FMO DATABASE

FMODB ID: Z6QGN

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	OptHSide
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	-1371419.123377
FMO2-HF: Nuclear repulsion	1314300.813609
FMO2-HF: Total energy	-57118.309768
FMO2-MP2: Total energy	-57285.925847

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.
94.045	96.971	-0.002	-1.259	-1.664	0.002

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 : 0.996 / q_NPA : 0.993

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	-0.052	-0.028	3.491	-5.655	-2.817	-0.001	-1.251	-1.585	0.002
4	A	14	SER	0	-0.008	-0.011	5.507	2.531	2.531	0.000	0.000	0.000	0.000
5	A	15	ASP	-1	-0.876	-0.910	7.413	-22.157	-22.157	0.000	0.000	0.000	0.000
6	A	16	LEU	0	-0.028	-0.015	9.652	-1.528	-1.528	0.000	0.000	0.000	0.000
7	A	17	ALA	0	-0.014	-0.005	11.861	1.536	1.536	0.000	0.000	0.000	0.000
8	A	18	ARG	1	0.856	0.913	13.460	15.830	15.830	0.000	0.000	0.000	0.000
9	A	19	ARG	1	0.902	0.949	12.815	20.786	20.786	0.000	0.000	0.000	0.000
10	A	20	ALA	0	0.011	0.010	17.796	0.589	0.589	0.000	0.000	0.000	0.000
11	A	21	THR	0	-0.032	-0.021	19.893	-0.707	-0.707	0.000	0.000	0.000	0.000
12	A	22	ALA	0	0.065	0.032	22.220	0.413	0.413	0.000	0.000	0.000	0.000
13	A	23	ILE	0	0.000	0.001	25.111	-0.271	-0.271	0.000	0.000	0.000	0.000
14	A	24	ILE	0	0.031	0.005	27.339	0.264	0.264	0.000	0.000	0.000	0.000
15	A	25	GLU	-1	-0.764	-0.853	30.232	-9.424	-9.424	0.000	0.000	0.000	0.000
16	A	26	MET	0	-0.016	-0.001	32.332	0.256	0.256	0.000	0.000	0.000	0.000
17	A	27	PRO	0	0.023	0.003	34.716	-0.041	-0.041	0.000	0.000	0.000	0.000
18	A	28	ASP	-1	-0.882	-0.930	35.511	-8.153	-8.153	0.000	0.000	0.000	0.000
19	A	29	GLY	0	-0.003	-0.004	31.891	-0.181	-0.181	0.000	0.000	0.000	0.000
20	A	30	VAL	0	-0.067	-0.034	26.788	0.008	0.008	0.000	0.000	0.000	0.000
21	A	31	LEU	0	0.010	0.015	27.187	-0.192	-0.192	0.000	0.000	0.000	0.000
22	A	32	VAL	0	-0.058	-0.022	23.154	-0.505	-0.505	0.000	0.000	0.000	0.000
23	A	33	THR	0	0.040	0.008	21.922	0.207	0.207	0.000	0.000	0.000	0.000
24	A	34	ALA	0	0.015	-0.015	20.036	-0.682	-0.682	0.000	0.000	0.000	0.000
25	A	35	SER	0	0.034	0.020	17.237	0.153	0.153	0.000	0.000	0.000	0.000
26	A	36	ARG	1	0.828	0.937	15.379	16.589	16.589	0.000	0.000	0.000	0.000
27	A	37	GLY	0	0.104	0.072	18.623	0.822	0.822	0.000	0.000	0.000	0.000
28	A	38	GLY	0	0.015	-0.015	17.873	-0.614	-0.614	0.000	0.000	0.000	0.000
29	A	39	ARG	1	0.808	0.892	13.871	17.933	17.933	0.000	0.000	0.000	0.000
30	A	40	TYR	0	0.082	0.044	18.441	-0.420	-0.420	0.000	0.000	0.000	0.000
31	A	41	ASN	0	-0.031	-0.030	16.110	-0.015	-0.015	0.000	0.000	0.000	0.000
32	A	42	LEU	0	0.010	0.010	19.597	0.484	0.484	0.000	0.000	0.000	0.000
33	A	43	PRO	0	0.006	0.025	20.489	-0.768	-0.768	0.000	0.000	0.000	0.000
34	A	44	GLY	0	0.029	-0.006	21.007	0.215	0.215	0.000	0.000	0.000	0.000
35	A	45	GLY	0	-0.007	0.017	17.387	-0.436	-0.436	0.000	0.000	0.000	0.000
36	A	46	LYS	1	0.927	0.959	12.828	20.018	20.018	0.000	0.000	0.000	0.000
37	A	47	ALA	0	0.038	0.019	17.191	0.576	0.576	0.000	0.000	0.000	0.000
38	A	48	ASN	0	-0.050	-0.041	18.338	-1.527	-1.527	0.000	0.000	0.000	0.000
39	A	49	ARG	1	0.976	0.971	15.538	17.848	17.848	0.000	0.000	0.000	0.000
40	A	50	GLY	0	0.035	0.017	20.802	0.315	0.315	0.000	0.000	0.000	0.000
41	A	51	GLU	-1	-0.749	-0.821	22.363	-12.968	-12.968	0.000	0.000	0.000	0.000
42	A	52	LEU	0	0.029	0.010	23.275	-0.728	-0.728	0.000	0.000	0.000	0.000
43	A	53	ARG	1	0.870	0.911	18.902	15.099	15.099	0.000	0.000	0.000	0.000
44	A	54	SER	0	0.031	0.016	23.579	-0.163	-0.163	0.000	0.000	0.000	0.000
45	A	55	GLN	0	0.069	0.028	26.552	-0.052	-0.052	0.000	0.000	0.000	0.000
46	A	56	ALA	0	0.025	0.022	21.901	0.110	0.110	0.000	0.000	0.000	0.000
47	A	57	LEU	0	-0.013	-0.004	23.158	-0.131	-0.131	0.000	0.000	0.000	0.000
48	A	58	ILE	0	0.001	0.001	24.874	0.042	0.042	0.000	0.000	0.000	0.000
49	A	59	ARG	1	0.806	0.893	20.882	13.803	13.803	0.000	0.000	0.000	0.000
50	A	60	GLU	-1	-0.813	-0.900	19.998	-15.231	-15.231	0.000	0.000	0.000	0.000
51	A	61	ILE	0	-0.011	-0.008	23.809	-0.059	-0.059	0.000	0.000	0.000	0.000
52	A	62	ARG	1	0.898	0.962	26.015	10.268	10.268	0.000	0.000	0.000	0.000
53	A	63	GLU	-1	-0.854	-0.934	24.138	-11.171	-11.171	0.000	0.000	0.000	0.000
54	A	64	GLH	0	-0.032	-0.019	20.328	0.105	0.105	0.000	0.000	0.000	0.000
55	A	65	THR	0	-0.035	-0.031	24.648	0.215	0.215	0.000	0.000	0.000	0.000
56	A	66	GLY	0	0.039	0.029	28.055	0.376	0.376	0.000	0.000	0.000	0.000
57	A	67	LEU	0	-0.076	-0.034	30.071	0.397	0.397	0.000	0.000	0.000	0.000
58	A	68	ARG	1	0.971	0.971	31.000	8.390	8.390	0.000	0.000	0.000	0.000
59	A	69	ILE	0	-0.015	-0.016	28.722	0.188	0.188	0.000	0.000	0.000	0.000
60	A	70	ASN	0	-0.009	0.009	32.903	0.053	0.053	0.000	0.000	0.000	0.000
61	A	71	SER	0	0.047	0.034	35.055	0.209	0.209	0.000	0.000	0.000	0.000
62	A	72	MET	0	-0.061	-0.043	28.411	-0.267	-0.267	0.000	0.000	0.000	0.000
63	A	73	LEU	0	0.030	0.030	31.984	0.170	0.170	0.000	0.000	0.000	0.000
64	A	74	TYR	0	-0.042	-0.048	25.580	-0.128	-0.128	0.000	0.000	0.000	0.000
65	A	75	LEU	0	0.010	0.019	27.082	0.305	0.305	0.000	0.000	0.000	0.000
66	A	76	PHE	0	0.034	0.001	22.550	0.148	0.148	0.000	0.000	0.000	0.000
67	A	77	ASP	-1	-0.766	-0.833	21.350	-13.269	-13.269	0.000	0.000	0.000	0.000
68	A	78	HIS	0	0.009	-0.006	16.770	0.860	0.860	0.000	0.000	0.000	0.000
69	A	79	ILE	0	0.028	0.014	15.068	-0.569	-0.569	0.000	0.000	0.000	0.000
70	A	80	THR	0	-0.043	-0.047	11.732	-0.147	-0.147	0.000	0.000	0.000	0.000
71	A	81	PRO	0	0.080	0.030	7.602	0.238	0.238	0.000	0.000	0.000	0.000
72	A	82	PHE	0	0.021	0.023	4.644	-1.101	-1.013	-0.001	-0.008	-0.079	0.000
73	A	83	ASN	0	-0.025	-0.012	9.604	0.569	0.569	0.000	0.000	0.000	0.000
74	A	84	ALA	0	0.072	0.048	13.362	0.748	0.748	0.000	0.000	0.000	0.000
75	A	85	HIS	1	0.771	0.865	14.742	18.225	18.225	0.000	0.000	0.000	0.000
76	A	86	LYS	1	0.854	0.925	18.951	12.958	12.958	0.000	0.000	0.000	0.000
77	A	87	VAL	0	0.012	0.002	21.685	-0.321	-0.321	0.000	0.000	0.000	0.000
78	A	88	TYR	0	0.024	0.000	24.156	0.240	0.240	0.000	0.000	0.000	0.000
79	A	89	LEU	0	0.043	0.050	27.612	-0.268	-0.268	0.000	0.000	0.000	0.000
80	A	90	CYS	0	-0.073	-0.045	28.947	0.051	0.051	0.000	0.000	0.000	0.000
81	A	91	ILE	0	0.078	0.042	31.658	0.001	0.001	0.000	0.000	0.000	0.000
82	A	92	ALA	0	0.002	-0.010	32.890	-0.084	-0.084	0.000	0.000	0.000	0.000
83	A	93	GLN	0	-0.034	-0.002	35.019	-0.089	-0.089	0.000	0.000	0.000	0.000
84	A	94	GLY	0	0.006	-0.007	36.212	0.040	0.040	0.000	0.000	0.000	0.000
85	A	95	GLN	0	0.028	0.009	35.628	-0.152	-0.152	0.000	0.000	0.000	0.000
86	A	96	PRO	0	-0.003	0.007	30.225	-0.091	-0.091	0.000	0.000	0.000	0.000
87	A	97	LYS	1	0.935	0.952	30.605	9.180	9.180	0.000	0.000	0.000	0.000
88	A	98	PRO	0	-0.031	0.013	26.871	-0.193	-0.193	0.000	0.000	0.000	0.000
89	A	99	GLN	0	0.003	-0.015	26.044	0.573	0.573	0.000	0.000	0.000	0.000
90	A	100	ASN	0	-0.044	-0.023	23.603	-0.384	-0.384	0.000	0.000	0.000	0.000
91	A	101	GLU	-1	-0.873	-0.938	18.294	-14.712	-14.712	0.000	0.000	0.000	0.000
92	A	102	ILE	0	-0.118	-0.055	20.462	-0.535	-0.535	0.000	0.000	0.000	0.000
93	A	103	GLU	-1	-0.894	-0.947	22.616	-12.400	-12.400	0.000	0.000	0.000	0.000
94	A	104	ARG	1	0.878	0.927	21.996	13.559	13.559	0.000	0.000	0.000	0.000
95	A	105	ILE	0	-0.009	-0.016	24.674	-0.543	-0.543	0.000	0.000	0.000	0.000
96	A	106	ALA	0	-0.024	-0.007	26.823	0.267	0.267	0.000	0.000	0.000	0.000
97	A	107	LEU	0	0.039	0.015	28.431	-0.179	-0.179	0.000	0.000	0.000	0.000
98	A	108	VAL	0	-0.029	-0.018	24.954	-0.010	-0.010	0.000	0.000	0.000	0.000
99	A	109	SER	0	0.049	0.024	28.408	0.057	0.057	0.000	0.000	0.000	0.000
100	A	110	SER	0	0.002	-0.009	29.058	0.185	0.185	0.000	0.000	0.000	0.000
101	A	111	PRO	0	-0.017	-0.033	24.841	-0.312	-0.312	0.000	0.000	0.000	0.000
102	A	112	ASP	-1	-0.952	-0.964	24.194	-10.819	-10.819	0.000	0.000	0.000	0.000
103	A	113	THR	0	0.025	0.031	24.685	0.057	0.057	0.000	0.000	0.000	0.000
104	A	114	ASP	-1	-0.799	-0.892	25.075	-10.615	-10.615	0.000	0.000	0.000	0.000
105	A	115	MET	0	-0.058	-0.009	23.790	-0.546	-0.546	0.000	0.000	0.000	0.000
106	A	116	ASP	-1	-0.773	-0.865	18.689	-15.751	-15.751	0.000	0.000	0.000	0.000
107	A	117	LEU	0	-0.058	-0.028	19.608	-0.503	-0.503	0.000	0.000	0.000	0.000
108	A	118	PHE	0	0.012	-0.004	10.661	-0.394	-0.394	0.000	0.000	0.000	0.000
109	A	119	VAL	0	0.056	0.023	12.137	0.764	0.764	0.000	0.000	0.000	0.000
110	A	120	GLU	-1	-0.788	-0.870	13.090	-20.063	-20.063	0.000	0.000	0.000	0.000
111	A	121	GLY	0	0.034	0.025	15.769	0.698	0.698	0.000	0.000	0.000	0.000
112	A	122	ARG	1	0.863	0.926	18.610	13.633	13.633	0.000	0.000	0.000	0.000
113	A	123	ALA	0	-0.042	-0.020	17.988	0.669	0.669	0.000	0.000	0.000	0.000
114	A	124	ILE	0	-0.022	-0.013	18.463	0.563	0.563	0.000	0.000	0.000	0.000
115	A	125	LEU	0	0.075	0.030	21.473	0.561	0.561	0.000	0.000	0.000	0.000
116	A	126	ARG	1	0.976	0.987	20.473	12.945	12.945	0.000	0.000	0.000	0.000
117	A	127	ARG	1	0.814	0.912	21.356	13.131	13.131	0.000	0.000	0.000	0.000
118	A	128	TYR	0	-0.033	-0.053	25.346	0.262	0.262	0.000	0.000	0.000	0.000
119	A	129	ALA	0	0.016	0.007	27.541	0.345	0.345	0.000	0.000	0.000	0.000
120	A	130	ARG	1	0.942	0.969	23.761	11.365	11.365	0.000	0.000	0.000	0.000
121	A	131	LEU	0	0.048	0.035	29.364	0.221	0.221	0.000	0.000	0.000	0.000
122	A	132	ARG	1	0.817	0.892	31.217	9.479	9.479	0.000	0.000	0.000	0.000
123	A	133	ASN	0	-0.033	-0.010	33.649	0.315	0.315	0.000	0.000	0.000	0.000
124	A	134	GLU	-1	-0.947	-0.958	31.684	-9.222	-9.222	0.000	0.000	0.000	0.000
125	A	135	GLU	-1	-0.890	-0.925	35.554	-7.302	-7.302	0.000	0.000	0.000	0.000
126	A	136	THR	0	0.004	-0.004	34.787	-0.017	-0.017	0.000	0.000	0.000	0.000
127	A	137	ALA	0	0.102	0.049	37.772	0.002	0.002	0.000	0.000	0.000	0.000
128	A	138	LYS	1	0.778	0.881	29.663	10.087	10.087	0.000	0.000	0.000	0.000
129	A	139	GLY	0	0.040	0.024	34.865	-0.102	-0.102	0.000	0.000	0.000	0.000
130	A	140	GLU	-1	-0.907	-0.959	35.735	-7.362	-7.362	0.000	0.000	0.000	0.000
131	A	141	ALA	0	-0.001	0.000	36.501	0.071	0.071	0.000	0.000	0.000	0.000
132	A	142	LEU	0	-0.031	-0.016	31.452	-0.044	-0.044	0.000	0.000	0.000	0.000
133	A	143	ARG	1	0.854	0.902	35.503	8.011	8.011	0.000	0.000	0.000	0.000
134	A	144	ALA	0	0.008	0.013	38.206	0.114	0.114	0.000	0.000	0.000	0.000
135	A	145	LEU	0	-0.013	-0.013	35.584	0.067	0.067	0.000	0.000	0.000	0.000
136	A	146	LEU	0	-0.029	-0.014	33.838	0.037	0.037	0.000	0.000	0.000	0.000
137	A	147	GLY	0	-0.042	-0.012	37.762	0.095	0.095	0.000	0.000	0.000	0.000
138	A	148	LEU	0	0.024	0.008	40.476	0.124	0.124	0.000	0.000	0.000	0.000
139	A	149	ALA	0	0.016	0.000	37.550	0.084	0.084	0.000	0.000	0.000	0.000
140	A	150	ARG	1	0.947	0.979	39.297	7.693	7.693	0.000	0.000	0.000	0.000
141	A	151	TYR	0	-0.009	-0.007	41.426	0.101	0.101	0.000	0.000	0.000	0.000
142	A	152	ILE	0	0.008	0.001	41.288	0.115	0.115	0.000	0.000	0.000	0.000
143	A	153	ALA	0	0.035	0.022	40.432	0.063	0.063	0.000	0.000	0.000	0.000
144	A	154	LYS	1	0.913	0.987	42.531	6.534	6.534	0.000	0.000	0.000	0.000
145	A	155	VAL	0	-0.070	-0.026	45.784	0.146	0.146	0.000	0.000	0.000	0.000
146	A	156	ASP	-1	-0.971	-1.005	43.421	-7.036	-7.036	0.000	0.000	0.000	0.000

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