FMO DATABASE

FMODB ID: ZVNJN

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	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	-1588779.04537
FMO2-HF: Nuclear repulsion	1528746.972325
FMO2-HF: Total energy	-60032.073045
FMO2-MP2: Total energy	-60212.883155

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.
-194.14	-193.749	28.775	-16.423	-12.742	0.179

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 : -0.802 / q_NPA : -0.889

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	-0.034	-0.029	2.841	-1.164	2.149	0.254	-1.564	-2.004	0.001
4	A	62	GLU	-1	-0.901	-0.926	3.252	36.195	37.013	0.018	-0.222	-0.614	0.000
5	A	63	LEU	0	-0.004	-0.006	4.773	-3.885	-3.778	-0.001	-0.012	-0.095	0.000
6	A	64	GLU	-1	-0.824	-0.911	8.333	22.879	22.879	0.000	0.000	0.000	0.000
7	A	65	ILE	0	-0.053	-0.033	11.090	-0.447	-0.447	0.000	0.000	0.000	0.000
8	A	66	GLY	0	-0.026	-0.015	14.719	-0.377	-0.377	0.000	0.000	0.000	0.000
9	A	67	ASP	-1	-0.832	-0.903	10.908	21.516	21.516	0.000	0.000	0.000	0.000
10	A	68	PRO	0	-0.068	-0.038	13.355	-0.435	-0.435	0.000	0.000	0.000	0.000
11	A	69	ILE	0	-0.030	-0.013	12.623	1.712	1.712	0.000	0.000	0.000	0.000
12	A	70	PRO	0	0.005	0.003	9.311	-0.602	-0.602	0.000	0.000	0.000	0.000
13	A	71	ASP	-1	-0.828	-0.891	11.771	16.500	16.500	0.000	0.000	0.000	0.000
14	A	72	LEU	0	0.001	0.007	8.896	0.269	0.269	0.000	0.000	0.000	0.000
15	A	73	SER	0	-0.028	-0.033	13.587	-1.816	-1.816	0.000	0.000	0.000	0.000
16	A	74	LEU	0	-0.026	-0.004	11.520	1.283	1.283	0.000	0.000	0.000	0.000
17	A	75	LEU	0	-0.007	0.014	15.674	-1.113	-1.113	0.000	0.000	0.000	0.000
18	A	76	ASN	0	0.092	0.043	18.251	0.932	0.932	0.000	0.000	0.000	0.000
19	A	77	GLU	-1	-0.799	-0.897	20.815	13.723	13.723	0.000	0.000	0.000	0.000
20	A	78	ASP	-1	-0.845	-0.930	23.063	11.482	11.482	0.000	0.000	0.000	0.000
21	A	79	ASN	0	-0.084	-0.039	22.484	0.098	0.098	0.000	0.000	0.000	0.000
22	A	80	ASP	-1	-0.839	-0.904	23.539	12.207	12.207	0.000	0.000	0.000	0.000
23	A	81	SER	0	-0.051	-0.034	19.802	1.116	1.116	0.000	0.000	0.000	0.000
24	A	82	ILE	0	-0.025	-0.016	18.827	-0.709	-0.709	0.000	0.000	0.000	0.000
25	A	83	SER	0	0.013	0.016	17.738	0.963	0.963	0.000	0.000	0.000	0.000
26	A	84	LEU	0	0.033	-0.009	12.238	-0.910	-0.910	0.000	0.000	0.000	0.000
27	A	85	LYS	1	0.869	0.929	16.650	-16.373	-16.373	0.000	0.000	0.000	0.000
28	A	86	LYS	1	0.858	0.925	18.487	-13.146	-13.146	0.000	0.000	0.000	0.000
29	A	87	ILE	0	0.001	-0.001	18.042	-0.710	-0.710	0.000	0.000	0.000	0.000
30	A	88	THR	0	-0.035	-0.020	17.891	-0.289	-0.289	0.000	0.000	0.000	0.000
31	A	89	GLU	-1	-0.868	-0.918	20.983	13.041	13.041	0.000	0.000	0.000	0.000
32	A	90	ASN	0	-0.037	-0.018	23.870	-0.626	-0.626	0.000	0.000	0.000	0.000
33	A	91	ASN	0	-0.048	-0.024	23.797	-0.852	-0.852	0.000	0.000	0.000	0.000
34	A	92	ARG	1	0.905	0.933	23.962	-10.561	-10.561	0.000	0.000	0.000	0.000
35	A	93	VAL	0	0.031	0.018	22.741	0.457	0.457	0.000	0.000	0.000	0.000
36	A	94	VAL	0	-0.014	0.000	18.978	-0.312	-0.312	0.000	0.000	0.000	0.000
37	A	95	VAL	0	0.002	0.012	19.060	0.590	0.590	0.000	0.000	0.000	0.000
38	A	96	PHE	0	0.039	0.012	14.690	0.001	0.001	0.000	0.000	0.000	0.000
39	A	97	PHE	0	-0.015	-0.013	15.902	0.663	0.663	0.000	0.000	0.000	0.000
40	A	98	VAL	0	0.030	0.007	11.403	0.160	0.160	0.000	0.000	0.000	0.000
41	A	99	TYR	0	-0.047	-0.053	14.605	-0.956	-0.956	0.000	0.000	0.000	0.000
42	A	100	PRO	0	-0.069	-0.043	14.610	0.821	0.821	0.000	0.000	0.000	0.000
43	A	101	ARG	1	0.981	0.980	15.652	-18.571	-18.571	0.000	0.000	0.000	0.000
44	A	102	ALA	0	0.051	0.055	18.396	-0.834	-0.834	0.000	0.000	0.000	0.000
45	A	103	SER	0	-0.024	-0.009	21.082	-0.382	-0.382	0.000	0.000	0.000	0.000
46	A	104	THR	0	0.009	0.007	21.769	-0.249	-0.249	0.000	0.000	0.000	0.000
47	A	105	PRO	0	0.074	0.032	24.549	0.055	0.055	0.000	0.000	0.000	0.000
48	A	106	GLY	0	-0.033	-0.011	22.730	-0.147	-0.147	0.000	0.000	0.000	0.000
49	A	107	SER	0	0.002	-0.046	20.145	0.162	0.162	0.000	0.000	0.000	0.000
50	A	108	THR	0	0.012	0.006	22.024	-0.077	-0.077	0.000	0.000	0.000	0.000
51	A	109	ARG	1	0.878	0.947	25.484	-12.590	-12.590	0.000	0.000	0.000	0.000
52	A	110	GLN	0	0.032	0.032	17.913	-0.057	-0.057	0.000	0.000	0.000	0.000
53	A	111	ALA	0	0.045	0.025	22.767	-0.161	-0.161	0.000	0.000	0.000	0.000
54	A	112	SER	0	-0.027	-0.033	24.014	-0.400	-0.400	0.000	0.000	0.000	0.000
55	A	113	GLY	0	0.060	0.035	26.792	-0.369	-0.369	0.000	0.000	0.000	0.000
56	A	114	PHE	0	0.012	-0.011	21.175	-0.220	-0.220	0.000	0.000	0.000	0.000
57	A	115	ARG	1	0.769	0.880	25.961	-10.683	-10.683	0.000	0.000	0.000	0.000
58	A	116	ASP	-1	-0.863	-0.915	28.568	9.925	9.925	0.000	0.000	0.000	0.000
59	A	117	ASN	0	-0.023	-0.025	28.167	-0.523	-0.523	0.000	0.000	0.000	0.000
60	A	118	TYR	0	0.025	0.021	26.129	0.030	0.030	0.000	0.000	0.000	0.000
61	A	119	GLN	0	-0.003	-0.007	29.506	0.000	0.000	0.000	0.000	0.000	0.000
62	A	120	GLU	-1	-0.804	-0.884	31.949	9.583	9.583	0.000	0.000	0.000	0.000
63	A	121	LEU	0	0.040	-0.010	25.665	0.048	0.048	0.000	0.000	0.000	0.000
64	A	122	LYS	1	0.790	0.899	28.530	-9.253	-9.253	0.000	0.000	0.000	0.000
65	A	123	GLU	-1	-0.840	-0.889	29.628	9.205	9.205	0.000	0.000	0.000	0.000
66	A	124	TYR	0	-0.070	-0.043	28.433	-0.172	-0.172	0.000	0.000	0.000	0.000
67	A	125	ALA	0	-0.047	-0.027	23.971	0.270	0.270	0.000	0.000	0.000	0.000
68	A	126	ALA	0	0.014	0.030	22.872	-0.239	-0.239	0.000	0.000	0.000	0.000
69	A	127	VAL	0	-0.015	-0.023	21.696	0.439	0.439	0.000	0.000	0.000	0.000
70	A	128	PHE	0	0.031	0.012	18.311	-0.342	-0.342	0.000	0.000	0.000	0.000
71	A	129	GLY	0	0.006	0.008	18.401	0.463	0.463	0.000	0.000	0.000	0.000
72	A	130	LEU	0	-0.011	0.003	11.132	0.124	0.124	0.000	0.000	0.000	0.000
73	A	131	SER	0	-0.010	-0.041	13.377	0.288	0.288	0.000	0.000	0.000	0.000
74	A	132	ALA	0	0.037	0.015	11.527	0.197	0.197	0.000	0.000	0.000	0.000
75	A	133	ASP	-1	-0.846	-0.879	13.157	17.948	17.948	0.000	0.000	0.000	0.000
76	A	134	SER	0	0.044	0.037	16.770	0.352	0.352	0.000	0.000	0.000	0.000
77	A	135	VAL	0	0.132	0.058	18.926	-0.216	-0.216	0.000	0.000	0.000	0.000
78	A	136	THR	0	0.020	0.011	21.027	-0.463	-0.463	0.000	0.000	0.000	0.000
79	A	137	SER	0	-0.062	-0.036	20.837	-0.838	-0.838	0.000	0.000	0.000	0.000
80	A	138	GLN	0	0.070	0.042	17.130	-1.345	-1.345	0.000	0.000	0.000	0.000
81	A	139	LYS	1	0.856	0.940	21.867	-12.276	-12.276	0.000	0.000	0.000	0.000
82	A	140	LYS	1	0.905	0.961	25.331	-12.232	-12.232	0.000	0.000	0.000	0.000
83	A	141	PHE	0	0.026	0.018	21.556	-0.557	-0.557	0.000	0.000	0.000	0.000
84	A	142	GLN	0	0.073	0.031	24.684	-0.429	-0.429	0.000	0.000	0.000	0.000
85	A	143	SER	0	-0.006	-0.022	26.298	-0.502	-0.502	0.000	0.000	0.000	0.000
86	A	144	LYS	1	0.812	0.893	29.135	-11.258	-11.258	0.000	0.000	0.000	0.000
87	A	145	GLN	0	-0.002	-0.002	27.308	-0.422	-0.422	0.000	0.000	0.000	0.000
88	A	146	ASN	0	-0.023	0.000	29.698	-0.224	-0.224	0.000	0.000	0.000	0.000
89	A	147	LEU	0	-0.018	-0.006	24.323	-0.129	-0.129	0.000	0.000	0.000	0.000
90	A	148	PRO	0	0.014	0.017	28.113	0.030	0.030	0.000	0.000	0.000	0.000
91	A	149	TYR	0	-0.044	-0.017	22.513	0.090	0.090	0.000	0.000	0.000	0.000
92	A	150	HIS	0	-0.012	-0.025	21.967	-0.041	-0.041	0.000	0.000	0.000	0.000
93	A	151	LEU	0	-0.094	-0.051	19.790	0.475	0.475	0.000	0.000	0.000	0.000
94	A	152	LEU	0	0.018	0.005	15.747	-0.252	-0.252	0.000	0.000	0.000	0.000
95	A	153	SER	0	-0.077	-0.061	15.857	0.786	0.786	0.000	0.000	0.000	0.000
96	A	154	ASP	-1	-0.721	-0.872	9.116	36.003	36.003	0.000	0.000	0.000	0.000
97	A	155	PRO	0	-0.013	-0.005	10.906	2.757	2.757	0.000	0.000	0.000	0.000
98	A	156	LYS	1	0.926	0.960	8.924	-27.257	-27.257	0.000	0.000	0.000	0.000
99	A	157	ARG	1	0.777	0.877	6.773	-38.673	-38.673	0.000	0.000	0.000	0.000
100	A	158	GLU	-1	-0.917	-0.958	5.239	45.738	45.851	-0.001	-0.002	-0.109	0.000
101	A	159	PHE	0	0.057	0.015	5.474	4.867	4.907	-0.001	0.000	-0.039	0.000
102	A	160	ILE	0	-0.039	-0.029	7.093	1.046	1.046	0.000	0.000	0.000	0.000
103	A	161	GLY	0	-0.034	-0.029	2.979	-2.902	-1.518	0.268	-0.774	-0.877	0.007
104	A	162	LEU	0	0.039	0.039	3.667	-2.898	-2.162	0.044	-0.126	-0.653	0.001
105	A	163	LEU	0	-0.045	-0.010	5.047	-6.178	-6.178	-0.001	-0.002	0.003	0.000
106	A	164	GLY	0	0.080	0.057	4.805	-4.337	-4.337	0.000	0.000	0.000	0.000
107	A	165	ALA	0	-0.063	-0.026	5.837	-3.346	-3.346	0.000	0.000	0.000	0.000
108	A	166	LYS	1	0.807	0.881	1.680	-163.598	-169.718	28.195	-13.721	-8.354	0.170
109	A	167	LYS	1	0.884	0.949	7.262	-25.182	-25.182	0.000	0.000	0.000	0.000
110	A	168	THR	0	-0.003	-0.002	9.164	-1.448	-1.448	0.000	0.000	0.000	0.000
111	A	169	PRO	0	0.104	0.036	5.370	2.298	2.298	0.000	0.000	0.000	0.000
112	A	170	LEU	0	0.029	0.031	6.296	2.796	2.796	0.000	0.000	0.000	0.000
113	A	171	SER	0	-0.022	-0.010	9.044	-1.550	-1.550	0.000	0.000	0.000	0.000
114	A	172	GLY	0	0.007	0.006	10.608	0.238	0.238	0.000	0.000	0.000	0.000
115	A	173	SER	0	0.068	0.028	9.730	5.111	5.111	0.000	0.000	0.000	0.000
116	A	174	ILE	0	-0.059	-0.023	11.028	-3.382	-3.382	0.000	0.000	0.000	0.000
117	A	175	ARG	1	0.852	0.940	12.791	-16.410	-16.410	0.000	0.000	0.000	0.000
118	A	176	SER	0	-0.004	-0.008	12.385	-0.007	-0.007	0.000	0.000	0.000	0.000
119	A	177	HIS	0	-0.058	-0.017	14.561	-0.145	-0.145	0.000	0.000	0.000	0.000
120	A	178	PHE	0	0.031	0.022	10.412	0.408	0.408	0.000	0.000	0.000	0.000
121	A	179	ILE	0	-0.021	0.004	15.091	-0.405	-0.405	0.000	0.000	0.000	0.000
122	A	180	PHE	0	0.054	0.023	12.395	0.271	0.271	0.000	0.000	0.000	0.000
123	A	181	VAL	0	0.035	-0.005	18.334	-0.759	-0.759	0.000	0.000	0.000	0.000
124	A	182	ASP	-1	-0.819	-0.890	21.069	12.131	12.131	0.000	0.000	0.000	0.000
125	A	183	GLY	0	0.007	-0.008	19.032	-0.012	-0.012	0.000	0.000	0.000	0.000
126	A	184	LYS	1	0.895	0.959	16.649	-13.363	-13.363	0.000	0.000	0.000	0.000
127	A	185	LEU	0	-0.033	0.008	11.414	-0.642	-0.642	0.000	0.000	0.000	0.000
128	A	186	LYS	1	0.852	0.926	15.507	-13.543	-13.543	0.000	0.000	0.000	0.000
129	A	187	PHE	0	0.014	0.000	17.306	-0.350	-0.350	0.000	0.000	0.000	0.000
130	A	188	LYS	1	0.826	0.878	7.736	-26.461	-26.461	0.000	0.000	0.000	0.000
131	A	189	ARG	1	0.757	0.865	14.047	-15.312	-15.312	0.000	0.000	0.000	0.000
132	A	190	VAL	0	0.095	0.035	9.652	0.067	0.067	0.000	0.000	0.000	0.000
133	A	191	LYS	1	0.912	0.954	12.751	-19.364	-19.364	0.000	0.000	0.000	0.000
134	A	192	ILE	0	-0.024	0.015	14.834	-1.198	-1.198	0.000	0.000	0.000	0.000
135	A	193	SER	0	-0.024	-0.040	18.301	0.380	0.380	0.000	0.000	0.000	0.000
136	A	194	PRO	0	-0.025	-0.039	21.238	0.313	0.313	0.000	0.000	0.000	0.000
137	A	195	GLU	-1	-0.718	-0.832	22.742	12.511	12.511	0.000	0.000	0.000	0.000
138	A	196	VAL	0	0.025	0.021	21.279	-0.247	-0.247	0.000	0.000	0.000	0.000
139	A	197	SER	0	-0.035	-0.015	19.484	0.089	0.089	0.000	0.000	0.000	0.000
140	A	198	VAL	0	0.009	0.014	21.201	-0.095	-0.095	0.000	0.000	0.000	0.000
141	A	199	ASN	0	-0.035	-0.035	24.439	-0.509	-0.509	0.000	0.000	0.000	0.000
142	A	200	ASP	-1	-0.803	-0.892	22.172	12.381	12.381	0.000	0.000	0.000	0.000
143	A	201	ALA	0	0.014	0.023	21.267	-0.036	-0.036	0.000	0.000	0.000	0.000
144	A	202	LYS	1	0.854	0.917	22.696	-10.131	-10.131	0.000	0.000	0.000	0.000
145	A	203	LYS	1	0.862	0.914	25.862	-11.604	-11.604	0.000	0.000	0.000	0.000
146	A	204	GLU	-1	-0.774	-0.871	20.289	14.662	14.662	0.000	0.000	0.000	0.000
147	A	205	VAL	0	0.004	-0.003	23.339	-0.042	-0.042	0.000	0.000	0.000	0.000
148	A	206	LEU	0	-0.019	-0.014	25.266	-0.217	-0.217	0.000	0.000	0.000	0.000
149	A	207	GLU	-1	-0.850	-0.900	25.197	11.676	11.676	0.000	0.000	0.000	0.000
150	A	208	VAL	0	-0.050	-0.038	23.101	-0.156	-0.156	0.000	0.000	0.000	0.000
151	A	209	ALA	0	-0.010	-0.007	26.509	-0.165	-0.165	0.000	0.000	0.000	0.000
152	A	210	GLU	-1	-0.814	-0.878	29.484	8.539	8.539	0.000	0.000	0.000	0.000
153	A	211	LYS	1	0.948	0.979	24.802	-11.707	-11.707	0.000	0.000	0.000	0.000
154	A	212	PHE	0	-0.090	-0.053	26.120	-0.007	-0.007	0.000	0.000	0.000	0.000
155	A	213	LYS	1	0.796	0.890	31.369	-8.769	-8.769	0.000	0.000	0.000	0.000
156	A	214	GLU	-1	-1.001	-0.971	33.385	8.643	8.643	0.000	0.000	0.000	0.000

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