FMO DATABASE

FMODB ID: LZ2Q9

Calculation Name: 3BDW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BDW

Chain ID: A

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	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	119
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1121554.509131
FMO2-HF: Nuclear repulsion	1068895.112053
FMO2-HF: Total energy	-52659.397078
FMO2-MP2: Total energy	-52806.354744

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:57:ASP)

Summations of interaction energy for fragment #1(A:57:ASP)

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.
-4.047	3.928	8.058	-7.393	-8.64	0.07

Interaction energy analysis for fragmet #1(A:57:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.886 / q_NPA : -0.965

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

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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	59	CYS	0	-0.063	-0.006	2.022	-31.803	-27.895	6.372	-5.254	-5.026	0.045
4	A	60	SER	0	0.040	0.026	2.715	-6.214	-3.189	1.627	-1.721	-2.931	0.021
5	A	61	CYS	0	-0.068	-0.033	3.689	-6.473	-6.015	0.053	-0.225	-0.286	0.003
6	A	62	GLN	0	-0.006	-0.013	7.434	-3.487	-3.487	0.000	0.000	0.000	0.000
7	A	63	GLU	-1	-0.777	-0.851	9.632	20.673	20.673	0.000	0.000	0.000	0.000
8	A	64	LYS	1	0.776	0.848	12.439	-19.728	-19.728	0.000	0.000	0.000	0.000
9	A	65	TRP	0	0.013	0.020	10.763	-1.058	-1.058	0.000	0.000	0.000	0.000
10	A	66	VAL	0	-0.031	-0.022	11.922	0.734	0.734	0.000	0.000	0.000	0.000
11	A	67	GLY	0	0.057	0.029	8.969	0.768	0.768	0.000	0.000	0.000	0.000
12	A	68	TYR	0	-0.084	-0.057	9.852	-1.472	-1.472	0.000	0.000	0.000	0.000
13	A	69	ARG	1	0.886	0.927	11.208	-18.270	-18.270	0.000	0.000	0.000	0.000
14	A	71	ASN	0	0.061	0.044	7.947	3.000	3.000	0.000	0.000	0.000	0.000
15	A	73	TYR	0	-0.029	-0.059	9.734	-1.244	-1.244	0.000	0.000	0.000	0.000
16	A	74	PHE	0	0.009	0.022	13.421	0.321	0.321	0.000	0.000	0.000	0.000
17	A	75	ILE	0	0.012	0.001	15.795	-0.753	-0.753	0.000	0.000	0.000	0.000
18	A	76	SER	0	-0.010	0.015	19.259	-0.187	-0.187	0.000	0.000	0.000	0.000
19	A	77	SER	0	0.038	-0.007	21.903	-0.447	-0.447	0.000	0.000	0.000	0.000
20	A	78	GLU	-1	-0.827	-0.903	24.606	12.029	12.029	0.000	0.000	0.000	0.000
21	A	79	GLN	0	-0.016	-0.011	25.910	0.294	0.294	0.000	0.000	0.000	0.000
22	A	80	LYS	1	0.845	0.912	26.077	-12.305	-12.305	0.000	0.000	0.000	0.000
23	A	81	THR	0	0.067	0.043	28.684	0.056	0.056	0.000	0.000	0.000	0.000
24	A	82	TRP	0	0.048	0.056	26.272	0.418	0.418	0.000	0.000	0.000	0.000
25	A	83	ASN	0	0.083	0.002	26.583	0.813	0.813	0.000	0.000	0.000	0.000
26	A	84	GLU	-1	-0.804	-0.887	26.612	10.910	10.910	0.000	0.000	0.000	0.000
27	A	85	SER	0	-0.024	-0.035	23.721	0.535	0.535	0.000	0.000	0.000	0.000
28	A	86	ARG	1	0.889	0.948	22.316	-11.785	-11.785	0.000	0.000	0.000	0.000
29	A	87	HIS	0	-0.005	-0.001	21.967	0.955	0.955	0.000	0.000	0.000	0.000
30	A	88	LEU	0	-0.003	0.012	21.535	0.514	0.514	0.000	0.000	0.000	0.000
31	A	89	CYS	0	-0.027	0.035	15.982	0.176	0.176	0.000	0.000	0.000	0.000
32	A	90	ALA	0	0.070	0.051	17.158	1.211	1.211	0.000	0.000	0.000	0.000
33	A	91	SER	0	-0.116	-0.073	18.322	0.540	0.540	0.000	0.000	0.000	0.000
34	A	92	GLN	0	-0.056	-0.022	14.805	1.140	1.140	0.000	0.000	0.000	0.000
35	A	93	LYS	1	0.890	0.946	10.910	-24.625	-24.625	0.000	0.000	0.000	0.000
36	A	94	SER	0	-0.065	-0.033	12.976	2.086	2.086	0.000	0.000	0.000	0.000
37	A	95	SER	0	0.045	0.020	14.674	-0.899	-0.899	0.000	0.000	0.000	0.000
38	A	96	LEU	0	0.005	0.014	17.152	0.762	0.762	0.000	0.000	0.000	0.000
39	A	97	LEU	0	-0.007	-0.010	17.641	0.190	0.190	0.000	0.000	0.000	0.000
40	A	98	GLN	0	0.041	0.035	17.885	-0.835	-0.835	0.000	0.000	0.000	0.000
41	A	99	LEU	0	-0.014	0.004	18.435	0.894	0.894	0.000	0.000	0.000	0.000
42	A	100	GLN	0	-0.023	-0.033	16.745	0.163	0.163	0.000	0.000	0.000	0.000
43	A	101	ASN	0	-0.029	-0.031	18.739	-0.482	-0.482	0.000	0.000	0.000	0.000
44	A	102	THR	0	0.079	0.035	21.440	0.474	0.474	0.000	0.000	0.000	0.000
45	A	103	ASP	-1	-0.884	-0.935	20.697	13.739	13.739	0.000	0.000	0.000	0.000
46	A	104	GLU	-1	-0.795	-0.852	16.453	19.435	19.435	0.000	0.000	0.000	0.000
47	A	105	LEU	0	-0.021	-0.018	17.234	1.057	1.057	0.000	0.000	0.000	0.000
48	A	106	ASP	-1	-0.812	-0.894	19.556	14.542	14.542	0.000	0.000	0.000	0.000
49	A	107	PHE	0	-0.027	-0.009	16.097	-0.550	-0.550	0.000	0.000	0.000	0.000
50	A	108	MET	0	-0.051	-0.020	19.575	-0.211	-0.211	0.000	0.000	0.000	0.000
51	A	109	SER	0	0.031	-0.001	21.860	-0.661	-0.661	0.000	0.000	0.000	0.000
52	A	110	SER	0	-0.043	-0.011	24.888	-0.384	-0.384	0.000	0.000	0.000	0.000
53	A	111	SER	0	-0.037	-0.011	24.998	-0.618	-0.618	0.000	0.000	0.000	0.000
54	A	112	GLN	0	0.015	-0.008	27.058	0.100	0.100	0.000	0.000	0.000	0.000
55	A	113	GLN	0	-0.006	0.012	26.700	-0.434	-0.434	0.000	0.000	0.000	0.000
56	A	114	PHE	0	0.041	0.011	27.524	0.279	0.279	0.000	0.000	0.000	0.000
57	A	115	TYR	0	-0.042	-0.029	23.540	0.010	0.010	0.000	0.000	0.000	0.000
58	A	116	TRP	0	-0.021	-0.006	25.446	0.151	0.151	0.000	0.000	0.000	0.000
59	A	117	ILE	0	-0.007	-0.008	22.822	0.766	0.766	0.000	0.000	0.000	0.000
60	A	118	GLY	0	-0.022	-0.025	22.331	-0.436	-0.436	0.000	0.000	0.000	0.000
61	A	119	LEU	0	-0.064	-0.021	23.325	0.025	0.025	0.000	0.000	0.000	0.000
62	A	120	SER	0	0.017	0.000	26.355	-0.204	-0.204	0.000	0.000	0.000	0.000
63	A	121	TYR	0	-0.009	-0.006	29.314	0.092	0.092	0.000	0.000	0.000	0.000
64	A	122	SER	0	-0.029	-0.027	30.800	-0.035	-0.035	0.000	0.000	0.000	0.000
65	A	123	GLU	-1	-0.816	-0.925	32.796	8.197	8.197	0.000	0.000	0.000	0.000
66	A	124	GLU	-1	-0.978	-0.987	34.080	8.498	8.498	0.000	0.000	0.000	0.000
67	A	125	HIS	0	-0.014	0.017	30.710	-0.059	-0.059	0.000	0.000	0.000	0.000
68	A	126	THR	0	-0.035	-0.006	34.220	-0.085	-0.085	0.000	0.000	0.000	0.000
69	A	127	ALA	0	0.013	0.013	32.026	-0.067	-0.067	0.000	0.000	0.000	0.000
70	A	128	TRP	0	0.000	0.004	29.854	0.208	0.208	0.000	0.000	0.000	0.000
71	A	129	LEU	0	-0.028	-0.012	26.455	0.134	0.134	0.000	0.000	0.000	0.000
72	A	130	TRP	0	0.042	0.017	21.647	0.211	0.211	0.000	0.000	0.000	0.000
73	A	131	GLU	-1	-0.807	-0.917	20.995	14.246	14.246	0.000	0.000	0.000	0.000
74	A	132	ASN	0	-0.054	-0.004	18.292	-0.613	-0.613	0.000	0.000	0.000	0.000
75	A	133	GLY	0	0.025	0.019	20.852	-0.061	-0.061	0.000	0.000	0.000	0.000
76	A	134	SER	0	-0.080	-0.051	21.524	-0.336	-0.336	0.000	0.000	0.000	0.000
77	A	135	ALA	0	0.047	0.009	23.637	-0.056	-0.056	0.000	0.000	0.000	0.000
78	A	136	LEU	0	-0.005	0.017	25.217	0.525	0.525	0.000	0.000	0.000	0.000
79	A	137	SER	0	-0.012	-0.013	26.146	-0.486	-0.486	0.000	0.000	0.000	0.000
80	A	138	GLN	0	0.040	0.006	27.920	-0.148	-0.148	0.000	0.000	0.000	0.000
81	A	139	TYR	0	-0.026	-0.024	29.247	-0.202	-0.202	0.000	0.000	0.000	0.000
82	A	140	LEU	0	-0.063	-0.007	24.226	0.019	0.019	0.000	0.000	0.000	0.000
83	A	141	PHE	0	0.062	0.022	25.978	0.092	0.092	0.000	0.000	0.000	0.000
84	A	142	PRO	0	0.043	0.012	30.985	-0.182	-0.182	0.000	0.000	0.000	0.000
85	A	143	SER	0	0.004	0.004	34.456	-0.140	-0.140	0.000	0.000	0.000	0.000
86	A	144	PHE	0	0.014	0.011	32.792	-0.179	-0.179	0.000	0.000	0.000	0.000
87	A	145	GLU	-1	-0.952	-0.967	34.740	7.941	7.941	0.000	0.000	0.000	0.000
88	A	146	THR	0	-0.101	-0.071	38.124	-0.166	-0.166	0.000	0.000	0.000	0.000
89	A	147	PHE	0	-0.032	0.009	31.344	0.034	0.034	0.000	0.000	0.000	0.000
90	A	148	ASN	0	0.027	0.015	36.880	-0.120	-0.120	0.000	0.000	0.000	0.000
91	A	149	THR	0	0.032	0.003	36.211	0.165	0.165	0.000	0.000	0.000	0.000
92	A	150	LYS	1	0.765	0.873	36.105	-8.102	-8.102	0.000	0.000	0.000	0.000
93	A	151	ASN	0	-0.067	-0.024	35.035	-0.017	-0.017	0.000	0.000	0.000	0.000
94	A	152	CYS	0	-0.022	-0.021	29.891	0.380	0.380	0.000	0.000	0.000	0.000
95	A	153	ILE	0	0.048	0.023	28.478	-0.206	-0.206	0.000	0.000	0.000	0.000
96	A	154	ALA	0	-0.009	0.003	28.010	0.522	0.522	0.000	0.000	0.000	0.000
97	A	155	TYR	0	0.022	-0.002	23.629	-0.266	-0.266	0.000	0.000	0.000	0.000
98	A	156	ASN	0	0.038	0.045	26.431	0.561	0.561	0.000	0.000	0.000	0.000
99	A	157	PRO	0	0.006	-0.014	23.266	-0.084	-0.084	0.000	0.000	0.000	0.000
100	A	158	ASN	0	-0.050	-0.023	25.192	-0.195	-0.195	0.000	0.000	0.000	0.000
101	A	159	GLY	0	-0.005	0.006	27.700	-0.075	-0.075	0.000	0.000	0.000	0.000
102	A	160	ASN	0	-0.082	-0.041	28.592	-0.204	-0.204	0.000	0.000	0.000	0.000
103	A	161	ALA	0	0.003	-0.002	29.379	0.292	0.292	0.000	0.000	0.000	0.000
104	A	162	LEU	0	0.006	0.003	30.775	-0.344	-0.344	0.000	0.000	0.000	0.000
105	A	163	ASP	-1	-0.834	-0.911	32.107	9.117	9.117	0.000	0.000	0.000	0.000
106	A	164	GLU	-1	-0.903	-0.959	33.156	8.812	8.812	0.000	0.000	0.000	0.000
107	A	165	SER	0	-0.010	-0.013	34.252	0.158	0.158	0.000	0.000	0.000	0.000
108	A	167	GLU	-1	-0.940	-0.988	32.376	9.877	9.877	0.000	0.000	0.000	0.000
109	A	168	ASP	-1	-0.857	-0.894	33.865	8.780	8.780	0.000	0.000	0.000	0.000
110	A	169	LYS	1	0.749	0.852	31.285	-9.682	-9.682	0.000	0.000	0.000	0.000
111	A	170	ASN	0	0.037	0.017	28.576	-0.240	-0.240	0.000	0.000	0.000	0.000
112	A	171	ARG	1	0.835	0.938	24.801	-11.096	-11.096	0.000	0.000	0.000	0.000
113	A	172	TYR	0	0.006	-0.015	20.634	0.078	0.078	0.000	0.000	0.000	0.000
114	A	173	ILE	0	0.025	0.009	17.740	0.375	0.375	0.000	0.000	0.000	0.000
115	A	175	LYS	1	0.817	0.887	13.433	-19.502	-19.502	0.000	0.000	0.000	0.000
116	A	176	GLN	0	-0.065	-0.034	9.431	1.642	1.642	0.000	0.000	0.000	0.000
117	A	177	GLN	0	0.033	0.007	9.929	0.728	0.728	0.000	0.000	0.000	0.000
118	A	178	LEU	0	0.009	-0.003	3.838	2.986	3.570	0.006	-0.193	-0.397	0.001
119	A	179	ILE	0	-0.011	0.012	6.344	0.036	0.036	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:57:ASP)