FMO DATABASE

FMODB ID: 395KL

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	OptH
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	-1119653.356256
FMO2-HF: Nuclear repulsion	1066994.883249
FMO2-HF: Total energy	-52658.473007
FMO2-MP2: Total energy	-52805.421497

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.
-3.095	3.035	10.369	-7.474	-9.027	0.074

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 : -0.876 / q_NPA : -0.959

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	-0.011	1.969	-31.509	-28.960	8.090	-5.451	-5.189	0.047
4	A	60	SER	0	0.041	0.030	2.738	-5.540	-2.846	2.211	-1.717	-3.188	0.022
5	A	61	CYS	0	-0.066	-0.037	3.604	-6.905	-6.448	0.066	-0.184	-0.339	0.004
6	A	62	GLN	0	0.008	-0.004	7.355	-3.291	-3.291	0.000	0.000	0.000	0.000
7	A	63	GLU	-1	-0.872	-0.915	9.535	21.619	21.619	0.000	0.000	0.000	0.000
8	A	64	LYS	1	0.867	0.908	12.341	-19.848	-19.848	0.000	0.000	0.000	0.000
9	A	65	TRP	0	0.014	0.024	10.662	-1.048	-1.048	0.000	0.000	0.000	0.000
10	A	66	VAL	0	-0.033	-0.021	11.831	0.806	0.806	0.000	0.000	0.000	0.000
11	A	67	GLY	0	0.063	0.026	8.896	0.756	0.756	0.000	0.000	0.000	0.000
12	A	68	TYR	0	-0.048	-0.031	9.783	-1.590	-1.590	0.000	0.000	0.000	0.000
13	A	69	ARG	1	0.934	0.960	11.230	-18.707	-18.707	0.000	0.000	0.000	0.000
14	A	71	ASN	0	0.059	0.043	7.967	2.550	2.550	0.000	0.000	0.000	0.000
15	A	73	TYR	0	-0.017	-0.029	9.688	-1.297	-1.297	0.000	0.000	0.000	0.000
16	A	74	PHE	0	0.007	0.021	13.368	0.398	0.398	0.000	0.000	0.000	0.000
17	A	75	ILE	0	0.014	0.001	15.732	-0.735	-0.735	0.000	0.000	0.000	0.000
18	A	76	SER	0	-0.005	0.023	19.193	-0.189	-0.189	0.000	0.000	0.000	0.000
19	A	77	SER	0	0.019	-0.016	21.836	-0.392	-0.392	0.000	0.000	0.000	0.000
20	A	78	GLU	-1	-0.941	-0.973	24.537	12.127	12.127	0.000	0.000	0.000	0.000
21	A	79	GLN	0	-0.021	-0.017	25.849	0.186	0.186	0.000	0.000	0.000	0.000
22	A	80	LYS	1	0.908	0.948	26.069	-11.772	-11.772	0.000	0.000	0.000	0.000
23	A	81	THR	0	0.106	0.070	28.638	0.042	0.042	0.000	0.000	0.000	0.000
24	A	82	TRP	0	0.074	0.057	26.368	0.376	0.376	0.000	0.000	0.000	0.000
25	A	83	ASN	0	0.049	-0.014	26.562	0.639	0.639	0.000	0.000	0.000	0.000
26	A	84	GLU	-1	-0.894	-0.958	26.592	10.891	10.891	0.000	0.000	0.000	0.000
27	A	85	SER	0	-0.010	-0.019	23.675	0.546	0.546	0.000	0.000	0.000	0.000
28	A	86	ARG	1	0.889	0.967	22.288	-11.676	-11.676	0.000	0.000	0.000	0.000
29	A	87	HIS	0	-0.016	-0.008	21.955	0.975	0.975	0.000	0.000	0.000	0.000
30	A	88	LEU	0	0.000	0.017	21.376	0.500	0.500	0.000	0.000	0.000	0.000
31	A	89	CYS	0	-0.034	0.039	15.859	0.184	0.184	0.000	0.000	0.000	0.000
32	A	90	ALA	0	0.069	0.041	17.139	1.192	1.192	0.000	0.000	0.000	0.000
33	A	91	SER	0	-0.115	-0.079	18.314	0.529	0.529	0.000	0.000	0.000	0.000
34	A	92	GLN	0	-0.052	-0.018	14.754	1.232	1.232	0.000	0.000	0.000	0.000
35	A	93	LYS	1	0.884	0.943	10.665	-24.783	-24.783	0.000	0.000	0.000	0.000
36	A	94	SER	0	-0.069	-0.036	12.975	2.069	2.069	0.000	0.000	0.000	0.000
37	A	95	SER	0	0.046	0.022	14.667	-0.919	-0.919	0.000	0.000	0.000	0.000
38	A	96	LEU	0	0.022	0.016	17.138	0.778	0.778	0.000	0.000	0.000	0.000
39	A	97	LEU	0	-0.024	-0.016	17.735	0.193	0.193	0.000	0.000	0.000	0.000
40	A	98	GLN	0	0.021	0.015	17.943	-0.982	-0.982	0.000	0.000	0.000	0.000
41	A	99	LEU	0	-0.029	-0.012	18.456	0.888	0.888	0.000	0.000	0.000	0.000
42	A	100	GLN	0	-0.039	-0.027	16.806	-0.158	-0.158	0.000	0.000	0.000	0.000
43	A	101	ASN	0	-0.027	-0.030	18.860	-0.488	-0.488	0.000	0.000	0.000	0.000
44	A	102	THR	0	0.084	0.034	21.456	0.486	0.486	0.000	0.000	0.000	0.000
45	A	103	ASP	-1	-0.870	-0.920	20.734	13.821	13.821	0.000	0.000	0.000	0.000
46	A	104	GLU	-1	-0.868	-0.936	16.402	19.229	19.229	0.000	0.000	0.000	0.000
47	A	105	LEU	0	-0.039	-0.034	17.205	1.102	1.102	0.000	0.000	0.000	0.000
48	A	106	ASP	-1	-0.870	-0.934	19.519	13.556	13.556	0.000	0.000	0.000	0.000
49	A	107	PHE	0	-0.059	-0.034	16.011	-0.457	-0.457	0.000	0.000	0.000	0.000
50	A	108	MET	0	-0.059	-0.024	19.125	-0.252	-0.252	0.000	0.000	0.000	0.000
51	A	109	SER	0	0.043	0.014	21.800	-0.637	-0.637	0.000	0.000	0.000	0.000
52	A	110	SER	0	-0.040	-0.010	24.837	-0.395	-0.395	0.000	0.000	0.000	0.000
53	A	111	SER	0	-0.027	-0.006	25.064	-0.601	-0.601	0.000	0.000	0.000	0.000
54	A	112	GLN	0	0.045	0.007	26.995	0.025	0.025	0.000	0.000	0.000	0.000
55	A	113	GLN	0	-0.055	-0.021	26.612	-0.594	-0.594	0.000	0.000	0.000	0.000
56	A	114	PHE	0	0.043	0.011	27.472	0.269	0.269	0.000	0.000	0.000	0.000
57	A	115	TYR	0	-0.052	-0.035	23.477	0.002	0.002	0.000	0.000	0.000	0.000
58	A	116	TRP	0	-0.015	-0.002	25.364	0.175	0.175	0.000	0.000	0.000	0.000
59	A	117	ILE	0	-0.011	-0.010	22.834	0.765	0.765	0.000	0.000	0.000	0.000
60	A	118	GLY	0	-0.024	-0.029	22.338	-0.434	-0.434	0.000	0.000	0.000	0.000
61	A	119	LEU	0	-0.049	-0.014	23.321	0.020	0.020	0.000	0.000	0.000	0.000
62	A	120	SER	0	-0.013	-0.019	26.373	-0.319	-0.319	0.000	0.000	0.000	0.000
63	A	121	TYR	0	0.019	0.011	29.334	0.085	0.085	0.000	0.000	0.000	0.000
64	A	122	SER	0	-0.032	-0.032	30.858	-0.041	-0.041	0.000	0.000	0.000	0.000
65	A	123	GLU	-1	-0.912	-0.984	32.841	8.043	8.043	0.000	0.000	0.000	0.000
66	A	124	GLU	-1	-0.985	-0.993	34.331	8.474	8.474	0.000	0.000	0.000	0.000
67	A	125	HIS	0	-0.007	0.025	30.622	-0.118	-0.118	0.000	0.000	0.000	0.000
68	A	126	THR	0	-0.018	0.001	34.287	-0.042	-0.042	0.000	0.000	0.000	0.000
69	A	127	ALA	0	-0.008	0.003	32.085	-0.059	-0.059	0.000	0.000	0.000	0.000
70	A	128	TRP	0	-0.001	0.003	29.901	0.210	0.210	0.000	0.000	0.000	0.000
71	A	129	LEU	0	-0.030	-0.012	26.470	0.140	0.140	0.000	0.000	0.000	0.000
72	A	130	TRP	0	0.040	0.018	21.684	0.192	0.192	0.000	0.000	0.000	0.000
73	A	131	GLU	-1	-0.840	-0.945	21.129	14.008	14.008	0.000	0.000	0.000	0.000
74	A	132	ASN	0	-0.052	-0.008	18.323	-0.710	-0.710	0.000	0.000	0.000	0.000
75	A	133	GLY	0	0.025	0.021	20.906	-0.071	-0.071	0.000	0.000	0.000	0.000
76	A	134	SER	0	-0.078	-0.041	21.517	-0.199	-0.199	0.000	0.000	0.000	0.000
77	A	135	ALA	0	0.043	0.008	23.711	-0.050	-0.050	0.000	0.000	0.000	0.000
78	A	136	LEU	0	-0.008	0.016	25.284	0.534	0.534	0.000	0.000	0.000	0.000
79	A	137	SER	0	-0.016	-0.015	26.192	-0.482	-0.482	0.000	0.000	0.000	0.000
80	A	138	GLN	0	0.039	0.005	27.938	-0.154	-0.154	0.000	0.000	0.000	0.000
81	A	139	TYR	0	-0.029	-0.025	29.268	-0.208	-0.208	0.000	0.000	0.000	0.000
82	A	140	LEU	0	-0.065	-0.008	24.772	0.043	0.043	0.000	0.000	0.000	0.000
83	A	141	PHE	0	0.063	0.022	25.886	0.100	0.100	0.000	0.000	0.000	0.000
84	A	142	PRO	0	0.052	0.019	31.013	-0.167	-0.167	0.000	0.000	0.000	0.000
85	A	143	SER	0	0.018	0.001	34.476	-0.146	-0.146	0.000	0.000	0.000	0.000
86	A	144	PHE	0	-0.003	0.010	32.830	-0.185	-0.185	0.000	0.000	0.000	0.000
87	A	145	GLU	-1	-0.951	-0.967	34.771	7.860	7.860	0.000	0.000	0.000	0.000
88	A	146	THR	0	-0.103	-0.070	38.161	-0.156	-0.156	0.000	0.000	0.000	0.000
89	A	147	PHE	0	-0.032	0.008	31.293	0.036	0.036	0.000	0.000	0.000	0.000
90	A	148	ASN	0	0.012	-0.002	36.898	-0.027	-0.027	0.000	0.000	0.000	0.000
91	A	149	THR	0	0.025	0.000	36.233	0.160	0.160	0.000	0.000	0.000	0.000
92	A	150	LYS	1	0.897	0.950	36.124	-7.732	-7.732	0.000	0.000	0.000	0.000
93	A	151	ASN	0	-0.041	-0.003	35.043	-0.017	-0.017	0.000	0.000	0.000	0.000
94	A	152	CYS	0	-0.013	-0.017	29.832	0.395	0.395	0.000	0.000	0.000	0.000
95	A	153	ILE	0	0.042	0.024	28.357	-0.201	-0.201	0.000	0.000	0.000	0.000
96	A	154	ALA	0	-0.009	-0.002	27.989	0.524	0.524	0.000	0.000	0.000	0.000
97	A	155	TYR	0	0.021	-0.007	23.638	-0.309	-0.309	0.000	0.000	0.000	0.000
98	A	156	ASN	0	0.010	0.031	26.392	0.492	0.492	0.000	0.000	0.000	0.000
99	A	157	PRO	0	-0.003	-0.015	23.274	-0.088	-0.088	0.000	0.000	0.000	0.000
100	A	158	ASN	0	0.008	0.014	25.150	0.232	0.232	0.000	0.000	0.000	0.000
101	A	159	GLY	0	-0.011	-0.001	27.678	-0.084	-0.084	0.000	0.000	0.000	0.000
102	A	160	ASN	0	-0.103	-0.048	28.565	-0.226	-0.226	0.000	0.000	0.000	0.000
103	A	161	ALA	0	-0.001	-0.004	29.385	0.312	0.312	0.000	0.000	0.000	0.000
104	A	162	LEU	0	-0.004	-0.004	30.753	-0.323	-0.323	0.000	0.000	0.000	0.000
105	A	163	ASP	-1	-0.837	-0.904	32.084	9.154	9.154	0.000	0.000	0.000	0.000
106	A	164	GLU	-1	-0.896	-0.958	33.157	8.812	8.812	0.000	0.000	0.000	0.000
107	A	165	SER	0	0.027	0.018	34.232	0.147	0.147	0.000	0.000	0.000	0.000
108	A	167	GLU	-1	-0.991	-1.002	32.349	9.640	9.640	0.000	0.000	0.000	0.000
109	A	168	ASP	-1	-0.892	-0.924	33.818	8.802	8.802	0.000	0.000	0.000	0.000
110	A	169	LYS	1	0.850	0.908	31.261	-9.593	-9.593	0.000	0.000	0.000	0.000
111	A	170	ASN	0	0.073	0.036	28.465	-0.249	-0.249	0.000	0.000	0.000	0.000
112	A	171	ARG	1	0.867	0.950	24.732	-11.094	-11.094	0.000	0.000	0.000	0.000
113	A	172	TYR	0	0.030	0.008	20.205	0.045	0.045	0.000	0.000	0.000	0.000
114	A	173	ILE	0	0.030	0.012	17.672	0.379	0.379	0.000	0.000	0.000	0.000
115	A	175	LYS	1	0.907	0.949	13.120	-20.106	-20.106	0.000	0.000	0.000	0.000
116	A	176	GLN	0	-0.050	-0.022	8.790	2.112	2.112	0.000	0.000	0.000	0.000
117	A	177	GLN	0	0.016	0.002	9.962	2.286	2.286	0.000	0.000	0.000	0.000
118	A	178	LEU	0	0.010	-0.006	3.973	3.186	3.616	0.002	-0.122	-0.311	0.001
119	A	179	ILE	0	-0.013	0.015	6.349	-0.069	-0.069	0.000	0.000	0.000	0.000

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