FMO DATABASE

FMODB ID: M3JYZ

Calculation Name: 2F9Z-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2F9Z

Chain ID: C

ChEMBL ID:

UniProt ID: Q9X006

Base Structure: X-ray

Registration Date: 2023-06-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	159
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1471595.379594
FMO2-HF: Nuclear repulsion	1411206.872941
FMO2-HF: Total energy	-60388.506653
FMO2-MP2: Total energy	-60559.750596

3D Structure Molmil

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(C:-1:ALA)

Summations of interaction energy for fragment #1(C:-1:ALA)

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.
1.523	3.172	-0.012	-0.805	-0.831	0.003

Interaction energy analysis for fragmet #1(C:-1:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.049 / q_NPA : 0.026

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	C	1	MET	0	0.025	0.021	3.893	0.346	1.995	-0.012	-0.805	-0.831	0.003
4	C	2	LYN	0	-0.005	-0.007	5.647	0.428	0.428	0.000	0.000	0.000	0.000
5	C	3	LYS	1	0.865	0.926	9.080	0.620	0.620	0.000	0.000	0.000	0.000
6	C	4	VAL	0	0.040	0.032	12.339	0.028	0.028	0.000	0.000	0.000	0.000
7	C	5	ILE	0	-0.042	-0.013	15.565	0.037	0.037	0.000	0.000	0.000	0.000
8	C	6	GLY	0	0.074	0.045	18.982	-0.001	-0.001	0.000	0.000	0.000	0.000
9	C	7	ILE	0	0.038	0.003	22.567	-0.006	-0.006	0.000	0.000	0.000	0.000
10	C	8	GLY	0	0.019	0.007	26.048	0.013	0.013	0.000	0.000	0.000	0.000
11	C	9	GLU	-1	-0.899	-0.927	21.654	-0.236	-0.236	0.000	0.000	0.000	0.000
12	C	10	TYR	0	-0.003	-0.026	21.414	-0.002	-0.002	0.000	0.000	0.000	0.000
13	C	11	ALA	0	-0.027	-0.003	16.186	0.001	0.001	0.000	0.000	0.000	0.000
14	C	12	VAL	0	0.011	-0.005	17.008	-0.004	-0.004	0.000	0.000	0.000	0.000
15	C	13	MET	0	-0.015	0.018	9.589	-0.032	-0.032	0.000	0.000	0.000	0.000
16	C	14	LYS	1	0.909	0.955	10.949	0.467	0.467	0.000	0.000	0.000	0.000
17	C	15	ASN	0	-0.025	-0.043	10.244	-0.069	-0.069	0.000	0.000	0.000	0.000
18	C	16	PRO	0	0.067	0.037	4.969	0.048	0.048	0.000	0.000	0.000	0.000
19	C	17	GLY	0	-0.003	-0.003	6.469	-0.669	-0.669	0.000	0.000	0.000	0.000
20	C	18	VAL	0	-0.029	-0.023	7.767	0.139	0.139	0.000	0.000	0.000	0.000
21	C	19	ILE	0	0.006	0.020	10.310	0.059	0.059	0.000	0.000	0.000	0.000
22	C	20	VAL	0	0.007	0.001	12.337	0.026	0.026	0.000	0.000	0.000	0.000
23	C	21	THR	0	-0.030	-0.031	15.166	0.068	0.068	0.000	0.000	0.000	0.000
24	C	22	LEU	0	0.031	0.008	16.923	-0.003	-0.003	0.000	0.000	0.000	0.000
25	C	23	GLY	0	0.040	0.025	20.697	0.016	0.016	0.000	0.000	0.000	0.000
26	C	24	LEU	0	-0.033	-0.017	21.943	0.014	0.014	0.000	0.000	0.000	0.000
27	C	25	GLY	0	0.062	0.019	25.572	0.006	0.006	0.000	0.000	0.000	0.000
28	C	26	SER	0	0.003	0.017	29.261	-0.007	-0.007	0.000	0.000	0.000	0.000
29	C	27	CYS	0	-0.024	0.006	27.264	0.007	0.007	0.000	0.000	0.000	0.000
30	C	28	VAL	0	0.001	-0.009	26.751	-0.004	-0.004	0.000	0.000	0.000	0.000
31	C	29	ALA	0	0.029	0.017	21.285	-0.002	-0.002	0.000	0.000	0.000	0.000
32	C	30	VAL	0	-0.001	-0.002	23.372	-0.005	-0.005	0.000	0.000	0.000	0.000
33	C	31	CYS	0	-0.039	-0.005	19.222	-0.032	-0.032	0.000	0.000	0.000	0.000
34	C	32	MET	0	0.021	0.015	20.046	0.033	0.033	0.000	0.000	0.000	0.000
35	C	33	ARG	1	0.832	0.900	15.911	0.372	0.372	0.000	0.000	0.000	0.000
36	C	34	ASP	-1	-0.692	-0.802	18.804	-0.211	-0.211	0.000	0.000	0.000	0.000
37	C	35	PRO	0	0.006	0.002	17.901	-0.033	-0.033	0.000	0.000	0.000	0.000
38	C	36	VAL	0	-0.028	-0.007	18.086	-0.008	-0.008	0.000	0.000	0.000	0.000
39	C	37	ALA	0	-0.004	-0.002	18.777	0.003	0.003	0.000	0.000	0.000	0.000
40	C	38	LYS	1	0.868	0.935	13.900	0.345	0.345	0.000	0.000	0.000	0.000
41	C	39	VAL	0	0.025	0.005	14.138	-0.061	-0.061	0.000	0.000	0.000	0.000
42	C	40	GLY	0	0.049	0.000	15.474	0.039	0.039	0.000	0.000	0.000	0.000
43	C	41	ALA	0	-0.021	-0.008	16.238	-0.031	-0.031	0.000	0.000	0.000	0.000
44	C	42	MET	0	-0.019	-0.006	16.892	0.006	0.006	0.000	0.000	0.000	0.000
45	C	43	ALA	0	0.045	0.013	19.784	0.010	0.010	0.000	0.000	0.000	0.000
46	C	44	HIS	0	-0.038	-0.013	22.493	0.025	0.025	0.000	0.000	0.000	0.000
47	C	45	VAL	0	0.022	0.022	24.396	0.017	0.017	0.000	0.000	0.000	0.000
48	C	46	MET	0	0.002	-0.006	28.028	0.000	0.000	0.000	0.000	0.000	0.000
49	C	47	LEU	0	-0.027	-0.008	30.451	0.010	0.010	0.000	0.000	0.000	0.000
50	C	48	PRO	0	0.012	-0.001	33.102	-0.007	-0.007	0.000	0.000	0.000	0.000
51	C	49	ASP	-1	-0.890	-0.962	35.051	-0.116	-0.116	0.000	0.000	0.000	0.000
52	C	50	SER	0	-0.025	-0.053	35.058	0.006	0.006	0.000	0.000	0.000	0.000
53	C	51	GLY	0	-0.006	0.003	36.866	0.004	0.004	0.000	0.000	0.000	0.000
54	C	52	GLY	0	-0.016	0.000	38.797	0.005	0.005	0.000	0.000	0.000	0.000
55	C	53	LYS	1	0.806	0.900	36.625	0.106	0.106	0.000	0.000	0.000	0.000
56	C	54	THR	0	0.044	0.014	35.065	-0.005	-0.005	0.000	0.000	0.000	0.000
57	C	55	ASP	-1	-0.816	-0.902	32.584	-0.119	-0.119	0.000	0.000	0.000	0.000
58	C	56	LYS	1	0.860	0.933	25.782	0.189	0.189	0.000	0.000	0.000	0.000
59	C	57	PRO	0	0.064	0.030	26.474	-0.002	-0.002	0.000	0.000	0.000	0.000
60	C	58	GLY	0	0.000	-0.011	25.586	-0.001	-0.001	0.000	0.000	0.000	0.000
61	C	59	LYS	1	0.822	0.916	26.522	0.122	0.122	0.000	0.000	0.000	0.000
62	C	60	TYR	0	0.041	0.023	29.535	0.004	0.004	0.000	0.000	0.000	0.000
63	C	61	ALA	0	0.044	0.020	30.469	-0.008	-0.008	0.000	0.000	0.000	0.000
64	C	62	ASP	-1	-0.778	-0.858	30.844	-0.143	-0.143	0.000	0.000	0.000	0.000
65	C	63	THR	0	0.041	0.008	30.696	-0.004	-0.004	0.000	0.000	0.000	0.000
66	C	64	ALA	0	-0.010	0.025	26.900	-0.009	-0.009	0.000	0.000	0.000	0.000
67	C	65	VAL	0	-0.009	-0.009	26.856	-0.015	-0.015	0.000	0.000	0.000	0.000
68	C	66	LYS	1	0.897	0.932	27.582	0.147	0.147	0.000	0.000	0.000	0.000
69	C	67	THR	0	-0.050	-0.029	25.442	0.008	0.008	0.000	0.000	0.000	0.000
70	C	68	LEU	0	-0.009	-0.014	22.034	-0.007	-0.007	0.000	0.000	0.000	0.000
71	C	69	VAL	0	0.004	0.005	23.623	-0.011	-0.011	0.000	0.000	0.000	0.000
72	C	70	GLU	-1	-0.857	-0.907	26.106	-0.152	-0.152	0.000	0.000	0.000	0.000
73	C	71	GLU	-1	-0.836	-0.919	21.733	-0.210	-0.210	0.000	0.000	0.000	0.000
74	C	72	LEU	0	0.030	0.013	18.569	-0.012	-0.012	0.000	0.000	0.000	0.000
75	C	73	LYS	1	0.872	0.946	21.642	0.166	0.166	0.000	0.000	0.000	0.000
76	C	74	LYS	1	0.790	0.883	23.501	0.189	0.189	0.000	0.000	0.000	0.000
77	C	75	MET	0	-0.035	0.002	17.876	-0.015	-0.015	0.000	0.000	0.000	0.000
78	C	76	GLY	0	0.024	0.012	19.685	-0.017	-0.017	0.000	0.000	0.000	0.000
79	C	77	ALA	0	-0.060	-0.020	21.342	0.013	0.013	0.000	0.000	0.000	0.000
80	C	78	LYS	1	0.852	0.918	22.769	0.189	0.189	0.000	0.000	0.000	0.000
81	C	79	VAL	0	0.038	0.018	25.601	-0.015	-0.015	0.000	0.000	0.000	0.000
82	C	80	GLU	-1	-0.841	-0.941	27.796	-0.158	-0.158	0.000	0.000	0.000	0.000
83	C	81	ARG	1	0.818	0.892	22.812	0.204	0.204	0.000	0.000	0.000	0.000
84	C	82	LEU	0	-0.036	-0.013	22.459	-0.025	-0.025	0.000	0.000	0.000	0.000
85	C	83	GLU	-1	-0.785	-0.860	20.979	-0.299	-0.299	0.000	0.000	0.000	0.000
86	C	84	ALA	0	0.010	-0.008	22.092	-0.028	-0.028	0.000	0.000	0.000	0.000
87	C	85	LYS	1	0.822	0.901	18.777	0.387	0.387	0.000	0.000	0.000	0.000
88	C	86	ILE	0	-0.004	0.010	23.238	-0.011	-0.011	0.000	0.000	0.000	0.000
89	C	87	ALA	0	0.037	0.009	22.454	0.006	0.006	0.000	0.000	0.000	0.000
90	C	88	GLY	0	0.011	0.014	24.546	-0.011	-0.011	0.000	0.000	0.000	0.000
91	C	89	GLY	0	0.022	0.017	27.003	0.007	0.007	0.000	0.000	0.000	0.000
92	C	90	ALA	0	-0.087	-0.032	30.229	0.010	0.010	0.000	0.000	0.000	0.000
93	C	91	SER	0	-0.031	-0.029	31.804	0.001	0.001	0.000	0.000	0.000	0.000
94	C	92	MET	0	-0.064	-0.015	29.848	-0.001	-0.001	0.000	0.000	0.000	0.000
95	C	93	PHE	0	0.033	0.026	33.616	0.005	0.005	0.000	0.000	0.000	0.000
96	C	94	GLU	-1	-0.816	-0.917	37.412	-0.085	-0.085	0.000	0.000	0.000	0.000
97	C	95	SER	0	-0.069	-0.050	39.098	-0.003	-0.003	0.000	0.000	0.000	0.000
98	C	96	LYS	1	0.965	1.006	41.148	0.064	0.064	0.000	0.000	0.000	0.000
99	C	97	GLY	0	0.013	0.004	44.038	0.002	0.002	0.000	0.000	0.000	0.000
100	C	98	MET	0	-0.007	-0.002	42.348	-0.003	-0.003	0.000	0.000	0.000	0.000
101	C	99	ASN	0	0.004	-0.015	37.161	-0.010	-0.010	0.000	0.000	0.000	0.000
102	C	100	ILE	0	0.087	0.024	34.620	-0.002	-0.002	0.000	0.000	0.000	0.000
103	C	101	GLY	0	0.005	0.021	33.215	-0.007	-0.007	0.000	0.000	0.000	0.000
104	C	102	ALA	0	0.000	-0.003	33.457	-0.008	-0.008	0.000	0.000	0.000	0.000
105	C	103	ARG	1	0.967	0.986	35.646	0.095	0.095	0.000	0.000	0.000	0.000
106	C	104	ASN	0	-0.020	-0.019	31.278	0.004	0.004	0.000	0.000	0.000	0.000
107	C	105	VAL	0	0.005	0.002	30.464	-0.007	-0.007	0.000	0.000	0.000	0.000
108	C	106	GLU	-1	-0.956	-0.973	32.402	-0.112	-0.112	0.000	0.000	0.000	0.000
109	C	107	ALA	0	0.041	0.019	34.573	0.000	0.000	0.000	0.000	0.000	0.000
110	C	108	VAL	0	-0.013	-0.011	28.473	-0.003	-0.003	0.000	0.000	0.000	0.000
111	C	109	LYS	1	0.788	0.868	31.258	0.152	0.152	0.000	0.000	0.000	0.000
112	C	110	LYS	1	0.837	0.907	32.607	0.115	0.115	0.000	0.000	0.000	0.000
113	C	111	HIS	0	0.059	0.024	32.538	0.006	0.006	0.000	0.000	0.000	0.000
114	C	112	LEU	0	-0.046	-0.022	26.838	-0.004	-0.004	0.000	0.000	0.000	0.000
115	C	113	LYS	1	0.961	0.988	30.822	0.116	0.116	0.000	0.000	0.000	0.000
116	C	114	ASP	-1	-0.846	-0.903	33.800	-0.115	-0.115	0.000	0.000	0.000	0.000
117	C	115	PHE	0	-0.025	-0.016	30.700	0.004	0.004	0.000	0.000	0.000	0.000
118	C	116	GLY	0	-0.012	0.003	31.823	-0.002	-0.002	0.000	0.000	0.000	0.000
119	C	117	ILE	0	-0.037	-0.013	26.468	-0.005	-0.005	0.000	0.000	0.000	0.000
120	C	118	LYS	1	0.906	0.943	28.054	0.167	0.167	0.000	0.000	0.000	0.000
121	C	119	LEU	0	0.020	0.012	26.162	-0.017	-0.017	0.000	0.000	0.000	0.000
122	C	120	LEU	0	-0.002	-0.003	22.911	0.020	0.020	0.000	0.000	0.000	0.000
123	C	121	ALA	0	-0.028	-0.010	23.628	0.006	0.006	0.000	0.000	0.000	0.000
124	C	122	GLU	-1	-0.785	-0.890	25.503	-0.180	-0.180	0.000	0.000	0.000	0.000
125	C	123	ASP	-1	-0.812	-0.868	24.432	-0.196	-0.196	0.000	0.000	0.000	0.000
126	C	124	THR	0	0.053	0.007	26.337	-0.005	-0.005	0.000	0.000	0.000	0.000
127	C	125	GLY	0	0.019	0.026	29.181	0.006	0.006	0.000	0.000	0.000	0.000
128	C	126	GLY	0	0.024	0.013	31.079	-0.009	-0.009	0.000	0.000	0.000	0.000
129	C	127	ASN	0	0.042	0.005	32.520	-0.006	-0.006	0.000	0.000	0.000	0.000
130	C	128	ARG	1	0.911	0.960	28.184	0.145	0.145	0.000	0.000	0.000	0.000
131	C	129	ALA	0	0.047	0.011	26.396	-0.006	-0.006	0.000	0.000	0.000	0.000
132	C	130	ARG	1	0.793	0.898	22.995	0.197	0.197	0.000	0.000	0.000	0.000
133	C	131	SER	0	-0.064	-0.009	18.217	-0.004	-0.004	0.000	0.000	0.000	0.000
134	C	132	VAL	0	0.014	-0.013	17.848	0.010	0.010	0.000	0.000	0.000	0.000
135	C	133	GLU	-1	-0.777	-0.877	11.894	-0.781	-0.781	0.000	0.000	0.000	0.000
136	C	134	TYR	0	-0.013	-0.021	14.412	0.012	0.012	0.000	0.000	0.000	0.000
137	C	135	ASN	0	0.057	0.038	8.492	0.126	0.126	0.000	0.000	0.000	0.000
138	C	136	ILE	0	-0.047	-0.018	11.425	0.165	0.165	0.000	0.000	0.000	0.000
139	C	137	GLU	-1	-0.886	-0.928	7.126	-1.273	-1.273	0.000	0.000	0.000	0.000
140	C	138	THR	0	-0.034	-0.036	11.025	0.185	0.185	0.000	0.000	0.000	0.000
141	C	139	GLY	0	0.009	-0.001	13.454	0.092	0.092	0.000	0.000	0.000	0.000
142	C	140	LYS	1	0.869	0.933	13.535	0.569	0.569	0.000	0.000	0.000	0.000
143	C	141	LEU	0	-0.024	-0.003	14.961	-0.068	-0.068	0.000	0.000	0.000	0.000
144	C	142	LEU	0	0.026	0.026	13.033	0.074	0.074	0.000	0.000	0.000	0.000
145	C	143	VAL	0	-0.016	-0.030	16.338	-0.005	-0.005	0.000	0.000	0.000	0.000
146	C	144	ARG	1	0.865	0.915	14.365	0.460	0.460	0.000	0.000	0.000	0.000
147	C	145	LYS	1	0.842	0.893	20.852	0.185	0.185	0.000	0.000	0.000	0.000
148	C	146	VAL	0	0.057	0.045	23.027	0.016	0.016	0.000	0.000	0.000	0.000
149	C	147	GLY	0	-0.009	-0.008	25.566	0.006	0.006	0.000	0.000	0.000	0.000
150	C	148	GLY	0	0.022	0.018	29.209	-0.003	-0.003	0.000	0.000	0.000	0.000
151	C	149	GLY	0	0.034	0.002	25.994	-0.006	-0.006	0.000	0.000	0.000	0.000
152	C	150	GLU	-1	-0.835	-0.923	25.436	-0.106	-0.106	0.000	0.000	0.000	0.000
153	C	151	GLN	0	-0.077	-0.042	27.404	0.004	0.004	0.000	0.000	0.000	0.000
154	C	152	LEU	0	-0.089	-0.043	26.021	-0.008	-0.008	0.000	0.000	0.000	0.000
155	C	153	GLU	-1	-0.893	-0.935	21.478	-0.199	-0.199	0.000	0.000	0.000	0.000
156	C	154	ILE	0	-0.007	-0.013	16.898	-0.025	-0.025	0.000	0.000	0.000	0.000
157	C	155	LYS	1	0.870	0.942	19.816	0.239	0.239	0.000	0.000	0.000	0.000
158	C	156	GLU	-1	-0.803	-0.893	13.722	-0.593	-0.593	0.000	0.000	0.000	0.000
159	C	157	ILE	0	-0.041	-0.004	18.409	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:-1:ALA)