FMO DATABASE

FMODB ID: 942Q2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1587754.442689
FMO2-HF: Nuclear repulsion	1524734.691776
FMO2-HF: Total energy	-63019.750913
FMO2-MP2: Total energy	-63206.242729

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.
-0.829	0.48	-0.006	-0.729	-0.575	0.003

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 : 0.025 / q_NPA : 0.013

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	0.012	0.006	3.875	-0.457	0.852	-0.006	-0.729	-0.575	0.003
4	A	1	MET	0	-0.009	0.000	5.293	0.454	0.454	0.000	0.000	0.000	0.000
5	A	2	THR	0	-0.012	-0.013	9.055	0.035	0.035	0.000	0.000	0.000	0.000
6	A	3	ASN	0	-0.060	-0.028	12.575	0.052	0.052	0.000	0.000	0.000	0.000
7	A	4	THR	0	0.023	0.003	15.171	0.016	0.016	0.000	0.000	0.000	0.000
8	A	5	VAL	0	0.000	0.018	18.583	0.025	0.025	0.000	0.000	0.000	0.000
9	A	6	THR	0	-0.020	-0.018	21.842	-0.010	-0.010	0.000	0.000	0.000	0.000
10	A	7	ILE	0	-0.015	-0.002	25.006	0.014	0.014	0.000	0.000	0.000	0.000
11	A	8	GLU	-1	-0.843	-0.902	28.243	-0.129	-0.129	0.000	0.000	0.000	0.000
12	A	9	LEU	0	-0.021	-0.016	31.563	0.009	0.009	0.000	0.000	0.000	0.000
13	A	10	LYS	1	0.854	0.912	34.418	0.106	0.106	0.000	0.000	0.000	0.000
14	A	11	ILE	0	0.014	0.026	36.708	0.005	0.005	0.000	0.000	0.000	0.000
15	A	12	GLY	0	0.069	0.044	40.381	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	13	TYR	0	-0.012	-0.037	42.458	0.001	0.001	0.000	0.000	0.000	0.000
17	A	14	LYS	1	0.848	0.939	43.526	0.063	0.063	0.000	0.000	0.000	0.000
18	A	15	TYR	0	0.089	0.029	41.800	0.001	0.001	0.000	0.000	0.000	0.000
19	A	16	ALA	0	0.014	0.034	39.272	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	17	ALA	0	0.072	0.023	37.686	-0.005	-0.005	0.000	0.000	0.000	0.000
21	A	18	GLU	-1	-0.897	-0.934	37.836	-0.074	-0.074	0.000	0.000	0.000	0.000
22	A	19	VAL	0	0.024	-0.015	36.055	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	20	VAL	0	-0.009	-0.005	32.394	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	21	LYS	1	0.860	0.935	32.747	0.075	0.075	0.000	0.000	0.000	0.000
25	A	22	ALA	0	0.007	0.007	33.173	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	23	VAL	0	0.058	0.027	29.379	0.001	0.001	0.000	0.000	0.000	0.000
27	A	24	LEU	0	0.034	0.022	27.622	-0.006	-0.006	0.000	0.000	0.000	0.000
28	A	25	GLY	0	0.007	0.008	28.508	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	26	VAL	0	0.033	0.002	29.206	0.006	0.006	0.000	0.000	0.000	0.000
30	A	27	ILE	0	-0.020	0.002	23.758	0.001	0.001	0.000	0.000	0.000	0.000
31	A	28	LEU	0	0.000	-0.013	24.347	0.000	0.000	0.000	0.000	0.000	0.000
32	A	29	PHE	0	-0.029	-0.001	25.957	0.008	0.008	0.000	0.000	0.000	0.000
33	A	30	HIS	0	-0.041	-0.023	24.229	0.021	0.021	0.000	0.000	0.000	0.000
34	A	31	ARG	1	0.748	0.807	18.708	0.159	0.159	0.000	0.000	0.000	0.000
35	A	32	GLN	0	-0.095	-0.034	21.809	-0.009	-0.009	0.000	0.000	0.000	0.000
36	A	33	PHE	0	0.031	0.002	18.984	0.009	0.009	0.000	0.000	0.000	0.000
37	A	34	SER	0	-0.024	0.018	24.438	0.010	0.010	0.000	0.000	0.000	0.000
38	A	35	THR	0	-0.002	-0.016	27.154	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	36	VAL	0	0.037	0.020	29.937	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	37	PRO	0	-0.047	-0.010	32.482	0.005	0.005	0.000	0.000	0.000	0.000
41	A	38	ALA	0	0.050	0.019	35.207	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	39	ARG	1	0.864	0.930	36.158	0.031	0.031	0.000	0.000	0.000	0.000
43	A	40	THR	0	0.060	0.035	36.527	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	41	ILE	0	-0.056	-0.013	37.229	0.003	0.003	0.000	0.000	0.000	0.000
45	A	42	ASP	-1	-0.824	-0.903	39.653	-0.044	-0.044	0.000	0.000	0.000	0.000
46	A	43	VAL	0	-0.026	0.001	39.087	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	44	LEU	0	-0.045	-0.020	41.139	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	45	ASP	-1	-0.795	-0.835	43.374	-0.046	-0.046	0.000	0.000	0.000	0.000
49	A	46	ILE	0	-0.017	0.000	37.505	0.002	0.002	0.000	0.000	0.000	0.000
50	A	47	THR	0	-0.029	-0.034	39.489	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	48	VAL	0	-0.028	-0.010	34.662	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	49	PRO	0	-0.026	-0.016	32.169	0.003	0.003	0.000	0.000	0.000	0.000
53	A	50	THR	0	0.007	-0.011	34.097	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	51	LEU	0	-0.009	0.010	28.565	0.006	0.006	0.000	0.000	0.000	0.000
55	A	52	VAL	0	-0.014	-0.015	33.287	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	53	GLY	0	0.046	0.005	34.065	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	54	ALA	0	-0.037	-0.006	35.437	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	55	GLU	-1	-0.822	-0.924	30.977	-0.120	-0.120	0.000	0.000	0.000	0.000
59	A	56	LEU	0	0.046	0.040	28.987	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	57	ASN	0	-0.048	-0.037	32.981	-0.005	-0.005	0.000	0.000	0.000	0.000
61	A	58	GLU	-1	-0.914	-0.936	35.990	-0.079	-0.079	0.000	0.000	0.000	0.000
62	A	59	GLN	0	-0.014	-0.020	28.885	-0.018	-0.018	0.000	0.000	0.000	0.000
63	A	60	LEU	0	-0.058	-0.032	30.073	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	61	ALA	0	0.010	-0.004	33.500	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	62	THR	0	-0.030	-0.017	35.520	0.001	0.001	0.000	0.000	0.000	0.000
66	A	63	LYS	1	0.918	0.955	28.006	0.179	0.179	0.000	0.000	0.000	0.000
67	A	64	ALA	0	0.016	-0.002	33.832	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	65	ALA	0	-0.020	-0.011	34.959	0.001	0.001	0.000	0.000	0.000	0.000
69	A	66	GLU	-1	-0.950	-0.967	34.281	-0.145	-0.145	0.000	0.000	0.000	0.000
70	A	67	PHE	0	-0.029	-0.003	32.201	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	68	ILE	0	0.006	-0.007	35.513	0.001	0.001	0.000	0.000	0.000	0.000
72	A	69	ASP	-1	-0.894	-0.959	38.360	-0.105	-0.105	0.000	0.000	0.000	0.000
73	A	70	THR	0	0.027	0.018	36.378	0.002	0.002	0.000	0.000	0.000	0.000
74	A	71	ILE	0	-0.065	-0.008	34.778	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	72	ARG	1	0.766	0.854	38.723	0.085	0.085	0.000	0.000	0.000	0.000
76	A	73	ASN	0	-0.095	-0.062	42.323	0.007	0.007	0.000	0.000	0.000	0.000
77	A	74	GLU	-1	-0.902	-0.920	39.592	-0.114	-0.114	0.000	0.000	0.000	0.000
78	A	75	ALA	0	-0.033	-0.020	37.183	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	76	GLY	0	-0.053	-0.034	38.809	-0.003	-0.003	0.000	0.000	0.000	0.000
80	A	77	ALA	0	-0.047	-0.025	39.501	0.007	0.007	0.000	0.000	0.000	0.000
81	A	78	ASN	0	-0.062	-0.050	35.168	-0.006	-0.006	0.000	0.000	0.000	0.000
82	A	79	GLY	0	0.089	0.044	33.572	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	80	GLN	0	-0.086	-0.060	27.465	-0.015	-0.015	0.000	0.000	0.000	0.000
84	A	81	MET	0	0.012	0.049	28.901	-0.008	-0.008	0.000	0.000	0.000	0.000
85	A	82	ILE	0	0.007	0.000	22.600	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	83	LEU	0	-0.014	0.006	22.429	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	84	LEU	0	-0.046	-0.018	18.757	-0.035	-0.035	0.000	0.000	0.000	0.000
88	A	85	LEU	0	0.017	0.011	17.295	0.035	0.035	0.000	0.000	0.000	0.000
89	A	86	TYR	0	-0.013	-0.047	14.854	-0.103	-0.103	0.000	0.000	0.000	0.000
90	A	87	GLU	-1	-0.796	-0.895	9.770	-0.424	-0.424	0.000	0.000	0.000	0.000
91	A	88	ARG	1	0.879	0.914	13.735	0.215	0.215	0.000	0.000	0.000	0.000
92	A	89	SER	0	0.004	0.000	16.210	-0.033	-0.033	0.000	0.000	0.000	0.000
93	A	90	PRO	0	0.149	0.072	17.774	0.001	0.001	0.000	0.000	0.000	0.000
94	A	91	LYS	1	0.941	0.978	18.833	0.182	0.182	0.000	0.000	0.000	0.000
95	A	92	LYS	1	0.931	0.932	19.356	0.158	0.158	0.000	0.000	0.000	0.000
96	A	93	SER	0	-0.002	0.011	14.496	0.035	0.035	0.000	0.000	0.000	0.000
97	A	94	TRP	0	0.047	0.025	14.530	-0.043	-0.043	0.000	0.000	0.000	0.000
98	A	95	PHE	0	-0.058	-0.021	15.929	-0.008	-0.008	0.000	0.000	0.000	0.000
99	A	96	GLY	0	0.011	0.000	13.664	0.030	0.030	0.000	0.000	0.000	0.000
100	A	97	LYS	1	0.873	0.954	12.687	0.272	0.272	0.000	0.000	0.000	0.000
101	A	98	GLY	0	0.021	0.028	9.150	-0.066	-0.066	0.000	0.000	0.000	0.000
102	A	99	ASN	0	-0.013	-0.017	8.093	-0.305	-0.305	0.000	0.000	0.000	0.000
103	A	100	THR	0	0.015	-0.014	10.919	0.142	0.142	0.000	0.000	0.000	0.000
104	A	101	ILE	0	-0.017	0.004	9.853	0.087	0.087	0.000	0.000	0.000	0.000
105	A	102	PRO	0	0.001	0.020	12.161	-0.036	-0.036	0.000	0.000	0.000	0.000
106	A	103	TRP	0	0.048	0.025	11.429	-0.093	-0.093	0.000	0.000	0.000	0.000
107	A	104	GLU	-1	-0.777	-0.847	12.563	-0.209	-0.209	0.000	0.000	0.000	0.000
108	A	105	GLN	0	-0.041	-0.029	15.914	0.003	0.003	0.000	0.000	0.000	0.000
109	A	106	TRP	0	0.025	0.000	18.795	0.020	0.020	0.000	0.000	0.000	0.000
110	A	107	ILE	0	0.024	0.022	21.953	0.003	0.003	0.000	0.000	0.000	0.000
111	A	108	LEU	0	0.026	0.011	24.909	0.014	0.014	0.000	0.000	0.000	0.000
112	A	109	HIS	0	0.031	0.009	28.442	-0.010	-0.010	0.000	0.000	0.000	0.000
113	A	110	THR	0	-0.001	0.000	30.448	0.013	0.013	0.000	0.000	0.000	0.000
114	A	111	THR	0	-0.023	-0.014	33.936	-0.004	-0.004	0.000	0.000	0.000	0.000
115	A	112	ILE	0	-0.040	-0.018	37.205	0.006	0.006	0.000	0.000	0.000	0.000
116	A	113	LEU	0	-0.040	-0.009	40.462	0.000	0.000	0.000	0.000	0.000	0.000
117	A	114	GLU	-1	-0.830	-0.885	43.768	-0.073	-0.073	0.000	0.000	0.000	0.000
118	A	115	GLU	-1	-0.808	-0.897	46.579	-0.069	-0.069	0.000	0.000	0.000	0.000
119	A	116	GLY	0	-0.049	-0.018	49.845	0.000	0.000	0.000	0.000	0.000	0.000
120	A	117	ASP	-1	-0.886	-0.968	49.985	-0.053	-0.053	0.000	0.000	0.000	0.000
121	A	118	SER	0	-0.014	-0.026	45.120	0.001	0.001	0.000	0.000	0.000	0.000
122	A	119	TYR	0	-0.098	-0.055	44.812	-0.005	-0.005	0.000	0.000	0.000	0.000
123	A	120	GLN	0	-0.028	-0.019	44.810	0.001	0.001	0.000	0.000	0.000	0.000
124	A	121	GLU	-1	-0.833	-0.928	42.727	-0.062	-0.062	0.000	0.000	0.000	0.000
125	A	122	SER	0	-0.021	-0.032	40.602	-0.006	-0.006	0.000	0.000	0.000	0.000
126	A	123	SER	0	-0.032	-0.056	39.969	-0.004	-0.004	0.000	0.000	0.000	0.000
127	A	124	LEU	0	0.029	0.020	40.160	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	125	SER	0	-0.022	0.009	35.975	-0.005	-0.005	0.000	0.000	0.000	0.000
129	A	126	LEU	0	-0.008	-0.019	35.038	-0.006	-0.006	0.000	0.000	0.000	0.000
130	A	127	GLU	-1	-0.932	-0.960	35.062	-0.057	-0.057	0.000	0.000	0.000	0.000
131	A	128	ALA	0	0.027	0.011	34.522	0.000	0.000	0.000	0.000	0.000	0.000
132	A	129	ALA	0	0.005	-0.008	31.401	-0.005	-0.005	0.000	0.000	0.000	0.000
133	A	130	VAL	0	-0.015	-0.022	30.270	-0.006	-0.006	0.000	0.000	0.000	0.000
134	A	131	GLU	-1	-0.900	-0.941	30.350	-0.064	-0.064	0.000	0.000	0.000	0.000
135	A	132	GLN	0	0.011	-0.008	28.056	0.004	0.004	0.000	0.000	0.000	0.000
136	A	133	ILE	0	-0.051	-0.010	25.546	-0.012	-0.012	0.000	0.000	0.000	0.000
137	A	134	VAL	0	0.010	0.007	25.395	-0.002	-0.002	0.000	0.000	0.000	0.000
138	A	135	GLN	0	-0.028	-0.013	25.968	-0.003	-0.003	0.000	0.000	0.000	0.000
139	A	136	ALA	0	-0.032	-0.009	22.365	0.002	0.002	0.000	0.000	0.000	0.000
140	A	137	VAL	0	-0.041	-0.030	21.543	-0.004	-0.004	0.000	0.000	0.000	0.000
141	A	138	ASN	0	-0.127	-0.061	21.575	0.024	0.024	0.000	0.000	0.000	0.000
142	A	139	LEU	0	0.058	0.038	21.102	0.013	0.013	0.000	0.000	0.000	0.000
143	A	140	ARG	1	0.817	0.904	16.368	0.019	0.019	0.000	0.000	0.000	0.000
144	A	141	SER	0	0.089	0.031	15.604	-0.047	-0.047	0.000	0.000	0.000	0.000
145	A	142	LEU	0	0.029	0.016	15.371	0.010	0.010	0.000	0.000	0.000	0.000
146	A	143	SER	0	-0.105	-0.039	14.094	0.024	0.024	0.000	0.000	0.000	0.000
147	A	144	TYR	0	-0.067	-0.054	8.919	0.154	0.154	0.000	0.000	0.000	0.000
148	A	145	LEU	0	0.035	0.057	12.618	-0.086	-0.086	0.000	0.000	0.000	0.000
149	A	146	PRO	0	0.018	0.016	11.267	0.072	0.072	0.000	0.000	0.000	0.000
150	A	147	PRO	0	0.003	0.024	11.489	0.034	0.034	0.000	0.000	0.000	0.000
151	A	148	VAL	0	0.025	0.013	14.480	-0.056	-0.056	0.000	0.000	0.000	0.000
152	A	149	ALA	0	-0.041	-0.015	15.542	0.026	0.026	0.000	0.000	0.000	0.000
153	A	150	MET	0	-0.051	-0.016	17.634	-0.012	-0.012	0.000	0.000	0.000	0.000
154	A	151	ASP	-1	-0.857	-0.921	21.169	-0.014	-0.014	0.000	0.000	0.000	0.000
155	A	152	SER	0	-0.075	-0.044	24.098	0.001	0.001	0.000	0.000	0.000	0.000
156	A	153	GLY	0	0.021	0.008	23.117	0.005	0.005	0.000	0.000	0.000	0.000
157	A	154	ASN	0	-0.008	-0.008	22.680	0.004	0.004	0.000	0.000	0.000	0.000
158	A	155	TYR	0	-0.016	-0.033	16.014	-0.005	-0.005	0.000	0.000	0.000	0.000
159	A	156	PRO	0	-0.068	-0.045	17.872	0.004	0.004	0.000	0.000	0.000	0.000
160	A	157	TYR	0	0.029	0.025	19.401	-0.031	-0.031	0.000	0.000	0.000	0.000
161	A	158	GLU	-1	-0.919	-0.937	21.113	-0.329	-0.329	0.000	0.000	0.000	0.000
162	A	159	ILE	0	0.001	-0.027	23.480	0.001	0.001	0.000	0.000	0.000	0.000
163	A	160	VAL	0	-0.002	0.014	23.198	0.014	0.014	0.000	0.000	0.000	0.000
164	A	161	THR	0	0.050	0.035	26.232	0.008	0.008	0.000	0.000	0.000	0.000

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