FMO DATABASE

FMODB ID: 948G2

Calculation Name: 5VKY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5VKY

Chain ID: A

ChEMBL ID:

UniProt ID: P40045

Base Structure: X-ray

Registration Date: 2023-06-21

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	122
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1008777.337527
FMO2-HF: Nuclear repulsion	960248.269244
FMO2-HF: Total energy	-48529.068283
FMO2-MP2: Total energy	-48673.155261

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:5:ILE)

Summations of interaction energy for fragment #1(A:5:ILE)

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.
-6.074	0.16	2.025	-3.404	-4.853	-0.015

Interaction energy analysis for fragmet #1(A:5:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / 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

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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	7	ILE	0	0.002	-0.010	3.634	-0.624	2.046	-0.023	-1.079	-1.568	0.006
4	A	8	LYS	1	0.817	0.916	4.993	1.456	1.481	-0.001	-0.003	-0.021	0.000
5	A	9	ASP	-1	-0.887	-0.952	8.309	-0.653	-0.653	0.000	0.000	0.000	0.000
6	A	10	GLY	0	-0.018	-0.015	11.312	0.074	0.074	0.000	0.000	0.000	0.000
7	A	11	ARG	1	0.878	0.942	14.174	0.401	0.401	0.000	0.000	0.000	0.000
8	A	12	SER	0	0.056	0.031	14.452	0.002	0.002	0.000	0.000	0.000	0.000
9	A	13	ASP	-1	-0.914	-0.943	16.393	-0.343	-0.343	0.000	0.000	0.000	0.000
10	A	14	ASN	0	-0.100	-0.084	13.467	0.052	0.052	0.000	0.000	0.000	0.000
11	A	15	SER	0	-0.063	-0.006	17.584	0.033	0.033	0.000	0.000	0.000	0.000
12	A	16	PRO	0	-0.042	-0.019	19.400	0.011	0.011	0.000	0.000	0.000	0.000
13	A	17	LEU	0	-0.019	0.000	22.159	0.027	0.027	0.000	0.000	0.000	0.000
14	A	18	PRO	0	0.019	-0.005	23.270	-0.018	-0.018	0.000	0.000	0.000	0.000
15	A	19	GLU	-1	-0.775	-0.897	20.282	-0.287	-0.287	0.000	0.000	0.000	0.000
16	A	20	ARG	1	0.968	0.979	23.929	0.150	0.150	0.000	0.000	0.000	0.000
17	A	21	LYS	1	0.879	0.937	27.162	0.138	0.138	0.000	0.000	0.000	0.000
18	A	22	LEU	0	0.055	0.036	20.388	0.013	0.013	0.000	0.000	0.000	0.000
19	A	23	VAL	0	0.022	0.011	24.913	0.012	0.012	0.000	0.000	0.000	0.000
20	A	24	THR	0	-0.040	-0.009	26.375	0.013	0.013	0.000	0.000	0.000	0.000
21	A	25	LEU	0	-0.021	0.006	25.310	0.010	0.010	0.000	0.000	0.000	0.000
22	A	26	ILE	0	-0.001	0.002	22.416	0.011	0.011	0.000	0.000	0.000	0.000
23	A	27	GLN	0	-0.017	-0.018	26.904	0.002	0.002	0.000	0.000	0.000	0.000
24	A	28	GLU	-1	-0.898	-0.948	29.818	-0.074	-0.074	0.000	0.000	0.000	0.000
25	A	29	SER	0	-0.065	-0.042	28.638	0.009	0.009	0.000	0.000	0.000	0.000
26	A	30	TYR	0	0.026	0.020	28.918	0.009	0.009	0.000	0.000	0.000	0.000
27	A	31	ASP	-1	-0.826	-0.924	30.770	-0.061	-0.061	0.000	0.000	0.000	0.000
28	A	32	SER	0	-0.088	-0.056	33.263	0.006	0.006	0.000	0.000	0.000	0.000
29	A	33	LEU	0	-0.028	-0.017	30.359	0.005	0.005	0.000	0.000	0.000	0.000
30	A	34	LYS	1	0.852	0.933	31.829	0.031	0.031	0.000	0.000	0.000	0.000
31	A	35	ASP	-1	-0.850	-0.896	36.105	-0.033	-0.033	0.000	0.000	0.000	0.000
32	A	36	ASP	-1	-0.942	-0.982	39.225	-0.018	-0.018	0.000	0.000	0.000	0.000
33	A	37	ASN	0	-0.152	-0.072	42.230	0.005	0.005	0.000	0.000	0.000	0.000
34	A	38	GLU	-1	-0.959	-0.960	38.126	-0.027	-0.027	0.000	0.000	0.000	0.000
35	A	39	ILE	0	-0.048	-0.024	40.766	0.003	0.003	0.000	0.000	0.000	0.000
36	A	40	ASN	0	0.048	0.028	35.226	0.001	0.001	0.000	0.000	0.000	0.000
37	A	41	LEU	0	-0.029	-0.019	38.898	0.002	0.002	0.000	0.000	0.000	0.000
38	A	42	SER	0	-0.069	-0.034	35.591	0.004	0.004	0.000	0.000	0.000	0.000
39	A	43	THR	0	0.023	-0.006	34.334	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	44	GLU	-1	-0.971	-0.984	30.308	0.027	0.027	0.000	0.000	0.000	0.000
41	A	45	SER	0	0.035	0.012	28.099	-0.006	-0.006	0.000	0.000	0.000	0.000
42	A	46	THR	0	0.117	0.046	29.487	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	47	SER	0	-0.002	0.011	24.256	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	48	ASN	0	0.034	-0.002	25.381	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	49	LEU	0	0.007	0.009	26.954	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	50	LEU	0	0.010	0.011	25.186	-0.006	-0.006	0.000	0.000	0.000	0.000
47	A	51	ILE	0	-0.027	-0.015	22.154	-0.010	-0.010	0.000	0.000	0.000	0.000
48	A	52	LYS	1	0.919	0.964	24.696	-0.021	-0.021	0.000	0.000	0.000	0.000
49	A	53	LEU	0	0.076	0.045	27.250	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	54	VAL	0	-0.026	-0.018	22.993	-0.010	-0.010	0.000	0.000	0.000	0.000
51	A	55	LEU	0	-0.018	-0.025	20.789	-0.014	-0.014	0.000	0.000	0.000	0.000
52	A	56	GLU	-1	-0.881	-0.925	24.614	-0.038	-0.038	0.000	0.000	0.000	0.000
53	A	57	LYS	1	0.898	0.938	27.804	0.064	0.064	0.000	0.000	0.000	0.000
54	A	58	LEU	0	-0.014	0.012	21.206	-0.012	-0.012	0.000	0.000	0.000	0.000
55	A	59	GLU	-1	-0.959	-0.985	24.498	-0.049	-0.049	0.000	0.000	0.000	0.000
56	A	60	LYS	1	0.836	0.919	25.879	0.054	0.054	0.000	0.000	0.000	0.000
57	A	61	HIS	0	-0.067	-0.035	26.226	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	62	SER	0	0.021	0.008	23.399	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	63	SER	0	0.056	0.046	24.114	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	64	LEU	0	-0.010	-0.020	21.816	0.011	0.011	0.000	0.000	0.000	0.000
61	A	65	TYR	0	0.016	0.003	17.100	-0.024	-0.024	0.000	0.000	0.000	0.000
62	A	66	LYS	1	0.883	0.940	17.028	0.051	0.051	0.000	0.000	0.000	0.000
63	A	67	TYR	0	0.040	0.004	17.292	-0.049	-0.049	0.000	0.000	0.000	0.000
64	A	68	ILE	0	-0.005	0.002	13.818	0.037	0.037	0.000	0.000	0.000	0.000
65	A	69	ALA	0	0.018	0.010	17.386	-0.036	-0.036	0.000	0.000	0.000	0.000
66	A	70	SER	0	-0.028	-0.004	15.763	0.034	0.034	0.000	0.000	0.000	0.000
67	A	71	VAL	0	0.058	0.017	18.132	-0.026	-0.026	0.000	0.000	0.000	0.000
68	A	72	THR	0	-0.041	-0.008	18.450	0.026	0.026	0.000	0.000	0.000	0.000
69	A	73	THR	0	0.007	-0.012	20.942	-0.015	-0.015	0.000	0.000	0.000	0.000
70	A	74	LEU	0	-0.047	-0.013	24.548	0.011	0.011	0.000	0.000	0.000	0.000
71	A	75	ASN	0	0.066	0.025	25.977	-0.010	-0.010	0.000	0.000	0.000	0.000
72	A	76	ILE	0	-0.068	-0.025	29.542	0.006	0.006	0.000	0.000	0.000	0.000
73	A	77	GLU	-1	-0.877	-0.942	31.666	0.011	0.011	0.000	0.000	0.000	0.000
74	A	78	GLY	0	-0.045	-0.021	34.796	0.001	0.001	0.000	0.000	0.000	0.000
75	A	79	LEU	0	-0.093	-0.058	33.770	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	80	ASN	0	0.005	0.014	35.986	0.003	0.003	0.000	0.000	0.000	0.000
77	A	81	GLU	-1	-0.843	-0.927	30.905	-0.040	-0.040	0.000	0.000	0.000	0.000
78	A	82	GLU	-1	-0.839	-0.937	32.562	-0.034	-0.034	0.000	0.000	0.000	0.000
79	A	83	ASN	0	-0.128	-0.066	34.555	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	84	ALA	0	0.000	0.014	31.602	0.003	0.003	0.000	0.000	0.000	0.000
81	A	85	ASN	0	-0.062	-0.031	30.336	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	86	PHE	0	0.012	0.007	25.203	0.005	0.005	0.000	0.000	0.000	0.000
83	A	87	SER	0	-0.067	-0.029	21.938	-0.015	-0.015	0.000	0.000	0.000	0.000
84	A	88	LEU	0	0.068	0.031	20.684	0.007	0.007	0.000	0.000	0.000	0.000
85	A	89	LYS	1	0.942	0.957	16.594	0.133	0.133	0.000	0.000	0.000	0.000
86	A	90	ASN	0	0.030	0.003	13.437	0.000	0.000	0.000	0.000	0.000	0.000
87	A	91	ASP	-1	-0.903	-0.931	9.430	-0.320	-0.320	0.000	0.000	0.000	0.000
88	A	92	ILE	0	0.020	0.005	8.141	0.101	0.101	0.000	0.000	0.000	0.000
89	A	93	GLY	0	0.000	0.007	4.277	-0.343	-0.305	-0.001	-0.010	-0.026	0.000
90	A	94	ALA	0	-0.027	0.001	4.273	0.274	0.516	-0.001	-0.054	-0.187	0.000
91	A	95	SER	0	-0.025	-0.022	2.494	-3.939	-1.662	2.028	-2.123	-2.182	-0.020
92	A	96	TRP	0	-0.044	-0.023	3.606	0.705	1.371	0.020	-0.069	-0.616	-0.001
93	A	97	GLU	-1	-0.883	-0.933	3.578	-4.808	-4.492	0.003	-0.066	-0.253	0.000
94	A	98	SER	0	-0.067	-0.027	5.711	0.631	0.631	0.000	0.000	0.000	0.000
95	A	99	LYS	1	0.983	0.965	9.455	1.087	1.087	0.000	0.000	0.000	0.000
96	A	100	LYS	1	0.930	0.991	11.847	0.433	0.433	0.000	0.000	0.000	0.000
97	A	101	ASP	-1	-0.767	-0.885	10.441	-0.443	-0.443	0.000	0.000	0.000	0.000
98	A	102	GLY	0	0.001	-0.009	12.064	-0.159	-0.159	0.000	0.000	0.000	0.000
99	A	103	ILE	0	-0.014	-0.004	11.355	0.079	0.079	0.000	0.000	0.000	0.000
100	A	104	PHE	0	0.048	0.025	14.250	-0.017	-0.017	0.000	0.000	0.000	0.000
101	A	105	ASN	0	0.000	0.007	14.190	0.054	0.054	0.000	0.000	0.000	0.000
102	A	106	TYR	0	-0.017	-0.011	18.117	-0.012	-0.012	0.000	0.000	0.000	0.000
103	A	107	LYS	1	0.878	0.943	21.744	0.116	0.116	0.000	0.000	0.000	0.000
104	A	108	LEU	0	-0.029	-0.004	23.851	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	109	GLU	-1	-0.896	-0.958	27.237	-0.054	-0.054	0.000	0.000	0.000	0.000
106	A	110	ASP	-1	-0.872	-0.947	29.794	-0.030	-0.030	0.000	0.000	0.000	0.000
107	A	111	LYS	1	0.981	0.986	32.782	0.052	0.052	0.000	0.000	0.000	0.000
108	A	112	ASN	0	-0.045	-0.013	34.932	0.003	0.003	0.000	0.000	0.000	0.000
109	A	113	ASN	0	-0.059	-0.020	34.477	0.006	0.006	0.000	0.000	0.000	0.000
110	A	114	ASN	0	-0.019	0.009	33.797	0.001	0.001	0.000	0.000	0.000	0.000
111	A	115	GLU	-1	-0.842	-0.931	29.748	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	116	CYS	0	-0.050	-0.011	26.099	-0.013	-0.013	0.000	0.000	0.000	0.000
113	A	117	TYR	0	-0.025	-0.024	24.457	0.010	0.010	0.000	0.000	0.000	0.000
114	A	118	LEU	0	-0.063	-0.027	18.134	-0.016	-0.016	0.000	0.000	0.000	0.000
115	A	119	ILE	0	-0.009	-0.006	20.153	0.015	0.015	0.000	0.000	0.000	0.000
116	A	120	THR	0	0.011	-0.007	13.891	-0.012	-0.012	0.000	0.000	0.000	0.000
117	A	121	ILE	0	-0.047	-0.018	17.185	0.031	0.031	0.000	0.000	0.000	0.000
118	A	122	LEU	0	0.020	0.013	11.229	-0.051	-0.051	0.000	0.000	0.000	0.000
119	A	123	TRP	0	0.030	0.012	14.897	0.082	0.082	0.000	0.000	0.000	0.000
120	A	124	LEU	0	0.003	-0.012	11.171	-0.068	-0.068	0.000	0.000	0.000	0.000
121	A	125	HIS	0	-0.005	-0.023	14.353	0.083	0.083	0.000	0.000	0.000	0.000
122	A	126	LYS	1	0.863	0.966	15.389	0.087	0.087	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:ILE)