FMO DATABASE

FMODB ID: 9GN22

Calculation Name: 4YKB-A-Xray319

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YKB

Chain ID: A

ChEMBL ID:

UniProt ID: A8I5N5

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	160
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1698519.934223
FMO2-HF: Nuclear repulsion	1634126.842469
FMO2-HF: Total energy	-64393.091755
FMO2-MP2: Total energy	-64583.057083

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:80:ACE )

Summations of interaction energy for fragment #1(A:80:ACE )

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.
-0.797	0.605	-0.006	-0.708	-0.688	-0.002

Interaction energy analysis for fragmet #1(A:80:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.019

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	82	GLY	0	0.019	0.022	3.859	0.293	1.695	-0.006	-0.708	-0.688	-0.002
4	A	83	LYS	1	0.956	0.993	6.009	0.696	0.696	0.000	0.000	0.000	0.000
5	A	84	GLU	-1	-0.885	-0.967	7.199	-0.978	-0.978	0.000	0.000	0.000	0.000
6	A	85	ALA	0	-0.004	0.008	6.036	0.178	0.178	0.000	0.000	0.000	0.000
7	A	86	VAL	0	-0.076	-0.033	8.060	0.194	0.194	0.000	0.000	0.000	0.000
8	A	87	MET	0	-0.055	-0.036	11.259	0.099	0.099	0.000	0.000	0.000	0.000
9	A	88	GLU	-1	-0.934	-0.949	8.582	-0.732	-0.732	0.000	0.000	0.000	0.000
10	A	89	VAL	0	-0.069	-0.019	12.665	0.072	0.072	0.000	0.000	0.000	0.000
11	A	90	GLN	0	0.017	0.010	14.517	0.003	0.003	0.000	0.000	0.000	0.000
12	A	91	LEU	0	-0.003	-0.006	17.522	0.019	0.019	0.000	0.000	0.000	0.000
13	A	92	SER	0	-0.030	-0.012	20.509	0.009	0.009	0.000	0.000	0.000	0.000
14	A	93	SER	0	0.008	-0.011	23.555	0.006	0.006	0.000	0.000	0.000	0.000
15	A	94	THR	0	-0.095	-0.045	26.555	0.001	0.001	0.000	0.000	0.000	0.000
16	A	95	ALA	0	-0.012	-0.008	29.510	0.002	0.002	0.000	0.000	0.000	0.000
17	A	96	GLY	0	-0.011	-0.001	30.178	0.001	0.001	0.000	0.000	0.000	0.000
18	A	97	ILE	0	-0.040	-0.019	26.072	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	98	ASP	-1	-0.820	-0.879	25.097	-0.101	-0.101	0.000	0.000	0.000	0.000
20	A	99	TYR	0	-0.050	-0.074	20.900	0.003	0.003	0.000	0.000	0.000	0.000
21	A	100	THR	0	-0.015	-0.040	20.850	-0.009	-0.009	0.000	0.000	0.000	0.000
22	A	101	VAL	0	0.073	0.053	20.672	-0.014	-0.014	0.000	0.000	0.000	0.000
23	A	102	LEU	0	0.022	0.012	18.813	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	103	ARG	1	0.815	0.894	16.287	0.194	0.194	0.000	0.000	0.000	0.000
25	A	104	ASP	-1	-0.818	-0.899	16.214	-0.218	-0.218	0.000	0.000	0.000	0.000
26	A	105	HIS	0	-0.053	-0.033	17.420	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	106	LEU	0	-0.049	-0.045	14.323	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	107	ALA	0	-0.024	-0.007	12.449	-0.015	-0.015	0.000	0.000	0.000	0.000
29	A	108	ASN	0	-0.058	-0.039	12.324	-0.095	-0.095	0.000	0.000	0.000	0.000
30	A	109	GLY	0	0.010	0.025	13.718	0.013	0.013	0.000	0.000	0.000	0.000
31	A	110	GLU	-1	-0.876	-0.921	14.250	-0.091	-0.091	0.000	0.000	0.000	0.000
32	A	111	PHE	0	0.036	-0.009	12.149	0.011	0.011	0.000	0.000	0.000	0.000
33	A	112	ARG	1	0.873	0.926	18.159	0.016	0.016	0.000	0.000	0.000	0.000
34	A	113	GLU	-1	-0.840	-0.928	21.584	-0.049	-0.049	0.000	0.000	0.000	0.000
35	A	114	ALA	0	0.052	0.034	18.735	0.001	0.001	0.000	0.000	0.000	0.000
36	A	115	GLU	-1	-0.860	-0.918	20.707	0.014	0.014	0.000	0.000	0.000	0.000
37	A	116	ASP	-1	-0.830	-0.899	22.455	-0.011	-0.011	0.000	0.000	0.000	0.000
38	A	117	GLU	-1	-0.877	-0.949	22.817	-0.052	-0.052	0.000	0.000	0.000	0.000
39	A	118	THR	0	-0.023	-0.057	21.551	0.002	0.002	0.000	0.000	0.000	0.000
40	A	119	ARG	1	0.838	0.912	23.834	0.007	0.007	0.000	0.000	0.000	0.000
41	A	120	ALA	0	0.026	0.013	27.247	0.002	0.002	0.000	0.000	0.000	0.000
42	A	121	LEU	0	-0.002	-0.003	23.745	0.000	0.000	0.000	0.000	0.000	0.000
43	A	122	LEU	0	0.002	0.012	26.579	0.002	0.002	0.000	0.000	0.000	0.000
44	A	123	ILE	0	-0.047	-0.021	28.531	0.002	0.002	0.000	0.000	0.000	0.000
45	A	124	LYS	1	0.909	0.949	28.479	0.044	0.044	0.000	0.000	0.000	0.000
46	A	125	LEU	0	-0.015	-0.009	26.503	0.001	0.001	0.000	0.000	0.000	0.000
47	A	126	ALA	0	-0.050	-0.004	31.189	0.002	0.002	0.000	0.000	0.000	0.000
48	A	127	GLY	0	0.033	0.021	33.780	0.002	0.002	0.000	0.000	0.000	0.000
49	A	128	PRO	0	0.022	-0.012	36.534	0.001	0.001	0.000	0.000	0.000	0.000
50	A	129	GLU	-1	-0.805	-0.886	39.386	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	130	ALA	0	0.009	-0.001	35.763	0.001	0.001	0.000	0.000	0.000	0.000
52	A	131	VAL	0	0.010	0.011	34.900	0.000	0.000	0.000	0.000	0.000	0.000
53	A	132	LYS	1	0.787	0.897	37.234	0.008	0.008	0.000	0.000	0.000	0.000
54	A	133	ARG	1	0.761	0.867	38.392	0.003	0.003	0.000	0.000	0.000	0.000
55	A	134	ASN	0	0.009	0.016	35.113	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	135	TRP	0	0.034	0.006	34.748	0.002	0.002	0.000	0.000	0.000	0.000
57	A	136	VAL	0	0.045	0.025	31.980	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	137	TYR	0	-0.040	-0.027	35.107	0.003	0.003	0.000	0.000	0.000	0.000
59	A	138	PHE	0	0.044	0.004	34.646	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	139	THR	0	-0.033	-0.014	35.261	0.001	0.001	0.000	0.000	0.000	0.000
61	A	140	GLU	-1	-0.766	-0.882	35.822	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	141	VAL	0	0.013	0.020	30.259	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	142	LYS	1	0.913	0.953	32.073	-0.013	-0.013	0.000	0.000	0.000	0.000
64	A	143	ASN	0	-0.004	0.003	33.933	0.000	0.000	0.000	0.000	0.000	0.000
65	A	144	ILE	0	-0.006	0.026	28.031	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	145	SER	0	0.013	-0.004	28.419	0.004	0.004	0.000	0.000	0.000	0.000
67	A	146	VAL	0	0.044	-0.003	25.446	0.001	0.001	0.000	0.000	0.000	0.000
68	A	147	THR	0	-0.011	-0.005	24.396	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	148	ASP	-1	-0.652	-0.759	23.259	-0.041	-0.041	0.000	0.000	0.000	0.000
70	A	149	PHE	0	0.042	0.011	23.155	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	150	GLN	0	0.006	-0.014	20.722	0.012	0.012	0.000	0.000	0.000	0.000
72	A	151	THR	0	-0.021	-0.002	18.980	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	152	LEU	0	0.032	0.016	18.208	-0.008	-0.008	0.000	0.000	0.000	0.000
74	A	153	ASP	-1	-0.781	-0.864	17.761	0.059	0.059	0.000	0.000	0.000	0.000
75	A	154	ASN	0	-0.041	-0.024	14.924	0.032	0.032	0.000	0.000	0.000	0.000
76	A	155	LEU	0	0.036	0.031	13.424	-0.007	-0.007	0.000	0.000	0.000	0.000
77	A	156	TRP	0	0.036	0.010	13.341	-0.005	-0.005	0.000	0.000	0.000	0.000
78	A	157	LYS	1	0.851	0.952	11.469	-0.051	-0.051	0.000	0.000	0.000	0.000
79	A	158	ALA	0	-0.017	-0.017	9.432	0.077	0.077	0.000	0.000	0.000	0.000
80	A	159	SER	0	-0.026	-0.010	8.559	-0.039	-0.039	0.000	0.000	0.000	0.000
81	A	160	SER	0	0.034	-0.020	9.982	0.047	0.047	0.000	0.000	0.000	0.000
82	A	161	ASN	0	-0.020	-0.015	5.259	0.111	0.111	0.000	0.000	0.000	0.000
83	A	162	ASN	0	-0.010	-0.015	7.357	-0.049	-0.049	0.000	0.000	0.000	0.000
84	A	163	LYS	1	0.821	0.913	10.596	-0.367	-0.367	0.000	0.000	0.000	0.000
85	A	164	PHE	0	-0.006	-0.006	12.789	-0.028	-0.028	0.000	0.000	0.000	0.000
86	A	165	GLY	0	0.042	0.013	14.676	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	166	TYR	0	0.030	0.017	17.405	0.007	0.007	0.000	0.000	0.000	0.000
88	A	167	SER	0	-0.060	-0.059	17.824	0.015	0.015	0.000	0.000	0.000	0.000
89	A	168	VAL	0	-0.017	0.009	15.041	0.007	0.007	0.000	0.000	0.000	0.000
90	A	169	GLN	0	0.013	-0.015	18.266	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	170	LYS	1	0.854	0.917	21.471	-0.057	-0.057	0.000	0.000	0.000	0.000
92	A	171	GLU	-1	-0.826	-0.864	17.827	0.203	0.203	0.000	0.000	0.000	0.000
93	A	172	ILE	0	0.002	-0.004	18.656	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	173	TRP	0	-0.016	-0.015	22.606	-0.007	-0.007	0.000	0.000	0.000	0.000
95	A	174	VAL	0	-0.019	-0.026	25.389	-0.006	-0.006	0.000	0.000	0.000	0.000
96	A	175	GLN	0	0.042	0.037	21.766	-0.009	-0.009	0.000	0.000	0.000	0.000
97	A	176	ASN	0	-0.071	-0.051	25.390	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	177	GLN	0	0.040	0.018	28.314	-0.011	-0.011	0.000	0.000	0.000	0.000
99	A	178	LYS	1	0.919	0.979	29.848	-0.054	-0.054	0.000	0.000	0.000	0.000
100	A	179	ARG	1	0.859	0.928	31.210	-0.061	-0.061	0.000	0.000	0.000	0.000
101	A	180	TRP	0	0.041	0.011	28.803	0.006	0.006	0.000	0.000	0.000	0.000
102	A	181	PRO	0	0.046	0.026	30.507	0.004	0.004	0.000	0.000	0.000	0.000
103	A	182	LYS	1	0.872	0.951	27.711	-0.099	-0.099	0.000	0.000	0.000	0.000
104	A	183	PHE	0	0.061	0.028	23.858	0.005	0.005	0.000	0.000	0.000	0.000
105	A	184	PHE	0	0.055	0.015	26.113	0.006	0.006	0.000	0.000	0.000	0.000
106	A	185	LYS	1	0.861	0.938	27.005	-0.086	-0.086	0.000	0.000	0.000	0.000
107	A	186	GLN	0	-0.043	-0.028	22.645	0.000	0.000	0.000	0.000	0.000	0.000
108	A	187	ILE	0	0.007	0.023	21.167	0.016	0.016	0.000	0.000	0.000	0.000
109	A	188	ASP	-1	-0.789	-0.873	22.453	0.105	0.105	0.000	0.000	0.000	0.000
110	A	189	TRP	0	-0.015	-0.012	22.979	-0.012	-0.012	0.000	0.000	0.000	0.000
111	A	190	THR	0	-0.051	-0.044	26.772	-0.006	-0.006	0.000	0.000	0.000	0.000
112	A	191	GLN	0	-0.056	-0.039	23.979	-0.010	-0.010	0.000	0.000	0.000	0.000
113	A	192	GLY	0	0.026	0.024	28.215	-0.005	-0.005	0.000	0.000	0.000	0.000
114	A	193	GLU	-1	-0.821	-0.910	28.597	0.062	0.062	0.000	0.000	0.000	0.000
115	A	194	ASN	0	-0.068	-0.032	32.455	0.001	0.001	0.000	0.000	0.000	0.000
116	A	195	ASN	0	-0.027	-0.014	35.456	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	196	ASN	0	-0.001	0.006	31.821	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	197	TYR	0	-0.031	-0.032	31.525	0.004	0.004	0.000	0.000	0.000	0.000
119	A	198	ARG	1	0.769	0.909	24.522	-0.076	-0.076	0.000	0.000	0.000	0.000
120	A	199	LYS	1	0.959	0.991	29.743	-0.019	-0.019	0.000	0.000	0.000	0.000
121	A	200	TRP	0	-0.008	0.028	27.304	0.000	0.000	0.000	0.000	0.000	0.000
122	A	201	PRO	0	-0.031	-0.044	27.542	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	202	MET	0	-0.030	-0.031	26.842	0.001	0.001	0.000	0.000	0.000	0.000
124	A	203	GLU	-1	-0.883	-0.937	27.103	0.034	0.034	0.000	0.000	0.000	0.000
125	A	204	PHE	0	-0.038	-0.020	23.651	0.006	0.006	0.000	0.000	0.000	0.000
126	A	205	ILE	0	0.019	0.015	18.522	-0.005	-0.005	0.000	0.000	0.000	0.000
127	A	206	TYR	0	-0.056	-0.033	19.028	0.008	0.008	0.000	0.000	0.000	0.000
128	A	207	SER	0	0.009	-0.047	15.417	-0.014	-0.014	0.000	0.000	0.000	0.000
129	A	208	MET	0	0.031	0.029	8.063	0.010	0.010	0.000	0.000	0.000	0.000
130	A	209	ASP	-1	-0.857	-0.874	12.586	0.218	0.218	0.000	0.000	0.000	0.000
131	A	210	ALA	0	-0.040	0.002	14.950	0.003	0.003	0.000	0.000	0.000	0.000
132	A	211	PRO	0	0.011	-0.006	15.458	0.045	0.045	0.000	0.000	0.000	0.000
133	A	212	ARG	1	0.790	0.862	13.796	-0.270	-0.270	0.000	0.000	0.000	0.000
134	A	213	GLY	0	0.033	-0.012	16.422	-0.018	-0.018	0.000	0.000	0.000	0.000
135	A	214	HIS	0	-0.068	-0.028	18.492	-0.029	-0.029	0.000	0.000	0.000	0.000
136	A	215	LEU	0	0.034	0.046	17.217	-0.020	-0.020	0.000	0.000	0.000	0.000
137	A	216	PRO	0	0.059	0.027	18.479	0.013	0.013	0.000	0.000	0.000	0.000
138	A	217	LEU	0	0.037	0.032	20.995	0.010	0.010	0.000	0.000	0.000	0.000
139	A	218	THR	0	-0.040	-0.046	24.701	-0.004	-0.004	0.000	0.000	0.000	0.000
140	A	219	ASN	0	-0.006	0.011	27.896	-0.002	-0.002	0.000	0.000	0.000	0.000
141	A	220	ALA	0	0.060	0.040	30.932	-0.003	-0.003	0.000	0.000	0.000	0.000
142	A	221	LEU	0	-0.042	-0.025	33.273	-0.002	-0.002	0.000	0.000	0.000	0.000
143	A	222	ARG	1	0.869	0.936	35.898	-0.008	-0.008	0.000	0.000	0.000	0.000
144	A	223	GLY	0	0.015	0.021	37.060	0.002	0.002	0.000	0.000	0.000	0.000
145	A	224	THR	0	0.022	-0.008	33.018	0.002	0.002	0.000	0.000	0.000	0.000
146	A	225	GLN	0	0.002	0.002	33.079	0.003	0.003	0.000	0.000	0.000	0.000
147	A	226	LEU	0	0.008	0.000	30.929	0.000	0.000	0.000	0.000	0.000	0.000
148	A	227	PHE	0	0.041	0.019	24.567	-0.001	-0.001	0.000	0.000	0.000	0.000
149	A	228	GLN	0	-0.019	-0.031	28.724	0.003	0.003	0.000	0.000	0.000	0.000
150	A	229	ALA	0	-0.020	-0.008	30.136	0.002	0.002	0.000	0.000	0.000	0.000
151	A	230	ILE	0	-0.003	0.005	25.499	-0.001	-0.001	0.000	0.000	0.000	0.000
152	A	231	MET	0	-0.049	-0.010	24.426	-0.001	-0.001	0.000	0.000	0.000	0.000
153	A	232	GLU	-1	-0.845	-0.937	26.811	0.038	0.038	0.000	0.000	0.000	0.000
154	A	233	HIS	0	-0.004	0.012	27.377	0.001	0.001	0.000	0.000	0.000	0.000
155	A	234	PRO	0	0.023	-0.001	27.566	0.004	0.004	0.000	0.000	0.000	0.000
156	A	235	ALA	0	-0.020	0.002	23.944	0.000	0.000	0.000	0.000	0.000	0.000
157	A	236	PHE	0	-0.034	-0.035	21.416	0.003	0.003	0.000	0.000	0.000	0.000
158	A	237	GLU	-1	-0.913	-0.936	23.646	0.059	0.059	0.000	0.000	0.000	0.000
159	A	238	LYS	1	0.831	0.922	22.626	-0.029	-0.029	0.000	0.000	0.000	0.000
160	A	239	NME	0	0.034	0.034	22.413	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:80:ACE )