FMO DATABASE

FMODB ID: KG273

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	OptH
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	-1408465.30171
FMO2-HF: Nuclear repulsion	1350646.266254
FMO2-HF: Total energy	-57819.035456
FMO2-MP2: Total energy	-57988.828884

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.
-14.738	-8.109	6.592	-4.817	-8.402	-0.028

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 : -0.007 / q_NPA : 0.003

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	0.007	0.003	3.205	-3.574	-1.111	0.061	-1.403	-1.121	0.000
4	A	588	SER	0	0.039	0.021	5.901	0.524	0.524	0.000	0.000	0.000	0.000
5	A	589	HIS	1	0.812	0.877	2.216	-4.240	-3.540	1.200	-0.683	-1.218	0.003
6	A	590	MET	0	0.059	0.040	6.560	0.203	0.203	0.000	0.000	0.000	0.000
7	A	591	SER	0	-0.008	-0.026	9.338	-0.009	-0.009	0.000	0.000	0.000	0.000
8	A	592	GLY	0	0.024	0.016	11.294	0.014	0.014	0.000	0.000	0.000	0.000
9	A	593	THR	0	0.010	0.011	14.376	-0.047	-0.047	0.000	0.000	0.000	0.000
10	A	594	VAL	0	-0.006	0.000	15.057	0.022	0.022	0.000	0.000	0.000	0.000
11	A	595	LEU	0	-0.015	-0.008	17.621	-0.019	-0.019	0.000	0.000	0.000	0.000
12	A	596	ILE	0	-0.044	-0.017	17.583	0.002	0.002	0.000	0.000	0.000	0.000
13	A	597	ASN	0	-0.004	-0.024	21.328	0.001	0.001	0.000	0.000	0.000	0.000
14	A	598	ASN	0	0.007	0.012	23.972	0.016	0.016	0.000	0.000	0.000	0.000
15	A	599	ILE	0	-0.013	-0.005	26.670	0.000	0.000	0.000	0.000	0.000	0.000
16	A	600	ASN	0	-0.009	-0.005	30.356	-0.008	-0.008	0.000	0.000	0.000	0.000
17	A	601	ALA	0	0.015	0.031	30.868	0.007	0.007	0.000	0.000	0.000	0.000
18	A	602	PRO	0	-0.008	-0.017	32.777	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	603	PHE	0	-0.037	-0.033	34.038	0.001	0.001	0.000	0.000	0.000	0.000
20	A	604	LEU	0	-0.016	-0.024	29.058	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	605	PRO	0	0.012	0.028	26.087	0.005	0.005	0.000	0.000	0.000	0.000
22	A	606	ASP	-1	-0.871	-0.920	25.575	-0.117	-0.117	0.000	0.000	0.000	0.000
23	A	607	PRO	0	-0.032	-0.020	21.311	-0.008	-0.008	0.000	0.000	0.000	0.000
24	A	608	VAL	0	0.001	0.016	17.960	0.010	0.010	0.000	0.000	0.000	0.000
25	A	609	ILE	0	-0.022	-0.013	17.209	-0.034	-0.034	0.000	0.000	0.000	0.000
26	A	610	VAL	0	0.006	0.007	12.509	0.025	0.025	0.000	0.000	0.000	0.000
27	A	611	THR	0	0.009	-0.001	13.517	-0.053	-0.053	0.000	0.000	0.000	0.000
28	A	612	GLY	0	0.030	0.024	9.975	-0.014	-0.014	0.000	0.000	0.000	0.000
29	A	613	ASN	0	-0.032	-0.007	4.671	-0.023	0.103	-0.001	-0.003	-0.121	0.000
30	A	614	MET	0	0.020	0.025	6.288	0.101	0.101	0.000	0.000	0.000	0.000
31	A	615	THR	0	-0.022	-0.014	2.329	-4.639	-3.723	3.740	-1.636	-3.020	-0.023
32	A	616	LEU	0	-0.006	0.016	4.515	0.621	0.701	-0.001	-0.037	-0.042	0.000
33	A	617	GLU	-1	-0.805	-0.908	5.108	0.366	0.440	-0.001	-0.001	-0.071	0.000
34	A	618	LYS	1	0.985	0.998	8.052	0.146	0.146	0.000	0.000	0.000	0.000
35	A	619	ASN	0	-0.038	-0.028	10.975	-0.020	-0.020	0.000	0.000	0.000	0.000
36	A	620	GLY	0	0.008	0.019	11.571	0.027	0.027	0.000	0.000	0.000	0.000
37	A	621	HIS	0	-0.048	-0.024	12.537	-0.026	-0.026	0.000	0.000	0.000	0.000
38	A	622	VAL	0	0.000	-0.005	12.766	0.012	0.012	0.000	0.000	0.000	0.000
39	A	623	ILE	0	0.007	-0.001	15.773	-0.010	-0.010	0.000	0.000	0.000	0.000
40	A	624	LEU	0	-0.024	-0.018	17.814	0.007	0.007	0.000	0.000	0.000	0.000
41	A	625	ASN	0	0.078	0.071	21.438	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	626	ASN	0	-0.040	-0.032	22.570	0.015	0.015	0.000	0.000	0.000	0.000
43	A	627	SER	0	0.021	0.004	26.567	0.010	0.010	0.000	0.000	0.000	0.000
44	A	628	SER	0	0.062	0.037	29.770	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	629	SER	0	-0.021	-0.014	31.773	0.000	0.000	0.000	0.000	0.000	0.000
46	A	630	ASN	0	-0.063	-0.027	29.513	0.003	0.003	0.000	0.000	0.000	0.000
47	A	631	VAL	0	0.065	0.044	27.621	-0.008	-0.008	0.000	0.000	0.000	0.000
48	A	632	GLY	0	-0.058	-0.032	26.348	0.007	0.007	0.000	0.000	0.000	0.000
49	A	633	GLN	0	-0.012	-0.011	22.549	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	634	THR	0	0.011	-0.004	19.569	-0.009	-0.009	0.000	0.000	0.000	0.000
51	A	635	TYR	0	-0.044	-0.013	11.716	0.032	0.032	0.000	0.000	0.000	0.000
52	A	636	VAL	0	0.054	0.012	16.065	-0.022	-0.022	0.000	0.000	0.000	0.000
53	A	637	GLN	0	0.035	0.016	9.296	0.010	0.010	0.000	0.000	0.000	0.000
54	A	638	LYS	1	0.928	0.955	12.771	0.261	0.261	0.000	0.000	0.000	0.000
55	A	639	GLY	0	0.019	-0.004	9.468	0.039	0.039	0.000	0.000	0.000	0.000
56	A	640	ASN	0	-0.004	0.001	5.797	0.111	0.111	0.000	0.000	0.000	0.000
57	A	641	TRP	0	0.017	-0.003	6.486	-0.217	-0.217	0.000	0.000	0.000	0.000
58	A	642	HIS	0	-0.069	-0.044	2.567	-2.255	-0.583	1.415	-0.904	-2.183	-0.009
59	A	643	GLY	0	0.027	0.019	4.625	-0.097	-0.064	-0.001	-0.005	-0.026	0.000
60	A	644	LYS	1	0.912	0.945	2.787	-1.303	-0.738	0.180	-0.145	-0.600	0.001
61	A	645	GLY	0	0.000	-0.007	7.525	0.215	0.215	0.000	0.000	0.000	0.000
62	A	646	GLY	0	0.014	0.026	10.474	0.098	0.098	0.000	0.000	0.000	0.000
63	A	647	ILE	0	-0.050	-0.042	12.287	-0.016	-0.016	0.000	0.000	0.000	0.000
64	A	648	LEU	0	0.015	0.013	14.479	-0.009	-0.009	0.000	0.000	0.000	0.000
65	A	649	SER	0	-0.073	-0.059	16.032	0.021	0.021	0.000	0.000	0.000	0.000
66	A	650	LEU	0	-0.002	-0.005	18.774	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	651	GLY	0	0.033	0.012	21.928	0.010	0.010	0.000	0.000	0.000	0.000
68	A	652	ALA	0	0.006	-0.006	25.649	-0.008	-0.008	0.000	0.000	0.000	0.000
69	A	653	VAL	0	-0.014	0.010	27.913	0.007	0.007	0.000	0.000	0.000	0.000
70	A	654	LEU	0	-0.058	-0.025	27.849	0.000	0.000	0.000	0.000	0.000	0.000
71	A	655	GLY	0	0.070	0.033	31.676	0.008	0.008	0.000	0.000	0.000	0.000
72	A	656	ASN	0	0.085	0.066	33.433	-0.007	-0.007	0.000	0.000	0.000	0.000
73	A	657	ASP	-1	-0.713	-0.864	30.808	-0.120	-0.120	0.000	0.000	0.000	0.000
74	A	658	ASN	0	-0.062	-0.028	30.243	-0.011	-0.011	0.000	0.000	0.000	0.000
75	A	659	SER	0	-0.031	-0.015	29.749	0.004	0.004	0.000	0.000	0.000	0.000
76	A	660	LYS	1	0.929	0.978	29.433	0.094	0.094	0.000	0.000	0.000	0.000
77	A	661	THR	0	-0.021	-0.034	24.117	0.004	0.004	0.000	0.000	0.000	0.000
78	A	662	ASP	-1	-0.725	-0.834	22.097	-0.164	-0.164	0.000	0.000	0.000	0.000
79	A	663	ARG	1	0.908	0.962	20.478	0.175	0.175	0.000	0.000	0.000	0.000
80	A	664	LEU	0	-0.016	0.007	12.432	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	665	GLU	-1	-0.949	-0.978	16.317	-0.247	-0.247	0.000	0.000	0.000	0.000
82	A	666	ILE	0	-0.059	-0.033	10.577	-0.037	-0.037	0.000	0.000	0.000	0.000
83	A	667	ALA	0	-0.020	-0.024	13.415	0.032	0.032	0.000	0.000	0.000	0.000
84	A	668	GLY	0	0.017	0.023	10.841	0.046	0.046	0.000	0.000	0.000	0.000
85	A	669	HIS	0	0.051	0.042	8.085	0.048	0.048	0.000	0.000	0.000	0.000
86	A	670	ALA	0	-0.012	-0.005	8.455	-0.206	-0.206	0.000	0.000	0.000	0.000
87	A	671	SER	0	0.035	0.026	5.585	-0.066	-0.066	0.000	0.000	0.000	0.000
88	A	672	GLY	0	-0.012	-0.007	7.005	-0.204	-0.204	0.000	0.000	0.000	0.000
89	A	673	ILE	0	0.020	0.010	7.766	0.175	0.175	0.000	0.000	0.000	0.000
90	A	674	THR	0	-0.024	0.003	9.802	-0.108	-0.108	0.000	0.000	0.000	0.000
91	A	675	TYR	0	-0.037	-0.019	11.973	0.045	0.045	0.000	0.000	0.000	0.000
92	A	676	VAL	0	0.034	0.011	15.662	-0.018	-0.018	0.000	0.000	0.000	0.000
93	A	677	ALA	0	-0.012	0.006	18.051	0.025	0.025	0.000	0.000	0.000	0.000
94	A	678	VAL	0	0.023	0.003	21.235	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	679	THR	0	-0.021	-0.005	23.937	0.014	0.014	0.000	0.000	0.000	0.000
96	A	680	ASN	0	0.009	-0.006	27.086	-0.006	-0.006	0.000	0.000	0.000	0.000
97	A	681	GLU	-1	-0.899	-0.977	28.413	-0.115	-0.115	0.000	0.000	0.000	0.000
98	A	682	GLY	0	-0.005	-0.004	31.639	0.002	0.002	0.000	0.000	0.000	0.000
99	A	683	GLY	0	0.007	0.005	33.802	0.003	0.003	0.000	0.000	0.000	0.000
100	A	684	SER	0	-0.025	-0.026	34.907	0.004	0.004	0.000	0.000	0.000	0.000
101	A	685	GLY	0	0.004	0.013	34.901	0.002	0.002	0.000	0.000	0.000	0.000
102	A	686	ASP	-1	-0.895	-0.955	35.254	-0.076	-0.076	0.000	0.000	0.000	0.000
103	A	687	LYS	1	0.841	0.950	34.050	0.091	0.091	0.000	0.000	0.000	0.000
104	A	688	THR	0	-0.025	0.004	30.502	0.000	0.000	0.000	0.000	0.000	0.000
105	A	689	LEU	0	-0.062	-0.027	33.509	0.004	0.004	0.000	0.000	0.000	0.000
106	A	690	GLU	-1	-0.774	-0.860	29.823	-0.120	-0.120	0.000	0.000	0.000	0.000
107	A	691	GLY	0	0.003	-0.007	27.989	-0.009	-0.009	0.000	0.000	0.000	0.000
108	A	692	VAL	0	-0.011	-0.004	26.160	0.000	0.000	0.000	0.000	0.000	0.000
109	A	693	GLN	0	-0.047	-0.023	22.364	-0.024	-0.024	0.000	0.000	0.000	0.000
110	A	694	ILE	0	0.006	0.003	20.043	0.003	0.003	0.000	0.000	0.000	0.000
111	A	695	ILE	0	-0.001	0.001	15.041	-0.016	-0.016	0.000	0.000	0.000	0.000
112	A	696	SER	0	-0.001	-0.004	17.404	0.035	0.035	0.000	0.000	0.000	0.000
113	A	697	THR	0	-0.059	-0.028	13.340	-0.043	-0.043	0.000	0.000	0.000	0.000
114	A	698	ASP	-1	-0.895	-0.933	14.192	-0.245	-0.245	0.000	0.000	0.000	0.000
115	A	699	SER	0	-0.029	-0.039	12.800	0.049	0.049	0.000	0.000	0.000	0.000
116	A	700	SER	0	-0.009	-0.019	12.513	-0.079	-0.079	0.000	0.000	0.000	0.000
117	A	701	ASP	-1	-0.840	-0.922	9.733	-0.547	-0.547	0.000	0.000	0.000	0.000
118	A	702	LYS	1	0.969	0.966	12.905	0.208	0.208	0.000	0.000	0.000	0.000
119	A	703	ASN	0	-0.059	-0.039	14.022	-0.013	-0.013	0.000	0.000	0.000	0.000
120	A	704	ALA	0	0.044	0.042	11.128	-0.014	-0.014	0.000	0.000	0.000	0.000
121	A	705	PHE	0	-0.013	-0.006	11.878	-0.070	-0.070	0.000	0.000	0.000	0.000
122	A	706	ILE	0	-0.014	-0.003	14.781	0.048	0.048	0.000	0.000	0.000	0.000
123	A	707	GLN	0	0.015	0.010	17.342	-0.009	-0.009	0.000	0.000	0.000	0.000
124	A	708	LYS	1	0.918	0.957	19.181	0.173	0.173	0.000	0.000	0.000	0.000
125	A	709	GLY	0	0.012	0.014	21.341	0.005	0.005	0.000	0.000	0.000	0.000
126	A	710	ARG	1	0.824	0.885	25.048	0.083	0.083	0.000	0.000	0.000	0.000
127	A	711	ILE	0	0.005	0.019	23.779	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	712	VAL	0	0.018	0.014	28.263	0.002	0.002	0.000	0.000	0.000	0.000
129	A	713	ALA	0	-0.012	-0.002	32.011	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	714	GLY	0	0.049	0.036	34.244	0.001	0.001	0.000	0.000	0.000	0.000
131	A	715	SER	0	-0.017	-0.010	37.672	0.001	0.001	0.000	0.000	0.000	0.000
132	A	716	TYR	0	-0.018	0.000	34.295	0.001	0.001	0.000	0.000	0.000	0.000
133	A	717	ASP	-1	-0.828	-0.913	30.997	-0.111	-0.111	0.000	0.000	0.000	0.000
134	A	718	TYR	0	-0.014	-0.060	27.839	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	719	ARG	1	0.928	0.955	23.645	0.151	0.151	0.000	0.000	0.000	0.000
136	A	720	LEU	0	-0.018	-0.006	18.168	0.000	0.000	0.000	0.000	0.000	0.000
137	A	721	LYS	1	0.862	0.945	22.625	0.165	0.165	0.000	0.000	0.000	0.000
138	A	722	GLN	0	-0.013	-0.005	16.797	-0.008	-0.008	0.000	0.000	0.000	0.000
139	A	723	GLY	0	-0.021	-0.024	20.652	0.016	0.016	0.000	0.000	0.000	0.000
140	A	724	THR	0	-0.077	-0.051	23.251	-0.001	-0.001	0.000	0.000	0.000	0.000
141	A	725	ALA	0	-0.013	-0.015	26.737	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	726	SER	0	-0.080	-0.070	29.495	0.004	0.004	0.000	0.000	0.000	0.000
143	A	727	GLY	0	-0.066	-0.026	26.604	0.004	0.004	0.000	0.000	0.000	0.000
144	A	728	LEU	0	0.019	0.012	26.533	-0.004	-0.004	0.000	0.000	0.000	0.000
145	A	729	ASN	0	-0.006	-0.004	23.456	-0.008	-0.008	0.000	0.000	0.000	0.000
146	A	730	THR	0	0.066	0.020	20.792	-0.015	-0.015	0.000	0.000	0.000	0.000
147	A	731	ASN	0	0.005	0.022	17.725	-0.004	-0.004	0.000	0.000	0.000	0.000
148	A	732	LYS	1	0.901	0.974	17.605	0.185	0.185	0.000	0.000	0.000	0.000
149	A	733	TRP	0	0.012	-0.002	15.235	0.018	0.018	0.000	0.000	0.000	0.000
150	A	734	TYR	0	0.024	-0.001	20.160	0.004	0.004	0.000	0.000	0.000	0.000
151	A	735	LEU	0	0.005	0.015	23.248	-0.006	-0.006	0.000	0.000	0.000	0.000
152	A	736	THR	0	-0.022	-0.009	25.767	0.011	0.011	0.000	0.000	0.000	0.000
153	A	737	SER	0	0.015	-0.022	28.913	-0.002	-0.002	0.000	0.000	0.000	0.000
154	A	738	GLN	0	-0.007	-0.014	31.954	0.005	0.005	0.000	0.000	0.000	0.000
155	A	739	MET	0	-0.016	0.001	34.830	-0.002	-0.002	0.000	0.000	0.000	0.000
156	A	740	ASP	-1	-0.885	-0.925	35.529	-0.079	-0.079	0.000	0.000	0.000	0.000

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