FMO DATABASE

FMODB ID: JLZ49

Calculation Name: 3BDW-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BDW

Chain ID: B

ChEMBL ID:

UniProt ID: Q13241

Base Structure: X-ray

Registration Date: 2023-09-20

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	117
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1032458.257479
FMO2-HF: Nuclear repulsion	982686.870558
FMO2-HF: Total energy	-49771.386921
FMO2-MP2: Total energy	-49911.292475

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(B:113:ALA)

Summations of interaction energy for fragment #1(B:113: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.
-5.563	-2.87	0.042	-1.405	-1.33	-0.003

Interaction energy analysis for fragmet #1(B:113:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : 0.002

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	B	115	HIS	0	0.044	0.039	3.878	-0.373	1.072	-0.018	-0.745	-0.682	0.003
4	B	116	CYS	0	-0.028	-0.012	6.764	0.070	0.070	0.000	0.000	0.000	0.000
5	B	117	GLY	0	0.033	0.013	10.555	-0.088	-0.088	0.000	0.000	0.000	0.000
6	B	118	HIS	0	0.004	-0.003	11.853	-0.040	-0.040	0.000	0.000	0.000	0.000
7	B	119	CYS	0	-0.063	-0.022	12.283	0.077	0.077	0.000	0.000	0.000	0.000
8	B	120	PRO	0	0.028	0.007	10.722	-0.074	-0.074	0.000	0.000	0.000	0.000
9	B	121	GLU	-1	-0.938	-0.967	3.185	-4.972	-3.724	0.060	-0.660	-0.648	-0.006
10	B	122	GLU	-1	-0.890	-0.952	6.830	-0.579	-0.579	0.000	0.000	0.000	0.000
11	B	123	TRP	0	-0.077	-0.035	8.974	0.198	0.198	0.000	0.000	0.000	0.000
12	B	124	ILE	0	-0.018	-0.008	11.004	0.032	0.032	0.000	0.000	0.000	0.000
13	B	125	THR	0	0.038	0.006	13.408	-0.018	-0.018	0.000	0.000	0.000	0.000
14	B	126	TYR	0	-0.052	-0.018	15.744	0.033	0.033	0.000	0.000	0.000	0.000
15	B	127	SER	0	0.028	0.008	19.058	0.016	0.016	0.000	0.000	0.000	0.000
16	B	128	ASN	0	-0.019	0.000	21.119	-0.010	-0.010	0.000	0.000	0.000	0.000
17	B	129	SER	0	0.043	0.022	20.148	-0.012	-0.012	0.000	0.000	0.000	0.000
18	B	131	TYR	0	-0.031	-0.050	16.328	-0.001	-0.001	0.000	0.000	0.000	0.000
19	B	132	TYR	0	0.026	0.036	13.603	0.019	0.019	0.000	0.000	0.000	0.000
20	B	133	ILE	0	0.037	0.009	16.238	0.012	0.012	0.000	0.000	0.000	0.000
21	B	134	GLY	0	0.096	0.042	16.961	-0.014	-0.014	0.000	0.000	0.000	0.000
22	B	135	LYS	1	0.832	0.905	15.062	0.102	0.102	0.000	0.000	0.000	0.000
23	B	136	GLU	-1	-0.767	-0.849	19.496	-0.172	-0.172	0.000	0.000	0.000	0.000
24	B	137	ARG	1	0.861	0.914	22.043	0.056	0.056	0.000	0.000	0.000	0.000
25	B	138	ARG	1	0.836	0.908	22.234	0.129	0.129	0.000	0.000	0.000	0.000
26	B	139	THR	0	0.042	0.021	27.671	0.010	0.010	0.000	0.000	0.000	0.000
27	B	140	TRP	0	-0.014	-0.006	29.192	-0.009	-0.009	0.000	0.000	0.000	0.000
28	B	141	GLU	-1	-0.861	-0.949	29.507	-0.075	-0.075	0.000	0.000	0.000	0.000
29	B	142	GLU	-1	-0.838	-0.907	27.398	-0.103	-0.103	0.000	0.000	0.000	0.000
30	B	143	SER	0	-0.034	-0.032	25.176	-0.012	-0.012	0.000	0.000	0.000	0.000
31	B	144	LEU	0	0.014	0.005	24.818	-0.010	-0.010	0.000	0.000	0.000	0.000
32	B	145	LEU	0	0.007	0.018	25.880	-0.010	-0.010	0.000	0.000	0.000	0.000
33	B	146	ALA	0	0.005	0.005	22.020	-0.014	-0.014	0.000	0.000	0.000	0.000
34	B	147	CYS	0	-0.081	-0.030	18.922	-0.015	-0.015	0.000	0.000	0.000	0.000
35	B	148	THR	0	-0.032	-0.017	21.410	-0.008	-0.008	0.000	0.000	0.000	0.000
36	B	149	SER	0	-0.042	-0.010	21.434	-0.016	-0.016	0.000	0.000	0.000	0.000
37	B	150	LYS	1	0.831	0.904	17.144	0.206	0.206	0.000	0.000	0.000	0.000
38	B	151	ASN	0	-0.039	-0.018	17.684	-0.008	-0.008	0.000	0.000	0.000	0.000
39	B	152	SER	0	-0.003	0.001	19.108	0.006	0.006	0.000	0.000	0.000	0.000
40	B	153	SER	0	-0.016	-0.013	21.343	0.017	0.017	0.000	0.000	0.000	0.000
41	B	154	LEU	0	0.015	0.016	23.020	-0.004	-0.004	0.000	0.000	0.000	0.000
42	B	155	LEU	0	-0.012	0.001	23.534	0.006	0.006	0.000	0.000	0.000	0.000
43	B	156	SER	0	-0.024	-0.020	25.235	0.003	0.003	0.000	0.000	0.000	0.000
44	B	157	ILE	0	-0.006	-0.018	26.948	0.002	0.002	0.000	0.000	0.000	0.000
45	B	158	ASP	-1	-0.776	-0.861	27.732	-0.032	-0.032	0.000	0.000	0.000	0.000
46	B	159	ASN	0	-0.004	-0.014	29.990	0.001	0.001	0.000	0.000	0.000	0.000
47	B	160	GLU	-1	-0.741	-0.852	30.558	0.008	0.008	0.000	0.000	0.000	0.000
48	B	161	GLU	-1	-0.920	-0.947	28.077	0.037	0.037	0.000	0.000	0.000	0.000
49	B	162	GLU	-1	-0.751	-0.830	24.999	-0.016	-0.016	0.000	0.000	0.000	0.000
50	B	163	MET	0	-0.021	0.011	26.377	0.000	0.000	0.000	0.000	0.000	0.000
51	B	164	LYS	1	0.836	0.935	28.320	-0.038	-0.038	0.000	0.000	0.000	0.000
52	B	165	PHE	0	0.047	0.025	19.232	0.006	0.006	0.000	0.000	0.000	0.000
53	B	166	LEU	0	0.035	0.008	21.777	0.004	0.004	0.000	0.000	0.000	0.000
54	B	167	SER	0	-0.082	-0.071	24.075	-0.001	-0.001	0.000	0.000	0.000	0.000
55	B	168	ILE	0	-0.053	-0.016	22.786	0.001	0.001	0.000	0.000	0.000	0.000
56	B	169	ILE	0	0.001	0.016	18.540	0.005	0.005	0.000	0.000	0.000	0.000
57	B	170	SER	0	-0.053	-0.040	20.841	-0.018	-0.018	0.000	0.000	0.000	0.000
58	B	171	PRO	0	0.013	0.029	23.427	0.000	0.000	0.000	0.000	0.000	0.000
59	B	172	SER	0	-0.045	-0.044	26.122	0.000	0.000	0.000	0.000	0.000	0.000
60	B	173	SER	0	-0.004	-0.010	24.827	-0.008	-0.008	0.000	0.000	0.000	0.000
61	B	174	TRP	0	-0.018	-0.015	26.730	0.010	0.010	0.000	0.000	0.000	0.000
62	B	175	ILE	0	0.020	0.018	27.134	-0.002	-0.002	0.000	0.000	0.000	0.000
63	B	176	GLY	0	0.009	0.023	28.983	-0.002	-0.002	0.000	0.000	0.000	0.000
64	B	177	VAL	0	-0.057	-0.046	30.257	0.002	0.002	0.000	0.000	0.000	0.000
65	B	178	PHE	0	-0.013	-0.003	34.001	0.000	0.000	0.000	0.000	0.000	0.000
66	B	179	ARG	1	0.841	0.919	36.860	0.028	0.028	0.000	0.000	0.000	0.000
67	B	180	ASN	0	0.019	-0.001	40.464	-0.004	-0.004	0.000	0.000	0.000	0.000
68	B	181	SER	0	-0.020	-0.023	42.815	0.000	0.000	0.000	0.000	0.000	0.000
69	B	182	SER	0	0.047	0.003	44.747	0.000	0.000	0.000	0.000	0.000	0.000
70	B	183	HIS	0	-0.031	-0.008	46.034	0.001	0.001	0.000	0.000	0.000	0.000
71	B	184	HIS	0	0.019	0.044	44.633	-0.001	-0.001	0.000	0.000	0.000	0.000
72	B	185	PRO	0	0.003	-0.010	43.611	0.000	0.000	0.000	0.000	0.000	0.000
73	B	186	TRP	0	0.048	0.027	37.425	-0.003	-0.003	0.000	0.000	0.000	0.000
74	B	187	VAL	0	-0.019	0.003	37.740	0.002	0.002	0.000	0.000	0.000	0.000
75	B	188	THR	0	-0.028	-0.031	33.324	-0.003	-0.003	0.000	0.000	0.000	0.000
76	B	189	MET	0	0.006	-0.003	30.155	0.001	0.001	0.000	0.000	0.000	0.000
77	B	190	ASN	0	-0.043	-0.019	30.642	-0.009	-0.009	0.000	0.000	0.000	0.000
78	B	191	GLY	0	0.022	0.022	33.527	0.001	0.001	0.000	0.000	0.000	0.000
79	B	192	LEU	0	-0.036	-0.006	35.728	0.004	0.004	0.000	0.000	0.000	0.000
80	B	193	ALA	0	0.039	0.024	37.781	-0.001	-0.001	0.000	0.000	0.000	0.000
81	B	194	PHE	0	0.003	-0.011	33.483	0.001	0.001	0.000	0.000	0.000	0.000
82	B	195	LYS	1	0.927	0.952	37.511	0.015	0.015	0.000	0.000	0.000	0.000
83	B	196	HIS	0	-0.036	0.002	33.623	0.005	0.005	0.000	0.000	0.000	0.000
84	B	197	GLU	-1	-0.931	-0.964	37.819	-0.005	-0.005	0.000	0.000	0.000	0.000
85	B	198	ILE	0	-0.052	-0.025	36.897	0.001	0.001	0.000	0.000	0.000	0.000
86	B	199	LYS	1	0.889	0.917	38.258	0.006	0.006	0.000	0.000	0.000	0.000
87	B	200	ASP	-1	-0.842	-0.899	39.106	-0.012	-0.012	0.000	0.000	0.000	0.000
88	B	201	SER	0	-0.014	-0.030	41.519	-0.001	-0.001	0.000	0.000	0.000	0.000
89	B	202	ASP	-1	-0.780	-0.845	43.637	-0.016	-0.016	0.000	0.000	0.000	0.000
90	B	203	ASN	0	-0.062	-0.027	46.023	-0.003	-0.003	0.000	0.000	0.000	0.000
91	B	204	ALA	0	-0.038	-0.015	45.228	0.001	0.001	0.000	0.000	0.000	0.000
92	B	205	GLU	-1	-0.828	-0.935	43.296	-0.035	-0.035	0.000	0.000	0.000	0.000
93	B	206	LEU	0	-0.070	-0.018	39.608	-0.003	-0.003	0.000	0.000	0.000	0.000
94	B	207	ASN	0	0.057	0.027	39.401	0.003	0.003	0.000	0.000	0.000	0.000
95	B	208	CYS	0	0.070	0.058	34.153	-0.004	-0.004	0.000	0.000	0.000	0.000
96	B	209	ALA	0	0.026	0.014	34.218	0.004	0.004	0.000	0.000	0.000	0.000
97	B	210	VAL	0	-0.019	-0.009	30.893	-0.005	-0.005	0.000	0.000	0.000	0.000
98	B	211	LEU	0	0.016	0.021	27.146	0.006	0.006	0.000	0.000	0.000	0.000
99	B	212	GLN	0	-0.009	-0.035	29.717	-0.005	-0.005	0.000	0.000	0.000	0.000
100	B	213	VAL	0	-0.002	-0.006	29.795	0.003	0.003	0.000	0.000	0.000	0.000
101	B	214	ASN	0	0.039	0.026	30.383	0.007	0.007	0.000	0.000	0.000	0.000
102	B	215	ARG	1	0.827	0.870	31.807	-0.005	-0.005	0.000	0.000	0.000	0.000
103	B	216	LEU	0	0.038	0.033	32.472	-0.003	-0.003	0.000	0.000	0.000	0.000
104	B	217	LYS	1	0.851	0.918	34.749	0.018	0.018	0.000	0.000	0.000	0.000
105	B	218	SER	0	0.033	0.023	35.653	-0.004	-0.004	0.000	0.000	0.000	0.000
106	B	219	ALA	0	-0.007	-0.020	34.819	0.002	0.002	0.000	0.000	0.000	0.000
107	B	220	GLN	0	0.027	0.006	36.937	-0.003	-0.003	0.000	0.000	0.000	0.000
108	B	222	GLY	0	0.049	0.026	33.912	-0.005	-0.005	0.000	0.000	0.000	0.000
109	B	223	SER	0	-0.073	-0.044	33.870	0.001	0.001	0.000	0.000	0.000	0.000
110	B	224	SER	0	0.031	0.013	29.998	-0.005	-0.005	0.000	0.000	0.000	0.000
111	B	225	ILE	0	-0.046	-0.017	28.658	0.006	0.006	0.000	0.000	0.000	0.000
112	B	226	ILE	0	-0.014	0.005	22.988	-0.008	-0.008	0.000	0.000	0.000	0.000
113	B	227	TYR	0	-0.020	-0.033	20.818	0.003	0.003	0.000	0.000	0.000	0.000
114	B	228	HIS	0	0.079	0.037	20.681	-0.021	-0.021	0.000	0.000	0.000	0.000
115	B	230	LYS	1	0.785	0.867	19.624	0.040	0.040	0.000	0.000	0.000	0.000
116	B	231	HIS	0	0.026	0.019	16.686	0.018	0.018	0.000	0.000	0.000	0.000
117	B	232	LYS	1	0.913	0.949	20.844	0.110	0.110	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:113:ALA)