FMO DATABASE

FMODB ID: V5J81

Calculation Name: 5XFS-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5XFS

Chain ID: B

ChEMBL ID:

UniProt ID: O53943

Base Structure: X-ray

Registration Date: 2023-06-26

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	OptHSide
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	173
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1194697.561108
FMO2-HF: Nuclear repulsion	1131038.71678
FMO2-HF: Total energy	-63658.844328
FMO2-MP2: Total energy	-63836.134824

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(B:1:MET)

Summations of interaction energy for fragment #1(B: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.
-6.759	-1.062	3.454	-3.218	-5.932	-0.016

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : -0.004

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	B	3	PHE	0	0.007	-0.001	2.912	-5.717	-1.224	0.393	-2.452	-2.433	-0.011
4	B	4	GLY	0	0.058	0.029	5.024	0.096	0.232	-0.001	-0.005	-0.129	0.000
5	B	5	ALA	0	-0.033	-0.007	2.304	0.086	0.199	1.188	-0.294	-1.008	-0.002
6	B	6	LEU	0	-0.096	-0.035	2.410	-1.439	-0.576	1.874	-0.450	-2.287	-0.003
7	B	7	PRO	0	0.043	0.025	4.367	0.389	0.481	0.000	-0.017	-0.075	0.000
8	B	8	PRO	0	0.036	0.027	8.058	-0.068	-0.068	0.000	0.000	0.000	0.000
9	B	9	GLU	-1	-0.793	-0.885	10.961	-0.674	-0.674	0.000	0.000	0.000	0.000
10	B	10	ILE	0	-0.071	-0.034	6.149	0.103	0.103	0.000	0.000	0.000	0.000
11	B	11	ASN	0	-0.018	-0.029	6.631	-0.100	-0.100	0.000	0.000	0.000	0.000
12	B	12	SER	0	0.084	0.038	9.710	0.119	0.119	0.000	0.000	0.000	0.000
13	B	13	ALA	0	-0.027	-0.008	12.106	0.106	0.106	0.000	0.000	0.000	0.000
14	B	14	ARG	1	0.819	0.905	5.499	1.879	1.879	0.000	0.000	0.000	0.000
15	B	15	MET	0	-0.015	0.018	12.241	0.041	0.041	0.000	0.000	0.000	0.000
16	B	16	TYR	0	-0.016	-0.019	14.277	0.084	0.084	0.000	0.000	0.000	0.000
17	B	17	ALA	0	-0.016	-0.001	15.995	0.067	0.067	0.000	0.000	0.000	0.000
18	B	18	GLY	0	0.008	0.007	16.577	-0.036	-0.036	0.000	0.000	0.000	0.000
19	B	19	ALA	0	-0.038	-0.031	18.483	0.017	0.017	0.000	0.000	0.000	0.000
20	B	20	GLY	0	0.050	0.035	19.923	0.021	0.021	0.000	0.000	0.000	0.000
21	B	21	ALA	0	0.064	0.025	21.155	0.002	0.002	0.000	0.000	0.000	0.000
22	B	22	GLY	0	-0.023	-0.011	22.968	0.014	0.014	0.000	0.000	0.000	0.000
23	B	23	PRO	0	-0.010	-0.014	21.874	0.016	0.016	0.000	0.000	0.000	0.000
24	B	24	MET	0	0.021	0.018	18.822	0.025	0.025	0.000	0.000	0.000	0.000
25	B	25	MET	0	0.046	0.019	23.622	0.009	0.009	0.000	0.000	0.000	0.000
26	B	26	ALA	0	-0.025	0.000	26.984	0.014	0.014	0.000	0.000	0.000	0.000
27	B	27	ALA	0	0.000	0.001	25.124	0.013	0.013	0.000	0.000	0.000	0.000
28	B	28	GLY	0	0.014	0.001	26.920	0.009	0.009	0.000	0.000	0.000	0.000
29	B	29	ALA	0	0.028	0.002	28.457	0.010	0.010	0.000	0.000	0.000	0.000
30	B	30	ALA	0	-0.018	0.004	30.389	0.010	0.010	0.000	0.000	0.000	0.000
31	B	31	TRP	0	0.020	0.006	26.211	0.015	0.015	0.000	0.000	0.000	0.000
32	B	32	ASN	0	0.003	-0.013	31.440	-0.001	-0.001	0.000	0.000	0.000	0.000
33	B	33	GLY	0	0.002	0.007	34.100	0.006	0.006	0.000	0.000	0.000	0.000
34	B	34	LEU	0	-0.013	-0.005	32.716	0.007	0.007	0.000	0.000	0.000	0.000
35	B	35	ALA	0	0.010	0.002	34.391	0.005	0.005	0.000	0.000	0.000	0.000
36	B	36	ALA	0	-0.049	-0.020	36.280	0.004	0.004	0.000	0.000	0.000	0.000
37	B	37	GLU	-1	-0.864	-0.921	39.260	-0.050	-0.050	0.000	0.000	0.000	0.000
38	B	38	LEU	0	-0.049	-0.003	35.729	0.006	0.006	0.000	0.000	0.000	0.000
39	B	39	GLY	0	0.056	0.027	40.121	0.004	0.004	0.000	0.000	0.000	0.000
40	B	40	THR	0	-0.032	-0.030	42.106	0.003	0.003	0.000	0.000	0.000	0.000
41	B	41	THR	0	-0.012	-0.014	43.235	0.005	0.005	0.000	0.000	0.000	0.000
42	B	42	ALA	0	-0.004	-0.006	43.090	0.004	0.004	0.000	0.000	0.000	0.000
43	B	43	ALA	0	-0.026	-0.018	45.161	0.002	0.002	0.000	0.000	0.000	0.000
44	B	44	SER	0	-0.025	-0.014	47.788	0.003	0.003	0.000	0.000	0.000	0.000
45	B	45	TYR	0	0.047	0.009	47.645	0.004	0.004	0.000	0.000	0.000	0.000
46	B	46	GLU	-1	-0.907	-0.948	47.494	-0.039	-0.039	0.000	0.000	0.000	0.000
47	B	47	SER	0	-0.049	-0.011	50.488	0.000	0.000	0.000	0.000	0.000	0.000
48	B	48	VAL	0	-0.052	-0.027	53.088	0.002	0.002	0.000	0.000	0.000	0.000
49	B	49	ILE	0	0.043	0.003	50.524	0.002	0.002	0.000	0.000	0.000	0.000
50	B	50	THR	0	0.014	0.003	52.951	0.002	0.002	0.000	0.000	0.000	0.000
51	B	51	ARG	1	0.858	0.930	55.677	0.025	0.025	0.000	0.000	0.000	0.000
52	B	52	LEU	0	-0.024	0.019	56.333	0.001	0.001	0.000	0.000	0.000	0.000
53	B	53	THR	0	-0.018	-0.038	56.465	0.002	0.002	0.000	0.000	0.000	0.000
54	B	54	THR	0	-0.070	-0.043	59.110	0.001	0.001	0.000	0.000	0.000	0.000
55	B	55	GLU	-1	-0.841	-0.890	61.427	-0.023	-0.023	0.000	0.000	0.000	0.000
56	B	56	SER	0	-0.042	-0.012	62.487	0.001	0.001	0.000	0.000	0.000	0.000
57	B	57	TRP	0	-0.038	-0.038	58.293	0.001	0.001	0.000	0.000	0.000	0.000
58	B	58	MET	0	-0.019	-0.010	59.557	0.001	0.001	0.000	0.000	0.000	0.000
59	B	59	GLY	0	0.044	0.025	64.076	0.001	0.001	0.000	0.000	0.000	0.000
60	B	60	PRO	0	0.009	-0.009	63.661	-0.001	-0.001	0.000	0.000	0.000	0.000
61	B	61	ALA	0	-0.001	0.007	61.330	0.000	0.000	0.000	0.000	0.000	0.000
62	B	62	SER	0	0.018	0.007	60.019	0.000	0.000	0.000	0.000	0.000	0.000
63	B	63	MET	0	0.037	0.012	57.041	-0.001	-0.001	0.000	0.000	0.000	0.000
64	B	64	ALA	0	0.003	0.006	55.704	-0.001	-0.001	0.000	0.000	0.000	0.000
65	B	65	MET	0	-0.008	-0.002	54.936	0.001	0.001	0.000	0.000	0.000	0.000
66	B	66	VAL	0	0.012	0.016	52.310	-0.001	-0.001	0.000	0.000	0.000	0.000
67	B	67	ALA	0	-0.024	-0.026	51.341	-0.001	-0.001	0.000	0.000	0.000	0.000
68	B	68	ALA	0	-0.023	-0.010	49.946	0.000	0.000	0.000	0.000	0.000	0.000
69	B	69	ALA	0	0.022	0.009	48.896	0.000	0.000	0.000	0.000	0.000	0.000
70	B	70	GLN	0	0.004	0.008	47.040	-0.003	-0.003	0.000	0.000	0.000	0.000
71	B	71	PRO	0	-0.029	-0.018	43.577	-0.003	-0.003	0.000	0.000	0.000	0.000
72	B	72	TYR	0	-0.010	-0.007	41.395	-0.001	-0.001	0.000	0.000	0.000	0.000
73	B	73	LEU	0	0.036	0.019	42.734	-0.003	-0.003	0.000	0.000	0.000	0.000
74	B	74	ALA	0	0.000	-0.001	41.501	-0.004	-0.004	0.000	0.000	0.000	0.000
75	B	75	TRP	0	-0.013	-0.002	35.345	-0.004	-0.004	0.000	0.000	0.000	0.000
76	B	76	LEU	0	-0.016	0.012	38.053	-0.005	-0.005	0.000	0.000	0.000	0.000
77	B	77	THR	0	0.016	0.004	38.998	-0.005	-0.005	0.000	0.000	0.000	0.000
78	B	78	TYR	0	-0.028	-0.013	31.112	-0.006	-0.006	0.000	0.000	0.000	0.000
79	B	79	THR	0	0.018	-0.016	33.373	-0.007	-0.007	0.000	0.000	0.000	0.000
80	B	80	ALA	0	-0.028	-0.015	34.152	-0.007	-0.007	0.000	0.000	0.000	0.000
81	B	81	GLU	-1	-0.947	-0.970	34.202	-0.095	-0.095	0.000	0.000	0.000	0.000
82	B	82	ALA	0	0.008	0.011	30.432	-0.011	-0.011	0.000	0.000	0.000	0.000
83	B	83	ALA	0	-0.026	-0.007	29.991	-0.011	-0.011	0.000	0.000	0.000	0.000
84	B	84	ALA	0	0.030	0.001	30.919	-0.010	-0.010	0.000	0.000	0.000	0.000
85	B	85	HIS	0	-0.065	-0.013	25.418	-0.005	-0.005	0.000	0.000	0.000	0.000
86	B	86	ALA	0	0.062	0.013	26.363	-0.018	-0.018	0.000	0.000	0.000	0.000
87	B	87	GLY	0	-0.010	0.001	26.728	-0.014	-0.014	0.000	0.000	0.000	0.000
88	B	88	SER	0	-0.069	-0.043	27.985	-0.013	-0.013	0.000	0.000	0.000	0.000
89	B	89	GLN	0	-0.011	-0.014	22.888	-0.026	-0.026	0.000	0.000	0.000	0.000
90	B	90	ALA	0	-0.005	0.014	22.978	-0.029	-0.029	0.000	0.000	0.000	0.000
91	B	91	MET	0	-0.042	-0.029	23.420	-0.019	-0.019	0.000	0.000	0.000	0.000
92	B	92	ALA	0	0.007	0.019	23.309	-0.019	-0.019	0.000	0.000	0.000	0.000
93	B	93	SER	0	-0.007	-0.030	19.483	-0.042	-0.042	0.000	0.000	0.000	0.000
94	B	94	ALA	0	-0.043	-0.012	19.387	-0.043	-0.043	0.000	0.000	0.000	0.000
95	B	95	ALA	0	0.020	0.001	21.187	-0.022	-0.022	0.000	0.000	0.000	0.000
96	B	96	ALA	0	0.010	0.014	17.862	-0.021	-0.021	0.000	0.000	0.000	0.000
97	B	97	TYR	0	-0.018	-0.006	16.345	-0.035	-0.035	0.000	0.000	0.000	0.000
98	B	98	GLU	-1	-0.923	-0.981	18.140	-0.330	-0.330	0.000	0.000	0.000	0.000
99	B	99	ALA	0	-0.049	-0.020	19.985	0.005	0.005	0.000	0.000	0.000	0.000
100	B	100	ALA	0	0.010	0.007	14.868	-0.018	-0.018	0.000	0.000	0.000	0.000
101	B	101	TYR	0	0.006	0.013	16.408	-0.044	-0.044	0.000	0.000	0.000	0.000
102	B	102	ALA	0	-0.050	-0.016	18.257	0.007	0.007	0.000	0.000	0.000	0.000
103	B	103	MET	0	-0.058	-0.014	17.561	0.001	0.001	0.000	0.000	0.000	0.000
104	B	104	THR	0	-0.025	-0.003	14.119	-0.067	-0.067	0.000	0.000	0.000	0.000
105	B	105	VAL	0	-0.022	-0.010	15.635	0.086	0.086	0.000	0.000	0.000	0.000
106	B	106	PRO	0	0.014	0.007	16.490	-0.035	-0.035	0.000	0.000	0.000	0.000
107	B	107	PRO	0	0.043	0.018	16.472	0.000	0.000	0.000	0.000	0.000	0.000
108	B	108	GLU	-1	-0.905	-0.968	17.567	-0.327	-0.327	0.000	0.000	0.000	0.000
109	B	109	VAL	0	-0.023	-0.014	20.047	0.023	0.023	0.000	0.000	0.000	0.000
110	B	110	VAL	0	0.036	0.015	14.265	0.013	0.013	0.000	0.000	0.000	0.000
111	B	111	ALA	0	0.001	-0.009	17.681	0.024	0.024	0.000	0.000	0.000	0.000
112	B	112	ALA	0	-0.015	0.005	18.987	0.035	0.035	0.000	0.000	0.000	0.000
113	B	113	ASN	0	0.011	0.000	19.050	0.010	0.010	0.000	0.000	0.000	0.000
114	B	114	ARG	1	0.828	0.900	15.760	0.435	0.435	0.000	0.000	0.000	0.000
115	B	115	ALA	0	-0.003	0.003	19.703	0.029	0.029	0.000	0.000	0.000	0.000
116	B	116	LEU	0	-0.013	-0.005	22.991	0.026	0.026	0.000	0.000	0.000	0.000
117	B	117	LEU	0	-0.007	0.008	19.369	0.022	0.022	0.000	0.000	0.000	0.000
118	B	118	ALA	0	-0.001	-0.007	22.680	0.020	0.020	0.000	0.000	0.000	0.000
119	B	119	ALA	0	-0.020	-0.005	24.274	0.020	0.020	0.000	0.000	0.000	0.000
120	B	120	LEU	0	-0.010	-0.017	26.283	0.016	0.016	0.000	0.000	0.000	0.000
121	B	121	VAL	0	0.010	0.002	23.932	0.012	0.012	0.000	0.000	0.000	0.000
122	B	122	ALA	0	-0.023	-0.001	27.310	0.013	0.013	0.000	0.000	0.000	0.000
123	B	123	THR	0	-0.027	-0.018	29.778	0.010	0.010	0.000	0.000	0.000	0.000
124	B	124	ASN	0	-0.028	0.006	29.201	0.005	0.005	0.000	0.000	0.000	0.000
125	B	125	VAL	0	-0.010	-0.012	31.938	0.004	0.004	0.000	0.000	0.000	0.000
126	B	126	LEU	0	-0.014	-0.013	34.675	0.005	0.005	0.000	0.000	0.000	0.000
127	B	127	GLY	0	0.007	0.007	32.167	0.000	0.000	0.000	0.000	0.000	0.000
128	B	128	ILE	0	-0.010	-0.011	32.918	-0.005	-0.005	0.000	0.000	0.000	0.000
129	B	129	ASN	0	0.048	0.018	30.422	-0.005	-0.005	0.000	0.000	0.000	0.000
130	B	130	THR	0	-0.004	0.004	27.468	-0.012	-0.012	0.000	0.000	0.000	0.000
131	B	131	PRO	0	0.020	-0.001	27.340	-0.013	-0.013	0.000	0.000	0.000	0.000
132	B	132	ALA	0	0.033	0.022	27.558	-0.013	-0.013	0.000	0.000	0.000	0.000
133	B	133	ILE	0	-0.037	0.003	23.642	-0.018	-0.018	0.000	0.000	0.000	0.000
134	B	134	MET	0	0.031	-0.004	22.256	-0.025	-0.025	0.000	0.000	0.000	0.000
135	B	135	ALA	0	-0.007	0.011	22.877	-0.019	-0.019	0.000	0.000	0.000	0.000
136	B	136	THR	0	-0.043	-0.035	21.340	-0.021	-0.021	0.000	0.000	0.000	0.000
137	B	137	GLU	-1	-0.799	-0.892	17.895	-0.374	-0.374	0.000	0.000	0.000	0.000
138	B	138	ALA	0	-0.034	-0.007	18.004	-0.046	-0.046	0.000	0.000	0.000	0.000
139	B	139	LEU	0	0.041	0.014	18.631	-0.037	-0.037	0.000	0.000	0.000	0.000
140	B	140	TYR	0	-0.061	-0.051	12.175	-0.045	-0.045	0.000	0.000	0.000	0.000
141	B	141	ALA	0	0.031	0.012	13.946	-0.084	-0.084	0.000	0.000	0.000	0.000
142	B	142	GLU	-1	-0.930	-0.961	14.484	-0.450	-0.450	0.000	0.000	0.000	0.000
143	B	143	MET	0	-0.011	0.011	15.302	-0.034	-0.034	0.000	0.000	0.000	0.000
144	B	144	TRP	0	-0.076	-0.040	6.708	0.073	0.073	0.000	0.000	0.000	0.000
145	B	145	ALA	0	-0.036	-0.025	10.994	-0.158	-0.158	0.000	0.000	0.000	0.000
146	B	146	GLN	0	-0.053	-0.031	13.119	-0.004	-0.004	0.000	0.000	0.000	0.000
147	B	147	ASP	-1	-0.767	-0.905	10.687	-0.955	-0.955	0.000	0.000	0.000	0.000
148	B	148	ALA	0	-0.051	-0.013	9.055	-0.103	-0.103	0.000	0.000	0.000	0.000
149	B	149	LEU	0	-0.019	-0.005	10.123	-0.034	-0.034	0.000	0.000	0.000	0.000
150	B	150	ALA	0	0.049	0.027	13.472	0.054	0.054	0.000	0.000	0.000	0.000
151	B	151	MET	0	-0.031	-0.019	8.651	-0.010	-0.010	0.000	0.000	0.000	0.000
152	B	152	TYR	0	-0.069	-0.066	7.635	0.153	0.153	0.000	0.000	0.000	0.000
153	B	153	GLY	0	0.009	0.005	11.492	0.092	0.092	0.000	0.000	0.000	0.000
154	B	154	TYR	0	0.008	0.005	12.246	0.086	0.086	0.000	0.000	0.000	0.000
155	B	155	ALA	0	-0.008	-0.012	10.109	0.090	0.090	0.000	0.000	0.000	0.000
156	B	156	ALA	0	-0.031	-0.011	12.206	0.116	0.116	0.000	0.000	0.000	0.000
157	B	157	ALA	0	0.003	-0.002	14.978	0.084	0.084	0.000	0.000	0.000	0.000
158	B	158	SER	0	0.001	-0.013	14.210	0.087	0.087	0.000	0.000	0.000	0.000
159	B	159	GLY	0	-0.023	0.002	15.491	0.049	0.049	0.000	0.000	0.000	0.000
160	B	160	ALA	0	-0.046	-0.027	16.114	0.064	0.064	0.000	0.000	0.000	0.000
161	B	161	ALA	0	0.011	0.019	19.041	0.043	0.043	0.000	0.000	0.000	0.000
162	B	162	GLY	0	0.007	0.015	17.940	0.033	0.033	0.000	0.000	0.000	0.000
163	B	163	MET	0	-0.071	-0.027	18.358	0.042	0.042	0.000	0.000	0.000	0.000
164	B	164	LEU	0	0.039	0.012	21.647	0.010	0.010	0.000	0.000	0.000	0.000
165	B	165	GLN	0	0.011	0.011	24.385	0.014	0.014	0.000	0.000	0.000	0.000
166	B	166	PRO	0	0.001	0.000	26.318	0.005	0.005	0.000	0.000	0.000	0.000
167	B	167	LEU	0	0.035	0.033	27.772	0.003	0.003	0.000	0.000	0.000	0.000
168	B	168	SER	0	-0.002	-0.006	30.142	0.006	0.006	0.000	0.000	0.000	0.000
169	B	169	PRO	0	-0.010	-0.007	32.885	-0.003	-0.003	0.000	0.000	0.000	0.000
170	B	170	PRO	0	0.005	0.013	36.211	-0.001	-0.001	0.000	0.000	0.000	0.000
171	B	171	SER	0	0.008	-0.013	39.083	0.006	0.006	0.000	0.000	0.000	0.000
172	B	172	GLN	0	-0.031	-0.003	41.035	-0.004	-0.004	0.000	0.000	0.000	0.000
173	B	173	THR	0	0.020	0.013	43.648	-0.001	-0.001	0.000	0.000	0.000	0.000

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