FMO DATABASE

FMODB ID: 3JM3L

Calculation Name: 2FD4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FD4

Chain ID: A

ChEMBL ID:

UniProt ID: Q8RSY1

Base Structure: X-ray

Registration Date: 2023-09-23

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	120
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-950126.914367
FMO2-HF: Nuclear repulsion	903764.546979
FMO2-HF: Total energy	-46362.367388
FMO2-MP2: Total energy	-46496.83451

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:435:LYS)

Summations of interaction energy for fragment #1(A:435:LYS)

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.
-46.424	-43.721	0.066	-1.439	-1.33	0.001

Interaction energy analysis for fragmet #1(A:435:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.988 / q_NPA : 0.986

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	436	ALA	0	0.015	0.001	3.261	-6.553	-3.850	0.066	-1.439	-1.330	0.001
4	A	437	ALA	0	0.001	0.006	5.969	2.420	2.420	0.000	0.000	0.000	0.000
5	A	438	LEU	0	0.008	0.003	9.605	-0.069	-0.069	0.000	0.000	0.000	0.000
6	A	439	ASP	-1	-0.755	-0.872	12.455	-16.465	-16.465	0.000	0.000	0.000	0.000
7	A	440	PRO	0	0.029	0.031	14.919	0.353	0.353	0.000	0.000	0.000	0.000
8	A	441	ILE	0	0.021	0.014	18.367	0.878	0.878	0.000	0.000	0.000	0.000
9	A	442	ALA	0	0.029	0.003	15.928	0.348	0.348	0.000	0.000	0.000	0.000
10	A	443	SER	0	-0.079	-0.055	16.168	0.333	0.333	0.000	0.000	0.000	0.000
11	A	444	GLN	0	-0.025	-0.026	17.585	0.727	0.727	0.000	0.000	0.000	0.000
12	A	445	PHE	0	0.042	0.027	19.536	0.554	0.554	0.000	0.000	0.000	0.000
13	A	446	SER	0	-0.010	-0.024	19.054	0.492	0.492	0.000	0.000	0.000	0.000
14	A	447	GLN	0	-0.040	-0.022	21.948	0.171	0.171	0.000	0.000	0.000	0.000
15	A	448	LEU	0	-0.040	0.005	24.266	0.445	0.445	0.000	0.000	0.000	0.000
16	A	449	ARG	1	0.810	0.909	26.610	9.221	9.221	0.000	0.000	0.000	0.000
17	A	450	THR	0	-0.016	-0.006	27.883	-0.220	-0.220	0.000	0.000	0.000	0.000
18	A	451	ILE	0	0.016	0.012	30.088	0.338	0.338	0.000	0.000	0.000	0.000
19	A	452	SER	0	0.004	0.001	30.959	-0.263	-0.263	0.000	0.000	0.000	0.000
20	A	453	LYS	1	0.855	0.933	29.087	10.746	10.746	0.000	0.000	0.000	0.000
21	A	454	ALA	0	-0.049	-0.046	32.947	0.099	0.099	0.000	0.000	0.000	0.000
22	A	455	ASP	-1	-0.890	-0.940	36.722	-7.549	-7.549	0.000	0.000	0.000	0.000
23	A	456	ALA	0	0.024	0.008	36.728	-0.059	-0.059	0.000	0.000	0.000	0.000
24	A	457	GLH	0	-0.011	0.012	38.692	-0.128	-0.128	0.000	0.000	0.000	0.000
25	A	458	SER	0	-0.059	-0.025	40.546	0.252	0.252	0.000	0.000	0.000	0.000
26	A	459	GLU	-1	-0.794	-0.893	39.421	-7.593	-7.593	0.000	0.000	0.000	0.000
27	A	460	GLU	-1	-0.859	-0.928	39.995	-7.979	-7.979	0.000	0.000	0.000	0.000
28	A	461	LEU	0	-0.042	-0.032	35.307	-0.242	-0.242	0.000	0.000	0.000	0.000
29	A	462	GLY	0	0.038	0.043	37.059	-0.074	-0.074	0.000	0.000	0.000	0.000
30	A	463	PHE	0	-0.083	-0.050	28.115	-0.190	-0.190	0.000	0.000	0.000	0.000
31	A	464	LYS	1	0.883	0.938	32.852	8.711	8.711	0.000	0.000	0.000	0.000
32	A	465	ASP	-1	-0.726	-0.835	28.047	-11.727	-11.727	0.000	0.000	0.000	0.000
33	A	466	ALA	0	0.059	0.029	26.790	0.306	0.306	0.000	0.000	0.000	0.000
34	A	467	ALA	0	-0.014	-0.009	27.246	0.146	0.146	0.000	0.000	0.000	0.000
35	A	468	ASH	0	-0.068	-0.028	28.907	0.518	0.518	0.000	0.000	0.000	0.000
36	A	469	HIS	1	0.873	0.915	29.760	9.523	9.523	0.000	0.000	0.000	0.000
37	A	470	HIS	1	0.824	0.921	30.101	9.768	9.768	0.000	0.000	0.000	0.000
38	A	471	THR	0	0.050	-0.010	28.959	-0.229	-0.229	0.000	0.000	0.000	0.000
39	A	472	ASP	-1	-0.817	-0.900	31.101	-9.257	-9.257	0.000	0.000	0.000	0.000
40	A	473	ASH	0	-0.041	-0.037	34.732	0.029	0.029	0.000	0.000	0.000	0.000
41	A	474	VAL	0	-0.009	0.031	28.926	0.079	0.079	0.000	0.000	0.000	0.000
42	A	475	THR	0	0.003	0.004	30.492	0.130	0.130	0.000	0.000	0.000	0.000
43	A	476	HIS	0	-0.017	-0.015	28.048	-0.628	-0.628	0.000	0.000	0.000	0.000
44	A	477	CYM	-1	-0.866	-0.787	24.752	-12.774	-12.774	0.000	0.000	0.000	0.000
45	A	478	LEU	0	0.040	0.029	26.978	0.165	0.165	0.000	0.000	0.000	0.000
46	A	479	PHE	0	0.003	-0.049	23.560	0.056	0.056	0.000	0.000	0.000	0.000
47	A	480	GLY	0	0.000	0.004	23.862	-0.556	-0.556	0.000	0.000	0.000	0.000
48	A	481	GLY	0	0.011	0.000	23.858	-0.645	-0.645	0.000	0.000	0.000	0.000
49	A	482	GLU	-1	-0.861	-0.902	24.999	-11.595	-11.595	0.000	0.000	0.000	0.000
50	A	483	LEU	0	0.019	0.030	24.121	-0.647	-0.647	0.000	0.000	0.000	0.000
51	A	484	SER	0	-0.036	-0.058	24.036	0.386	0.386	0.000	0.000	0.000	0.000
52	A	485	LEU	0	-0.035	-0.019	23.504	-0.490	-0.490	0.000	0.000	0.000	0.000
53	A	486	SER	0	-0.061	-0.040	23.093	0.146	0.146	0.000	0.000	0.000	0.000
54	A	487	ASN	0	0.002	0.015	18.804	-0.925	-0.925	0.000	0.000	0.000	0.000
55	A	488	PRO	0	-0.019	-0.010	15.747	0.213	0.213	0.000	0.000	0.000	0.000
56	A	489	ASP	-1	-0.933	-0.958	13.245	-23.006	-23.006	0.000	0.000	0.000	0.000
57	A	490	GLN	0	-0.075	-0.054	15.887	0.601	0.601	0.000	0.000	0.000	0.000
58	A	491	GLN	0	-0.038	-0.030	17.284	0.049	0.049	0.000	0.000	0.000	0.000
59	A	492	VAL	0	0.002	0.004	20.253	0.356	0.356	0.000	0.000	0.000	0.000
60	A	493	ILE	0	-0.010	-0.018	23.771	0.192	0.192	0.000	0.000	0.000	0.000
61	A	494	GLY	0	0.025	0.021	26.251	0.104	0.104	0.000	0.000	0.000	0.000
62	A	495	LEU	0	-0.049	-0.044	27.727	-0.166	-0.166	0.000	0.000	0.000	0.000
63	A	496	ALA	0	0.067	0.042	30.420	0.119	0.119	0.000	0.000	0.000	0.000
64	A	497	GLY	0	0.021	0.017	33.576	-0.220	-0.220	0.000	0.000	0.000	0.000
65	A	498	ASN	0	-0.067	-0.052	36.181	0.041	0.041	0.000	0.000	0.000	0.000
66	A	499	PRO	0	-0.048	-0.007	34.186	-0.131	-0.131	0.000	0.000	0.000	0.000
67	A	500	THR	0	0.035	0.002	35.168	0.333	0.333	0.000	0.000	0.000	0.000
68	A	501	ASP	-1	-0.848	-0.910	34.896	-8.248	-8.248	0.000	0.000	0.000	0.000
69	A	502	THR	0	0.005	-0.010	30.645	-0.012	-0.012	0.000	0.000	0.000	0.000
70	A	503	SER	0	-0.062	-0.051	33.402	-0.111	-0.111	0.000	0.000	0.000	0.000
71	A	504	GLN	0	-0.018	0.014	35.146	0.219	0.219	0.000	0.000	0.000	0.000
72	A	505	PRO	0	0.004	-0.011	36.125	-0.287	-0.287	0.000	0.000	0.000	0.000
73	A	506	TYR	0	0.035	0.016	35.204	0.028	0.028	0.000	0.000	0.000	0.000
74	A	507	SER	0	-0.013	-0.024	37.155	0.230	0.230	0.000	0.000	0.000	0.000
75	A	508	GLN	0	-0.016	-0.005	39.897	-0.078	-0.078	0.000	0.000	0.000	0.000
76	A	509	GLU	-1	-0.839	-0.910	42.102	-7.002	-7.002	0.000	0.000	0.000	0.000
77	A	510	GLY	0	-0.041	-0.019	38.648	0.037	0.037	0.000	0.000	0.000	0.000
78	A	511	ASN	0	-0.112	-0.059	37.932	-0.310	-0.310	0.000	0.000	0.000	0.000
79	A	512	LYS	1	0.800	0.870	38.829	7.368	7.368	0.000	0.000	0.000	0.000
80	A	513	ASP	-1	-0.829	-0.901	37.574	-8.082	-8.082	0.000	0.000	0.000	0.000
81	A	514	LEU	0	-0.041	0.000	32.411	-0.232	-0.232	0.000	0.000	0.000	0.000
82	A	515	ALA	0	0.030	0.020	31.501	0.035	0.035	0.000	0.000	0.000	0.000
83	A	516	PHE	0	0.013	-0.008	29.441	-0.280	-0.280	0.000	0.000	0.000	0.000
84	A	517	MET	0	0.010	-0.018	25.239	-0.122	-0.122	0.000	0.000	0.000	0.000
85	A	518	ASP	-1	-0.743	-0.900	19.465	-16.139	-16.139	0.000	0.000	0.000	0.000
86	A	519	MET	0	-0.025	-0.002	20.545	-0.054	-0.054	0.000	0.000	0.000	0.000
87	A	520	LYS	1	0.890	0.940	13.630	19.675	19.675	0.000	0.000	0.000	0.000
88	A	521	LYS	1	0.790	0.841	17.871	13.852	13.852	0.000	0.000	0.000	0.000
89	A	522	LEU	0	0.008	0.014	19.927	0.182	0.182	0.000	0.000	0.000	0.000
90	A	523	ALA	0	-0.011	-0.009	18.080	0.280	0.280	0.000	0.000	0.000	0.000
91	A	524	GLN	0	-0.044	-0.019	16.438	-0.564	-0.564	0.000	0.000	0.000	0.000
92	A	525	PHE	0	-0.026	-0.009	18.525	0.140	0.140	0.000	0.000	0.000	0.000
93	A	526	LEU	0	-0.008	-0.010	22.230	0.218	0.218	0.000	0.000	0.000	0.000
94	A	527	ALA	0	-0.050	-0.024	18.429	0.307	0.307	0.000	0.000	0.000	0.000
95	A	528	GLY	0	-0.037	-0.009	20.450	-0.065	-0.065	0.000	0.000	0.000	0.000
96	A	529	LYS	1	0.801	0.883	22.396	11.026	11.026	0.000	0.000	0.000	0.000
97	A	530	PRO	0	0.033	0.042	25.302	0.072	0.072	0.000	0.000	0.000	0.000
98	A	531	GLU	-1	-0.761	-0.841	26.586	-9.535	-9.535	0.000	0.000	0.000	0.000
99	A	532	HIS	0	0.058	0.001	28.656	-0.498	-0.498	0.000	0.000	0.000	0.000
100	A	533	PRO	0	-0.039	-0.022	27.849	0.225	0.225	0.000	0.000	0.000	0.000
101	A	534	MET	0	-0.052	-0.026	30.265	0.035	0.035	0.000	0.000	0.000	0.000
102	A	535	THR	0	0.019	0.005	33.914	0.170	0.170	0.000	0.000	0.000	0.000
103	A	536	ARG	1	0.761	0.851	33.008	9.489	9.489	0.000	0.000	0.000	0.000
104	A	537	GLU	-1	-0.856	-0.917	33.955	-8.396	-8.396	0.000	0.000	0.000	0.000
105	A	538	THR	0	-0.045	-0.020	30.201	-0.248	-0.248	0.000	0.000	0.000	0.000
106	A	539	LEU	0	-0.038	0.005	27.176	0.114	0.114	0.000	0.000	0.000	0.000
107	A	540	ASN	0	0.047	0.005	25.253	-0.283	-0.283	0.000	0.000	0.000	0.000
108	A	541	ALA	0	0.031	0.021	22.258	0.060	0.060	0.000	0.000	0.000	0.000
109	A	542	GLU	-1	-0.859	-0.926	24.224	-11.484	-11.484	0.000	0.000	0.000	0.000
110	A	543	ASN	0	-0.051	-0.045	27.651	0.163	0.163	0.000	0.000	0.000	0.000
111	A	544	ILE	0	0.089	0.065	23.831	0.240	0.240	0.000	0.000	0.000	0.000
112	A	545	ALA	0	0.036	0.010	26.763	0.199	0.199	0.000	0.000	0.000	0.000
113	A	546	LYS	1	0.846	0.913	28.200	9.764	9.764	0.000	0.000	0.000	0.000
114	A	547	TYR	0	0.045	0.030	30.079	0.263	0.263	0.000	0.000	0.000	0.000
115	A	548	ALA	0	-0.039	-0.007	26.702	0.075	0.075	0.000	0.000	0.000	0.000
116	A	549	PHE	0	0.021	0.000	28.766	0.142	0.142	0.000	0.000	0.000	0.000
117	A	550	ARG	1	0.884	0.951	23.160	11.754	11.754	0.000	0.000	0.000	0.000
118	A	551	ILE	0	0.006	0.012	26.493	0.369	0.369	0.000	0.000	0.000	0.000
119	A	552	VAL	0	-0.033	-0.015	26.321	-0.522	-0.522	0.000	0.000	0.000	0.000
120	A	553	PRO	0	0.025	0.007	27.043	0.429	0.429	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:435:LYS)