FMO DATABASE

FMODB ID: 5JNZZ

Calculation Name: 3ML3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ML3

Chain ID: A

ChEMBL ID:

UniProt ID: Q7BCK4

Base Structure: X-ray

Registration Date: 2023-09-21

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	156
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1411156.647833
FMO2-HF: Nuclear repulsion	1353336.949008
FMO2-HF: Total energy	-57819.698824
FMO2-MP2: Total energy	-57989.433565

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:585:PRO)

Summations of interaction energy for fragment #1(A:585:PRO)

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.
-19.421	-12	4.65	-3.999	-8.07	-0.011

Interaction energy analysis for fragmet #1(A:585:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / q_NPA : 0.013

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	587	GLY	0	0.039	0.008	3.879	-1.707	0.019	-0.006	-0.783	-0.936	0.002
4	A	588	SER	0	0.055	0.036	5.586	0.654	0.654	0.000	0.000	0.000	0.000
5	A	589	HIS	1	0.798	0.873	2.570	-12.024	-10.594	1.572	-1.102	-1.900	0.011
6	A	590	MET	0	0.052	0.042	7.112	-0.157	-0.157	0.000	0.000	0.000	0.000
7	A	591	SER	0	0.004	-0.020	9.345	0.011	0.011	0.000	0.000	0.000	0.000
8	A	592	GLY	0	0.038	0.026	11.474	-0.042	-0.042	0.000	0.000	0.000	0.000
9	A	593	THR	0	-0.003	-0.006	14.551	-0.027	-0.027	0.000	0.000	0.000	0.000
10	A	594	VAL	0	-0.011	-0.002	15.255	0.014	0.014	0.000	0.000	0.000	0.000
11	A	595	LEU	0	-0.002	0.001	17.897	-0.020	-0.020	0.000	0.000	0.000	0.000
12	A	596	ILE	0	-0.042	-0.019	17.732	0.006	0.006	0.000	0.000	0.000	0.000
13	A	597	ASN	0	0.016	-0.015	21.640	-0.013	-0.013	0.000	0.000	0.000	0.000
14	A	598	ASN	0	-0.003	0.007	24.056	0.013	0.013	0.000	0.000	0.000	0.000
15	A	599	ILE	0	0.000	-0.007	26.897	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	600	ASN	0	-0.053	-0.041	30.552	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	601	ALA	0	0.038	0.037	30.875	0.003	0.003	0.000	0.000	0.000	0.000
18	A	602	PRO	0	-0.016	-0.013	32.877	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	603	PHE	0	-0.020	-0.026	34.085	0.000	0.000	0.000	0.000	0.000	0.000
20	A	604	LEU	0	0.012	-0.005	29.107	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	605	PRO	0	0.005	0.019	26.371	0.003	0.003	0.000	0.000	0.000	0.000
22	A	606	ASP	-1	-0.872	-0.919	25.653	-0.008	-0.008	0.000	0.000	0.000	0.000
23	A	607	PRO	0	-0.040	-0.021	21.416	0.001	0.001	0.000	0.000	0.000	0.000
24	A	608	VAL	0	-0.001	0.011	18.005	0.011	0.011	0.000	0.000	0.000	0.000
25	A	609	ILE	0	-0.028	-0.017	17.133	-0.015	-0.015	0.000	0.000	0.000	0.000
26	A	610	VAL	0	-0.009	0.000	12.116	0.028	0.028	0.000	0.000	0.000	0.000
27	A	611	THR	0	0.024	0.012	13.279	-0.033	-0.033	0.000	0.000	0.000	0.000
28	A	612	GLY	0	0.033	0.027	9.908	0.043	0.043	0.000	0.000	0.000	0.000
29	A	613	ASN	0	-0.042	-0.011	4.876	-0.052	-0.052	0.000	0.000	0.000	0.000
30	A	614	MET	0	0.004	0.017	6.233	0.329	0.329	0.000	0.000	0.000	0.000
31	A	615	THR	0	-0.049	-0.026	2.570	-3.023	-1.395	1.254	-0.935	-1.946	-0.013
32	A	616	LEU	0	-0.006	0.019	4.782	0.556	0.584	-0.001	-0.010	-0.017	0.000
33	A	617	GLU	-1	-0.743	-0.879	4.961	2.042	2.173	-0.001	-0.003	-0.127	0.000
34	A	618	LYS	1	0.948	0.990	7.828	-0.074	-0.074	0.000	0.000	0.000	0.000
35	A	619	ASN	0	0.012	-0.001	10.851	-0.063	-0.063	0.000	0.000	0.000	0.000
36	A	620	GLY	0	-0.002	0.020	11.325	0.015	0.015	0.000	0.000	0.000	0.000
37	A	621	HIS	0	-0.074	-0.052	12.300	-0.095	-0.095	0.000	0.000	0.000	0.000
38	A	622	VAL	0	0.012	-0.001	13.110	0.030	0.030	0.000	0.000	0.000	0.000
39	A	623	ILE	0	0.021	0.013	16.053	-0.028	-0.028	0.000	0.000	0.000	0.000
40	A	624	LEU	0	-0.040	0.001	18.474	0.011	0.011	0.000	0.000	0.000	0.000
41	A	625	ASN	0	0.101	0.075	22.174	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	626	ASN	0	-0.092	-0.066	22.574	0.009	0.009	0.000	0.000	0.000	0.000
43	A	627	SER	0	0.026	0.014	26.620	0.004	0.004	0.000	0.000	0.000	0.000
44	A	628	SER	0	0.084	0.056	30.011	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	629	SER	0	-0.030	-0.014	31.900	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	630	ASN	0	-0.056	-0.033	29.761	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	631	VAL	0	0.044	0.047	28.102	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	632	GLY	0	-0.041	-0.031	27.079	0.001	0.001	0.000	0.000	0.000	0.000
49	A	633	GLN	0	-0.018	-0.006	23.100	0.002	0.002	0.000	0.000	0.000	0.000
50	A	634	THR	0	-0.008	-0.017	19.769	-0.014	-0.014	0.000	0.000	0.000	0.000
51	A	635	TYR	0	-0.010	0.000	11.761	0.031	0.031	0.000	0.000	0.000	0.000
52	A	636	VAL	0	0.027	-0.006	16.310	-0.026	-0.026	0.000	0.000	0.000	0.000
53	A	637	GLN	0	0.036	0.019	9.454	0.048	0.048	0.000	0.000	0.000	0.000
54	A	638	LYS	1	0.811	0.887	12.785	0.066	0.066	0.000	0.000	0.000	0.000
55	A	639	GLY	0	0.021	-0.005	9.834	0.045	0.045	0.000	0.000	0.000	0.000
56	A	640	ASN	0	-0.031	-0.013	6.310	-0.013	-0.013	0.000	0.000	0.000	0.000
57	A	641	TRP	0	0.029	-0.001	6.976	0.061	0.061	0.000	0.000	0.000	0.000
58	A	642	HIS	0	-0.064	-0.036	2.563	-3.624	-1.667	1.768	-1.046	-2.680	-0.012
59	A	643	GLY	0	0.033	0.036	4.937	0.414	0.440	-0.001	-0.003	-0.021	0.000
60	A	644	LYS	1	0.843	0.901	3.050	-2.188	-1.693	0.065	-0.117	-0.443	0.001
61	A	645	GLY	0	0.014	-0.003	8.069	0.148	0.148	0.000	0.000	0.000	0.000
62	A	646	GLY	0	0.014	0.024	10.414	0.069	0.069	0.000	0.000	0.000	0.000
63	A	647	ILE	0	-0.077	-0.060	11.982	-0.069	-0.069	0.000	0.000	0.000	0.000
64	A	648	LEU	0	0.035	0.031	14.849	0.029	0.029	0.000	0.000	0.000	0.000
65	A	649	SER	0	-0.068	-0.061	16.139	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	650	LEU	0	0.014	0.011	19.476	0.006	0.006	0.000	0.000	0.000	0.000
67	A	651	GLY	0	0.064	0.037	22.512	0.002	0.002	0.000	0.000	0.000	0.000
68	A	652	ALA	0	-0.014	-0.016	26.311	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	653	VAL	0	-0.002	0.010	28.772	0.003	0.003	0.000	0.000	0.000	0.000
70	A	654	LEU	0	-0.061	-0.019	28.328	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	655	GLY	0	0.082	0.030	32.232	0.005	0.005	0.000	0.000	0.000	0.000
72	A	656	ASN	0	0.026	0.032	33.094	-0.006	-0.006	0.000	0.000	0.000	0.000
73	A	657	ASP	-1	-0.712	-0.859	30.583	-0.070	-0.070	0.000	0.000	0.000	0.000
74	A	658	ASN	0	-0.050	-0.031	30.348	-0.004	-0.004	0.000	0.000	0.000	0.000
75	A	659	SER	0	-0.035	-0.012	29.989	0.004	0.004	0.000	0.000	0.000	0.000
76	A	660	LYS	1	0.871	0.947	29.847	0.021	0.021	0.000	0.000	0.000	0.000
77	A	661	THR	0	-0.013	-0.028	24.875	0.001	0.001	0.000	0.000	0.000	0.000
78	A	662	ASP	-1	-0.748	-0.860	22.887	-0.036	-0.036	0.000	0.000	0.000	0.000
79	A	663	ARG	1	0.836	0.908	21.168	0.069	0.069	0.000	0.000	0.000	0.000
80	A	664	LEU	0	-0.004	0.008	13.221	0.011	0.011	0.000	0.000	0.000	0.000
81	A	665	GLU	-1	-0.845	-0.909	16.712	-0.134	-0.134	0.000	0.000	0.000	0.000
82	A	666	ILE	0	-0.008	-0.005	10.806	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	667	ALA	0	0.002	0.005	13.633	-0.007	-0.007	0.000	0.000	0.000	0.000
84	A	668	GLY	0	0.015	-0.003	11.214	0.018	0.018	0.000	0.000	0.000	0.000
85	A	669	HIS	0	0.014	0.028	7.768	0.080	0.080	0.000	0.000	0.000	0.000
86	A	670	ALA	0	0.002	0.004	8.562	-0.102	-0.102	0.000	0.000	0.000	0.000
87	A	671	SER	0	0.010	0.006	5.210	-0.214	-0.214	0.000	0.000	0.000	0.000
88	A	672	GLY	0	-0.019	-0.008	6.808	-0.160	-0.160	0.000	0.000	0.000	0.000
89	A	673	ILE	0	0.005	-0.008	7.533	0.190	0.190	0.000	0.000	0.000	0.000
90	A	674	THR	0	-0.006	0.013	10.234	-0.022	-0.022	0.000	0.000	0.000	0.000
91	A	675	TYR	0	-0.059	-0.024	11.955	0.019	0.019	0.000	0.000	0.000	0.000
92	A	676	VAL	0	0.036	0.013	15.551	0.003	0.003	0.000	0.000	0.000	0.000
93	A	677	ALA	0	-0.011	0.002	18.223	0.005	0.005	0.000	0.000	0.000	0.000
94	A	678	VAL	0	0.022	-0.005	21.393	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	679	THR	0	0.001	0.011	24.341	0.004	0.004	0.000	0.000	0.000	0.000
96	A	680	ASN	0	-0.011	-0.019	27.352	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	681	GLU	-1	-0.900	-0.981	28.412	-0.016	-0.016	0.000	0.000	0.000	0.000
98	A	682	GLY	0	0.018	0.003	32.162	0.001	0.001	0.000	0.000	0.000	0.000
99	A	683	GLY	0	-0.008	0.005	34.168	0.000	0.000	0.000	0.000	0.000	0.000
100	A	684	SER	0	-0.006	-0.013	35.270	0.001	0.001	0.000	0.000	0.000	0.000
101	A	685	GLY	0	-0.008	0.003	35.276	0.000	0.000	0.000	0.000	0.000	0.000
102	A	686	ASP	-1	-0.857	-0.929	35.441	-0.042	-0.042	0.000	0.000	0.000	0.000
103	A	687	LYS	1	0.833	0.924	33.792	0.061	0.061	0.000	0.000	0.000	0.000
104	A	688	THR	0	-0.014	-0.007	30.231	0.000	0.000	0.000	0.000	0.000	0.000
105	A	689	LEU	0	-0.063	-0.021	33.361	0.000	0.000	0.000	0.000	0.000	0.000
106	A	690	GLU	-1	-0.760	-0.845	29.654	-0.094	-0.094	0.000	0.000	0.000	0.000
107	A	691	GLY	0	0.017	-0.015	27.747	-0.009	-0.009	0.000	0.000	0.000	0.000
108	A	692	VAL	0	-0.013	0.006	26.577	0.001	0.001	0.000	0.000	0.000	0.000
109	A	693	GLN	0	0.014	0.022	22.832	-0.015	-0.015	0.000	0.000	0.000	0.000
110	A	694	ILE	0	0.004	0.004	20.711	0.009	0.009	0.000	0.000	0.000	0.000
111	A	695	ILE	0	-0.009	-0.002	15.274	0.001	0.001	0.000	0.000	0.000	0.000
112	A	696	SER	0	0.002	0.005	17.523	0.011	0.011	0.000	0.000	0.000	0.000
113	A	697	THR	0	-0.069	-0.039	13.243	-0.023	-0.023	0.000	0.000	0.000	0.000
114	A	698	ASP	-1	-0.883	-0.923	14.417	-0.190	-0.190	0.000	0.000	0.000	0.000
115	A	699	SER	0	-0.012	-0.032	12.433	0.035	0.035	0.000	0.000	0.000	0.000
116	A	700	SER	0	0.005	-0.015	12.177	-0.047	-0.047	0.000	0.000	0.000	0.000
117	A	701	ASP	-1	-0.825	-0.905	9.107	-0.708	-0.708	0.000	0.000	0.000	0.000
118	A	702	LYS	1	0.966	0.977	12.403	0.243	0.243	0.000	0.000	0.000	0.000
119	A	703	ASN	0	-0.036	-0.032	14.119	-0.015	-0.015	0.000	0.000	0.000	0.000
120	A	704	ALA	0	0.030	0.030	10.604	-0.005	-0.005	0.000	0.000	0.000	0.000
121	A	705	PHE	0	-0.011	-0.009	11.594	-0.031	-0.031	0.000	0.000	0.000	0.000
122	A	706	ILE	0	-0.015	-0.010	14.451	0.029	0.029	0.000	0.000	0.000	0.000
123	A	707	GLN	0	0.011	0.002	17.180	0.004	0.004	0.000	0.000	0.000	0.000
124	A	708	LYS	1	0.897	0.952	18.458	0.058	0.058	0.000	0.000	0.000	0.000
125	A	709	GLY	0	0.047	0.019	21.174	0.013	0.013	0.000	0.000	0.000	0.000
126	A	710	ARG	1	0.739	0.827	24.954	0.045	0.045	0.000	0.000	0.000	0.000
127	A	711	ILE	0	-0.012	0.009	23.765	0.002	0.002	0.000	0.000	0.000	0.000
128	A	712	VAL	0	-0.002	-0.008	28.410	-0.002	-0.002	0.000	0.000	0.000	0.000
129	A	713	ALA	0	0.001	0.009	32.156	0.003	0.003	0.000	0.000	0.000	0.000
130	A	714	GLY	0	0.051	0.030	34.777	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	715	SER	0	-0.020	-0.010	38.356	0.001	0.001	0.000	0.000	0.000	0.000
132	A	716	TYR	0	0.023	0.017	34.432	-0.002	-0.002	0.000	0.000	0.000	0.000
133	A	717	ASP	-1	-0.798	-0.892	30.026	-0.069	-0.069	0.000	0.000	0.000	0.000
134	A	718	TYR	0	-0.012	-0.033	27.970	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	719	ARG	1	0.916	0.960	24.524	0.099	0.099	0.000	0.000	0.000	0.000
136	A	720	LEU	0	0.007	0.005	18.203	0.001	0.001	0.000	0.000	0.000	0.000
137	A	721	LYS	1	0.787	0.897	22.065	0.134	0.134	0.000	0.000	0.000	0.000
138	A	722	GLN	0	0.018	0.015	16.186	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	723	GLY	0	0.024	0.006	20.206	0.011	0.011	0.000	0.000	0.000	0.000
140	A	724	THR	0	-0.071	-0.063	22.820	0.000	0.000	0.000	0.000	0.000	0.000
141	A	725	ALA	0	-0.022	-0.019	26.410	-0.006	-0.006	0.000	0.000	0.000	0.000
142	A	726	SER	0	-0.052	-0.050	29.061	0.000	0.000	0.000	0.000	0.000	0.000
143	A	727	GLY	0	-0.046	-0.015	26.304	0.001	0.001	0.000	0.000	0.000	0.000
144	A	728	LEU	0	0.006	0.011	25.802	-0.008	-0.008	0.000	0.000	0.000	0.000
145	A	729	ASN	0	-0.009	-0.005	23.431	-0.007	-0.007	0.000	0.000	0.000	0.000
146	A	730	THR	0	0.060	0.018	20.180	-0.008	-0.008	0.000	0.000	0.000	0.000
147	A	731	ASN	0	-0.022	0.008	17.164	-0.012	-0.012	0.000	0.000	0.000	0.000
148	A	732	LYS	1	0.873	0.945	17.494	0.127	0.127	0.000	0.000	0.000	0.000
149	A	733	TRP	0	-0.010	-0.016	14.748	0.005	0.005	0.000	0.000	0.000	0.000
150	A	734	TYR	0	0.022	0.005	20.121	0.011	0.011	0.000	0.000	0.000	0.000
151	A	735	LEU	0	0.005	0.017	23.551	-0.006	-0.006	0.000	0.000	0.000	0.000
152	A	736	THR	0	-0.015	-0.020	25.701	0.006	0.006	0.000	0.000	0.000	0.000
153	A	737	SER	0	0.013	0.002	28.679	-0.002	-0.002	0.000	0.000	0.000	0.000
154	A	738	GLN	0	-0.034	-0.020	31.573	0.003	0.003	0.000	0.000	0.000	0.000
155	A	739	MET	0	0.009	0.024	34.464	0.001	0.001	0.000	0.000	0.000	0.000
156	A	740	ASP	-1	-0.858	-0.904	35.827	-0.045	-0.045	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:585:PRO)