FMO DATABASE

FMODB ID: R8YL8

Calculation Name: 2XFA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2XFA

Chain ID: A

ChEMBL ID:

UniProt ID: Q3YPH0

Base Structure: X-ray

Registration Date: 2023-09-22

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	143
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1443008.800226
FMO2-HF: Nuclear repulsion	1383809.404565
FMO2-HF: Total energy	-59199.395661
FMO2-MP2: Total energy	-59369.534704

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:1:MET)

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

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.
-8.471	-3.565	2.727	-1.366	-6.265	-0.004

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.079 / q_NPA : 0.082

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	3	SER	0	-0.018	-0.017	2.864	-5.218	-2.075	0.930	-0.329	-3.744	0.001
4	A	4	GLY	0	-0.003	0.003	3.558	0.525	0.601	0.021	0.047	-0.144	0.000
5	A	5	VAL	0	0.040	0.044	7.303	0.337	0.337	0.000	0.000	0.000	0.000
6	A	6	ASN	0	-0.011	-0.004	9.778	-0.137	-0.137	0.000	0.000	0.000	0.000
7	A	7	VAL	0	-0.014	-0.027	12.177	0.000	0.000	0.000	0.000	0.000	0.000
8	A	8	SER	0	-0.017	-0.004	14.472	0.080	0.080	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.822	-0.925	18.180	-0.435	-0.435	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.870	-0.952	20.723	-0.289	-0.289	0.000	0.000	0.000	0.000
11	A	11	CYS	0	-0.065	-0.013	16.299	0.023	0.023	0.000	0.000	0.000	0.000
12	A	12	ILE	0	0.014	0.005	17.594	0.022	0.022	0.000	0.000	0.000	0.000
13	A	13	TYR	0	-0.057	-0.008	20.549	0.045	0.045	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.737	-0.893	22.848	-0.233	-0.233	0.000	0.000	0.000	0.000
15	A	15	PHE	0	0.007	0.004	20.472	0.023	0.023	0.000	0.000	0.000	0.000
16	A	16	ASN	0	0.008	-0.004	22.601	0.030	0.030	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.913	0.964	25.158	0.229	0.229	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.012	0.012	23.561	0.016	0.016	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.914	0.964	23.443	0.228	0.228	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.048	-0.037	26.510	0.017	0.017	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.877	0.937	29.416	0.156	0.156	0.000	0.000	0.000	0.000
22	A	22	HIS	1	0.923	0.981	30.108	0.153	0.153	0.000	0.000	0.000	0.000
23	A	23	LEU	0	0.002	-0.007	30.530	0.007	0.007	0.000	0.000	0.000	0.000
24	A	24	ASN	0	-0.064	-0.017	26.154	0.009	0.009	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.959	0.979	28.415	0.138	0.138	0.000	0.000	0.000	0.000
26	A	26	TYR	0	-0.027	-0.040	23.877	0.004	0.004	0.000	0.000	0.000	0.000
27	A	27	ILE	0	-0.021	0.005	20.655	0.003	0.003	0.000	0.000	0.000	0.000
28	A	28	ILE	0	0.000	0.010	19.395	-0.010	-0.010	0.000	0.000	0.000	0.000
29	A	29	TYR	0	-0.015	-0.007	15.884	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.964	0.969	15.494	0.429	0.429	0.000	0.000	0.000	0.000
31	A	31	ILE	0	-0.035	-0.013	9.969	-0.020	-0.020	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.950	-0.977	14.321	-0.403	-0.403	0.000	0.000	0.000	0.000
33	A	33	ASN	0	-0.026	-0.029	15.545	-0.045	-0.045	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.042	-0.031	11.315	-0.008	-0.008	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.901	-0.944	10.793	-1.028	-1.028	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.957	0.986	12.324	0.568	0.568	0.000	0.000	0.000	0.000
37	A	37	ILE	0	-0.060	-0.025	10.212	0.047	0.047	0.000	0.000	0.000	0.000
38	A	38	VAL	0	-0.005	-0.023	14.541	0.053	0.053	0.000	0.000	0.000	0.000
39	A	39	VAL	0	0.035	0.012	18.203	-0.025	-0.025	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.966	-0.997	20.110	-0.341	-0.341	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.021	0.015	21.874	0.030	0.030	0.000	0.000	0.000	0.000
42	A	42	LEU	0	0.005	-0.004	23.768	-0.020	-0.020	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.869	-0.921	26.432	-0.154	-0.154	0.000	0.000	0.000	0.000
44	A	44	HIS	0	0.015	-0.010	28.982	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	45	ASP	-1	-0.819	-0.900	31.705	-0.115	-0.115	0.000	0.000	0.000	0.000
46	A	46	MET	0	-0.072	-0.052	33.384	0.000	0.000	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.973	-0.980	34.338	-0.087	-0.087	0.000	0.000	0.000	0.000
48	A	48	LEU	0	-0.029	0.008	31.203	0.006	0.006	0.000	0.000	0.000	0.000
49	A	49	THR	0	-0.032	-0.035	33.864	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	50	SER	0	-0.003	0.004	34.626	0.001	0.001	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.072	0.019	28.081	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.813	-0.926	30.314	-0.085	-0.085	0.000	0.000	0.000	0.000
53	A	53	ASN	0	-0.002	-0.006	31.586	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	54	ILE	0	0.013	0.017	26.287	-0.007	-0.007	0.000	0.000	0.000	0.000
55	A	55	ILE	0	-0.002	-0.007	26.341	-0.014	-0.014	0.000	0.000	0.000	0.000
56	A	56	MET	0	0.002	0.018	27.302	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.803	0.904	29.236	0.132	0.132	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.020	0.015	22.718	-0.011	-0.011	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.980	1.000	24.767	0.102	0.102	0.000	0.000	0.000	0.000
60	A	60	ASN	0	-0.046	-0.024	25.884	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	61	ASN	0	-0.024	0.000	24.379	0.005	0.005	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.025	0.005	19.984	-0.031	-0.031	0.000	0.000	0.000	0.000
63	A	63	LYS	1	0.952	0.973	21.519	0.257	0.257	0.000	0.000	0.000	0.000
64	A	64	ASN	0	0.045	-0.012	21.034	-0.021	-0.021	0.000	0.000	0.000	0.000
65	A	65	THR	0	-0.015	-0.014	19.826	0.013	0.013	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.951	-0.982	17.266	-0.377	-0.377	0.000	0.000	0.000	0.000
67	A	67	CYS	0	-0.054	-0.008	13.057	0.043	0.043	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.825	0.919	15.101	0.401	0.401	0.000	0.000	0.000	0.000
69	A	69	TYR	0	-0.038	-0.044	8.575	-0.029	-0.029	0.000	0.000	0.000	0.000
70	A	70	ILE	0	0.019	0.008	15.171	0.014	0.014	0.000	0.000	0.000	0.000
71	A	71	ILE	0	-0.048	-0.009	17.414	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	72	ALA	0	0.043	0.013	20.076	0.010	0.010	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.895	-0.949	23.531	-0.159	-0.159	0.000	0.000	0.000	0.000
74	A	74	MET	0	-0.039	-0.012	24.127	0.010	0.010	0.000	0.000	0.000	0.000
75	A	75	PRO	0	0.058	0.033	27.795	0.004	0.004	0.000	0.000	0.000	0.000
76	A	76	ILE	0	-0.003	-0.016	27.559	0.006	0.006	0.000	0.000	0.000	0.000
77	A	77	PRO	0	-0.012	0.016	31.727	0.000	0.000	0.000	0.000	0.000	0.000
78	A	78	THR	0	0.025	0.024	34.062	0.001	0.001	0.000	0.000	0.000	0.000
79	A	79	PRO	0	0.030	0.009	34.027	0.000	0.000	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-1.045	-0.957	36.720	-0.033	-0.033	0.000	0.000	0.000	0.000
81	A	81	GLY	0	0.085	-0.026	37.893	0.003	0.003	0.000	0.000	0.000	0.000
82	A	82	VAL	0	-0.062	-0.037	38.132	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	83	LEU	0	0.000	-0.027	34.351	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.886	0.958	32.282	0.067	0.067	0.000	0.000	0.000	0.000
85	A	85	ASP	-1	-0.872	-0.916	29.581	-0.117	-0.117	0.000	0.000	0.000	0.000
86	A	86	ARG	1	0.837	0.917	25.755	0.099	0.099	0.000	0.000	0.000	0.000
87	A	87	ILE	0	0.056	0.032	21.113	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	88	TYR	0	0.033	0.014	20.844	0.007	0.007	0.000	0.000	0.000	0.000
89	A	89	PHE	0	-0.023	-0.013	12.483	-0.026	-0.026	0.000	0.000	0.000	0.000
90	A	90	ILE	0	0.022	0.002	16.759	0.028	0.028	0.000	0.000	0.000	0.000
91	A	91	PHE	0	-0.034	-0.025	9.295	-0.097	-0.097	0.000	0.000	0.000	0.000
92	A	92	TRP	0	0.026	0.013	14.013	0.068	0.068	0.000	0.000	0.000	0.000
93	A	93	SER	0	0.060	0.009	11.788	-0.081	-0.081	0.000	0.000	0.000	0.000
94	A	94	PRO	0	0.077	0.060	14.599	0.059	0.059	0.000	0.000	0.000	0.000
95	A	95	GLY	0	0.036	0.008	16.241	-0.023	-0.023	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.013	-0.003	17.515	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	97	SER	0	-0.014	0.028	14.976	-0.038	-0.038	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.973	0.984	13.670	0.409	0.409	0.000	0.000	0.000	0.000
99	A	99	PRO	0	0.078	0.017	11.005	-0.083	-0.083	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.897	0.931	8.911	0.479	0.479	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.828	-0.890	8.904	-0.804	-0.804	0.000	0.000	0.000	0.000
102	A	102	LYS	1	0.910	0.935	9.944	0.026	0.026	0.000	0.000	0.000	0.000
103	A	103	MET	0	-0.042	-0.025	4.345	-0.174	-0.017	-0.001	-0.007	-0.149	0.000
104	A	104	LEU	0	0.031	0.031	5.540	-0.386	-0.386	0.000	0.000	0.000	0.000
105	A	105	TYR	0	0.081	0.042	6.665	-0.388	-0.388	0.000	0.000	0.000	0.000
106	A	106	ALA	0	0.008	0.018	6.085	-0.153	-0.153	0.000	0.000	0.000	0.000
107	A	107	ALA	0	-0.042	-0.014	2.242	-0.771	0.139	1.778	-0.994	-1.693	0.000
108	A	108	SER	0	0.012	0.005	3.037	-2.120	-1.805	-0.003	0.025	-0.336	-0.004
109	A	109	LYS	1	0.958	0.997	6.020	0.944	0.944	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.881	-0.947	3.765	-3.357	-3.052	0.002	-0.108	-0.199	-0.001
111	A	111	SER	0	-0.040	-0.042	7.161	0.398	0.398	0.000	0.000	0.000	0.000
112	A	112	LEU	0	0.024	0.011	9.119	0.277	0.277	0.000	0.000	0.000	0.000
113	A	113	VAL	0	0.036	0.013	10.979	0.145	0.145	0.000	0.000	0.000	0.000
114	A	114	ARG	1	0.935	0.983	8.234	1.412	1.412	0.000	0.000	0.000	0.000
115	A	115	LYS	1	0.823	0.921	12.602	0.951	0.951	0.000	0.000	0.000	0.000
116	A	116	ILE	0	-0.037	0.010	14.796	0.059	0.059	0.000	0.000	0.000	0.000
117	A	117	ASN	0	0.043	0.016	17.533	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	118	GLY	0	-0.072	-0.061	19.822	0.007	0.007	0.000	0.000	0.000	0.000
119	A	119	ILE	0	0.000	0.015	16.299	0.015	0.015	0.000	0.000	0.000	0.000
120	A	120	PHE	0	-0.035	-0.006	20.295	0.016	0.016	0.000	0.000	0.000	0.000
121	A	121	LYS	1	0.947	0.969	19.566	0.069	0.069	0.000	0.000	0.000	0.000
122	A	122	SER	0	-0.011	-0.001	13.874	-0.020	-0.020	0.000	0.000	0.000	0.000
123	A	123	LEU	0	-0.018	-0.012	16.345	0.047	0.047	0.000	0.000	0.000	0.000
124	A	124	GLU	-1	-0.973	-0.986	11.181	0.030	0.030	0.000	0.000	0.000	0.000
125	A	125	ILE	0	-0.006	0.013	14.917	0.035	0.035	0.000	0.000	0.000	0.000
126	A	126	THR	0	0.009	-0.023	15.541	-0.037	-0.037	0.000	0.000	0.000	0.000
127	A	127	CYS	0	-0.034	0.024	17.384	0.004	0.004	0.000	0.000	0.000	0.000
128	A	128	ASP	-1	-0.770	-0.869	20.767	-0.117	-0.117	0.000	0.000	0.000	0.000
129	A	129	ILE	0	-0.032	-0.040	23.357	0.000	0.000	0.000	0.000	0.000	0.000
130	A	130	ASN	0	-0.066	-0.043	24.482	-0.008	-0.008	0.000	0.000	0.000	0.000
131	A	131	GLU	-1	-0.875	-0.935	25.471	-0.041	-0.041	0.000	0.000	0.000	0.000
132	A	132	PHE	0	-0.049	-0.018	20.309	0.000	0.000	0.000	0.000	0.000	0.000
133	A	133	GLU	-1	-0.934	-0.984	24.379	-0.095	-0.095	0.000	0.000	0.000	0.000
134	A	134	GLU	-1	-0.922	-0.960	27.309	-0.037	-0.037	0.000	0.000	0.000	0.000
135	A	135	GLU	-1	-0.855	-0.944	21.510	-0.033	-0.033	0.000	0.000	0.000	0.000
136	A	136	LEU	0	-0.011	-0.018	21.974	0.003	0.003	0.000	0.000	0.000	0.000
137	A	137	LYS	1	0.918	0.978	24.258	0.068	0.068	0.000	0.000	0.000	0.000
138	A	138	ALA	0	0.029	0.022	26.710	0.005	0.005	0.000	0.000	0.000	0.000
139	A	139	ILE	0	-0.029	-0.026	20.660	0.007	0.007	0.000	0.000	0.000	0.000
140	A	140	ILE	0	-0.073	-0.037	24.496	0.003	0.003	0.000	0.000	0.000	0.000
141	A	141	LEU	0	-0.024	-0.014	26.080	0.003	0.003	0.000	0.000	0.000	0.000
142	A	142	ASN	0	-0.052	0.004	27.196	0.009	0.009	0.000	0.000	0.000	0.000
143	A	143	THR	0	-0.061	-0.042	25.191	-0.003	-0.003	0.000	0.000	0.000	0.000

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