FMO DATABASE

FMODB ID: R9JK8

Calculation Name: 3F13-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3F13

Chain ID: A

ChEMBL ID:

UniProt ID: Q7NWQ3

Base Structure: X-ray

Registration Date: 2023-09-20

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	146
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1372324.156545
FMO2-HF: Nuclear repulsion	1315205.25494
FMO2-HF: Total energy	-57118.901605
FMO2-MP2: Total energy	-57286.466959

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:11:ARG)

Summations of interaction energy for fragment #1(A:11:ARG)

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.
84.8	88.68	0.354	-1.894	-2.34	-0.01

Interaction energy analysis for fragmet #1(A:11:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.998 / q_NPA : 0.996

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	13	PRO	0	-0.047	-0.028	2.789	-9.422	-5.755	0.356	-1.877	-2.146	-0.010
4	A	14	SER	0	0.000	-0.017	5.013	1.819	1.920	-0.001	-0.005	-0.095	0.000
5	A	15	ASP	-1	-0.884	-0.909	7.451	-22.436	-22.436	0.000	0.000	0.000	0.000
6	A	16	LEU	0	-0.036	-0.012	9.361	-1.652	-1.652	0.000	0.000	0.000	0.000
7	A	17	ALA	0	0.007	0.003	11.833	1.795	1.795	0.000	0.000	0.000	0.000
8	A	18	ARG	1	0.832	0.901	13.414	15.767	15.767	0.000	0.000	0.000	0.000
9	A	19	ARG	1	0.898	0.938	13.291	20.716	20.716	0.000	0.000	0.000	0.000
10	A	20	ALA	0	0.010	0.014	17.481	0.646	0.646	0.000	0.000	0.000	0.000
11	A	21	THR	0	-0.056	-0.034	20.025	-0.872	-0.872	0.000	0.000	0.000	0.000
12	A	22	ALA	0	0.066	0.040	22.310	0.385	0.385	0.000	0.000	0.000	0.000
13	A	23	ILE	0	0.006	0.001	24.992	-0.346	-0.346	0.000	0.000	0.000	0.000
14	A	24	ILE	0	0.032	0.004	27.525	0.249	0.249	0.000	0.000	0.000	0.000
15	A	25	GLU	-1	-0.785	-0.858	30.514	-9.501	-9.501	0.000	0.000	0.000	0.000
16	A	26	MET	0	0.021	0.026	32.776	0.291	0.291	0.000	0.000	0.000	0.000
17	A	27	PRO	0	0.019	-0.005	34.900	-0.080	-0.080	0.000	0.000	0.000	0.000
18	A	28	ASP	-1	-0.856	-0.911	35.080	-8.207	-8.207	0.000	0.000	0.000	0.000
19	A	29	GLY	0	-0.011	-0.007	31.738	-0.152	-0.152	0.000	0.000	0.000	0.000
20	A	30	VAL	0	-0.071	-0.039	26.712	0.009	0.009	0.000	0.000	0.000	0.000
21	A	31	LEU	0	0.005	0.013	27.481	-0.191	-0.191	0.000	0.000	0.000	0.000
22	A	32	VAL	0	-0.063	-0.028	23.253	-0.488	-0.488	0.000	0.000	0.000	0.000
23	A	33	THR	0	0.027	-0.004	22.077	0.175	0.175	0.000	0.000	0.000	0.000
24	A	34	ALA	0	0.023	-0.007	20.106	-0.758	-0.758	0.000	0.000	0.000	0.000
25	A	35	SER	0	-0.052	-0.026	17.354	0.240	0.240	0.000	0.000	0.000	0.000
26	A	36	ARG	1	0.820	0.921	15.266	16.002	16.002	0.000	0.000	0.000	0.000
27	A	37	GLY	0	0.105	0.074	18.258	0.775	0.775	0.000	0.000	0.000	0.000
28	A	38	GLY	0	-0.007	-0.024	18.140	-0.371	-0.371	0.000	0.000	0.000	0.000
29	A	39	ARG	1	0.811	0.882	13.829	17.618	17.618	0.000	0.000	0.000	0.000
30	A	40	TYR	0	0.062	0.044	18.466	-0.504	-0.504	0.000	0.000	0.000	0.000
31	A	41	ASN	0	-0.016	-0.028	16.528	-0.149	-0.149	0.000	0.000	0.000	0.000
32	A	42	LEU	0	0.019	0.017	19.704	0.465	0.465	0.000	0.000	0.000	0.000
33	A	43	PRO	0	0.003	0.031	20.556	-0.770	-0.770	0.000	0.000	0.000	0.000
34	A	44	GLY	0	0.038	-0.005	21.465	0.301	0.301	0.000	0.000	0.000	0.000
35	A	45	GLY	0	-0.008	0.008	17.759	-0.568	-0.568	0.000	0.000	0.000	0.000
36	A	46	LYS	1	0.884	0.932	14.016	17.899	17.899	0.000	0.000	0.000	0.000
37	A	47	ALA	0	0.016	0.016	17.693	0.431	0.431	0.000	0.000	0.000	0.000
38	A	48	ASN	0	-0.021	-0.025	18.731	-1.628	-1.628	0.000	0.000	0.000	0.000
39	A	49	ARG	1	0.966	0.964	14.983	18.287	18.287	0.000	0.000	0.000	0.000
40	A	50	GLY	0	0.061	0.029	20.759	0.320	0.320	0.000	0.000	0.000	0.000
41	A	51	GLU	-1	-0.757	-0.814	22.344	-13.118	-13.118	0.000	0.000	0.000	0.000
42	A	52	LEU	0	0.046	0.007	23.709	-0.678	-0.678	0.000	0.000	0.000	0.000
43	A	53	ARG	1	0.848	0.898	18.817	15.244	15.244	0.000	0.000	0.000	0.000
44	A	54	SER	0	0.044	0.031	23.782	-0.213	-0.213	0.000	0.000	0.000	0.000
45	A	55	GLN	0	0.081	0.040	26.671	-0.103	-0.103	0.000	0.000	0.000	0.000
46	A	56	ALA	0	0.012	0.017	21.904	0.086	0.086	0.000	0.000	0.000	0.000
47	A	57	LEU	0	-0.013	-0.002	23.274	-0.135	-0.135	0.000	0.000	0.000	0.000
48	A	58	ILE	0	0.011	0.005	25.040	0.095	0.095	0.000	0.000	0.000	0.000
49	A	59	ARG	1	0.799	0.884	21.034	13.855	13.855	0.000	0.000	0.000	0.000
50	A	60	GLU	-1	-0.793	-0.895	20.229	-15.277	-15.277	0.000	0.000	0.000	0.000
51	A	61	ILE	0	0.002	-0.004	23.930	-0.093	-0.093	0.000	0.000	0.000	0.000
52	A	62	ARG	1	0.896	0.966	26.324	10.339	10.339	0.000	0.000	0.000	0.000
53	A	63	GLU	-1	-0.843	-0.921	24.332	-11.190	-11.190	0.000	0.000	0.000	0.000
54	A	64	GLH	0	-0.026	-0.014	20.075	0.033	0.033	0.000	0.000	0.000	0.000
55	A	65	THR	0	-0.025	-0.029	24.699	0.203	0.203	0.000	0.000	0.000	0.000
56	A	66	GLY	0	0.032	0.028	28.175	0.365	0.365	0.000	0.000	0.000	0.000
57	A	67	LEU	0	-0.071	-0.032	30.380	0.400	0.400	0.000	0.000	0.000	0.000
58	A	68	ARG	1	0.966	0.963	31.636	8.430	8.430	0.000	0.000	0.000	0.000
59	A	69	ILE	0	-0.021	-0.019	29.144	0.209	0.209	0.000	0.000	0.000	0.000
60	A	70	ASN	0	-0.011	0.005	33.481	0.066	0.066	0.000	0.000	0.000	0.000
61	A	71	SER	0	0.043	0.031	35.591	0.206	0.206	0.000	0.000	0.000	0.000
62	A	72	MET	0	-0.061	-0.038	28.519	-0.251	-0.251	0.000	0.000	0.000	0.000
63	A	73	LEU	0	0.027	0.028	32.092	0.150	0.150	0.000	0.000	0.000	0.000
64	A	74	TYR	0	-0.041	-0.054	25.800	-0.138	-0.138	0.000	0.000	0.000	0.000
65	A	75	LEU	0	0.009	0.029	26.911	0.261	0.261	0.000	0.000	0.000	0.000
66	A	76	PHE	0	0.032	-0.006	22.576	0.142	0.142	0.000	0.000	0.000	0.000
67	A	77	ASP	-1	-0.772	-0.835	21.620	-13.164	-13.164	0.000	0.000	0.000	0.000
68	A	78	HIS	0	0.014	0.008	17.125	0.870	0.870	0.000	0.000	0.000	0.000
69	A	79	ILE	0	0.017	0.010	14.963	-0.526	-0.526	0.000	0.000	0.000	0.000
70	A	80	THR	0	-0.008	-0.016	11.549	-0.103	-0.103	0.000	0.000	0.000	0.000
71	A	81	PRO	0	0.057	0.009	7.577	0.305	0.305	0.000	0.000	0.000	0.000
72	A	82	PHE	0	0.054	0.040	4.458	-1.302	-1.190	-0.001	-0.012	-0.099	0.000
73	A	83	ASN	0	-0.038	-0.017	9.609	0.662	0.662	0.000	0.000	0.000	0.000
74	A	84	ALA	0	0.071	0.049	13.404	0.857	0.857	0.000	0.000	0.000	0.000
75	A	85	HIS	1	0.778	0.874	14.730	18.295	18.295	0.000	0.000	0.000	0.000
76	A	86	LYS	1	0.829	0.913	18.881	12.807	12.807	0.000	0.000	0.000	0.000
77	A	87	VAL	0	0.007	-0.003	21.657	-0.266	-0.266	0.000	0.000	0.000	0.000
78	A	88	TYR	0	0.010	-0.008	24.139	0.208	0.208	0.000	0.000	0.000	0.000
79	A	89	LEU	0	0.064	0.059	27.683	-0.214	-0.214	0.000	0.000	0.000	0.000
80	A	90	CYS	0	-0.090	-0.055	29.132	0.035	0.035	0.000	0.000	0.000	0.000
81	A	91	ILE	0	0.068	0.034	31.918	0.008	0.008	0.000	0.000	0.000	0.000
82	A	92	ALA	0	-0.002	-0.008	33.426	-0.084	-0.084	0.000	0.000	0.000	0.000
83	A	93	GLN	0	-0.014	-0.018	35.533	-0.092	-0.092	0.000	0.000	0.000	0.000
84	A	94	GLY	0	-0.014	-0.002	36.896	-0.069	-0.069	0.000	0.000	0.000	0.000
85	A	95	GLN	0	0.020	0.005	35.752	-0.037	-0.037	0.000	0.000	0.000	0.000
86	A	96	PRO	0	0.000	0.010	30.361	-0.033	-0.033	0.000	0.000	0.000	0.000
87	A	97	LYS	1	0.900	0.938	30.729	9.153	9.153	0.000	0.000	0.000	0.000
88	A	98	PRO	0	-0.001	0.020	26.915	-0.223	-0.223	0.000	0.000	0.000	0.000
89	A	99	GLN	0	-0.024	-0.034	26.072	0.621	0.621	0.000	0.000	0.000	0.000
90	A	100	ASN	0	-0.055	-0.043	23.719	-0.392	-0.392	0.000	0.000	0.000	0.000
91	A	101	GLU	-1	-0.779	-0.880	18.541	-14.897	-14.897	0.000	0.000	0.000	0.000
92	A	102	ILE	0	-0.104	-0.035	20.721	-0.464	-0.464	0.000	0.000	0.000	0.000
93	A	103	GLU	-1	-0.840	-0.918	22.339	-12.488	-12.488	0.000	0.000	0.000	0.000
94	A	104	ARG	1	0.839	0.912	21.867	13.576	13.576	0.000	0.000	0.000	0.000
95	A	105	ILE	0	0.004	-0.014	24.598	-0.522	-0.522	0.000	0.000	0.000	0.000
96	A	106	ALA	0	0.004	0.005	26.674	0.191	0.191	0.000	0.000	0.000	0.000
97	A	107	LEU	0	0.032	0.016	28.340	-0.184	-0.184	0.000	0.000	0.000	0.000
98	A	108	VAL	0	-0.013	-0.012	25.227	-0.036	-0.036	0.000	0.000	0.000	0.000
99	A	109	SER	0	0.037	0.009	28.647	-0.014	-0.014	0.000	0.000	0.000	0.000
100	A	110	SER	0	-0.020	-0.026	29.210	0.168	0.168	0.000	0.000	0.000	0.000
101	A	111	PRO	0	-0.028	-0.031	24.571	-0.301	-0.301	0.000	0.000	0.000	0.000
102	A	112	ASP	-1	-0.873	-0.932	24.096	-11.101	-11.101	0.000	0.000	0.000	0.000
103	A	113	THR	0	-0.016	0.024	25.002	-0.021	-0.021	0.000	0.000	0.000	0.000
104	A	114	ASP	-1	-0.787	-0.895	24.933	-10.604	-10.604	0.000	0.000	0.000	0.000
105	A	115	MET	0	-0.038	0.005	23.855	-0.520	-0.520	0.000	0.000	0.000	0.000
106	A	116	ASP	-1	-0.753	-0.848	18.700	-15.644	-15.644	0.000	0.000	0.000	0.000
107	A	117	LEU	0	-0.058	-0.037	19.916	-0.586	-0.586	0.000	0.000	0.000	0.000
108	A	118	PHE	0	-0.004	-0.017	10.728	-0.242	-0.242	0.000	0.000	0.000	0.000
109	A	119	VAL	0	0.037	0.015	12.285	0.651	0.651	0.000	0.000	0.000	0.000
110	A	120	GLU	-1	-0.797	-0.870	13.132	-20.269	-20.269	0.000	0.000	0.000	0.000
111	A	121	GLY	0	0.055	0.029	15.952	0.730	0.730	0.000	0.000	0.000	0.000
112	A	122	ARG	1	0.841	0.920	18.847	13.723	13.723	0.000	0.000	0.000	0.000
113	A	123	ALA	0	-0.012	-0.006	18.011	0.622	0.622	0.000	0.000	0.000	0.000
114	A	124	ILE	0	-0.035	-0.018	18.602	0.581	0.581	0.000	0.000	0.000	0.000
115	A	125	LEU	0	0.062	0.026	21.595	0.584	0.584	0.000	0.000	0.000	0.000
116	A	126	ARG	1	0.962	0.985	21.248	12.514	12.514	0.000	0.000	0.000	0.000
117	A	127	ARG	1	0.796	0.905	21.558	13.045	13.045	0.000	0.000	0.000	0.000
118	A	128	TYR	0	-0.020	-0.055	25.427	0.284	0.284	0.000	0.000	0.000	0.000
119	A	129	ALA	0	-0.008	-0.013	27.649	0.356	0.356	0.000	0.000	0.000	0.000
120	A	130	ARG	1	0.917	0.961	24.158	11.237	11.237	0.000	0.000	0.000	0.000
121	A	131	LEU	0	0.064	0.033	29.271	0.232	0.232	0.000	0.000	0.000	0.000
122	A	132	ARG	1	0.810	0.883	31.239	9.504	9.504	0.000	0.000	0.000	0.000
123	A	133	ASN	0	-0.017	-0.009	33.834	0.298	0.298	0.000	0.000	0.000	0.000
124	A	134	GLU	-1	-0.921	-0.944	31.525	-9.244	-9.244	0.000	0.000	0.000	0.000
125	A	135	GLU	-1	-0.909	-0.934	35.482	-7.303	-7.303	0.000	0.000	0.000	0.000
126	A	136	THR	0	0.000	-0.013	35.108	-0.012	-0.012	0.000	0.000	0.000	0.000
127	A	137	ALA	0	0.106	0.053	37.928	-0.074	-0.074	0.000	0.000	0.000	0.000
128	A	138	LYS	1	0.785	0.893	29.667	10.109	10.109	0.000	0.000	0.000	0.000
129	A	139	GLY	0	0.054	0.025	34.860	-0.127	-0.127	0.000	0.000	0.000	0.000
130	A	140	GLU	-1	-0.912	-0.958	35.710	-7.387	-7.387	0.000	0.000	0.000	0.000
131	A	141	ALA	0	0.004	0.002	36.760	0.076	0.076	0.000	0.000	0.000	0.000
132	A	142	LEU	0	-0.045	-0.021	31.610	-0.042	-0.042	0.000	0.000	0.000	0.000
133	A	143	ARG	1	0.855	0.904	35.631	8.002	8.002	0.000	0.000	0.000	0.000
134	A	144	ALA	0	0.008	0.014	38.440	0.115	0.115	0.000	0.000	0.000	0.000
135	A	145	LEU	0	-0.016	-0.012	35.467	0.072	0.072	0.000	0.000	0.000	0.000
136	A	146	LEU	0	-0.017	-0.016	34.054	0.024	0.024	0.000	0.000	0.000	0.000
137	A	147	GLY	0	-0.030	-0.006	37.971	0.107	0.107	0.000	0.000	0.000	0.000
138	A	148	LEU	0	0.012	0.004	40.370	0.114	0.114	0.000	0.000	0.000	0.000
139	A	149	ALA	0	0.012	-0.003	37.513	0.078	0.078	0.000	0.000	0.000	0.000
140	A	150	ARG	1	0.950	0.981	39.091	7.708	7.708	0.000	0.000	0.000	0.000
141	A	151	TYR	0	-0.015	-0.005	41.561	0.108	0.108	0.000	0.000	0.000	0.000
142	A	152	ILE	0	0.004	-0.002	41.724	0.113	0.113	0.000	0.000	0.000	0.000
143	A	153	ALA	0	0.044	0.027	40.476	0.086	0.086	0.000	0.000	0.000	0.000
144	A	154	LYS	1	0.907	0.963	42.578	6.516	6.516	0.000	0.000	0.000	0.000
145	A	155	VAL	0	-0.060	-0.021	45.916	0.166	0.166	0.000	0.000	0.000	0.000
146	A	156	ASP	-1	-0.934	-0.954	43.274	-7.107	-7.107	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:11:ARG)