FMO DATABASE

FMODB ID: 6YGMZ

Calculation Name: 2A4V-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2A4V

Chain ID: A

ChEMBL ID:

UniProt ID: P40553

Base Structure: X-ray

Registration Date: 2023-09-22

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	-1588220.379842
FMO2-HF: Nuclear repulsion	1528189.041523
FMO2-HF: Total energy	-60031.338318
FMO2-MP2: Total energy	-60212.154971

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:59:ASP)

Summations of interaction energy for fragment #1(A:59: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.
-163.954	-150.174	7.354	-10.789	-10.344	0.118

Interaction energy analysis for fragmet #1(A:59:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.861 / q_NPA : -0.938

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	61	ASN	0	-0.026	-0.024	2.858	0.189	3.100	0.424	-1.303	-2.031	-0.003
4	A	62	GLU	-1	-0.866	-0.908	2.950	36.313	37.240	0.034	-0.283	-0.678	-0.001
5	A	63	LEU	0	-0.018	-0.017	4.739	-3.569	-3.466	-0.001	-0.012	-0.090	0.000
6	A	64	GLU	-1	-0.905	-0.957	8.403	23.985	23.985	0.000	0.000	0.000	0.000
7	A	65	ILE	0	-0.049	-0.039	10.873	-0.556	-0.556	0.000	0.000	0.000	0.000
8	A	66	GLY	0	-0.030	-0.018	14.570	-0.349	-0.349	0.000	0.000	0.000	0.000
9	A	67	ASP	-1	-0.820	-0.894	11.065	20.984	20.984	0.000	0.000	0.000	0.000
10	A	68	PRO	0	-0.079	-0.047	13.571	-0.492	-0.492	0.000	0.000	0.000	0.000
11	A	69	ILE	0	-0.013	-0.005	12.608	1.598	1.598	0.000	0.000	0.000	0.000
12	A	70	PRO	0	0.001	0.001	9.415	-0.561	-0.561	0.000	0.000	0.000	0.000
13	A	71	ASP	-1	-0.857	-0.907	11.761	16.250	16.250	0.000	0.000	0.000	0.000
14	A	72	LEU	0	0.012	0.010	9.347	0.234	0.234	0.000	0.000	0.000	0.000
15	A	73	SER	0	-0.017	-0.029	14.109	-1.752	-1.752	0.000	0.000	0.000	0.000
16	A	74	LEU	0	-0.035	-0.011	11.905	1.145	1.145	0.000	0.000	0.000	0.000
17	A	75	LEU	0	0.001	0.024	16.135	-1.016	-1.016	0.000	0.000	0.000	0.000
18	A	76	ASN	0	0.094	0.040	18.624	0.856	0.856	0.000	0.000	0.000	0.000
19	A	77	GLU	-1	-0.814	-0.916	21.195	13.384	13.384	0.000	0.000	0.000	0.000
20	A	78	ASP	-1	-0.859	-0.942	23.377	11.319	11.319	0.000	0.000	0.000	0.000
21	A	79	ASN	0	-0.093	-0.055	22.852	0.334	0.334	0.000	0.000	0.000	0.000
22	A	80	ASP	-1	-0.855	-0.896	23.908	11.990	11.990	0.000	0.000	0.000	0.000
23	A	81	SER	0	-0.074	-0.051	20.329	1.025	1.025	0.000	0.000	0.000	0.000
24	A	82	ILE	0	0.002	0.000	19.251	-0.678	-0.678	0.000	0.000	0.000	0.000
25	A	83	SER	0	0.015	0.018	18.255	0.909	0.909	0.000	0.000	0.000	0.000
26	A	84	LEU	0	0.040	-0.006	12.964	-0.846	-0.846	0.000	0.000	0.000	0.000
27	A	85	LYS	1	0.902	0.950	17.194	-15.724	-15.724	0.000	0.000	0.000	0.000
28	A	86	LYS	1	0.872	0.921	18.626	-12.961	-12.961	0.000	0.000	0.000	0.000
29	A	87	ILE	0	-0.019	-0.007	18.448	-0.672	-0.672	0.000	0.000	0.000	0.000
30	A	88	THR	0	-0.052	-0.037	17.927	-0.290	-0.290	0.000	0.000	0.000	0.000
31	A	89	GLU	-1	-0.881	-0.917	21.186	12.783	12.783	0.000	0.000	0.000	0.000
32	A	90	ASN	0	-0.032	-0.016	23.903	-0.733	-0.733	0.000	0.000	0.000	0.000
33	A	91	ASN	0	-0.052	-0.013	24.226	-0.808	-0.808	0.000	0.000	0.000	0.000
34	A	92	ARG	1	0.872	0.910	24.146	-10.435	-10.435	0.000	0.000	0.000	0.000
35	A	93	VAL	0	0.031	0.020	23.052	0.456	0.456	0.000	0.000	0.000	0.000
36	A	94	VAL	0	-0.010	0.000	19.261	-0.308	-0.308	0.000	0.000	0.000	0.000
37	A	95	VAL	0	0.005	0.014	19.381	0.573	0.573	0.000	0.000	0.000	0.000
38	A	96	PHE	0	0.031	0.012	14.971	-0.013	-0.013	0.000	0.000	0.000	0.000
39	A	97	PHE	0	-0.012	-0.016	16.159	0.655	0.655	0.000	0.000	0.000	0.000
40	A	98	VAL	0	0.024	0.004	11.492	0.163	0.163	0.000	0.000	0.000	0.000
41	A	99	TYR	0	-0.048	-0.049	14.736	-0.842	-0.842	0.000	0.000	0.000	0.000
42	A	100	PRO	0	-0.075	-0.048	14.535	0.815	0.815	0.000	0.000	0.000	0.000
43	A	101	ARG	1	0.977	0.979	15.608	-18.332	-18.332	0.000	0.000	0.000	0.000
44	A	102	ALA	0	0.050	0.037	18.363	-0.755	-0.755	0.000	0.000	0.000	0.000
45	A	103	SER	0	-0.030	-0.011	21.128	-0.374	-0.374	0.000	0.000	0.000	0.000
46	A	104	THR	0	0.008	0.014	21.718	-0.275	-0.275	0.000	0.000	0.000	0.000
47	A	105	PRO	0	0.081	0.022	24.486	0.042	0.042	0.000	0.000	0.000	0.000
48	A	106	GLY	0	-0.036	-0.012	22.636	-0.143	-0.143	0.000	0.000	0.000	0.000
49	A	107	SER	0	-0.002	-0.036	19.892	0.174	0.174	0.000	0.000	0.000	0.000
50	A	108	THR	0	0.014	0.017	22.029	-0.077	-0.077	0.000	0.000	0.000	0.000
51	A	109	ARG	1	0.861	0.930	25.237	-12.494	-12.494	0.000	0.000	0.000	0.000
52	A	110	GLN	0	0.031	0.023	18.006	-0.061	-0.061	0.000	0.000	0.000	0.000
53	A	111	ALA	0	0.044	0.026	22.923	-0.158	-0.158	0.000	0.000	0.000	0.000
54	A	112	SER	0	-0.046	-0.025	24.151	-0.434	-0.434	0.000	0.000	0.000	0.000
55	A	113	GLY	0	0.083	0.045	26.908	-0.340	-0.340	0.000	0.000	0.000	0.000
56	A	114	PHE	0	0.003	-0.019	21.486	-0.170	-0.170	0.000	0.000	0.000	0.000
57	A	115	ARG	1	0.795	0.910	26.159	-10.527	-10.527	0.000	0.000	0.000	0.000
58	A	116	ASP	-1	-0.904	-0.952	28.786	9.720	9.720	0.000	0.000	0.000	0.000
59	A	117	ASN	0	0.004	-0.002	27.781	-0.600	-0.600	0.000	0.000	0.000	0.000
60	A	118	TYR	0	0.005	0.008	26.527	0.013	0.013	0.000	0.000	0.000	0.000
61	A	119	GLN	0	-0.021	-0.020	29.791	-0.019	-0.019	0.000	0.000	0.000	0.000
62	A	120	GLU	-1	-0.828	-0.913	32.279	9.457	9.457	0.000	0.000	0.000	0.000
63	A	121	LEU	0	0.029	-0.012	25.794	0.047	0.047	0.000	0.000	0.000	0.000
64	A	122	LYS	1	0.851	0.944	28.882	-9.139	-9.139	0.000	0.000	0.000	0.000
65	A	123	GLU	-1	-0.890	-0.929	29.996	9.079	9.079	0.000	0.000	0.000	0.000
66	A	124	TYR	0	-0.076	-0.042	28.615	-0.142	-0.142	0.000	0.000	0.000	0.000
67	A	125	ALA	0	-0.046	-0.030	24.304	0.260	0.260	0.000	0.000	0.000	0.000
68	A	126	ALA	0	0.013	0.028	23.233	-0.241	-0.241	0.000	0.000	0.000	0.000
69	A	127	VAL	0	-0.017	-0.019	22.063	0.422	0.422	0.000	0.000	0.000	0.000
70	A	128	PHE	0	0.026	0.010	18.596	-0.314	-0.314	0.000	0.000	0.000	0.000
71	A	129	GLY	0	0.007	0.005	18.646	0.440	0.440	0.000	0.000	0.000	0.000
72	A	130	LEU	0	-0.007	0.007	11.287	0.096	0.096	0.000	0.000	0.000	0.000
73	A	131	SER	0	-0.012	-0.034	13.526	0.332	0.332	0.000	0.000	0.000	0.000
74	A	132	ALA	0	0.035	0.013	11.569	0.211	0.211	0.000	0.000	0.000	0.000
75	A	133	ASP	-1	-0.845	-0.884	13.259	17.473	17.473	0.000	0.000	0.000	0.000
76	A	134	SER	0	0.036	0.031	16.951	0.370	0.370	0.000	0.000	0.000	0.000
77	A	135	VAL	0	0.130	0.058	19.090	-0.225	-0.225	0.000	0.000	0.000	0.000
78	A	136	THR	0	0.000	0.000	21.274	-0.332	-0.332	0.000	0.000	0.000	0.000
79	A	137	SER	0	-0.024	-0.020	20.968	-0.822	-0.822	0.000	0.000	0.000	0.000
80	A	138	GLN	0	0.067	0.039	17.381	-1.296	-1.296	0.000	0.000	0.000	0.000
81	A	139	LYS	1	0.904	0.977	22.063	-11.826	-11.826	0.000	0.000	0.000	0.000
82	A	140	LYS	1	0.881	0.937	25.561	-11.905	-11.905	0.000	0.000	0.000	0.000
83	A	141	PHE	0	0.026	0.005	21.781	-0.524	-0.524	0.000	0.000	0.000	0.000
84	A	142	GLN	0	0.090	0.035	24.953	-0.376	-0.376	0.000	0.000	0.000	0.000
85	A	143	SER	0	-0.029	-0.035	26.517	-0.484	-0.484	0.000	0.000	0.000	0.000
86	A	144	LYS	1	0.844	0.936	29.175	-11.125	-11.125	0.000	0.000	0.000	0.000
87	A	145	GLN	0	-0.014	-0.002	27.277	-0.476	-0.476	0.000	0.000	0.000	0.000
88	A	146	ASN	0	-0.009	0.009	29.855	-0.168	-0.168	0.000	0.000	0.000	0.000
89	A	147	LEU	0	-0.028	-0.013	24.459	-0.126	-0.126	0.000	0.000	0.000	0.000
90	A	148	PRO	0	0.016	0.019	28.288	0.012	0.012	0.000	0.000	0.000	0.000
91	A	149	TYR	0	-0.037	-0.012	22.725	0.084	0.084	0.000	0.000	0.000	0.000
92	A	150	HIS	0	-0.017	-0.023	22.440	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	151	LEU	0	-0.093	-0.048	20.084	0.467	0.467	0.000	0.000	0.000	0.000
94	A	152	LEU	0	0.025	0.006	16.074	-0.217	-0.217	0.000	0.000	0.000	0.000
95	A	153	SER	0	-0.078	-0.053	16.109	0.800	0.800	0.000	0.000	0.000	0.000
96	A	154	ASP	-1	-0.716	-0.868	9.595	33.462	33.462	0.000	0.000	0.000	0.000
97	A	155	PRO	0	-0.019	-0.008	11.102	2.616	2.616	0.000	0.000	0.000	0.000
98	A	156	LYS	1	0.928	0.952	8.974	-25.574	-25.574	0.000	0.000	0.000	0.000
99	A	157	ARG	1	0.791	0.891	6.786	-36.747	-36.747	0.000	0.000	0.000	0.000
100	A	158	GLU	-1	-0.922	-0.956	5.490	42.637	42.739	-0.001	-0.001	-0.100	0.000
101	A	159	PHE	0	0.055	0.011	5.983	3.918	3.918	0.000	0.000	0.000	0.000
102	A	160	ILE	0	-0.041	-0.030	7.273	0.956	0.956	0.000	0.000	0.000	0.000
103	A	161	GLY	0	-0.036	-0.026	3.276	-1.598	-0.602	0.082	-0.451	-0.627	0.003
104	A	162	LEU	0	0.031	0.041	3.903	-1.509	-0.941	0.011	-0.138	-0.441	0.000
105	A	163	LEU	0	-0.038	-0.005	5.305	-4.952	-4.943	-0.001	0.000	-0.008	0.000
106	A	164	GLY	0	0.081	0.056	5.031	-3.934	-3.934	0.000	0.000	0.000	0.000
107	A	165	ALA	0	-0.058	-0.022	6.079	-2.860	-2.860	0.000	0.000	0.000	0.000
108	A	166	LYS	1	0.859	0.911	1.943	-138.571	-130.407	6.806	-8.601	-6.369	0.119
109	A	167	LYS	1	0.880	0.947	7.022	-24.587	-24.587	0.000	0.000	0.000	0.000
110	A	168	THR	0	0.001	-0.002	9.026	-1.262	-1.262	0.000	0.000	0.000	0.000
111	A	169	PRO	0	0.100	0.035	5.929	1.977	1.977	0.000	0.000	0.000	0.000
112	A	170	LEU	0	0.041	0.032	6.704	2.477	2.477	0.000	0.000	0.000	0.000
113	A	171	SER	0	-0.024	-0.009	9.437	-1.557	-1.557	0.000	0.000	0.000	0.000
114	A	172	GLY	0	-0.009	-0.003	10.632	0.270	0.270	0.000	0.000	0.000	0.000
115	A	173	SER	0	0.071	0.030	9.512	4.831	4.831	0.000	0.000	0.000	0.000
116	A	174	ILE	0	-0.057	-0.020	10.673	-3.177	-3.177	0.000	0.000	0.000	0.000
117	A	175	ARG	1	0.865	0.948	12.557	-16.124	-16.124	0.000	0.000	0.000	0.000
118	A	176	SER	0	0.002	-0.001	12.360	0.099	0.099	0.000	0.000	0.000	0.000
119	A	177	HIS	0	-0.063	-0.020	14.608	-0.138	-0.138	0.000	0.000	0.000	0.000
120	A	178	PHE	0	0.020	0.016	10.478	0.377	0.377	0.000	0.000	0.000	0.000
121	A	179	ILE	0	-0.011	0.010	15.380	-0.398	-0.398	0.000	0.000	0.000	0.000
122	A	180	PHE	0	0.047	0.018	12.583	0.337	0.337	0.000	0.000	0.000	0.000
123	A	181	VAL	0	0.018	-0.013	18.566	-0.723	-0.723	0.000	0.000	0.000	0.000
124	A	182	ASP	-1	-0.799	-0.869	21.040	11.974	11.974	0.000	0.000	0.000	0.000
125	A	183	GLY	0	0.003	-0.003	19.012	0.035	0.035	0.000	0.000	0.000	0.000
126	A	184	LYS	1	0.916	0.964	16.625	-13.947	-13.947	0.000	0.000	0.000	0.000
127	A	185	LEU	0	-0.028	0.010	11.643	-0.628	-0.628	0.000	0.000	0.000	0.000
128	A	186	LYS	1	0.956	0.985	15.716	-13.466	-13.466	0.000	0.000	0.000	0.000
129	A	187	PHE	0	0.015	0.003	17.383	-0.225	-0.225	0.000	0.000	0.000	0.000
130	A	188	LYS	1	0.856	0.903	7.448	-26.665	-26.665	0.000	0.000	0.000	0.000
131	A	189	ARG	1	0.764	0.867	14.090	-15.245	-15.245	0.000	0.000	0.000	0.000
132	A	190	VAL	0	0.099	0.036	9.553	-0.004	-0.004	0.000	0.000	0.000	0.000
133	A	191	LYS	1	0.906	0.952	12.786	-19.181	-19.181	0.000	0.000	0.000	0.000
134	A	192	ILE	0	-0.018	0.016	14.871	-1.118	-1.118	0.000	0.000	0.000	0.000
135	A	193	SER	0	-0.005	-0.015	18.362	0.390	0.390	0.000	0.000	0.000	0.000
136	A	194	PRO	0	-0.033	-0.044	21.251	0.296	0.296	0.000	0.000	0.000	0.000
137	A	195	GLU	-1	-0.749	-0.875	22.686	12.180	12.180	0.000	0.000	0.000	0.000
138	A	196	VAL	0	0.007	0.013	21.278	-0.216	-0.216	0.000	0.000	0.000	0.000
139	A	197	SER	0	-0.039	-0.018	19.632	0.044	0.044	0.000	0.000	0.000	0.000
140	A	198	VAL	0	0.026	0.021	21.307	-0.063	-0.063	0.000	0.000	0.000	0.000
141	A	199	ASN	0	-0.034	-0.032	24.531	-0.397	-0.397	0.000	0.000	0.000	0.000
142	A	200	ASP	-1	-0.842	-0.921	22.267	12.417	12.417	0.000	0.000	0.000	0.000
143	A	201	ALA	0	0.012	0.020	21.433	-0.026	-0.026	0.000	0.000	0.000	0.000
144	A	202	LYS	1	0.911	0.960	22.941	-9.925	-9.925	0.000	0.000	0.000	0.000
145	A	203	LYS	1	0.914	0.952	26.026	-11.010	-11.010	0.000	0.000	0.000	0.000
146	A	204	GLU	-1	-0.730	-0.850	20.680	14.308	14.308	0.000	0.000	0.000	0.000
147	A	205	VAL	0	-0.011	-0.009	23.594	-0.046	-0.046	0.000	0.000	0.000	0.000
148	A	206	LEU	0	-0.031	-0.023	25.560	-0.215	-0.215	0.000	0.000	0.000	0.000
149	A	207	GLU	-1	-0.933	-0.950	25.550	11.254	11.254	0.000	0.000	0.000	0.000
150	A	208	VAL	0	-0.071	-0.049	23.215	-0.147	-0.147	0.000	0.000	0.000	0.000
151	A	209	ALA	0	0.025	0.006	26.667	-0.158	-0.158	0.000	0.000	0.000	0.000
152	A	210	GLU	-1	-0.845	-0.911	29.734	8.499	8.499	0.000	0.000	0.000	0.000
153	A	211	LYS	1	0.939	0.973	25.068	-11.371	-11.371	0.000	0.000	0.000	0.000
154	A	212	PHE	0	-0.090	-0.054	26.383	0.000	0.000	0.000	0.000	0.000	0.000
155	A	213	LYS	1	0.835	0.928	31.551	-8.633	-8.633	0.000	0.000	0.000	0.000
156	A	214	GLU	-1	-1.001	-0.972	32.955	8.740	8.740	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:59:ASP)