FMO DATABASE

FMODB ID: N9MZQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1030088.847967
FMO2-HF: Nuclear repulsion	980317.948895
FMO2-HF: Total energy	-49770.899072
FMO2-MP2: Total energy	-49910.801776

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.
-4.395	-2.756	-0.023	-0.766	-0.85	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 : -0.009 / q_NPA : -0.010

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	0.041	0.018	3.835	-1.093	0.396	-0.022	-0.740	-0.726	0.003
4	B	116	CYS	0	-0.042	-0.017	6.759	0.113	0.113	0.000	0.000	0.000	0.000
5	B	117	GLY	0	0.041	0.021	10.532	-0.116	-0.116	0.000	0.000	0.000	0.000
6	B	118	HIS	0	0.001	-0.005	12.182	-0.064	-0.064	0.000	0.000	0.000	0.000
7	B	119	CYS	0	-0.093	-0.035	12.729	0.053	0.053	0.000	0.000	0.000	0.000
8	B	120	PRO	0	0.029	0.000	11.184	-0.043	-0.043	0.000	0.000	0.000	0.000
9	B	121	GLU	-1	-0.937	-0.956	4.324	-2.850	-2.700	-0.001	-0.026	-0.124	0.000
10	B	122	GLU	-1	-0.907	-0.957	6.607	-0.954	-0.954	0.000	0.000	0.000	0.000
11	B	123	TRP	0	-0.097	-0.039	8.897	0.225	0.225	0.000	0.000	0.000	0.000
12	B	124	ILE	0	-0.020	-0.012	11.058	0.014	0.014	0.000	0.000	0.000	0.000
13	B	125	THR	0	0.043	0.014	13.433	-0.007	-0.007	0.000	0.000	0.000	0.000
14	B	126	TYR	0	-0.035	-0.024	15.559	0.027	0.027	0.000	0.000	0.000	0.000
15	B	127	SER	0	0.017	0.013	18.792	0.022	0.022	0.000	0.000	0.000	0.000
16	B	128	ASN	0	-0.040	-0.018	20.764	-0.006	-0.006	0.000	0.000	0.000	0.000
17	B	129	SER	0	0.058	0.031	20.031	-0.011	-0.011	0.000	0.000	0.000	0.000
18	B	131	TYR	0	-0.030	-0.055	16.295	0.009	0.009	0.000	0.000	0.000	0.000
19	B	132	TYR	0	0.047	0.041	13.505	0.001	0.001	0.000	0.000	0.000	0.000
20	B	133	ILE	0	0.019	-0.001	15.968	0.024	0.024	0.000	0.000	0.000	0.000
21	B	134	GLY	0	0.067	0.030	16.729	-0.021	-0.021	0.000	0.000	0.000	0.000
22	B	135	LYS	1	0.839	0.899	14.742	0.197	0.197	0.000	0.000	0.000	0.000
23	B	136	GLU	-1	-0.757	-0.840	19.459	-0.221	-0.221	0.000	0.000	0.000	0.000
24	B	137	ARG	1	0.858	0.923	21.995	0.087	0.087	0.000	0.000	0.000	0.000
25	B	138	ARG	1	0.863	0.925	21.888	0.171	0.171	0.000	0.000	0.000	0.000
26	B	139	THR	0	0.071	0.048	27.440	0.010	0.010	0.000	0.000	0.000	0.000
27	B	140	TRP	0	0.007	0.016	29.219	-0.009	-0.009	0.000	0.000	0.000	0.000
28	B	141	GLU	-1	-0.865	-0.952	29.734	-0.089	-0.089	0.000	0.000	0.000	0.000
29	B	142	GLU	-1	-0.862	-0.933	27.700	-0.123	-0.123	0.000	0.000	0.000	0.000
30	B	143	SER	0	-0.049	-0.039	25.382	-0.015	-0.015	0.000	0.000	0.000	0.000
31	B	144	LEU	0	0.004	0.002	25.066	-0.012	-0.012	0.000	0.000	0.000	0.000
32	B	145	LEU	0	0.007	0.006	26.134	-0.009	-0.009	0.000	0.000	0.000	0.000
33	B	146	ALA	0	0.005	0.013	22.300	-0.013	-0.013	0.000	0.000	0.000	0.000
34	B	147	CYS	0	-0.091	-0.042	19.171	-0.013	-0.013	0.000	0.000	0.000	0.000
35	B	148	THR	0	-0.016	-0.015	21.601	-0.010	-0.010	0.000	0.000	0.000	0.000
36	B	149	SER	0	-0.042	-0.001	21.847	-0.011	-0.011	0.000	0.000	0.000	0.000
37	B	150	LYS	1	0.854	0.932	17.226	0.265	0.265	0.000	0.000	0.000	0.000
38	B	151	ASN	0	-0.032	-0.013	18.242	0.003	0.003	0.000	0.000	0.000	0.000
39	B	152	SER	0	-0.033	-0.017	19.488	0.008	0.008	0.000	0.000	0.000	0.000
40	B	153	SER	0	0.017	0.017	21.772	0.010	0.010	0.000	0.000	0.000	0.000
41	B	154	LEU	0	0.038	0.010	23.358	-0.006	-0.006	0.000	0.000	0.000	0.000
42	B	155	LEU	0	-0.012	0.014	23.573	0.006	0.006	0.000	0.000	0.000	0.000
43	B	156	SER	0	0.004	0.014	25.252	0.004	0.004	0.000	0.000	0.000	0.000
44	B	157	ILE	0	-0.014	-0.024	26.917	0.000	0.000	0.000	0.000	0.000	0.000
45	B	158	ASP	-1	-0.842	-0.909	27.581	-0.041	-0.041	0.000	0.000	0.000	0.000
46	B	159	ASN	0	-0.002	-0.011	29.836	0.001	0.001	0.000	0.000	0.000	0.000
47	B	160	GLU	-1	-0.761	-0.880	31.142	-0.010	-0.010	0.000	0.000	0.000	0.000
48	B	161	GLU	-1	-0.937	-0.958	28.185	0.027	0.027	0.000	0.000	0.000	0.000
49	B	162	GLU	-1	-0.744	-0.838	25.018	-0.038	-0.038	0.000	0.000	0.000	0.000
50	B	163	MET	0	-0.011	0.014	26.193	-0.003	-0.003	0.000	0.000	0.000	0.000
51	B	164	LYS	1	0.953	0.982	27.759	-0.017	-0.017	0.000	0.000	0.000	0.000
52	B	165	PHE	0	0.026	0.024	19.174	0.003	0.003	0.000	0.000	0.000	0.000
53	B	166	LEU	0	0.050	0.009	21.930	0.000	0.000	0.000	0.000	0.000	0.000
54	B	167	SER	0	-0.117	-0.071	24.212	-0.005	-0.005	0.000	0.000	0.000	0.000
55	B	168	ILE	0	-0.054	-0.026	22.263	0.001	0.001	0.000	0.000	0.000	0.000
56	B	169	ILE	0	0.002	0.019	18.398	0.001	0.001	0.000	0.000	0.000	0.000
57	B	170	SER	0	-0.031	-0.039	20.722	-0.024	-0.024	0.000	0.000	0.000	0.000
58	B	171	PRO	0	-0.005	0.030	23.170	0.003	0.003	0.000	0.000	0.000	0.000
59	B	172	SER	0	-0.028	-0.026	26.312	0.005	0.005	0.000	0.000	0.000	0.000
60	B	173	SER	0	0.010	-0.008	24.989	-0.014	-0.014	0.000	0.000	0.000	0.000
61	B	174	TRP	0	-0.024	0.003	26.904	0.013	0.013	0.000	0.000	0.000	0.000
62	B	175	ILE	0	0.008	0.005	27.271	-0.004	-0.004	0.000	0.000	0.000	0.000
63	B	176	GLY	0	-0.007	0.002	29.054	0.000	0.000	0.000	0.000	0.000	0.000
64	B	177	VAL	0	-0.065	-0.055	30.504	0.004	0.004	0.000	0.000	0.000	0.000
65	B	178	PHE	0	-0.047	-0.023	34.176	-0.002	-0.002	0.000	0.000	0.000	0.000
66	B	179	ARG	1	0.881	0.937	37.046	0.039	0.039	0.000	0.000	0.000	0.000
67	B	180	ASN	0	0.006	-0.003	40.475	-0.005	-0.005	0.000	0.000	0.000	0.000
68	B	181	SER	0	-0.033	-0.021	42.738	0.000	0.000	0.000	0.000	0.000	0.000
69	B	182	SER	0	0.078	0.019	44.970	0.000	0.000	0.000	0.000	0.000	0.000
70	B	183	HIS	0	-0.051	-0.025	46.323	0.000	0.000	0.000	0.000	0.000	0.000
71	B	184	HIS	0	0.046	0.050	44.835	-0.001	-0.001	0.000	0.000	0.000	0.000
72	B	185	PRO	0	0.016	-0.005	43.605	0.000	0.000	0.000	0.000	0.000	0.000
73	B	186	TRP	0	0.036	0.026	37.669	-0.003	-0.003	0.000	0.000	0.000	0.000
74	B	187	VAL	0	-0.012	0.005	38.117	0.003	0.003	0.000	0.000	0.000	0.000
75	B	188	THR	0	-0.033	-0.014	33.555	-0.004	-0.004	0.000	0.000	0.000	0.000
76	B	189	MET	0	0.033	0.010	30.670	0.001	0.001	0.000	0.000	0.000	0.000
77	B	190	ASN	0	-0.040	-0.024	30.652	-0.008	-0.008	0.000	0.000	0.000	0.000
78	B	191	GLY	0	0.016	0.026	33.863	0.003	0.003	0.000	0.000	0.000	0.000
79	B	192	LEU	0	-0.029	-0.011	35.708	0.004	0.004	0.000	0.000	0.000	0.000
80	B	193	ALA	0	0.037	0.014	38.409	-0.002	-0.002	0.000	0.000	0.000	0.000
81	B	194	PHE	0	0.000	-0.014	33.322	0.001	0.001	0.000	0.000	0.000	0.000
82	B	195	LYS	1	0.947	0.961	38.050	0.020	0.020	0.000	0.000	0.000	0.000
83	B	196	HIS	0	-0.023	0.016	33.729	0.005	0.005	0.000	0.000	0.000	0.000
84	B	197	GLU	-1	-0.921	-0.956	38.129	-0.015	-0.015	0.000	0.000	0.000	0.000
85	B	198	ILE	0	-0.045	-0.028	37.011	-0.001	-0.001	0.000	0.000	0.000	0.000
86	B	199	LYS	1	0.888	0.914	37.850	0.024	0.024	0.000	0.000	0.000	0.000
87	B	200	ASP	-1	-0.845	-0.901	39.091	-0.029	-0.029	0.000	0.000	0.000	0.000
88	B	201	SER	0	0.002	-0.026	41.220	-0.001	-0.001	0.000	0.000	0.000	0.000
89	B	202	ASP	-1	-0.821	-0.869	43.601	-0.025	-0.025	0.000	0.000	0.000	0.000
90	B	203	ASN	0	-0.059	-0.014	46.271	-0.003	-0.003	0.000	0.000	0.000	0.000
91	B	204	ALA	0	-0.046	-0.021	44.686	0.001	0.001	0.000	0.000	0.000	0.000
92	B	205	GLU	-1	-0.849	-0.942	43.362	-0.045	-0.045	0.000	0.000	0.000	0.000
93	B	206	LEU	0	-0.077	-0.022	39.576	-0.004	-0.004	0.000	0.000	0.000	0.000
94	B	207	ASN	0	0.067	0.028	39.605	0.004	0.004	0.000	0.000	0.000	0.000
95	B	208	CYS	0	0.057	0.046	34.305	-0.005	-0.005	0.000	0.000	0.000	0.000
96	B	209	ALA	0	0.026	0.020	33.880	0.003	0.003	0.000	0.000	0.000	0.000
97	B	210	VAL	0	-0.001	-0.007	30.749	-0.007	-0.007	0.000	0.000	0.000	0.000
98	B	211	LEU	0	-0.009	0.008	27.414	0.007	0.007	0.000	0.000	0.000	0.000
99	B	212	GLN	0	-0.020	-0.035	29.344	-0.006	-0.006	0.000	0.000	0.000	0.000
100	B	213	VAL	0	-0.024	-0.023	29.172	0.005	0.005	0.000	0.000	0.000	0.000
101	B	214	ASN	0	0.002	0.004	29.973	0.002	0.002	0.000	0.000	0.000	0.000
102	B	215	ARG	1	0.845	0.890	31.674	0.012	0.012	0.000	0.000	0.000	0.000
103	B	216	LEU	0	0.031	0.038	32.638	-0.005	-0.005	0.000	0.000	0.000	0.000
104	B	217	LYS	1	0.831	0.912	34.610	0.037	0.037	0.000	0.000	0.000	0.000
105	B	218	SER	0	0.033	0.021	35.746	-0.004	-0.004	0.000	0.000	0.000	0.000
106	B	219	ALA	0	0.006	-0.022	34.879	0.002	0.002	0.000	0.000	0.000	0.000
107	B	220	GLN	0	0.034	0.007	37.014	-0.003	-0.003	0.000	0.000	0.000	0.000
108	B	222	GLY	0	0.048	0.026	34.213	-0.006	-0.006	0.000	0.000	0.000	0.000
109	B	223	SER	0	-0.070	-0.036	33.714	0.000	0.000	0.000	0.000	0.000	0.000
110	B	224	SER	0	0.009	0.007	29.406	-0.006	-0.006	0.000	0.000	0.000	0.000
111	B	225	ILE	0	-0.049	-0.044	28.242	0.006	0.006	0.000	0.000	0.000	0.000
112	B	226	ILE	0	-0.025	0.005	22.487	-0.009	-0.009	0.000	0.000	0.000	0.000
113	B	227	TYR	0	-0.002	-0.023	20.600	0.007	0.007	0.000	0.000	0.000	0.000
114	B	228	HIS	0	0.066	0.034	20.733	-0.028	-0.028	0.000	0.000	0.000	0.000
115	B	230	LYS	1	0.799	0.871	19.899	0.051	0.051	0.000	0.000	0.000	0.000
116	B	231	HIS	0	-0.006	0.008	17.417	0.018	0.018	0.000	0.000	0.000	0.000
117	B	232	LYS	1	0.969	0.980	21.380	0.122	0.122	0.000	0.000	0.000	0.000

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