FMO DATABASE

FMODB ID: 946L2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1122172.390127
FMO2-HF: Nuclear repulsion	1069512.628433
FMO2-HF: Total energy	-52659.761694
FMO2-MP2: Total energy	-52806.766658

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.
-33.157	-34.735	27.819	-13.27	-12.972	0.148

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 : -0.810 / q_NPA : -0.915

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	-0.019	-0.020	1.793	-30.874	-32.840	14.435	-6.705	-5.764	0.065
4	A	60	SER	0	-0.030	-0.023	1.825	-30.944	-33.820	12.814	-4.904	-5.034	0.062
5	A	61	CYS	0	-0.079	-0.010	3.588	-9.931	-8.835	0.108	-0.621	-0.583	0.008
6	A	62	GLN	0	-0.040	-0.031	6.955	-5.854	-5.854	0.000	0.000	0.000	0.000
7	A	63	GLU	-1	-0.778	-0.861	9.584	20.848	20.848	0.000	0.000	0.000	0.000
8	A	64	LYS	1	0.773	0.843	12.332	-19.723	-19.723	0.000	0.000	0.000	0.000
9	A	65	TRP	0	0.000	0.016	10.944	-0.969	-0.969	0.000	0.000	0.000	0.000
10	A	66	VAL	0	-0.016	-0.006	11.915	0.202	0.202	0.000	0.000	0.000	0.000
11	A	67	GLY	0	0.050	0.006	8.514	1.222	1.222	0.000	0.000	0.000	0.000
12	A	68	TYR	0	-0.092	-0.074	9.374	-1.572	-1.572	0.000	0.000	0.000	0.000
13	A	69	ARG	1	0.843	0.909	10.588	-18.192	-18.192	0.000	0.000	0.000	0.000
14	A	71	ASN	0	0.018	0.009	7.126	4.946	4.946	0.000	0.000	0.000	0.000
15	A	73	TYR	0	-0.032	-0.054	9.177	-1.395	-1.395	0.000	0.000	0.000	0.000
16	A	74	PHE	0	0.016	0.015	12.856	0.368	0.368	0.000	0.000	0.000	0.000
17	A	75	ILE	0	0.019	0.004	15.553	-0.667	-0.667	0.000	0.000	0.000	0.000
18	A	76	SER	0	-0.015	0.006	19.051	-0.242	-0.242	0.000	0.000	0.000	0.000
19	A	77	SER	0	0.033	-0.001	21.813	-0.480	-0.480	0.000	0.000	0.000	0.000
20	A	78	GLU	-1	-0.810	-0.885	24.577	12.171	12.171	0.000	0.000	0.000	0.000
21	A	79	GLN	0	-0.007	0.002	25.911	0.336	0.336	0.000	0.000	0.000	0.000
22	A	80	LYS	1	0.818	0.898	25.870	-12.444	-12.444	0.000	0.000	0.000	0.000
23	A	81	THR	0	0.026	-0.005	28.622	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	82	TRP	0	0.005	0.030	25.944	0.458	0.458	0.000	0.000	0.000	0.000
25	A	83	ASN	0	0.081	0.002	25.994	0.836	0.836	0.000	0.000	0.000	0.000
26	A	84	GLU	-1	-0.809	-0.885	26.117	11.019	11.019	0.000	0.000	0.000	0.000
27	A	85	SER	0	-0.001	-0.021	23.419	0.521	0.521	0.000	0.000	0.000	0.000
28	A	86	ARG	1	0.893	0.952	21.866	-12.104	-12.104	0.000	0.000	0.000	0.000
29	A	87	HIS	0	-0.002	-0.004	21.324	1.021	1.021	0.000	0.000	0.000	0.000
30	A	88	LEU	0	-0.021	0.003	21.273	0.425	0.425	0.000	0.000	0.000	0.000
31	A	89	CYS	0	-0.034	0.029	15.890	0.071	0.071	0.000	0.000	0.000	0.000
32	A	90	ALA	0	0.048	0.043	16.814	1.225	1.225	0.000	0.000	0.000	0.000
33	A	91	SER	0	-0.093	-0.060	17.734	0.719	0.719	0.000	0.000	0.000	0.000
34	A	92	GLN	0	-0.059	-0.027	14.691	1.128	1.128	0.000	0.000	0.000	0.000
35	A	93	LYS	1	0.903	0.949	10.540	-25.429	-25.429	0.000	0.000	0.000	0.000
36	A	94	SER	0	-0.070	-0.041	12.416	2.359	2.359	0.000	0.000	0.000	0.000
37	A	95	SER	0	0.032	0.021	14.293	-0.930	-0.930	0.000	0.000	0.000	0.000
38	A	96	LEU	0	-0.005	-0.007	16.849	0.758	0.758	0.000	0.000	0.000	0.000
39	A	97	LEU	0	-0.016	-0.019	17.261	0.207	0.207	0.000	0.000	0.000	0.000
40	A	98	GLN	0	0.037	0.037	17.643	-0.649	-0.649	0.000	0.000	0.000	0.000
41	A	99	LEU	0	-0.013	0.007	17.891	0.992	0.992	0.000	0.000	0.000	0.000
42	A	100	GLN	0	-0.003	-0.025	16.438	0.029	0.029	0.000	0.000	0.000	0.000
43	A	101	ASN	0	-0.048	-0.042	18.996	-0.416	-0.416	0.000	0.000	0.000	0.000
44	A	102	THR	0	0.067	0.024	21.008	0.483	0.483	0.000	0.000	0.000	0.000
45	A	103	ASP	-1	-0.859	-0.915	21.216	13.921	13.921	0.000	0.000	0.000	0.000
46	A	104	GLU	-1	-0.809	-0.841	15.845	20.383	20.383	0.000	0.000	0.000	0.000
47	A	105	LEU	0	0.008	-0.010	16.648	1.142	1.142	0.000	0.000	0.000	0.000
48	A	106	ASP	-1	-0.750	-0.856	18.951	15.930	15.930	0.000	0.000	0.000	0.000
49	A	107	PHE	0	-0.023	0.010	15.890	-0.639	-0.639	0.000	0.000	0.000	0.000
50	A	108	MET	0	-0.034	-0.015	19.251	-0.119	-0.119	0.000	0.000	0.000	0.000
51	A	109	SER	0	-0.017	-0.028	21.464	-0.730	-0.730	0.000	0.000	0.000	0.000
52	A	110	SER	0	-0.023	-0.003	24.427	-0.367	-0.367	0.000	0.000	0.000	0.000
53	A	111	SER	0	-0.040	-0.015	24.494	-0.679	-0.679	0.000	0.000	0.000	0.000
54	A	112	GLN	0	0.060	0.022	26.472	0.208	0.208	0.000	0.000	0.000	0.000
55	A	113	GLN	0	-0.041	-0.014	26.354	-0.375	-0.375	0.000	0.000	0.000	0.000
56	A	114	PHE	0	0.058	0.023	27.341	0.252	0.252	0.000	0.000	0.000	0.000
57	A	115	TYR	0	-0.048	-0.028	23.151	0.033	0.033	0.000	0.000	0.000	0.000
58	A	116	TRP	0	-0.017	-0.015	25.031	0.123	0.123	0.000	0.000	0.000	0.000
59	A	117	ILE	0	-0.011	-0.007	22.424	0.800	0.800	0.000	0.000	0.000	0.000
60	A	118	GLY	0	-0.007	0.010	21.661	-0.535	-0.535	0.000	0.000	0.000	0.000
61	A	119	LEU	0	-0.060	-0.035	22.656	0.137	0.137	0.000	0.000	0.000	0.000
62	A	120	SER	0	0.011	-0.001	25.775	-0.198	-0.198	0.000	0.000	0.000	0.000
63	A	121	TYR	0	0.000	-0.002	29.009	0.072	0.072	0.000	0.000	0.000	0.000
64	A	122	SER	0	-0.034	-0.030	30.719	0.022	0.022	0.000	0.000	0.000	0.000
65	A	123	GLU	-1	-0.800	-0.921	32.737	8.383	8.383	0.000	0.000	0.000	0.000
66	A	124	GLU	-1	-0.966	-0.978	33.918	8.597	8.597	0.000	0.000	0.000	0.000
67	A	125	HIS	0	-0.014	0.009	30.795	0.023	0.023	0.000	0.000	0.000	0.000
68	A	126	THR	0	-0.045	-0.011	34.020	-0.094	-0.094	0.000	0.000	0.000	0.000
69	A	127	ALA	0	0.015	0.017	31.910	-0.075	-0.075	0.000	0.000	0.000	0.000
70	A	128	TRP	0	-0.002	0.002	29.455	0.255	0.255	0.000	0.000	0.000	0.000
71	A	129	LEU	0	-0.021	-0.011	26.334	0.159	0.159	0.000	0.000	0.000	0.000
72	A	130	TRP	0	0.041	0.012	21.481	0.220	0.220	0.000	0.000	0.000	0.000
73	A	131	GLU	-1	-0.792	-0.903	20.439	14.932	14.932	0.000	0.000	0.000	0.000
74	A	132	ASN	0	-0.048	0.006	18.111	-0.609	-0.609	0.000	0.000	0.000	0.000
75	A	133	GLY	0	0.022	0.015	20.657	-0.073	-0.073	0.000	0.000	0.000	0.000
76	A	134	SER	0	-0.059	-0.043	21.288	-0.355	-0.355	0.000	0.000	0.000	0.000
77	A	135	ALA	0	0.049	0.009	23.480	-0.074	-0.074	0.000	0.000	0.000	0.000
78	A	136	LEU	0	0.001	0.012	24.941	0.538	0.538	0.000	0.000	0.000	0.000
79	A	137	SER	0	-0.023	-0.010	25.782	-0.544	-0.544	0.000	0.000	0.000	0.000
80	A	138	GLN	0	0.043	0.006	27.493	-0.102	-0.102	0.000	0.000	0.000	0.000
81	A	139	TYR	0	-0.023	-0.020	29.270	-0.269	-0.269	0.000	0.000	0.000	0.000
82	A	140	LEU	0	-0.046	-0.003	23.339	0.013	0.013	0.000	0.000	0.000	0.000
83	A	141	PHE	0	0.035	0.006	25.299	0.125	0.125	0.000	0.000	0.000	0.000
84	A	142	PRO	0	0.031	0.012	30.386	-0.226	-0.226	0.000	0.000	0.000	0.000
85	A	143	SER	0	0.013	0.016	33.936	-0.162	-0.162	0.000	0.000	0.000	0.000
86	A	144	PHE	0	0.025	0.008	32.206	-0.156	-0.156	0.000	0.000	0.000	0.000
87	A	145	GLU	-1	-0.960	-0.974	34.179	8.150	8.150	0.000	0.000	0.000	0.000
88	A	146	THR	0	-0.122	-0.077	37.344	-0.247	-0.247	0.000	0.000	0.000	0.000
89	A	147	PHE	0	-0.019	0.013	30.872	0.002	0.002	0.000	0.000	0.000	0.000
90	A	148	ASN	0	0.030	0.010	36.277	-0.160	-0.160	0.000	0.000	0.000	0.000
91	A	149	THR	0	0.011	0.002	35.924	0.198	0.198	0.000	0.000	0.000	0.000
92	A	150	LYS	1	0.739	0.860	36.008	-8.392	-8.392	0.000	0.000	0.000	0.000
93	A	151	ASN	0	-0.050	-0.012	34.628	-0.118	-0.118	0.000	0.000	0.000	0.000
94	A	152	CYS	0	-0.045	-0.037	29.526	0.376	0.376	0.000	0.000	0.000	0.000
95	A	153	ILE	0	0.035	0.015	27.874	-0.172	-0.172	0.000	0.000	0.000	0.000
96	A	154	ALA	0	-0.005	0.003	27.256	0.500	0.500	0.000	0.000	0.000	0.000
97	A	155	TYR	0	0.017	-0.010	22.922	-0.307	-0.307	0.000	0.000	0.000	0.000
98	A	156	ASN	0	0.032	0.019	26.230	0.409	0.409	0.000	0.000	0.000	0.000
99	A	157	PRO	0	-0.004	-0.014	22.949	-0.075	-0.075	0.000	0.000	0.000	0.000
100	A	158	ASN	0	-0.030	-0.006	24.867	-0.183	-0.183	0.000	0.000	0.000	0.000
101	A	159	GLY	0	-0.027	0.002	26.898	-0.171	-0.171	0.000	0.000	0.000	0.000
102	A	160	ASN	0	-0.072	-0.040	27.855	-0.289	-0.289	0.000	0.000	0.000	0.000
103	A	161	ALA	0	0.003	-0.004	28.467	0.397	0.397	0.000	0.000	0.000	0.000
104	A	162	LEU	0	-0.006	0.011	30.180	-0.373	-0.373	0.000	0.000	0.000	0.000
105	A	163	ASP	-1	-0.813	-0.904	31.389	9.352	9.352	0.000	0.000	0.000	0.000
106	A	164	GLU	-1	-0.879	-0.930	32.760	8.993	8.993	0.000	0.000	0.000	0.000
107	A	165	SER	0	-0.010	-0.037	34.073	0.123	0.123	0.000	0.000	0.000	0.000
108	A	167	GLU	-1	-0.872	-0.924	31.577	10.211	10.211	0.000	0.000	0.000	0.000
109	A	168	ASP	-1	-0.839	-0.880	33.596	8.913	8.913	0.000	0.000	0.000	0.000
110	A	169	LYS	1	0.780	0.865	31.067	-9.718	-9.718	0.000	0.000	0.000	0.000
111	A	170	ASN	0	0.040	0.036	28.561	-0.178	-0.178	0.000	0.000	0.000	0.000
112	A	171	ARG	1	0.801	0.908	24.781	-11.256	-11.256	0.000	0.000	0.000	0.000
113	A	172	TYR	0	-0.008	-0.029	20.554	0.104	0.104	0.000	0.000	0.000	0.000
114	A	173	ILE	0	0.023	0.014	17.438	0.378	0.378	0.000	0.000	0.000	0.000
115	A	175	LYS	1	0.798	0.875	13.056	-19.886	-19.886	0.000	0.000	0.000	0.000
116	A	176	GLN	0	-0.025	-0.009	9.014	2.058	2.058	0.000	0.000	0.000	0.000
117	A	177	GLN	0	0.032	0.003	8.913	-0.629	-0.629	0.000	0.000	0.000	0.000
118	A	178	LEU	0	-0.031	-0.001	2.761	-2.037	0.088	0.463	-1.036	-1.552	0.013
119	A	179	ILE	0	-0.003	0.009	5.085	1.455	1.498	-0.001	-0.004	-0.039	0.000

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