FMO DATABASE

FMODB ID: YZ1Q2

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:

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	102
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-668454.021958
FMO2-HF: Nuclear repulsion	626224.085134
FMO2-HF: Total energy	-42229.936824
FMO2-MP2: Total energy	-42349.099858

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.
-4.582	-0.301	1.785	-3.057	-3.009	-0.017

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 : 0.019 / q_NPA : 0.015

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	0.014	0.002	3.796	-0.267	1.770	-0.020	-0.996	-1.021	0.005
4	A	21	GLY	0	0.063	0.022	5.714	0.194	0.194	0.000	0.000	0.000	0.000
5	A	22	GLU	-1	-0.852	-0.927	2.467	-5.378	-3.134	1.805	-2.061	-1.988	-0.022
6	A	23	LEU	0	0.009	0.007	7.078	0.240	0.240	0.000	0.000	0.000	0.000
7	A	24	THR	0	0.054	0.031	9.419	0.083	0.083	0.000	0.000	0.000	0.000
8	A	25	LEU	0	0.018	0.021	9.942	0.086	0.086	0.000	0.000	0.000	0.000
9	A	26	MET	0	-0.021	-0.021	8.732	0.103	0.103	0.000	0.000	0.000	0.000
10	A	27	LEU	0	0.038	0.026	12.141	0.058	0.058	0.000	0.000	0.000	0.000
11	A	28	TYR	0	0.038	0.015	15.124	0.048	0.048	0.000	0.000	0.000	0.000
12	A	29	ASN	0	-0.048	-0.037	13.769	0.055	0.055	0.000	0.000	0.000	0.000
13	A	30	GLY	0	-0.018	-0.001	16.114	0.033	0.033	0.000	0.000	0.000	0.000
14	A	31	CYS	0	-0.010	-0.017	17.800	0.022	0.022	0.000	0.000	0.000	0.000
15	A	32	LEU	0	-0.001	0.004	19.063	0.013	0.013	0.000	0.000	0.000	0.000
16	A	33	LYS	1	0.919	0.971	18.183	0.020	0.020	0.000	0.000	0.000	0.000
17	A	34	PHE	0	-0.003	-0.013	20.039	0.012	0.012	0.000	0.000	0.000	0.000
18	A	35	ILE	0	0.063	0.032	24.153	0.007	0.007	0.000	0.000	0.000	0.000
19	A	36	ARG	1	0.929	0.958	21.128	0.129	0.129	0.000	0.000	0.000	0.000
20	A	37	LEU	0	-0.018	-0.005	24.432	0.006	0.006	0.000	0.000	0.000	0.000
21	A	38	ALA	0	0.001	0.006	27.881	0.006	0.006	0.000	0.000	0.000	0.000
22	A	39	ALA	0	-0.002	0.003	29.921	0.003	0.003	0.000	0.000	0.000	0.000
23	A	40	GLN	0	0.031	0.008	28.300	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	41	ALA	0	-0.015	0.003	32.084	0.003	0.003	0.000	0.000	0.000	0.000
25	A	42	ILE	0	-0.019	-0.009	33.925	0.003	0.003	0.000	0.000	0.000	0.000
26	A	43	GLU	-1	-0.942	-0.956	35.622	-0.036	-0.036	0.000	0.000	0.000	0.000
27	A	44	ASN	0	-0.129	-0.067	35.423	0.004	0.004	0.000	0.000	0.000	0.000
28	A	45	ASP	-1	-0.884	-0.938	38.351	-0.011	-0.011	0.000	0.000	0.000	0.000
29	A	46	ASP	-1	-0.839	-0.892	34.745	0.007	0.007	0.000	0.000	0.000	0.000
30	A	47	MET	0	0.021	-0.015	35.578	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	48	GLU	-1	-0.891	-0.939	35.395	0.008	0.008	0.000	0.000	0.000	0.000
32	A	49	ARG	1	0.874	0.893	30.974	-0.014	-0.014	0.000	0.000	0.000	0.000
33	A	50	LYS	1	0.899	0.964	30.664	0.012	0.012	0.000	0.000	0.000	0.000
34	A	51	ASN	0	-0.026	-0.008	31.263	-0.008	-0.008	0.000	0.000	0.000	0.000
35	A	52	GLU	-1	-0.812	-0.892	27.593	0.022	0.022	0.000	0.000	0.000	0.000
36	A	53	ASN	0	-0.085	-0.067	26.144	0.000	0.000	0.000	0.000	0.000	0.000
37	A	54	LEU	0	0.055	0.023	26.440	-0.008	-0.008	0.000	0.000	0.000	0.000
38	A	55	ILE	0	0.009	0.016	27.646	-0.007	-0.007	0.000	0.000	0.000	0.000
39	A	56	LYS	1	0.856	0.932	23.150	-0.028	-0.028	0.000	0.000	0.000	0.000
40	A	57	ALA	0	0.004	-0.005	22.993	-0.007	-0.007	0.000	0.000	0.000	0.000
41	A	58	GLN	0	-0.007	-0.009	23.767	-0.013	-0.013	0.000	0.000	0.000	0.000
42	A	59	ASN	0	0.001	-0.008	23.266	-0.009	-0.009	0.000	0.000	0.000	0.000
43	A	60	ILE	0	-0.020	0.000	18.622	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	61	ILE	0	0.002	-0.001	20.350	-0.017	-0.017	0.000	0.000	0.000	0.000
45	A	62	GLN	0	-0.014	-0.011	22.664	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	63	GLU	-1	-0.903	-0.934	17.371	-0.047	-0.047	0.000	0.000	0.000	0.000
47	A	64	LEU	0	-0.060	-0.036	16.140	-0.017	-0.017	0.000	0.000	0.000	0.000
48	A	65	ASN	0	-0.002	-0.006	19.158	-0.020	-0.020	0.000	0.000	0.000	0.000
49	A	66	PHE	0	0.030	0.021	20.506	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	67	THR	0	0.013	-0.004	15.527	0.002	0.002	0.000	0.000	0.000	0.000
51	A	68	LEU	0	-0.035	-0.008	18.994	-0.010	-0.010	0.000	0.000	0.000	0.000
52	A	69	ASN	0	-0.044	-0.043	20.290	0.002	0.002	0.000	0.000	0.000	0.000
53	A	70	ARG	1	0.827	0.899	20.551	0.073	0.073	0.000	0.000	0.000	0.000
54	A	71	ASN	0	-0.014	-0.024	15.626	0.024	0.024	0.000	0.000	0.000	0.000
55	A	72	ILE	0	-0.047	-0.015	19.922	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	73	GLU	-1	-0.830	-0.863	23.036	-0.071	-0.071	0.000	0.000	0.000	0.000
57	A	74	LEU	0	-0.020	-0.012	19.259	0.006	0.006	0.000	0.000	0.000	0.000
58	A	75	SER	0	-0.014	-0.001	22.708	0.001	0.001	0.000	0.000	0.000	0.000
59	A	76	ALA	0	0.037	-0.003	20.460	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	77	SER	0	-0.023	0.001	20.755	-0.007	-0.007	0.000	0.000	0.000	0.000
61	A	78	MET	0	0.034	0.021	17.570	0.006	0.006	0.000	0.000	0.000	0.000
62	A	79	GLY	0	-0.007	-0.003	16.642	-0.005	-0.005	0.000	0.000	0.000	0.000
63	A	80	ALA	0	0.030	0.013	16.753	-0.015	-0.015	0.000	0.000	0.000	0.000
64	A	81	MET	0	-0.013	-0.002	18.733	0.006	0.006	0.000	0.000	0.000	0.000
65	A	82	TYR	0	0.007	-0.006	13.212	0.012	0.012	0.000	0.000	0.000	0.000
66	A	83	ASP	-1	-0.912	-0.946	13.943	-0.300	-0.300	0.000	0.000	0.000	0.000
67	A	84	TYR	0	-0.140	-0.098	15.168	0.011	0.011	0.000	0.000	0.000	0.000
68	A	85	MET	0	0.025	0.020	15.199	0.031	0.031	0.000	0.000	0.000	0.000
69	A	86	TYR	0	-0.005	0.010	8.143	0.040	0.040	0.000	0.000	0.000	0.000
70	A	87	ARG	1	0.951	0.965	12.724	0.191	0.191	0.000	0.000	0.000	0.000
71	A	88	ARG	1	0.860	0.911	15.258	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	89	LEU	0	0.043	0.033	11.896	0.028	0.028	0.000	0.000	0.000	0.000
73	A	90	VAL	0	-0.012	-0.002	11.466	0.038	0.038	0.000	0.000	0.000	0.000
74	A	91	GLN	0	0.011	0.002	13.932	0.018	0.018	0.000	0.000	0.000	0.000
75	A	92	ALA	0	0.023	-0.005	16.985	0.006	0.006	0.000	0.000	0.000	0.000
76	A	93	ASN	0	-0.044	-0.018	13.336	0.034	0.034	0.000	0.000	0.000	0.000
77	A	94	ILE	0	-0.038	-0.013	15.783	0.005	0.005	0.000	0.000	0.000	0.000
78	A	95	LYS	1	0.883	0.933	18.564	-0.067	-0.067	0.000	0.000	0.000	0.000
79	A	96	ASN	0	-0.044	-0.002	20.013	0.012	0.012	0.000	0.000	0.000	0.000
80	A	97	ASP	-1	-0.836	-0.913	20.877	0.079	0.079	0.000	0.000	0.000	0.000
81	A	98	THR	0	0.041	-0.007	21.048	0.004	0.004	0.000	0.000	0.000	0.000
82	A	99	GLY	0	0.026	0.026	22.698	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	100	MET	0	-0.077	-0.043	20.146	-0.008	-0.008	0.000	0.000	0.000	0.000
84	A	101	LEU	0	-0.016	-0.002	16.564	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	102	ALA	0	0.047	0.027	19.435	0.000	0.000	0.000	0.000	0.000	0.000
86	A	103	GLU	-1	-0.770	-0.819	21.669	0.012	0.012	0.000	0.000	0.000	0.000
87	A	104	VAL	0	0.000	-0.018	15.549	-0.011	-0.011	0.000	0.000	0.000	0.000
88	A	105	GLU	-1	-0.956	-0.973	18.683	0.156	0.156	0.000	0.000	0.000	0.000
89	A	106	GLY	0	0.013	0.017	19.620	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	107	TYR	0	-0.036	-0.048	19.290	-0.011	-0.011	0.000	0.000	0.000	0.000
91	A	108	VAL	0	0.005	-0.005	15.392	-0.010	-0.010	0.000	0.000	0.000	0.000
92	A	109	THR	0	-0.050	-0.025	18.212	0.004	0.004	0.000	0.000	0.000	0.000
93	A	110	ASP	-1	-0.884	-0.930	21.160	0.021	0.021	0.000	0.000	0.000	0.000
94	A	111	PHE	0	-0.045	-0.052	17.905	-0.011	-0.011	0.000	0.000	0.000	0.000
95	A	112	ARG	1	0.845	0.906	18.594	-0.101	-0.101	0.000	0.000	0.000	0.000
96	A	113	ASP	-1	-0.788	-0.863	19.997	0.064	0.064	0.000	0.000	0.000	0.000
97	A	114	ALA	0	0.043	0.021	23.081	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	115	TRP	0	0.010	0.000	18.167	-0.010	-0.010	0.000	0.000	0.000	0.000
99	A	116	LYS	1	0.828	0.899	21.983	-0.072	-0.072	0.000	0.000	0.000	0.000
100	A	117	GLN	0	-0.048	-0.016	23.615	0.000	0.000	0.000	0.000	0.000	0.000
101	A	118	ALA	0	-0.026	-0.004	23.776	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	119	ILE	0	-0.084	-0.029	20.723	-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)