.012	11.900	-0.008	-0.008	0.000	0.000	0.000	0.000
91	A	90	PRO	0	-0.003	-0.013	14.294	0.019	0.019	0.000	0.000	0.000	0.000
92	A	91	VAL	0	0.014	0.008	16.102	-0.013	-0.013	0.000	0.000	0.000	0.000
93	A	92	VAL	0	-0.041	-0.017	17.264	0.012	0.012	0.000	0.000	0.000	0.000
94	A	93	LEU	0	-0.029	-0.017	19.512	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	94	TRP	0	-0.012	-0.007	20.208	0.006	0.006	0.000	0.000	0.000	0.000
96	A	95	ASP	-1	-0.833	-0.952	22.306	-0.031	-0.031	0.000	0.000	0.000	0.000
97	A	96	GLU	-1	-0.925	-0.940	22.586	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	97	ARG	1	0.941	0.959	21.889	0.041	0.041	0.000	0.000	0.000	0.000
99	A	98	LEU	0	0.065	0.037	23.045	0.001	0.001	0.000	0.000	0.000	0.000
100	A	99	THR	0	0.021	0.007	25.128	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	100	THR	0	0.041	0.012	28.044	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	101	MET	0	0.005	0.005	29.416	0.000	0.000	0.000	0.000	0.000	0.000
103	A	102	ALA	0	0.030	0.017	29.052	0.001	0.001	0.000	0.000	0.000	0.000
104	A	103	ALA	0	0.038	0.016	27.441	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	104	GLU	-1	-0.790	-0.913	29.267	-0.036	-0.036	0.000	0.000	0.000	0.000
106	A	105	LYS	1	0.921	0.961	32.637	0.023	0.023	0.000	0.000	0.000	0.000
107	A	106	MET	0	0.013	0.011	26.843	0.001	0.001	0.000	0.000	0.000	0.000
108	A	107	LEU	0	-0.021	-0.008	28.482	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	108	ILE	0	-0.066	-0.044	32.054	0.000	0.000	0.000	0.000	0.000	0.000
110	A	109	ALA	0	-0.004	0.014	34.276	0.000	0.000	0.000	0.000	0.000	0.000
111	A	110	ALA	0	-0.041	-0.011	31.879	0.000	0.000	0.000	0.000	0.000	0.000
112	A	111	ASP	-1	-0.879	-0.930	33.922	-0.034	-0.034	0.000	0.000	0.000	0.000
113	A	112	VAL	0	-0.096	-0.039	31.436	-0.002	-0.002	0.000	0.000	0.000	0.000
114	A	113	SER	0	0.006	-0.002	34.571	0.002	0.002	0.000	0.000	0.000	0.000
115	A	114	ARG	1	1.062	1.002	35.373	0.029	0.029	0.000	0.000	0.000	0.000
116	A	115	GLN	0	0.016	0.002	35.259	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	116	LYS	1	0.946	0.973	30.203	0.054	0.054	0.000	0.000	0.000	0.000
118	A	117	ARG	1	0.908	0.956	30.920	0.033	0.033	0.000	0.000	0.000	0.000
119	A	118	LYS	1	0.894	0.944	30.729	0.045	0.045	0.000	0.000	0.000	0.000
120	A	119	LYS	1	0.941	0.967	29.423	0.057	0.057	0.000	0.000	0.000	0.000
121	A	120	VAL	0	-0.028	-0.019	26.533	-0.005	-0.005	0.000	0.000	0.000	0.000
122	A	121	ILE	0	0.019	0.012	25.706	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	122	ASP	-1	-0.865	-0.912	26.392	-0.053	-0.053	0.000	0.000	0.000	0.000
124	A	123	LYS	1	0.911	0.947	22.858	0.082	0.082	0.000	0.000	0.000	0.000
125	A	124	MET	0	-0.007	-0.003	19.647	-0.010	-0.010	0.000	0.000	0.000	0.000
126	A	125	ALA	0	-0.012	0.021	21.220	0.003	0.003	0.000	0.000	0.000	0.000
127	A	126	ALA	0	0.052	0.019	17.891	0.006	0.006	0.000	0.000	0.000	0.000
128	A	127	VAL	0	0.021	0.017	16.085	0.006	0.006	0.000	0.000	0.000	0.000
129	A	128	MET	0	-0.048	-0.027	17.465	0.013	0.013	0.000	0.000	0.000	0.000
130	A	129	ILE	0	-0.027	-0.003	18.411	0.009	0.009	0.000	0.000	0.000	0.000
131	A	130	LEU	0	-0.005	0.000	11.542	0.002	0.002	0.000	0.000	0.000	0.000
132	A	131	GLN	0	-0.033	-0.040	15.247	0.006	0.006	0.000	0.000	0.000	0.000
133	A	132	GLY	0	0.034	0.023	16.461	0.008	0.008	0.000	0.000	0.000	0.000
134	A	133	TYR	0	0.015	0.011	13.425	0.006	0.006	0.000	0.000	0.000	0.000
135	A	134	LEU	0	-0.021	-0.027	10.888	0.014	0.014	0.000	0.000	0.000	0.000
136	A	135	ASP	-1	-0.843	-0.910	14.563	0.013	0.013	0.000	0.000	0.000	0.000
137	A	136	SER	0	-0.067	-0.022	17.524	0.001	0.001	0.000	0.000	0.000	0.000
138	A	137	LEU	0	-0.080	-0.048	12.081	-0.002	-0.002	0.000	0.000	0.000	0.000
139	A	138	ASN	0	-0.055	-0.030	12.880	0.019	0.019	0.000	0.000	0.000	0.000
140	A	139	GLU	-1	-1.015	-0.981	15.883	0.014	0.014	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:SER)