FMO DATABASE

FMODB ID: YZJ62

Calculation Name: 5XFS-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1194317.704664
FMO2-HF: Nuclear repulsion	1130659.606317
FMO2-HF: Total energy	-63658.098347
FMO2-MP2: Total energy	-63835.428088

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(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.
-3.25	0.99	2.704	-2.757	-4.186	-0.014

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 : -0.024

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	0.001	-0.002	2.994	-3.252	0.298	0.227	-1.966	-1.811	-0.010
4	B	4	GLY	0	0.066	0.029	5.195	0.265	0.393	-0.001	-0.005	-0.122	0.000
5	B	5	ALA	0	-0.034	-0.008	2.113	0.499	-0.068	2.319	-0.601	-1.150	-0.003
6	B	6	LEU	0	-0.100	-0.036	2.841	-0.793	0.290	0.160	-0.183	-1.060	-0.001
7	B	7	PRO	0	0.059	0.031	5.045	0.229	0.275	-0.001	-0.002	-0.043	0.000
8	B	8	PRO	0	0.049	0.034	8.532	0.017	0.017	0.000	0.000	0.000	0.000
9	B	9	GLU	-1	-0.846	-0.921	11.609	-0.360	-0.360	0.000	0.000	0.000	0.000
10	B	10	ILE	0	-0.068	-0.032	6.866	0.133	0.133	0.000	0.000	0.000	0.000
11	B	11	ASN	0	-0.028	-0.029	7.331	0.108	0.108	0.000	0.000	0.000	0.000
12	B	12	SER	0	0.066	0.030	9.998	0.109	0.109	0.000	0.000	0.000	0.000
13	B	13	ALA	0	-0.017	-0.001	12.438	0.080	0.080	0.000	0.000	0.000	0.000
14	B	14	ARG	1	0.866	0.921	5.067	0.427	0.427	0.000	0.000	0.000	0.000
15	B	15	MET	0	-0.006	0.017	12.224	0.049	0.049	0.000	0.000	0.000	0.000
16	B	16	TYR	0	-0.006	-0.007	14.530	0.044	0.044	0.000	0.000	0.000	0.000
17	B	17	ALA	0	-0.021	-0.003	16.004	0.032	0.032	0.000	0.000	0.000	0.000
18	B	18	GLY	0	0.003	0.004	16.549	0.002	0.002	0.000	0.000	0.000	0.000
19	B	19	ALA	0	-0.033	-0.028	18.450	-0.009	-0.009	0.000	0.000	0.000	0.000
20	B	20	GLY	0	0.055	0.029	19.841	-0.004	-0.004	0.000	0.000	0.000	0.000
21	B	21	ALA	0	0.063	0.024	21.063	0.013	0.013	0.000	0.000	0.000	0.000
22	B	22	GLY	0	-0.025	-0.011	22.847	0.008	0.008	0.000	0.000	0.000	0.000
23	B	23	PRO	0	-0.009	-0.009	21.558	0.005	0.005	0.000	0.000	0.000	0.000
24	B	24	MET	0	0.019	0.015	18.951	0.014	0.014	0.000	0.000	0.000	0.000
25	B	25	MET	0	0.046	0.011	23.557	-0.003	-0.003	0.000	0.000	0.000	0.000
26	B	26	ALA	0	-0.031	0.000	26.892	0.001	0.001	0.000	0.000	0.000	0.000
27	B	27	ALA	0	-0.005	-0.001	25.112	0.004	0.004	0.000	0.000	0.000	0.000
28	B	28	GLY	0	0.020	0.000	26.856	0.000	0.000	0.000	0.000	0.000	0.000
29	B	29	ALA	0	0.033	0.005	28.387	0.001	0.001	0.000	0.000	0.000	0.000
30	B	30	ALA	0	-0.022	0.003	30.350	0.001	0.001	0.000	0.000	0.000	0.000
31	B	31	TRP	0	0.016	0.006	26.377	0.002	0.002	0.000	0.000	0.000	0.000
32	B	32	ASN	0	0.008	-0.013	31.408	-0.002	-0.002	0.000	0.000	0.000	0.000
33	B	33	GLY	0	0.000	0.009	34.036	-0.001	-0.001	0.000	0.000	0.000	0.000
34	B	34	LEU	0	-0.002	-0.002	32.718	0.002	0.002	0.000	0.000	0.000	0.000
35	B	35	ALA	0	0.006	0.000	34.499	0.000	0.000	0.000	0.000	0.000	0.000
36	B	36	ALA	0	-0.051	-0.022	36.407	-0.001	-0.001	0.000	0.000	0.000	0.000
37	B	37	GLU	-1	-0.898	-0.961	39.274	0.010	0.010	0.000	0.000	0.000	0.000
38	B	38	LEU	0	-0.051	0.014	36.035	0.003	0.003	0.000	0.000	0.000	0.000
39	B	39	GLY	0	0.056	0.026	40.428	0.000	0.000	0.000	0.000	0.000	0.000
40	B	40	THR	0	-0.012	-0.006	42.400	-0.001	-0.001	0.000	0.000	0.000	0.000
41	B	41	THR	0	-0.034	-0.031	43.419	0.001	0.001	0.000	0.000	0.000	0.000
42	B	42	ALA	0	-0.003	-0.004	43.580	0.001	0.001	0.000	0.000	0.000	0.000
43	B	43	ALA	0	-0.024	-0.017	45.648	-0.001	-0.001	0.000	0.000	0.000	0.000
44	B	44	SER	0	-0.018	-0.008	48.165	0.000	0.000	0.000	0.000	0.000	0.000
45	B	45	TYR	0	0.062	0.021	48.078	0.001	0.001	0.000	0.000	0.000	0.000
46	B	46	GLU	-1	-0.900	-0.947	47.921	-0.004	-0.004	0.000	0.000	0.000	0.000
47	B	47	SER	0	-0.019	0.073	50.934	-0.001	-0.001	0.000	0.000	0.000	0.000
48	B	48	VAL	0	-0.028	-0.027	53.588	0.000	0.000	0.000	0.000	0.000	0.000
49	B	49	ILE	0	0.050	0.006	50.972	0.000	0.000	0.000	0.000	0.000	0.000
50	B	50	THR	0	-0.054	-0.089	53.416	0.000	0.000	0.000	0.000	0.000	0.000
51	B	51	ARG	1	0.927	0.966	56.087	-0.004	-0.004	0.000	0.000	0.000	0.000
52	B	52	LEU	0	-0.037	0.019	56.953	0.000	0.000	0.000	0.000	0.000	0.000
53	B	53	THR	0	-0.023	-0.047	56.829	0.000	0.000	0.000	0.000	0.000	0.000
54	B	54	THR	0	-0.049	-0.014	59.603	0.000	0.000	0.000	0.000	0.000	0.000
55	B	55	GLU	-1	-0.925	-0.970	61.805	0.001	0.001	0.000	0.000	0.000	0.000
56	B	56	SER	0	-0.055	-0.021	62.896	0.000	0.000	0.000	0.000	0.000	0.000
57	B	57	TRP	0	0.002	0.002	58.983	0.001	0.001	0.000	0.000	0.000	0.000
58	B	58	MET	0	-0.031	-0.024	60.271	0.001	0.001	0.000	0.000	0.000	0.000
59	B	59	GLY	0	0.037	0.021	64.471	0.000	0.000	0.000	0.000	0.000	0.000
60	B	60	PRO	0	0.004	-0.012	64.022	0.000	0.000	0.000	0.000	0.000	0.000
61	B	61	ALA	0	-0.001	0.007	61.675	0.000	0.000	0.000	0.000	0.000	0.000
62	B	62	SER	0	0.033	0.021	60.402	0.001	0.001	0.000	0.000	0.000	0.000
63	B	63	MET	0	0.046	0.021	57.009	0.000	0.000	0.000	0.000	0.000	0.000
64	B	64	ALA	0	-0.009	0.000	56.063	0.000	0.000	0.000	0.000	0.000	0.000
65	B	65	MET	0	-0.006	-0.002	55.333	0.002	0.002	0.000	0.000	0.000	0.000
66	B	66	VAL	0	0.020	0.025	52.791	0.001	0.001	0.000	0.000	0.000	0.000
67	B	67	ALA	0	-0.041	-0.033	51.728	0.000	0.000	0.000	0.000	0.000	0.000
68	B	68	ALA	0	-0.019	-0.010	50.322	0.001	0.001	0.000	0.000	0.000	0.000
69	B	69	ALA	0	0.022	0.007	49.334	0.002	0.002	0.000	0.000	0.000	0.000
70	B	70	GLN	0	0.013	0.010	47.335	0.000	0.000	0.000	0.000	0.000	0.000
71	B	71	PRO	0	-0.032	-0.020	44.006	-0.001	-0.001	0.000	0.000	0.000	0.000
72	B	72	TYR	0	0.004	0.002	42.340	0.001	0.001	0.000	0.000	0.000	0.000
73	B	73	LEU	0	0.024	0.009	43.216	0.000	0.000	0.000	0.000	0.000	0.000
74	B	74	ALA	0	-0.001	0.002	41.774	-0.002	-0.002	0.000	0.000	0.000	0.000
75	B	75	TRP	0	-0.011	-0.001	35.848	-0.003	-0.003	0.000	0.000	0.000	0.000
76	B	76	LEU	0	-0.015	0.025	38.515	0.000	0.000	0.000	0.000	0.000	0.000
77	B	77	THR	0	0.023	0.006	39.473	-0.001	-0.001	0.000	0.000	0.000	0.000
78	B	78	TYR	0	-0.021	0.003	31.419	-0.005	-0.005	0.000	0.000	0.000	0.000
79	B	79	THR	0	0.018	-0.034	33.900	-0.001	-0.001	0.000	0.000	0.000	0.000
80	B	80	ALA	0	-0.027	-0.016	34.647	0.000	0.000	0.000	0.000	0.000	0.000
81	B	81	GLU	-1	-0.946	-0.971	34.567	-0.026	-0.026	0.000	0.000	0.000	0.000
82	B	82	ALA	0	-0.003	0.008	30.932	-0.005	-0.005	0.000	0.000	0.000	0.000
83	B	83	ALA	0	-0.014	-0.001	30.415	-0.001	-0.001	0.000	0.000	0.000	0.000
84	B	84	ALA	0	0.031	0.001	31.037	-0.003	-0.003	0.000	0.000	0.000	0.000
85	B	85	HIS	0	-0.056	-0.004	25.843	-0.005	-0.005	0.000	0.000	0.000	0.000
86	B	86	ALA	0	0.057	0.010	26.552	-0.008	-0.008	0.000	0.000	0.000	0.000
87	B	87	GLY	0	-0.003	0.001	26.659	-0.002	-0.002	0.000	0.000	0.000	0.000
88	B	88	SER	0	-0.074	-0.040	27.879	-0.009	-0.009	0.000	0.000	0.000	0.000
89	B	89	GLN	0	-0.023	-0.019	23.163	-0.022	-0.022	0.000	0.000	0.000	0.000
90	B	90	ALA	0	0.009	0.009	22.864	-0.006	-0.006	0.000	0.000	0.000	0.000
91	B	91	MET	0	-0.055	-0.033	23.309	-0.007	-0.007	0.000	0.000	0.000	0.000
92	B	92	ALA	0	0.004	0.018	23.101	-0.013	-0.013	0.000	0.000	0.000	0.000
93	B	93	SER	0	0.005	-0.012	19.621	-0.021	-0.021	0.000	0.000	0.000	0.000
94	B	94	ALA	0	-0.030	-0.007	19.223	-0.019	-0.019	0.000	0.000	0.000	0.000
95	B	95	ALA	0	0.015	0.005	20.998	-0.016	-0.016	0.000	0.000	0.000	0.000
96	B	96	ALA	0	0.004	0.011	17.652	-0.026	-0.026	0.000	0.000	0.000	0.000
97	B	97	TYR	0	0.001	0.002	16.467	-0.030	-0.030	0.000	0.000	0.000	0.000
98	B	98	GLU	-1	-0.949	-0.993	17.937	-0.135	-0.135	0.000	0.000	0.000	0.000
99	B	99	ALA	0	-0.038	-0.012	19.863	-0.007	-0.007	0.000	0.000	0.000	0.000
100	B	100	ALA	0	0.013	0.007	14.931	-0.027	-0.027	0.000	0.000	0.000	0.000
101	B	101	TYR	0	0.001	0.019	16.652	-0.039	-0.039	0.000	0.000	0.000	0.000
102	B	102	ALA	0	-0.052	-0.013	18.514	-0.004	-0.004	0.000	0.000	0.000	0.000
103	B	103	MET	0	-0.056	-0.018	17.446	-0.010	-0.010	0.000	0.000	0.000	0.000
104	B	104	THR	0	-0.031	-0.012	14.463	-0.060	-0.060	0.000	0.000	0.000	0.000
105	B	105	VAL	0	-0.032	-0.016	16.236	0.063	0.063	0.000	0.000	0.000	0.000
106	B	106	PRO	0	0.012	0.007	17.127	-0.007	-0.007	0.000	0.000	0.000	0.000
107	B	107	PRO	0	0.041	0.017	17.093	-0.014	-0.014	0.000	0.000	0.000	0.000
108	B	108	GLU	-1	-0.901	-0.968	18.087	-0.151	-0.151	0.000	0.000	0.000	0.000
109	B	109	VAL	0	-0.022	-0.014	20.576	0.006	0.006	0.000	0.000	0.000	0.000
110	B	110	VAL	0	0.034	0.010	14.769	-0.005	-0.005	0.000	0.000	0.000	0.000
111	B	111	ALA	0	0.010	-0.007	18.189	0.007	0.007	0.000	0.000	0.000	0.000
112	B	112	ALA	0	-0.011	0.006	19.467	0.019	0.019	0.000	0.000	0.000	0.000
113	B	113	ASN	0	0.016	0.019	19.407	0.004	0.004	0.000	0.000	0.000	0.000
114	B	114	ARG	1	0.887	0.932	16.328	0.320	0.320	0.000	0.000	0.000	0.000
115	B	115	ALA	0	0.004	0.008	20.048	0.017	0.017	0.000	0.000	0.000	0.000
116	B	116	LEU	0	-0.020	-0.006	23.415	0.016	0.016	0.000	0.000	0.000	0.000
117	B	117	LEU	0	0.009	0.009	19.590	0.010	0.010	0.000	0.000	0.000	0.000
118	B	118	ALA	0	0.001	-0.004	23.116	0.011	0.011	0.000	0.000	0.000	0.000
119	B	119	ALA	0	-0.020	-0.006	24.616	0.013	0.013	0.000	0.000	0.000	0.000
120	B	120	LEU	0	-0.022	-0.029	26.535	0.010	0.010	0.000	0.000	0.000	0.000
121	B	121	VAL	0	0.016	0.008	24.458	0.005	0.005	0.000	0.000	0.000	0.000
122	B	122	ALA	0	-0.022	-0.001	27.726	0.008	0.008	0.000	0.000	0.000	0.000
123	B	123	THR	0	-0.038	-0.019	30.147	0.007	0.007	0.000	0.000	0.000	0.000
124	B	124	ASN	0	0.006	0.021	29.847	0.004	0.004	0.000	0.000	0.000	0.000
125	B	125	VAL	0	-0.011	-0.011	32.408	0.000	0.000	0.000	0.000	0.000	0.000
126	B	126	LEU	0	-0.016	-0.014	35.186	0.003	0.003	0.000	0.000	0.000	0.000
127	B	127	GLY	0	0.005	0.005	32.739	-0.002	-0.002	0.000	0.000	0.000	0.000
128	B	128	ILE	0	-0.007	-0.006	33.482	-0.007	-0.007	0.000	0.000	0.000	0.000
129	B	129	ASN	0	0.061	0.014	30.696	-0.007	-0.007	0.000	0.000	0.000	0.000
130	B	130	THR	0	-0.031	-0.003	28.165	-0.009	-0.009	0.000	0.000	0.000	0.000
131	B	131	PRO	0	0.018	-0.002	27.849	-0.014	-0.014	0.000	0.000	0.000	0.000
132	B	132	ALA	0	0.034	0.022	27.991	-0.013	-0.013	0.000	0.000	0.000	0.000
133	B	133	ILE	0	-0.036	-0.008	24.205	-0.013	-0.013	0.000	0.000	0.000	0.000
134	B	134	MET	0	0.026	-0.003	22.377	-0.022	-0.022	0.000	0.000	0.000	0.000
135	B	135	ALA	0	-0.007	0.011	23.325	-0.022	-0.022	0.000	0.000	0.000	0.000
136	B	136	THR	0	-0.029	-0.015	21.501	-0.016	-0.016	0.000	0.000	0.000	0.000
137	B	137	GLU	-1	-0.906	-0.970	18.217	-0.324	-0.324	0.000	0.000	0.000	0.000
138	B	138	ALA	0	-0.015	0.001	18.468	-0.045	-0.045	0.000	0.000	0.000	0.000
139	B	139	LEU	0	0.048	0.018	19.268	-0.033	-0.033	0.000	0.000	0.000	0.000
140	B	140	TYR	0	-0.070	-0.030	12.574	-0.054	-0.054	0.000	0.000	0.000	0.000
141	B	141	ALA	0	0.035	0.014	14.574	-0.064	-0.064	0.000	0.000	0.000	0.000
142	B	142	GLU	-1	-0.915	-0.961	15.243	-0.422	-0.422	0.000	0.000	0.000	0.000
143	B	143	MET	0	-0.028	0.010	15.721	-0.020	-0.020	0.000	0.000	0.000	0.000
144	B	144	TRP	0	-0.115	-0.052	7.175	0.144	0.144	0.000	0.000	0.000	0.000
145	B	145	ALA	0	-0.003	-0.022	11.907	-0.146	-0.146	0.000	0.000	0.000	0.000
146	B	146	GLN	0	-0.050	-0.038	13.821	-0.019	-0.019	0.000	0.000	0.000	0.000
147	B	147	ASP	-1	-0.753	-0.894	11.393	-0.613	-0.613	0.000	0.000	0.000	0.000
148	B	148	ALA	0	-0.053	-0.014	9.684	-0.060	-0.060	0.000	0.000	0.000	0.000
149	B	149	LEU	0	-0.016	-0.006	10.627	-0.016	-0.016	0.000	0.000	0.000	0.000
150	B	150	ALA	0	0.032	0.023	13.710	0.057	0.057	0.000	0.000	0.000	0.000
151	B	151	MET	0	-0.021	-0.014	9.014	0.086	0.086	0.000	0.000	0.000	0.000
152	B	152	TYR	0	-0.068	-0.051	7.212	0.237	0.237	0.000	0.000	0.000	0.000
153	B	153	GLY	0	0.015	0.010	11.434	0.089	0.089	0.000	0.000	0.000	0.000
154	B	154	TYR	0	-0.008	0.000	11.914	0.103	0.103	0.000	0.000	0.000	0.000
155	B	155	ALA	0	-0.008	-0.015	9.871	0.088	0.088	0.000	0.000	0.000	0.000
156	B	156	ALA	0	-0.034	-0.012	11.971	0.092	0.092	0.000	0.000	0.000	0.000
157	B	157	ALA	0	0.006	-0.002	14.916	0.068	0.068	0.000	0.000	0.000	0.000
158	B	158	SER	0	0.025	-0.002	14.140	0.072	0.072	0.000	0.000	0.000	0.000
159	B	159	GLY	0	-0.027	0.005	15.617	0.054	0.054	0.000	0.000	0.000	0.000
160	B	160	ALA	0	-0.043	-0.023	16.352	0.041	0.041	0.000	0.000	0.000	0.000
161	B	161	ALA	0	0.011	0.020	19.139	0.025	0.025	0.000	0.000	0.000	0.000
162	B	162	GLY	0	0.009	0.010	18.363	0.029	0.029	0.000	0.000	0.000	0.000
163	B	163	MET	0	-0.069	-0.029	19.019	0.023	0.023	0.000	0.000	0.000	0.000
164	B	164	LEU	0	0.016	-0.008	21.951	-0.001	-0.001	0.000	0.000	0.000	0.000
165	B	165	GLN	0	0.005	0.010	24.771	0.008	0.008	0.000	0.000	0.000	0.000
166	B	166	PRO	0	-0.003	-0.001	26.676	0.010	0.010	0.000	0.000	0.000	0.000
167	B	167	LEU	0	0.040	0.022	28.120	-0.004	-0.004	0.000	0.000	0.000	0.000
168	B	168	SER	0	-0.025	-0.020	30.572	0.006	0.006	0.000	0.000	0.000	0.000
169	B	169	PRO	0	-0.008	-0.001	33.315	-0.003	-0.003	0.000	0.000	0.000	0.000
170	B	170	PRO	0	0.033	0.021	36.683	-0.003	-0.003	0.000	0.000	0.000	0.000
171	B	171	SER	0	0.008	-0.004	39.480	0.005	0.005	0.000	0.000	0.000	0.000
172	B	172	GLN	0	-0.047	-0.013	41.396	-0.002	-0.002	0.000	0.000	0.000	0.000
173	B	173	THR	0	0.020	0.014	43.922	-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)