FMO DATABASE

FMODB ID: QVNLY

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	OptHSide
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	-1444893.932776
FMO2-HF: Nuclear repulsion	1385693.391645
FMO2-HF: Total energy	-59200.54113
FMO2-MP2: Total energy	-59370.6549

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.
-7.456	-1.961	2.237	-2.056	-5.677	-0.003

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 : 0.065 / q_NPA : 0.067

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	-0.012	-0.010	2.940	-6.039	-2.032	0.479	-1.151	-3.334	0.000
4	A	4	GLY	0	0.006	0.006	3.775	0.474	0.572	0.008	-0.001	-0.105	0.000
5	A	5	VAL	0	0.018	0.029	7.491	0.348	0.348	0.000	0.000	0.000	0.000
6	A	6	ASN	0	-0.023	-0.007	9.923	-0.034	-0.034	0.000	0.000	0.000	0.000
7	A	7	VAL	0	-0.006	-0.023	12.068	-0.002	-0.002	0.000	0.000	0.000	0.000
8	A	8	SER	0	0.028	0.014	14.523	0.069	0.069	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.836	-0.916	18.226	-0.432	-0.432	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.872	-0.956	20.778	-0.293	-0.293	0.000	0.000	0.000	0.000
11	A	11	CYS	0	-0.057	-0.009	17.682	0.009	0.009	0.000	0.000	0.000	0.000
12	A	12	ILE	0	-0.006	-0.012	17.442	0.022	0.022	0.000	0.000	0.000	0.000
13	A	13	TYR	0	-0.035	0.000	20.602	0.043	0.043	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.665	-0.802	23.115	-0.211	-0.211	0.000	0.000	0.000	0.000
15	A	15	PHE	0	0.011	0.012	20.492	0.023	0.023	0.000	0.000	0.000	0.000
16	A	16	ASN	0	0.001	-0.008	22.642	0.030	0.030	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.835	0.885	25.208	0.234	0.234	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.029	0.007	23.751	0.015	0.015	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.842	0.923	23.116	0.218	0.218	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.056	-0.044	26.553	0.017	0.017	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.889	0.943	29.465	0.145	0.145	0.000	0.000	0.000	0.000
22	A	22	HIS	1	0.876	0.961	29.549	0.148	0.148	0.000	0.000	0.000	0.000
23	A	23	LEU	0	0.029	0.014	30.565	0.007	0.007	0.000	0.000	0.000	0.000
24	A	24	ASN	0	-0.066	-0.037	26.277	0.006	0.006	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.835	0.903	28.439	0.131	0.131	0.000	0.000	0.000	0.000
26	A	26	TYR	0	-0.012	-0.046	23.930	0.005	0.005	0.000	0.000	0.000	0.000
27	A	27	ILE	0	-0.026	0.004	20.766	0.002	0.002	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.003	0.008	19.376	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	29	TYR	0	-0.022	-0.010	15.941	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.882	0.935	15.485	0.437	0.437	0.000	0.000	0.000	0.000
31	A	31	ILE	0	-0.035	-0.011	9.836	-0.025	-0.025	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.892	-0.955	14.316	-0.407	-0.407	0.000	0.000	0.000	0.000
33	A	33	ASN	0	-0.025	-0.032	15.756	-0.045	-0.045	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.033	-0.021	11.332	-0.015	-0.015	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.879	-0.936	10.966	-1.038	-1.038	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.898	0.943	12.536	0.602	0.602	0.000	0.000	0.000	0.000
37	A	37	ILE	0	-0.058	-0.017	10.127	0.043	0.043	0.000	0.000	0.000	0.000
38	A	38	VAL	0	0.007	-0.019	14.564	0.055	0.055	0.000	0.000	0.000	0.000
39	A	39	VAL	0	0.035	0.013	18.223	-0.022	-0.022	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.856	-0.925	19.940	-0.374	-0.374	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.004	-0.003	21.874	0.029	0.029	0.000	0.000	0.000	0.000
42	A	42	LEU	0	0.013	0.005	23.775	-0.019	-0.019	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.830	-0.889	26.442	-0.146	-0.146	0.000	0.000	0.000	0.000
44	A	44	HIS	0	-0.001	-0.019	28.989	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	45	ASP	-1	-0.802	-0.873	31.720	-0.111	-0.111	0.000	0.000	0.000	0.000
46	A	46	MET	0	-0.064	-0.041	33.400	0.000	0.000	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.972	-0.977	34.355	-0.083	-0.083	0.000	0.000	0.000	0.000
48	A	48	LEU	0	-0.024	0.012	30.987	0.006	0.006	0.000	0.000	0.000	0.000
49	A	49	THR	0	-0.018	-0.028	33.871	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	50	SER	0	-0.018	-0.003	34.628	0.001	0.001	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.079	0.025	28.091	-0.007	-0.007	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.803	-0.885	30.302	-0.076	-0.076	0.000	0.000	0.000	0.000
53	A	53	ASN	0	0.003	-0.008	31.566	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	54	ILE	0	0.028	0.026	26.501	-0.008	-0.008	0.000	0.000	0.000	0.000
55	A	55	ILE	0	-0.017	-0.017	26.027	-0.013	-0.013	0.000	0.000	0.000	0.000
56	A	56	MET	0	-0.005	0.012	27.278	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.747	0.841	29.209	0.127	0.127	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.005	0.008	22.729	-0.013	-0.013	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.897	0.943	24.742	0.098	0.098	0.000	0.000	0.000	0.000
60	A	60	ASN	0	-0.040	-0.025	25.853	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	61	ASN	0	-0.032	0.000	24.434	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.020	0.005	19.810	-0.033	-0.033	0.000	0.000	0.000	0.000
63	A	63	LYS	1	0.902	0.933	21.474	0.288	0.288	0.000	0.000	0.000	0.000
64	A	64	ASN	0	0.034	-0.012	20.982	-0.021	-0.021	0.000	0.000	0.000	0.000
65	A	65	THR	0	0.002	-0.006	19.703	0.011	0.011	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.877	-0.920	17.239	-0.398	-0.398	0.000	0.000	0.000	0.000
67	A	67	CYS	0	-0.056	0.001	12.983	0.044	0.044	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.742	0.851	15.057	0.401	0.401	0.000	0.000	0.000	0.000
69	A	69	TYR	0	-0.022	-0.027	8.574	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	70	ILE	0	0.006	0.001	15.166	0.012	0.012	0.000	0.000	0.000	0.000
71	A	71	ILE	0	-0.043	-0.004	17.653	0.002	0.002	0.000	0.000	0.000	0.000
72	A	72	ALA	0	0.046	0.015	20.090	0.008	0.008	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.831	-0.907	23.541	-0.140	-0.140	0.000	0.000	0.000	0.000
74	A	74	MET	0	-0.004	0.001	23.969	0.009	0.009	0.000	0.000	0.000	0.000
75	A	75	PRO	0	0.055	0.027	27.803	0.006	0.006	0.000	0.000	0.000	0.000
76	A	76	ILE	0	-0.004	-0.010	27.327	0.006	0.006	0.000	0.000	0.000	0.000
77	A	77	PRO	0	-0.011	0.016	31.735	0.001	0.001	0.000	0.000	0.000	0.000
78	A	78	THR	0	0.026	0.012	33.907	0.001	0.001	0.000	0.000	0.000	0.000
79	A	79	PRO	0	0.020	0.005	34.009	0.000	0.000	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-1.016	-0.969	36.726	-0.023	-0.023	0.000	0.000	0.000	0.000
81	A	81	GLY	0	0.062	0.003	37.847	0.002	0.002	0.000	0.000	0.000	0.000
82	A	82	VAL	0	-0.058	-0.042	38.127	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	83	LEU	0	0.007	-0.018	34.890	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.889	0.960	32.098	0.054	0.054	0.000	0.000	0.000	0.000
85	A	85	ASP	-1	-0.799	-0.890	29.606	-0.112	-0.112	0.000	0.000	0.000	0.000
86	A	86	ARG	1	0.837	0.929	25.866	0.080	0.080	0.000	0.000	0.000	0.000
87	A	87	ILE	0	0.038	0.025	21.148	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	88	TYR	0	0.037	0.013	20.851	0.007	0.007	0.000	0.000	0.000	0.000
89	A	89	PHE	0	-0.012	-0.010	12.545	-0.028	-0.028	0.000	0.000	0.000	0.000
90	A	90	ILE	0	0.023	0.000	16.722	0.031	0.031	0.000	0.000	0.000	0.000
91	A	91	PHE	0	-0.052	-0.024	9.261	-0.097	-0.097	0.000	0.000	0.000	0.000
92	A	92	TRP	0	0.023	0.017	13.993	0.068	0.068	0.000	0.000	0.000	0.000
93	A	93	SER	0	0.046	-0.002	11.577	-0.087	-0.087	0.000	0.000	0.000	0.000
94	A	94	PRO	0	0.078	0.057	14.544	0.057	0.057	0.000	0.000	0.000	0.000
95	A	95	GLY	0	0.048	0.017	16.133	-0.029	-0.029	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.021	-0.005	17.426	-0.005	-0.005	0.000	0.000	0.000	0.000
97	A	97	SER	0	-0.041	-0.004	14.878	-0.036	-0.036	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.906	0.942	14.089	0.482	0.482	0.000	0.000	0.000	0.000
99	A	99	PRO	0	0.088	0.020	11.267	-0.091	-0.091	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.911	0.946	9.061	0.552	0.552	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.749	-0.836	9.277	-0.796	-0.796	0.000	0.000	0.000	0.000
102	A	102	LYS	1	0.896	0.931	9.912	0.070	0.070	0.000	0.000	0.000	0.000
103	A	103	MET	0	-0.040	-0.025	4.410	-0.132	0.011	-0.001	-0.005	-0.137	0.000
104	A	104	LEU	0	0.031	0.030	5.498	-0.431	-0.431	0.000	0.000	0.000	0.000
105	A	105	TYR	0	0.071	0.041	6.639	-0.375	-0.375	0.000	0.000	0.000	0.000
106	A	106	ALA	0	0.022	0.018	6.060	-0.123	-0.123	0.000	0.000	0.000	0.000
107	A	107	ALA	0	-0.048	-0.018	2.311	-0.902	0.030	1.759	-1.024	-1.668	0.000
108	A	108	SER	0	0.000	-0.012	3.010	-1.683	-1.529	-0.007	0.151	-0.299	-0.003
109	A	109	LYS	1	0.909	0.967	6.044	0.762	0.762	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.877	-0.944	4.144	-1.982	-1.821	-0.001	-0.026	-0.134	0.000
111	A	111	SER	0	-0.038	-0.031	7.430	0.406	0.406	0.000	0.000	0.000	0.000
112	A	112	LEU	0	0.033	0.021	9.186	0.262	0.262	0.000	0.000	0.000	0.000
113	A	113	VAL	0	0.031	0.013	11.021	0.137	0.137	0.000	0.000	0.000	0.000
114	A	114	ARG	1	0.911	0.974	7.234	1.606	1.606	0.000	0.000	0.000	0.000
115	A	115	LYS	1	0.839	0.915	12.764	0.900	0.900	0.000	0.000	0.000	0.000
116	A	116	ILE	0	-0.044	0.000	14.857	0.055	0.055	0.000	0.000	0.000	0.000
117	A	117	ASN	0	0.064	0.029	17.587	0.016	0.016	0.000	0.000	0.000	0.000
118	A	118	GLY	0	-0.032	-0.045	19.791	0.003	0.003	0.000	0.000	0.000	0.000
119	A	119	ILE	0	-0.009	0.016	16.231	0.013	0.013	0.000	0.000	0.000	0.000
120	A	120	PHE	0	-0.029	-0.007	20.276	0.018	0.018	0.000	0.000	0.000	0.000
121	A	121	LYS	1	0.911	0.950	19.583	0.046	0.046	0.000	0.000	0.000	0.000
122	A	122	SER	0	-0.003	0.003	14.226	-0.029	-0.029	0.000	0.000	0.000	0.000
123	A	123	LEU	0	-0.023	-0.015	16.295	0.051	0.051	0.000	0.000	0.000	0.000
124	A	124	GLU	-1	-0.880	-0.944	10.840	-0.022	-0.022	0.000	0.000	0.000	0.000
125	A	125	ILE	0	0.004	0.013	14.886	0.036	0.036	0.000	0.000	0.000	0.000
126	A	126	THR	0	-0.008	-0.035	15.326	-0.038	-0.038	0.000	0.000	0.000	0.000
127	A	127	CYS	0	-0.049	0.030	17.325	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	128	ASP	-1	-0.754	-0.849	20.651	-0.123	-0.123	0.000	0.000	0.000	0.000
129	A	129	ILE	0	-0.030	-0.040	23.106	0.000	0.000	0.000	0.000	0.000	0.000
130	A	130	ASN	0	-0.106	-0.069	24.427	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	131	GLU	-1	-0.827	-0.919	25.226	-0.044	-0.044	0.000	0.000	0.000	0.000
132	A	132	PHE	0	-0.042	-0.017	20.319	0.001	0.001	0.000	0.000	0.000	0.000
133	A	133	GLU	-1	-0.859	-0.928	24.334	-0.099	-0.099	0.000	0.000	0.000	0.000
134	A	134	GLU	-1	-0.915	-0.960	27.272	-0.032	-0.032	0.000	0.000	0.000	0.000
135	A	135	GLU	-1	-0.868	-0.946	21.082	-0.025	-0.025	0.000	0.000	0.000	0.000
136	A	136	LEU	0	-0.002	-0.015	22.113	0.005	0.005	0.000	0.000	0.000	0.000
137	A	137	LYS	1	0.877	0.926	24.230	0.063	0.063	0.000	0.000	0.000	0.000
138	A	138	ALA	0	0.029	0.025	26.746	0.006	0.006	0.000	0.000	0.000	0.000
139	A	139	ILE	0	-0.016	-0.011	20.646	0.008	0.008	0.000	0.000	0.000	0.000
140	A	140	ILE	0	-0.068	-0.035	24.372	0.004	0.004	0.000	0.000	0.000	0.000
141	A	141	LEU	0	-0.006	-0.010	26.069	0.003	0.003	0.000	0.000	0.000	0.000
142	A	142	ASN	0	-0.075	-0.019	27.177	0.010	0.010	0.000	0.000	0.000	0.000
143	A	143	THR	0	-0.035	-0.020	25.207	0.000	0.000	0.000	0.000	0.000	0.000

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