FMO DATABASE

FMODB ID: 3Q57L

Calculation Name: 4RFT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4RFT

Chain ID: A

ChEMBL ID:

UniProt ID: Q8JNX5

Base Structure: X-ray

Registration Date: 2023-06-20

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	163
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1538615.884083
FMO2-HF: Nuclear repulsion	1476121.104935
FMO2-HF: Total energy	-62494.779148
FMO2-MP2: Total energy	-62677.300045

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:52:THR)

Summations of interaction energy for fragment #1(A:52:THR)

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.
-12.712	-4.728	2.28	-4.452	-5.811	0.01

Interaction energy analysis for fragmet #1(A:52:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : 0.008

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	54	ASP	-1	-0.827	-0.875	2.391	-4.259	1.251	1.831	-3.322	-4.019	0.021
4	A	55	VAL	0	0.017	0.012	2.905	-4.849	-3.566	0.317	-0.682	-0.918	-0.007
5	A	56	HIS	0	-0.054	-0.031	3.189	-2.684	-1.493	0.132	-0.448	-0.874	-0.004
6	A	57	LEU	0	-0.023	-0.006	6.643	0.185	0.185	0.000	0.000	0.000	0.000
7	A	58	SER	0	0.028	-0.004	10.421	0.084	0.084	0.000	0.000	0.000	0.000
8	A	59	GLY	0	-0.039	-0.016	13.337	0.003	0.003	0.000	0.000	0.000	0.000
9	A	60	MET	0	0.000	0.021	17.130	0.014	0.014	0.000	0.000	0.000	0.000
10	A	61	SER	0	-0.056	-0.030	20.630	-0.018	-0.018	0.000	0.000	0.000	0.000
11	A	62	ARG	1	0.885	0.952	23.064	0.157	0.157	0.000	0.000	0.000	0.000
12	A	63	ILE	0	0.008	0.017	22.955	0.002	0.002	0.000	0.000	0.000	0.000
13	A	64	SER	0	0.031	0.010	26.775	0.007	0.007	0.000	0.000	0.000	0.000
14	A	65	GLN	0	-0.017	-0.031	30.610	-0.014	-0.014	0.000	0.000	0.000	0.000
15	A	66	ALA	0	0.004	0.014	33.803	0.003	0.003	0.000	0.000	0.000	0.000
16	A	67	VAL	0	-0.025	-0.013	36.987	0.000	0.000	0.000	0.000	0.000	0.000
17	A	68	LEU	0	0.008	0.015	40.488	0.002	0.002	0.000	0.000	0.000	0.000
18	A	69	PRO	0	0.038	-0.008	42.792	0.000	0.000	0.000	0.000	0.000	0.000
19	A	70	ALA	0	0.008	0.001	46.526	0.001	0.001	0.000	0.000	0.000	0.000
20	A	71	GLY	0	0.017	0.024	48.601	0.001	0.001	0.000	0.000	0.000	0.000
21	A	72	THR	0	-0.045	-0.022	45.661	0.002	0.002	0.000	0.000	0.000	0.000
22	A	73	GLY	0	0.015	0.016	44.255	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	74	THR	0	0.005	-0.021	44.678	0.001	0.001	0.000	0.000	0.000	0.000
24	A	75	ASP	-1	-0.870	-0.933	43.737	-0.033	-0.033	0.000	0.000	0.000	0.000
25	A	76	GLY	0	0.030	0.022	41.210	0.003	0.003	0.000	0.000	0.000	0.000
26	A	77	TYR	0	-0.044	-0.021	40.849	0.000	0.000	0.000	0.000	0.000	0.000
27	A	78	VAL	0	0.039	0.022	35.759	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	79	VAL	0	-0.018	-0.020	36.252	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	80	VAL	0	-0.063	-0.036	30.882	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	81	ASP	-1	-0.752	-0.842	31.384	-0.055	-0.055	0.000	0.000	0.000	0.000
31	A	82	ALA	0	-0.004	-0.001	27.775	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	83	THR	0	0.033	0.007	25.072	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	84	ILE	0	-0.038	-0.002	20.248	-0.013	-0.013	0.000	0.000	0.000	0.000
34	A	85	VAL	0	0.062	0.032	20.593	0.012	0.012	0.000	0.000	0.000	0.000
35	A	86	PRO	0	0.051	0.012	17.157	-0.013	-0.013	0.000	0.000	0.000	0.000
36	A	87	ASP	-1	-0.782	-0.879	19.241	-0.256	-0.256	0.000	0.000	0.000	0.000
37	A	88	LEU	0	-0.040	-0.001	22.512	0.001	0.001	0.000	0.000	0.000	0.000
38	A	89	LEU	0	-0.043	-0.018	18.181	0.001	0.001	0.000	0.000	0.000	0.000
39	A	90	PRO	0	0.055	0.011	19.568	-0.044	-0.044	0.000	0.000	0.000	0.000
40	A	91	ARG	1	0.866	0.927	14.993	0.577	0.577	0.000	0.000	0.000	0.000
41	A	92	LEU	0	0.008	0.007	14.187	-0.045	-0.045	0.000	0.000	0.000	0.000
42	A	93	GLY	0	0.031	0.025	16.596	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	94	HIS	0	0.012	-0.004	18.400	0.013	0.013	0.000	0.000	0.000	0.000
44	A	95	ALA	0	0.005	0.006	12.934	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	96	ALA	0	0.001	-0.016	14.396	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	97	ARG	1	0.852	0.915	16.275	0.297	0.297	0.000	0.000	0.000	0.000
47	A	98	ILE	0	-0.016	0.004	12.972	0.013	0.013	0.000	0.000	0.000	0.000
48	A	99	PHE	0	-0.036	-0.012	8.452	-0.059	-0.059	0.000	0.000	0.000	0.000
49	A	100	GLN	0	0.047	0.024	13.211	0.061	0.061	0.000	0.000	0.000	0.000
50	A	101	ARG	1	0.886	0.942	11.732	-0.146	-0.146	0.000	0.000	0.000	0.000
51	A	102	TYR	0	-0.039	-0.024	10.172	-0.117	-0.117	0.000	0.000	0.000	0.000
52	A	103	ALA	0	0.054	0.038	9.240	0.135	0.135	0.000	0.000	0.000	0.000
53	A	104	VAL	0	-0.013	-0.001	10.440	-0.187	-0.187	0.000	0.000	0.000	0.000
54	A	105	GLU	-1	-0.836	-0.928	7.552	-1.280	-1.280	0.000	0.000	0.000	0.000
55	A	106	THR	0	-0.033	-0.029	11.839	0.068	0.068	0.000	0.000	0.000	0.000
56	A	107	LEU	0	0.027	0.007	14.888	-0.037	-0.037	0.000	0.000	0.000	0.000
57	A	108	GLU	-1	-0.822	-0.873	18.209	-0.163	-0.163	0.000	0.000	0.000	0.000
58	A	109	PHE	0	0.038	0.000	21.634	-0.021	-0.021	0.000	0.000	0.000	0.000
59	A	110	GLU	-1	-0.803	-0.883	24.884	-0.162	-0.162	0.000	0.000	0.000	0.000
60	A	111	ILE	0	-0.010	0.005	27.026	-0.005	-0.005	0.000	0.000	0.000	0.000
61	A	112	GLN	0	0.017	0.006	29.591	0.014	0.014	0.000	0.000	0.000	0.000
62	A	113	PRO	0	0.008	0.008	32.334	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	114	MET	0	-0.016	-0.014	34.224	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	115	CYS	0	0.011	0.019	38.786	0.002	0.002	0.000	0.000	0.000	0.000
65	A	116	PRO	0	0.028	0.029	42.439	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	117	ALA	0	0.055	0.011	44.593	0.001	0.001	0.000	0.000	0.000	0.000
67	A	118	ASN	0	-0.066	-0.015	45.506	0.004	0.004	0.000	0.000	0.000	0.000
68	A	119	THR	0	0.010	-0.012	44.293	0.001	0.001	0.000	0.000	0.000	0.000
69	A	120	GLY	0	-0.015	-0.011	45.755	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	121	GLY	0	0.022	0.005	44.979	0.003	0.003	0.000	0.000	0.000	0.000
71	A	122	GLY	0	-0.020	-0.022	40.956	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	123	TYR	0	-0.053	-0.028	33.695	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	124	VAL	0	0.038	0.024	34.660	0.001	0.001	0.000	0.000	0.000	0.000
74	A	125	ALA	0	-0.011	-0.004	31.218	-0.004	-0.004	0.000	0.000	0.000	0.000
75	A	126	GLY	0	0.050	0.012	29.397	0.003	0.003	0.000	0.000	0.000	0.000
76	A	127	PHE	0	-0.038	-0.013	21.688	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	128	LEU	0	0.116	0.060	26.389	0.007	0.007	0.000	0.000	0.000	0.000
78	A	129	PRO	0	-0.083	-0.042	22.232	-0.007	-0.007	0.000	0.000	0.000	0.000
79	A	130	ASP	-1	-0.783	-0.860	23.621	0.019	0.019	0.000	0.000	0.000	0.000
80	A	131	PRO	0	-0.023	-0.009	23.748	-0.004	-0.004	0.000	0.000	0.000	0.000
81	A	132	THR	0	-0.050	-0.052	26.466	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	133	ASP	-1	-0.871	-0.939	29.480	-0.007	-0.007	0.000	0.000	0.000	0.000
83	A	134	ASN	0	-0.058	-0.037	31.518	-0.014	-0.014	0.000	0.000	0.000	0.000
84	A	135	ASP	-1	-0.857	-0.913	34.178	-0.010	-0.010	0.000	0.000	0.000	0.000
85	A	136	HIS	0	-0.082	-0.062	32.397	0.001	0.001	0.000	0.000	0.000	0.000
86	A	137	THR	0	0.017	0.009	35.951	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	138	PHE	0	0.018	-0.006	36.631	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	139	ASP	-1	-0.867	-0.933	36.714	-0.014	-0.014	0.000	0.000	0.000	0.000
89	A	140	ALA	0	0.032	0.026	34.202	0.002	0.002	0.000	0.000	0.000	0.000
90	A	141	LEU	0	0.006	-0.005	32.312	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	142	GLN	0	-0.040	-0.015	31.903	-0.007	-0.007	0.000	0.000	0.000	0.000
92	A	143	ALA	0	0.038	0.045	32.649	0.003	0.003	0.000	0.000	0.000	0.000
93	A	144	THR	0	-0.097	-0.063	27.694	0.003	0.003	0.000	0.000	0.000	0.000
94	A	145	ARG	1	0.869	0.894	25.441	-0.010	-0.010	0.000	0.000	0.000	0.000
95	A	146	GLY	0	-0.013	0.011	26.481	0.001	0.001	0.000	0.000	0.000	0.000
96	A	147	ALA	0	-0.013	0.009	27.472	-0.013	-0.013	0.000	0.000	0.000	0.000
97	A	148	VAL	0	-0.053	-0.025	30.200	0.003	0.003	0.000	0.000	0.000	0.000
98	A	149	VAL	0	0.042	0.022	32.883	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	150	ALA	0	-0.037	-0.012	35.763	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	151	LYS	1	0.936	0.966	37.803	0.054	0.054	0.000	0.000	0.000	0.000
101	A	152	TRP	0	0.061	0.000	38.475	-0.004	-0.004	0.000	0.000	0.000	0.000
102	A	153	TRP	0	-0.013	0.001	39.415	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	154	GLU	-1	-0.853	-0.906	36.361	-0.059	-0.059	0.000	0.000	0.000	0.000
104	A	155	SER	0	0.017	-0.004	32.436	0.003	0.003	0.000	0.000	0.000	0.000
105	A	156	ARG	1	0.852	0.921	31.448	0.070	0.070	0.000	0.000	0.000	0.000
106	A	157	THR	0	-0.050	-0.032	24.797	-0.011	-0.011	0.000	0.000	0.000	0.000
107	A	158	VAL	0	0.033	0.049	26.144	0.008	0.008	0.000	0.000	0.000	0.000
108	A	159	ARG	1	0.828	0.878	22.085	0.121	0.121	0.000	0.000	0.000	0.000
109	A	160	PRO	0	0.017	0.024	21.920	0.014	0.014	0.000	0.000	0.000	0.000
110	A	161	GLN	0	0.028	0.017	21.165	-0.010	-0.010	0.000	0.000	0.000	0.000
111	A	162	TYR	0	-0.032	-0.030	14.759	0.012	0.012	0.000	0.000	0.000	0.000
112	A	163	THR	0	0.021	0.012	16.923	0.010	0.010	0.000	0.000	0.000	0.000
113	A	164	ARG	1	0.842	0.922	13.213	0.177	0.177	0.000	0.000	0.000	0.000
114	A	165	THR	0	0.040	0.033	13.199	0.055	0.055	0.000	0.000	0.000	0.000
115	A	166	LEU	0	-0.038	-0.021	9.467	-0.075	-0.075	0.000	0.000	0.000	0.000
116	A	167	LEU	0	-0.029	0.006	12.794	0.031	0.031	0.000	0.000	0.000	0.000
117	A	168	TRP	0	0.015	-0.018	14.005	0.012	0.012	0.000	0.000	0.000	0.000
118	A	169	THR	0	-0.042	-0.035	14.428	0.001	0.001	0.000	0.000	0.000	0.000
119	A	170	SER	0	0.016	0.001	17.269	-0.021	-0.021	0.000	0.000	0.000	0.000
120	A	171	SER	0	-0.029	-0.001	21.008	0.014	0.014	0.000	0.000	0.000	0.000
121	A	172	GLY	0	0.055	0.030	23.416	0.007	0.007	0.000	0.000	0.000	0.000
122	A	173	LYS	1	0.911	0.946	24.261	-0.031	-0.031	0.000	0.000	0.000	0.000
123	A	174	GLU	-1	-0.819	-0.905	23.942	0.033	0.033	0.000	0.000	0.000	0.000
124	A	175	GLN	0	0.006	-0.013	23.205	-0.011	-0.011	0.000	0.000	0.000	0.000
125	A	176	ARG	1	0.835	0.890	22.560	-0.038	-0.038	0.000	0.000	0.000	0.000
126	A	177	LEU	0	-0.022	-0.002	17.166	0.005	0.005	0.000	0.000	0.000	0.000
127	A	178	THR	0	0.009	0.008	18.655	-0.005	-0.005	0.000	0.000	0.000	0.000
128	A	179	SER	0	-0.008	-0.010	19.611	-0.030	-0.030	0.000	0.000	0.000	0.000
129	A	180	PRO	0	-0.037	-0.023	17.732	0.024	0.024	0.000	0.000	0.000	0.000
130	A	181	GLY	0	0.029	0.007	19.758	0.014	0.014	0.000	0.000	0.000	0.000
131	A	182	ARG	1	0.791	0.883	23.511	0.030	0.030	0.000	0.000	0.000	0.000
132	A	183	LEU	0	-0.063	-0.014	25.997	0.006	0.006	0.000	0.000	0.000	0.000
133	A	184	ILE	0	0.017	0.013	27.651	-0.001	-0.001	0.000	0.000	0.000	0.000
134	A	185	LEU	0	-0.038	-0.028	31.425	-0.002	-0.002	0.000	0.000	0.000	0.000
135	A	186	LEU	0	0.023	0.019	33.961	0.001	0.001	0.000	0.000	0.000	0.000
136	A	187	CYS	0	-0.064	-0.010	37.523	-0.002	-0.002	0.000	0.000	0.000	0.000
137	A	188	VAL	0	-0.007	-0.004	39.941	0.004	0.004	0.000	0.000	0.000	0.000
138	A	189	GLY	0	0.019	0.008	42.638	-0.002	-0.002	0.000	0.000	0.000	0.000
139	A	190	ASN	0	0.002	-0.006	45.563	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	191	ASN	0	-0.091	-0.058	44.567	0.002	0.002	0.000	0.000	0.000	0.000
141	A	192	THR	0	-0.014	-0.009	46.551	0.002	0.002	0.000	0.000	0.000	0.000
142	A	193	ASP	-1	-0.801	-0.895	46.869	-0.055	-0.055	0.000	0.000	0.000	0.000
143	A	194	VAL	0	-0.073	-0.035	43.593	-0.001	-0.001	0.000	0.000	0.000	0.000
144	A	195	VAL	0	-0.012	-0.006	39.282	-0.002	-0.002	0.000	0.000	0.000	0.000
145	A	196	ASN	0	-0.013	0.002	38.173	-0.001	-0.001	0.000	0.000	0.000	0.000
146	A	197	VAL	0	0.029	0.027	33.925	-0.006	-0.006	0.000	0.000	0.000	0.000
147	A	198	SER	0	0.001	0.001	31.017	-0.005	-0.005	0.000	0.000	0.000	0.000
148	A	199	VAL	0	0.002	0.011	27.919	0.002	0.002	0.000	0.000	0.000	0.000
149	A	200	LEU	0	-0.011	-0.018	25.457	-0.011	-0.011	0.000	0.000	0.000	0.000
150	A	201	CYS	0	-0.008	0.025	20.773	-0.006	-0.006	0.000	0.000	0.000	0.000
151	A	202	ARG	1	0.797	0.874	19.368	0.206	0.206	0.000	0.000	0.000	0.000
152	A	203	TRP	0	0.055	0.003	13.767	0.007	0.007	0.000	0.000	0.000	0.000
153	A	204	SER	0	0.001	0.007	11.133	-0.107	-0.107	0.000	0.000	0.000	0.000
154	A	205	VAL	0	0.002	-0.001	10.943	0.127	0.127	0.000	0.000	0.000	0.000
155	A	206	ARG	1	0.863	0.935	5.074	-0.366	-0.366	0.000	0.000	0.000	0.000
156	A	207	LEU	0	-0.012	-0.010	7.426	0.459	0.459	0.000	0.000	0.000	0.000
157	A	208	SER	0	-0.031	-0.029	6.580	-0.314	-0.314	0.000	0.000	0.000	0.000
158	A	209	VAL	0	-0.006	0.002	7.799	-0.020	-0.020	0.000	0.000	0.000	0.000
159	A	210	PRO	0	0.025	0.021	9.764	-0.099	-0.099	0.000	0.000	0.000	0.000
160	A	211	SER	0	-0.076	-0.052	12.277	0.109	0.109	0.000	0.000	0.000	0.000
161	A	212	LEU	0	0.025	-0.001	16.035	-0.055	-0.055	0.000	0.000	0.000	0.000
162	A	213	GLU	-1	-0.868	-0.902	18.964	-0.081	-0.081	0.000	0.000	0.000	0.000
163	A	214	ASN	0	-0.083	-0.046	20.985	0.013	0.013	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:52:THR)