FMO DATABASE

FMODB ID: KG2V3

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	OptAll
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	-1446845.291113
FMO2-HF: Nuclear repulsion	1387644.282345
FMO2-HF: Total energy	-59201.008768
FMO2-MP2: Total energy	-59371.166181

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.
-7.091	-2.022	3.162	-2.196	-6.034	-0.009

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 : 0.057 / q_NPA : 0.047

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	-0.013	-0.015	2.949	-6.861	-2.687	1.009	-1.545	-3.638	-0.007
4	A	4	GLY	0	-0.010	0.001	3.480	1.018	1.113	0.023	0.075	-0.192	0.000
5	A	5	VAL	0	0.000	0.007	7.052	0.343	0.343	0.000	0.000	0.000	0.000
6	A	6	ASN	0	-0.031	-0.003	9.735	0.062	0.062	0.000	0.000	0.000	0.000
7	A	7	VAL	0	-0.015	-0.020	12.639	-0.011	-0.011	0.000	0.000	0.000	0.000
8	A	8	SER	0	0.009	0.008	15.088	0.047	0.047	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.837	-0.918	18.871	-0.470	-0.470	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.901	-0.960	20.975	-0.354	-0.354	0.000	0.000	0.000	0.000
11	A	11	CYS	0	0.005	0.015	18.349	0.016	0.016	0.000	0.000	0.000	0.000
12	A	12	ILE	0	-0.027	-0.015	17.610	0.018	0.018	0.000	0.000	0.000	0.000
13	A	13	TYR	0	-0.021	-0.005	21.122	0.043	0.043	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.687	-0.814	23.493	-0.221	-0.221	0.000	0.000	0.000	0.000
15	A	15	PHE	0	0.013	0.011	20.858	0.022	0.022	0.000	0.000	0.000	0.000
16	A	16	ASN	0	0.000	-0.018	23.012	0.035	0.035	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.848	0.896	25.850	0.244	0.244	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.012	0.023	23.971	0.015	0.015	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.855	0.914	23.711	0.221	0.221	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.048	-0.033	26.727	0.017	0.017	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.878	0.935	29.832	0.150	0.150	0.000	0.000	0.000	0.000
22	A	22	HIS	1	0.836	0.923	29.389	0.153	0.153	0.000	0.000	0.000	0.000
23	A	23	LEU	0	0.019	0.012	31.010	0.007	0.007	0.000	0.000	0.000	0.000
24	A	24	ASN	0	-0.048	-0.027	26.405	0.003	0.003	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.830	0.905	28.411	0.125	0.125	0.000	0.000	0.000	0.000
26	A	26	TYR	0	-0.019	-0.051	24.149	0.009	0.009	0.000	0.000	0.000	0.000
27	A	27	ILE	0	-0.022	0.004	21.201	0.003	0.003	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.010	0.004	19.588	-0.007	-0.007	0.000	0.000	0.000	0.000
29	A	29	TYR	0	-0.013	-0.015	16.212	0.001	0.001	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.862	0.921	15.567	0.472	0.472	0.000	0.000	0.000	0.000
31	A	31	ILE	0	-0.015	-0.001	9.697	-0.021	-0.021	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.870	-0.937	14.067	-0.458	-0.458	0.000	0.000	0.000	0.000
33	A	33	ASN	0	-0.017	-0.028	15.506	-0.057	-0.057	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.039	-0.020	11.298	-0.021	-0.021	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.863	-0.925	10.675	-1.213	-1.213	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.892	0.927	12.312	0.631	0.631	0.000	0.000	0.000	0.000
37	A	37	ILE	0	-0.033	-0.008	10.176	0.073	0.073	0.000	0.000	0.000	0.000
38	A	38	VAL	0	-0.007	-0.015	14.664	0.053	0.053	0.000	0.000	0.000	0.000
39	A	39	VAL	0	0.048	0.013	18.304	-0.018	-0.018	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.850	-0.916	20.165	-0.411	-0.411	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.004	0.005	22.197	0.028	0.028	0.000	0.000	0.000	0.000
42	A	42	LEU	0	0.007	0.006	23.980	-0.019	-0.019	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.818	-0.885	26.704	-0.148	-0.148	0.000	0.000	0.000	0.000
44	A	44	HIS	0	-0.017	-0.030	29.155	0.000	0.000	0.000	0.000	0.000	0.000
45	A	45	ASP	-1	-0.805	-0.878	32.092	-0.110	-0.110	0.000	0.000	0.000	0.000
46	A	46	MET	0	-0.048	-0.036	33.427	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.956	-0.965	34.530	-0.086	-0.086	0.000	0.000	0.000	0.000
48	A	48	LEU	0	-0.041	-0.008	31.060	0.008	0.008	0.000	0.000	0.000	0.000
49	A	49	THR	0	0.000	-0.010	33.858	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	50	SER	0	-0.056	-0.020	35.128	0.003	0.003	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.058	0.015	28.491	-0.007	-0.007	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.788	-0.879	30.452	-0.067	-0.067	0.000	0.000	0.000	0.000
53	A	53	ASN	0	0.005	0.007	31.555	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	54	ILE	0	0.035	0.022	26.504	-0.008	-0.008	0.000	0.000	0.000	0.000
55	A	55	ILE	0	-0.020	-0.015	26.460	-0.014	-0.014	0.000	0.000	0.000	0.000
56	A	56	MET	0	-0.006	0.007	27.172	-0.008	-0.008	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.715	0.830	29.204	0.128	0.128	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.024	0.014	22.704	-0.013	-0.013	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.832	0.910	24.798	0.092	0.092	0.000	0.000	0.000	0.000
60	A	60	ASN	0	-0.016	-0.012	25.923	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	61	ASN	0	-0.037	-0.010	24.700	-0.009	-0.009	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.020	0.008	19.807	-0.034	-0.034	0.000	0.000	0.000	0.000
63	A	63	LYS	1	0.913	0.934	21.504	0.295	0.295	0.000	0.000	0.000	0.000
64	A	64	ASN	0	0.041	-0.006	20.705	-0.025	-0.025	0.000	0.000	0.000	0.000
65	A	65	THR	0	-0.007	-0.003	19.542	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.844	-0.900	17.131	-0.413	-0.413	0.000	0.000	0.000	0.000
67	A	67	CYS	0	-0.052	0.000	13.231	0.051	0.051	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.715	0.831	15.241	0.414	0.414	0.000	0.000	0.000	0.000
69	A	69	TYR	0	-0.013	-0.026	8.674	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	70	ILE	0	0.007	0.006	15.338	0.013	0.013	0.000	0.000	0.000	0.000
71	A	71	ILE	0	-0.037	-0.007	18.190	0.001	0.001	0.000	0.000	0.000	0.000
72	A	72	ALA	0	0.040	0.007	20.379	0.007	0.007	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.795	-0.875	23.756	-0.138	-0.138	0.000	0.000	0.000	0.000
74	A	74	MET	0	0.001	0.005	24.269	0.011	0.011	0.000	0.000	0.000	0.000
75	A	75	PRO	0	0.050	0.028	27.899	0.006	0.006	0.000	0.000	0.000	0.000
76	A	76	ILE	0	-0.003	-0.006	27.341	0.005	0.005	0.000	0.000	0.000	0.000
77	A	77	PRO	0	-0.017	0.010	31.840	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	78	THR	0	0.027	0.008	33.911	0.001	0.001	0.000	0.000	0.000	0.000
79	A	79	PRO	0	0.002	-0.001	34.430	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.976	-0.973	37.135	-0.017	-0.017	0.000	0.000	0.000	0.000
81	A	81	GLY	0	0.021	0.003	38.682	0.002	0.002	0.000	0.000	0.000	0.000
82	A	82	VAL	0	-0.026	-0.019	38.323	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	83	LEU	0	0.001	-0.007	34.942	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.874	0.929	32.371	0.051	0.051	0.000	0.000	0.000	0.000
85	A	85	ASP	-1	-0.785	-0.869	29.678	-0.109	-0.109	0.000	0.000	0.000	0.000
86	A	86	ARG	1	0.817	0.908	26.090	0.079	0.079	0.000	0.000	0.000	0.000
87	A	87	ILE	0	0.034	0.026	21.436	-0.005	-0.005	0.000	0.000	0.000	0.000
88	A	88	TYR	0	0.042	0.012	21.253	0.007	0.007	0.000	0.000	0.000	0.000
89	A	89	PHE	0	-0.011	-0.010	12.698	-0.033	-0.033	0.000	0.000	0.000	0.000
90	A	90	ILE	0	0.021	0.004	16.701	0.042	0.042	0.000	0.000	0.000	0.000
91	A	91	PHE	0	-0.045	-0.018	9.091	-0.098	-0.098	0.000	0.000	0.000	0.000
92	A	92	TRP	0	0.028	0.016	13.980	0.080	0.080	0.000	0.000	0.000	0.000
93	A	93	SER	0	0.052	0.001	11.446	-0.097	-0.097	0.000	0.000	0.000	0.000
94	A	94	PRO	0	0.051	0.040	14.388	0.067	0.067	0.000	0.000	0.000	0.000
95	A	95	GLY	0	0.040	0.014	15.977	-0.021	-0.021	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.018	-0.006	17.398	0.003	0.003	0.000	0.000	0.000	0.000
97	A	97	SER	0	-0.045	-0.018	14.329	-0.038	-0.038	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.878	0.915	14.326	0.479	0.479	0.000	0.000	0.000	0.000
99	A	99	PRO	0	0.067	0.011	11.374	-0.108	-0.108	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.915	0.955	8.394	0.562	0.562	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.696	-0.797	8.854	-0.839	-0.839	0.000	0.000	0.000	0.000
102	A	102	LYS	1	0.885	0.941	9.759	0.001	0.001	0.000	0.000	0.000	0.000
103	A	103	MET	0	-0.038	-0.025	4.304	-0.090	0.058	-0.001	-0.006	-0.141	0.000
104	A	104	LEU	0	0.005	0.017	5.106	-0.595	-0.507	-0.001	-0.002	-0.084	0.000
105	A	105	TYR	0	0.057	0.029	6.686	-0.418	-0.418	0.000	0.000	0.000	0.000
106	A	106	ALA	0	0.024	0.024	5.842	-0.082	-0.082	0.000	0.000	0.000	0.000
107	A	107	ALA	0	-0.055	-0.023	2.305	-0.760	-0.038	2.146	-1.060	-1.808	-0.001
108	A	108	SER	0	0.006	-0.007	3.031	-0.935	-1.155	-0.013	0.343	-0.111	-0.001
109	A	109	LYS	1	0.874	0.947	6.239	0.705	0.705	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.876	-0.952	4.884	-1.635	-1.573	-0.001	-0.001	-0.060	0.000
111	A	111	SER	0	-0.018	-0.017	7.640	0.297	0.297	0.000	0.000	0.000	0.000
112	A	112	LEU	0	0.029	0.034	9.530	0.203	0.203	0.000	0.000	0.000	0.000
113	A	113	VAL	0	0.040	0.007	11.506	0.112	0.112	0.000	0.000	0.000	0.000
114	A	114	ARG	1	0.887	0.954	7.335	1.598	1.598	0.000	0.000	0.000	0.000
115	A	115	LYS	1	0.878	0.938	13.326	0.884	0.884	0.000	0.000	0.000	0.000
116	A	116	ILE	0	-0.045	0.002	15.034	0.055	0.055	0.000	0.000	0.000	0.000
117	A	117	ASN	0	0.026	0.005	17.928	0.047	0.047	0.000	0.000	0.000	0.000
118	A	118	GLY	0	-0.010	-0.012	20.093	0.010	0.010	0.000	0.000	0.000	0.000
119	A	119	ILE	0	-0.009	0.009	16.436	0.011	0.011	0.000	0.000	0.000	0.000
120	A	120	PHE	0	-0.018	-0.005	20.497	0.018	0.018	0.000	0.000	0.000	0.000
121	A	121	LYS	1	0.863	0.922	20.035	0.032	0.032	0.000	0.000	0.000	0.000
122	A	122	SER	0	-0.006	-0.004	14.208	-0.028	-0.028	0.000	0.000	0.000	0.000
123	A	123	LEU	0	0.000	-0.001	16.327	0.051	0.051	0.000	0.000	0.000	0.000
124	A	124	GLU	-1	-0.895	-0.955	10.905	-0.017	-0.017	0.000	0.000	0.000	0.000
125	A	125	ILE	0	0.010	0.021	14.939	0.034	0.034	0.000	0.000	0.000	0.000
126	A	126	THR	0	-0.030	-0.038	15.465	-0.035	-0.035	0.000	0.000	0.000	0.000
127	A	127	CYS	0	-0.079	0.001	17.440	0.000	0.000	0.000	0.000	0.000	0.000
128	A	128	ASP	-1	-0.776	-0.857	20.754	-0.107	-0.107	0.000	0.000	0.000	0.000
129	A	129	ILE	0	-0.062	-0.051	23.161	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	130	ASN	0	-0.094	-0.060	24.617	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	131	GLU	-1	-0.786	-0.900	24.906	-0.025	-0.025	0.000	0.000	0.000	0.000
132	A	132	PHE	0	-0.037	-0.018	20.313	0.001	0.001	0.000	0.000	0.000	0.000
133	A	133	GLU	-1	-0.785	-0.895	24.370	-0.099	-0.099	0.000	0.000	0.000	0.000
134	A	134	GLU	-1	-0.930	-0.962	27.571	-0.017	-0.017	0.000	0.000	0.000	0.000
135	A	135	GLU	-1	-0.825	-0.921	20.737	0.001	0.001	0.000	0.000	0.000	0.000
136	A	136	LEU	0	-0.002	-0.008	21.643	0.006	0.006	0.000	0.000	0.000	0.000
137	A	137	LYS	1	0.886	0.918	24.051	0.051	0.051	0.000	0.000	0.000	0.000
138	A	138	ALA	0	0.017	0.012	26.696	0.005	0.005	0.000	0.000	0.000	0.000
139	A	139	ILE	0	-0.004	-0.005	20.531	0.009	0.009	0.000	0.000	0.000	0.000
140	A	140	ILE	0	-0.064	-0.029	24.426	0.002	0.002	0.000	0.000	0.000	0.000
141	A	141	LEU	0	0.013	0.005	26.147	0.005	0.005	0.000	0.000	0.000	0.000
142	A	142	ASN	0	-0.049	-0.009	27.277	0.009	0.009	0.000	0.000	0.000	0.000
143	A	143	THR	0	-0.042	-0.012	25.455	0.002	0.002	0.000	0.000	0.000	0.000

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