FMO DATABASE

FMODB ID: 1N9MZ

Calculation Name: 3D3M-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D3M

Chain ID: A

ChEMBL ID:

UniProt ID: P78344

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	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	161
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1754514.430324
FMO2-HF: Nuclear repulsion	1688793.111118
FMO2-HF: Total energy	-65721.319207
FMO2-MP2: Total energy	-65915.430562

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:730:LEU)

Summations of interaction energy for fragment #1(A:730:LEU)

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.
-25.48	-17.99	9.526	-5.967	-11.047	0.002

Interaction energy analysis for fragmet #1(A:730:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.048 / q_NPA : 0.007

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	732	LYS	1	0.962	0.968	3.179	-8.240	-5.289	0.169	-1.498	-1.622	0.011
4	A	733	LEU	0	-0.001	0.009	2.167	-5.684	-4.154	3.691	-2.399	-2.821	0.003
5	A	734	GLU	-1	-0.802	-0.918	3.568	-2.075	-1.602	0.005	-0.123	-0.355	0.000
6	A	735	LYS	1	0.826	0.929	5.418	-1.791	-1.791	0.000	0.000	0.000	0.000
7	A	736	GLU	-1	-0.909	-0.947	7.231	0.756	0.756	0.000	0.000	0.000	0.000
8	A	737	LEU	0	0.037	0.023	6.519	-0.256	-0.256	0.000	0.000	0.000	0.000
9	A	738	LEU	0	0.016	0.018	9.138	-0.125	-0.125	0.000	0.000	0.000	0.000
10	A	739	LYS	1	0.874	0.944	11.330	-0.812	-0.812	0.000	0.000	0.000	0.000
11	A	740	GLN	0	-0.050	-0.056	12.075	-0.169	-0.169	0.000	0.000	0.000	0.000
12	A	741	ILE	0	0.011	0.011	11.835	-0.060	-0.060	0.000	0.000	0.000	0.000
13	A	742	LYS	1	0.927	0.955	15.054	-0.247	-0.247	0.000	0.000	0.000	0.000
14	A	743	LEU	0	-0.077	-0.039	16.132	-0.007	-0.007	0.000	0.000	0.000	0.000
15	A	744	ASP	-1	-0.798	-0.879	17.955	0.080	0.080	0.000	0.000	0.000	0.000
16	A	745	PRO	0	-0.010	0.007	17.900	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	746	SER	0	0.045	0.028	18.995	-0.045	-0.045	0.000	0.000	0.000	0.000
18	A	747	PRO	0	0.040	0.004	17.810	0.006	0.006	0.000	0.000	0.000	0.000
19	A	748	GLN	0	-0.036	-0.019	17.377	0.001	0.001	0.000	0.000	0.000	0.000
20	A	749	THR	0	-0.034	-0.021	17.131	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	750	ILE	0	0.009	0.025	12.523	0.025	0.025	0.000	0.000	0.000	0.000
22	A	751	TYR	0	-0.009	-0.009	13.078	0.024	0.024	0.000	0.000	0.000	0.000
23	A	752	LYS	1	0.909	0.960	13.902	-0.093	-0.093	0.000	0.000	0.000	0.000
24	A	753	TRP	0	0.065	0.026	7.961	0.032	0.032	0.000	0.000	0.000	0.000
25	A	754	ILE	0	0.044	0.017	8.581	0.077	0.077	0.000	0.000	0.000	0.000
26	A	755	LYS	1	0.847	0.922	10.310	0.063	0.063	0.000	0.000	0.000	0.000
27	A	756	ASP	-1	-0.919	-0.955	12.755	0.097	0.097	0.000	0.000	0.000	0.000
28	A	757	ASN	0	-0.105	-0.052	10.100	0.132	0.132	0.000	0.000	0.000	0.000
29	A	758	ILE	0	-0.048	-0.001	5.213	0.244	0.244	0.000	0.000	0.000	0.000
30	A	759	SER	0	0.005	-0.001	8.067	-0.167	-0.167	0.000	0.000	0.000	0.000
31	A	760	PRO	0	0.117	0.047	7.949	-0.207	-0.207	0.000	0.000	0.000	0.000
32	A	761	LYS	1	0.916	0.950	9.104	0.277	0.277	0.000	0.000	0.000	0.000
33	A	762	LEU	0	0.013	0.003	3.026	-0.780	-0.014	0.087	-0.148	-0.705	0.000
34	A	763	HIS	0	-0.060	-0.034	5.448	-0.409	-0.409	0.000	0.000	0.000	0.000
35	A	764	VAL	0	0.042	0.027	7.844	0.053	0.053	0.000	0.000	0.000	0.000
36	A	765	ASP	-1	-0.866	-0.916	3.124	-6.216	-5.036	0.123	-0.594	-0.710	-0.005
37	A	766	LYS	1	0.842	0.924	6.055	0.842	0.842	0.000	0.000	0.000	0.000
38	A	767	GLY	0	0.016	0.013	2.572	-0.019	0.311	0.416	-0.293	-0.452	-0.001
39	A	768	PHE	0	-0.042	-0.035	2.615	-2.243	-0.578	0.713	-0.646	-1.731	-0.004
40	A	769	VAL	0	0.035	0.020	3.485	0.997	0.777	0.043	0.335	-0.158	0.000
41	A	770	ASN	0	-0.023	-0.008	5.625	0.340	0.340	0.000	0.000	0.000	0.000
42	A	771	ILE	0	0.009	0.007	2.182	0.922	-0.307	4.280	-0.600	-2.451	-0.002
43	A	772	LEU	0	-0.038	0.000	5.388	0.567	0.611	-0.001	-0.001	-0.042	0.000
44	A	773	MET	0	0.005	-0.005	7.620	0.295	0.295	0.000	0.000	0.000	0.000
45	A	774	THR	0	0.015	0.000	8.419	0.227	0.227	0.000	0.000	0.000	0.000
46	A	775	SER	0	-0.037	-0.028	8.161	0.258	0.258	0.000	0.000	0.000	0.000
47	A	776	PHE	0	0.017	0.007	10.829	0.109	0.109	0.000	0.000	0.000	0.000
48	A	777	LEU	0	0.004	0.005	13.246	0.067	0.067	0.000	0.000	0.000	0.000
49	A	778	GLN	0	0.002	0.000	11.812	0.110	0.110	0.000	0.000	0.000	0.000
50	A	779	TYR	0	0.010	0.002	14.920	0.040	0.040	0.000	0.000	0.000	0.000
51	A	780	ILE	0	0.043	0.016	16.853	0.023	0.023	0.000	0.000	0.000	0.000
52	A	781	SER	0	-0.004	-0.008	18.562	0.004	0.004	0.000	0.000	0.000	0.000
53	A	782	SER	0	-0.108	-0.051	19.095	0.026	0.026	0.000	0.000	0.000	0.000
54	A	783	GLU	-1	-0.929	-0.958	21.053	0.054	0.054	0.000	0.000	0.000	0.000
55	A	784	VAL	0	-0.037	-0.009	22.918	0.002	0.002	0.000	0.000	0.000	0.000
56	A	785	ASN	0	-0.092	-0.058	24.045	0.009	0.009	0.000	0.000	0.000	0.000
57	A	786	PRO	0	0.073	0.064	24.791	0.003	0.003	0.000	0.000	0.000	0.000
58	A	787	PRO	0	-0.012	-0.029	24.436	-0.005	-0.005	0.000	0.000	0.000	0.000
59	A	788	SER	0	-0.058	-0.010	27.480	0.006	0.006	0.000	0.000	0.000	0.000
60	A	796	ALA	0	0.008	-0.005	29.840	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	797	PRO	0	-0.058	-0.018	28.221	0.006	0.006	0.000	0.000	0.000	0.000
62	A	798	SER	0	0.062	0.034	30.664	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	799	LYS	1	0.972	0.964	31.887	0.033	0.033	0.000	0.000	0.000	0.000
64	A	800	GLU	-1	-0.838	-0.934	32.483	-0.038	-0.038	0.000	0.000	0.000	0.000
65	A	801	GLN	0	-0.001	0.009	28.245	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	802	LEU	0	-0.034	-0.019	27.753	-0.009	-0.009	0.000	0.000	0.000	0.000
67	A	803	GLU	-1	-0.974	-0.981	27.990	-0.061	-0.061	0.000	0.000	0.000	0.000
68	A	804	GLN	0	0.042	0.015	25.944	-0.007	-0.007	0.000	0.000	0.000	0.000
69	A	805	GLU	-1	-0.792	-0.887	22.685	-0.138	-0.138	0.000	0.000	0.000	0.000
70	A	806	LYS	1	0.956	0.976	23.448	0.100	0.100	0.000	0.000	0.000	0.000
71	A	807	GLN	0	0.008	0.009	24.630	-0.011	-0.011	0.000	0.000	0.000	0.000
72	A	808	LEU	0	0.025	0.013	20.774	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	809	LEU	0	0.008	0.008	18.560	-0.014	-0.014	0.000	0.000	0.000	0.000
74	A	810	LEU	0	0.006	-0.016	20.628	-0.020	-0.020	0.000	0.000	0.000	0.000
75	A	811	SER	0	-0.094	-0.034	21.229	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	812	PHE	0	0.029	-0.007	16.553	0.000	0.000	0.000	0.000	0.000	0.000
77	A	813	LYS	1	0.964	0.983	17.370	0.147	0.147	0.000	0.000	0.000	0.000
78	A	814	PRO	0	0.006	0.001	18.558	-0.032	-0.032	0.000	0.000	0.000	0.000
79	A	815	VAL	0	-0.024	0.001	13.591	-0.017	-0.017	0.000	0.000	0.000	0.000
80	A	816	MET	0	-0.028	0.005	13.788	-0.067	-0.067	0.000	0.000	0.000	0.000
81	A	817	GLN	0	0.048	0.011	14.732	-0.049	-0.049	0.000	0.000	0.000	0.000
82	A	818	LYS	1	0.891	0.966	14.982	0.248	0.248	0.000	0.000	0.000	0.000
83	A	819	PHE	0	-0.033	-0.048	10.693	0.003	0.003	0.000	0.000	0.000	0.000
84	A	820	LEU	0	-0.007	-0.002	11.828	-0.093	-0.093	0.000	0.000	0.000	0.000
85	A	821	HIS	0	-0.067	-0.009	14.637	0.005	0.005	0.000	0.000	0.000	0.000
86	A	822	ASP	-1	-0.841	-0.917	17.267	-0.350	-0.350	0.000	0.000	0.000	0.000
87	A	823	HIS	0	-0.033	-0.005	14.171	-0.045	-0.045	0.000	0.000	0.000	0.000
88	A	824	VAL	0	0.093	0.037	15.501	-0.072	-0.072	0.000	0.000	0.000	0.000
89	A	825	ASP	-1	-0.817	-0.935	13.425	-0.877	-0.877	0.000	0.000	0.000	0.000
90	A	826	LEU	0	0.008	0.017	9.367	-0.120	-0.120	0.000	0.000	0.000	0.000
91	A	827	GLN	0	-0.023	-0.016	12.126	-0.035	-0.035	0.000	0.000	0.000	0.000
92	A	828	VAL	0	0.012	0.016	14.218	0.013	0.013	0.000	0.000	0.000	0.000
93	A	829	SER	0	-0.002	-0.016	9.058	0.020	0.020	0.000	0.000	0.000	0.000
94	A	830	ALA	0	-0.002	0.012	11.124	-0.052	-0.052	0.000	0.000	0.000	0.000
95	A	831	LEU	0	0.021	0.017	12.264	0.059	0.059	0.000	0.000	0.000	0.000
96	A	832	TYR	0	-0.055	-0.083	11.938	0.078	0.078	0.000	0.000	0.000	0.000
97	A	833	ALA	0	0.013	0.008	9.986	0.038	0.038	0.000	0.000	0.000	0.000
98	A	834	LEU	0	0.007	0.018	11.796	0.105	0.105	0.000	0.000	0.000	0.000
99	A	835	GLN	0	-0.046	-0.038	15.258	0.071	0.071	0.000	0.000	0.000	0.000
100	A	836	VAL	0	0.001	-0.005	11.864	0.075	0.075	0.000	0.000	0.000	0.000
101	A	837	HIS	0	0.036	0.026	14.083	0.064	0.064	0.000	0.000	0.000	0.000
102	A	838	CYS	0	-0.042	-0.025	15.524	0.077	0.077	0.000	0.000	0.000	0.000
103	A	839	TYR	0	-0.027	-0.017	16.779	0.044	0.044	0.000	0.000	0.000	0.000
104	A	840	ASN	0	-0.004	-0.021	13.529	0.057	0.057	0.000	0.000	0.000	0.000
105	A	841	SER	0	-0.056	-0.006	17.818	0.047	0.047	0.000	0.000	0.000	0.000
106	A	842	ASN	0	-0.068	-0.043	20.912	0.005	0.005	0.000	0.000	0.000	0.000
107	A	843	PHE	0	-0.082	-0.044	20.396	0.013	0.013	0.000	0.000	0.000	0.000
108	A	844	PRO	0	0.082	0.053	23.097	0.009	0.009	0.000	0.000	0.000	0.000
109	A	845	LYS	1	1.030	1.001	26.106	0.086	0.086	0.000	0.000	0.000	0.000
110	A	846	GLY	0	-0.078	-0.050	28.106	0.005	0.005	0.000	0.000	0.000	0.000
111	A	847	MET	0	0.004	0.022	19.796	0.001	0.001	0.000	0.000	0.000	0.000
112	A	848	LEU	0	0.061	0.036	19.893	-0.009	-0.009	0.000	0.000	0.000	0.000
113	A	849	LEU	0	0.015	0.010	22.640	-0.012	-0.012	0.000	0.000	0.000	0.000
114	A	850	ARG	1	0.821	0.893	24.451	0.128	0.128	0.000	0.000	0.000	0.000
115	A	851	PHE	0	-0.006	-0.012	19.369	0.000	0.000	0.000	0.000	0.000	0.000
116	A	852	PHE	0	0.045	0.023	19.727	-0.017	-0.017	0.000	0.000	0.000	0.000
117	A	853	VAL	0	-0.007	0.000	22.700	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	854	HIS	0	-0.006	-0.004	22.383	0.003	0.003	0.000	0.000	0.000	0.000
119	A	855	PHE	0	-0.037	-0.034	16.269	-0.003	-0.003	0.000	0.000	0.000	0.000
120	A	856	TYR	0	0.014	0.014	21.224	-0.008	-0.008	0.000	0.000	0.000	0.000
121	A	857	ASP	-1	-0.884	-0.936	24.077	-0.164	-0.164	0.000	0.000	0.000	0.000
122	A	858	MET	0	-0.194	-0.097	20.351	0.016	0.016	0.000	0.000	0.000	0.000
123	A	859	GLU	-1	-0.916	-0.957	23.142	-0.206	-0.206	0.000	0.000	0.000	0.000
124	A	860	ILE	0	-0.100	-0.049	16.940	-0.009	-0.009	0.000	0.000	0.000	0.000
125	A	861	ILE	0	-0.066	-0.027	15.837	-0.057	-0.057	0.000	0.000	0.000	0.000
126	A	862	GLU	-1	-0.833	-0.922	19.598	-0.311	-0.311	0.000	0.000	0.000	0.000
127	A	863	GLU	-1	-0.885	-0.955	22.143	-0.238	-0.238	0.000	0.000	0.000	0.000
128	A	864	GLU	-1	-0.853	-0.944	22.692	-0.289	-0.289	0.000	0.000	0.000	0.000
129	A	865	ALA	0	-0.011	0.000	17.954	-0.020	-0.020	0.000	0.000	0.000	0.000
130	A	866	PHE	0	-0.001	-0.022	19.583	-0.024	-0.024	0.000	0.000	0.000	0.000
131	A	867	LEU	0	0.001	0.006	21.618	-0.006	-0.006	0.000	0.000	0.000	0.000
132	A	868	ALA	0	0.011	0.005	19.162	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	869	TRP	0	-0.050	-0.029	16.274	0.020	0.020	0.000	0.000	0.000	0.000
134	A	870	LYS	1	0.873	0.925	18.919	0.226	0.226	0.000	0.000	0.000	0.000
135	A	871	GLU	-1	-0.932	-0.971	22.351	-0.243	-0.243	0.000	0.000	0.000	0.000
136	A	872	ASP	-1	-0.827	-0.824	16.188	-0.550	-0.550	0.000	0.000	0.000	0.000
137	A	873	ILE	0	-0.020	-0.024	19.667	0.015	0.015	0.000	0.000	0.000	0.000
138	A	874	THR	0	-0.125	-0.078	16.248	-0.022	-0.022	0.000	0.000	0.000	0.000
139	A	875	GLN	0	-0.008	0.010	10.598	-0.139	-0.139	0.000	0.000	0.000	0.000
140	A	876	GLU	-1	-0.941	-0.962	13.758	-0.376	-0.376	0.000	0.000	0.000	0.000
141	A	877	PHE	0	-0.025	-0.003	9.061	-0.037	-0.037	0.000	0.000	0.000	0.000
142	A	878	PRO	0	0.005	0.009	14.169	0.047	0.047	0.000	0.000	0.000	0.000
143	A	879	GLY	0	0.023	-0.007	17.300	-0.022	-0.022	0.000	0.000	0.000	0.000
144	A	880	LYS	1	0.954	1.000	18.575	0.402	0.402	0.000	0.000	0.000	0.000
145	A	881	GLY	0	0.047	0.023	20.493	0.012	0.012	0.000	0.000	0.000	0.000
146	A	882	LYS	1	0.926	0.959	23.738	0.150	0.150	0.000	0.000	0.000	0.000
147	A	883	ALA	0	0.018	0.018	20.906	0.012	0.012	0.000	0.000	0.000	0.000
148	A	884	LEU	0	0.060	0.015	23.034	0.011	0.011	0.000	0.000	0.000	0.000
149	A	885	PHE	0	-0.067	-0.024	24.975	0.013	0.013	0.000	0.000	0.000	0.000
150	A	886	GLN	0	-0.077	-0.052	24.259	0.016	0.016	0.000	0.000	0.000	0.000
151	A	887	VAL	0	0.015	0.014	23.773	0.011	0.011	0.000	0.000	0.000	0.000
152	A	888	ASN	0	0.060	0.019	26.996	-0.007	-0.007	0.000	0.000	0.000	0.000
153	A	889	GLN	0	-0.018	0.008	28.931	0.001	0.001	0.000	0.000	0.000	0.000
154	A	890	TRP	0	0.002	0.001	24.699	0.004	0.004	0.000	0.000	0.000	0.000
155	A	891	LEU	0	0.045	0.006	23.995	-0.002	-0.002	0.000	0.000	0.000	0.000
156	A	892	THR	0	-0.047	-0.017	28.213	-0.002	-0.002	0.000	0.000	0.000	0.000
157	A	893	TRP	0	-0.024	-0.014	31.446	0.010	0.010	0.000	0.000	0.000	0.000
158	A	894	LEU	0	-0.043	-0.017	26.170	0.002	0.002	0.000	0.000	0.000	0.000
159	A	895	GLU	-1	-0.872	-0.933	29.407	-0.207	-0.207	0.000	0.000	0.000	0.000
160	A	896	THR	0	-0.100	-0.023	30.974	0.011	0.011	0.000	0.000	0.000	0.000
161	A	897	ALA	0	-0.051	-0.040	34.774	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:730:LEU)