FMO DATABASE

FMODB ID: V5RN1

Calculation Name: 3EAA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EAA

Chain ID: A

ChEMBL ID:

UniProt ID: Q6EE19

Base Structure: X-ray

Registration Date: 2023-06-21

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

DOI:

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	162
LigandCharge	DLY=1,DAR=1,CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1454045.678771
FMO2-HF: Nuclear repulsion	1390515.090039
FMO2-HF: Total energy	-63530.588732
FMO2-MP2: Total energy	-63711.510409

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:2:ALA)

Summations of interaction energy for fragment #1(A:2:ALA)

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.
-23.309	-27.144	24.5	-11.222	-9.442	0.008

Interaction energy analysis for fragmet #1(A:2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : -0.015

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	4	ASP	-1	-0.738	-0.843	2.906	-11.470	-6.848	0.157	-2.460	-2.319	-0.013
4	A	5	THR	0	-0.002	-0.001	5.050	1.236	1.316	-0.001	-0.005	-0.074	0.000
5	A	6	TYR	0	0.013	0.012	7.796	0.021	0.021	0.000	0.000	0.000	0.000
6	A	7	ILE	0	-0.028	-0.027	11.767	0.060	0.060	0.000	0.000	0.000	0.000
7	A	8	LYS	1	0.839	0.918	15.449	0.345	0.345	0.000	0.000	0.000	0.000
8	A	9	LEU	0	0.042	0.014	18.680	0.015	0.015	0.000	0.000	0.000	0.000
9	A	10	ASP	-1	-0.852	-0.936	22.246	-0.242	-0.242	0.000	0.000	0.000	0.000
10	A	11	LYS	1	0.892	0.934	25.438	0.181	0.181	0.000	0.000	0.000	0.000
11	A	12	VAL	0	-0.008	-0.014	22.910	0.014	0.014	0.000	0.000	0.000	0.000
12	A	13	ASP	-1	-0.842	-0.895	21.688	-0.271	-0.271	0.000	0.000	0.000	0.000
13	A	14	GLY	0	0.049	0.015	18.238	0.001	0.001	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.854	-0.963	16.855	-0.322	-0.322	0.000	0.000	0.000	0.000
15	A	16	SER	0	-0.084	-0.027	12.851	-0.024	-0.024	0.000	0.000	0.000	0.000
16	A	17	THR	0	0.005	-0.013	13.081	0.115	0.115	0.000	0.000	0.000	0.000
17	A	18	ASP	-1	-0.860	-0.908	10.408	-0.463	-0.463	0.000	0.000	0.000	0.000
18	A	19	ASP	-1	-0.812	-0.907	12.489	-0.035	-0.035	0.000	0.000	0.000	0.000
19	A	20	LYS	1	0.832	0.918	12.150	-0.072	-0.072	0.000	0.000	0.000	0.000
20	A	21	HIS	1	0.792	0.875	10.753	0.616	0.616	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.854	0.920	14.443	0.083	0.083	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.838	0.912	17.101	0.242	0.242	0.000	0.000	0.000	0.000
23	A	24	TRP	0	0.002	0.017	14.634	-0.019	-0.019	0.000	0.000	0.000	0.000
24	A	25	ILE	0	0.000	0.013	15.480	0.006	0.006	0.000	0.000	0.000	0.000
25	A	26	GLU	-1	-0.899	-0.949	10.920	-1.024	-1.024	0.000	0.000	0.000	0.000
26	A	27	VAL	0	-0.070	-0.043	11.006	0.132	0.132	0.000	0.000	0.000	0.000
27	A	28	LEU	0	-0.032	-0.007	9.337	-0.359	-0.359	0.000	0.000	0.000	0.000
28	A	29	GLY	0	0.010	0.006	9.621	-0.302	-0.302	0.000	0.000	0.000	0.000
29	A	30	PHE	0	-0.016	-0.030	10.087	0.166	0.166	0.000	0.000	0.000	0.000
30	A	31	ALA	0	0.041	0.022	14.246	0.113	0.113	0.000	0.000	0.000	0.000
31	A	32	TRP	0	0.053	0.001	16.259	0.031	0.031	0.000	0.000	0.000	0.000
32	A	33	GLY	0	0.030	0.022	18.516	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	34	ALA	0	-0.036	-0.013	21.172	0.013	0.013	0.000	0.000	0.000	0.000
34	A	35	GLY	0	0.022	0.013	24.078	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	36	ASN	0	-0.043	-0.017	26.715	0.007	0.007	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.843	-0.912	30.457	-0.131	-0.131	0.000	0.000	0.000	0.000
37	A	38	CYS	0	-0.012	0.004	32.107	0.011	0.011	0.000	0.000	0.000	0.000
38	A	39	THR	0	-0.015	-0.014	33.254	-0.007	-0.007	0.000	0.000	0.000	0.000
39	A	40	MET	0	-0.014	-0.009	35.259	0.002	0.002	0.000	0.000	0.000	0.000
40	A	41	GLU	-1	-0.778	-0.864	36.557	-0.077	-0.077	0.000	0.000	0.000	0.000
41	A	42	SER	0	-0.055	-0.012	39.839	0.003	0.003	0.000	0.000	0.000	0.000
42	A	43	GLY	0	0.017	0.000	42.058	0.002	0.002	0.000	0.000	0.000	0.000
43	A	44	THR	0	-0.116	-0.074	41.720	0.004	0.004	0.000	0.000	0.000	0.000
44	A	45	GLN	0	-0.011	-0.001	42.795	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	46	GLY	0	0.014	0.010	41.438	0.001	0.001	0.000	0.000	0.000	0.000
46	A	47	LEU	0	-0.013	-0.010	34.348	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	48	ASN	0	-0.043	-0.036	38.085	0.000	0.000	0.000	0.000	0.000	0.000
48	A	49	THR	0	-0.022	-0.022	32.867	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	50	GLY	0	0.037	0.032	34.559	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	51	LYS	1	0.786	0.894	32.859	0.154	0.154	0.000	0.000	0.000	0.000
51	A	52	ALA	0	0.031	0.005	30.404	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	53	MET	0	0.027	0.021	28.816	0.003	0.003	0.000	0.000	0.000	0.000
53	A	54	MET	0	-0.018	-0.025	24.943	0.000	0.000	0.000	0.000	0.000	0.000
54	A	55	SER	0	-0.020	-0.003	22.416	0.008	0.008	0.000	0.000	0.000	0.000
55	A	56	VAL	0	0.010	0.020	23.876	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	57	LEU	0	-0.027	0.007	16.823	-0.015	-0.015	0.000	0.000	0.000	0.000
57	A	58	ARG	1	0.845	0.887	18.731	0.450	0.450	0.000	0.000	0.000	0.000
58	A	59	VAL	0	0.012	0.008	15.667	-0.080	-0.080	0.000	0.000	0.000	0.000
59	A	60	THR	0	-0.012	0.001	14.248	0.095	0.095	0.000	0.000	0.000	0.000
60	A	61	LYS	1	0.777	0.873	14.003	0.376	0.376	0.000	0.000	0.000	0.000
61	A	62	TRP	0	0.022	0.020	11.837	0.101	0.101	0.000	0.000	0.000	0.000
62	A	63	MET	0	0.019	0.010	16.808	0.014	0.014	0.000	0.000	0.000	0.000
63	A	64	ASP	-1	-0.788	-0.884	17.727	-0.546	-0.546	0.000	0.000	0.000	0.000
64	A	65	CYS	0	-0.071	-0.027	20.146	0.028	0.028	0.000	0.000	0.000	0.000
65	A	66	ALA	0	-0.018	-0.009	20.527	0.029	0.029	0.000	0.000	0.000	0.000
66	A	67	SER	0	0.017	-0.017	22.053	0.017	0.017	0.000	0.000	0.000	0.000
67	A	68	VAL	0	0.045	0.031	23.636	0.014	0.014	0.000	0.000	0.000	0.000
68	A	69	LYS	1	0.878	0.948	25.508	0.238	0.238	0.000	0.000	0.000	0.000
69	A	70	LEU	0	0.042	0.024	20.821	0.011	0.011	0.000	0.000	0.000	0.000
70	A	71	ALA	0	-0.002	-0.002	25.463	0.010	0.010	0.000	0.000	0.000	0.000
71	A	72	SER	0	-0.056	-0.060	28.105	0.018	0.018	0.000	0.000	0.000	0.000
72	A	73	ALA	0	0.000	-0.007	27.480	0.013	0.013	0.000	0.000	0.000	0.000
73	A	74	ALA	0	0.020	0.011	28.463	0.012	0.012	0.000	0.000	0.000	0.000
74	A	75	VAL	0	-0.024	-0.009	30.093	0.011	0.011	0.000	0.000	0.000	0.000
75	A	76	GLN	0	-0.058	-0.015	32.780	0.013	0.013	0.000	0.000	0.000	0.000
76	A	77	GLY	0	0.002	0.016	32.816	0.010	0.010	0.000	0.000	0.000	0.000
77	A	78	GLN	0	-0.081	-0.034	29.529	0.011	0.011	0.000	0.000	0.000	0.000
78	A	79	ASN	0	-0.061	-0.033	30.235	-0.010	-0.010	0.000	0.000	0.000	0.000
79	A	80	PHE	0	-0.002	-0.004	26.586	0.006	0.006	0.000	0.000	0.000	0.000
80	A	81	PRO	0	0.014	0.002	27.812	0.001	0.001	0.000	0.000	0.000	0.000
81	A	82	THR	0	-0.045	-0.033	23.163	0.010	0.010	0.000	0.000	0.000	0.000
82	A	83	LEU	0	-0.003	0.032	19.733	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	84	GLU	-1	-0.818	-0.896	18.232	-0.326	-0.326	0.000	0.000	0.000	0.000
84	A	85	LEU	0	-0.011	-0.001	12.786	-0.043	-0.043	0.000	0.000	0.000	0.000
85	A	86	GLU	-1	-0.823	-0.909	11.896	-0.425	-0.425	0.000	0.000	0.000	0.000
86	A	87	ILE	0	0.001	0.022	6.586	-0.209	-0.209	0.000	0.000	0.000	0.000
87	A	88	CYS	0	-0.040	-0.009	7.214	0.513	0.513	0.000	0.000	0.000	0.000
88	A	89	THR	0	-0.028	-0.009	4.130	-1.146	-1.140	0.000	-0.023	0.017	0.000
89	A	90	GLN	0	0.013	0.023	1.806	-10.305	-18.957	24.307	-8.834	-6.821	0.021
90	A	91	ALA	0	0.027	0.016	3.462	-1.002	-0.944	0.038	0.102	-0.198	0.000
91	A	92	GLY	0	0.059	0.031	6.248	-0.644	-0.644	0.000	0.000	0.000	0.000
92	A	93	ASP	-1	-0.851	-0.930	9.341	0.281	0.281	0.000	0.000	0.000	0.000
93	A	94	LYS	1	0.812	0.897	4.282	0.981	1.032	-0.001	-0.002	-0.047	0.000
94	A	95	PHE	0	-0.018	-0.003	8.534	-0.279	-0.279	0.000	0.000	0.000	0.000
95	A	96	ALA	0	0.084	0.024	8.731	-0.082	-0.082	0.000	0.000	0.000	0.000
96	A	97	PHE	0	-0.058	-0.018	5.741	0.184	0.184	0.000	0.000	0.000	0.000
97	A	98	CYS	0	-0.046	-0.035	10.700	0.049	0.049	0.000	0.000	0.000	0.000
98	A	99	ILE	0	-0.045	-0.018	12.523	-0.085	-0.085	0.000	0.000	0.000	0.000
99	A	100	TYR	0	0.035	0.018	15.212	0.056	0.056	0.000	0.000	0.000	0.000
100	A	101	LYS	1	0.837	0.898	17.444	0.260	0.260	0.000	0.000	0.000	0.000
101	A	102	PHE	0	0.007	0.007	18.562	0.025	0.025	0.000	0.000	0.000	0.000
102	A	103	THR	0	0.040	0.012	23.432	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	104	HIS	0	-0.040	-0.038	26.971	0.003	0.003	0.000	0.000	0.000	0.000
104	A	105	VAL	0	-0.021	-0.008	23.818	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	106	ALA	0	0.027	0.012	27.208	0.017	0.017	0.000	0.000	0.000	0.000
106	A	107	VAL	0	0.016	0.012	24.640	-0.022	-0.022	0.000	0.000	0.000	0.000
107	A	108	SER	0	-0.103	-0.060	26.662	0.022	0.022	0.000	0.000	0.000	0.000
108	A	109	SER	0	-0.042	-0.044	25.877	0.021	0.021	0.000	0.000	0.000	0.000
109	A	110	TYR	0	0.013	-0.022	23.486	-0.023	-0.023	0.000	0.000	0.000	0.000
110	A	111	GLN	0	-0.077	-0.031	23.955	0.037	0.037	0.000	0.000	0.000	0.000
111	A	112	CYM	-1	-0.800	-0.887	23.561	-0.358	-0.358	0.000	0.000	0.000	0.000
112	A	113	SER	0	-0.029	-0.005	22.389	0.019	0.019	0.000	0.000	0.000	0.000
113	A	114	GLY	0	0.057	0.005	22.808	-0.029	-0.029	0.000	0.000	0.000	0.000
114	A	115	ALA	0	-0.013	0.001	21.125	0.022	0.022	0.000	0.000	0.000	0.000
115	A	116	THR	0	-0.022	-0.008	23.269	0.025	0.025	0.000	0.000	0.000	0.000
116	A	117	GLY	0	0.016	-0.005	24.966	0.012	0.012	0.000	0.000	0.000	0.000
117	A	118	GLY	0	-0.016	-0.006	22.016	0.017	0.017	0.000	0.000	0.000	0.000
118	A	119	SER	0	-0.038	0.003	17.109	0.005	0.005	0.000	0.000	0.000	0.000
119	A	120	ASP	-1	-0.835	-0.913	17.467	-0.281	-0.281	0.000	0.000	0.000	0.000
120	A	121	DAR	1	0.826	0.909	13.488	0.493	0.493	0.000	0.000	0.000	0.000
121	A	122	PRO	0	0.013	-0.004	18.839	-0.018	-0.018	0.000	0.000	0.000	0.000
122	A	123	GLN	0	-0.030	-0.017	16.217	-0.064	-0.064	0.000	0.000	0.000	0.000
123	A	124	GLU	-1	-0.709	-0.823	18.794	-0.399	-0.399	0.000	0.000	0.000	0.000
124	A	125	THR	0	-0.037	-0.028	18.607	-0.061	-0.061	0.000	0.000	0.000	0.000
125	A	126	ILE	0	-0.017	-0.010	19.509	0.055	0.055	0.000	0.000	0.000	0.000
126	A	127	ASP	-1	-0.787	-0.816	20.928	-0.441	-0.441	0.000	0.000	0.000	0.000
127	A	128	PHE	0	0.054	0.011	19.743	0.041	0.041	0.000	0.000	0.000	0.000
128	A	129	ALA	0	0.008	0.005	23.954	-0.002	-0.002	0.000	0.000	0.000	0.000
129	A	130	TYR	0	-0.011	-0.023	23.559	0.003	0.003	0.000	0.000	0.000	0.000
130	A	131	LYS	1	0.941	0.982	27.420	0.196	0.196	0.000	0.000	0.000	0.000
131	A	132	GLU	-1	-0.888	-0.916	27.619	-0.161	-0.161	0.000	0.000	0.000	0.000
132	A	133	VAL	0	0.029	0.002	21.435	-0.021	-0.021	0.000	0.000	0.000	0.000
133	A	134	THR	0	-0.035	-0.033	21.000	0.041	0.041	0.000	0.000	0.000	0.000
134	A	135	TRP	0	-0.002	-0.007	18.618	-0.034	-0.034	0.000	0.000	0.000	0.000
135	A	136	GLU	-1	-0.738	-0.834	17.416	-0.254	-0.254	0.000	0.000	0.000	0.000
136	A	137	TYR	0	0.039	0.027	11.042	-0.024	-0.024	0.000	0.000	0.000	0.000
137	A	138	VAL	0	-0.052	-0.030	13.113	0.051	0.051	0.000	0.000	0.000	0.000
138	A	139	PRO	0	0.031	0.022	12.300	-0.005	-0.005	0.000	0.000	0.000	0.000
139	A	140	GLN	0	-0.008	-0.020	7.726	0.057	0.057	0.000	0.000	0.000	0.000
140	A	141	ASP	-1	-0.803	-0.888	12.372	0.375	0.375	0.000	0.000	0.000	0.000
141	A	142	GLN	0	0.006	0.003	13.338	0.094	0.094	0.000	0.000	0.000	0.000
142	A	143	ASN	0	-0.119	-0.058	14.247	0.104	0.104	0.000	0.000	0.000	0.000
143	A	144	GLY	0	-0.040	-0.017	11.678	0.006	0.006	0.000	0.000	0.000	0.000
144	A	145	DLY	1	0.806	0.875	11.565	-0.602	-0.602	0.000	0.000	0.000	0.000
145	A	146	ALA	0	0.046	0.034	13.186	0.027	0.027	0.000	0.000	0.000	0.000
146	A	147	GLY	0	0.038	0.017	14.202	0.012	0.012	0.000	0.000	0.000	0.000
147	A	148	GLY	0	-0.024	-0.009	17.002	-0.027	-0.027	0.000	0.000	0.000	0.000
148	A	149	LYS	1	0.884	0.927	16.926	0.179	0.179	0.000	0.000	0.000	0.000
149	A	150	ILE	0	-0.031	-0.028	17.606	0.013	0.013	0.000	0.000	0.000	0.000
150	A	151	GLY	0	0.009	-0.003	19.873	-0.027	-0.027	0.000	0.000	0.000	0.000
151	A	152	PRO	0	0.026	0.013	21.334	-0.015	-0.015	0.000	0.000	0.000	0.000
152	A	153	GLU	-1	-0.862	-0.903	22.217	-0.106	-0.106	0.000	0.000	0.000	0.000
153	A	154	GLY	0	0.076	0.034	22.993	-0.028	-0.028	0.000	0.000	0.000	0.000
154	A	155	TRP	0	-0.044	-0.017	25.067	0.025	0.025	0.000	0.000	0.000	0.000
155	A	156	SER	0	0.018	-0.017	27.808	-0.012	-0.012	0.000	0.000	0.000	0.000
156	A	157	LEU	0	0.011	-0.010	28.912	0.015	0.015	0.000	0.000	0.000	0.000
157	A	158	ILE	0	-0.022	-0.003	32.284	0.007	0.007	0.000	0.000	0.000	0.000
158	A	159	THR	0	-0.026	-0.009	34.341	0.012	0.012	0.000	0.000	0.000	0.000
159	A	160	ASN	0	-0.064	-0.031	33.484	0.001	0.001	0.000	0.000	0.000	0.000
160	A	161	LYS	1	0.942	0.973	33.389	0.111	0.111	0.000	0.000	0.000	0.000
161	A	162	LYS	1	1.003	0.997	29.662	0.087	0.087	0.000	0.000	0.000	0.000
162	A	163	LYS	1	0.801	0.902	26.392	0.133	0.133	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ALA)