FMO DATABASE

FMODB ID: 4JLRN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1409481.385884
FMO2-HF: Nuclear repulsion	1351661.846056
FMO2-HF: Total energy	-57819.539828
FMO2-MP2: Total energy	-57989.300221

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.
-15.56	-8.226	5.179	-4.413	-8.098	-0.021

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 : 0.001 / q_NPA : 0.005

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	0.003	0.000	3.225	-3.425	-1.091	0.052	-1.300	-1.085	0.001
4	A	588	SER	0	0.037	0.020	5.896	0.528	0.528	0.000	0.000	0.000	0.000
5	A	589	HIS	1	0.819	0.889	2.255	-5.265	-4.195	0.989	-0.694	-1.366	0.004
6	A	590	MET	0	0.057	0.045	6.730	0.141	0.141	0.000	0.000	0.000	0.000
7	A	591	SER	0	0.000	-0.023	9.579	-0.017	-0.017	0.000	0.000	0.000	0.000
8	A	592	GLY	0	0.024	0.017	11.621	-0.002	-0.002	0.000	0.000	0.000	0.000
9	A	593	THR	0	0.004	0.006	14.599	-0.045	-0.045	0.000	0.000	0.000	0.000
10	A	594	VAL	0	0.000	0.001	15.119	0.021	0.021	0.000	0.000	0.000	0.000
11	A	595	LEU	0	-0.010	-0.002	17.704	-0.021	-0.021	0.000	0.000	0.000	0.000
12	A	596	ILE	0	-0.046	-0.019	17.877	0.003	0.003	0.000	0.000	0.000	0.000
13	A	597	ASN	0	0.004	-0.018	21.694	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	598	ASN	0	0.002	0.008	24.401	0.017	0.017	0.000	0.000	0.000	0.000
15	A	599	ILE	0	-0.004	-0.006	27.166	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	600	ASN	0	-0.043	-0.026	30.905	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	601	ALA	0	0.034	0.039	31.290	0.007	0.007	0.000	0.000	0.000	0.000
18	A	602	PRO	0	-0.012	-0.014	33.298	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	603	PHE	0	-0.024	-0.027	34.500	0.001	0.001	0.000	0.000	0.000	0.000
20	A	604	LEU	0	-0.013	-0.020	29.459	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	605	PRO	0	0.001	0.017	26.580	0.005	0.005	0.000	0.000	0.000	0.000
22	A	606	ASP	-1	-0.871	-0.919	25.975	-0.096	-0.096	0.000	0.000	0.000	0.000
23	A	607	PRO	0	-0.033	-0.021	21.748	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	608	VAL	0	-0.005	0.013	18.421	0.011	0.011	0.000	0.000	0.000	0.000
25	A	609	ILE	0	-0.023	-0.015	17.186	-0.031	-0.031	0.000	0.000	0.000	0.000
26	A	610	VAL	0	0.002	0.006	12.588	0.027	0.027	0.000	0.000	0.000	0.000
27	A	611	THR	0	0.029	0.011	13.521	-0.049	-0.049	0.000	0.000	0.000	0.000
28	A	612	GLY	0	0.024	0.020	9.993	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	613	ASN	0	-0.027	0.000	4.719	-0.081	0.027	-0.001	-0.002	-0.104	0.000
30	A	614	MET	0	0.032	0.026	6.473	0.141	0.141	0.000	0.000	0.000	0.000
31	A	615	THR	0	-0.028	-0.013	2.424	-4.165	-2.708	2.024	-1.253	-2.227	-0.018
32	A	616	LEU	0	-0.002	0.019	4.756	0.610	0.658	-0.001	-0.016	-0.030	0.000
33	A	617	GLU	-1	-0.762	-0.884	5.293	0.710	0.710	0.000	0.000	0.000	0.000
34	A	618	LYS	1	0.983	1.002	8.286	0.126	0.126	0.000	0.000	0.000	0.000
35	A	619	ASN	0	-0.019	-0.023	10.964	-0.029	-0.029	0.000	0.000	0.000	0.000
36	A	620	GLY	0	0.017	0.026	11.791	0.027	0.027	0.000	0.000	0.000	0.000
37	A	621	HIS	0	-0.076	-0.043	12.777	-0.040	-0.040	0.000	0.000	0.000	0.000
38	A	622	VAL	0	0.008	0.003	13.163	0.017	0.017	0.000	0.000	0.000	0.000
39	A	623	ILE	0	0.010	-0.002	16.066	-0.014	-0.014	0.000	0.000	0.000	0.000
40	A	624	LEU	0	-0.022	-0.007	18.209	0.009	0.009	0.000	0.000	0.000	0.000
41	A	625	ASN	0	0.095	0.076	21.902	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	626	ASN	0	-0.060	-0.047	22.751	0.013	0.013	0.000	0.000	0.000	0.000
43	A	627	SER	0	0.027	0.014	26.900	0.010	0.010	0.000	0.000	0.000	0.000
44	A	628	SER	0	0.071	0.045	30.227	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	629	SER	0	-0.026	-0.013	32.191	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	630	ASN	0	-0.071	-0.037	29.961	0.003	0.003	0.000	0.000	0.000	0.000
47	A	631	VAL	0	0.082	0.055	27.859	-0.007	-0.007	0.000	0.000	0.000	0.000
48	A	632	GLY	0	-0.053	-0.027	26.661	0.007	0.007	0.000	0.000	0.000	0.000
49	A	633	GLN	0	-0.011	-0.008	23.060	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	634	THR	0	0.001	-0.013	20.088	-0.011	-0.011	0.000	0.000	0.000	0.000
51	A	635	TYR	0	-0.025	-0.007	12.393	0.030	0.030	0.000	0.000	0.000	0.000
52	A	636	VAL	0	0.040	0.002	16.433	-0.024	-0.024	0.000	0.000	0.000	0.000
53	A	637	GLN	0	0.023	0.015	9.768	0.022	0.022	0.000	0.000	0.000	0.000
54	A	638	LYS	1	0.862	0.923	13.010	0.229	0.229	0.000	0.000	0.000	0.000
55	A	639	GLY	0	0.013	-0.008	9.506	0.044	0.044	0.000	0.000	0.000	0.000
56	A	640	ASN	0	-0.028	-0.012	5.863	0.078	0.078	0.000	0.000	0.000	0.000
57	A	641	TRP	0	0.013	-0.005	6.711	-0.134	-0.134	0.000	0.000	0.000	0.000
58	A	642	HIS	0	-0.063	-0.039	2.669	-2.781	-1.025	1.970	-1.013	-2.713	-0.009
59	A	643	GLY	0	0.033	0.026	4.492	0.042	0.095	-0.001	-0.015	-0.038	0.000
60	A	644	LYS	1	0.840	0.891	2.705	-1.575	-1.067	0.147	-0.120	-0.535	0.001
61	A	645	GLY	0	0.006	-0.004	7.522	0.213	0.213	0.000	0.000	0.000	0.000
62	A	646	GLY	0	0.010	0.023	10.417	0.098	0.098	0.000	0.000	0.000	0.000
63	A	647	ILE	0	-0.070	-0.050	12.240	-0.028	-0.028	0.000	0.000	0.000	0.000
64	A	648	LEU	0	0.017	0.017	14.649	0.000	0.000	0.000	0.000	0.000	0.000
65	A	649	SER	0	-0.068	-0.060	16.296	0.015	0.015	0.000	0.000	0.000	0.000
66	A	650	LEU	0	0.001	-0.002	18.924	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	651	GLY	0	0.040	0.023	22.191	0.009	0.009	0.000	0.000	0.000	0.000
68	A	652	ALA	0	-0.007	-0.014	25.896	-0.007	-0.007	0.000	0.000	0.000	0.000
69	A	653	VAL	0	-0.012	0.012	28.105	0.006	0.006	0.000	0.000	0.000	0.000
70	A	654	LEU	0	-0.054	-0.020	27.825	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	655	GLY	0	0.066	0.030	31.754	0.008	0.008	0.000	0.000	0.000	0.000
72	A	656	ASN	0	0.048	0.031	33.392	-0.007	-0.007	0.000	0.000	0.000	0.000
73	A	657	ASP	-1	-0.716	-0.858	30.725	-0.117	-0.117	0.000	0.000	0.000	0.000
74	A	658	ASN	0	-0.070	-0.035	30.218	-0.009	-0.009	0.000	0.000	0.000	0.000
75	A	659	SER	0	-0.041	-0.018	29.706	0.004	0.004	0.000	0.000	0.000	0.000
76	A	660	LYS	1	0.905	0.961	29.542	0.087	0.087	0.000	0.000	0.000	0.000
77	A	661	THR	0	-0.024	-0.038	24.317	0.003	0.003	0.000	0.000	0.000	0.000
78	A	662	ASP	-1	-0.736	-0.847	22.395	-0.145	-0.145	0.000	0.000	0.000	0.000
79	A	663	ARG	1	0.877	0.936	20.667	0.158	0.158	0.000	0.000	0.000	0.000
80	A	664	LEU	0	-0.011	0.010	12.690	0.002	0.002	0.000	0.000	0.000	0.000
81	A	665	GLU	-1	-0.863	-0.936	16.580	-0.238	-0.238	0.000	0.000	0.000	0.000
82	A	666	ILE	0	-0.056	-0.032	10.548	-0.028	-0.028	0.000	0.000	0.000	0.000
83	A	667	ALA	0	-0.007	-0.016	13.490	0.025	0.025	0.000	0.000	0.000	0.000
84	A	668	GLY	0	0.008	0.019	10.895	0.041	0.041	0.000	0.000	0.000	0.000
85	A	669	HIS	0	0.029	0.016	7.912	0.073	0.073	0.000	0.000	0.000	0.000
86	A	670	ALA	0	-0.021	-0.006	8.188	-0.207	-0.207	0.000	0.000	0.000	0.000
87	A	671	SER	0	0.037	0.024	5.477	-0.104	-0.104	0.000	0.000	0.000	0.000
88	A	672	GLY	0	-0.019	-0.007	7.078	-0.197	-0.197	0.000	0.000	0.000	0.000
89	A	673	ILE	0	0.018	0.003	7.882	0.191	0.191	0.000	0.000	0.000	0.000
90	A	674	THR	0	-0.023	0.006	9.905	-0.093	-0.093	0.000	0.000	0.000	0.000
91	A	675	TYR	0	-0.043	-0.019	11.898	0.038	0.038	0.000	0.000	0.000	0.000
92	A	676	VAL	0	0.033	0.012	15.622	-0.012	-0.012	0.000	0.000	0.000	0.000
93	A	677	ALA	0	-0.010	0.006	18.073	0.021	0.021	0.000	0.000	0.000	0.000
94	A	678	VAL	0	0.018	0.000	21.340	-0.007	-0.007	0.000	0.000	0.000	0.000
95	A	679	THR	0	-0.011	0.002	24.058	0.012	0.012	0.000	0.000	0.000	0.000
96	A	680	ASN	0	0.009	-0.010	27.278	-0.005	-0.005	0.000	0.000	0.000	0.000
97	A	681	GLU	-1	-0.898	-0.975	28.529	-0.097	-0.097	0.000	0.000	0.000	0.000
98	A	682	GLY	0	0.004	-0.001	31.902	0.002	0.002	0.000	0.000	0.000	0.000
99	A	683	GLY	0	0.006	0.007	33.979	0.003	0.003	0.000	0.000	0.000	0.000
100	A	684	SER	0	-0.026	-0.024	35.053	0.003	0.003	0.000	0.000	0.000	0.000
101	A	685	GLY	0	0.010	0.016	34.901	0.002	0.002	0.000	0.000	0.000	0.000
102	A	686	ASP	-1	-0.857	-0.934	35.206	-0.074	-0.074	0.000	0.000	0.000	0.000
103	A	687	LYS	1	0.821	0.932	33.678	0.092	0.092	0.000	0.000	0.000	0.000
104	A	688	THR	0	-0.030	-0.004	30.285	0.000	0.000	0.000	0.000	0.000	0.000
105	A	689	LEU	0	-0.054	-0.024	33.361	0.003	0.003	0.000	0.000	0.000	0.000
106	A	690	GLU	-1	-0.762	-0.849	29.539	-0.124	-0.124	0.000	0.000	0.000	0.000
107	A	691	GLY	0	0.004	-0.005	27.778	-0.010	-0.010	0.000	0.000	0.000	0.000
108	A	692	VAL	0	-0.011	-0.005	26.370	0.001	0.001	0.000	0.000	0.000	0.000
109	A	693	GLN	0	0.017	0.018	22.393	-0.024	-0.024	0.000	0.000	0.000	0.000
110	A	694	ILE	0	-0.002	-0.002	20.259	0.006	0.006	0.000	0.000	0.000	0.000
111	A	695	ILE	0	-0.010	-0.002	14.962	-0.012	-0.012	0.000	0.000	0.000	0.000
112	A	696	SER	0	0.018	0.023	17.427	0.032	0.032	0.000	0.000	0.000	0.000
113	A	697	THR	0	-0.066	-0.037	13.069	-0.043	-0.043	0.000	0.000	0.000	0.000
114	A	698	ASP	-1	-0.883	-0.922	14.214	-0.245	-0.245	0.000	0.000	0.000	0.000
115	A	699	SER	0	-0.025	-0.034	12.640	0.053	0.053	0.000	0.000	0.000	0.000
116	A	700	SER	0	-0.002	-0.016	12.183	-0.078	-0.078	0.000	0.000	0.000	0.000
117	A	701	ASP	-1	-0.822	-0.906	9.698	-0.646	-0.646	0.000	0.000	0.000	0.000
118	A	702	LYS	1	0.975	0.970	12.869	0.239	0.239	0.000	0.000	0.000	0.000
119	A	703	ASN	0	-0.062	-0.041	14.117	-0.018	-0.018	0.000	0.000	0.000	0.000
120	A	704	ALA	0	0.051	0.046	10.845	-0.015	-0.015	0.000	0.000	0.000	0.000
121	A	705	PHE	0	-0.011	-0.008	11.736	-0.062	-0.062	0.000	0.000	0.000	0.000
122	A	706	ILE	0	-0.018	-0.008	14.511	0.047	0.047	0.000	0.000	0.000	0.000
123	A	707	GLN	0	0.020	0.017	17.175	-0.007	-0.007	0.000	0.000	0.000	0.000
124	A	708	LYS	1	0.929	0.961	18.959	0.165	0.165	0.000	0.000	0.000	0.000
125	A	709	GLY	0	0.013	0.013	21.274	0.007	0.007	0.000	0.000	0.000	0.000
126	A	710	ARG	1	0.764	0.834	25.011	0.083	0.083	0.000	0.000	0.000	0.000
127	A	711	ILE	0	-0.005	0.014	23.681	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	712	VAL	0	0.010	0.007	28.238	0.001	0.001	0.000	0.000	0.000	0.000
129	A	713	ALA	0	-0.007	0.005	32.001	0.000	0.000	0.000	0.000	0.000	0.000
130	A	714	GLY	0	0.055	0.036	34.279	0.000	0.000	0.000	0.000	0.000	0.000
131	A	715	SER	0	-0.016	-0.011	37.658	0.000	0.000	0.000	0.000	0.000	0.000
132	A	716	TYR	0	-0.003	0.009	34.198	0.000	0.000	0.000	0.000	0.000	0.000
133	A	717	ASP	-1	-0.789	-0.888	30.338	-0.114	-0.114	0.000	0.000	0.000	0.000
134	A	718	TYR	0	-0.022	-0.048	27.802	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	719	ARG	1	0.926	0.959	24.121	0.148	0.148	0.000	0.000	0.000	0.000
136	A	720	LEU	0	-0.007	-0.004	17.964	0.000	0.000	0.000	0.000	0.000	0.000
137	A	721	LYS	1	0.856	0.946	22.350	0.175	0.175	0.000	0.000	0.000	0.000
138	A	722	GLN	0	-0.003	0.010	16.469	-0.008	-0.008	0.000	0.000	0.000	0.000
139	A	723	GLY	0	-0.009	-0.020	20.360	0.016	0.016	0.000	0.000	0.000	0.000
140	A	724	THR	0	-0.085	-0.069	22.892	-0.001	-0.001	0.000	0.000	0.000	0.000
141	A	725	ALA	0	-0.022	-0.022	26.394	-0.003	-0.003	0.000	0.000	0.000	0.000
142	A	726	SER	0	-0.055	-0.049	29.169	0.004	0.004	0.000	0.000	0.000	0.000
143	A	727	GLY	0	-0.069	-0.028	26.351	0.003	0.003	0.000	0.000	0.000	0.000
144	A	728	LEU	0	0.020	0.014	26.257	-0.004	-0.004	0.000	0.000	0.000	0.000
145	A	729	ASN	0	-0.001	-0.003	23.280	-0.009	-0.009	0.000	0.000	0.000	0.000
146	A	730	THR	0	0.068	0.018	20.550	-0.013	-0.013	0.000	0.000	0.000	0.000
147	A	731	ASN	0	-0.013	0.013	17.250	-0.008	-0.008	0.000	0.000	0.000	0.000
148	A	732	LYS	1	0.851	0.937	17.334	0.187	0.187	0.000	0.000	0.000	0.000
149	A	733	TRP	0	0.001	-0.008	14.853	0.016	0.016	0.000	0.000	0.000	0.000
150	A	734	TYR	0	0.018	-0.007	19.933	0.007	0.007	0.000	0.000	0.000	0.000
151	A	735	LEU	0	0.003	0.017	23.220	-0.007	-0.007	0.000	0.000	0.000	0.000
152	A	736	THR	0	-0.007	-0.003	25.613	0.011	0.011	0.000	0.000	0.000	0.000
153	A	737	SER	0	0.011	-0.015	28.685	-0.002	-0.002	0.000	0.000	0.000	0.000
154	A	738	GLN	0	-0.010	-0.010	31.756	0.006	0.006	0.000	0.000	0.000	0.000
155	A	739	MET	0	-0.003	0.009	34.587	-0.001	-0.001	0.000	0.000	0.000	0.000
156	A	740	ASP	-1	-0.867	-0.917	35.348	-0.076	-0.076	0.000	0.000	0.000	0.000

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