FMO DATABASE

FMODB ID: 437RN

Calculation Name: 3EWL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EWL

Chain ID: A

ChEMBL ID:

UniProt ID: Q5LE83

Base Structure: X-ray

Registration Date: 2023-06-20

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	138
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1356734.814451
FMO2-HF: Nuclear repulsion	1299782.886858
FMO2-HF: Total energy	-56951.927594
FMO2-MP2: Total energy	-57114.88926

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:SER)

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

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.
-39.541	-35.024	22.682	-12.456	-14.738	-0.033

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

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 : 0.015

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	0	ALA	0	0.077	0.031	3.886	-1.294	0.466	-0.013	-0.903	-0.843	0.003
4	A	1	GLY	0	-0.004	0.004	6.577	0.247	0.247	0.000	0.000	0.000	0.000
5	A	2	MET	0	-0.012	-0.006	3.539	0.241	0.463	0.004	-0.032	-0.193	0.000
6	A	3	LYS	1	0.920	0.954	4.642	-2.414	-2.308	-0.001	-0.013	-0.093	0.000
7	A	4	ALA	0	0.028	0.016	2.377	-0.131	1.147	1.387	-1.370	-1.295	0.003
8	A	5	ALA	0	0.002	0.003	1.910	-7.352	-9.995	8.290	-2.579	-3.067	0.029
9	A	6	ASP	-1	-0.786	-0.854	3.779	-1.750	-1.505	0.018	-0.065	-0.198	0.002
10	A	7	PHE	0	0.029	0.021	6.283	-0.219	-0.219	0.000	0.000	0.000	0.000
11	A	8	THR	0	-0.045	-0.032	9.114	0.056	0.056	0.000	0.000	0.000	0.000
12	A	9	TYR	0	0.010	0.007	12.528	-0.100	-0.100	0.000	0.000	0.000	0.000
13	A	10	VAL	0	-0.023	-0.006	14.558	0.061	0.061	0.000	0.000	0.000	0.000
14	A	11	THR	0	0.028	-0.004	18.180	-0.041	-0.041	0.000	0.000	0.000	0.000
15	A	12	VAL	0	0.018	0.003	20.496	0.011	0.011	0.000	0.000	0.000	0.000
16	A	13	HIS	0	0.000	0.015	23.767	0.014	0.014	0.000	0.000	0.000	0.000
17	A	14	GLY	0	0.001	0.013	23.931	0.012	0.012	0.000	0.000	0.000	0.000
18	A	15	ASP	-1	-0.898	-0.929	20.872	-0.053	-0.053	0.000	0.000	0.000	0.000
19	A	16	ASN	0	0.006	-0.013	17.492	-0.025	-0.025	0.000	0.000	0.000	0.000
20	A	17	SER	0	-0.020	-0.007	16.794	0.046	0.046	0.000	0.000	0.000	0.000
21	A	18	ARG	1	0.881	0.916	11.205	-0.498	-0.498	0.000	0.000	0.000	0.000
22	A	19	MET	0	0.027	0.046	6.409	-0.090	-0.090	0.000	0.000	0.000	0.000
23	A	20	SER	0	-0.046	-0.069	10.466	-0.062	-0.062	0.000	0.000	0.000	0.000
24	A	21	ARG	1	0.925	0.961	11.522	-0.272	-0.272	0.000	0.000	0.000	0.000
25	A	22	LEU	0	0.012	0.028	13.661	-0.036	-0.036	0.000	0.000	0.000	0.000
26	A	23	LYS	1	0.946	0.976	14.848	-0.078	-0.078	0.000	0.000	0.000	0.000
27	A	24	ALA	0	0.038	0.015	15.425	-0.032	-0.032	0.000	0.000	0.000	0.000
28	A	25	GLN	0	-0.007	0.002	15.674	0.057	0.057	0.000	0.000	0.000	0.000
29	A	26	TYR	0	0.045	0.026	13.470	0.012	0.012	0.000	0.000	0.000	0.000
30	A	27	THR	0	-0.054	-0.021	10.288	0.069	0.069	0.000	0.000	0.000	0.000
31	A	28	MET	0	0.029	0.024	10.234	-0.053	-0.053	0.000	0.000	0.000	0.000
32	A	29	LEU	0	-0.029	-0.006	5.332	0.078	0.078	0.000	0.000	0.000	0.000
33	A	30	PHE	0	0.010	-0.002	9.451	-0.143	-0.143	0.000	0.000	0.000	0.000
34	A	31	PHE	0	0.019	0.010	5.823	0.023	0.023	0.000	0.000	0.000	0.000
35	A	32	TYR	0	0.005	-0.013	11.067	0.044	0.044	0.000	0.000	0.000	0.000
36	A	33	ASP	-1	-0.778	-0.920	14.663	-0.345	-0.345	0.000	0.000	0.000	0.000
37	A	34	PRO	0	0.015	0.011	17.644	0.016	0.016	0.000	0.000	0.000	0.000
38	A	35	ASP	-1	-0.973	-0.981	21.211	-0.168	-0.168	0.000	0.000	0.000	0.000
39	A	36	CYS	0	0.040	0.039	18.025	0.001	0.001	0.000	0.000	0.000	0.000
40	A	37	SER	0	0.033	0.014	21.194	-0.014	-0.014	0.000	0.000	0.000	0.000
41	A	38	ASN	0	0.041	0.009	18.962	0.022	0.022	0.000	0.000	0.000	0.000
42	A	39	CYS	0	-0.042	-0.003	17.203	-0.036	-0.036	0.000	0.000	0.000	0.000
43	A	40	ARG	1	0.794	0.862	18.986	0.278	0.278	0.000	0.000	0.000	0.000
44	A	41	LYS	1	0.879	0.933	22.205	0.246	0.246	0.000	0.000	0.000	0.000
45	A	42	PHE	0	0.037	0.015	15.532	0.003	0.003	0.000	0.000	0.000	0.000
46	A	43	GLU	-1	-0.749	-0.864	19.368	-0.290	-0.290	0.000	0.000	0.000	0.000
47	A	44	LYS	1	0.804	0.886	21.206	0.165	0.165	0.000	0.000	0.000	0.000
48	A	45	LEU	0	-0.011	-0.013	22.205	0.009	0.009	0.000	0.000	0.000	0.000
49	A	46	PHE	0	0.012	-0.008	16.970	0.004	0.004	0.000	0.000	0.000	0.000
50	A	47	ALA	0	-0.015	-0.009	21.454	0.013	0.013	0.000	0.000	0.000	0.000
51	A	48	GLU	-1	-0.817	-0.879	24.451	-0.135	-0.135	0.000	0.000	0.000	0.000
52	A	49	ILE	0	-0.009	0.006	21.807	0.008	0.008	0.000	0.000	0.000	0.000
53	A	50	PRO	0	-0.006	-0.009	24.509	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	51	ALA	0	0.104	0.050	23.831	0.000	0.000	0.000	0.000	0.000	0.000
55	A	52	PHE	0	-0.029	-0.026	19.017	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	53	VAL	0	0.021	0.015	21.538	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	54	GLU	-1	-0.843	-0.919	23.963	-0.078	-0.078	0.000	0.000	0.000	0.000
58	A	55	MET	0	-0.040	-0.023	19.094	0.009	0.009	0.000	0.000	0.000	0.000
59	A	56	VAL	0	-0.052	-0.014	19.154	0.006	0.006	0.000	0.000	0.000	0.000
60	A	57	GLU	-1	-0.960	-0.974	21.377	-0.065	-0.065	0.000	0.000	0.000	0.000
61	A	58	ASN	0	-0.083	-0.052	24.412	0.019	0.019	0.000	0.000	0.000	0.000
62	A	59	GLY	0	-0.055	-0.021	20.943	0.014	0.014	0.000	0.000	0.000	0.000
63	A	60	THR	0	-0.055	-0.033	19.549	0.013	0.013	0.000	0.000	0.000	0.000
64	A	61	LEU	0	0.014	-0.001	14.820	0.004	0.004	0.000	0.000	0.000	0.000
65	A	62	ARG	1	0.957	0.979	15.105	0.051	0.051	0.000	0.000	0.000	0.000
66	A	63	VAL	0	0.022	0.028	13.996	-0.028	-0.028	0.000	0.000	0.000	0.000
67	A	64	LEU	0	-0.036	-0.023	10.701	0.069	0.069	0.000	0.000	0.000	0.000
68	A	65	ALA	0	0.023	0.026	12.285	-0.125	-0.125	0.000	0.000	0.000	0.000
69	A	66	ILE	0	-0.058	-0.036	10.767	0.068	0.068	0.000	0.000	0.000	0.000
70	A	67	TYR	0	0.061	0.037	12.884	-0.102	-0.102	0.000	0.000	0.000	0.000
71	A	68	PRO	0	-0.039	-0.039	10.615	0.031	0.031	0.000	0.000	0.000	0.000
72	A	69	ASP	-1	-0.766	-0.842	12.664	-0.542	-0.542	0.000	0.000	0.000	0.000
73	A	70	GLU	-1	-0.886	-0.954	15.753	-0.188	-0.188	0.000	0.000	0.000	0.000
74	A	71	ASN	0	-0.013	0.010	19.184	0.042	0.042	0.000	0.000	0.000	0.000
75	A	72	ARG	1	0.978	0.965	21.504	0.121	0.121	0.000	0.000	0.000	0.000
76	A	73	GLU	-1	-0.895	-0.947	22.401	-0.112	-0.112	0.000	0.000	0.000	0.000
77	A	74	GLU	-1	-0.758	-0.847	24.013	-0.157	-0.157	0.000	0.000	0.000	0.000
78	A	75	TRP	0	-0.044	-0.022	18.598	0.005	0.005	0.000	0.000	0.000	0.000
79	A	76	ALA	0	-0.011	-0.014	22.172	0.001	0.001	0.000	0.000	0.000	0.000
80	A	77	THR	0	-0.045	-0.031	24.380	0.011	0.011	0.000	0.000	0.000	0.000
81	A	78	LYS	1	0.838	0.893	23.435	0.172	0.172	0.000	0.000	0.000	0.000
82	A	79	ALA	0	-0.034	-0.013	21.864	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	80	VAL	0	-0.036	-0.018	23.295	0.003	0.003	0.000	0.000	0.000	0.000
84	A	81	TYR	0	-0.052	-0.020	25.830	0.013	0.013	0.000	0.000	0.000	0.000
85	A	82	MET	0	-0.064	-0.002	18.791	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	83	PRO	0	0.001	-0.003	21.005	0.018	0.018	0.000	0.000	0.000	0.000
87	A	84	GLN	0	0.069	0.026	22.530	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	85	GLY	0	0.004	0.013	23.066	-0.008	-0.008	0.000	0.000	0.000	0.000
89	A	86	TRP	0	-0.034	-0.028	17.882	-0.013	-0.013	0.000	0.000	0.000	0.000
90	A	87	ILE	0	-0.046	-0.014	16.507	0.023	0.023	0.000	0.000	0.000	0.000
91	A	88	VAL	0	0.027	0.010	16.907	-0.047	-0.047	0.000	0.000	0.000	0.000
92	A	89	GLY	0	0.010	-0.010	16.380	0.042	0.042	0.000	0.000	0.000	0.000
93	A	90	TRP	0	-0.013	0.000	15.785	-0.021	-0.021	0.000	0.000	0.000	0.000
94	A	91	ASN	0	-0.018	-0.033	11.361	-0.026	-0.026	0.000	0.000	0.000	0.000
95	A	92	LYS	1	0.896	0.942	13.789	0.074	0.074	0.000	0.000	0.000	0.000
96	A	93	ALA	0	-0.043	-0.014	13.859	0.031	0.031	0.000	0.000	0.000	0.000
97	A	94	GLY	0	0.077	0.045	13.764	0.027	0.027	0.000	0.000	0.000	0.000
98	A	95	ASP	-1	-0.884	-0.927	10.194	-0.294	-0.294	0.000	0.000	0.000	0.000
99	A	96	ILE	0	-0.017	-0.021	6.774	-0.131	-0.131	0.000	0.000	0.000	0.000
100	A	97	ARG	1	0.834	0.886	7.658	0.396	0.396	0.000	0.000	0.000	0.000
101	A	98	THR	0	-0.026	-0.030	10.271	0.071	0.071	0.000	0.000	0.000	0.000
102	A	99	ARG	1	0.903	0.951	8.534	0.173	0.173	0.000	0.000	0.000	0.000
103	A	100	GLN	0	0.005	0.012	6.242	-0.110	-0.110	0.000	0.000	0.000	0.000
104	A	101	LEU	0	-0.057	-0.012	4.010	-0.201	0.335	0.000	-0.224	-0.311	-0.001
105	A	102	TYR	0	-0.038	-0.062	1.982	-23.547	-21.981	12.345	-7.131	-6.779	-0.067
106	A	103	ASP	-1	-0.880	-0.925	3.158	2.210	1.790	0.037	0.732	-0.349	0.000
107	A	104	ILE	0	0.003	-0.001	5.355	-0.650	-0.646	-0.001	0.000	-0.002	0.000
108	A	105	ARG	1	0.885	0.913	8.230	0.665	0.665	0.000	0.000	0.000	0.000
109	A	106	ALA	0	0.002	0.016	11.056	0.098	0.098	0.000	0.000	0.000	0.000
110	A	107	THR	0	0.013	0.039	12.156	-0.106	-0.106	0.000	0.000	0.000	0.000
111	A	108	PRO	0	0.010	-0.021	13.959	0.075	0.075	0.000	0.000	0.000	0.000
112	A	109	THR	0	-0.047	-0.023	7.776	0.005	0.005	0.000	0.000	0.000	0.000
113	A	110	ILE	0	-0.014	-0.006	10.096	-0.096	-0.096	0.000	0.000	0.000	0.000
114	A	111	TYR	0	-0.053	-0.043	3.420	-1.593	-0.876	0.020	-0.275	-0.462	-0.002
115	A	112	LEU	0	0.022	0.016	7.666	0.254	0.254	0.000	0.000	0.000	0.000
116	A	113	LEU	0	-0.028	-0.016	5.092	-0.068	-0.068	0.000	0.000	0.000	0.000
117	A	114	ASP	-1	-0.696	-0.844	8.830	0.222	0.222	0.000	0.000	0.000	0.000
118	A	115	GLY	0	0.079	0.042	11.413	0.086	0.086	0.000	0.000	0.000	0.000
119	A	116	ARG	1	0.835	0.917	11.849	-0.251	-0.251	0.000	0.000	0.000	0.000
120	A	117	LYS	1	0.779	0.880	8.149	-0.070	-0.070	0.000	0.000	0.000	0.000
121	A	118	ARG	1	0.854	0.925	6.301	0.478	0.478	0.000	0.000	0.000	0.000
122	A	119	VAL	0	-0.003	-0.001	2.684	-0.588	-0.167	0.578	-0.291	-0.708	-0.002
123	A	120	ILE	0	-0.047	-0.020	5.885	0.000	0.000	0.000	0.000	0.000	0.000
124	A	121	LEU	0	0.028	0.022	8.462	0.046	0.046	0.000	0.000	0.000	0.000
125	A	122	LYS	1	0.842	0.906	3.275	-1.507	-0.782	0.018	-0.305	-0.438	0.002
126	A	123	ASP	-1	-0.842	-0.891	7.191	-0.431	-0.431	0.000	0.000	0.000	0.000
127	A	124	THR	0	0.014	0.016	8.766	0.216	0.216	0.000	0.000	0.000	0.000
128	A	125	SER	0	-0.017	-0.024	11.959	0.026	0.026	0.000	0.000	0.000	0.000
129	A	126	MET	0	0.006	0.012	15.521	-0.004	-0.004	0.000	0.000	0.000	0.000
130	A	127	GLU	-1	-0.856	-0.936	18.182	-0.271	-0.271	0.000	0.000	0.000	0.000
131	A	128	GLN	0	0.027	0.020	14.050	-0.044	-0.044	0.000	0.000	0.000	0.000
132	A	129	LEU	0	-0.024	-0.007	12.728	0.006	0.006	0.000	0.000	0.000	0.000
133	A	130	ILE	0	0.005	0.000	16.429	0.029	0.029	0.000	0.000	0.000	0.000
134	A	131	ASP	-1	-0.919	-0.958	19.330	-0.164	-0.164	0.000	0.000	0.000	0.000
135	A	132	TYR	0	-0.027	-0.007	15.145	0.021	0.021	0.000	0.000	0.000	0.000
136	A	133	LEU	0	-0.051	-0.029	15.902	0.019	0.019	0.000	0.000	0.000	0.000
137	A	134	ALA	0	0.000	0.028	19.236	0.020	0.020	0.000	0.000	0.000	0.000
138	A	135	THR	0	-0.135	-0.077	20.968	0.031	0.031	0.000	0.000	0.000	0.000

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