FMO DATABASE

FMODB ID: YVVK2

Calculation Name: 3ER0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ER0

Chain ID: A

ChEMBL ID:

UniProt ID: P23301

Base Structure: X-ray

Registration Date: 2023-09-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	146
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1157659.896305
FMO2-HF: Nuclear repulsion	1100531.124204
FMO2-HF: Total energy	-57128.772101
FMO2-MP2: Total energy	-57289.885909

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:12:ASP)

Summations of interaction energy for fragment #1(A:12: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.
56.507	58.994	-0.008	-1.338	-1.141	0.005

Interaction energy analysis for fragmet #1(A:12:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.927 / q_NPA : -0.966

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	14	GLY	0	0.039	0.012	3.862	0.977	3.464	-0.008	-1.338	-1.141	0.005
4	A	15	SER	0	0.015	-0.017	6.562	-1.276	-1.276	0.000	0.000	0.000	0.000
5	A	16	SER	0	-0.054	0.017	8.936	-1.696	-1.696	0.000	0.000	0.000	0.000
6	A	17	ALA	0	-0.052	-0.005	12.727	0.009	0.009	0.000	0.000	0.000	0.000
7	A	18	THR	0	-0.032	-0.073	13.327	1.201	1.201	0.000	0.000	0.000	0.000
8	A	19	TYR	0	0.027	-0.014	15.892	-0.391	-0.391	0.000	0.000	0.000	0.000
9	A	20	PRO	0	0.008	0.008	16.204	-0.673	-0.673	0.000	0.000	0.000	0.000
10	A	21	MET	0	-0.015	0.002	18.824	-0.723	-0.723	0.000	0.000	0.000	0.000
11	A	22	GLN	0	0.031	0.022	21.956	-0.072	-0.072	0.000	0.000	0.000	0.000
12	A	23	CYS	0	-0.016	-0.009	23.532	-0.217	-0.217	0.000	0.000	0.000	0.000
13	A	24	SER	0	-0.048	-0.036	24.870	-0.326	-0.326	0.000	0.000	0.000	0.000
14	A	25	ALA	0	-0.035	0.000	27.023	-0.376	-0.376	0.000	0.000	0.000	0.000
15	A	26	LEU	0	0.007	0.024	23.201	-0.178	-0.178	0.000	0.000	0.000	0.000
16	A	27	ARG	1	0.982	0.970	27.830	-9.068	-9.068	0.000	0.000	0.000	0.000
17	A	28	LYS	1	0.836	0.885	29.687	-8.439	-8.439	0.000	0.000	0.000	0.000
18	A	29	ASN	0	-0.010	-0.013	30.842	-0.012	-0.012	0.000	0.000	0.000	0.000
19	A	30	GLY	0	0.028	0.045	27.892	0.120	0.120	0.000	0.000	0.000	0.000
20	A	31	PHE	0	0.020	0.002	23.172	-0.135	-0.135	0.000	0.000	0.000	0.000
21	A	32	VAL	0	0.009	-0.007	20.304	-0.057	-0.057	0.000	0.000	0.000	0.000
22	A	33	VAL	0	0.028	0.019	14.422	-0.052	-0.052	0.000	0.000	0.000	0.000
23	A	34	ILE	0	-0.037	-0.014	17.236	0.042	0.042	0.000	0.000	0.000	0.000
24	A	35	LYS	1	0.814	0.883	15.349	-13.894	-13.894	0.000	0.000	0.000	0.000
25	A	36	SER	0	0.036	0.018	10.613	0.014	0.014	0.000	0.000	0.000	0.000
26	A	37	ARG	1	0.834	0.881	13.516	-15.235	-15.235	0.000	0.000	0.000	0.000
27	A	38	PRO	0	-0.003	0.020	16.360	-0.593	-0.593	0.000	0.000	0.000	0.000
28	A	39	CYS	0	-0.031	-0.012	18.943	-0.580	-0.580	0.000	0.000	0.000	0.000
29	A	40	LYS	1	0.894	0.940	22.383	-10.176	-10.176	0.000	0.000	0.000	0.000
30	A	41	ILE	0	-0.040	-0.013	24.884	-0.166	-0.166	0.000	0.000	0.000	0.000
31	A	42	VAL	0	0.021	0.011	27.691	-0.327	-0.327	0.000	0.000	0.000	0.000
32	A	43	ASP	-1	-0.871	-0.944	30.067	8.334	8.334	0.000	0.000	0.000	0.000
33	A	44	MET	0	-0.017	0.001	28.411	0.518	0.518	0.000	0.000	0.000	0.000
34	A	45	SER	0	0.049	0.051	30.827	-0.431	-0.431	0.000	0.000	0.000	0.000
35	A	46	THR	0	-0.027	-0.032	31.087	0.297	0.297	0.000	0.000	0.000	0.000
36	A	47	SER	0	0.019	0.024	32.323	-0.352	-0.352	0.000	0.000	0.000	0.000
37	A	48	LYS	1	1.009	0.993	33.006	-7.181	-7.181	0.000	0.000	0.000	0.000
38	A	49	THR	0	-0.009	0.009	31.439	0.014	0.014	0.000	0.000	0.000	0.000
39	A	50	GLY	0	0.067	0.033	31.833	0.286	0.286	0.000	0.000	0.000	0.000
40	A	51	LYS	1	0.953	0.984	32.386	-7.732	-7.732	0.000	0.000	0.000	0.000
41	A	52	HIS	0	0.037	0.016	34.452	0.245	0.245	0.000	0.000	0.000	0.000
42	A	53	GLY	0	-0.002	0.006	34.868	0.006	0.006	0.000	0.000	0.000	0.000
43	A	54	HIS	0	-0.028	-0.022	29.990	0.282	0.282	0.000	0.000	0.000	0.000
44	A	55	ALA	0	0.030	0.012	31.533	-0.280	-0.280	0.000	0.000	0.000	0.000
45	A	56	LYS	1	0.853	0.931	27.459	-9.431	-9.431	0.000	0.000	0.000	0.000
46	A	57	VAL	0	0.035	0.014	26.922	-0.400	-0.400	0.000	0.000	0.000	0.000
47	A	58	HIS	0	-0.062	-0.035	26.872	0.126	0.126	0.000	0.000	0.000	0.000
48	A	59	LEU	0	0.002	-0.009	23.690	-0.236	-0.236	0.000	0.000	0.000	0.000
49	A	60	VAL	0	0.007	0.011	26.000	0.243	0.243	0.000	0.000	0.000	0.000
50	A	61	ALA	0	0.018	0.005	23.920	-0.203	-0.203	0.000	0.000	0.000	0.000
51	A	62	ILE	0	0.006	0.008	25.783	-0.054	-0.054	0.000	0.000	0.000	0.000
52	A	63	ASP	-1	-0.749	-0.851	21.988	13.711	13.711	0.000	0.000	0.000	0.000
53	A	64	ILE	0	-0.062	-0.035	21.063	-0.493	-0.493	0.000	0.000	0.000	0.000
54	A	65	PHE	0	0.006	0.022	19.028	-0.177	-0.177	0.000	0.000	0.000	0.000
55	A	66	THR	0	-0.018	-0.050	22.445	-0.523	-0.523	0.000	0.000	0.000	0.000
56	A	67	GLY	0	0.051	0.030	25.161	-0.404	-0.404	0.000	0.000	0.000	0.000
57	A	68	LYS	1	0.896	0.942	23.070	-12.124	-12.124	0.000	0.000	0.000	0.000
58	A	69	LYS	1	0.895	0.934	24.350	-9.580	-9.580	0.000	0.000	0.000	0.000
59	A	70	LEU	0	-0.031	-0.010	19.513	0.155	0.155	0.000	0.000	0.000	0.000
60	A	71	GLU	-1	-0.819	-0.898	23.246	9.686	9.686	0.000	0.000	0.000	0.000
61	A	72	ASP	-1	-0.818	-0.898	20.194	13.956	13.956	0.000	0.000	0.000	0.000
62	A	73	LEU	0	-0.014	-0.004	23.097	-0.610	-0.610	0.000	0.000	0.000	0.000
63	A	74	SER	0	0.049	0.025	21.716	0.361	0.361	0.000	0.000	0.000	0.000
64	A	75	PRO	0	-0.038	-0.030	23.103	-0.503	-0.503	0.000	0.000	0.000	0.000
65	A	76	SER	0	0.011	-0.018	25.316	0.275	0.275	0.000	0.000	0.000	0.000
66	A	77	THR	0	-0.019	-0.018	26.592	0.127	0.127	0.000	0.000	0.000	0.000
67	A	78	HIS	0	0.011	0.019	18.010	-0.146	-0.146	0.000	0.000	0.000	0.000
68	A	79	ASN	0	-0.006	-0.005	19.145	-0.746	-0.746	0.000	0.000	0.000	0.000
69	A	80	MET	0	-0.007	0.002	18.229	0.655	0.655	0.000	0.000	0.000	0.000
70	A	81	GLU	-1	-0.825	-0.884	13.509	20.310	20.310	0.000	0.000	0.000	0.000
71	A	82	VAL	0	-0.037	-0.013	17.586	-0.531	-0.531	0.000	0.000	0.000	0.000
72	A	83	PRO	0	0.045	0.028	18.092	0.687	0.687	0.000	0.000	0.000	0.000
73	A	84	VAL	0	-0.015	-0.016	18.357	-0.756	-0.756	0.000	0.000	0.000	0.000
74	A	85	VAL	0	0.006	0.008	20.281	0.361	0.361	0.000	0.000	0.000	0.000
75	A	86	LYS	1	0.933	0.967	18.968	-15.753	-15.753	0.000	0.000	0.000	0.000
76	A	87	ARG	1	0.869	0.923	24.400	-10.959	-10.959	0.000	0.000	0.000	0.000
77	A	88	ASN	0	0.000	0.007	25.879	0.282	0.282	0.000	0.000	0.000	0.000
78	A	89	GLU	-1	-0.858	-0.935	28.928	9.825	9.825	0.000	0.000	0.000	0.000
79	A	90	TYR	0	0.020	0.014	26.287	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	91	GLN	0	-0.037	-0.022	31.921	-0.313	-0.313	0.000	0.000	0.000	0.000
81	A	92	LEU	0	0.026	0.006	33.293	0.242	0.242	0.000	0.000	0.000	0.000
82	A	93	LEU	0	-0.053	-0.031	34.857	-0.189	-0.189	0.000	0.000	0.000	0.000
83	A	94	ASP	-1	-0.829	-0.922	34.783	8.085	8.085	0.000	0.000	0.000	0.000
84	A	95	ILE	0	-0.055	-0.003	33.249	0.288	0.288	0.000	0.000	0.000	0.000
85	A	96	ASP	-1	-0.954	-0.963	32.157	9.089	9.089	0.000	0.000	0.000	0.000
86	A	97	ASP	-1	-0.921	-0.978	31.508	9.841	9.841	0.000	0.000	0.000	0.000
87	A	98	GLY	0	0.008	-0.015	30.070	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	99	PHE	0	-0.061	-0.064	27.014	0.050	0.050	0.000	0.000	0.000	0.000
89	A	100	LEU	0	-0.077	0.005	27.832	0.331	0.331	0.000	0.000	0.000	0.000
90	A	101	SER	0	0.035	0.011	29.951	-0.383	-0.383	0.000	0.000	0.000	0.000
91	A	102	LEU	0	-0.091	-0.047	27.699	0.353	0.353	0.000	0.000	0.000	0.000
92	A	103	MET	0	0.042	0.045	30.835	-0.241	-0.241	0.000	0.000	0.000	0.000
93	A	104	ASN	0	-0.061	-0.079	29.558	0.399	0.399	0.000	0.000	0.000	0.000
94	A	105	MET	0	-0.048	-0.021	32.513	-0.250	-0.250	0.000	0.000	0.000	0.000
95	A	106	ASP	-1	-0.961	-0.969	31.139	9.805	9.805	0.000	0.000	0.000	0.000
96	A	107	GLY	0	0.005	-0.010	31.337	-0.197	-0.197	0.000	0.000	0.000	0.000
97	A	108	ASP	-1	-0.892	-0.917	28.852	10.705	10.705	0.000	0.000	0.000	0.000
98	A	109	THR	0	-0.044	-0.029	26.128	-0.075	-0.075	0.000	0.000	0.000	0.000
99	A	110	LYS	1	0.710	0.838	22.156	-13.715	-13.715	0.000	0.000	0.000	0.000
100	A	111	ASP	-1	-0.925	-0.946	24.673	11.944	11.944	0.000	0.000	0.000	0.000
101	A	112	ASP	-1	-0.821	-0.906	21.474	13.668	13.668	0.000	0.000	0.000	0.000
102	A	113	VAL	0	-0.014	-0.010	22.685	-0.436	-0.436	0.000	0.000	0.000	0.000
103	A	114	LYS	1	0.872	0.907	23.222	-12.076	-12.076	0.000	0.000	0.000	0.000
104	A	115	ALA	0	-0.036	-0.032	26.113	-0.161	-0.161	0.000	0.000	0.000	0.000
105	A	116	PRO	0	0.060	0.043	27.896	-0.174	-0.174	0.000	0.000	0.000	0.000
106	A	117	GLU	-1	-0.851	-0.916	26.489	11.492	11.492	0.000	0.000	0.000	0.000
107	A	118	GLY	0	-0.067	-0.031	30.224	-0.254	-0.254	0.000	0.000	0.000	0.000
108	A	119	GLU	-1	-0.930	-0.954	33.377	8.547	8.547	0.000	0.000	0.000	0.000
109	A	120	LEU	0	-0.030	-0.028	31.703	-0.176	-0.176	0.000	0.000	0.000	0.000
110	A	121	GLY	0	0.049	0.015	33.839	-0.069	-0.069	0.000	0.000	0.000	0.000
111	A	122	ASP	-1	-0.865	-0.918	34.493	8.178	8.178	0.000	0.000	0.000	0.000
112	A	123	SER	0	-0.052	-0.029	37.606	-0.228	-0.228	0.000	0.000	0.000	0.000
113	A	124	LEU	0	-0.051	-0.035	32.732	-0.131	-0.131	0.000	0.000	0.000	0.000
114	A	125	GLN	0	-0.009	0.005	35.078	0.054	0.054	0.000	0.000	0.000	0.000
115	A	126	THR	0	-0.025	-0.009	38.601	-0.150	-0.150	0.000	0.000	0.000	0.000
116	A	127	ALA	0	0.009	0.002	40.796	-0.128	-0.128	0.000	0.000	0.000	0.000
117	A	128	PHE	0	-0.059	-0.017	38.781	-0.094	-0.094	0.000	0.000	0.000	0.000
118	A	129	ASP	-1	-0.889	-0.957	41.088	7.600	7.600	0.000	0.000	0.000	0.000
119	A	130	GLU	-1	-1.012	-0.996	43.300	6.706	6.706	0.000	0.000	0.000	0.000
120	A	131	GLY	0	-0.006	-0.001	44.329	-0.177	-0.177	0.000	0.000	0.000	0.000
121	A	132	LYS	1	0.679	0.843	43.066	-7.227	-7.227	0.000	0.000	0.000	0.000
122	A	133	ASP	-1	-0.800	-0.891	41.011	7.434	7.434	0.000	0.000	0.000	0.000
123	A	134	LEU	0	0.032	0.013	37.919	-0.107	-0.107	0.000	0.000	0.000	0.000
124	A	135	MET	0	-0.060	-0.016	35.534	0.098	0.098	0.000	0.000	0.000	0.000
125	A	136	VAL	0	0.017	-0.008	30.820	-0.084	-0.084	0.000	0.000	0.000	0.000
126	A	137	THR	0	-0.037	-0.011	30.212	0.269	0.269	0.000	0.000	0.000	0.000
127	A	138	ILE	0	0.035	0.029	23.834	0.042	0.042	0.000	0.000	0.000	0.000
128	A	139	ILE	0	-0.049	-0.033	24.074	-0.107	-0.107	0.000	0.000	0.000	0.000
129	A	140	SER	0	0.021	0.007	19.724	0.405	0.405	0.000	0.000	0.000	0.000
130	A	141	ALA	0	-0.022	-0.020	18.264	-0.340	-0.340	0.000	0.000	0.000	0.000
131	A	142	MET	0	-0.062	-0.034	12.933	0.033	0.033	0.000	0.000	0.000	0.000
132	A	143	GLY	0	0.024	0.012	13.587	0.051	0.051	0.000	0.000	0.000	0.000
133	A	144	GLU	-1	-0.813	-0.842	14.590	17.046	17.046	0.000	0.000	0.000	0.000
134	A	145	GLU	-1	-0.861	-0.954	16.873	13.631	13.631	0.000	0.000	0.000	0.000
135	A	146	ALA	0	-0.006	0.013	20.687	0.002	0.002	0.000	0.000	0.000	0.000
136	A	147	ALA	0	0.069	0.036	24.155	-0.042	-0.042	0.000	0.000	0.000	0.000
137	A	148	ILE	0	-0.086	-0.045	27.460	0.093	0.093	0.000	0.000	0.000	0.000
138	A	149	SER	0	-0.056	-0.031	30.101	-0.217	-0.217	0.000	0.000	0.000	0.000
139	A	150	PHE	0	0.085	0.052	33.489	0.086	0.086	0.000	0.000	0.000	0.000
140	A	151	LYS	1	0.845	0.925	35.923	-8.170	-8.170	0.000	0.000	0.000	0.000
141	A	152	GLU	-1	-0.823	-0.903	38.625	7.537	7.537	0.000	0.000	0.000	0.000
142	A	153	ALA	0	0.005	0.006	40.727	0.078	0.078	0.000	0.000	0.000	0.000
143	A	154	ALA	0	0.004	-0.015	42.407	-0.156	-0.156	0.000	0.000	0.000	0.000
144	A	155	ARG	1	0.935	0.973	45.222	-6.603	-6.603	0.000	0.000	0.000	0.000
145	A	156	THR	0	-0.015	-0.003	46.604	-0.179	-0.179	0.000	0.000	0.000	0.000
146	A	157	ASP	-1	-0.955	-0.976	46.646	6.345	6.345	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:12:ASP)