FMO DATABASE

FMODB ID: 726GK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1011977.878103
FMO2-HF: Nuclear repulsion	963447.251042
FMO2-HF: Total energy	-48530.627062
FMO2-MP2: Total energy	-48674.687828

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.
-4.794	1.1	3.298	-3.751	-5.438	-0.022

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 : 0.003 / q_NPA : 0.000

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	0.014	-0.007	3.433	-0.416	1.928	0.008	-1.002	-1.350	0.003
4	A	8	LYS	1	0.772	0.881	4.890	1.300	1.341	-0.001	-0.004	-0.036	0.000
5	A	9	ASP	-1	-0.844	-0.930	8.177	-0.584	-0.584	0.000	0.000	0.000	0.000
6	A	10	GLY	0	0.007	0.001	11.251	0.055	0.055	0.000	0.000	0.000	0.000
7	A	11	ARG	1	0.856	0.922	14.170	0.442	0.442	0.000	0.000	0.000	0.000
8	A	12	SER	0	0.045	0.027	14.746	-0.026	-0.026	0.000	0.000	0.000	0.000
9	A	13	ASP	-1	-0.896	-0.931	16.726	-0.360	-0.360	0.000	0.000	0.000	0.000
10	A	14	ASN	0	-0.075	-0.073	14.517	0.039	0.039	0.000	0.000	0.000	0.000
11	A	15	SER	0	0.013	0.015	17.402	0.027	0.027	0.000	0.000	0.000	0.000
12	A	16	PRO	0	-0.065	-0.028	19.210	0.012	0.012	0.000	0.000	0.000	0.000
13	A	17	LEU	0	-0.021	-0.005	21.982	0.027	0.027	0.000	0.000	0.000	0.000
14	A	18	PRO	0	0.024	-0.001	23.334	-0.019	-0.019	0.000	0.000	0.000	0.000
15	A	19	GLU	-1	-0.825	-0.912	20.102	-0.294	-0.294	0.000	0.000	0.000	0.000
16	A	20	ARG	1	0.955	0.975	23.587	0.147	0.147	0.000	0.000	0.000	0.000
17	A	21	LYS	1	0.876	0.931	26.990	0.119	0.119	0.000	0.000	0.000	0.000
18	A	22	LEU	0	0.025	0.029	20.056	0.013	0.013	0.000	0.000	0.000	0.000
19	A	23	VAL	0	0.038	0.018	24.506	0.010	0.010	0.000	0.000	0.000	0.000
20	A	24	THR	0	-0.052	-0.026	26.095	0.011	0.011	0.000	0.000	0.000	0.000
21	A	25	LEU	0	-0.028	0.006	24.693	0.009	0.009	0.000	0.000	0.000	0.000
22	A	26	ILE	0	0.015	0.014	22.066	0.011	0.011	0.000	0.000	0.000	0.000
23	A	27	GLN	0	-0.026	-0.019	26.495	0.001	0.001	0.000	0.000	0.000	0.000
24	A	28	GLU	-1	-0.826	-0.926	29.637	-0.085	-0.085	0.000	0.000	0.000	0.000
25	A	29	SER	0	-0.033	-0.027	28.434	0.009	0.009	0.000	0.000	0.000	0.000
26	A	30	TYR	0	-0.001	-0.008	28.760	0.007	0.007	0.000	0.000	0.000	0.000
27	A	31	ASP	-1	-0.781	-0.892	30.567	-0.072	-0.072	0.000	0.000	0.000	0.000
28	A	32	SER	0	-0.016	-0.018	33.441	0.003	0.003	0.000	0.000	0.000	0.000
29	A	33	LEU	0	-0.085	-0.041	30.164	0.005	0.005	0.000	0.000	0.000	0.000
30	A	34	LYS	1	0.788	0.895	32.344	0.046	0.046	0.000	0.000	0.000	0.000
31	A	35	ASP	-1	-0.861	-0.905	35.931	-0.040	-0.040	0.000	0.000	0.000	0.000
32	A	36	ASP	-1	-0.932	-0.969	39.141	-0.026	-0.026	0.000	0.000	0.000	0.000
33	A	37	ASN	0	-0.134	-0.074	42.288	0.005	0.005	0.000	0.000	0.000	0.000
34	A	38	GLU	-1	-0.955	-0.966	37.750	-0.029	-0.029	0.000	0.000	0.000	0.000
35	A	39	ILE	0	-0.043	-0.020	40.444	0.003	0.003	0.000	0.000	0.000	0.000
36	A	40	ASN	0	0.033	0.022	34.578	0.004	0.004	0.000	0.000	0.000	0.000
37	A	41	LEU	0	-0.045	-0.013	38.267	0.002	0.002	0.000	0.000	0.000	0.000
38	A	42	SER	0	-0.067	-0.050	35.380	0.005	0.005	0.000	0.000	0.000	0.000
39	A	43	THR	0	0.028	-0.001	33.933	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	44	GLU	-1	-0.855	-0.891	29.918	0.015	0.015	0.000	0.000	0.000	0.000
41	A	45	SER	0	0.026	0.000	27.750	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	46	THR	0	0.089	0.028	29.354	0.001	0.001	0.000	0.000	0.000	0.000
43	A	47	SER	0	0.003	0.014	23.689	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	48	ASN	0	-0.037	-0.028	25.563	-0.007	-0.007	0.000	0.000	0.000	0.000
45	A	49	LEU	0	0.024	0.019	26.871	0.002	0.002	0.000	0.000	0.000	0.000
46	A	50	LEU	0	0.032	0.022	25.352	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	51	ILE	0	-0.027	-0.019	21.541	-0.009	-0.009	0.000	0.000	0.000	0.000
48	A	52	LYS	1	0.790	0.895	24.205	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	53	LEU	0	0.066	0.043	26.774	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	54	VAL	0	-0.011	-0.008	22.534	-0.009	-0.009	0.000	0.000	0.000	0.000
51	A	55	LEU	0	-0.021	-0.016	20.213	-0.011	-0.011	0.000	0.000	0.000	0.000
52	A	56	GLU	-1	-0.872	-0.944	24.070	-0.037	-0.037	0.000	0.000	0.000	0.000
53	A	57	LYS	1	0.839	0.905	27.419	0.075	0.075	0.000	0.000	0.000	0.000
54	A	58	LEU	0	-0.003	0.010	20.835	-0.008	-0.008	0.000	0.000	0.000	0.000
55	A	59	GLU	-1	-0.965	-0.991	24.164	-0.037	-0.037	0.000	0.000	0.000	0.000
56	A	60	LYS	1	0.829	0.919	25.894	0.050	0.050	0.000	0.000	0.000	0.000
57	A	61	HIS	0	-0.051	-0.022	26.358	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	62	SER	0	0.001	-0.004	23.844	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	63	SER	0	0.087	0.057	23.996	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	64	LEU	0	0.015	0.011	22.189	0.013	0.013	0.000	0.000	0.000	0.000
61	A	65	TYR	0	0.002	0.011	16.256	0.015	0.015	0.000	0.000	0.000	0.000
62	A	66	LYS	1	0.927	0.970	16.832	-0.009	-0.009	0.000	0.000	0.000	0.000
63	A	67	TYR	0	0.022	-0.005	17.166	-0.042	-0.042	0.000	0.000	0.000	0.000
64	A	68	ILE	0	-0.002	-0.004	13.635	0.038	0.038	0.000	0.000	0.000	0.000
65	A	69	ALA	0	0.021	0.016	17.182	-0.038	-0.038	0.000	0.000	0.000	0.000
66	A	70	SER	0	-0.010	0.001	16.173	0.032	0.032	0.000	0.000	0.000	0.000
67	A	71	VAL	0	0.038	0.009	18.357	-0.027	-0.027	0.000	0.000	0.000	0.000
68	A	72	THR	0	0.014	0.016	18.274	0.023	0.023	0.000	0.000	0.000	0.000
69	A	73	THR	0	0.006	-0.014	20.773	-0.013	-0.013	0.000	0.000	0.000	0.000
70	A	74	LEU	0	-0.039	-0.002	24.499	0.010	0.010	0.000	0.000	0.000	0.000
71	A	75	ASN	0	0.026	0.004	26.100	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	76	ILE	0	-0.069	-0.027	29.348	0.005	0.005	0.000	0.000	0.000	0.000
73	A	77	GLU	-1	-0.831	-0.911	31.744	-0.010	-0.010	0.000	0.000	0.000	0.000
74	A	78	GLY	0	-0.071	-0.039	34.744	0.000	0.000	0.000	0.000	0.000	0.000
75	A	79	LEU	0	-0.088	-0.047	33.400	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	80	ASN	0	-0.006	-0.013	35.888	0.004	0.004	0.000	0.000	0.000	0.000
77	A	81	GLU	-1	-0.789	-0.909	29.839	-0.073	-0.073	0.000	0.000	0.000	0.000
78	A	82	GLU	-1	-0.828	-0.915	32.495	-0.054	-0.054	0.000	0.000	0.000	0.000
79	A	83	ASN	0	-0.099	-0.053	34.563	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	84	ALA	0	0.012	0.031	31.340	0.002	0.002	0.000	0.000	0.000	0.000
81	A	85	ASN	0	-0.090	-0.050	30.583	-0.005	-0.005	0.000	0.000	0.000	0.000
82	A	86	PHE	0	-0.002	-0.003	25.159	0.003	0.003	0.000	0.000	0.000	0.000
83	A	87	SER	0	-0.027	-0.017	21.338	-0.015	-0.015	0.000	0.000	0.000	0.000
84	A	88	LEU	0	0.036	0.016	20.081	0.008	0.008	0.000	0.000	0.000	0.000
85	A	89	LYS	1	0.936	0.964	16.378	0.215	0.215	0.000	0.000	0.000	0.000
86	A	90	ASN	0	0.064	0.016	13.218	-0.013	-0.013	0.000	0.000	0.000	0.000
87	A	91	ASP	-1	-0.901	-0.932	9.802	-0.446	-0.446	0.000	0.000	0.000	0.000
88	A	92	ILE	0	0.004	-0.005	7.991	0.101	0.101	0.000	0.000	0.000	0.000
89	A	93	GLY	0	0.013	0.010	4.027	-0.400	-0.328	0.000	-0.022	-0.050	0.000
90	A	94	ALA	0	-0.019	0.011	3.853	0.211	0.596	0.004	-0.106	-0.282	0.000
91	A	95	SER	0	-0.018	-0.021	2.463	-4.658	-2.229	3.272	-2.753	-2.947	-0.025
92	A	96	TRP	0	-0.047	-0.031	3.554	1.099	1.451	0.014	0.186	-0.551	0.000
93	A	97	GLU	-1	-0.847	-0.903	3.622	-3.765	-3.494	0.001	-0.050	-0.222	0.000
94	A	98	SER	0	-0.061	-0.053	5.645	0.656	0.656	0.000	0.000	0.000	0.000
95	A	99	LYS	1	0.834	0.897	7.658	1.823	1.823	0.000	0.000	0.000	0.000
96	A	100	LYS	1	0.849	0.949	11.845	0.347	0.347	0.000	0.000	0.000	0.000
97	A	101	ASP	-1	-0.739	-0.857	10.400	-0.295	-0.295	0.000	0.000	0.000	0.000
98	A	102	GLY	0	0.001	-0.009	11.779	-0.176	-0.176	0.000	0.000	0.000	0.000
99	A	103	ILE	0	0.000	0.005	10.545	0.085	0.085	0.000	0.000	0.000	0.000
100	A	104	PHE	0	0.018	0.009	13.884	-0.011	-0.011	0.000	0.000	0.000	0.000
101	A	105	ASN	0	-0.001	0.021	13.940	0.047	0.047	0.000	0.000	0.000	0.000
102	A	106	TYR	0	-0.031	-0.024	17.833	-0.009	-0.009	0.000	0.000	0.000	0.000
103	A	107	LYS	1	0.878	0.939	21.580	0.143	0.143	0.000	0.000	0.000	0.000
104	A	108	LEU	0	-0.023	0.006	23.962	0.000	0.000	0.000	0.000	0.000	0.000
105	A	109	GLU	-1	-0.855	-0.925	27.181	-0.083	-0.083	0.000	0.000	0.000	0.000
106	A	110	ASP	-1	-0.766	-0.868	29.896	-0.044	-0.044	0.000	0.000	0.000	0.000
107	A	111	LYS	1	0.812	0.883	32.468	0.074	0.074	0.000	0.000	0.000	0.000
108	A	112	ASN	0	-0.049	-0.018	35.350	0.004	0.004	0.000	0.000	0.000	0.000
109	A	113	ASN	0	-0.044	-0.033	34.798	0.007	0.007	0.000	0.000	0.000	0.000
110	A	114	ASN	0	0.013	0.024	33.864	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	115	GLU	-1	-0.802	-0.866	29.695	-0.034	-0.034	0.000	0.000	0.000	0.000
112	A	116	CYS	0	-0.060	-0.026	26.516	-0.012	-0.012	0.000	0.000	0.000	0.000
113	A	117	TYR	0	-0.042	-0.056	24.487	0.004	0.004	0.000	0.000	0.000	0.000
114	A	118	LEU	0	-0.078	-0.040	17.859	-0.014	-0.014	0.000	0.000	0.000	0.000
115	A	119	ILE	0	-0.011	0.003	20.015	0.011	0.011	0.000	0.000	0.000	0.000
116	A	120	THR	0	-0.008	-0.020	13.781	-0.011	-0.011	0.000	0.000	0.000	0.000
117	A	121	ILE	0	-0.034	-0.018	17.115	0.036	0.036	0.000	0.000	0.000	0.000
118	A	122	LEU	0	0.026	0.009	11.044	-0.055	-0.055	0.000	0.000	0.000	0.000
119	A	123	TRP	0	-0.026	0.002	14.516	0.082	0.082	0.000	0.000	0.000	0.000
120	A	124	LEU	0	0.019	0.005	11.237	-0.063	-0.063	0.000	0.000	0.000	0.000
121	A	125	HIS	0	0.025	-0.001	14.200	0.073	0.073	0.000	0.000	0.000	0.000
122	A	126	LYS	1	0.787	0.895	15.618	0.070	0.070	0.000	0.000	0.000	0.000

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