FMO DATABASE

FMODB ID: 5JN1Z

Calculation Name: 1VHF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VHF

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X0E6

Base Structure: X-ray

Registration Date: 2023-09-22

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	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	101
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-812892.425294
FMO2-HF: Nuclear repulsion	771025.395401
FMO2-HF: Total energy	-41867.029894
FMO2-MP2: Total energy	-41991.317263

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.
-39.475	-48.777	34.444	-15.191	-9.95	-0.118

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 : -0.063 / q_NPA : -0.057

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	ILE	0	0.012	0.009	3.887	0.732	2.974	-0.010	-1.134	-1.097	0.004
4	A	3	LEU	0	-0.014	-0.016	6.259	0.003	0.003	0.000	0.000	0.000	0.000
5	A	4	VAL	0	-0.005	-0.001	9.916	0.034	0.034	0.000	0.000	0.000	0.000
6	A	5	TYR	0	0.035	0.013	12.614	0.090	0.090	0.000	0.000	0.000	0.000
7	A	6	SER	0	-0.042	-0.045	15.784	-0.040	-0.040	0.000	0.000	0.000	0.000
8	A	7	THR	0	-0.050	-0.041	19.355	0.026	0.026	0.000	0.000	0.000	0.000
9	A	8	PHE	0	0.015	0.001	20.717	-0.023	-0.023	0.000	0.000	0.000	0.000
10	A	9	PRO	0	0.034	0.027	26.033	0.013	0.013	0.000	0.000	0.000	0.000
11	A	10	ASN	0	-0.045	-0.046	28.844	0.004	0.004	0.000	0.000	0.000	0.000
12	A	11	GLU	-1	-0.863	-0.925	27.463	-0.090	-0.090	0.000	0.000	0.000	0.000
13	A	12	GLU	-1	-0.840	-0.919	27.082	-0.114	-0.114	0.000	0.000	0.000	0.000
14	A	13	LYS	1	0.848	0.905	26.380	0.181	0.181	0.000	0.000	0.000	0.000
15	A	14	ALA	0	0.045	0.030	23.514	-0.024	-0.024	0.000	0.000	0.000	0.000
16	A	15	LEU	0	-0.025	-0.015	22.644	-0.027	-0.027	0.000	0.000	0.000	0.000
17	A	16	GLU	-1	-0.922	-0.935	23.436	-0.205	-0.205	0.000	0.000	0.000	0.000
18	A	17	ILE	0	0.010	0.005	20.023	-0.018	-0.018	0.000	0.000	0.000	0.000
19	A	18	GLY	0	0.038	0.019	18.822	-0.041	-0.041	0.000	0.000	0.000	0.000
20	A	19	ARG	1	0.834	0.901	18.917	0.137	0.137	0.000	0.000	0.000	0.000
21	A	20	LYS	1	0.869	0.929	20.686	0.206	0.206	0.000	0.000	0.000	0.000
22	A	21	LEU	0	0.014	0.009	15.774	-0.025	-0.025	0.000	0.000	0.000	0.000
23	A	22	LEU	0	-0.009	0.008	15.686	-0.046	-0.046	0.000	0.000	0.000	0.000
24	A	23	GLU	-1	-0.877	-0.934	17.643	-0.193	-0.193	0.000	0.000	0.000	0.000
25	A	24	LYS	1	0.769	0.865	17.835	0.390	0.390	0.000	0.000	0.000	0.000
26	A	25	ARG	1	0.900	0.960	14.301	0.222	0.222	0.000	0.000	0.000	0.000
27	A	26	LEU	0	0.019	0.010	12.549	-0.079	-0.079	0.000	0.000	0.000	0.000
28	A	27	ILE	0	-0.036	0.000	11.097	-0.231	-0.231	0.000	0.000	0.000	0.000
29	A	28	ALA	0	0.010	0.018	10.472	0.099	0.099	0.000	0.000	0.000	0.000
30	A	29	CYM	-1	-0.817	-0.807	12.309	-0.066	-0.066	0.000	0.000	0.000	0.000
31	A	30	PHE	0	0.000	0.001	13.765	-0.092	-0.092	0.000	0.000	0.000	0.000
32	A	31	ASN	0	-0.026	-0.005	16.100	0.042	0.042	0.000	0.000	0.000	0.000
33	A	32	ALA	0	0.022	0.003	18.340	-0.031	-0.031	0.000	0.000	0.000	0.000
34	A	33	PHE	0	-0.023	-0.012	19.213	0.024	0.024	0.000	0.000	0.000	0.000
35	A	34	GLU	-1	-0.812	-0.875	24.322	-0.062	-0.062	0.000	0.000	0.000	0.000
36	A	35	ILE	0	-0.047	-0.028	23.784	0.012	0.012	0.000	0.000	0.000	0.000
37	A	36	ARG	1	0.789	0.867	27.123	0.047	0.047	0.000	0.000	0.000	0.000
38	A	37	SER	0	-0.028	-0.033	27.450	0.006	0.006	0.000	0.000	0.000	0.000
39	A	38	GLY	0	0.038	0.003	29.357	0.006	0.006	0.000	0.000	0.000	0.000
40	A	39	TYR	0	-0.073	-0.049	29.726	-0.005	-0.005	0.000	0.000	0.000	0.000
41	A	40	TRP	0	0.002	0.004	31.692	0.007	0.007	0.000	0.000	0.000	0.000
42	A	41	TRP	0	0.038	0.004	33.344	-0.012	-0.012	0.000	0.000	0.000	0.000
43	A	42	LYS	1	0.921	0.950	35.770	0.104	0.104	0.000	0.000	0.000	0.000
44	A	43	GLY	0	0.002	0.011	38.432	0.002	0.002	0.000	0.000	0.000	0.000
45	A	44	GLU	-1	-0.954	-0.959	39.240	-0.060	-0.060	0.000	0.000	0.000	0.000
46	A	45	ILE	0	-0.024	-0.015	34.886	-0.006	-0.006	0.000	0.000	0.000	0.000
47	A	46	VAL	0	0.002	0.008	33.916	0.006	0.006	0.000	0.000	0.000	0.000
48	A	47	GLN	0	-0.070	-0.050	33.464	0.006	0.006	0.000	0.000	0.000	0.000
49	A	48	ASP	-1	-0.826	-0.883	31.364	-0.100	-0.100	0.000	0.000	0.000	0.000
50	A	49	LYN	0	-0.046	-0.023	31.605	0.010	0.010	0.000	0.000	0.000	0.000
51	A	50	GLU	-1	-0.742	-0.799	26.713	-0.155	-0.155	0.000	0.000	0.000	0.000
52	A	51	TRP	0	0.003	-0.003	24.944	0.012	0.012	0.000	0.000	0.000	0.000
53	A	52	ALA	0	0.010	0.014	20.972	-0.024	-0.024	0.000	0.000	0.000	0.000
54	A	53	ALA	0	-0.004	-0.020	19.035	0.014	0.014	0.000	0.000	0.000	0.000
55	A	54	ILE	0	-0.032	-0.007	13.799	-0.015	-0.015	0.000	0.000	0.000	0.000
56	A	55	PHE	0	0.006	-0.013	13.806	0.055	0.055	0.000	0.000	0.000	0.000
57	A	56	LYS	1	0.798	0.849	9.927	0.007	0.007	0.000	0.000	0.000	0.000
58	A	57	THR	0	0.009	-0.033	7.734	0.125	0.125	0.000	0.000	0.000	0.000
59	A	58	THR	0	0.001	-0.017	3.457	-0.102	0.142	0.003	-0.107	-0.140	0.000
60	A	59	GLU	-1	-0.816	-0.883	1.621	-38.581	-50.984	32.010	-12.631	-6.976	-0.118
61	A	60	GLU	-1	-0.867	-0.920	3.727	-3.198	-2.823	0.002	-0.137	-0.241	-0.001
62	A	61	LYS	1	0.797	0.895	6.881	1.712	1.712	0.000	0.000	0.000	0.000
63	A	62	GLU	-1	-0.845	-0.880	8.261	-1.344	-1.344	0.000	0.000	0.000	0.000
64	A	63	LYS	1	0.875	0.919	10.045	1.072	1.072	0.000	0.000	0.000	0.000
65	A	64	GLU	-1	-0.827	-0.912	12.360	-0.747	-0.747	0.000	0.000	0.000	0.000
66	A	65	LEU	0	0.013	0.011	11.234	0.166	0.166	0.000	0.000	0.000	0.000
67	A	66	TYR	0	0.015	-0.029	12.214	0.217	0.217	0.000	0.000	0.000	0.000
68	A	67	GLU	-1	-0.862	-0.905	15.918	-0.446	-0.446	0.000	0.000	0.000	0.000
69	A	68	GLU	-1	-0.817	-0.895	17.454	-0.326	-0.326	0.000	0.000	0.000	0.000
70	A	69	LEU	0	0.003	0.003	16.799	0.065	0.065	0.000	0.000	0.000	0.000
71	A	70	ARG	1	0.863	0.920	19.243	0.378	0.378	0.000	0.000	0.000	0.000
72	A	71	LYS	1	0.830	0.901	20.952	0.479	0.479	0.000	0.000	0.000	0.000
73	A	72	LEU	0	-0.029	-0.005	21.168	0.036	0.036	0.000	0.000	0.000	0.000
74	A	73	HIS	0	-0.009	0.010	21.900	0.038	0.038	0.000	0.000	0.000	0.000
75	A	74	PRO	0	-0.042	-0.014	25.006	0.014	0.014	0.000	0.000	0.000	0.000
76	A	75	TYR	0	-0.065	-0.060	25.491	0.016	0.016	0.000	0.000	0.000	0.000
77	A	76	GLU	-1	-0.885	-0.921	26.837	-0.218	-0.218	0.000	0.000	0.000	0.000
78	A	77	THR	0	-0.015	-0.037	25.205	-0.031	-0.031	0.000	0.000	0.000	0.000
79	A	78	PRO	0	-0.024	0.005	22.056	0.015	0.015	0.000	0.000	0.000	0.000
80	A	79	ALA	0	0.020	0.012	21.299	-0.019	-0.019	0.000	0.000	0.000	0.000
81	A	80	ILE	0	-0.013	0.000	15.984	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	81	PHE	0	-0.027	-0.002	14.425	0.010	0.010	0.000	0.000	0.000	0.000
83	A	82	THR	0	0.008	-0.018	8.483	0.107	0.107	0.000	0.000	0.000	0.000
84	A	83	LEU	0	-0.054	-0.010	9.980	0.099	0.099	0.000	0.000	0.000	0.000
85	A	84	LYN	0	0.067	0.042	5.025	-0.369	-0.317	-0.001	-0.004	-0.046	0.000
86	A	85	VAL	0	-0.023	-0.023	4.690	-0.624	-0.538	-0.001	-0.009	-0.076	0.000
87	A	86	GLU	-1	-0.898	-0.948	4.740	2.287	2.371	-0.001	-0.002	-0.080	0.000
88	A	87	ASN	0	-0.086	-0.056	6.417	-0.141	-0.141	0.000	0.000	0.000	0.000
89	A	88	VAL	0	0.005	0.006	4.264	-0.289	-0.215	-0.001	-0.014	-0.060	0.000
90	A	89	LEU	0	-0.016	0.011	7.106	0.103	0.103	0.000	0.000	0.000	0.000
91	A	90	THR	0	0.037	-0.006	8.370	0.063	0.063	0.000	0.000	0.000	0.000
92	A	91	GLU	-1	-0.868	-0.927	8.973	0.726	0.726	0.000	0.000	0.000	0.000
93	A	92	TYR	0	-0.013	-0.031	9.918	-0.070	-0.070	0.000	0.000	0.000	0.000
94	A	93	MET	0	0.018	0.010	3.029	0.476	0.420	2.443	-1.153	-1.234	-0.003
95	A	94	ASN	0	0.015	0.002	6.235	0.112	0.112	0.000	0.000	0.000	0.000
96	A	95	TRP	0	0.018	0.000	8.570	-0.163	-0.163	0.000	0.000	0.000	0.000
97	A	96	LEU	0	-0.009	-0.006	6.636	-0.103	-0.103	0.000	0.000	0.000	0.000
98	A	97	ARG	1	0.866	0.930	5.253	-2.033	-2.033	0.000	0.000	0.000	0.000
99	A	98	GLU	-1	-0.894	-0.951	7.782	0.277	0.277	0.000	0.000	0.000	0.000
100	A	99	SER	0	-0.064	-0.025	11.153	-0.011	-0.011	0.000	0.000	0.000	0.000
101	A	100	VAL	0	-0.096	-0.035	8.000	0.038	0.038	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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