FMO DATABASE

FMODB ID: KG243

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

Total energy (hartree)

FMO2-HF: Electronic energy	-811670.538391
FMO2-HF: Nuclear repulsion	769804.399565
FMO2-HF: Total energy	-41866.138826
FMO2-MP2: Total energy	-41990.494918

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.
-25.032	-13.409	5.646	-8.339	-8.928	-0.051

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 : 0.004 / q_NPA : 0.002

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	2	ILE	0	0.042	0.023	3.809	-0.281	2.815	-0.014	-1.675	-1.407	0.007
4	A	3	LEU	0	-0.012	-0.012	6.047	-0.159	-0.159	0.000	0.000	0.000	0.000
5	A	4	VAL	0	0.004	0.014	9.691	0.019	0.019	0.000	0.000	0.000	0.000
6	A	5	TYR	0	0.001	-0.003	12.301	0.056	0.056	0.000	0.000	0.000	0.000
7	A	6	SER	0	-0.024	-0.027	15.659	-0.028	-0.028	0.000	0.000	0.000	0.000
8	A	7	THR	0	-0.041	-0.030	19.100	0.019	0.019	0.000	0.000	0.000	0.000
9	A	8	PHE	0	-0.022	-0.015	20.024	-0.019	-0.019	0.000	0.000	0.000	0.000
10	A	9	PRO	0	0.056	0.030	25.549	0.011	0.011	0.000	0.000	0.000	0.000
11	A	10	ASN	0	-0.011	-0.012	28.337	0.006	0.006	0.000	0.000	0.000	0.000
12	A	11	GLU	-1	-0.845	-0.921	27.338	-0.061	-0.061	0.000	0.000	0.000	0.000
13	A	12	GLU	-1	-0.895	-0.953	26.907	-0.075	-0.075	0.000	0.000	0.000	0.000
14	A	13	LYS	1	0.852	0.922	25.657	0.129	0.129	0.000	0.000	0.000	0.000
15	A	14	ALA	0	0.040	0.027	22.959	-0.018	-0.018	0.000	0.000	0.000	0.000
16	A	15	LEU	0	-0.017	-0.012	22.283	-0.020	-0.020	0.000	0.000	0.000	0.000
17	A	16	GLU	-1	-0.929	-0.950	23.289	-0.145	-0.145	0.000	0.000	0.000	0.000
18	A	17	ILE	0	0.006	-0.008	19.831	-0.013	-0.013	0.000	0.000	0.000	0.000
19	A	18	GLY	0	0.049	0.027	18.624	-0.031	-0.031	0.000	0.000	0.000	0.000
20	A	19	ARG	1	0.924	0.966	18.869	0.089	0.089	0.000	0.000	0.000	0.000
21	A	20	LYS	1	0.935	0.967	20.660	0.154	0.154	0.000	0.000	0.000	0.000
22	A	21	LEU	0	0.000	-0.003	15.656	-0.018	-0.018	0.000	0.000	0.000	0.000
23	A	22	LEU	0	-0.021	-0.004	15.550	-0.032	-0.032	0.000	0.000	0.000	0.000
24	A	23	GLU	-1	-0.983	-0.994	17.331	-0.151	-0.151	0.000	0.000	0.000	0.000
25	A	24	LYS	1	0.848	0.925	17.445	0.283	0.283	0.000	0.000	0.000	0.000
26	A	25	ARG	1	0.928	0.972	14.394	0.141	0.141	0.000	0.000	0.000	0.000
27	A	26	LEU	0	0.016	0.007	12.338	-0.059	-0.059	0.000	0.000	0.000	0.000
28	A	27	ILE	0	-0.045	-0.003	10.897	-0.192	-0.192	0.000	0.000	0.000	0.000
29	A	28	ALA	0	0.011	0.004	10.259	0.078	0.078	0.000	0.000	0.000	0.000
30	A	29	CYM	-1	-0.816	-0.830	12.131	-0.027	-0.027	0.000	0.000	0.000	0.000
31	A	30	PHE	0	0.014	0.010	13.887	-0.068	-0.068	0.000	0.000	0.000	0.000
32	A	31	ASN	0	-0.019	-0.004	16.281	0.025	0.025	0.000	0.000	0.000	0.000
33	A	32	ALA	0	0.011	0.002	18.226	-0.016	-0.016	0.000	0.000	0.000	0.000
34	A	33	PHE	0	-0.045	-0.026	19.038	0.019	0.019	0.000	0.000	0.000	0.000
35	A	34	GLU	-1	-0.915	-0.942	23.848	-0.045	-0.045	0.000	0.000	0.000	0.000
36	A	35	ILE	0	-0.061	-0.031	23.921	0.011	0.011	0.000	0.000	0.000	0.000
37	A	36	ARG	1	0.921	0.946	27.241	0.027	0.027	0.000	0.000	0.000	0.000
38	A	37	SER	0	-0.041	-0.044	27.497	0.004	0.004	0.000	0.000	0.000	0.000
39	A	38	GLY	0	0.024	0.000	29.126	0.004	0.004	0.000	0.000	0.000	0.000
40	A	39	TYR	0	-0.101	-0.059	29.211	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	40	TRP	0	-0.012	0.001	31.225	0.005	0.005	0.000	0.000	0.000	0.000
42	A	41	TRP	0	0.034	0.000	32.825	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	42	LYS	1	0.932	0.966	35.381	0.078	0.078	0.000	0.000	0.000	0.000
44	A	43	GLY	0	0.001	0.003	37.742	0.004	0.004	0.000	0.000	0.000	0.000
45	A	44	GLU	-1	-0.927	-0.949	38.505	-0.044	-0.044	0.000	0.000	0.000	0.000
46	A	45	ILE	0	-0.029	-0.014	34.822	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	46	VAL	0	-0.019	-0.008	33.674	0.004	0.004	0.000	0.000	0.000	0.000
48	A	47	GLN	0	-0.028	-0.027	33.794	0.002	0.002	0.000	0.000	0.000	0.000
49	A	48	ASP	-1	-0.847	-0.903	31.134	-0.076	-0.076	0.000	0.000	0.000	0.000
50	A	49	LYN	0	-0.025	0.003	31.181	0.008	0.008	0.000	0.000	0.000	0.000
51	A	50	GLU	-1	-0.742	-0.814	26.724	-0.110	-0.110	0.000	0.000	0.000	0.000
52	A	51	TRP	0	0.035	0.022	24.807	0.009	0.009	0.000	0.000	0.000	0.000
53	A	52	ALA	0	0.005	0.002	20.700	-0.019	-0.019	0.000	0.000	0.000	0.000
54	A	53	ALA	0	-0.005	-0.015	18.978	0.014	0.014	0.000	0.000	0.000	0.000
55	A	54	ILE	0	-0.024	0.000	13.298	-0.013	-0.013	0.000	0.000	0.000	0.000
56	A	55	PHE	0	-0.005	-0.020	13.327	0.041	0.041	0.000	0.000	0.000	0.000
57	A	56	LYS	1	0.802	0.834	9.577	0.003	0.003	0.000	0.000	0.000	0.000
58	A	57	THR	0	0.016	-0.029	7.341	0.065	0.065	0.000	0.000	0.000	0.000
59	A	58	THR	0	-0.017	-0.011	3.283	-0.041	0.255	0.007	-0.129	-0.174	0.000
60	A	59	GLU	-1	-0.858	-0.932	2.253	-20.797	-14.463	4.861	-5.444	-5.750	-0.052
61	A	60	GLU	-1	-0.894	-0.948	3.069	-3.391	-2.281	0.069	-0.522	-0.657	-0.005
62	A	61	LYS	1	0.925	0.983	6.197	1.485	1.485	0.000	0.000	0.000	0.000
63	A	62	GLU	-1	-0.849	-0.895	7.564	-1.137	-1.137	0.000	0.000	0.000	0.000
64	A	63	LYS	1	0.853	0.919	9.264	0.883	0.883	0.000	0.000	0.000	0.000
65	A	64	GLU	-1	-0.892	-0.967	11.953	-0.613	-0.613	0.000	0.000	0.000	0.000
66	A	65	LEU	0	-0.003	0.011	10.958	0.140	0.140	0.000	0.000	0.000	0.000
67	A	66	TYR	0	-0.006	-0.039	12.098	0.178	0.178	0.000	0.000	0.000	0.000
68	A	67	GLU	-1	-0.935	-0.949	15.188	-0.418	-0.418	0.000	0.000	0.000	0.000
69	A	68	GLU	-1	-0.873	-0.960	16.820	-0.240	-0.240	0.000	0.000	0.000	0.000
70	A	69	LEU	0	-0.004	0.001	16.417	0.055	0.055	0.000	0.000	0.000	0.000
71	A	70	ARG	1	0.879	0.928	18.681	0.309	0.309	0.000	0.000	0.000	0.000
72	A	71	LYS	1	0.916	0.952	20.988	0.343	0.343	0.000	0.000	0.000	0.000
73	A	72	LEU	0	-0.055	-0.012	20.238	0.031	0.031	0.000	0.000	0.000	0.000
74	A	73	HIS	0	-0.019	0.015	21.285	0.028	0.028	0.000	0.000	0.000	0.000
75	A	74	PRO	0	-0.033	-0.014	24.315	0.009	0.009	0.000	0.000	0.000	0.000
76	A	75	TYR	0	-0.055	-0.066	25.545	0.011	0.011	0.000	0.000	0.000	0.000
77	A	76	GLU	-1	-0.914	-0.952	26.433	-0.158	-0.158	0.000	0.000	0.000	0.000
78	A	77	THR	0	-0.042	-0.034	25.136	-0.021	-0.021	0.000	0.000	0.000	0.000
79	A	78	PRO	0	-0.042	-0.003	21.917	0.011	0.011	0.000	0.000	0.000	0.000
80	A	79	ALA	0	0.045	0.035	20.443	-0.015	-0.015	0.000	0.000	0.000	0.000
81	A	80	ILE	0	-0.009	-0.017	15.565	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	81	PHE	0	-0.020	-0.005	14.336	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	82	THR	0	0.000	-0.014	8.302	0.064	0.064	0.000	0.000	0.000	0.000
84	A	83	LEU	0	-0.055	-0.009	10.045	0.040	0.040	0.000	0.000	0.000	0.000
85	A	84	LYN	0	0.054	0.031	5.190	-0.172	-0.119	-0.001	-0.004	-0.047	0.000
86	A	85	VAL	0	-0.051	-0.028	4.790	-0.651	-0.567	-0.001	-0.007	-0.075	0.000
87	A	86	GLU	-1	-0.881	-0.951	5.218	1.673	1.673	0.000	0.000	0.000	0.000
88	A	87	ASN	0	-0.063	-0.037	6.477	0.060	0.060	0.000	0.000	0.000	0.000
89	A	88	VAL	0	0.008	-0.001	4.851	-0.099	-0.099	0.000	0.000	0.000	0.000
90	A	89	LEU	0	-0.019	0.004	7.346	0.066	0.066	0.000	0.000	0.000	0.000
91	A	90	THR	0	0.063	0.026	8.920	0.083	0.083	0.000	0.000	0.000	0.000
92	A	91	GLU	-1	-0.875	-0.955	9.424	0.572	0.572	0.000	0.000	0.000	0.000
93	A	92	TYR	0	-0.003	0.002	9.215	-0.068	-0.068	0.000	0.000	0.000	0.000
94	A	93	MET	0	0.015	0.007	3.316	0.179	0.725	0.726	-0.532	-0.740	-0.001
95	A	94	ASN	0	-0.032	-0.027	6.758	0.162	0.162	0.000	0.000	0.000	0.000
96	A	95	TRP	0	0.021	0.018	9.084	-0.102	-0.102	0.000	0.000	0.000	0.000
97	A	96	LEU	0	-0.010	0.004	6.431	-0.072	-0.072	0.000	0.000	0.000	0.000
98	A	97	ARG	1	0.945	0.972	3.797	-3.115	-3.011	-0.001	-0.026	-0.078	0.000
99	A	98	GLU	-1	-0.977	-0.985	7.658	0.174	0.174	0.000	0.000	0.000	0.000
100	A	99	SER	0	-0.092	-0.042	11.158	-0.058	-0.058	0.000	0.000	0.000	0.000
101	A	100	VAL	0	-0.075	-0.029	7.542	0.011	0.011	0.000	0.000	0.000	0.000

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