FMO DATABASE

FMODB ID: LZ6R9

Calculation Name: 4YK8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YK8

Chain ID: A

ChEMBL ID:

UniProt ID: O36019

Base Structure: X-ray

Registration Date: 2023-06-26

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	164
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1589057.88289
FMO2-HF: Nuclear repulsion	1526039.397973
FMO2-HF: Total energy	-63018.484917
FMO2-MP2: Total energy	-63205.143961

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:-2:GLY)

Summations of interaction energy for fragment #1(A:-2:GLY)

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.
-0.981	-0.171	-0.004	-0.406	-0.399	0.001

Interaction energy analysis for fragmet #1(A:-2:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / 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	0	HIS	0	0.019	0.008	3.875	-0.738	0.072	-0.004	-0.406	-0.399	0.001
4	A	1	MET	0	-0.007	0.002	5.884	0.592	0.592	0.000	0.000	0.000	0.000
5	A	2	THR	0	-0.002	0.003	9.046	-0.014	-0.014	0.000	0.000	0.000	0.000
6	A	3	ASN	0	-0.045	-0.022	12.562	0.096	0.096	0.000	0.000	0.000	0.000
7	A	4	THR	0	0.013	0.002	15.166	0.000	0.000	0.000	0.000	0.000	0.000
8	A	5	VAL	0	-0.009	0.017	18.575	0.028	0.028	0.000	0.000	0.000	0.000
9	A	6	THR	0	-0.025	-0.019	21.837	-0.008	-0.008	0.000	0.000	0.000	0.000
10	A	7	ILE	0	-0.026	-0.006	24.998	0.012	0.012	0.000	0.000	0.000	0.000
11	A	8	GLU	-1	-0.901	-0.955	28.236	-0.091	-0.091	0.000	0.000	0.000	0.000
12	A	9	LEU	0	-0.020	-0.017	31.555	0.004	0.004	0.000	0.000	0.000	0.000
13	A	10	LYS	1	0.918	0.966	34.408	0.075	0.075	0.000	0.000	0.000	0.000
14	A	11	ILE	0	0.019	0.037	36.914	0.003	0.003	0.000	0.000	0.000	0.000
15	A	12	GLY	0	0.055	0.037	40.369	0.000	0.000	0.000	0.000	0.000	0.000
16	A	13	TYR	0	-0.010	-0.029	42.384	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	14	LYS	1	0.864	0.952	43.506	0.054	0.054	0.000	0.000	0.000	0.000
18	A	15	TYR	0	0.090	0.025	41.803	0.000	0.000	0.000	0.000	0.000	0.000
19	A	16	ALA	0	0.022	0.035	39.272	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	17	ALA	0	0.078	0.018	37.666	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	18	GLU	-1	-0.973	-0.966	37.817	-0.081	-0.081	0.000	0.000	0.000	0.000
22	A	19	VAL	0	0.027	-0.017	35.980	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	20	VAL	0	0.003	0.006	32.363	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	21	LYS	1	0.932	0.974	32.730	0.089	0.089	0.000	0.000	0.000	0.000
25	A	22	ALA	0	0.018	0.012	33.158	-0.006	-0.006	0.000	0.000	0.000	0.000
26	A	23	VAL	0	0.047	0.029	29.274	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	24	LEU	0	0.026	0.019	27.675	-0.011	-0.011	0.000	0.000	0.000	0.000
28	A	25	GLY	0	0.014	0.009	28.493	-0.010	-0.010	0.000	0.000	0.000	0.000
29	A	26	VAL	0	0.039	0.006	29.071	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	27	ILE	0	-0.021	0.000	23.909	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	28	LEU	0	0.000	-0.017	24.154	-0.011	-0.011	0.000	0.000	0.000	0.000
32	A	29	PHE	0	-0.038	-0.008	25.945	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	30	HIS	0	-0.030	-0.014	24.190	0.011	0.011	0.000	0.000	0.000	0.000
34	A	31	ARG	1	0.788	0.847	18.255	0.235	0.235	0.000	0.000	0.000	0.000
35	A	32	GLN	0	-0.093	-0.028	21.796	-0.019	-0.019	0.000	0.000	0.000	0.000
36	A	33	PHE	0	0.027	0.000	18.878	0.011	0.011	0.000	0.000	0.000	0.000
37	A	34	SER	0	-0.049	0.006	24.430	0.016	0.016	0.000	0.000	0.000	0.000
38	A	35	THR	0	0.020	-0.008	27.143	0.001	0.001	0.000	0.000	0.000	0.000
39	A	36	VAL	0	0.036	0.025	29.735	0.000	0.000	0.000	0.000	0.000	0.000
40	A	37	PRO	0	-0.058	-0.020	32.473	0.005	0.005	0.000	0.000	0.000	0.000
41	A	38	ALA	0	0.058	0.024	35.200	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	39	ARG	1	0.860	0.930	36.152	0.077	0.077	0.000	0.000	0.000	0.000
43	A	40	THR	0	0.068	0.032	36.520	-0.005	-0.005	0.000	0.000	0.000	0.000
44	A	41	ILE	0	-0.087	-0.030	37.310	0.003	0.003	0.000	0.000	0.000	0.000
45	A	42	ASP	-1	-0.820	-0.918	39.647	-0.065	-0.065	0.000	0.000	0.000	0.000
46	A	43	VAL	0	-0.029	0.003	38.797	0.000	0.000	0.000	0.000	0.000	0.000
47	A	44	LEU	0	-0.069	-0.036	41.214	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	45	ASP	-1	-0.827	-0.895	43.339	-0.050	-0.050	0.000	0.000	0.000	0.000
49	A	46	ILE	0	-0.031	-0.003	37.489	0.000	0.000	0.000	0.000	0.000	0.000
50	A	47	THR	0	-0.008	-0.005	39.136	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	48	VAL	0	-0.028	-0.014	34.640	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	49	PRO	0	-0.034	-0.015	32.001	0.003	0.003	0.000	0.000	0.000	0.000
53	A	50	THR	0	-0.021	-0.026	34.088	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	51	LEU	0	0.000	0.010	28.615	0.002	0.002	0.000	0.000	0.000	0.000
55	A	52	VAL	0	-0.018	-0.013	33.273	0.002	0.002	0.000	0.000	0.000	0.000
56	A	53	GLY	0	0.041	0.000	34.048	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	54	ALA	0	-0.056	-0.016	35.417	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	55	GLU	-1	-0.836	-0.927	31.215	-0.154	-0.154	0.000	0.000	0.000	0.000
59	A	56	LEU	0	0.064	0.039	29.117	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	57	ASN	0	0.027	0.009	32.958	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	58	GLU	-1	-0.939	-0.946	35.968	-0.095	-0.095	0.000	0.000	0.000	0.000
62	A	59	GLN	0	-0.013	-0.031	29.090	-0.009	-0.009	0.000	0.000	0.000	0.000
63	A	60	LEU	0	-0.067	-0.034	30.218	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	61	ALA	0	-0.033	-0.034	33.476	0.001	0.001	0.000	0.000	0.000	0.000
65	A	62	THR	0	-0.008	-0.003	35.446	0.004	0.004	0.000	0.000	0.000	0.000
66	A	63	LYS	1	0.925	0.974	27.660	0.194	0.194	0.000	0.000	0.000	0.000
67	A	64	ALA	0	-0.001	0.000	33.804	0.000	0.000	0.000	0.000	0.000	0.000
68	A	65	ALA	0	-0.020	-0.013	34.935	0.004	0.004	0.000	0.000	0.000	0.000
69	A	66	GLU	-1	-0.959	-0.966	34.294	-0.128	-0.128	0.000	0.000	0.000	0.000
70	A	67	PHE	0	-0.026	0.023	31.989	0.001	0.001	0.000	0.000	0.000	0.000
71	A	68	ILE	0	0.006	-0.011	35.487	0.004	0.004	0.000	0.000	0.000	0.000
72	A	69	ASP	-1	-0.849	-0.928	38.337	-0.090	-0.090	0.000	0.000	0.000	0.000
73	A	70	THR	0	-0.037	-0.035	36.295	0.004	0.004	0.000	0.000	0.000	0.000
74	A	71	ILE	0	-0.077	-0.019	35.131	0.001	0.001	0.000	0.000	0.000	0.000
75	A	72	ARG	1	0.827	0.916	38.699	0.068	0.068	0.000	0.000	0.000	0.000
76	A	73	ASN	0	-0.053	-0.042	42.322	0.006	0.006	0.000	0.000	0.000	0.000
77	A	74	GLU	-1	-0.901	-0.908	39.274	-0.079	-0.079	0.000	0.000	0.000	0.000
78	A	75	ALA	0	-0.047	-0.037	37.168	0.001	0.001	0.000	0.000	0.000	0.000
79	A	76	GLY	0	-0.049	-0.032	38.798	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	77	ALA	0	-0.047	-0.027	39.479	0.004	0.004	0.000	0.000	0.000	0.000
81	A	78	ASN	0	-0.058	-0.049	35.142	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	79	GLY	0	0.099	0.055	33.554	0.001	0.001	0.000	0.000	0.000	0.000
83	A	80	GLN	0	-0.063	-0.053	27.827	-0.009	-0.009	0.000	0.000	0.000	0.000
84	A	81	MET	0	0.025	0.043	28.865	-0.008	-0.008	0.000	0.000	0.000	0.000
85	A	82	ILE	0	0.015	0.004	22.420	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	83	LEU	0	-0.017	0.000	22.475	-0.007	-0.007	0.000	0.000	0.000	0.000
87	A	84	LEU	0	-0.042	-0.020	18.797	-0.028	-0.028	0.000	0.000	0.000	0.000
88	A	85	LEU	0	0.028	0.022	17.143	0.021	0.021	0.000	0.000	0.000	0.000
89	A	86	TYR	0	0.006	-0.013	14.834	-0.096	-0.096	0.000	0.000	0.000	0.000
90	A	87	GLU	-1	-0.820	-0.920	9.676	-0.895	-0.895	0.000	0.000	0.000	0.000
91	A	88	ARG	1	0.898	0.943	13.612	0.521	0.521	0.000	0.000	0.000	0.000
92	A	89	SER	0	-0.005	-0.010	16.178	-0.005	-0.005	0.000	0.000	0.000	0.000
93	A	90	PRO	0	0.155	0.077	17.808	-0.010	-0.010	0.000	0.000	0.000	0.000
94	A	91	LYS	1	0.956	0.985	18.827	0.235	0.235	0.000	0.000	0.000	0.000
95	A	92	LYS	1	0.917	0.940	19.350	0.279	0.279	0.000	0.000	0.000	0.000
96	A	93	SER	0	-0.016	-0.003	14.605	0.013	0.013	0.000	0.000	0.000	0.000
97	A	94	TRP	0	0.055	0.027	14.611	-0.057	-0.057	0.000	0.000	0.000	0.000
98	A	95	PHE	0	-0.048	-0.015	15.961	0.001	0.001	0.000	0.000	0.000	0.000
99	A	96	GLY	0	0.015	0.003	13.768	0.002	0.002	0.000	0.000	0.000	0.000
100	A	97	LYS	1	0.869	0.940	12.918	0.429	0.429	0.000	0.000	0.000	0.000
101	A	98	GLY	0	0.016	0.024	9.260	-0.125	-0.125	0.000	0.000	0.000	0.000
102	A	99	ASN	0	-0.004	-0.012	8.181	-0.157	-0.157	0.000	0.000	0.000	0.000
103	A	100	THR	0	0.011	-0.011	10.921	0.061	0.061	0.000	0.000	0.000	0.000
104	A	101	ILE	0	-0.013	0.001	9.712	0.112	0.112	0.000	0.000	0.000	0.000
105	A	102	PRO	0	-0.019	0.011	12.129	-0.083	-0.083	0.000	0.000	0.000	0.000
106	A	103	TRP	0	0.058	0.018	11.383	-0.071	-0.071	0.000	0.000	0.000	0.000
107	A	104	GLU	-1	-0.784	-0.863	12.544	-0.273	-0.273	0.000	0.000	0.000	0.000
108	A	105	GLN	0	-0.050	-0.048	15.900	0.021	0.021	0.000	0.000	0.000	0.000
109	A	106	TRP	0	0.011	-0.001	18.779	0.031	0.031	0.000	0.000	0.000	0.000
110	A	107	ILE	0	0.025	0.023	22.320	0.002	0.002	0.000	0.000	0.000	0.000
111	A	108	LEU	0	0.029	0.009	24.893	0.012	0.012	0.000	0.000	0.000	0.000
112	A	109	HIS	0	0.002	-0.012	28.428	-0.006	-0.006	0.000	0.000	0.000	0.000
113	A	110	THR	0	0.009	0.006	30.433	0.008	0.008	0.000	0.000	0.000	0.000
114	A	111	THR	0	-0.006	-0.007	33.920	0.000	0.000	0.000	0.000	0.000	0.000
115	A	112	ILE	0	-0.064	-0.021	37.190	0.003	0.003	0.000	0.000	0.000	0.000
116	A	113	LEU	0	-0.008	0.000	40.446	0.002	0.002	0.000	0.000	0.000	0.000
117	A	114	GLU	-1	-0.911	-0.969	43.754	-0.056	-0.056	0.000	0.000	0.000	0.000
118	A	115	GLU	-1	-0.881	-0.953	46.317	-0.051	-0.051	0.000	0.000	0.000	0.000
119	A	116	GLY	0	-0.048	-0.025	49.832	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	117	ASP	-1	-0.922	-0.980	50.232	-0.048	-0.048	0.000	0.000	0.000	0.000
121	A	118	SER	0	0.037	0.024	44.844	0.000	0.000	0.000	0.000	0.000	0.000
122	A	119	TYR	0	-0.064	-0.035	44.803	-0.004	-0.004	0.000	0.000	0.000	0.000
123	A	120	GLN	0	0.029	0.017	44.803	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	121	GLU	-1	-0.853	-0.944	42.637	-0.052	-0.052	0.000	0.000	0.000	0.000
125	A	122	SER	0	-0.036	-0.037	40.591	-0.005	-0.005	0.000	0.000	0.000	0.000
126	A	123	SER	0	-0.022	-0.011	39.963	-0.005	-0.005	0.000	0.000	0.000	0.000
127	A	124	LEU	0	0.061	0.027	40.157	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	125	SER	0	-0.018	0.011	36.083	-0.004	-0.004	0.000	0.000	0.000	0.000
129	A	126	LEU	0	-0.001	-0.021	35.293	-0.006	-0.006	0.000	0.000	0.000	0.000
130	A	127	GLU	-1	-0.951	-0.964	35.058	-0.064	-0.064	0.000	0.000	0.000	0.000
131	A	128	ALA	0	0.050	0.023	34.487	-0.003	-0.003	0.000	0.000	0.000	0.000
132	A	129	ALA	0	-0.006	-0.013	31.396	-0.006	-0.006	0.000	0.000	0.000	0.000
133	A	130	VAL	0	-0.020	-0.022	30.268	-0.009	-0.009	0.000	0.000	0.000	0.000
134	A	131	GLU	-1	-0.944	-0.962	30.351	-0.074	-0.074	0.000	0.000	0.000	0.000
135	A	132	GLN	0	0.010	-0.003	28.085	0.004	0.004	0.000	0.000	0.000	0.000
136	A	133	ILE	0	-0.068	-0.022	25.699	-0.013	-0.013	0.000	0.000	0.000	0.000
137	A	134	VAL	0	0.020	0.012	25.397	-0.009	-0.009	0.000	0.000	0.000	0.000
138	A	135	GLN	0	0.013	-0.010	25.976	-0.004	-0.004	0.000	0.000	0.000	0.000
139	A	136	ALA	0	-0.028	-0.005	22.329	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	137	VAL	0	-0.050	-0.038	21.551	-0.013	-0.013	0.000	0.000	0.000	0.000
141	A	138	ASN	0	-0.103	-0.043	21.585	0.001	0.001	0.000	0.000	0.000	0.000
142	A	139	LEU	0	0.032	0.030	20.944	0.018	0.018	0.000	0.000	0.000	0.000
143	A	140	ARG	1	0.839	0.918	16.284	0.067	0.067	0.000	0.000	0.000	0.000
144	A	141	SER	0	0.074	0.021	15.630	-0.039	-0.039	0.000	0.000	0.000	0.000
145	A	142	LEU	0	0.049	0.024	15.382	-0.023	-0.023	0.000	0.000	0.000	0.000
146	A	143	SER	0	-0.110	-0.042	13.953	0.012	0.012	0.000	0.000	0.000	0.000
147	A	144	TYR	0	-0.043	-0.037	8.604	0.023	0.023	0.000	0.000	0.000	0.000
148	A	145	LEU	0	0.042	0.062	12.631	-0.042	-0.042	0.000	0.000	0.000	0.000
149	A	146	PRO	0	-0.008	0.003	11.270	0.019	0.019	0.000	0.000	0.000	0.000
150	A	147	PRO	0	0.022	0.030	11.256	0.085	0.085	0.000	0.000	0.000	0.000
151	A	148	VAL	0	0.033	0.026	14.473	-0.039	-0.039	0.000	0.000	0.000	0.000
152	A	149	ALA	0	-0.046	-0.019	15.543	0.025	0.025	0.000	0.000	0.000	0.000
153	A	150	MET	0	-0.101	-0.039	17.614	-0.003	-0.003	0.000	0.000	0.000	0.000
154	A	151	ASP	-1	-0.849	-0.925	21.147	-0.188	-0.188	0.000	0.000	0.000	0.000
155	A	152	SER	0	-0.077	-0.050	23.913	0.014	0.014	0.000	0.000	0.000	0.000
156	A	153	GLY	0	0.055	0.026	23.103	0.014	0.014	0.000	0.000	0.000	0.000
157	A	154	ASN	0	-0.018	-0.008	22.677	0.000	0.000	0.000	0.000	0.000	0.000
158	A	155	TYR	0	-0.023	-0.037	15.669	-0.004	-0.004	0.000	0.000	0.000	0.000
159	A	156	PRO	0	-0.083	-0.052	17.746	0.026	0.026	0.000	0.000	0.000	0.000
160	A	157	TYR	0	0.028	0.015	19.374	-0.031	-0.031	0.000	0.000	0.000	0.000
161	A	158	GLU	-1	-0.949	-0.970	21.213	-0.306	-0.306	0.000	0.000	0.000	0.000
162	A	159	ILE	0	-0.001	-0.027	23.451	0.001	0.001	0.000	0.000	0.000	0.000
163	A	160	VAL	0	0.000	0.010	23.169	0.014	0.014	0.000	0.000	0.000	0.000
164	A	161	THR	0	0.057	0.039	26.202	0.009	0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-2:GLY)