FMO DATABASE

FMODB ID: R8YZ8

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	OptAll
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	-1588348.316317
FMO2-HF: Nuclear repulsion	1528315.905699
FMO2-HF: Total energy	-60032.410619
FMO2-MP2: Total energy	-60213.093875

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.
-207.776	-207.816	33.042	-17.46	-15.538	0.191

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 : -0.753 / q_NPA : -0.861

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	-0.012	-0.014	2.814	-2.888	1.144	0.656	-2.149	-2.539	-0.003
4	A	62	GLU	-1	-0.896	-0.923	2.715	36.166	37.672	0.115	-0.551	-1.070	-0.002
5	A	63	LEU	0	-0.003	0.003	4.419	-3.783	-3.621	0.000	-0.035	-0.126	0.000
6	A	64	GLU	-1	-0.824	-0.923	8.025	22.232	22.232	0.000	0.000	0.000	0.000
7	A	65	ILE	0	-0.082	-0.038	10.891	-0.476	-0.476	0.000	0.000	0.000	0.000
8	A	66	GLY	0	0.003	0.006	14.536	-0.701	-0.701	0.000	0.000	0.000	0.000
9	A	67	ASP	-1	-0.834	-0.901	10.740	21.452	21.452	0.000	0.000	0.000	0.000
10	A	68	PRO	0	-0.049	-0.031	13.290	-0.442	-0.442	0.000	0.000	0.000	0.000
11	A	69	ILE	0	-0.023	-0.007	12.470	1.648	1.648	0.000	0.000	0.000	0.000
12	A	70	PRO	0	-0.006	-0.005	9.106	-0.588	-0.588	0.000	0.000	0.000	0.000
13	A	71	ASP	-1	-0.833	-0.890	11.614	16.665	16.665	0.000	0.000	0.000	0.000
14	A	72	LEU	0	0.002	0.005	8.884	0.349	0.349	0.000	0.000	0.000	0.000
15	A	73	SER	0	-0.001	-0.015	13.495	-1.509	-1.509	0.000	0.000	0.000	0.000
16	A	74	LEU	0	-0.046	-0.008	11.058	1.565	1.565	0.000	0.000	0.000	0.000
17	A	75	LEU	0	-0.021	0.004	15.170	-1.159	-1.159	0.000	0.000	0.000	0.000
18	A	76	ASN	0	0.046	0.023	17.822	0.913	0.913	0.000	0.000	0.000	0.000
19	A	77	GLU	-1	-0.772	-0.888	20.356	14.142	14.142	0.000	0.000	0.000	0.000
20	A	78	ASP	-1	-0.841	-0.923	22.430	11.742	11.742	0.000	0.000	0.000	0.000
21	A	79	ASN	0	-0.060	-0.030	21.926	-0.113	-0.113	0.000	0.000	0.000	0.000
22	A	80	ASP	-1	-0.849	-0.909	22.790	12.662	12.662	0.000	0.000	0.000	0.000
23	A	81	SER	0	-0.034	-0.038	19.409	1.117	1.117	0.000	0.000	0.000	0.000
24	A	82	ILE	0	-0.016	-0.003	18.448	-0.534	-0.534	0.000	0.000	0.000	0.000
25	A	83	SER	0	0.011	0.010	17.331	0.981	0.981	0.000	0.000	0.000	0.000
26	A	84	LEU	0	0.033	-0.007	11.805	-0.882	-0.882	0.000	0.000	0.000	0.000
27	A	85	LYS	1	0.868	0.923	16.261	-16.559	-16.559	0.000	0.000	0.000	0.000
28	A	86	LYS	1	0.850	0.932	18.149	-13.371	-13.371	0.000	0.000	0.000	0.000
29	A	87	ILE	0	0.005	0.010	17.537	-0.748	-0.748	0.000	0.000	0.000	0.000
30	A	88	THR	0	-0.043	-0.032	17.772	-0.461	-0.461	0.000	0.000	0.000	0.000
31	A	89	GLU	-1	-0.864	-0.929	20.939	13.052	13.052	0.000	0.000	0.000	0.000
32	A	90	ASN	0	-0.022	-0.009	23.621	-0.574	-0.574	0.000	0.000	0.000	0.000
33	A	91	ASN	0	-0.052	-0.027	23.262	-0.769	-0.769	0.000	0.000	0.000	0.000
34	A	92	ARG	1	0.914	0.938	23.323	-10.426	-10.426	0.000	0.000	0.000	0.000
35	A	93	VAL	0	0.038	0.022	22.374	0.295	0.295	0.000	0.000	0.000	0.000
36	A	94	VAL	0	-0.002	0.003	18.566	-0.344	-0.344	0.000	0.000	0.000	0.000
37	A	95	VAL	0	-0.016	0.003	18.695	0.780	0.780	0.000	0.000	0.000	0.000
38	A	96	PHE	0	0.052	0.013	14.354	0.003	0.003	0.000	0.000	0.000	0.000
39	A	97	PHE	0	-0.011	-0.006	15.321	0.954	0.954	0.000	0.000	0.000	0.000
40	A	98	VAL	0	0.017	0.005	10.923	0.270	0.270	0.000	0.000	0.000	0.000
41	A	99	TYR	0	-0.056	-0.056	14.265	-1.118	-1.118	0.000	0.000	0.000	0.000
42	A	100	PRO	0	-0.070	-0.039	14.187	0.934	0.934	0.000	0.000	0.000	0.000
43	A	101	ARG	1	0.983	0.986	15.036	-18.448	-18.448	0.000	0.000	0.000	0.000
44	A	102	ALA	0	0.046	0.040	17.777	-0.744	-0.744	0.000	0.000	0.000	0.000
45	A	103	SER	0	-0.027	-0.017	20.558	-0.375	-0.375	0.000	0.000	0.000	0.000
46	A	104	THR	0	0.014	0.020	21.073	-0.451	-0.451	0.000	0.000	0.000	0.000
47	A	105	PRO	0	0.055	0.019	23.898	0.114	0.114	0.000	0.000	0.000	0.000
48	A	106	GLY	0	-0.027	0.003	22.525	-0.313	-0.313	0.000	0.000	0.000	0.000
49	A	107	SER	0	0.039	-0.027	19.627	0.111	0.111	0.000	0.000	0.000	0.000
50	A	108	THR	0	-0.007	-0.009	21.596	-0.147	-0.147	0.000	0.000	0.000	0.000
51	A	109	ARG	1	0.867	0.939	25.197	-12.659	-12.659	0.000	0.000	0.000	0.000
52	A	110	GLN	0	0.051	0.044	17.573	-0.185	-0.185	0.000	0.000	0.000	0.000
53	A	111	ALA	0	0.037	0.021	22.520	-0.181	-0.181	0.000	0.000	0.000	0.000
54	A	112	SER	0	-0.023	-0.025	23.843	-0.376	-0.376	0.000	0.000	0.000	0.000
55	A	113	GLY	0	0.066	0.030	26.935	-0.319	-0.319	0.000	0.000	0.000	0.000
56	A	114	PHE	0	0.011	-0.007	20.835	-0.185	-0.185	0.000	0.000	0.000	0.000
57	A	115	ARG	1	0.743	0.835	25.698	-10.798	-10.798	0.000	0.000	0.000	0.000
58	A	116	ASP	-1	-0.833	-0.889	28.322	10.012	10.012	0.000	0.000	0.000	0.000
59	A	117	ASN	0	-0.002	-0.008	28.238	-0.532	-0.532	0.000	0.000	0.000	0.000
60	A	118	TYR	0	-0.009	0.000	25.647	-0.053	-0.053	0.000	0.000	0.000	0.000
61	A	119	GLN	0	-0.013	-0.011	29.206	0.013	0.013	0.000	0.000	0.000	0.000
62	A	120	GLU	-1	-0.838	-0.900	31.681	9.667	9.667	0.000	0.000	0.000	0.000
63	A	121	LEU	0	0.025	-0.018	25.639	0.056	0.056	0.000	0.000	0.000	0.000
64	A	122	LYS	1	0.792	0.887	28.282	-9.311	-9.311	0.000	0.000	0.000	0.000
65	A	123	GLU	-1	-0.830	-0.881	29.298	9.317	9.317	0.000	0.000	0.000	0.000
66	A	124	TYR	0	-0.074	-0.036	28.342	-0.208	-0.208	0.000	0.000	0.000	0.000
67	A	125	ALA	0	-0.030	-0.021	23.781	0.286	0.286	0.000	0.000	0.000	0.000
68	A	126	ALA	0	0.015	0.029	22.511	-0.200	-0.200	0.000	0.000	0.000	0.000
69	A	127	VAL	0	-0.022	-0.026	21.330	0.455	0.455	0.000	0.000	0.000	0.000
70	A	128	PHE	0	0.025	0.013	17.967	-0.356	-0.356	0.000	0.000	0.000	0.000
71	A	129	GLY	0	-0.005	0.006	17.800	0.308	0.308	0.000	0.000	0.000	0.000
72	A	130	LEU	0	-0.009	0.002	10.549	0.040	0.040	0.000	0.000	0.000	0.000
73	A	131	SER	0	-0.008	-0.044	12.778	0.476	0.476	0.000	0.000	0.000	0.000
74	A	132	ALA	0	0.038	0.017	11.444	0.189	0.189	0.000	0.000	0.000	0.000
75	A	133	ASP	-1	-0.813	-0.859	12.951	18.257	18.257	0.000	0.000	0.000	0.000
76	A	134	SER	0	0.073	0.054	16.657	0.235	0.235	0.000	0.000	0.000	0.000
77	A	135	VAL	0	0.093	0.052	18.486	-0.431	-0.431	0.000	0.000	0.000	0.000
78	A	136	THR	0	0.037	0.017	20.557	-0.431	-0.431	0.000	0.000	0.000	0.000
79	A	137	SER	0	-0.086	-0.050	20.466	-0.966	-0.966	0.000	0.000	0.000	0.000
80	A	138	GLN	0	0.053	0.023	16.641	-1.463	-1.463	0.000	0.000	0.000	0.000
81	A	139	LYS	1	0.840	0.926	21.459	-12.542	-12.542	0.000	0.000	0.000	0.000
82	A	140	LYS	1	0.924	0.977	24.982	-12.453	-12.453	0.000	0.000	0.000	0.000
83	A	141	PHE	0	0.018	0.018	21.207	-0.563	-0.563	0.000	0.000	0.000	0.000
84	A	142	GLN	0	0.072	0.039	24.106	-0.542	-0.542	0.000	0.000	0.000	0.000
85	A	143	SER	0	-0.018	-0.029	25.817	-0.529	-0.529	0.000	0.000	0.000	0.000
86	A	144	LYS	1	0.810	0.893	28.447	-11.378	-11.378	0.000	0.000	0.000	0.000
87	A	145	GLN	0	0.021	0.001	26.948	-0.468	-0.468	0.000	0.000	0.000	0.000
88	A	146	ASN	0	-0.012	0.009	29.196	-0.223	-0.223	0.000	0.000	0.000	0.000
89	A	147	LEU	0	0.009	0.021	23.930	-0.183	-0.183	0.000	0.000	0.000	0.000
90	A	148	PRO	0	-0.002	0.013	27.760	0.104	0.104	0.000	0.000	0.000	0.000
91	A	149	TYR	0	-0.027	-0.031	21.994	0.136	0.136	0.000	0.000	0.000	0.000
92	A	150	HIS	0	0.004	-0.007	21.233	0.007	0.007	0.000	0.000	0.000	0.000
93	A	151	LEU	0	-0.086	-0.047	19.137	0.479	0.479	0.000	0.000	0.000	0.000
94	A	152	LEU	0	0.026	0.009	15.060	-0.162	-0.162	0.000	0.000	0.000	0.000
95	A	153	SER	0	-0.077	-0.061	15.366	0.862	0.862	0.000	0.000	0.000	0.000
96	A	154	ASP	-1	-0.713	-0.872	8.650	37.631	37.631	0.000	0.000	0.000	0.000
97	A	155	PRO	0	-0.029	-0.018	10.549	2.686	2.686	0.000	0.000	0.000	0.000
98	A	156	LYS	1	0.834	0.907	8.281	-31.180	-31.180	0.000	0.000	0.000	0.000
99	A	157	ARG	1	0.770	0.871	6.566	-39.038	-39.038	0.000	0.000	0.000	0.000
100	A	158	GLU	-1	-0.833	-0.905	4.850	48.384	48.556	-0.001	-0.005	-0.166	0.000
101	A	159	PHE	0	0.042	0.011	4.960	5.832	5.887	-0.001	0.000	-0.054	0.000
102	A	160	ILE	0	-0.023	-0.013	6.759	0.693	0.693	0.000	0.000	0.000	0.000
103	A	161	GLY	0	-0.030	-0.020	2.457	-4.695	-3.312	2.023	-1.716	-1.689	0.018
104	A	162	LEU	0	0.042	0.027	3.270	-7.921	-8.020	0.159	0.983	-1.042	0.003
105	A	163	LEU	0	-0.042	-0.012	4.780	-6.798	-6.776	-0.001	-0.005	-0.016	0.000
106	A	164	GLY	0	0.061	0.056	4.530	-4.723	-4.717	-0.001	-0.004	-0.001	0.000
107	A	165	ALA	0	-0.057	-0.033	5.543	-4.385	-4.385	0.000	0.000	0.000	0.000
108	A	166	LYS	1	0.803	0.883	1.694	-165.904	-173.309	30.094	-13.972	-8.717	0.175
109	A	167	LYS	1	0.873	0.939	7.068	-24.991	-24.991	0.000	0.000	0.000	0.000
110	A	168	THR	0	-0.011	-0.014	8.561	-2.543	-2.543	0.000	0.000	0.000	0.000
111	A	169	PRO	0	0.102	0.044	4.992	2.752	2.878	-0.001	-0.006	-0.118	0.000
112	A	170	LEU	0	0.032	0.037	5.992	2.277	2.277	0.000	0.000	0.000	0.000
113	A	171	SER	0	-0.006	-0.010	8.971	-0.882	-0.882	0.000	0.000	0.000	0.000
114	A	172	GLY	0	0.015	0.016	10.427	0.251	0.251	0.000	0.000	0.000	0.000
115	A	173	SER	0	0.060	0.026	9.593	5.475	5.475	0.000	0.000	0.000	0.000
116	A	174	ILE	0	-0.054	-0.020	10.291	-3.524	-3.524	0.000	0.000	0.000	0.000
117	A	175	ARG	1	0.825	0.924	12.297	-16.723	-16.723	0.000	0.000	0.000	0.000
118	A	176	SER	0	0.002	-0.002	11.990	-0.119	-0.119	0.000	0.000	0.000	0.000
119	A	177	HIS	0	-0.045	-0.017	14.186	-0.245	-0.245	0.000	0.000	0.000	0.000
120	A	178	PHE	0	0.025	0.026	9.986	0.426	0.426	0.000	0.000	0.000	0.000
121	A	179	ILE	0	-0.014	0.001	14.526	-0.528	-0.528	0.000	0.000	0.000	0.000
122	A	180	PHE	0	0.051	0.029	11.624	0.205	0.205	0.000	0.000	0.000	0.000
123	A	181	VAL	0	0.026	-0.009	17.672	-0.754	-0.754	0.000	0.000	0.000	0.000
124	A	182	ASP	-1	-0.784	-0.872	20.484	12.114	12.114	0.000	0.000	0.000	0.000
125	A	183	GLY	0	0.018	0.007	19.126	-0.100	-0.100	0.000	0.000	0.000	0.000
126	A	184	LYS	1	0.880	0.934	16.177	-13.199	-13.199	0.000	0.000	0.000	0.000
127	A	185	LEU	0	-0.036	0.010	11.030	-0.619	-0.619	0.000	0.000	0.000	0.000
128	A	186	LYS	1	0.846	0.906	15.161	-13.561	-13.561	0.000	0.000	0.000	0.000
129	A	187	PHE	0	0.016	-0.004	16.618	-0.530	-0.530	0.000	0.000	0.000	0.000
130	A	188	LYS	1	0.823	0.873	7.182	-26.460	-26.460	0.000	0.000	0.000	0.000
131	A	189	ARG	1	0.764	0.870	13.287	-15.178	-15.178	0.000	0.000	0.000	0.000
132	A	190	VAL	0	0.089	0.026	9.261	-0.065	-0.065	0.000	0.000	0.000	0.000
133	A	191	LYS	1	0.899	0.951	12.272	-19.680	-19.680	0.000	0.000	0.000	0.000
134	A	192	ILE	0	-0.023	0.016	14.378	-1.271	-1.271	0.000	0.000	0.000	0.000
135	A	193	SER	0	-0.013	-0.039	17.887	0.344	0.344	0.000	0.000	0.000	0.000
136	A	194	PRO	0	-0.049	-0.045	20.859	0.345	0.345	0.000	0.000	0.000	0.000
137	A	195	GLU	-1	-0.723	-0.828	22.394	12.663	12.663	0.000	0.000	0.000	0.000
138	A	196	VAL	0	0.029	0.020	20.672	-0.226	-0.226	0.000	0.000	0.000	0.000
139	A	197	SER	0	-0.020	-0.012	18.903	0.115	0.115	0.000	0.000	0.000	0.000
140	A	198	VAL	0	0.009	0.011	20.722	-0.040	-0.040	0.000	0.000	0.000	0.000
141	A	199	ASN	0	-0.035	-0.036	23.981	-0.565	-0.565	0.000	0.000	0.000	0.000
142	A	200	ASP	-1	-0.805	-0.865	21.796	12.336	12.336	0.000	0.000	0.000	0.000
143	A	201	ALA	0	0.013	0.016	20.691	-0.140	-0.140	0.000	0.000	0.000	0.000
144	A	202	LYS	1	0.860	0.924	22.185	-10.267	-10.267	0.000	0.000	0.000	0.000
145	A	203	LYS	1	0.847	0.897	25.281	-11.725	-11.725	0.000	0.000	0.000	0.000
146	A	204	GLU	-1	-0.784	-0.878	19.768	14.854	14.854	0.000	0.000	0.000	0.000
147	A	205	VAL	0	0.003	-0.009	23.011	-0.022	-0.022	0.000	0.000	0.000	0.000
148	A	206	LEU	0	0.002	0.001	24.875	-0.232	-0.232	0.000	0.000	0.000	0.000
149	A	207	GLU	-1	-0.853	-0.898	24.386	11.918	11.918	0.000	0.000	0.000	0.000
150	A	208	VAL	0	-0.022	-0.026	22.528	-0.138	-0.138	0.000	0.000	0.000	0.000
151	A	209	ALA	0	-0.014	-0.006	25.950	-0.143	-0.143	0.000	0.000	0.000	0.000
152	A	210	GLU	-1	-0.823	-0.880	28.968	8.616	8.616	0.000	0.000	0.000	0.000
153	A	211	LYS	1	0.895	0.949	24.470	-11.883	-11.883	0.000	0.000	0.000	0.000
154	A	212	PHE	0	-0.111	-0.057	25.854	-0.034	-0.034	0.000	0.000	0.000	0.000
155	A	213	LYS	1	0.811	0.892	31.275	-8.827	-8.827	0.000	0.000	0.000	0.000
156	A	214	GLU	-1	-1.007	-0.977	32.767	8.739	8.739	0.000	0.000	0.000	0.000

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