FMO DATABASE

FMODB ID: VR281

Calculation Name: 4C9Y-A-Xray321

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4C9Y

Chain ID: A

ChEMBL ID:

UniProt ID: Q96BD8

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	123
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1107443.250833
FMO2-HF: Nuclear repulsion	1056672.209831
FMO2-HF: Total energy	-50771.041002
FMO2-MP2: Total energy	-50918.918023

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:SER )

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

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.
-3.63	-2.308	-0.006	-0.536	-0.78	0.002

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.016

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	4	LYS	1	0.909	0.972	3.814	-1.016	0.128	-0.006	-0.483	-0.655	0.002
4	A	5	GLU	-1	-0.916	-0.960	6.388	1.671	1.671	0.000	0.000	0.000	0.000
5	A	6	MET	0	-0.038	-0.010	8.702	-0.243	-0.243	0.000	0.000	0.000	0.000
6	A	7	PRO	0	0.043	0.023	11.860	0.088	0.088	0.000	0.000	0.000	0.000
7	A	8	PHE	0	0.029	0.013	13.699	0.025	0.025	0.000	0.000	0.000	0.000
8	A	9	ILE	0	-0.007	0.011	17.013	-0.045	-0.045	0.000	0.000	0.000	0.000
9	A	10	THR	0	0.044	0.022	20.231	0.027	0.027	0.000	0.000	0.000	0.000
10	A	11	CYS	0	0.019	-0.006	22.227	0.009	0.009	0.000	0.000	0.000	0.000
11	A	12	ASP	-1	-0.848	-0.926	25.463	-0.082	-0.082	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-0.787	-0.870	20.544	-0.139	-0.139	0.000	0.000	0.000	0.000
13	A	14	PHE	0	0.019	-0.001	24.876	0.010	0.010	0.000	0.000	0.000	0.000
14	A	15	ASN	0	-0.013	-0.011	26.410	0.014	0.014	0.000	0.000	0.000	0.000
15	A	16	GLY	0	0.029	0.030	28.305	0.002	0.002	0.000	0.000	0.000	0.000
16	A	17	VAL	0	-0.049	0.003	26.012	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	18	PRO	0	0.030	-0.001	29.030	0.009	0.009	0.000	0.000	0.000	0.000
18	A	19	SER	0	0.056	0.012	32.088	0.006	0.006	0.000	0.000	0.000	0.000
19	A	20	TYR	0	0.026	0.005	32.683	0.009	0.009	0.000	0.000	0.000	0.000
20	A	21	MET	0	-0.068	-0.021	27.822	0.004	0.004	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.834	0.924	29.476	0.028	0.028	0.000	0.000	0.000	0.000
22	A	23	SER	0	0.000	0.016	31.178	0.014	0.014	0.000	0.000	0.000	0.000
23	A	24	ARG	1	0.942	0.944	32.811	-0.051	-0.051	0.000	0.000	0.000	0.000
24	A	25	LEU	0	-0.071	-0.019	27.282	0.008	0.008	0.000	0.000	0.000	0.000
25	A	26	THR	0	0.085	0.034	28.939	-0.007	-0.007	0.000	0.000	0.000	0.000
26	A	27	TYR	0	-0.010	-0.017	22.502	0.013	0.013	0.000	0.000	0.000	0.000
27	A	28	ASN	0	0.047	0.013	24.277	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	29	GLN	0	0.034	0.026	23.785	0.010	0.010	0.000	0.000	0.000	0.000
29	A	30	ILE	0	0.006	0.002	21.478	0.018	0.018	0.000	0.000	0.000	0.000
30	A	31	ASN	0	0.049	0.024	19.680	0.012	0.012	0.000	0.000	0.000	0.000
31	A	32	ASP	-1	-0.888	-0.943	19.001	0.217	0.217	0.000	0.000	0.000	0.000
32	A	33	VAL	0	-0.033	-0.024	19.705	0.042	0.042	0.000	0.000	0.000	0.000
33	A	34	ILE	0	-0.012	-0.005	15.253	0.041	0.041	0.000	0.000	0.000	0.000
34	A	35	LYS	1	0.942	0.980	15.164	-0.187	-0.187	0.000	0.000	0.000	0.000
35	A	36	GLU	-1	-0.907	-0.955	15.218	0.517	0.517	0.000	0.000	0.000	0.000
36	A	37	ILE	0	-0.029	-0.021	14.721	0.065	0.065	0.000	0.000	0.000	0.000
37	A	38	ASN	0	0.045	0.017	11.242	0.033	0.033	0.000	0.000	0.000	0.000
38	A	39	LYS	1	0.949	0.997	11.401	-0.298	-0.298	0.000	0.000	0.000	0.000
39	A	40	ALA	0	-0.009	-0.003	12.952	0.155	0.155	0.000	0.000	0.000	0.000
40	A	41	VAL	0	-0.005	0.001	8.859	0.088	0.088	0.000	0.000	0.000	0.000
41	A	42	ILE	0	0.009	-0.002	7.422	0.364	0.364	0.000	0.000	0.000	0.000
42	A	43	SER	0	-0.045	-0.022	9.145	0.299	0.299	0.000	0.000	0.000	0.000
43	A	44	LYS	1	0.904	0.978	11.939	-0.478	-0.478	0.000	0.000	0.000	0.000
44	A	45	TYR	0	0.015	-0.009	6.877	-0.113	-0.113	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.925	0.965	6.616	-3.289	-3.289	0.000	0.000	0.000	0.000
46	A	47	ILE	0	0.001	0.016	8.751	-0.194	-0.194	0.000	0.000	0.000	0.000
47	A	48	LEU	0	-0.035	-0.022	9.848	-0.129	-0.129	0.000	0.000	0.000	0.000
48	A	49	HIS	0	-0.026	-0.006	4.587	-0.810	-0.705	0.000	-0.011	-0.094	0.000
49	A	50	GLN	0	-0.007	0.019	8.777	-0.031	-0.031	0.000	0.000	0.000	0.000
50	A	51	PRO	0	0.021	0.006	11.669	-0.165	-0.165	0.000	0.000	0.000	0.000
51	A	52	LYS	1	1.037	0.981	14.384	-0.371	-0.371	0.000	0.000	0.000	0.000
52	A	53	LYS	1	0.946	0.979	17.273	-0.352	-0.352	0.000	0.000	0.000	0.000
53	A	54	SER	0	-0.012	-0.004	16.146	-0.023	-0.023	0.000	0.000	0.000	0.000
54	A	55	MET	0	-0.082	0.003	14.703	-0.012	-0.012	0.000	0.000	0.000	0.000
55	A	56	ASN	0	0.069	0.044	18.765	-0.046	-0.046	0.000	0.000	0.000	0.000
56	A	57	SER	0	0.031	-0.010	21.415	0.022	0.022	0.000	0.000	0.000	0.000
57	A	58	VAL	0	0.063	0.029	20.869	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	59	THR	0	0.012	-0.002	16.258	0.031	0.031	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.899	0.959	18.253	-0.328	-0.328	0.000	0.000	0.000	0.000
60	A	61	ASN	0	0.018	0.007	20.219	-0.022	-0.022	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.011	0.014	17.510	-0.014	-0.014	0.000	0.000	0.000	0.000
62	A	63	TYR	0	0.008	-0.008	14.168	-0.035	-0.035	0.000	0.000	0.000	0.000
63	A	64	HIS	0	0.025	-0.007	17.206	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	65	ARG	1	0.908	0.972	18.840	-0.406	-0.406	0.000	0.000	0.000	0.000
65	A	66	PHE	0	-0.039	-0.037	14.623	0.005	0.005	0.000	0.000	0.000	0.000
66	A	67	ILE	0	-0.052	-0.027	15.616	-0.037	-0.037	0.000	0.000	0.000	0.000
67	A	68	ASP	-1	-0.902	-0.943	18.193	0.157	0.157	0.000	0.000	0.000	0.000
68	A	69	GLU	-1	-0.926	-0.971	18.666	0.256	0.256	0.000	0.000	0.000	0.000
69	A	70	GLU	-1	-0.930	-0.937	14.094	0.167	0.167	0.000	0.000	0.000	0.000
70	A	71	THR	0	-0.016	-0.011	17.925	-0.032	-0.032	0.000	0.000	0.000	0.000
71	A	72	LYS	1	0.949	0.947	17.829	0.032	0.032	0.000	0.000	0.000	0.000
72	A	73	ASP	-1	-0.886	-0.926	18.014	-0.154	-0.154	0.000	0.000	0.000	0.000
73	A	74	THR	0	-0.079	-0.052	15.282	-0.037	-0.037	0.000	0.000	0.000	0.000
74	A	75	LYS	1	0.992	1.005	12.529	0.263	0.263	0.000	0.000	0.000	0.000
75	A	76	GLY	0	-0.029	-0.016	9.509	-0.086	-0.086	0.000	0.000	0.000	0.000
76	A	77	ARG	1	0.890	0.958	9.269	0.114	0.114	0.000	0.000	0.000	0.000
77	A	78	TYR	0	0.038	0.016	4.234	0.669	0.742	0.000	-0.042	-0.031	0.000
78	A	79	PHE	0	0.016	-0.003	10.845	-0.087	-0.087	0.000	0.000	0.000	0.000
79	A	80	ILE	0	0.025	0.025	13.864	0.120	0.120	0.000	0.000	0.000	0.000
80	A	81	VAL	0	0.013	0.005	16.208	-0.084	-0.084	0.000	0.000	0.000	0.000
81	A	82	GLU	-1	-0.832	-0.937	19.874	0.178	0.178	0.000	0.000	0.000	0.000
82	A	83	ALA	0	-0.004	-0.007	21.847	0.013	0.013	0.000	0.000	0.000	0.000
83	A	84	ASP	-1	-0.695	-0.849	16.850	0.471	0.471	0.000	0.000	0.000	0.000
84	A	85	ILE	0	-0.035	-0.008	18.341	0.037	0.037	0.000	0.000	0.000	0.000
85	A	86	LYS	1	0.885	0.944	20.297	-0.207	-0.207	0.000	0.000	0.000	0.000
86	A	87	GLU	-1	-0.928	-0.944	19.175	0.423	0.423	0.000	0.000	0.000	0.000
87	A	88	PHE	0	0.016	0.005	15.914	0.042	0.042	0.000	0.000	0.000	0.000
88	A	89	THR	0	-0.061	-0.036	18.090	0.012	0.012	0.000	0.000	0.000	0.000
89	A	90	THR	0	0.040	0.015	20.620	-0.017	-0.017	0.000	0.000	0.000	0.000
90	A	91	LEU	0	-0.028	-0.009	20.708	-0.040	-0.040	0.000	0.000	0.000	0.000
91	A	92	LYS	1	0.964	0.975	24.279	-0.178	-0.178	0.000	0.000	0.000	0.000
92	A	93	ALA	0	0.002	0.011	25.348	-0.009	-0.009	0.000	0.000	0.000	0.000
93	A	94	ASP	-1	-0.842	-0.933	26.929	0.113	0.113	0.000	0.000	0.000	0.000
94	A	95	LYS	1	0.955	0.959	29.322	-0.070	-0.070	0.000	0.000	0.000	0.000
95	A	96	LYS	1	0.966	0.981	28.805	-0.110	-0.110	0.000	0.000	0.000	0.000
96	A	97	PHE	0	0.089	0.058	21.454	-0.010	-0.010	0.000	0.000	0.000	0.000
97	A	98	HIS	1	0.874	0.920	25.477	-0.111	-0.111	0.000	0.000	0.000	0.000
98	A	99	VAL	0	-0.038	-0.010	27.243	-0.014	-0.014	0.000	0.000	0.000	0.000
99	A	100	LEU	0	0.015	0.001	22.960	-0.013	-0.013	0.000	0.000	0.000	0.000
100	A	101	LEU	0	0.016	0.008	21.451	-0.013	-0.013	0.000	0.000	0.000	0.000
101	A	102	ASN	0	-0.010	0.002	23.289	-0.026	-0.026	0.000	0.000	0.000	0.000
102	A	103	ILE	0	0.002	0.005	23.592	-0.018	-0.018	0.000	0.000	0.000	0.000
103	A	104	LEU	0	0.024	0.011	18.691	-0.020	-0.020	0.000	0.000	0.000	0.000
104	A	105	ARG	1	0.952	1.001	20.551	0.027	0.027	0.000	0.000	0.000	0.000
105	A	106	HIS	0	-0.029	-0.013	22.359	-0.028	-0.028	0.000	0.000	0.000	0.000
106	A	107	CYS	0	-0.047	-0.016	21.119	-0.014	-0.014	0.000	0.000	0.000	0.000
107	A	108	ARG	1	0.926	0.960	19.092	0.217	0.217	0.000	0.000	0.000	0.000
108	A	109	ARG	1	0.745	0.830	15.744	0.091	0.091	0.000	0.000	0.000	0.000
109	A	110	LEU	0	0.031	0.020	15.498	0.004	0.004	0.000	0.000	0.000	0.000
110	A	111	SER	0	-0.035	-0.026	17.490	-0.005	-0.005	0.000	0.000	0.000	0.000
111	A	112	GLU	-1	-0.914	-0.982	19.262	0.041	0.041	0.000	0.000	0.000	0.000
112	A	113	VAL	0	0.021	0.025	18.916	-0.021	-0.021	0.000	0.000	0.000	0.000
113	A	114	ARG	1	0.909	0.967	21.669	0.007	0.007	0.000	0.000	0.000	0.000
114	A	115	GLY	0	0.070	0.037	24.525	-0.012	-0.012	0.000	0.000	0.000	0.000
115	A	116	GLY	0	0.043	0.010	25.406	0.013	0.013	0.000	0.000	0.000	0.000
116	A	117	GLY	0	-0.025	-0.006	27.585	0.011	0.011	0.000	0.000	0.000	0.000
117	A	118	LEU	0	0.017	0.021	21.764	0.008	0.008	0.000	0.000	0.000	0.000
118	A	119	THR	0	-0.038	-0.049	23.115	-0.020	-0.020	0.000	0.000	0.000	0.000
119	A	120	ARG	1	0.830	0.926	18.629	-0.056	-0.056	0.000	0.000	0.000	0.000
120	A	121	TYR	0	-0.023	-0.017	18.012	-0.049	-0.049	0.000	0.000	0.000	0.000
121	A	122	VAL	0	-0.027	-0.022	14.076	0.048	0.048	0.000	0.000	0.000	0.000
122	A	123	ILE	0	-0.006	-0.009	10.777	-0.028	-0.028	0.000	0.000	0.000	0.000
123	A	124	THR	-1	-0.918	-0.975	11.764	-0.510	-0.510	0.000	0.000	0.000	0.000

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