FMO DATABASE

FMODB ID: 3JRRL

Calculation Name: 4B9I-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4B9I

Chain ID: A

ChEMBL ID:

UniProt ID: P53508

Base Structure: X-ray

Registration Date: 2023-09-23

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	137
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1218004.393925
FMO2-HF: Nuclear repulsion	1164571.809183
FMO2-HF: Total energy	-53432.584742
FMO2-MP2: Total energy	-53590.482351

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:13:PHE)

Summations of interaction energy for fragment #1(A:13:PHE)

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.
-17.013	-2.75	8.669	-6.247	-16.685	0.006

Interaction energy analysis for fragmet #1(A:13:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / 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	15	ALA	0	0.022	0.016	2.626	-2.432	1.482	0.626	-1.792	-2.748	0.011
4	A	16	PRO	0	-0.019	0.000	4.684	-0.704	-0.519	0.001	-0.049	-0.137	0.000
5	A	17	GLU	-1	-0.861	-0.935	7.850	-0.527	-0.527	0.000	0.000	0.000	0.000
6	A	18	PRO	0	-0.025	-0.008	7.701	0.063	0.063	0.000	0.000	0.000	0.000
7	A	19	GLN	0	-0.018	-0.004	10.614	0.028	0.028	0.000	0.000	0.000	0.000
8	A	20	ILE	0	0.039	0.024	14.413	0.012	0.012	0.000	0.000	0.000	0.000
9	A	21	GLN	0	-0.073	-0.043	16.331	0.014	0.014	0.000	0.000	0.000	0.000
10	A	22	PRO	0	0.068	0.033	20.294	0.002	0.002	0.000	0.000	0.000	0.000
11	A	23	SER	0	-0.054	-0.029	23.423	0.006	0.006	0.000	0.000	0.000	0.000
12	A	24	PHE	0	0.051	0.018	26.026	0.001	0.001	0.000	0.000	0.000	0.000
13	A	25	GLY	0	0.062	-0.001	29.713	0.004	0.004	0.000	0.000	0.000	0.000
14	A	26	LYS	1	0.915	0.974	31.494	0.043	0.043	0.000	0.000	0.000	0.000
15	A	27	ASN	0	-0.048	-0.034	28.229	0.004	0.004	0.000	0.000	0.000	0.000
16	A	28	VAL	0	0.055	0.031	28.151	0.003	0.003	0.000	0.000	0.000	0.000
17	A	29	GLY	0	0.032	0.021	29.957	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	30	LYS	1	0.888	0.954	32.118	0.040	0.040	0.000	0.000	0.000	0.000
19	A	31	GLU	-1	-0.783	-0.884	30.801	-0.036	-0.036	0.000	0.000	0.000	0.000
20	A	32	GLY	0	-0.034	-0.014	27.639	0.003	0.003	0.000	0.000	0.000	0.000
21	A	33	GLY	0	-0.034	-0.012	27.447	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	34	LEU	0	-0.061	-0.029	21.949	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	35	LEU	0	0.023	0.027	23.468	0.002	0.002	0.000	0.000	0.000	0.000
24	A	36	PHE	0	0.001	-0.004	16.975	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	37	SER	0	-0.010	-0.006	18.316	0.012	0.012	0.000	0.000	0.000	0.000
26	A	38	VAL	0	0.041	0.023	12.134	-0.011	-0.011	0.000	0.000	0.000	0.000
27	A	39	SER	0	-0.004	0.006	13.819	0.014	0.014	0.000	0.000	0.000	0.000
28	A	40	LEU	0	-0.032	-0.010	7.263	-0.032	-0.032	0.000	0.000	0.000	0.000
29	A	41	THR	0	0.021	0.005	9.374	0.032	0.032	0.000	0.000	0.000	0.000
30	A	42	VAL	0	-0.009	0.005	6.232	-0.077	-0.077	0.000	0.000	0.000	0.000
31	A	43	PRO	0	-0.007	0.001	2.415	-1.295	-0.030	1.069	-0.545	-1.788	0.003
32	A	44	GLU	-1	-0.823	-0.911	4.096	0.424	0.689	-0.001	-0.035	-0.229	0.000
33	A	45	ASN	0	-0.092	-0.055	3.171	-2.877	-1.123	0.065	-0.681	-1.138	-0.005
34	A	46	VAL	0	0.000	0.007	2.408	-1.135	-0.314	0.795	-0.314	-1.302	-0.004
35	A	47	SER	0	-0.029	-0.020	5.479	0.036	0.036	0.000	0.000	0.000	0.000
36	A	48	GLN	0	0.009	0.005	7.593	-0.106	-0.106	0.000	0.000	0.000	0.000
37	A	49	VAL	0	-0.007	-0.008	5.575	-0.057	-0.057	0.000	0.000	0.000	0.000
38	A	50	THR	0	-0.014	-0.011	8.059	0.071	0.071	0.000	0.000	0.000	0.000
39	A	51	VAL	0	0.005	0.001	8.991	-0.106	-0.106	0.000	0.000	0.000	0.000
40	A	52	TYR	0	-0.055	-0.034	10.765	0.039	0.039	0.000	0.000	0.000	0.000
41	A	53	PRO	0	0.015	0.015	14.114	-0.030	-0.030	0.000	0.000	0.000	0.000
42	A	54	VAL	0	0.026	-0.004	15.233	0.013	0.013	0.000	0.000	0.000	0.000
43	A	55	TYR	0	-0.043	-0.003	18.037	0.006	0.006	0.000	0.000	0.000	0.000
44	A	56	ASP	-1	-0.867	-0.939	21.214	-0.028	-0.028	0.000	0.000	0.000	0.000
45	A	57	GLU	-1	-0.805	-0.913	15.203	-0.087	-0.087	0.000	0.000	0.000	0.000
46	A	58	ASP	-1	-0.940	-0.958	18.444	0.001	0.001	0.000	0.000	0.000	0.000
47	A	59	TYR	0	-0.074	-0.043	20.971	0.014	0.014	0.000	0.000	0.000	0.000
48	A	60	GLY	0	0.019	0.009	18.773	0.000	0.000	0.000	0.000	0.000	0.000
49	A	61	LEU	0	-0.078	-0.048	19.631	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	62	GLY	0	0.025	-0.005	20.978	-0.008	-0.008	0.000	0.000	0.000	0.000
51	A	63	ARG	1	0.863	0.920	21.639	0.092	0.092	0.000	0.000	0.000	0.000
52	A	64	LEU	0	0.000	0.023	21.796	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	65	VAL	0	-0.003	-0.001	24.476	0.011	0.011	0.000	0.000	0.000	0.000
54	A	66	ASN	0	0.006	0.003	26.881	-0.011	-0.011	0.000	0.000	0.000	0.000
55	A	67	THR	0	-0.026	-0.044	26.378	0.002	0.002	0.000	0.000	0.000	0.000
56	A	68	ALA	0	-0.054	-0.020	29.012	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	69	ASP	-1	-0.849	-0.904	32.119	-0.058	-0.058	0.000	0.000	0.000	0.000
58	A	70	ASP	-1	-0.873	-0.934	31.301	-0.084	-0.084	0.000	0.000	0.000	0.000
59	A	71	SER	0	-0.140	-0.095	32.014	0.002	0.002	0.000	0.000	0.000	0.000
60	A	72	GLN	0	-0.038	-0.011	32.873	0.004	0.004	0.000	0.000	0.000	0.000
61	A	73	SER	0	-0.025	-0.020	28.730	-0.008	-0.008	0.000	0.000	0.000	0.000
62	A	74	ILE	0	-0.027	-0.001	26.685	0.006	0.006	0.000	0.000	0.000	0.000
63	A	75	ILE	0	0.013	0.007	25.922	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	76	TYR	0	-0.079	-0.072	18.883	0.001	0.001	0.000	0.000	0.000	0.000
65	A	77	GLN	0	0.073	0.045	21.024	0.004	0.004	0.000	0.000	0.000	0.000
66	A	78	ILE	0	0.007	0.005	15.415	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	79	VAL	0	-0.023	0.001	18.464	0.013	0.013	0.000	0.000	0.000	0.000
68	A	80	ASP	-1	-0.667	-0.836	15.901	-0.023	-0.023	0.000	0.000	0.000	0.000
69	A	81	ASP	-1	-0.867	-0.917	16.491	-0.011	-0.011	0.000	0.000	0.000	0.000
70	A	82	LYS	1	0.792	0.869	18.977	0.000	0.000	0.000	0.000	0.000	0.000
71	A	83	GLY	0	-0.037	-0.015	20.615	0.003	0.003	0.000	0.000	0.000	0.000
72	A	84	ARG	1	0.819	0.900	15.721	-0.041	-0.041	0.000	0.000	0.000	0.000
73	A	85	LYS	1	0.862	0.930	19.137	0.021	0.021	0.000	0.000	0.000	0.000
74	A	86	MET	0	-0.097	-0.004	14.231	0.011	0.011	0.000	0.000	0.000	0.000
75	A	87	LEU	0	0.023	0.003	15.215	-0.007	-0.007	0.000	0.000	0.000	0.000
76	A	88	LYS	1	0.936	0.968	12.615	-0.039	-0.039	0.000	0.000	0.000	0.000
77	A	89	ASP	-1	-0.830	-0.867	11.489	0.132	0.132	0.000	0.000	0.000	0.000
78	A	90	HIS	0	-0.055	-0.026	12.555	0.061	0.061	0.000	0.000	0.000	0.000
79	A	91	GLY	0	0.051	0.004	11.811	-0.042	-0.042	0.000	0.000	0.000	0.000
80	A	92	ALA	0	-0.029	-0.006	12.095	0.036	0.036	0.000	0.000	0.000	0.000
81	A	93	GLU	-1	-0.817	-0.889	11.076	0.275	0.275	0.000	0.000	0.000	0.000
82	A	94	VAL	0	-0.081	-0.041	8.466	-0.038	-0.038	0.000	0.000	0.000	0.000
83	A	95	THR	0	-0.006	-0.007	10.976	0.080	0.080	0.000	0.000	0.000	0.000
84	A	96	PRO	0	0.006	-0.005	7.432	-0.089	-0.089	0.000	0.000	0.000	0.000
85	A	97	ASN	0	-0.067	-0.052	8.570	-0.061	-0.061	0.000	0.000	0.000	0.000
86	A	98	GLN	0	0.007	0.029	10.527	0.000	0.000	0.000	0.000	0.000	0.000
87	A	99	GLN	0	-0.008	-0.006	10.810	-0.044	-0.044	0.000	0.000	0.000	0.000
88	A	100	ILE	0	-0.010	0.000	9.292	0.033	0.033	0.000	0.000	0.000	0.000
89	A	101	THR	0	-0.015	-0.024	13.180	-0.024	-0.024	0.000	0.000	0.000	0.000
90	A	102	PHE	0	0.006	0.004	10.403	0.025	0.025	0.000	0.000	0.000	0.000
91	A	103	ARG	1	0.855	0.911	15.676	0.044	0.044	0.000	0.000	0.000	0.000
92	A	104	ALA	0	0.036	0.031	18.939	0.007	0.007	0.000	0.000	0.000	0.000
93	A	105	LEU	0	-0.045	-0.025	20.408	0.004	0.004	0.000	0.000	0.000	0.000
94	A	106	ASN	0	0.053	0.005	23.958	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	107	TYR	0	-0.052	-0.033	25.839	0.008	0.008	0.000	0.000	0.000	0.000
96	A	108	THR	0	0.005	0.011	27.862	0.003	0.003	0.000	0.000	0.000	0.000
97	A	109	SER	0	-0.026	-0.016	30.621	0.000	0.000	0.000	0.000	0.000	0.000
98	A	110	GLY	0	-0.006	0.008	33.967	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	111	ASP	-1	-0.918	-0.963	37.180	-0.028	-0.028	0.000	0.000	0.000	0.000
100	A	112	LYS	1	0.812	0.886	33.899	0.038	0.038	0.000	0.000	0.000	0.000
101	A	113	GLU	-1	-0.940	-0.963	35.341	-0.042	-0.042	0.000	0.000	0.000	0.000
102	A	114	ILE	0	0.016	0.018	29.761	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	115	PRO	0	0.013	0.025	33.767	0.000	0.000	0.000	0.000	0.000	0.000
104	A	116	PRO	0	-0.019	-0.018	33.073	-0.005	-0.005	0.000	0.000	0.000	0.000
105	A	117	GLY	0	0.006	0.014	31.518	0.001	0.001	0.000	0.000	0.000	0.000
106	A	118	ILE	0	-0.008	0.005	25.960	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	119	TYR	0	-0.011	-0.015	25.623	0.003	0.003	0.000	0.000	0.000	0.000
108	A	120	ASN	0	-0.026	-0.032	20.720	-0.004	-0.004	0.000	0.000	0.000	0.000
109	A	121	ASP	-1	-0.726	-0.838	20.029	-0.124	-0.124	0.000	0.000	0.000	0.000
110	A	122	GLN	0	-0.106	-0.067	14.811	-0.023	-0.023	0.000	0.000	0.000	0.000
111	A	123	VAL	0	-0.028	-0.007	12.652	0.022	0.022	0.000	0.000	0.000	0.000
112	A	124	MET	0	0.005	0.009	9.492	-0.063	-0.063	0.000	0.000	0.000	0.000
113	A	125	VAL	0	-0.006	0.001	5.936	0.063	0.063	0.000	0.000	0.000	0.000
114	A	126	GLY	0	0.014	0.001	5.790	-0.078	-0.078	0.000	0.000	0.000	0.000
115	A	127	TYR	0	0.016	-0.012	2.672	-3.604	-1.242	2.172	-1.192	-3.342	-0.010
116	A	128	TYR	0	-0.013	0.003	4.698	0.754	0.858	-0.001	-0.008	-0.095	0.000
117	A	129	VAL	0	0.012	-0.006	2.318	-2.192	-0.798	3.257	-0.941	-3.710	0.004
118	A	130	ASN	0	-0.043	-0.039	5.256	-0.512	-0.443	-0.001	-0.004	-0.064	0.000
119	A	131	ASP	-1	-0.818	-0.890	6.892	0.846	0.846	0.000	0.000	0.000	0.000
120	A	132	ASN	0	-0.002	0.001	9.689	-0.220	-0.220	0.000	0.000	0.000	0.000
121	A	133	LYS	1	0.885	0.931	12.151	-0.419	-0.419	0.000	0.000	0.000	0.000
122	A	134	GLN	0	-0.056	-0.032	12.329	-0.143	-0.143	0.000	0.000	0.000	0.000
123	A	135	GLY	0	0.068	0.047	9.227	0.197	0.197	0.000	0.000	0.000	0.000
124	A	136	ASN	0	-0.055	-0.016	7.142	0.137	0.137	0.000	0.000	0.000	0.000
125	A	137	TRP	0	0.034	0.023	7.152	0.318	0.318	0.000	0.000	0.000	0.000
126	A	138	GLN	0	-0.052	-0.018	2.957	-2.866	-0.962	0.688	-0.672	-1.920	0.007
127	A	139	TYR	0	-0.050	-0.079	4.611	-0.681	-0.455	-0.001	-0.014	-0.212	0.000
128	A	140	LYS	1	0.816	0.910	5.332	0.302	0.302	0.000	0.000	0.000	0.000
129	A	141	SER	0	0.071	0.041	7.049	0.080	0.080	0.000	0.000	0.000	0.000
130	A	142	LEU	0	-0.035	-0.027	10.586	-0.056	-0.056	0.000	0.000	0.000	0.000
131	A	143	ASP	-1	-0.830	-0.903	12.453	-0.258	-0.258	0.000	0.000	0.000	0.000
132	A	144	VAL	0	-0.024	-0.004	16.241	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	145	ASN	0	-0.015	-0.013	18.210	0.025	0.025	0.000	0.000	0.000	0.000
134	A	146	VAL	0	-0.015	-0.003	20.764	-0.003	-0.003	0.000	0.000	0.000	0.000
135	A	147	ASN	0	-0.058	-0.038	23.462	-0.001	-0.001	0.000	0.000	0.000	0.000
136	A	148	ILE	0	-0.008	-0.002	24.871	0.000	0.000	0.000	0.000	0.000	0.000
137	A	149	GLU	-1	-0.874	-0.922	28.663	-0.078	-0.078	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:13:PHE)