FMO DATABASE

FMODB ID: 3QNML

Calculation Name: 4RFT-A-Xray322

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4RFT

Chain ID: A

ChEMBL ID:

UniProt ID: Q8JNX5

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

Apendix: None

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. 1.20200129
Remarks	Structural optimization was performed under the unconstrained condition of hydrogen and heavy atoms fixed using MOE with Auto-FMO protocol as OptH.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	165
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1543193.034521
FMO2-HF: Nuclear repulsion	1480529.162537
FMO2-HF: Total energy	-62663.871984
FMO2-MP2: Total energy	-62846.988822

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(A:51:ACE )

Summations of interaction energy for fragment #1(A:51:ACE )

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.
0.676	1.455	-0.005	-0.345	-0.428	0

Interaction energy analysis for fragmet #1(A:51:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : -0.011

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].
3	A	53	ASN	0	-0.030	-0.007	3.848	0.881	1.660	-0.005	-0.345	-0.428
4	A	54	ASP	-1	-0.833	-0.887	6.682	-0.592	-0.592	0.000	0.000	0.000
5	A	55	VAL	0	0.015	0.007	8.318	-0.048	-0.048	0.000	0.000	0.000
6	A	56	HIS	0	-0.005	0.006	9.208	-0.094	-0.094	0.000	0.000	0.000
7	A	57	LEU	0	-0.029	-0.016	12.492	0.066	0.066	0.000	0.000	0.000
8	A	58	SER	0	0.049	0.013	16.003	-0.017	-0.017	0.000	0.000	0.000
9	A	59	GLY	0	-0.051	-0.029	18.921	0.019	0.019	0.000	0.000	0.000
10	A	60	MET	0	-0.039	-0.016	22.568	-0.007	-0.007	0.000	0.000	0.000
11	A	61	SER	0	0.016	0.037	26.051	0.005	0.005	0.000	0.000	0.000
12	A	62	ARG	1	0.963	0.981	28.593	0.039	0.039	0.000	0.000	0.000
13	A	63	ILE	0	-0.027	0.012	29.370	-0.002	-0.002	0.000	0.000	0.000
14	A	64	SER	0	-0.009	-0.020	32.736	0.002	0.002	0.000	0.000	0.000
15	A	65	GLN	0	0.024	0.000	36.480	0.000	0.000	0.000	0.000	0.000
16	A	66	ALA	0	0.009	0.032	39.688	0.000	0.000	0.000	0.000	0.000
17	A	67	VAL	0	-0.024	-0.017	42.913	0.001	0.001	0.000	0.000	0.000
18	A	68	LEU	0	0.004	-0.003	46.209	0.000	0.000	0.000	0.000	0.000
19	A	69	PRO	0	0.021	0.000	48.404	0.001	0.001	0.000	0.000	0.000
20	A	70	ALA	0	0.021	-0.017	52.015	0.000	0.000	0.000	0.000	0.000
21	A	71	GLY	0	0.060	0.049	54.526	0.000	0.000	0.000	0.000	0.000
22	A	72	THR	0	-0.090	-0.043	51.399	0.000	0.000	0.000	0.000	0.000
23	A	73	GLY	0	0.033	0.029	50.696	-0.001	-0.001	0.000	0.000	0.000
24	A	74	THR	0	0.007	-0.025	50.888	0.001	0.001	0.000	0.000	0.000
25	A	75	ASP	-1	-0.898	-0.940	50.009	-0.032	-0.032	0.000	0.000	0.000
26	A	76	GLY	0	0.001	0.014	47.919	0.000	0.000	0.000	0.000	0.000
27	A	77	TYR	0	-0.029	-0.020	47.124	-0.002	-0.002	0.000	0.000	0.000
28	A	78	VAL	0	0.048	0.016	42.575	-0.001	-0.001	0.000	0.000	0.000
29	A	79	VAL	0	-0.031	-0.018	42.201	0.001	0.001	0.000	0.000	0.000
30	A	80	VAL	0	-0.073	-0.039	37.313	0.000	0.000	0.000	0.000	0.000
31	A	81	ASP	-1	-0.765	-0.866	38.053	-0.062	-0.062	0.000	0.000	0.000
32	A	82	ALA	0	-0.007	0.009	34.367	0.000	0.000	0.000	0.000	0.000
33	A	83	THR	0	0.013	-0.008	31.818	-0.004	-0.004	0.000	0.000	0.000
34	A	84	ILE	0	-0.040	-0.013	26.754	0.000	0.000	0.000	0.000	0.000
35	A	85	VAL	0	0.061	0.048	27.355	-0.009	-0.009	0.000	0.000	0.000
36	A	86	PRO	0	0.034	-0.005	23.591	0.004	0.004	0.000	0.000	0.000
37	A	87	ASP	-1	-0.869	-0.939	25.562	-0.076	-0.076	0.000	0.000	0.000
38	A	88	LEU	0	-0.063	-0.017	28.475	0.006	0.006	0.000	0.000	0.000
39	A	89	LEU	0	-0.031	-0.013	24.336	0.004	0.004	0.000	0.000	0.000
40	A	90	PRO	0	0.049	0.015	25.559	-0.005	-0.005	0.000	0.000	0.000
41	A	91	ARG	1	0.894	0.948	19.646	0.075	0.075	0.000	0.000	0.000
42	A	92	LEU	0	0.008	0.005	20.097	-0.004	-0.004	0.000	0.000	0.000
43	A	93	GLY	0	0.047	0.035	22.589	-0.007	-0.007	0.000	0.000	0.000
44	A	94	HIS	0	-0.036	-0.021	23.316	-0.001	-0.001	0.000	0.000	0.000
45	A	95	ALA	0	-0.006	-0.004	18.503	-0.002	-0.002	0.000	0.000	0.000
46	A	96	ALA	0	0.052	0.014	19.673	-0.016	-0.016	0.000	0.000	0.000
47	A	97	ARG	1	0.924	0.974	21.334	0.067	0.067	0.000	0.000	0.000
48	A	98	ILE	0	0.022	0.022	16.825	0.010	0.010	0.000	0.000	0.000
49	A	99	PHE	0	-0.018	-0.020	12.517	-0.011	-0.011	0.000	0.000	0.000
50	A	100	GLN	0	0.012	0.004	17.564	0.006	0.006	0.000	0.000	0.000
51	A	101	ARG	1	0.925	0.961	17.472	0.242	0.242	0.000	0.000	0.000
52	A	102	TYR	0	-0.006	0.010	16.882	-0.030	-0.030	0.000	0.000	0.000
53	A	103	ALA	0	0.054	0.037	16.047	0.017	0.017	0.000	0.000	0.000
54	A	104	VAL	0	-0.014	-0.002	17.475	-0.005	-0.005	0.000	0.000	0.000
55	A	105	GLU	-1	-0.858	-0.953	13.855	-0.477	-0.477	0.000	0.000	0.000
56	A	106	THR	0	-0.103	-0.051	18.138	0.014	0.014	0.000	0.000	0.000
57	A	107	LEU	0	0.050	-0.001	20.954	-0.002	-0.002	0.000	0.000	0.000
58	A	108	GLU	-1	-0.885	-0.914	24.428	-0.083	-0.083	0.000	0.000	0.000
59	A	109	PHE	0	0.028	0.010	27.555	0.000	0.000	0.000	0.000	0.000
60	A	110	GLU	-1	-0.909	-0.959	30.725	-0.048	-0.048	0.000	0.000	0.000
61	A	111	ILE	0	-0.004	-0.005	32.817	0.001	0.001	0.000	0.000	0.000
62	A	112	GLN	0	0.036	0.036	35.303	0.005	0.005	0.000	0.000	0.000
63	A	113	PRO	0	-0.025	0.001	38.138	0.001	0.001	0.000	0.000	0.000
64	A	114	MET	0	-0.030	-0.015	39.649	0.002	0.002	0.000	0.000	0.000
65	A	115	CYS	0	-0.016	0.006	44.194	0.001	0.001	0.000	0.000	0.000
66	A	116	PRO	0	0.059	0.047	47.819	0.000	0.000	0.000	0.000	0.000
67	A	117	ALA	0	0.052	0.006	49.695	-0.001	-0.001	0.000	0.000	0.000
68	A	118	ASN	0	-0.092	-0.033	50.590	0.000	0.000	0.000	0.000	0.000
69	A	119	THR	0	0.049	0.003	50.012	0.000	0.000	0.000	0.000	0.000
70	A	120	GLY	0	-0.028	-0.022	51.555	-0.001	-0.001	0.000	0.000	0.000
71	A	121	GLY	0	-0.046	-0.040	49.357	0.000	0.000	0.000	0.000	0.000
72	A	122	GLY	0	0.040	0.006	46.909	0.000	0.000	0.000	0.000	0.000
73	A	123	TYR	0	-0.048	-0.028	39.449	-0.002	-0.002	0.000	0.000	0.000
74	A	124	VAL	0	0.052	0.023	40.737	0.000	0.000	0.000	0.000	0.000
75	A	125	ALA	0	-0.005	0.000	37.008	0.000	0.000	0.000	0.000	0.000
76	A	126	GLY	0	0.028	0.012	35.285	0.000	0.000	0.000	0.000	0.000
77	A	127	PHE	0	-0.066	-0.024	28.220	-0.001	-0.001	0.000	0.000	0.000
78	A	128	LEU	0	0.081	0.032	32.565	-0.004	-0.004	0.000	0.000	0.000
79	A	129	PRO	0	-0.080	-0.053	29.274	-0.002	-0.002	0.000	0.000	0.000
80	A	130	ASP	-1	-0.841	-0.908	30.517	-0.095	-0.095	0.000	0.000	0.000
81	A	131	PRO	0	-0.056	-0.022	30.552	0.006	0.006	0.000	0.000	0.000
82	A	132	THR	0	-0.013	-0.036	33.359	0.003	0.003	0.000	0.000	0.000
83	A	133	ASP	-1	-0.912	-0.963	36.147	-0.060	-0.060	0.000	0.000	0.000
84	A	134	ASN	0	-0.082	-0.040	38.353	0.001	0.001	0.000	0.000	0.000
85	A	135	ASP	-1	-0.858	-0.906	40.783	-0.048	-0.048	0.000	0.000	0.000
86	A	136	HIS	0	-0.048	-0.024	39.448	-0.002	-0.002	0.000	0.000	0.000
87	A	137	THR	0	0.018	0.007	42.806	0.004	0.004	0.000	0.000	0.000
88	A	138	PHE	0	0.053	0.011	43.043	-0.003	-0.003	0.000	0.000	0.000
89	A	139	ASP	-1	-0.905	-0.960	43.144	-0.044	-0.044	0.000	0.000	0.000
90	A	140	ALA	0	0.050	0.036	40.827	-0.002	-0.002	0.000	0.000	0.000
91	A	141	LEU	0	-0.011	-0.017	38.577	-0.004	-0.004	0.000	0.000	0.000
92	A	142	GLN	0	-0.080	-0.037	38.337	-0.002	-0.002	0.000	0.000	0.000
93	A	143	ALA	0	0.040	0.045	39.187	-0.001	-0.001	0.000	0.000	0.000
94	A	144	THR	0	-0.142	-0.075	34.099	-0.006	-0.006	0.000	0.000	0.000
95	A	145	ARG	1	0.947	0.952	30.685	0.092	0.092	0.000	0.000	0.000
96	A	146	GLY	0	-0.028	-0.012	32.205	0.002	0.002	0.000	0.000	0.000
97	A	147	ALA	0	-0.024	0.009	32.882	0.003	0.003	0.000	0.000	0.000
98	A	148	VAL	0	-0.019	-0.004	35.637	0.002	0.002	0.000	0.000	0.000
99	A	149	VAL	0	0.048	0.017	38.436	0.000	0.000	0.000	0.000	0.000
100	A	150	ALA	0	-0.049	-0.019	41.440	0.001	0.001	0.000	0.000	0.000
101	A	151	LYS	1	1.002	1.007	43.501	0.028	0.028	0.000	0.000	0.000
102	A	152	TRP	0	0.052	0.016	43.961	0.000	0.000	0.000	0.000	0.000
103	A	153	TRP	0	-0.011	0.002	44.988	0.000	0.000	0.000	0.000	0.000
104	A	154	GLU	-1	-0.912	-0.960	42.170	-0.032	-0.032	0.000	0.000	0.000
105	A	155	SER	0	-0.005	-0.027	37.518	-0.002	-0.002	0.000	0.000	0.000
106	A	156	ARG	1	0.932	0.966	36.975	0.044	0.044	0.000	0.000	0.000
107	A	157	THR	0	-0.038	-0.022	30.450	0.000	0.000	0.000	0.000	0.000
108	A	158	VAL	0	0.005	0.022	31.632	0.000	0.000	0.000	0.000	0.000
109	A	159	ARG	1	0.911	0.940	27.762	0.067	0.067	0.000	0.000	0.000
110	A	160	PRO	0	0.008	0.024	27.667	0.001	0.001	0.000	0.000	0.000
111	A	161	GLN	0	-0.010	-0.017	26.860	-0.008	-0.008	0.000	0.000	0.000
112	A	162	TYR	0	-0.033	-0.020	21.056	0.010	0.010	0.000	0.000	0.000
113	A	163	THR	0	0.059	0.019	23.297	-0.013	-0.013	0.000	0.000	0.000
114	A	164	ARG	1	0.908	0.963	19.277	0.195	0.195	0.000	0.000	0.000
115	A	165	THR	0	0.052	0.038	19.634	-0.031	-0.031	0.000	0.000	0.000
116	A	166	LEU	0	-0.053	-0.027	16.057	-0.004	-0.004	0.000	0.000	0.000
117	A	167	LEU	0	-0.030	-0.007	19.428	0.024	0.024	0.000	0.000	0.000
118	A	168	TRP	0	0.014	-0.023	20.772	-0.018	-0.018	0.000	0.000	0.000
119	A	169	THR	0	-0.001	-0.018	20.419	0.008	0.008	0.000	0.000	0.000
120	A	170	SER	0	0.020	0.025	23.503	0.014	0.014	0.000	0.000	0.000
121	A	171	SER	0	-0.019	-0.007	26.932	-0.003	-0.003	0.000	0.000	0.000
122	A	172	GLY	0	0.041	0.023	29.719	-0.003	-0.003	0.000	0.000	0.000
123	A	173	LYS	1	0.919	0.958	30.468	0.076	0.076	0.000	0.000	0.000
124	A	174	GLU	-1	-0.884	-0.933	30.577	-0.087	-0.087	0.000	0.000	0.000
125	A	175	GLN	0	-0.020	-0.036	29.495	-0.012	-0.012	0.000	0.000	0.000
126	A	176	ARG	1	0.970	0.986	29.249	0.092	0.092	0.000	0.000	0.000
127	A	177	LEU	0	-0.047	-0.020	23.716	-0.011	-0.011	0.000	0.000	0.000
128	A	178	THR	0	0.010	-0.034	25.294	0.005	0.005	0.000	0.000	0.000
129	A	179	SER	0	-0.007	0.013	26.321	0.006	0.006	0.000	0.000	0.000
130	A	180	PRO	0	-0.048	-0.014	24.569	-0.002	-0.002	0.000	0.000	0.000
131	A	181	GLY	0	0.034	0.001	26.608	0.001	0.001	0.000	0.000	0.000
132	A	182	ARG	1	0.822	0.916	30.271	0.067	0.067	0.000	0.000	0.000
133	A	183	LEU	0	-0.048	-0.001	32.564	0.000	0.000	0.000	0.000	0.000
134	A	184	ILE	0	0.043	0.021	34.349	0.003	0.003	0.000	0.000	0.000
135	A	185	LEU	0	-0.031	-0.028	38.062	0.000	0.000	0.000	0.000	0.000
136	A	186	LEU	0	0.017	0.011	40.320	0.001	0.001	0.000	0.000	0.000
137	A	187	CYS	0	-0.071	-0.016	43.914	0.001	0.001	0.000	0.000	0.000
138	A	188	VAL	0	-0.015	0.000	45.864	-0.001	-0.001	0.000	0.000	0.000
139	A	189	GLY	0	0.045	0.040	48.537	0.001	0.001	0.000	0.000	0.000
140	A	190	ASN	0	0.015	-0.019	51.429	-0.002	-0.002	0.000	0.000	0.000
141	A	191	ASN	0	-0.079	-0.036	50.268	0.000	0.000	0.000	0.000	0.000
142	A	192	THR	0	-0.015	0.000	52.322	0.000	0.000	0.000	0.000	0.000
143	A	193	ASP	-1	-0.813	-0.919	52.224	-0.019	-0.019	0.000	0.000	0.000
144	A	194	VAL	0	-0.088	-0.033	49.394	-0.001	-0.001	0.000	0.000	0.000
145	A	195	VAL	0	-0.008	-0.003	44.799	0.000	0.000	0.000	0.000	0.000
146	A	196	ASN	0	-0.040	-0.021	43.160	-0.003	-0.003	0.000	0.000	0.000
147	A	197	VAL	0	0.030	0.030	39.607	0.000	0.000	0.000	0.000	0.000
148	A	198	SER	0	0.009	-0.015	37.157	0.000	0.000	0.000	0.000	0.000
149	A	199	VAL	0	0.005	0.028	33.118	0.000	0.000	0.000	0.000	0.000
150	A	200	LEU	0	-0.002	-0.007	30.820	-0.002	-0.002	0.000	0.000	0.000
151	A	201	CYS	0	0.011	0.016	27.009	-0.005	-0.005	0.000	0.000	0.000
152	A	202	ARG	1	0.864	0.925	23.611	0.076	0.076	0.000	0.000	0.000
153	A	203	TRP	0	0.015	-0.022	19.445	-0.008	-0.008	0.000	0.000	0.000
154	A	204	SER	0	-0.027	-0.010	17.159	-0.001	-0.001	0.000	0.000	0.000
155	A	205	VAL	0	-0.001	-0.007	16.985	-0.007	-0.007	0.000	0.000	0.000
156	A	206	ARG	1	0.910	0.953	11.261	0.648	0.648	0.000	0.000	0.000
157	A	207	LEU	0	-0.035	-0.029	13.548	0.021	0.021	0.000	0.000	0.000
158	A	208	SER	0	-0.019	-0.014	12.610	-0.041	-0.041	0.000	0.000	0.000
159	A	209	VAL	0	0.009	0.010	12.501	-0.032	-0.032	0.000	0.000	0.000
160	A	210	PRO	0	0.034	0.028	12.772	0.034	0.034	0.000	0.000	0.000
161	A	211	SER	0	-0.083	-0.047	15.595	0.007	0.007	0.000	0.000	0.000
162	A	212	LEU	0	0.029	0.001	19.271	0.008	0.008	0.000	0.000	0.000
163	A	213	GLU	-1	-0.919	-0.944	22.438	-0.089	-0.089	0.000	0.000	0.000
164	A	214	ASN	0	-0.108	-0.048	25.557	0.001	0.001	0.000	0.000	0.000
165	A	215	NME	0	0.033	0.021	28.473	0.005	0.005	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:51:ACE )