FMO DATABASE

FMODB ID: N1M2Q

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1537038.374396
FMO2-HF: Nuclear repulsion	1474545.385275
FMO2-HF: Total energy	-62492.989121
FMO2-MP2: Total energy	-62675.579138

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.
-7.6	-0.715	1.137	-3.619	-4.403	0

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 : 0.013 / q_NPA : 0.007

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	-0.839	-0.893	2.349	-2.989	2.340	0.542	-2.778	-3.093	0.011
4	A	55	VAL	0	0.018	0.008	2.699	-3.743	-2.439	0.594	-0.803	-1.095	-0.011
5	A	56	HIS	0	-0.008	0.004	4.100	-0.644	-0.392	0.001	-0.038	-0.215	0.000
6	A	57	LEU	0	-0.027	-0.015	7.343	0.126	0.126	0.000	0.000	0.000	0.000
7	A	58	SER	0	0.049	0.013	10.977	0.070	0.070	0.000	0.000	0.000	0.000
8	A	59	GLY	0	-0.051	-0.030	14.099	0.002	0.002	0.000	0.000	0.000	0.000
9	A	60	MET	0	-0.037	-0.017	17.777	0.006	0.006	0.000	0.000	0.000	0.000
10	A	61	SER	0	0.017	0.039	21.114	0.006	0.006	0.000	0.000	0.000	0.000
11	A	62	ARG	1	0.962	0.981	23.387	0.178	0.178	0.000	0.000	0.000	0.000
12	A	63	ILE	0	-0.022	0.014	23.698	-0.006	-0.006	0.000	0.000	0.000	0.000
13	A	64	SER	0	-0.013	-0.022	27.123	0.009	0.009	0.000	0.000	0.000	0.000
14	A	65	GLN	0	0.026	0.001	30.891	-0.014	-0.014	0.000	0.000	0.000	0.000
15	A	66	ALA	0	0.005	0.032	34.216	0.003	0.003	0.000	0.000	0.000	0.000
16	A	67	VAL	0	-0.025	-0.018	37.365	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	68	LEU	0	0.005	-0.002	40.754	0.002	0.002	0.000	0.000	0.000	0.000
18	A	69	PRO	0	0.020	0.000	42.917	0.000	0.000	0.000	0.000	0.000	0.000
19	A	70	ALA	0	0.020	-0.017	46.543	0.001	0.001	0.000	0.000	0.000	0.000
20	A	71	GLY	0	0.058	0.047	49.076	0.001	0.001	0.000	0.000	0.000	0.000
21	A	72	THR	0	-0.086	-0.042	45.762	0.001	0.001	0.000	0.000	0.000	0.000
22	A	73	GLY	0	0.033	0.029	45.130	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	74	THR	0	0.008	-0.023	45.234	0.002	0.002	0.000	0.000	0.000	0.000
24	A	75	ASP	-1	-0.901	-0.942	44.241	-0.041	-0.041	0.000	0.000	0.000	0.000
25	A	76	GLY	0	0.000	0.013	41.949	0.003	0.003	0.000	0.000	0.000	0.000
26	A	77	TYR	0	-0.028	-0.020	41.185	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	78	VAL	0	0.044	0.015	36.770	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	79	VAL	0	-0.028	-0.017	36.636	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	80	VAL	0	-0.074	-0.040	31.676	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	81	ASP	-1	-0.762	-0.865	32.068	-0.076	-0.076	0.000	0.000	0.000	0.000
31	A	82	ALA	0	-0.010	0.009	28.536	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	83	THR	0	0.012	-0.008	25.878	0.000	0.000	0.000	0.000	0.000	0.000
33	A	84	ILE	0	-0.037	-0.012	20.867	-0.014	-0.014	0.000	0.000	0.000	0.000
34	A	85	VAL	0	0.057	0.047	21.412	0.007	0.007	0.000	0.000	0.000	0.000
35	A	86	PRO	0	0.038	-0.003	17.786	-0.012	-0.012	0.000	0.000	0.000	0.000
36	A	87	ASP	-1	-0.870	-0.940	19.719	-0.269	-0.269	0.000	0.000	0.000	0.000
37	A	88	LEU	0	-0.063	-0.018	22.772	0.001	0.001	0.000	0.000	0.000	0.000
38	A	89	LEU	0	-0.031	-0.013	18.675	0.003	0.003	0.000	0.000	0.000	0.000
39	A	90	PRO	0	0.047	0.015	20.066	-0.041	-0.041	0.000	0.000	0.000	0.000
40	A	91	ARG	1	0.896	0.948	15.305	0.619	0.619	0.000	0.000	0.000	0.000
41	A	92	LEU	0	0.008	0.005	14.311	-0.043	-0.043	0.000	0.000	0.000	0.000
42	A	93	GLY	0	0.047	0.034	17.103	-0.009	-0.009	0.000	0.000	0.000	0.000
43	A	94	HIS	0	-0.036	-0.021	18.481	0.009	0.009	0.000	0.000	0.000	0.000
44	A	95	ALA	0	-0.006	-0.004	13.210	-0.015	-0.015	0.000	0.000	0.000	0.000
45	A	96	ALA	0	0.055	0.015	14.517	-0.032	-0.032	0.000	0.000	0.000	0.000
46	A	97	ARG	1	0.920	0.972	16.320	0.305	0.305	0.000	0.000	0.000	0.000
47	A	98	ILE	0	0.020	0.022	12.646	0.013	0.013	0.000	0.000	0.000	0.000
48	A	99	PHE	0	-0.017	-0.020	8.446	-0.065	-0.065	0.000	0.000	0.000	0.000
49	A	100	GLN	0	0.013	0.004	13.100	0.093	0.093	0.000	0.000	0.000	0.000
50	A	101	ARG	1	0.925	0.961	12.651	-0.052	-0.052	0.000	0.000	0.000	0.000
51	A	102	TYR	0	-0.003	0.011	11.238	-0.113	-0.113	0.000	0.000	0.000	0.000
52	A	103	ALA	0	0.051	0.036	9.779	0.143	0.143	0.000	0.000	0.000	0.000
53	A	104	VAL	0	-0.016	-0.002	11.459	-0.152	-0.152	0.000	0.000	0.000	0.000
54	A	105	GLU	-1	-0.858	-0.954	7.859	-1.081	-1.081	0.000	0.000	0.000	0.000
55	A	106	THR	0	-0.103	-0.051	12.371	0.046	0.046	0.000	0.000	0.000	0.000
56	A	107	LEU	0	0.048	-0.001	15.470	-0.028	-0.028	0.000	0.000	0.000	0.000
57	A	108	GLU	-1	-0.885	-0.913	18.865	-0.202	-0.202	0.000	0.000	0.000	0.000
58	A	109	PHE	0	0.029	0.011	22.107	-0.020	-0.020	0.000	0.000	0.000	0.000
59	A	110	GLU	-1	-0.903	-0.957	25.258	-0.182	-0.182	0.000	0.000	0.000	0.000
60	A	111	ILE	0	-0.015	-0.009	27.542	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	112	GLN	0	0.039	0.037	30.313	0.013	0.013	0.000	0.000	0.000	0.000
62	A	113	PRO	0	-0.018	0.004	32.971	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	114	MET	0	-0.032	-0.017	34.749	0.000	0.000	0.000	0.000	0.000	0.000
64	A	115	CYS	0	-0.017	0.007	39.129	0.004	0.004	0.000	0.000	0.000	0.000
65	A	116	PRO	0	0.060	0.049	42.735	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	117	ALA	0	0.054	0.006	44.690	0.001	0.001	0.000	0.000	0.000	0.000
67	A	118	ASN	0	-0.094	-0.034	45.616	0.005	0.005	0.000	0.000	0.000	0.000
68	A	119	THR	0	0.049	0.004	44.719	0.001	0.001	0.000	0.000	0.000	0.000
69	A	120	GLY	0	-0.026	-0.021	46.301	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	121	GLY	0	-0.048	-0.040	43.962	0.001	0.001	0.000	0.000	0.000	0.000
71	A	122	GLY	0	0.040	0.007	41.484	0.003	0.003	0.000	0.000	0.000	0.000
72	A	123	TYR	0	-0.048	-0.028	34.025	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	124	VAL	0	0.053	0.024	34.988	0.002	0.002	0.000	0.000	0.000	0.000
74	A	125	ALA	0	-0.010	-0.001	31.469	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	126	GLY	0	0.034	0.013	29.536	0.003	0.003	0.000	0.000	0.000	0.000
76	A	127	PHE	0	-0.068	-0.025	22.045	-0.007	-0.007	0.000	0.000	0.000	0.000
77	A	128	LEU	0	0.081	0.032	26.448	0.005	0.005	0.000	0.000	0.000	0.000
78	A	129	PRO	0	-0.080	-0.053	22.936	-0.009	-0.009	0.000	0.000	0.000	0.000
79	A	130	ASP	-1	-0.839	-0.906	24.183	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	131	PRO	0	-0.058	-0.023	24.304	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	132	THR	0	-0.011	-0.036	27.148	0.001	0.001	0.000	0.000	0.000	0.000
82	A	133	ASP	-1	-0.912	-0.962	29.947	-0.023	-0.023	0.000	0.000	0.000	0.000
83	A	134	ASN	0	-0.083	-0.040	32.056	-0.011	-0.011	0.000	0.000	0.000	0.000
84	A	135	ASP	-1	-0.861	-0.907	34.451	-0.018	-0.018	0.000	0.000	0.000	0.000
85	A	136	HIS	0	-0.046	-0.023	33.254	0.000	0.000	0.000	0.000	0.000	0.000
86	A	137	THR	0	0.016	0.008	36.601	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	138	PHE	0	0.054	0.011	36.922	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	139	ASP	-1	-0.905	-0.961	37.148	-0.024	-0.024	0.000	0.000	0.000	0.000
89	A	140	ALA	0	0.050	0.037	34.541	0.003	0.003	0.000	0.000	0.000	0.000
90	A	141	LEU	0	-0.010	-0.017	32.591	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	142	GLN	0	-0.080	-0.038	32.371	-0.007	-0.007	0.000	0.000	0.000	0.000
92	A	143	ALA	0	0.041	0.045	33.010	0.004	0.004	0.000	0.000	0.000	0.000
93	A	144	THR	0	-0.142	-0.074	28.041	0.001	0.001	0.000	0.000	0.000	0.000
94	A	145	ARG	1	0.943	0.951	24.559	0.021	0.021	0.000	0.000	0.000	0.000
95	A	146	GLY	0	-0.028	-0.012	26.639	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	147	ALA	0	-0.021	0.009	27.332	-0.008	-0.008	0.000	0.000	0.000	0.000
97	A	148	VAL	0	-0.021	-0.005	30.281	0.003	0.003	0.000	0.000	0.000	0.000
98	A	149	VAL	0	0.050	0.018	33.049	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	150	ALA	0	-0.050	-0.020	36.169	0.000	0.000	0.000	0.000	0.000	0.000
100	A	151	LYS	1	1.002	1.007	38.195	0.063	0.063	0.000	0.000	0.000	0.000
101	A	152	TRP	0	0.057	0.017	38.495	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	153	TRP	0	-0.015	-0.002	39.765	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	154	GLU	-1	-0.913	-0.960	37.176	-0.073	-0.073	0.000	0.000	0.000	0.000
104	A	155	SER	0	-0.006	-0.027	32.533	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	156	ARG	1	0.934	0.966	31.871	0.086	0.086	0.000	0.000	0.000	0.000
106	A	157	THR	0	-0.039	-0.022	25.337	-0.009	-0.009	0.000	0.000	0.000	0.000
107	A	158	VAL	0	0.006	0.022	26.097	0.009	0.009	0.000	0.000	0.000	0.000
108	A	159	ARG	1	0.909	0.939	22.597	0.136	0.136	0.000	0.000	0.000	0.000
109	A	160	PRO	0	0.014	0.026	22.021	0.018	0.018	0.000	0.000	0.000	0.000
110	A	161	GLN	0	-0.012	-0.019	20.906	0.000	0.000	0.000	0.000	0.000	0.000
111	A	162	TYR	0	-0.036	-0.020	15.259	0.018	0.018	0.000	0.000	0.000	0.000
112	A	163	THR	0	0.064	0.020	16.955	0.015	0.015	0.000	0.000	0.000	0.000
113	A	164	ARG	1	0.904	0.962	13.586	0.175	0.175	0.000	0.000	0.000	0.000
114	A	165	THR	0	0.052	0.038	13.401	0.060	0.060	0.000	0.000	0.000	0.000
115	A	166	LEU	0	-0.051	-0.026	10.458	-0.065	-0.065	0.000	0.000	0.000	0.000
116	A	167	LEU	0	-0.029	-0.007	13.425	0.028	0.028	0.000	0.000	0.000	0.000
117	A	168	TRP	0	0.015	-0.023	15.229	0.014	0.014	0.000	0.000	0.000	0.000
118	A	169	THR	0	-0.004	-0.019	14.888	0.006	0.006	0.000	0.000	0.000	0.000
119	A	170	SER	0	0.023	0.027	17.956	-0.017	-0.017	0.000	0.000	0.000	0.000
120	A	171	SER	0	-0.019	-0.008	21.617	0.013	0.013	0.000	0.000	0.000	0.000
121	A	172	GLY	0	0.040	0.023	24.468	0.006	0.006	0.000	0.000	0.000	0.000
122	A	173	LYS	1	0.920	0.959	25.241	-0.004	-0.004	0.000	0.000	0.000	0.000
123	A	174	GLU	-1	-0.884	-0.933	25.101	0.023	0.023	0.000	0.000	0.000	0.000
124	A	175	GLN	0	-0.021	-0.036	23.753	-0.014	-0.014	0.000	0.000	0.000	0.000
125	A	176	ARG	1	0.970	0.986	23.275	-0.022	-0.022	0.000	0.000	0.000	0.000
126	A	177	LEU	0	-0.049	-0.021	17.823	0.007	0.007	0.000	0.000	0.000	0.000
127	A	178	THR	0	0.013	-0.033	19.546	-0.011	-0.011	0.000	0.000	0.000	0.000
128	A	179	SER	0	-0.009	0.013	20.532	-0.022	-0.022	0.000	0.000	0.000	0.000
129	A	180	PRO	0	-0.043	-0.012	18.327	0.024	0.024	0.000	0.000	0.000	0.000
130	A	181	GLY	0	0.032	-0.001	20.352	0.018	0.018	0.000	0.000	0.000	0.000
131	A	182	ARG	1	0.817	0.914	24.030	0.052	0.052	0.000	0.000	0.000	0.000
132	A	183	LEU	0	-0.044	0.001	26.847	0.006	0.006	0.000	0.000	0.000	0.000
133	A	184	ILE	0	0.042	0.021	28.515	-0.002	-0.002	0.000	0.000	0.000	0.000
134	A	185	LEU	0	-0.030	-0.029	32.203	-0.002	-0.002	0.000	0.000	0.000	0.000
135	A	186	LEU	0	0.015	0.011	34.679	0.001	0.001	0.000	0.000	0.000	0.000
136	A	187	CYS	0	-0.066	-0.014	38.190	-0.003	-0.003	0.000	0.000	0.000	0.000
137	A	188	VAL	0	-0.020	-0.002	40.293	0.004	0.004	0.000	0.000	0.000	0.000
138	A	189	GLY	0	0.045	0.040	42.974	-0.002	-0.002	0.000	0.000	0.000	0.000
139	A	190	ASN	0	0.015	-0.020	45.858	-0.002	-0.002	0.000	0.000	0.000	0.000
140	A	191	ASN	0	-0.080	-0.036	44.814	0.002	0.002	0.000	0.000	0.000	0.000
141	A	192	THR	0	-0.013	0.001	46.869	0.001	0.001	0.000	0.000	0.000	0.000
142	A	193	ASP	-1	-0.814	-0.919	47.003	-0.062	-0.062	0.000	0.000	0.000	0.000
143	A	194	VAL	0	-0.089	-0.033	44.131	-0.001	-0.001	0.000	0.000	0.000	0.000
144	A	195	VAL	0	-0.004	-0.001	39.472	-0.002	-0.002	0.000	0.000	0.000	0.000
145	A	196	ASN	0	-0.044	-0.021	37.969	-0.007	-0.007	0.000	0.000	0.000	0.000
146	A	197	VAL	0	0.032	0.030	34.226	-0.005	-0.005	0.000	0.000	0.000	0.000
147	A	198	SER	0	0.003	-0.016	31.964	-0.005	-0.005	0.000	0.000	0.000	0.000
148	A	199	VAL	0	0.013	0.031	27.660	-0.001	-0.001	0.000	0.000	0.000	0.000
149	A	200	LEU	0	-0.008	-0.010	25.710	-0.011	-0.011	0.000	0.000	0.000	0.000
150	A	201	CYS	0	0.020	0.020	21.480	0.001	0.001	0.000	0.000	0.000	0.000
151	A	202	ARG	1	0.852	0.921	18.660	0.257	0.257	0.000	0.000	0.000	0.000
152	A	203	TRP	0	0.017	-0.022	14.119	0.002	0.002	0.000	0.000	0.000	0.000
153	A	204	SER	0	-0.029	-0.011	11.946	-0.075	-0.075	0.000	0.000	0.000	0.000
154	A	205	VAL	0	-0.001	-0.007	11.182	0.087	0.087	0.000	0.000	0.000	0.000
155	A	206	ARG	1	0.913	0.954	5.093	0.004	0.004	0.000	0.000	0.000	0.000
156	A	207	LEU	0	-0.037	-0.029	7.681	0.395	0.395	0.000	0.000	0.000	0.000
157	A	208	SER	0	-0.017	-0.013	7.032	-0.257	-0.257	0.000	0.000	0.000	0.000
158	A	209	VAL	0	0.007	0.010	8.314	-0.102	-0.102	0.000	0.000	0.000	0.000
159	A	210	PRO	0	0.035	0.028	9.554	-0.009	-0.009	0.000	0.000	0.000	0.000
160	A	211	SER	0	-0.080	-0.047	12.291	0.131	0.131	0.000	0.000	0.000	0.000
161	A	212	LEU	0	0.019	-0.003	16.023	-0.053	-0.053	0.000	0.000	0.000	0.000
162	A	213	GLU	-1	-0.950	-0.952	18.966	-0.138	-0.138	0.000	0.000	0.000	0.000
163	A	214	ASN	0	-0.032	-0.012	21.507	0.006	0.006	0.000	0.000	0.000	0.000

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