FMO DATABASE

FMODB ID: 3J8JL

Calculation Name: 3B93-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B93

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UNG2

Base Structure: X-ray

Registration Date: 2023-09-23

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	122
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1051201.23064
FMO2-HF: Nuclear repulsion	1002115.120958
FMO2-HF: Total energy	-49086.109682
FMO2-MP2: Total energy	-49229.006809

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:55:LYS)

Summations of interaction energy for fragment #1(A:55:LYS)

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.
-11.254	-10.216	0.087	0.788	-1.913	-0.002

Interaction energy analysis for fragmet #1(A:55:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.900 / q_NPA : 0.925

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	A	57	PRO	0	0.048	-0.025	2.671	2.901	2.579	0.007	1.521	-1.206	0.001
4	A	58	CYS	0	-0.015	0.017	4.141	7.165	7.299	-0.002	-0.013	-0.119	0.000
5	A	59	MET	0	-0.017	-0.005	6.771	3.867	3.867	0.000	0.000	0.000	0.000
6	A	60	ALA	0	0.004	0.013	9.839	0.690	0.690	0.000	0.000	0.000	0.000
7	A	61	LYS	1	0.939	0.979	13.409	16.686	16.686	0.000	0.000	0.000	0.000
8	A	62	PHE	0	0.014	0.009	16.305	0.385	0.385	0.000	0.000	0.000	0.000
9	A	63	GLY	0	0.019	0.033	19.737	0.321	0.321	0.000	0.000	0.000	0.000
10	A	64	PRO	0	0.017	-0.005	20.001	-0.829	-0.829	0.000	0.000	0.000	0.000
11	A	65	LEU	0	-0.051	-0.035	23.261	-0.122	-0.122	0.000	0.000	0.000	0.000
12	A	66	PRO	0	0.013	-0.006	24.422	0.170	0.170	0.000	0.000	0.000	0.000
13	A	67	SER	0	-0.012	0.012	19.626	-0.216	-0.216	0.000	0.000	0.000	0.000
14	A	68	LYS	1	0.951	0.967	20.608	11.926	11.926	0.000	0.000	0.000	0.000
15	A	69	TRP	0	-0.001	0.008	16.891	-0.587	-0.587	0.000	0.000	0.000	0.000
16	A	70	GLN	0	-0.099	-0.057	14.254	-0.029	-0.029	0.000	0.000	0.000	0.000
17	A	71	MET	0	0.007	-0.017	11.110	0.357	0.357	0.000	0.000	0.000	0.000
18	A	72	ALA	0	0.009	0.016	6.708	0.543	0.543	0.000	0.000	0.000	0.000
19	A	73	SER	0	0.017	0.034	3.349	-5.911	-4.708	0.083	-0.720	-0.567	-0.003
20	A	74	SER	0	-0.028	-0.018	5.371	-1.778	-1.755	-0.001	0.000	-0.021	0.000
21	A	75	GLU	-1	-0.917	-0.937	6.709	-22.527	-22.527	0.000	0.000	0.000	0.000
22	A	76	PRO	0	0.034	0.034	6.406	-3.320	-3.320	0.000	0.000	0.000	0.000
23	A	77	PRO	0	0.003	-0.007	9.194	-1.871	-1.871	0.000	0.000	0.000	0.000
24	A	79	VAL	0	0.009	0.003	11.961	1.507	1.507	0.000	0.000	0.000	0.000
25	A	80	ASN	0	-0.015	0.002	14.829	-0.409	-0.409	0.000	0.000	0.000	0.000
26	A	81	LYS	1	0.936	0.972	17.479	15.892	15.892	0.000	0.000	0.000	0.000
27	A	82	VAL	0	0.021	0.006	19.653	0.380	0.380	0.000	0.000	0.000	0.000
28	A	83	SER	0	0.000	0.002	23.290	0.598	0.598	0.000	0.000	0.000	0.000
29	A	84	ASP	-1	-0.928	-0.962	23.676	-12.187	-12.187	0.000	0.000	0.000	0.000
30	A	85	TRP	0	-0.041	-0.031	23.503	0.161	0.161	0.000	0.000	0.000	0.000
31	A	86	LYS	1	1.012	1.030	23.270	11.649	11.649	0.000	0.000	0.000	0.000
32	A	87	LEU	0	-0.089	-0.052	15.777	-0.177	-0.177	0.000	0.000	0.000	0.000
33	A	88	GLU	-1	-0.844	-0.935	19.651	-13.787	-13.787	0.000	0.000	0.000	0.000
34	A	89	ILE	0	-0.019	-0.008	15.695	-1.105	-1.105	0.000	0.000	0.000	0.000
35	A	90	LEU	0	-0.017	-0.015	14.932	0.830	0.830	0.000	0.000	0.000	0.000
36	A	91	GLN	0	0.001	-0.005	11.212	-1.201	-1.201	0.000	0.000	0.000	0.000
37	A	92	ASN	0	0.060	0.044	14.443	0.258	0.258	0.000	0.000	0.000	0.000
38	A	93	GLY	0	-0.003	0.003	13.053	-1.857	-1.857	0.000	0.000	0.000	0.000
39	A	94	LEU	0	0.015	0.021	12.866	1.760	1.760	0.000	0.000	0.000	0.000
40	A	95	TYR	0	0.014	-0.035	11.949	-3.303	-3.303	0.000	0.000	0.000	0.000
41	A	96	LEU	0	-0.026	-0.003	13.107	1.739	1.739	0.000	0.000	0.000	0.000
42	A	97	ILE	0	0.011	-0.007	14.483	-0.883	-0.883	0.000	0.000	0.000	0.000
43	A	98	TYR	0	-0.010	0.003	13.880	1.040	1.040	0.000	0.000	0.000	0.000
44	A	99	GLY	0	0.051	-0.001	18.418	-0.116	-0.116	0.000	0.000	0.000	0.000
45	A	100	GLN	0	-0.055	-0.011	20.930	0.067	0.067	0.000	0.000	0.000	0.000
46	A	101	VAL	0	0.070	0.028	24.225	0.059	0.059	0.000	0.000	0.000	0.000
47	A	102	ALA	0	-0.017	-0.021	27.447	0.242	0.242	0.000	0.000	0.000	0.000
48	A	103	PRO	0	0.008	0.010	30.137	0.134	0.134	0.000	0.000	0.000	0.000
49	A	104	ASN	0	-0.012	0.003	33.461	0.089	0.089	0.000	0.000	0.000	0.000
50	A	105	ALA	0	-0.001	-0.012	36.434	0.176	0.176	0.000	0.000	0.000	0.000
51	A	106	ASN	0	-0.026	-0.013	38.768	0.277	0.277	0.000	0.000	0.000	0.000
52	A	107	TYR	0	-0.089	-0.077	39.002	0.103	0.103	0.000	0.000	0.000	0.000
53	A	108	ASN	0	-0.056	-0.060	41.047	0.000	0.000	0.000	0.000	0.000	0.000
54	A	109	ASP	-1	-0.867	-0.896	42.755	-7.240	-7.240	0.000	0.000	0.000	0.000
55	A	110	VAL	0	0.008	0.000	44.818	-0.016	-0.016	0.000	0.000	0.000	0.000
56	A	111	ALA	0	0.020	0.030	41.102	0.021	0.021	0.000	0.000	0.000	0.000
57	A	112	PRO	0	0.069	0.063	41.448	-0.050	-0.050	0.000	0.000	0.000	0.000
58	A	113	PHE	0	-0.025	-0.019	34.075	-0.154	-0.154	0.000	0.000	0.000	0.000
59	A	114	GLU	-1	-0.887	-0.929	34.292	-8.943	-8.943	0.000	0.000	0.000	0.000
60	A	115	VAL	0	-0.023	-0.002	29.370	-0.046	-0.046	0.000	0.000	0.000	0.000
61	A	116	ARG	1	0.917	0.961	29.951	9.217	9.217	0.000	0.000	0.000	0.000
62	A	117	LEU	0	-0.001	0.011	22.324	-0.225	-0.225	0.000	0.000	0.000	0.000
63	A	118	TYR	0	-0.022	-0.015	25.835	0.439	0.439	0.000	0.000	0.000	0.000
64	A	119	LYS	1	1.009	1.004	22.691	12.985	12.985	0.000	0.000	0.000	0.000
65	A	120	ASN	0	-0.035	-0.030	24.642	0.298	0.298	0.000	0.000	0.000	0.000
66	A	121	LYS	1	0.927	0.955	26.978	10.106	10.106	0.000	0.000	0.000	0.000
67	A	122	ASP	-1	-0.886	-0.932	28.451	-10.249	-10.249	0.000	0.000	0.000	0.000
68	A	123	MET	0	-0.039	0.000	28.224	-0.508	-0.508	0.000	0.000	0.000	0.000
69	A	124	ILE	0	0.003	-0.003	23.306	0.062	0.062	0.000	0.000	0.000	0.000
70	A	125	GLN	0	0.024	0.003	25.284	-0.625	-0.625	0.000	0.000	0.000	0.000
71	A	126	THR	0	-0.037	-0.023	28.303	0.043	0.043	0.000	0.000	0.000	0.000
72	A	127	LEU	0	-0.029	-0.020	28.404	-0.036	-0.036	0.000	0.000	0.000	0.000
73	A	128	THR	0	0.082	0.037	32.456	0.084	0.084	0.000	0.000	0.000	0.000
74	A	129	ASN	0	0.003	0.013	35.098	0.306	0.306	0.000	0.000	0.000	0.000
75	A	130	LYS	1	0.965	0.971	34.972	7.410	7.410	0.000	0.000	0.000	0.000
76	A	131	SER	0	-0.047	-0.035	36.876	0.030	0.030	0.000	0.000	0.000	0.000
77	A	132	LYS	1	0.952	0.979	32.738	9.503	9.503	0.000	0.000	0.000	0.000
78	A	133	ILE	0	0.039	0.021	27.961	-0.061	-0.061	0.000	0.000	0.000	0.000
79	A	134	GLN	0	-0.123	-0.061	28.466	0.023	0.023	0.000	0.000	0.000	0.000
80	A	135	ASN	0	0.057	0.020	22.443	0.112	0.112	0.000	0.000	0.000	0.000
81	A	136	VAL	0	-0.053	-0.013	22.238	0.490	0.490	0.000	0.000	0.000	0.000
82	A	137	GLY	0	-0.007	-0.009	20.463	-0.712	-0.712	0.000	0.000	0.000	0.000
83	A	138	GLY	0	0.008	0.001	19.477	0.823	0.823	0.000	0.000	0.000	0.000
84	A	139	THR	0	-0.046	-0.017	15.806	-1.299	-1.299	0.000	0.000	0.000	0.000
85	A	140	TYR	0	0.001	-0.007	17.306	1.239	1.239	0.000	0.000	0.000	0.000
86	A	141	GLU	-1	-0.880	-0.942	17.090	-17.277	-17.277	0.000	0.000	0.000	0.000
87	A	142	LEU	0	-0.104	-0.054	16.665	0.985	0.985	0.000	0.000	0.000	0.000
88	A	143	HIS	0	0.050	0.000	17.442	-0.947	-0.947	0.000	0.000	0.000	0.000
89	A	144	VAL	0	-0.005	0.002	17.620	0.107	0.107	0.000	0.000	0.000	0.000
90	A	145	GLY	0	0.005	0.011	19.585	0.748	0.748	0.000	0.000	0.000	0.000
91	A	146	ASP	-1	-0.834	-0.892	20.369	-13.915	-13.915	0.000	0.000	0.000	0.000
92	A	147	THR	0	-0.062	-0.044	21.077	-0.322	-0.322	0.000	0.000	0.000	0.000
93	A	148	ILE	0	-0.022	-0.014	18.960	0.148	0.148	0.000	0.000	0.000	0.000
94	A	149	ASP	-1	-0.842	-0.935	22.276	-11.947	-11.947	0.000	0.000	0.000	0.000
95	A	150	LEU	0	-0.039	-0.014	24.413	0.072	0.072	0.000	0.000	0.000	0.000
96	A	151	ILE	0	-0.004	0.004	26.212	0.193	0.193	0.000	0.000	0.000	0.000
97	A	152	PHE	0	-0.008	-0.023	27.509	0.087	0.087	0.000	0.000	0.000	0.000
98	A	153	ASN	0	-0.009	-0.005	32.685	-0.048	-0.048	0.000	0.000	0.000	0.000
99	A	154	SER	0	-0.003	-0.002	36.255	0.195	0.195	0.000	0.000	0.000	0.000
100	A	155	GLU	-1	-0.792	-0.905	32.395	-9.883	-9.883	0.000	0.000	0.000	0.000
101	A	156	HIS	0	0.006	0.015	34.429	-0.343	-0.343	0.000	0.000	0.000	0.000
102	A	157	GLN	0	0.014	0.001	35.303	-0.102	-0.102	0.000	0.000	0.000	0.000
103	A	158	VAL	0	-0.034	-0.001	30.093	-0.075	-0.075	0.000	0.000	0.000	0.000
104	A	159	LEU	0	0.041	0.020	31.753	0.172	0.172	0.000	0.000	0.000	0.000
105	A	160	LYS	1	0.871	0.932	28.340	9.718	9.718	0.000	0.000	0.000	0.000
106	A	161	ASN	0	0.004	0.013	27.076	-0.533	-0.533	0.000	0.000	0.000	0.000
107	A	162	ASN	0	-0.004	0.000	26.320	-0.547	-0.547	0.000	0.000	0.000	0.000
108	A	163	THR	0	-0.014	-0.013	26.063	-0.064	-0.064	0.000	0.000	0.000	0.000
109	A	164	TYR	0	-0.027	-0.028	19.699	-0.398	-0.398	0.000	0.000	0.000	0.000
110	A	165	TRP	0	-0.010	0.000	17.768	-0.036	-0.036	0.000	0.000	0.000	0.000
111	A	166	GLY	0	0.026	0.013	15.913	-0.069	-0.069	0.000	0.000	0.000	0.000
112	A	167	ILE	0	-0.039	-0.008	13.146	0.713	0.713	0.000	0.000	0.000	0.000
113	A	168	ILE	0	0.009	-0.011	7.768	-1.311	-1.311	0.000	0.000	0.000	0.000
114	A	169	LEU	0	0.011	0.010	7.325	1.994	1.994	0.000	0.000	0.000	0.000
115	A	170	LEU	0	-0.046	-0.028	7.543	-4.914	-4.914	0.000	0.000	0.000	0.000
116	A	171	ALA	0	0.028	0.008	8.547	-2.147	-2.147	0.000	0.000	0.000	0.000
117	A	172	ASN	0	0.062	0.034	9.969	2.586	2.586	0.000	0.000	0.000	0.000
118	A	173	PRO	0	-0.005	0.013	11.809	-0.360	-0.360	0.000	0.000	0.000	0.000
119	A	174	GLN	0	0.017	0.004	13.229	2.228	2.228	0.000	0.000	0.000	0.000
120	A	175	PHE	0	-0.076	-0.022	16.094	0.491	0.491	0.000	0.000	0.000	0.000
121	A	176	ILE	0	0.043	0.065	15.909	1.063	1.063	0.000	0.000	0.000	0.000
122	A	177	SER	0	-0.127	-0.090	17.927	-0.300	-0.300	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:55:LYS)