FMO DATABASE

FMODB ID: V5N21

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

Total energy (hartree)

FMO2-HF: Electronic energy	-670128.54655
FMO2-HF: Nuclear repulsion	627898.366919
FMO2-HF: Total energy	-42230.17963
FMO2-MP2: Total energy	-42349.304927

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.
-6.032	-0.754	1.771	-3.687	-3.361	-0.024

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 : 0.053 / q_NPA : 0.033

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	0.000	0.007	3.893	-0.526	1.536	-0.012	-1.115	-0.934	0.004
4	A	21	GLY	0	0.073	0.029	5.856	0.247	0.247	0.000	0.000	0.000	0.000
5	A	22	GLU	-1	-0.876	-0.934	2.582	-6.860	-3.644	1.783	-2.572	-2.427	-0.028
6	A	23	LEU	0	0.045	0.018	6.560	0.291	0.291	0.000	0.000	0.000	0.000
7	A	24	THR	0	0.034	0.019	8.938	0.097	0.097	0.000	0.000	0.000	0.000
8	A	25	LEU	0	0.009	0.008	9.736	0.094	0.094	0.000	0.000	0.000	0.000
9	A	26	MET	0	-0.011	-0.003	8.465	0.111	0.111	0.000	0.000	0.000	0.000
10	A	27	LEU	0	0.043	0.025	11.870	0.065	0.065	0.000	0.000	0.000	0.000
11	A	28	TYR	0	0.035	0.016	14.859	0.052	0.052	0.000	0.000	0.000	0.000
12	A	29	ASN	0	-0.052	-0.039	13.828	0.064	0.064	0.000	0.000	0.000	0.000
13	A	30	GLY	0	-0.022	-0.001	15.944	0.036	0.036	0.000	0.000	0.000	0.000
14	A	31	CYS	0	-0.001	0.007	17.620	0.023	0.023	0.000	0.000	0.000	0.000
15	A	32	LEU	0	-0.002	-0.003	18.690	0.015	0.015	0.000	0.000	0.000	0.000
16	A	33	LYS	1	0.914	0.963	17.241	0.031	0.031	0.000	0.000	0.000	0.000
17	A	34	PHE	0	0.003	-0.008	19.678	0.014	0.014	0.000	0.000	0.000	0.000
18	A	35	ILE	0	0.058	0.022	23.750	0.007	0.007	0.000	0.000	0.000	0.000
19	A	36	ARG	1	0.920	0.968	20.412	0.141	0.141	0.000	0.000	0.000	0.000
20	A	37	LEU	0	0.004	0.001	23.897	0.007	0.007	0.000	0.000	0.000	0.000
21	A	38	ALA	0	0.011	0.008	27.404	0.006	0.006	0.000	0.000	0.000	0.000
22	A	39	ALA	0	-0.006	0.002	29.537	0.003	0.003	0.000	0.000	0.000	0.000
23	A	40	GLN	0	0.036	0.003	27.622	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	41	ALA	0	-0.026	0.001	31.537	0.004	0.004	0.000	0.000	0.000	0.000
25	A	42	ILE	0	-0.021	-0.018	33.322	0.003	0.003	0.000	0.000	0.000	0.000
26	A	43	GLU	-1	-0.972	-0.980	34.550	-0.040	-0.040	0.000	0.000	0.000	0.000
27	A	44	ASN	0	-0.097	-0.057	35.240	0.004	0.004	0.000	0.000	0.000	0.000
28	A	45	ASP	-1	-0.881	-0.932	38.080	-0.012	-0.012	0.000	0.000	0.000	0.000
29	A	46	ASP	-1	-0.814	-0.868	34.226	0.007	0.007	0.000	0.000	0.000	0.000
30	A	47	MET	0	0.020	-0.003	35.057	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	48	GLU	-1	-0.864	-0.928	34.838	0.006	0.006	0.000	0.000	0.000	0.000
32	A	49	ARG	1	0.861	0.893	30.485	-0.016	-0.016	0.000	0.000	0.000	0.000
33	A	50	LYS	1	0.867	0.935	30.170	0.011	0.011	0.000	0.000	0.000	0.000
34	A	51	ASN	0	-0.041	-0.015	30.832	-0.008	-0.008	0.000	0.000	0.000	0.000
35	A	52	GLU	-1	-0.795	-0.888	27.224	0.024	0.024	0.000	0.000	0.000	0.000
36	A	53	ASN	0	-0.060	-0.046	25.709	0.004	0.004	0.000	0.000	0.000	0.000
37	A	54	LEU	0	0.042	0.021	25.991	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	55	ILE	0	0.020	0.020	27.164	-0.007	-0.007	0.000	0.000	0.000	0.000
39	A	56	LYS	1	0.795	0.901	22.571	-0.023	-0.023	0.000	0.000	0.000	0.000
40	A	57	ALA	0	0.006	-0.004	22.815	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	58	GLN	0	0.019	-0.006	23.479	-0.012	-0.012	0.000	0.000	0.000	0.000
42	A	59	ASN	0	0.005	0.012	22.999	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	60	ILE	0	-0.019	-0.004	18.065	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	61	ILE	0	-0.012	-0.014	19.873	-0.019	-0.019	0.000	0.000	0.000	0.000
45	A	62	GLN	0	-0.036	-0.024	22.295	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	63	GLU	-1	-0.884	-0.926	17.121	-0.044	-0.044	0.000	0.000	0.000	0.000
47	A	64	LEU	0	-0.048	-0.021	15.558	-0.018	-0.018	0.000	0.000	0.000	0.000
48	A	65	ASN	0	0.015	0.002	18.681	-0.021	-0.021	0.000	0.000	0.000	0.000
49	A	66	PHE	0	0.022	0.018	20.182	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	67	THR	0	0.003	-0.014	15.122	0.002	0.002	0.000	0.000	0.000	0.000
51	A	68	LEU	0	-0.044	-0.016	18.562	-0.011	-0.011	0.000	0.000	0.000	0.000
52	A	69	ASN	0	-0.052	-0.038	20.064	0.002	0.002	0.000	0.000	0.000	0.000
53	A	70	ARG	1	0.837	0.898	20.104	0.068	0.068	0.000	0.000	0.000	0.000
54	A	71	ASN	0	0.009	-0.009	15.396	0.025	0.025	0.000	0.000	0.000	0.000
55	A	72	ILE	0	-0.058	-0.020	19.692	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	73	GLU	-1	-0.842	-0.878	22.911	-0.070	-0.070	0.000	0.000	0.000	0.000
57	A	74	LEU	0	0.004	-0.002	19.307	0.006	0.006	0.000	0.000	0.000	0.000
58	A	75	SER	0	-0.013	0.007	22.408	0.001	0.001	0.000	0.000	0.000	0.000
59	A	76	ALA	0	0.023	-0.012	20.217	-0.008	-0.008	0.000	0.000	0.000	0.000
60	A	77	SER	0	-0.046	-0.014	20.690	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	78	MET	0	0.055	0.038	17.688	0.008	0.008	0.000	0.000	0.000	0.000
62	A	79	GLY	0	-0.007	0.001	16.503	-0.005	-0.005	0.000	0.000	0.000	0.000
63	A	80	ALA	0	0.009	-0.008	16.739	-0.012	-0.012	0.000	0.000	0.000	0.000
64	A	81	MET	0	0.008	0.021	18.944	0.007	0.007	0.000	0.000	0.000	0.000
65	A	82	TYR	0	0.003	-0.011	13.284	0.011	0.011	0.000	0.000	0.000	0.000
66	A	83	ASP	-1	-0.829	-0.885	14.308	-0.216	-0.216	0.000	0.000	0.000	0.000
67	A	84	TYR	0	-0.106	-0.076	15.362	0.009	0.009	0.000	0.000	0.000	0.000
68	A	85	MET	0	0.020	0.016	15.476	0.029	0.029	0.000	0.000	0.000	0.000
69	A	86	TYR	0	-0.012	0.005	9.004	0.045	0.045	0.000	0.000	0.000	0.000
70	A	87	ARG	1	0.842	0.891	13.088	0.193	0.193	0.000	0.000	0.000	0.000
71	A	88	ARG	1	0.838	0.900	15.814	-0.008	-0.008	0.000	0.000	0.000	0.000
72	A	89	LEU	0	0.050	0.023	12.295	0.026	0.026	0.000	0.000	0.000	0.000
73	A	90	VAL	0	-0.023	-0.005	11.888	0.041	0.041	0.000	0.000	0.000	0.000
74	A	91	GLN	0	0.022	0.007	14.361	0.015	0.015	0.000	0.000	0.000	0.000
75	A	92	ALA	0	0.029	0.008	17.142	0.006	0.006	0.000	0.000	0.000	0.000
76	A	93	ASN	0	-0.012	-0.001	14.353	0.042	0.042	0.000	0.000	0.000	0.000
77	A	94	ILE	0	-0.038	-0.015	15.922	0.001	0.001	0.000	0.000	0.000	0.000
78	A	95	LYS	1	0.876	0.931	18.776	-0.076	-0.076	0.000	0.000	0.000	0.000
79	A	96	ASN	0	-0.053	-0.016	20.254	0.010	0.010	0.000	0.000	0.000	0.000
80	A	97	ASP	-1	-0.849	-0.917	20.899	0.089	0.089	0.000	0.000	0.000	0.000
81	A	98	THR	0	0.054	-0.004	21.251	0.002	0.002	0.000	0.000	0.000	0.000
82	A	99	GLY	0	0.019	0.027	22.844	0.001	0.001	0.000	0.000	0.000	0.000
83	A	100	MET	0	-0.079	-0.043	20.360	-0.007	-0.007	0.000	0.000	0.000	0.000
84	A	101	LEU	0	-0.022	-0.006	16.636	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	102	ALA	0	0.046	0.023	19.443	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	103	GLU	-1	-0.782	-0.831	21.629	0.019	0.019	0.000	0.000	0.000	0.000
87	A	104	VAL	0	-0.003	-0.014	15.583	-0.013	-0.013	0.000	0.000	0.000	0.000
88	A	105	GLU	-1	-0.949	-0.971	18.800	0.175	0.175	0.000	0.000	0.000	0.000
89	A	106	GLY	0	0.011	0.011	19.775	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	107	TYR	0	-0.017	-0.036	19.611	-0.008	-0.008	0.000	0.000	0.000	0.000
91	A	108	VAL	0	-0.009	-0.008	15.597	-0.010	-0.010	0.000	0.000	0.000	0.000
92	A	109	THR	0	-0.039	-0.020	18.344	0.004	0.004	0.000	0.000	0.000	0.000
93	A	110	ASP	-1	-0.893	-0.941	21.440	0.029	0.029	0.000	0.000	0.000	0.000
94	A	111	PHE	0	-0.013	-0.037	18.185	-0.010	-0.010	0.000	0.000	0.000	0.000
95	A	112	ARG	1	0.817	0.901	18.597	-0.114	-0.114	0.000	0.000	0.000	0.000
96	A	113	ASP	-1	-0.774	-0.853	19.848	0.073	0.073	0.000	0.000	0.000	0.000
97	A	114	ALA	0	0.036	0.022	22.929	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	115	TRP	0	0.007	0.000	17.564	-0.010	-0.010	0.000	0.000	0.000	0.000
99	A	116	LYS	1	0.830	0.893	21.745	-0.080	-0.080	0.000	0.000	0.000	0.000
100	A	117	GLN	0	-0.032	-0.015	23.518	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	118	ALA	0	-0.018	-0.007	23.724	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	119	ILE	0	-0.101	-0.030	20.671	-0.005	-0.005	0.000	0.000	0.000	0.000

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