FMO DATABASE

FMODB ID: J3Z29

Calculation Name: 4RFT-A-Xray372

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: 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:

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	163
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1537546.305228
FMO2-HF: Nuclear repulsion	1475052.261973
FMO2-HF: Total energy	-62494.043255
FMO2-MP2: Total energy	-62676.540862

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: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.
-9.809	-1.434	0.656	-4.322	-4.708	0.015

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 : 0.034 / q_NPA : 0.017

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	-0.804	-0.878	2.682	-3.464	3.312	0.467	-3.568	-3.675	0.022
4	A	55	VAL	0	0.021	0.017	2.963	-4.472	-3.205	0.187	-0.684	-0.769	-0.007
5	A	56	HIS	0	-0.022	-0.008	4.149	-1.230	-0.898	0.002	-0.070	-0.264	0.000
6	A	57	LEU	0	-0.029	-0.013	7.425	0.162	0.162	0.000	0.000	0.000	0.000
7	A	58	SER	0	0.033	0.020	11.054	0.122	0.122	0.000	0.000	0.000	0.000
8	A	59	GLY	0	-0.031	-0.021	14.157	0.001	0.001	0.000	0.000	0.000	0.000
9	A	60	MET	0	-0.036	-0.005	17.823	0.008	0.008	0.000	0.000	0.000	0.000
10	A	61	SER	0	0.003	0.028	21.206	0.003	0.003	0.000	0.000	0.000	0.000
11	A	62	ARG	1	0.884	0.933	23.538	0.176	0.176	0.000	0.000	0.000	0.000
12	A	63	ILE	0	0.007	0.018	23.478	-0.005	-0.005	0.000	0.000	0.000	0.000
13	A	64	SER	0	0.006	-0.006	27.210	0.008	0.008	0.000	0.000	0.000	0.000
14	A	65	GLN	0	0.019	-0.005	31.003	-0.013	-0.013	0.000	0.000	0.000	0.000
15	A	66	ALA	0	0.007	0.033	34.392	0.003	0.003	0.000	0.000	0.000	0.000
16	A	67	VAL	0	-0.010	-0.005	37.423	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	68	LEU	0	-0.003	-0.004	40.869	0.003	0.003	0.000	0.000	0.000	0.000
18	A	69	PRO	0	0.002	-0.013	42.891	0.000	0.000	0.000	0.000	0.000	0.000
19	A	70	ALA	0	0.027	0.001	46.554	0.001	0.001	0.000	0.000	0.000	0.000
20	A	71	GLY	0	0.053	0.043	48.963	0.001	0.001	0.000	0.000	0.000	0.000
21	A	72	THR	0	-0.059	-0.028	45.607	0.002	0.002	0.000	0.000	0.000	0.000
22	A	73	GLY	0	0.026	0.024	44.889	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	74	THR	0	-0.022	-0.029	44.908	0.003	0.003	0.000	0.000	0.000	0.000
24	A	75	ASP	-1	-0.829	-0.910	43.990	-0.040	-0.040	0.000	0.000	0.000	0.000
25	A	76	GLY	0	0.009	0.016	41.720	0.003	0.003	0.000	0.000	0.000	0.000
26	A	77	TYR	0	-0.028	-0.020	40.907	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	78	VAL	0	0.052	0.024	36.169	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	79	VAL	0	-0.028	-0.018	36.519	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	80	VAL	0	-0.066	-0.037	31.510	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	81	ASP	-1	-0.750	-0.848	31.808	-0.068	-0.068	0.000	0.000	0.000	0.000
31	A	82	ALA	0	-0.007	0.011	28.444	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	83	THR	0	0.034	0.004	25.537	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	84	ILE	0	-0.039	-0.014	20.653	-0.015	-0.015	0.000	0.000	0.000	0.000
34	A	85	VAL	0	0.048	0.040	21.193	0.008	0.008	0.000	0.000	0.000	0.000
35	A	86	PRO	0	0.040	0.003	17.763	-0.013	-0.013	0.000	0.000	0.000	0.000
36	A	87	ASP	-1	-0.797	-0.889	19.838	-0.271	-0.271	0.000	0.000	0.000	0.000
37	A	88	LEU	0	-0.038	0.000	23.079	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	89	LEU	0	-0.038	-0.014	18.778	0.000	0.000	0.000	0.000	0.000	0.000
39	A	90	PRO	0	0.058	0.014	20.318	-0.044	-0.044	0.000	0.000	0.000	0.000
40	A	91	ARG	1	0.889	0.946	15.402	0.628	0.628	0.000	0.000	0.000	0.000
41	A	92	LEU	0	0.011	0.007	14.552	-0.040	-0.040	0.000	0.000	0.000	0.000
42	A	93	GLY	0	0.039	0.032	17.369	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	94	HIS	0	-0.033	-0.024	18.721	0.011	0.011	0.000	0.000	0.000	0.000
44	A	95	ALA	0	-0.004	-0.004	13.466	-0.013	-0.013	0.000	0.000	0.000	0.000
45	A	96	ALA	0	0.039	0.009	14.858	-0.023	-0.023	0.000	0.000	0.000	0.000
46	A	97	ARG	1	0.832	0.906	16.744	0.294	0.294	0.000	0.000	0.000	0.000
47	A	98	ILE	0	0.010	0.015	13.248	0.010	0.010	0.000	0.000	0.000	0.000
48	A	99	PHE	0	-0.009	-0.011	8.593	-0.061	-0.061	0.000	0.000	0.000	0.000
49	A	100	GLN	0	0.012	0.007	13.290	0.087	0.087	0.000	0.000	0.000	0.000
50	A	101	ARG	1	0.920	0.963	12.222	-0.132	-0.132	0.000	0.000	0.000	0.000
51	A	102	TYR	0	0.000	0.012	10.892	-0.104	-0.104	0.000	0.000	0.000	0.000
52	A	103	ALA	0	0.059	0.039	9.587	0.145	0.145	0.000	0.000	0.000	0.000
53	A	104	VAL	0	-0.014	0.000	11.077	-0.172	-0.172	0.000	0.000	0.000	0.000
54	A	105	GLU	-1	-0.839	-0.935	7.735	-1.155	-1.155	0.000	0.000	0.000	0.000
55	A	106	THR	0	-0.060	-0.039	12.221	0.051	0.051	0.000	0.000	0.000	0.000
56	A	107	LEU	0	0.022	-0.003	15.462	-0.030	-0.030	0.000	0.000	0.000	0.000
57	A	108	GLU	-1	-0.823	-0.871	18.749	-0.193	-0.193	0.000	0.000	0.000	0.000
58	A	109	PHE	0	0.024	0.010	22.169	-0.022	-0.022	0.000	0.000	0.000	0.000
59	A	110	GLU	-1	-0.853	-0.921	25.288	-0.192	-0.192	0.000	0.000	0.000	0.000
60	A	111	ILE	0	-0.006	-0.001	27.688	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	112	GLN	0	0.023	0.020	30.241	0.014	0.014	0.000	0.000	0.000	0.000
62	A	113	PRO	0	-0.002	0.005	33.125	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	114	MET	0	-0.021	-0.013	34.683	0.000	0.000	0.000	0.000	0.000	0.000
64	A	115	CYS	0	0.008	0.008	39.290	0.002	0.002	0.000	0.000	0.000	0.000
65	A	116	PRO	0	0.037	0.042	42.891	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	117	ALA	0	0.056	0.003	44.810	0.001	0.001	0.000	0.000	0.000	0.000
67	A	118	ASN	0	-0.078	-0.025	45.739	0.005	0.005	0.000	0.000	0.000	0.000
68	A	119	THR	0	0.024	0.003	44.788	0.001	0.001	0.000	0.000	0.000	0.000
69	A	120	GLY	0	-0.022	-0.025	46.437	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	121	GLY	0	-0.035	-0.031	44.024	0.002	0.002	0.000	0.000	0.000	0.000
71	A	122	GLY	0	0.029	0.010	41.499	0.003	0.003	0.000	0.000	0.000	0.000
72	A	123	TYR	0	-0.059	-0.039	34.016	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	124	VAL	0	0.050	0.029	34.921	0.001	0.001	0.000	0.000	0.000	0.000
74	A	125	ALA	0	-0.008	0.001	31.298	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	126	GLY	0	0.050	0.012	29.371	0.003	0.003	0.000	0.000	0.000	0.000
76	A	127	PHE	0	-0.060	-0.025	21.771	-0.007	-0.007	0.000	0.000	0.000	0.000
77	A	128	LEU	0	0.073	0.032	26.324	0.006	0.006	0.000	0.000	0.000	0.000
78	A	129	PRO	0	-0.067	-0.052	22.781	-0.008	-0.008	0.000	0.000	0.000	0.000
79	A	130	ASP	-1	-0.798	-0.850	24.060	0.020	0.020	0.000	0.000	0.000	0.000
80	A	131	PRO	0	-0.020	-0.015	24.074	-0.004	-0.004	0.000	0.000	0.000	0.000
81	A	132	THR	0	-0.020	-0.038	26.862	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	133	ASP	-1	-0.905	-0.961	29.708	-0.014	-0.014	0.000	0.000	0.000	0.000
83	A	134	ASN	0	-0.050	-0.024	31.864	-0.014	-0.014	0.000	0.000	0.000	0.000
84	A	135	ASP	-1	-0.867	-0.909	34.276	-0.015	-0.015	0.000	0.000	0.000	0.000
85	A	136	HIS	0	-0.081	-0.051	32.655	0.001	0.001	0.000	0.000	0.000	0.000
86	A	137	THR	0	0.042	0.018	36.390	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	138	PHE	0	0.038	0.008	36.791	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	139	ASP	-1	-0.899	-0.960	37.068	-0.020	-0.020	0.000	0.000	0.000	0.000
89	A	140	ALA	0	0.039	0.031	34.516	0.003	0.003	0.000	0.000	0.000	0.000
90	A	141	LEU	0	-0.008	-0.016	32.540	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	142	GLN	0	-0.072	-0.037	32.309	-0.007	-0.007	0.000	0.000	0.000	0.000
92	A	143	ALA	0	0.043	0.043	33.219	0.004	0.004	0.000	0.000	0.000	0.000
93	A	144	THR	0	-0.136	-0.071	28.018	0.002	0.002	0.000	0.000	0.000	0.000
94	A	145	ARG	1	0.919	0.936	24.966	0.005	0.005	0.000	0.000	0.000	0.000
95	A	146	GLY	0	-0.024	-0.013	26.571	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	147	ALA	0	-0.027	0.006	27.290	-0.009	-0.009	0.000	0.000	0.000	0.000
97	A	148	VAL	0	-0.014	-0.005	30.530	0.003	0.003	0.000	0.000	0.000	0.000
98	A	149	VAL	0	0.043	0.018	32.989	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	150	ALA	0	-0.045	-0.013	36.320	0.000	0.000	0.000	0.000	0.000	0.000
100	A	151	LYS	1	0.974	0.973	38.313	0.066	0.066	0.000	0.000	0.000	0.000
101	A	152	TRP	0	0.054	0.006	38.479	-0.004	-0.004	0.000	0.000	0.000	0.000
102	A	153	TRP	0	-0.018	0.002	39.911	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	154	GLU	-1	-0.863	-0.915	36.763	-0.072	-0.072	0.000	0.000	0.000	0.000
104	A	155	SER	0	0.004	-0.007	32.748	0.002	0.002	0.000	0.000	0.000	0.000
105	A	156	ARG	1	0.909	0.948	31.990	0.086	0.086	0.000	0.000	0.000	0.000
106	A	157	THR	0	-0.041	-0.028	25.421	-0.008	-0.008	0.000	0.000	0.000	0.000
107	A	158	VAL	0	0.000	0.024	26.098	0.009	0.009	0.000	0.000	0.000	0.000
108	A	159	ARG	1	0.864	0.896	22.558	0.143	0.143	0.000	0.000	0.000	0.000
109	A	160	PRO	0	0.017	0.019	22.038	0.017	0.017	0.000	0.000	0.000	0.000
110	A	161	GLN	0	0.013	0.006	21.115	-0.010	-0.010	0.000	0.000	0.000	0.000
111	A	162	TYR	0	-0.019	-0.016	15.090	0.014	0.014	0.000	0.000	0.000	0.000
112	A	163	THR	0	0.050	0.019	17.056	0.015	0.015	0.000	0.000	0.000	0.000
113	A	164	ARG	1	0.868	0.941	13.504	0.184	0.184	0.000	0.000	0.000	0.000
114	A	165	THR	0	0.046	0.033	13.515	0.073	0.073	0.000	0.000	0.000	0.000
115	A	166	LEU	0	-0.061	-0.025	10.069	-0.073	-0.073	0.000	0.000	0.000	0.000
116	A	167	LEU	0	-0.026	-0.006	13.281	0.021	0.021	0.000	0.000	0.000	0.000
117	A	168	TRP	0	0.019	-0.026	14.866	0.027	0.027	0.000	0.000	0.000	0.000
118	A	169	THR	0	-0.014	-0.017	15.039	0.000	0.000	0.000	0.000	0.000	0.000
119	A	170	SER	0	0.017	0.022	17.887	-0.021	-0.021	0.000	0.000	0.000	0.000
120	A	171	SER	0	-0.022	-0.011	21.574	0.014	0.014	0.000	0.000	0.000	0.000
121	A	172	GLY	0	0.048	0.027	24.065	0.007	0.007	0.000	0.000	0.000	0.000
122	A	173	LYS	1	0.916	0.957	24.818	-0.023	-0.023	0.000	0.000	0.000	0.000
123	A	174	GLU	-1	-0.849	-0.930	24.479	0.029	0.029	0.000	0.000	0.000	0.000
124	A	175	GLN	0	-0.030	-0.025	23.432	-0.011	-0.011	0.000	0.000	0.000	0.000
125	A	176	ARG	1	0.857	0.923	23.065	-0.035	-0.035	0.000	0.000	0.000	0.000
126	A	177	LEU	0	-0.045	-0.026	17.632	0.011	0.011	0.000	0.000	0.000	0.000
127	A	178	THR	0	0.003	-0.009	19.091	-0.008	-0.008	0.000	0.000	0.000	0.000
128	A	179	SER	0	-0.007	-0.016	20.122	-0.025	-0.025	0.000	0.000	0.000	0.000
129	A	180	PRO	0	-0.040	-0.017	18.036	0.025	0.025	0.000	0.000	0.000	0.000
130	A	181	GLY	0	0.028	0.002	20.081	0.018	0.018	0.000	0.000	0.000	0.000
131	A	182	ARG	1	0.812	0.904	23.765	0.042	0.042	0.000	0.000	0.000	0.000
132	A	183	LEU	0	-0.053	-0.008	26.439	0.006	0.006	0.000	0.000	0.000	0.000
133	A	184	ILE	0	0.019	0.016	28.185	-0.002	-0.002	0.000	0.000	0.000	0.000
134	A	185	LEU	0	-0.036	-0.027	31.895	-0.003	-0.003	0.000	0.000	0.000	0.000
135	A	186	LEU	0	0.018	0.013	34.360	0.001	0.001	0.000	0.000	0.000	0.000
136	A	187	CYS	0	-0.091	-0.034	37.904	-0.004	-0.004	0.000	0.000	0.000	0.000
137	A	188	VAL	0	-0.022	-0.006	40.071	0.003	0.003	0.000	0.000	0.000	0.000
138	A	189	GLY	0	0.030	0.020	42.752	-0.002	-0.002	0.000	0.000	0.000	0.000
139	A	190	ASN	0	-0.007	-0.020	45.646	-0.002	-0.002	0.000	0.000	0.000	0.000
140	A	191	ASN	0	-0.084	-0.067	44.791	0.002	0.002	0.000	0.000	0.000	0.000
141	A	192	THR	0	-0.012	0.001	46.844	0.001	0.001	0.000	0.000	0.000	0.000
142	A	193	ASP	-1	-0.803	-0.896	47.205	-0.064	-0.064	0.000	0.000	0.000	0.000
143	A	194	VAL	0	-0.083	-0.034	44.191	-0.001	-0.001	0.000	0.000	0.000	0.000
144	A	195	VAL	0	-0.014	-0.006	39.633	-0.003	-0.003	0.000	0.000	0.000	0.000
145	A	196	ASN	0	-0.030	-0.011	38.299	-0.004	-0.004	0.000	0.000	0.000	0.000
146	A	197	VAL	0	0.031	0.027	34.295	-0.006	-0.006	0.000	0.000	0.000	0.000
147	A	198	SER	0	0.017	-0.003	31.890	-0.006	-0.006	0.000	0.000	0.000	0.000
148	A	199	VAL	0	-0.001	0.023	28.036	-0.002	-0.002	0.000	0.000	0.000	0.000
149	A	200	LEU	0	0.006	-0.001	25.902	-0.010	-0.010	0.000	0.000	0.000	0.000
150	A	201	CYS	0	0.012	0.025	21.358	0.001	0.001	0.000	0.000	0.000	0.000
151	A	202	ARG	1	0.784	0.859	19.666	0.237	0.237	0.000	0.000	0.000	0.000
152	A	203	TRP	0	0.046	-0.005	14.313	0.005	0.005	0.000	0.000	0.000	0.000
153	A	204	SER	0	-0.015	-0.012	11.977	-0.094	-0.094	0.000	0.000	0.000	0.000
154	A	205	VAL	0	0.002	-0.008	11.367	0.106	0.106	0.000	0.000	0.000	0.000
155	A	206	ARG	1	0.861	0.923	5.655	-0.445	-0.445	0.000	0.000	0.000	0.000
156	A	207	LEU	0	-0.044	-0.031	7.942	0.457	0.457	0.000	0.000	0.000	0.000
157	A	208	SER	0	-0.038	-0.019	7.270	-0.252	-0.252	0.000	0.000	0.000	0.000
158	A	209	VAL	0	-0.006	0.005	8.412	-0.041	-0.041	0.000	0.000	0.000	0.000
159	A	210	PRO	0	0.037	0.032	9.976	-0.051	-0.051	0.000	0.000	0.000	0.000
160	A	211	SER	0	-0.073	-0.049	12.711	0.126	0.126	0.000	0.000	0.000	0.000
161	A	212	LEU	0	0.032	0.003	16.440	-0.055	-0.055	0.000	0.000	0.000	0.000
162	A	213	GLU	-1	-0.930	-0.944	19.338	-0.108	-0.108	0.000	0.000	0.000	0.000
163	A	214	ASN	0	-0.056	-0.027	21.924	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)