FMO DATABASE

FMODB ID: YZY12

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	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	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	-1453252.03287
FMO2-HF: Nuclear repulsion	1389722.548554
FMO2-HF: Total energy	-63529.484316
FMO2-MP2: Total energy	-63710.425675

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.
-19.677	-20.249	18.613	-9.608	-8.43	0.015

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 : 0.016 / q_NPA : -0.028

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	-0.762	-0.849	2.919	-10.999	-6.676	0.122	-2.332	-2.112	-0.011
4	A	5	THR	0	-0.002	-0.001	5.019	1.171	1.246	-0.001	-0.005	-0.068	0.000
5	A	6	TYR	0	0.013	0.006	7.990	0.056	0.056	0.000	0.000	0.000	0.000
6	A	7	ILE	0	-0.020	-0.021	11.741	0.062	0.062	0.000	0.000	0.000	0.000
7	A	8	LYS	1	0.980	0.997	15.420	0.306	0.306	0.000	0.000	0.000	0.000
8	A	9	LEU	0	0.044	0.012	18.659	0.013	0.013	0.000	0.000	0.000	0.000
9	A	10	ASP	-1	-0.850	-0.937	22.220	-0.222	-0.222	0.000	0.000	0.000	0.000
10	A	11	LYS	1	0.885	0.930	25.417	0.168	0.168	0.000	0.000	0.000	0.000
11	A	12	VAL	0	-0.022	-0.017	22.438	0.012	0.012	0.000	0.000	0.000	0.000
12	A	13	ASP	-1	-0.943	-0.961	21.655	-0.260	-0.260	0.000	0.000	0.000	0.000
13	A	14	GLY	0	0.052	0.013	18.195	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.832	-0.951	16.631	-0.325	-0.325	0.000	0.000	0.000	0.000
15	A	16	SER	0	-0.066	-0.010	12.619	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	17	THR	0	0.001	-0.016	13.068	0.110	0.110	0.000	0.000	0.000	0.000
17	A	18	ASP	-1	-0.860	-0.928	10.392	-0.408	-0.408	0.000	0.000	0.000	0.000
18	A	19	ASP	-1	-0.903	-0.957	12.501	0.040	0.040	0.000	0.000	0.000	0.000
19	A	20	LYS	1	0.810	0.895	12.100	-0.177	-0.177	0.000	0.000	0.000	0.000
20	A	21	HIS	1	0.796	0.906	11.450	0.511	0.511	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.987	0.993	14.447	0.046	0.046	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.960	0.982	17.101	0.211	0.211	0.000	0.000	0.000	0.000
23	A	24	TRP	0	0.007	0.026	14.612	-0.017	-0.017	0.000	0.000	0.000	0.000
24	A	25	ILE	0	0.007	0.015	15.364	0.007	0.007	0.000	0.000	0.000	0.000
25	A	26	GLU	-1	-0.928	-0.962	10.971	-1.003	-1.003	0.000	0.000	0.000	0.000
26	A	27	VAL	0	-0.067	-0.034	10.952	0.116	0.116	0.000	0.000	0.000	0.000
27	A	28	LEU	0	-0.025	-0.008	9.405	-0.344	-0.344	0.000	0.000	0.000	0.000
28	A	29	GLY	0	0.006	0.003	9.688	-0.298	-0.298	0.000	0.000	0.000	0.000
29	A	30	PHE	0	-0.009	-0.025	10.017	0.166	0.166	0.000	0.000	0.000	0.000
30	A	31	ALA	0	0.039	0.019	14.234	0.112	0.112	0.000	0.000	0.000	0.000
31	A	32	TRP	0	0.044	-0.009	16.247	0.033	0.033	0.000	0.000	0.000	0.000
32	A	33	GLY	0	0.024	0.022	18.486	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	34	ALA	0	-0.036	-0.014	21.139	0.014	0.014	0.000	0.000	0.000	0.000
34	A	35	GLY	0	0.024	0.015	24.038	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	36	ASN	0	-0.051	-0.029	26.673	0.005	0.005	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.891	-0.940	30.415	-0.126	-0.126	0.000	0.000	0.000	0.000
37	A	38	CYS	0	-0.021	0.003	32.087	0.011	0.011	0.000	0.000	0.000	0.000
38	A	39	THR	0	-0.008	0.009	33.223	-0.007	-0.007	0.000	0.000	0.000	0.000
39	A	40	MET	0	-0.003	-0.007	35.209	0.002	0.002	0.000	0.000	0.000	0.000
40	A	41	GLU	-1	-0.794	-0.888	36.511	-0.075	-0.075	0.000	0.000	0.000	0.000
41	A	42	SER	0	-0.056	-0.013	39.890	0.003	0.003	0.000	0.000	0.000	0.000
42	A	43	GLY	0	0.012	-0.003	42.030	0.002	0.002	0.000	0.000	0.000	0.000
43	A	44	THR	0	-0.113	-0.070	41.651	0.004	0.004	0.000	0.000	0.000	0.000
44	A	45	GLN	0	-0.021	-0.001	42.755	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	46	GLY	0	0.028	0.012	41.388	0.001	0.001	0.000	0.000	0.000	0.000
46	A	47	LEU	0	-0.006	-0.009	34.106	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	48	ASN	0	-0.050	-0.036	38.037	0.000	0.000	0.000	0.000	0.000	0.000
48	A	49	THR	0	-0.014	-0.007	33.065	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	50	GLY	0	0.054	0.038	34.513	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	51	LYS	1	0.846	0.907	33.089	0.147	0.147	0.000	0.000	0.000	0.000
51	A	52	ALA	0	0.033	-0.002	30.357	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	53	MET	0	0.015	0.037	28.759	0.005	0.005	0.000	0.000	0.000	0.000
53	A	54	MET	0	-0.010	-0.020	24.627	0.001	0.001	0.000	0.000	0.000	0.000
54	A	55	SER	0	-0.018	-0.005	22.592	0.009	0.009	0.000	0.000	0.000	0.000
55	A	56	VAL	0	0.004	0.023	23.444	-0.006	-0.006	0.000	0.000	0.000	0.000
56	A	57	LEU	0	-0.021	0.008	16.730	-0.016	-0.016	0.000	0.000	0.000	0.000
57	A	58	ARG	1	0.915	0.960	18.853	0.454	0.454	0.000	0.000	0.000	0.000
58	A	59	VAL	0	0.012	0.006	15.739	-0.080	-0.080	0.000	0.000	0.000	0.000
59	A	60	THR	0	-0.016	0.002	14.329	0.087	0.087	0.000	0.000	0.000	0.000
60	A	61	LYS	1	0.819	0.919	14.075	0.372	0.372	0.000	0.000	0.000	0.000
61	A	62	TRP	0	0.025	0.017	12.370	0.094	0.094	0.000	0.000	0.000	0.000
62	A	63	MET	0	0.004	0.001	16.873	0.018	0.018	0.000	0.000	0.000	0.000
63	A	64	ASP	-1	-0.793	-0.898	17.446	-0.554	-0.554	0.000	0.000	0.000	0.000
64	A	65	CYS	0	-0.096	-0.036	20.093	0.026	0.026	0.000	0.000	0.000	0.000
65	A	66	ALA	0	-0.019	-0.010	20.511	0.029	0.029	0.000	0.000	0.000	0.000
66	A	67	SER	0	0.037	0.017	21.958	0.020	0.020	0.000	0.000	0.000	0.000
67	A	68	VAL	0	0.045	0.033	23.580	0.013	0.013	0.000	0.000	0.000	0.000
68	A	69	LYS	1	0.910	0.959	25.475	0.235	0.235	0.000	0.000	0.000	0.000
69	A	70	LEU	0	0.035	0.023	20.996	0.009	0.009	0.000	0.000	0.000	0.000
70	A	71	ALA	0	-0.007	-0.005	25.410	0.009	0.009	0.000	0.000	0.000	0.000
71	A	72	SER	0	-0.068	-0.060	28.047	0.018	0.018	0.000	0.000	0.000	0.000
72	A	73	ALA	0	0.004	-0.005	27.450	0.012	0.012	0.000	0.000	0.000	0.000
73	A	74	ALA	0	0.015	0.007	28.516	0.012	0.012	0.000	0.000	0.000	0.000
74	A	75	VAL	0	-0.025	-0.010	30.037	0.011	0.011	0.000	0.000	0.000	0.000
75	A	76	GLN	0	-0.050	-0.007	32.735	0.013	0.013	0.000	0.000	0.000	0.000
76	A	77	GLY	0	-0.005	0.009	32.767	0.010	0.010	0.000	0.000	0.000	0.000
77	A	78	GLN	0	-0.064	-0.026	29.810	0.009	0.009	0.000	0.000	0.000	0.000
78	A	79	ASN	0	-0.075	-0.041	30.194	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	80	PHE	0	-0.024	-0.015	26.620	0.006	0.006	0.000	0.000	0.000	0.000
80	A	81	PRO	0	-0.008	0.001	27.588	0.002	0.002	0.000	0.000	0.000	0.000
81	A	82	THR	0	-0.032	-0.029	23.194	0.009	0.009	0.000	0.000	0.000	0.000
82	A	83	LEU	0	-0.014	0.028	19.695	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	84	GLU	-1	-0.944	-0.964	18.130	-0.292	-0.292	0.000	0.000	0.000	0.000
84	A	85	LEU	0	0.001	0.000	12.628	-0.044	-0.044	0.000	0.000	0.000	0.000
85	A	86	GLU	-1	-0.854	-0.934	11.981	-0.356	-0.356	0.000	0.000	0.000	0.000
86	A	87	ILE	0	-0.005	0.014	6.647	-0.211	-0.211	0.000	0.000	0.000	0.000
87	A	88	CYS	0	-0.030	-0.011	7.230	0.481	0.481	0.000	0.000	0.000	0.000
88	A	89	THR	0	-0.020	-0.004	4.116	-1.052	-1.039	0.000	-0.024	0.011	0.000
89	A	90	GLN	0	-0.009	0.032	1.923	-6.323	-11.462	18.449	-7.310	-5.999	0.026
90	A	91	ALA	0	0.038	0.023	3.476	-1.341	-1.233	0.044	0.065	-0.217	0.000
91	A	92	GLY	0	0.057	0.027	6.255	-0.633	-0.633	0.000	0.000	0.000	0.000
92	A	93	ASP	-1	-0.856	-0.934	9.345	0.341	0.341	0.000	0.000	0.000	0.000
93	A	94	LYS	1	0.838	0.918	4.335	0.598	0.646	-0.001	-0.002	-0.045	0.000
94	A	95	PHE	0	-0.024	-0.004	8.543	-0.296	-0.296	0.000	0.000	0.000	0.000
95	A	96	ALA	0	0.077	0.023	8.731	-0.050	-0.050	0.000	0.000	0.000	0.000
96	A	97	PHE	0	-0.056	-0.016	5.679	0.155	0.155	0.000	0.000	0.000	0.000
97	A	98	CYS	0	-0.014	-0.025	10.692	0.049	0.049	0.000	0.000	0.000	0.000
98	A	99	ILE	0	-0.040	-0.009	12.514	-0.087	-0.087	0.000	0.000	0.000	0.000
99	A	100	TYR	0	0.047	0.022	15.049	0.048	0.048	0.000	0.000	0.000	0.000
100	A	101	LYS	1	0.880	0.940	17.437	0.227	0.227	0.000	0.000	0.000	0.000
101	A	102	PHE	0	0.006	0.011	18.646	0.023	0.023	0.000	0.000	0.000	0.000
102	A	103	THR	0	0.031	0.011	23.427	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	104	HIS	0	-0.033	-0.038	26.967	0.002	0.002	0.000	0.000	0.000	0.000
104	A	105	VAL	0	-0.010	-0.003	23.812	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	106	ALA	0	0.018	0.006	27.174	0.017	0.017	0.000	0.000	0.000	0.000
106	A	107	VAL	0	0.019	0.012	24.678	-0.022	-0.022	0.000	0.000	0.000	0.000
107	A	108	SER	0	-0.102	-0.061	26.645	0.021	0.021	0.000	0.000	0.000	0.000
108	A	109	SER	0	-0.009	-0.017	25.923	0.015	0.015	0.000	0.000	0.000	0.000
109	A	110	TYR	0	0.035	0.008	23.841	-0.026	-0.026	0.000	0.000	0.000	0.000
110	A	111	GLN	0	-0.050	-0.021	24.104	0.029	0.029	0.000	0.000	0.000	0.000
111	A	112	CYM	-1	-0.830	-0.916	23.626	-0.361	-0.361	0.000	0.000	0.000	0.000
112	A	113	SER	0	-0.044	-0.015	22.327	0.023	0.023	0.000	0.000	0.000	0.000
113	A	114	GLY	0	0.065	0.010	22.858	-0.030	-0.030	0.000	0.000	0.000	0.000
114	A	115	ALA	0	-0.011	0.000	21.151	0.023	0.023	0.000	0.000	0.000	0.000
115	A	116	THR	0	-0.033	-0.014	23.300	0.026	0.026	0.000	0.000	0.000	0.000
116	A	117	GLY	0	0.024	0.000	25.001	0.013	0.013	0.000	0.000	0.000	0.000
117	A	118	GLY	0	-0.015	-0.007	22.028	0.016	0.016	0.000	0.000	0.000	0.000
118	A	119	SER	0	-0.035	0.004	17.069	0.002	0.002	0.000	0.000	0.000	0.000
119	A	120	ASP	-1	-0.842	-0.917	17.593	-0.273	-0.273	0.000	0.000	0.000	0.000
120	A	121	DAR	1	0.812	0.904	13.644	0.490	0.490	0.000	0.000	0.000	0.000
121	A	122	PRO	0	0.032	0.006	18.944	-0.012	-0.012	0.000	0.000	0.000	0.000
122	A	123	GLN	0	-0.036	-0.019	17.008	-0.071	-0.071	0.000	0.000	0.000	0.000
123	A	124	GLU	-1	-0.747	-0.876	18.853	-0.391	-0.391	0.000	0.000	0.000	0.000
124	A	125	THR	0	-0.068	-0.047	18.673	-0.075	-0.075	0.000	0.000	0.000	0.000
125	A	126	ILE	0	-0.018	-0.010	19.556	0.054	0.054	0.000	0.000	0.000	0.000
126	A	127	ASP	-1	-0.862	-0.902	21.001	-0.446	-0.446	0.000	0.000	0.000	0.000
127	A	128	PHE	0	0.031	0.006	19.515	0.041	0.041	0.000	0.000	0.000	0.000
128	A	129	ALA	0	0.015	0.007	23.946	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	130	TYR	0	-0.030	-0.025	23.611	0.001	0.001	0.000	0.000	0.000	0.000
130	A	131	LYS	1	0.940	0.984	27.420	0.185	0.185	0.000	0.000	0.000	0.000
131	A	132	GLU	-1	-0.876	-0.917	27.611	-0.150	-0.150	0.000	0.000	0.000	0.000
132	A	133	VAL	0	0.035	0.005	21.423	-0.020	-0.020	0.000	0.000	0.000	0.000
133	A	134	THR	0	-0.054	-0.045	21.446	0.038	0.038	0.000	0.000	0.000	0.000
134	A	135	TRP	0	0.004	-0.006	18.500	-0.036	-0.036	0.000	0.000	0.000	0.000
135	A	136	GLU	-1	-0.804	-0.900	17.407	-0.217	-0.217	0.000	0.000	0.000	0.000
136	A	137	TYR	0	0.057	0.040	11.255	-0.018	-0.018	0.000	0.000	0.000	0.000
137	A	138	VAL	0	-0.071	-0.033	13.168	0.046	0.046	0.000	0.000	0.000	0.000
138	A	139	PRO	0	0.029	0.023	12.289	0.004	0.004	0.000	0.000	0.000	0.000
139	A	140	GLN	0	-0.014	-0.029	7.434	0.093	0.093	0.000	0.000	0.000	0.000
140	A	141	ASP	-1	-0.801	-0.883	12.363	0.400	0.400	0.000	0.000	0.000	0.000
141	A	142	GLN	0	0.007	0.002	13.307	0.095	0.095	0.000	0.000	0.000	0.000
142	A	143	ASN	0	-0.124	-0.063	14.242	0.100	0.100	0.000	0.000	0.000	0.000
143	A	144	GLY	0	-0.040	-0.017	11.676	0.005	0.005	0.000	0.000	0.000	0.000
144	A	145	DLY	1	0.806	0.877	11.563	-0.667	-0.667	0.000	0.000	0.000	0.000
145	A	146	ALA	0	0.055	0.036	13.198	0.029	0.029	0.000	0.000	0.000	0.000
146	A	147	GLY	0	0.037	0.017	14.198	0.005	0.005	0.000	0.000	0.000	0.000
147	A	148	GLY	0	-0.028	-0.010	16.995	-0.025	-0.025	0.000	0.000	0.000	0.000
148	A	149	LYS	1	0.921	0.952	17.133	0.122	0.122	0.000	0.000	0.000	0.000
149	A	150	ILE	0	-0.029	-0.025	17.664	0.010	0.010	0.000	0.000	0.000	0.000
150	A	151	GLY	0	-0.003	-0.008	19.862	-0.026	-0.026	0.000	0.000	0.000	0.000
151	A	152	PRO	0	0.035	0.021	21.336	-0.015	-0.015	0.000	0.000	0.000	0.000
152	A	153	GLU	-1	-0.962	-0.976	22.208	-0.098	-0.098	0.000	0.000	0.000	0.000
153	A	154	GLY	0	0.075	0.038	22.983	-0.025	-0.025	0.000	0.000	0.000	0.000
154	A	155	TRP	0	-0.047	-0.021	25.057	0.023	0.023	0.000	0.000	0.000	0.000
155	A	156	SER	0	0.016	-0.007	27.799	-0.012	-0.012	0.000	0.000	0.000	0.000
156	A	157	LEU	0	0.006	-0.009	28.849	0.014	0.014	0.000	0.000	0.000	0.000
157	A	158	ILE	0	-0.023	-0.009	32.229	0.006	0.006	0.000	0.000	0.000	0.000
158	A	159	THR	0	-0.033	-0.008	34.331	0.012	0.012	0.000	0.000	0.000	0.000
159	A	160	ASN	0	-0.067	-0.034	33.459	0.000	0.000	0.000	0.000	0.000	0.000
160	A	161	LYS	1	0.935	0.969	33.296	0.102	0.102	0.000	0.000	0.000	0.000
161	A	162	LYS	1	1.000	0.998	29.664	0.076	0.076	0.000	0.000	0.000	0.000
162	A	163	LYS	1	0.887	0.947	26.199	0.118	0.118	0.000	0.000	0.000	0.000

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