FMO DATABASE

FMODB ID: MN2YZ

Calculation Name: 2D3E-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D3E

Chain ID: A

ChEMBL ID:

UniProt ID: P03069

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	130
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-680457.127823
FMO2-HF: Nuclear repulsion	627455.162112
FMO2-HF: Total energy	-53001.965711
FMO2-MP2: Total energy	-53157.673517

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:153:ASP)

Summations of interaction energy for fragment #1(A:153:ASP)

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.
27.694	34.459	0.338	-3.337	-3.767	0.027

Interaction energy analysis for fragmet #1(A:153:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.850 / q_NPA : -0.920

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	155	VAL	0	-0.006	-0.013	3.021	-19.906	-15.488	0.116	-2.311	-2.224	0.018
4	A	156	GLU	-1	-0.912	-0.950	3.051	27.779	29.919	0.223	-0.971	-1.392	0.009
5	A	157	GLU	-1	-0.842	-0.907	4.255	30.369	30.576	-0.001	-0.055	-0.151	0.000
6	A	158	LEU	0	-0.047	-0.033	6.041	-5.408	-5.408	0.000	0.000	0.000	0.000
7	A	159	LEU	0	0.003	0.013	7.121	-4.064	-4.064	0.000	0.000	0.000	0.000
8	A	160	SER	0	0.006	0.010	8.312	-3.679	-3.679	0.000	0.000	0.000	0.000
9	A	161	LYS	1	0.837	0.898	9.375	-30.713	-30.713	0.000	0.000	0.000	0.000
10	A	162	ASN	0	0.020	0.006	12.151	-1.531	-1.531	0.000	0.000	0.000	0.000
11	A	163	TYR	0	0.042	0.036	13.509	-1.719	-1.719	0.000	0.000	0.000	0.000
12	A	164	HIS	0	-0.002	-0.002	14.516	-0.970	-0.970	0.000	0.000	0.000	0.000
13	A	165	LEU	0	0.013	-0.003	15.815	-1.136	-1.136	0.000	0.000	0.000	0.000
14	A	166	GLU	-1	-0.973	-0.983	17.520	15.360	15.360	0.000	0.000	0.000	0.000
15	A	167	ASN	0	-0.017	-0.015	19.241	-1.277	-1.277	0.000	0.000	0.000	0.000
16	A	168	GLU	-1	-0.974	-0.981	20.504	13.387	13.387	0.000	0.000	0.000	0.000
17	A	169	VAL	0	0.005	-0.001	22.182	-0.803	-0.803	0.000	0.000	0.000	0.000
18	A	170	ALA	0	-0.019	-0.007	23.851	-0.656	-0.656	0.000	0.000	0.000	0.000
19	A	171	ARG	1	0.948	0.950	24.529	-12.310	-12.310	0.000	0.000	0.000	0.000
20	A	172	LEU	0	0.013	0.009	25.602	-0.524	-0.524	0.000	0.000	0.000	0.000
21	A	173	LYS	1	0.958	0.979	27.143	-11.743	-11.743	0.000	0.000	0.000	0.000
22	A	174	LYS	1	0.878	0.957	29.892	-9.299	-9.299	0.000	0.000	0.000	0.000
23	A	175	LEU	0	-0.069	-0.045	30.127	-0.371	-0.371	0.000	0.000	0.000	0.000
24	A	176	LEU	0	0.026	0.003	32.398	-0.224	-0.224	0.000	0.000	0.000	0.000
25	A	177	GLU	-1	-0.829	-0.897	34.156	8.657	8.657	0.000	0.000	0.000	0.000
26	A	178	ARG	1	0.971	0.967	33.645	-8.988	-8.988	0.000	0.000	0.000	0.000
27	A	179	ALA	0	-0.087	-0.024	36.897	-0.222	-0.222	0.000	0.000	0.000	0.000
28	A	180	GLU	-1	-0.933	-0.971	38.047	8.151	8.151	0.000	0.000	0.000	0.000
29	A	181	GLU	-1	-0.903	-0.939	39.801	7.569	7.569	0.000	0.000	0.000	0.000
30	A	182	ARG	1	0.927	0.943	41.526	-7.734	-7.734	0.000	0.000	0.000	0.000
31	A	183	ALA	0	-0.073	-0.033	42.607	-0.187	-0.187	0.000	0.000	0.000	0.000
32	A	184	GLU	-1	-0.810	-0.923	42.918	7.199	7.199	0.000	0.000	0.000	0.000
33	A	185	LEU	0	-0.036	0.007	45.950	-0.184	-0.184	0.000	0.000	0.000	0.000
34	A	186	SER	0	-0.154	-0.082	47.517	-0.178	-0.178	0.000	0.000	0.000	0.000
35	A	187	GLU	-1	-0.904	-0.941	47.725	6.673	6.673	0.000	0.000	0.000	0.000
36	A	188	GLY	0	0.032	0.011	50.001	-0.124	-0.124	0.000	0.000	0.000	0.000
37	A	189	LYS	1	0.877	0.928	51.988	-5.881	-5.881	0.000	0.000	0.000	0.000
38	A	190	CYS	0	0.003	0.007	53.603	-0.115	-0.115	0.000	0.000	0.000	0.000
39	A	191	ALA	0	0.031	0.018	55.219	-0.115	-0.115	0.000	0.000	0.000	0.000
40	A	192	GLU	-1	-0.952	-0.958	56.995	5.435	5.435	0.000	0.000	0.000	0.000
41	A	193	LEU	0	0.009	-0.007	56.702	-0.087	-0.087	0.000	0.000	0.000	0.000
42	A	194	GLU	-1	-0.975	-0.993	58.844	5.394	5.394	0.000	0.000	0.000	0.000
43	A	195	GLU	-1	-0.882	-0.932	60.879	5.005	5.005	0.000	0.000	0.000	0.000
44	A	196	GLU	-1	-0.923	-0.966	62.370	4.972	4.972	0.000	0.000	0.000	0.000
45	A	197	LEU	0	-0.040	-0.022	62.318	-0.117	-0.117	0.000	0.000	0.000	0.000
46	A	198	LYS	1	0.962	1.004	65.377	-4.930	-4.930	0.000	0.000	0.000	0.000
47	A	199	THR	0	-0.052	-0.034	67.211	-0.113	-0.113	0.000	0.000	0.000	0.000
48	A	200	VAL	0	-0.017	-0.010	67.909	-0.102	-0.102	0.000	0.000	0.000	0.000
49	A	201	THR	0	0.018	0.000	68.133	-0.084	-0.084	0.000	0.000	0.000	0.000
50	A	202	ASN	0	-0.041	-0.024	70.927	-0.097	-0.097	0.000	0.000	0.000	0.000
51	A	203	ASN	0	-0.014	-0.038	73.057	-0.082	-0.082	0.000	0.000	0.000	0.000
52	A	204	LEU	0	0.050	0.050	73.307	-0.055	-0.055	0.000	0.000	0.000	0.000
53	A	205	LYS	1	0.877	0.936	74.223	-4.368	-4.368	0.000	0.000	0.000	0.000
54	A	206	SER	0	-0.080	-0.029	76.830	-0.079	-0.079	0.000	0.000	0.000	0.000
55	A	207	LEU	0	0.058	0.024	78.739	-0.049	-0.049	0.000	0.000	0.000	0.000
56	A	208	GLU	-1	-0.883	-0.926	78.621	4.047	4.047	0.000	0.000	0.000	0.000
57	A	209	ALA	0	0.002	-0.011	80.932	-0.058	-0.058	0.000	0.000	0.000	0.000
58	A	210	GLN	0	-0.085	-0.048	83.249	-0.073	-0.073	0.000	0.000	0.000	0.000
59	A	211	ALA	0	0.015	0.016	83.612	-0.060	-0.060	0.000	0.000	0.000	0.000
60	A	212	GLU	-1	-0.894	-0.932	84.969	3.733	3.733	0.000	0.000	0.000	0.000
61	A	213	LYS	1	0.912	0.932	86.714	-3.745	-3.745	0.000	0.000	0.000	0.000
62	A	214	TYR	0	-0.106	-0.087	88.138	-0.065	-0.065	0.000	0.000	0.000	0.000
63	A	215	SER	0	0.086	0.068	88.537	-0.031	-0.031	0.000	0.000	0.000	0.000
64	A	216	GLN	0	0.005	0.008	90.555	-0.067	-0.067	0.000	0.000	0.000	0.000
65	A	217	LYS	1	0.857	0.943	92.749	-3.465	-3.465	0.000	0.000	0.000	0.000
66	A	218	GLU	-1	-0.945	-0.984	91.738	3.491	3.491	0.000	0.000	0.000	0.000
67	A	219	ASP	-1	-0.854	-0.911	94.033	3.438	3.438	0.000	0.000	0.000	0.000
68	A	220	LYS	1	0.833	0.920	96.667	-3.259	-3.259	0.000	0.000	0.000	0.000
69	A	221	TYR	0	-0.043	-0.052	97.249	-0.033	-0.033	0.000	0.000	0.000	0.000
70	A	222	GLU	-1	-0.856	-0.921	97.835	3.266	3.266	0.000	0.000	0.000	0.000
71	A	223	GLU	-1	-0.976	-0.969	100.328	3.159	3.159	0.000	0.000	0.000	0.000
72	A	224	GLU	-1	-0.900	-0.953	102.560	3.125	3.125	0.000	0.000	0.000	0.000
73	A	225	ILE	0	0.018	0.001	101.693	-0.048	-0.048	0.000	0.000	0.000	0.000
74	A	226	LYS	1	0.940	0.958	104.851	-3.074	-3.074	0.000	0.000	0.000	0.000
75	A	227	VAL	0	0.014	0.011	106.635	-0.038	-0.038	0.000	0.000	0.000	0.000
76	A	228	LEU	0	-0.050	-0.024	107.748	-0.042	-0.042	0.000	0.000	0.000	0.000
77	A	229	SER	0	-0.045	-0.030	107.964	-0.037	-0.037	0.000	0.000	0.000	0.000
78	A	230	ASP	-1	-0.915	-0.950	110.098	2.936	2.936	0.000	0.000	0.000	0.000
79	A	231	LYS	1	0.953	0.968	112.678	-2.910	-2.910	0.000	0.000	0.000	0.000
80	A	232	LEU	0	-0.035	0.000	112.927	-0.025	-0.025	0.000	0.000	0.000	0.000
81	A	233	LYS	1	0.975	0.989	111.724	-2.924	-2.924	0.000	0.000	0.000	0.000
82	A	234	GLU	-1	-0.915	-0.951	116.529	2.755	2.755	0.000	0.000	0.000	0.000
83	A	235	ALA	0	-0.062	-0.015	118.477	-0.035	-0.035	0.000	0.000	0.000	0.000
84	A	236	GLU	-1	-0.909	-0.973	117.313	2.751	2.751	0.000	0.000	0.000	0.000
85	A	237	THR	0	-0.040	-0.015	120.079	-0.024	-0.024	0.000	0.000	0.000	0.000
86	A	238	ARG	1	0.930	0.963	122.642	-2.658	-2.658	0.000	0.000	0.000	0.000
87	A	239	ALA	0	0.004	0.000	124.302	-0.028	-0.028	0.000	0.000	0.000	0.000
88	A	240	GLU	-1	-0.822	-0.912	122.400	2.633	2.633	0.000	0.000	0.000	0.000
89	A	241	PHE	0	-0.113	-0.050	126.398	-0.031	-0.031	0.000	0.000	0.000	0.000
90	A	242	ALA	0	-0.006	-0.023	128.653	-0.026	-0.026	0.000	0.000	0.000	0.000
91	A	243	GLU	-1	-0.893	-0.943	127.824	2.527	2.527	0.000	0.000	0.000	0.000
92	A	244	ARG	1	0.927	0.971	130.720	-2.499	-2.499	0.000	0.000	0.000	0.000
93	A	245	SER	0	-0.073	-0.051	132.408	-0.027	-0.027	0.000	0.000	0.000	0.000
94	A	246	VAL	0	0.047	0.028	134.237	-0.023	-0.023	0.000	0.000	0.000	0.000
95	A	247	THR	0	0.046	0.037	134.890	-0.019	-0.019	0.000	0.000	0.000	0.000
96	A	248	LYS	1	0.854	0.917	135.841	-2.413	-2.413	0.000	0.000	0.000	0.000
97	A	249	LEU	0	-0.027	-0.025	138.111	-0.019	-0.019	0.000	0.000	0.000	0.000
98	A	250	GLU	-1	-0.904	-0.948	138.633	2.341	2.341	0.000	0.000	0.000	0.000
99	A	251	LYS	1	0.917	0.977	141.451	-2.282	-2.282	0.000	0.000	0.000	0.000
100	A	252	SER	0	-0.065	-0.036	143.212	-0.019	-0.019	0.000	0.000	0.000	0.000
101	A	253	ILE	0	-0.013	-0.009	143.833	-0.017	-0.017	0.000	0.000	0.000	0.000
102	A	254	ASP	-1	-0.845	-0.914	145.388	2.228	2.228	0.000	0.000	0.000	0.000
103	A	255	ASP	-1	-0.881	-0.943	147.450	2.203	2.203	0.000	0.000	0.000	0.000
104	A	256	LEU	0	-0.052	-0.033	148.226	-0.020	-0.020	0.000	0.000	0.000	0.000
105	A	257	GLU	-1	-0.990	-0.996	149.374	2.172	2.172	0.000	0.000	0.000	0.000
106	A	258	ASP	-1	-0.903	-0.939	151.546	2.136	2.136	0.000	0.000	0.000	0.000
107	A	259	GLU	-1	-0.982	-0.997	153.628	2.108	2.108	0.000	0.000	0.000	0.000
108	A	260	LEU	0	-0.066	-0.036	154.932	-0.024	-0.024	0.000	0.000	0.000	0.000
109	A	261	TYR	0	-0.002	0.002	156.351	-0.025	-0.025	0.000	0.000	0.000	0.000
110	A	262	ALA	0	0.044	0.021	158.124	-0.019	-0.019	0.000	0.000	0.000	0.000
111	A	263	GLN	0	-0.054	-0.025	159.717	-0.032	-0.032	0.000	0.000	0.000	0.000
112	A	264	LYS	1	0.948	0.954	157.688	-2.086	-2.086	0.000	0.000	0.000	0.000
113	A	265	LEU	0	0.018	0.009	161.030	-0.018	-0.018	0.000	0.000	0.000	0.000
114	A	266	LYS	1	0.898	0.953	163.877	-2.009	-2.009	0.000	0.000	0.000	0.000
115	A	267	TYR	0	-0.033	-0.017	165.654	-0.015	-0.015	0.000	0.000	0.000	0.000
116	A	268	LYS	1	0.867	0.932	166.202	-1.955	-1.955	0.000	0.000	0.000	0.000
117	A	269	ALA	0	0.044	0.029	168.524	-0.011	-0.011	0.000	0.000	0.000	0.000
118	A	270	ILE	0	-0.002	0.008	170.498	-0.012	-0.012	0.000	0.000	0.000	0.000
119	A	271	SER	0	-0.048	-0.023	171.415	-0.017	-0.017	0.000	0.000	0.000	0.000
120	A	272	GLU	-1	-0.841	-0.926	170.938	1.908	1.908	0.000	0.000	0.000	0.000
121	A	273	GLU	-1	-0.926	-0.949	174.530	1.841	1.841	0.000	0.000	0.000	0.000
122	A	274	LEU	0	-0.060	-0.047	176.189	-0.013	-0.013	0.000	0.000	0.000	0.000
123	A	275	ASP	-1	-0.949	-0.980	177.055	1.826	1.826	0.000	0.000	0.000	0.000
124	A	276	HIS	0	-0.015	-0.010	178.520	-0.016	-0.016	0.000	0.000	0.000	0.000
125	A	277	ALA	0	-0.023	-0.008	180.454	-0.012	-0.012	0.000	0.000	0.000	0.000
126	A	278	LEU	0	-0.009	-0.018	181.776	-0.014	-0.014	0.000	0.000	0.000	0.000
127	A	279	ASN	0	-0.076	-0.045	182.707	-0.010	-0.010	0.000	0.000	0.000	0.000
128	A	280	ASP	-1	-0.928	-0.948	184.830	1.753	1.753	0.000	0.000	0.000	0.000
129	A	281	MET	0	-0.086	-0.022	186.170	-0.012	-0.012	0.000	0.000	0.000	0.000
130	A	282	THR	0	-0.077	-0.030	188.605	-0.015	-0.015	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:153:ASP)