FMO DATABASE

FMODB ID: 52Y3Z

Calculation Name: 1VH6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VH6

Chain ID: A

ChEMBL ID:

UniProt ID: P39739

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:

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	102
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-669276.06808
FMO2-HF: Nuclear repulsion	627046.766031
FMO2-HF: Total energy	-42229.30205
FMO2-MP2: Total energy	-42348.57826

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:18:ALA)

Summations of interaction energy for fragment #1(A:18:ALA)

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.
-5.129	-0.206	0.716	-2.922	-2.716	-0.013

Interaction energy analysis for fragmet #1(A:18:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : 0.009

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	20	PRO	0	0.027	0.002	3.796	-0.244	1.819	-0.020	-1.010	-1.033	0.005
4	A	21	GLY	0	0.068	0.027	5.639	0.219	0.219	0.000	0.000	0.000	0.000
5	A	22	GLU	-1	-0.866	-0.925	2.759	-5.961	-3.101	0.736	-1.912	-1.683	-0.018
6	A	23	LEU	0	0.039	0.017	7.142	0.252	0.252	0.000	0.000	0.000	0.000
7	A	24	THR	0	0.042	0.025	9.366	0.115	0.115	0.000	0.000	0.000	0.000
8	A	25	LEU	0	0.007	0.020	9.703	0.084	0.084	0.000	0.000	0.000	0.000
9	A	26	MET	0	-0.043	-0.038	8.676	0.109	0.109	0.000	0.000	0.000	0.000
10	A	27	LEU	0	0.031	0.023	12.123	0.066	0.066	0.000	0.000	0.000	0.000
11	A	28	TYR	0	0.040	0.017	15.101	0.034	0.034	0.000	0.000	0.000	0.000
12	A	29	ASN	0	0.003	-0.007	13.130	0.050	0.050	0.000	0.000	0.000	0.000
13	A	30	GLY	0	-0.027	-0.004	16.099	0.036	0.036	0.000	0.000	0.000	0.000
14	A	31	CYS	0	0.001	-0.017	17.786	0.023	0.023	0.000	0.000	0.000	0.000
15	A	32	LEU	0	-0.001	0.003	19.052	0.015	0.015	0.000	0.000	0.000	0.000
16	A	33	LYS	1	0.927	0.974	18.887	0.025	0.025	0.000	0.000	0.000	0.000
17	A	34	PHE	0	-0.010	-0.016	20.272	0.015	0.015	0.000	0.000	0.000	0.000
18	A	35	ILE	0	0.057	0.033	24.139	0.007	0.007	0.000	0.000	0.000	0.000
19	A	36	ARG	1	0.930	0.955	21.377	0.138	0.138	0.000	0.000	0.000	0.000
20	A	37	LEU	0	-0.032	-0.010	24.688	0.007	0.007	0.000	0.000	0.000	0.000
21	A	38	ALA	0	0.001	0.007	27.872	0.007	0.007	0.000	0.000	0.000	0.000
22	A	39	ALA	0	0.005	0.005	29.911	0.003	0.003	0.000	0.000	0.000	0.000
23	A	40	GLN	0	0.013	-0.001	28.325	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	41	ALA	0	-0.027	-0.011	32.075	0.004	0.004	0.000	0.000	0.000	0.000
25	A	42	ILE	0	-0.033	-0.021	33.915	0.003	0.003	0.000	0.000	0.000	0.000
26	A	43	GLU	-1	-0.946	-0.957	35.689	-0.040	-0.040	0.000	0.000	0.000	0.000
27	A	44	ASN	0	-0.076	-0.029	34.974	0.000	0.000	0.000	0.000	0.000	0.000
28	A	45	ASP	-1	-0.897	-0.942	38.343	-0.013	-0.013	0.000	0.000	0.000	0.000
29	A	46	ASP	-1	-0.858	-0.923	34.944	0.004	0.004	0.000	0.000	0.000	0.000
30	A	47	MET	0	0.004	-0.037	35.567	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	48	GLU	-1	-0.915	-0.947	35.377	0.007	0.007	0.000	0.000	0.000	0.000
32	A	49	ARG	1	0.896	0.925	31.025	-0.012	-0.012	0.000	0.000	0.000	0.000
33	A	50	LYS	1	0.947	1.007	30.652	0.018	0.018	0.000	0.000	0.000	0.000
34	A	51	ASN	0	-0.033	-0.013	31.248	-0.009	-0.009	0.000	0.000	0.000	0.000
35	A	52	GLU	-1	-0.860	-0.913	27.273	0.014	0.014	0.000	0.000	0.000	0.000
36	A	53	ASN	0	-0.077	-0.083	26.238	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	54	LEU	0	0.050	0.017	26.424	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	55	ILE	0	0.019	0.025	27.487	-0.007	-0.007	0.000	0.000	0.000	0.000
39	A	56	LYS	1	0.892	0.957	23.106	-0.023	-0.023	0.000	0.000	0.000	0.000
40	A	57	ALA	0	0.004	-0.007	22.970	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	58	GLN	0	0.001	-0.004	23.745	-0.015	-0.015	0.000	0.000	0.000	0.000
42	A	59	ASN	0	0.010	-0.004	23.172	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	60	ILE	0	-0.032	-0.001	18.657	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	61	ILE	0	0.005	0.000	20.298	-0.017	-0.017	0.000	0.000	0.000	0.000
45	A	62	GLN	0	-0.025	-0.016	22.607	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	63	GLU	-1	-0.912	-0.938	17.283	-0.057	-0.057	0.000	0.000	0.000	0.000
47	A	64	LEU	0	-0.043	-0.029	16.233	-0.016	-0.016	0.000	0.000	0.000	0.000
48	A	65	ASN	0	-0.020	-0.014	19.100	-0.021	-0.021	0.000	0.000	0.000	0.000
49	A	66	PHE	0	0.006	0.004	20.572	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	67	THR	0	0.011	-0.010	15.497	0.002	0.002	0.000	0.000	0.000	0.000
51	A	68	LEU	0	-0.029	0.000	18.944	-0.010	-0.010	0.000	0.000	0.000	0.000
52	A	69	ASN	0	-0.015	-0.023	20.230	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	70	ARG	1	0.822	0.886	20.546	0.080	0.080	0.000	0.000	0.000	0.000
54	A	71	ASN	0	-0.005	-0.016	15.816	0.032	0.032	0.000	0.000	0.000	0.000
55	A	72	ILE	0	-0.052	-0.017	19.870	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	73	GLU	-1	-0.831	-0.858	22.980	-0.074	-0.074	0.000	0.000	0.000	0.000
57	A	74	LEU	0	0.000	-0.002	19.106	0.006	0.006	0.000	0.000	0.000	0.000
58	A	75	SER	0	-0.012	0.008	22.657	0.002	0.002	0.000	0.000	0.000	0.000
59	A	76	ALA	0	0.035	-0.006	20.410	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	77	SER	0	-0.032	-0.010	20.712	-0.007	-0.007	0.000	0.000	0.000	0.000
61	A	78	MET	0	0.023	0.018	17.408	0.007	0.007	0.000	0.000	0.000	0.000
62	A	79	GLY	0	-0.009	-0.004	16.602	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	80	ALA	0	0.041	0.021	16.721	-0.015	-0.015	0.000	0.000	0.000	0.000
64	A	81	MET	0	-0.013	-0.005	18.691	0.007	0.007	0.000	0.000	0.000	0.000
65	A	82	TYR	0	0.011	-0.006	13.240	0.015	0.015	0.000	0.000	0.000	0.000
66	A	83	ASP	-1	-0.904	-0.943	13.904	-0.304	-0.304	0.000	0.000	0.000	0.000
67	A	84	TYR	0	-0.112	-0.080	15.137	0.015	0.015	0.000	0.000	0.000	0.000
68	A	85	MET	0	0.008	0.015	15.154	0.034	0.034	0.000	0.000	0.000	0.000
69	A	86	TYR	0	0.004	0.015	7.662	0.032	0.032	0.000	0.000	0.000	0.000
70	A	87	ARG	1	0.940	0.957	12.700	0.181	0.181	0.000	0.000	0.000	0.000
71	A	88	ARG	1	0.922	0.964	15.242	-0.008	-0.008	0.000	0.000	0.000	0.000
72	A	89	LEU	0	0.019	0.024	11.739	0.030	0.030	0.000	0.000	0.000	0.000
73	A	90	VAL	0	-0.020	-0.002	11.596	0.039	0.039	0.000	0.000	0.000	0.000
74	A	91	GLN	0	-0.025	-0.021	13.938	0.016	0.016	0.000	0.000	0.000	0.000
75	A	92	ALA	0	0.027	-0.007	17.064	0.006	0.006	0.000	0.000	0.000	0.000
76	A	93	ASN	0	-0.062	-0.026	12.653	0.003	0.003	0.000	0.000	0.000	0.000
77	A	94	ILE	0	-0.017	0.001	16.051	0.003	0.003	0.000	0.000	0.000	0.000
78	A	95	LYS	1	0.868	0.925	18.588	-0.076	-0.076	0.000	0.000	0.000	0.000
79	A	96	ASN	0	-0.029	0.008	20.039	0.014	0.014	0.000	0.000	0.000	0.000
80	A	97	ASP	-1	-0.841	-0.925	20.890	0.089	0.089	0.000	0.000	0.000	0.000
81	A	98	THR	0	0.020	-0.011	21.062	0.005	0.005	0.000	0.000	0.000	0.000
82	A	99	GLY	0	0.036	0.025	22.713	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	100	MET	0	-0.070	-0.036	20.236	-0.010	-0.010	0.000	0.000	0.000	0.000
84	A	101	LEU	0	-0.011	0.000	16.514	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	102	ALA	0	0.054	0.031	19.439	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	103	GLU	-1	-0.788	-0.853	21.589	0.022	0.022	0.000	0.000	0.000	0.000
87	A	104	VAL	0	-0.023	-0.024	15.590	-0.011	-0.011	0.000	0.000	0.000	0.000
88	A	105	GLU	-1	-0.945	-0.970	18.719	0.165	0.165	0.000	0.000	0.000	0.000
89	A	106	GLY	0	0.014	0.014	19.648	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	107	TYR	0	-0.045	-0.050	19.223	-0.012	-0.012	0.000	0.000	0.000	0.000
91	A	108	VAL	0	-0.003	-0.009	15.454	-0.011	-0.011	0.000	0.000	0.000	0.000
92	A	109	THR	0	-0.055	-0.028	18.221	0.004	0.004	0.000	0.000	0.000	0.000
93	A	110	ASP	-1	-0.853	-0.909	21.173	0.024	0.024	0.000	0.000	0.000	0.000
94	A	111	PHE	0	-0.051	-0.051	17.849	-0.012	-0.012	0.000	0.000	0.000	0.000
95	A	112	ARG	1	0.862	0.934	18.564	-0.108	-0.108	0.000	0.000	0.000	0.000
96	A	113	ASP	-1	-0.864	-0.929	19.994	0.058	0.058	0.000	0.000	0.000	0.000
97	A	114	ALA	0	0.023	0.004	23.070	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	115	TRP	0	0.010	0.001	18.281	-0.011	-0.011	0.000	0.000	0.000	0.000
99	A	116	LYS	1	0.903	0.942	21.875	-0.084	-0.084	0.000	0.000	0.000	0.000
100	A	117	GLN	0	-0.058	-0.020	23.604	0.001	0.001	0.000	0.000	0.000	0.000
101	A	118	ALA	0	-0.032	-0.006	23.737	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	119	ILE	0	-0.064	-0.017	20.941	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:18:ALA)