FMO DATABASE

FMODB ID: 17Y4Z

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	OptHSide
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	-1205015.858692
FMO2-HF: Nuclear repulsion	1150591.461306
FMO2-HF: Total energy	-54424.397385
FMO2-MP2: Total energy	-54581.585286

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.
-20.135	-24.753	25.034	-12.874	-7.543	-0.052

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 : -0.029 / q_NPA : -0.042

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	0.783	0.880	2.619	6.586	10.652	0.241	-2.138	-2.170	0.009
4	A	3	ILE	0	0.038	0.021	5.473	-0.303	-0.251	-0.001	-0.006	-0.044	0.000
5	A	4	LEU	0	0.007	-0.001	9.070	-0.122	-0.122	0.000	0.000	0.000	0.000
6	A	5	GLY	0	0.026	0.019	11.620	0.117	0.117	0.000	0.000	0.000	0.000
7	A	6	LEU	0	-0.045	-0.043	14.750	-0.046	-0.046	0.000	0.000	0.000	0.000
8	A	7	ASP	-1	-0.905	-0.965	18.050	-0.143	-0.143	0.000	0.000	0.000	0.000
9	A	8	LEU	0	0.011	0.009	21.641	-0.012	-0.012	0.000	0.000	0.000	0.000
10	A	9	GLY	0	0.028	0.015	24.402	0.018	0.018	0.000	0.000	0.000	0.000
11	A	10	THR	0	-0.058	-0.040	27.531	-0.004	-0.004	0.000	0.000	0.000	0.000
12	A	11	LYS	1	0.910	0.928	29.760	0.126	0.126	0.000	0.000	0.000	0.000
13	A	12	THR	0	-0.034	-0.017	24.851	0.001	0.001	0.000	0.000	0.000	0.000
14	A	13	LEU	0	0.028	0.030	20.054	0.014	0.014	0.000	0.000	0.000	0.000
15	A	14	GLY	0	-0.046	-0.012	20.332	-0.023	-0.023	0.000	0.000	0.000	0.000
16	A	15	VAL	0	0.027	0.004	14.183	0.009	0.009	0.000	0.000	0.000	0.000
17	A	16	ALA	0	-0.003	-0.002	13.882	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	17	LEU	0	0.054	0.029	7.943	0.014	0.014	0.000	0.000	0.000	0.000
19	A	18	SER	0	0.024	0.034	6.230	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	19	ASP	-1	-0.750	-0.838	6.598	-0.580	-0.580	0.000	0.000	0.000	0.000
21	A	20	GLU	-1	-0.808	-0.883	1.597	-26.770	-36.442	24.788	-10.414	-4.703	-0.060
22	A	21	MET	0	-0.069	-0.034	3.919	1.669	1.826	-0.001	-0.008	-0.148	0.000
23	A	22	GLY	0	0.013	0.031	6.830	0.184	0.184	0.000	0.000	0.000	0.000
24	A	23	TRP	0	-0.063	-0.024	8.168	-0.081	-0.081	0.000	0.000	0.000	0.000
25	A	24	THR	0	-0.056	-0.056	10.483	-0.052	-0.052	0.000	0.000	0.000	0.000
26	A	25	ALA	0	0.014	0.015	10.316	-0.060	-0.060	0.000	0.000	0.000	0.000
27	A	26	GLN	0	-0.016	-0.022	8.509	-0.206	-0.206	0.000	0.000	0.000	0.000
28	A	27	GLY	0	-0.033	-0.029	12.555	-0.017	-0.017	0.000	0.000	0.000	0.000
29	A	28	ILE	0	-0.024	-0.001	10.691	-0.033	-0.033	0.000	0.000	0.000	0.000
30	A	29	GLU	-1	-0.788	-0.876	14.769	-0.373	-0.373	0.000	0.000	0.000	0.000
31	A	30	THR	0	-0.074	-0.041	18.299	0.010	0.010	0.000	0.000	0.000	0.000
32	A	31	ILE	0	0.040	0.039	18.299	0.017	0.017	0.000	0.000	0.000	0.000
33	A	32	LYS	1	0.885	0.941	22.316	0.210	0.210	0.000	0.000	0.000	0.000
34	A	33	ILE	0	0.017	0.035	24.345	-0.009	-0.009	0.000	0.000	0.000	0.000
35	A	34	ASN	0	-0.041	-0.038	27.361	0.021	0.021	0.000	0.000	0.000	0.000
36	A	35	GLU	-1	-0.705	-0.815	30.291	-0.124	-0.124	0.000	0.000	0.000	0.000
37	A	36	ALA	0	-0.054	-0.005	32.004	0.003	0.003	0.000	0.000	0.000	0.000
38	A	37	GLU	-1	-0.898	-0.948	32.670	-0.102	-0.102	0.000	0.000	0.000	0.000
39	A	38	GLY	0	-0.064	-0.023	31.427	0.000	0.000	0.000	0.000	0.000	0.000
40	A	39	ASP	-1	-0.929	-0.980	26.538	-0.207	-0.207	0.000	0.000	0.000	0.000
41	A	40	TYR	0	0.044	0.007	24.965	0.005	0.005	0.000	0.000	0.000	0.000
42	A	41	GLY	0	0.039	0.006	22.809	-0.014	-0.014	0.000	0.000	0.000	0.000
43	A	42	LEU	0	0.027	0.008	20.451	-0.031	-0.031	0.000	0.000	0.000	0.000
44	A	43	SER	0	-0.002	-0.001	19.397	-0.033	-0.033	0.000	0.000	0.000	0.000
45	A	44	ARG	1	0.798	0.871	18.264	0.389	0.389	0.000	0.000	0.000	0.000
46	A	45	LEU	0	0.013	0.005	15.489	-0.048	-0.048	0.000	0.000	0.000	0.000
47	A	46	SER	0	0.034	0.009	14.749	-0.079	-0.079	0.000	0.000	0.000	0.000
48	A	47	GLU	-1	-0.941	-0.946	14.039	-0.434	-0.434	0.000	0.000	0.000	0.000
49	A	48	LEU	0	-0.050	-0.043	13.459	-0.075	-0.075	0.000	0.000	0.000	0.000
50	A	49	ILE	0	-0.001	-0.005	10.036	-0.150	-0.150	0.000	0.000	0.000	0.000
51	A	50	LYS	1	0.903	0.974	9.175	0.264	0.264	0.000	0.000	0.000	0.000
52	A	51	ASP	-1	-0.939	-0.972	8.107	-0.814	-0.814	0.000	0.000	0.000	0.000
53	A	52	TYR	0	-0.053	-0.022	4.696	-0.481	-0.312	-0.001	-0.015	-0.153	0.000
54	A	53	THR	0	-0.012	-0.004	3.092	0.896	1.590	0.009	-0.279	-0.425	-0.001
55	A	54	ILE	0	-0.014	-0.009	5.362	-0.171	-0.255	-0.001	-0.014	0.100	0.000
56	A	55	ASP	-1	-0.795	-0.896	8.202	0.209	0.209	0.000	0.000	0.000	0.000
57	A	56	LYS	1	0.841	0.923	9.848	0.013	0.013	0.000	0.000	0.000	0.000
58	A	57	ILE	0	0.018	0.013	11.705	-0.089	-0.089	0.000	0.000	0.000	0.000
59	A	58	VAL	0	-0.010	0.011	14.078	0.058	0.058	0.000	0.000	0.000	0.000
60	A	59	LEU	0	-0.042	-0.024	16.393	-0.041	-0.041	0.000	0.000	0.000	0.000
61	A	60	GLY	0	0.011	0.008	19.727	0.025	0.025	0.000	0.000	0.000	0.000
62	A	61	PHE	0	-0.034	-0.020	22.264	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	62	PRO	0	-0.041	-0.011	25.378	0.007	0.007	0.000	0.000	0.000	0.000
64	A	63	LYS	1	0.828	0.881	28.693	0.064	0.064	0.000	0.000	0.000	0.000
65	A	64	ASN	0	0.033	0.018	30.756	-0.007	-0.007	0.000	0.000	0.000	0.000
66	A	65	MET	0	-0.025	-0.010	33.485	0.001	0.001	0.000	0.000	0.000	0.000
67	A	66	ASN	0	-0.024	-0.035	36.621	0.003	0.003	0.000	0.000	0.000	0.000
68	A	67	GLY	0	0.042	0.022	35.838	0.002	0.002	0.000	0.000	0.000	0.000
69	A	68	THR	0	-0.019	0.005	36.463	0.000	0.000	0.000	0.000	0.000	0.000
70	A	69	VAL	0	0.016	0.021	31.944	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	70	GLY	0	0.024	0.016	34.058	0.002	0.002	0.000	0.000	0.000	0.000
72	A	71	PRO	0	0.055	0.005	33.990	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	72	ARG	1	0.831	0.876	29.064	0.118	0.118	0.000	0.000	0.000	0.000
74	A	73	GLY	0	0.064	0.039	29.395	-0.009	-0.009	0.000	0.000	0.000	0.000
75	A	74	GLU	-1	-0.818	-0.905	29.513	-0.084	-0.084	0.000	0.000	0.000	0.000
76	A	75	ALA	0	0.000	-0.004	30.081	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	76	SER	0	-0.009	-0.026	25.613	-0.013	-0.013	0.000	0.000	0.000	0.000
78	A	77	GLN	0	-0.032	-0.021	25.408	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	78	THR	0	-0.032	-0.009	26.628	0.000	0.000	0.000	0.000	0.000	0.000
80	A	79	PHE	0	0.022	0.017	21.116	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	80	ALA	0	0.044	0.009	22.006	-0.017	-0.017	0.000	0.000	0.000	0.000
82	A	81	LYS	1	0.902	0.963	21.982	0.083	0.083	0.000	0.000	0.000	0.000
83	A	82	VAL	0	0.020	0.027	22.366	-0.005	-0.005	0.000	0.000	0.000	0.000
84	A	83	LEU	0	-0.003	0.013	17.790	-0.017	-0.017	0.000	0.000	0.000	0.000
85	A	84	GLU	-1	-0.912	-0.959	18.414	-0.137	-0.137	0.000	0.000	0.000	0.000
86	A	85	THR	0	-0.083	-0.061	19.215	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	86	THR	0	-0.094	-0.044	18.013	0.007	0.007	0.000	0.000	0.000	0.000
88	A	87	TYR	0	-0.055	-0.058	14.039	-0.020	-0.020	0.000	0.000	0.000	0.000
89	A	88	ASN	0	-0.056	-0.012	14.662	-0.011	-0.011	0.000	0.000	0.000	0.000
90	A	89	VAL	0	-0.023	0.001	11.956	0.005	0.005	0.000	0.000	0.000	0.000
91	A	90	PRO	0	0.006	-0.003	14.384	0.011	0.011	0.000	0.000	0.000	0.000
92	A	91	VAL	0	-0.004	0.003	15.996	-0.029	-0.029	0.000	0.000	0.000	0.000
93	A	92	VAL	0	-0.031	-0.014	16.915	0.027	0.027	0.000	0.000	0.000	0.000
94	A	93	LEU	0	-0.029	-0.013	19.219	-0.021	-0.021	0.000	0.000	0.000	0.000
95	A	94	TRP	0	-0.004	-0.004	19.846	0.015	0.015	0.000	0.000	0.000	0.000
96	A	95	ASP	-1	-0.767	-0.877	21.895	-0.080	-0.080	0.000	0.000	0.000	0.000
97	A	96	GLU	-1	-0.878	-0.908	22.179	-0.009	-0.009	0.000	0.000	0.000	0.000
98	A	97	ARG	1	0.939	0.961	21.535	0.113	0.113	0.000	0.000	0.000	0.000
99	A	98	LEU	0	0.065	0.043	22.731	0.009	0.009	0.000	0.000	0.000	0.000
100	A	99	THR	0	0.031	0.001	24.806	-0.012	-0.012	0.000	0.000	0.000	0.000
101	A	100	THR	0	0.045	0.010	27.728	-0.005	-0.005	0.000	0.000	0.000	0.000
102	A	101	MET	0	0.000	0.004	29.069	0.001	0.001	0.000	0.000	0.000	0.000
103	A	102	ALA	0	0.027	0.014	28.729	0.003	0.003	0.000	0.000	0.000	0.000
104	A	103	ALA	0	0.042	0.020	27.033	0.001	0.001	0.000	0.000	0.000	0.000
105	A	104	GLU	-1	-0.751	-0.868	28.869	-0.083	-0.083	0.000	0.000	0.000	0.000
106	A	105	LYS	1	0.916	0.961	32.229	0.051	0.051	0.000	0.000	0.000	0.000
107	A	106	MET	0	0.022	0.014	26.516	0.002	0.002	0.000	0.000	0.000	0.000
108	A	107	LEU	0	-0.013	-0.012	28.057	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	108	ILE	0	-0.066	-0.038	31.659	0.001	0.001	0.000	0.000	0.000	0.000
110	A	109	ALA	0	-0.005	0.015	33.845	0.002	0.002	0.000	0.000	0.000	0.000
111	A	110	ALA	0	-0.039	-0.014	31.586	0.001	0.001	0.000	0.000	0.000	0.000
112	A	111	ASP	-1	-0.897	-0.937	33.629	-0.063	-0.063	0.000	0.000	0.000	0.000
113	A	112	VAL	0	-0.090	-0.041	30.859	-0.004	-0.004	0.000	0.000	0.000	0.000
114	A	113	SER	0	0.041	0.010	34.248	0.002	0.002	0.000	0.000	0.000	0.000
115	A	114	ARG	1	1.037	1.004	34.995	0.066	0.066	0.000	0.000	0.000	0.000
116	A	115	GLN	0	0.016	0.000	34.910	-0.006	-0.006	0.000	0.000	0.000	0.000
117	A	116	LYS	1	0.959	0.980	29.975	0.113	0.113	0.000	0.000	0.000	0.000
118	A	117	ARG	1	0.850	0.903	30.520	0.069	0.069	0.000	0.000	0.000	0.000
119	A	118	LYS	1	0.854	0.914	30.291	0.112	0.112	0.000	0.000	0.000	0.000
120	A	119	LYS	1	0.952	0.965	29.132	0.132	0.132	0.000	0.000	0.000	0.000
121	A	120	VAL	0	-0.030	-0.012	25.975	-0.014	-0.014	0.000	0.000	0.000	0.000
122	A	121	ILE	0	0.026	0.013	25.272	-0.011	-0.011	0.000	0.000	0.000	0.000
123	A	122	ASP	-1	-0.849	-0.892	26.003	-0.134	-0.134	0.000	0.000	0.000	0.000
124	A	123	LYS	1	0.891	0.943	22.175	0.210	0.210	0.000	0.000	0.000	0.000
125	A	124	MET	0	0.007	-0.002	19.162	-0.029	-0.029	0.000	0.000	0.000	0.000
126	A	125	ALA	0	-0.006	0.025	20.831	-0.001	-0.001	0.000	0.000	0.000	0.000
127	A	126	ALA	0	0.058	0.025	17.571	0.013	0.013	0.000	0.000	0.000	0.000
128	A	127	VAL	0	0.012	0.008	15.844	0.002	0.002	0.000	0.000	0.000	0.000
129	A	128	MET	0	-0.043	-0.024	17.108	0.027	0.027	0.000	0.000	0.000	0.000
130	A	129	ILE	0	-0.020	-0.006	18.096	0.026	0.026	0.000	0.000	0.000	0.000
131	A	130	LEU	0	-0.010	0.003	11.217	0.020	0.020	0.000	0.000	0.000	0.000
132	A	131	GLN	0	-0.026	-0.037	14.665	-0.021	-0.021	0.000	0.000	0.000	0.000
133	A	132	GLY	0	0.029	0.021	16.152	0.030	0.030	0.000	0.000	0.000	0.000
134	A	133	TYR	0	-0.001	-0.009	12.907	0.029	0.029	0.000	0.000	0.000	0.000
135	A	134	LEU	0	-0.018	-0.025	10.411	0.028	0.028	0.000	0.000	0.000	0.000
136	A	135	ASP	-1	-0.851	-0.915	14.166	0.010	0.010	0.000	0.000	0.000	0.000
137	A	136	SER	0	-0.065	-0.036	17.152	0.020	0.020	0.000	0.000	0.000	0.000
138	A	137	LEU	0	-0.097	-0.052	12.006	0.014	0.014	0.000	0.000	0.000	0.000
139	A	138	ASN	0	-0.085	-0.063	12.272	0.075	0.075	0.000	0.000	0.000	0.000
140	A	139	GLU	-1	-1.010	-0.974	15.816	0.082	0.082	0.000	0.000	0.000	0.000

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