FMO DATABASE

FMODB ID: KR6N3

Calculation Name: 2J4B-A-Xray311

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2J4B

Chain ID: A

ChEMBL ID:

UniProt ID: Q8SQS4

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	133
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1315937.440747
FMO2-HF: Nuclear repulsion	1260874.383002
FMO2-HF: Total energy	-55063.057744
FMO2-MP2: Total energy	-55227.151916

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:17:ACE )

Summations of interaction energy for fragment #1(A:17:ACE )

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.
2.249	3.167	-0.005	-0.412	-0.5	0

Interaction energy analysis for fragmet #1(A:17:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.031 / q_NPA : 0.007

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].
3	A	19	MET	0	0.019	0.028	3.873	1.000	1.836	-0.005	-0.397	-0.435
4	A	20	GLU	-1	-0.839	-0.917	6.947	-0.136	-0.136	0.000	0.000	0.000
5	A	21	THR	0	0.024	0.003	5.104	0.108	0.108	0.000	0.000	0.000
6	A	22	SER	0	-0.024	-0.022	4.681	0.524	0.595	0.000	-0.005	-0.065
7	A	23	TYR	0	0.021	0.018	7.201	0.105	0.105	0.000	0.000	0.000
8	A	24	VAL	0	0.038	0.027	10.525	0.068	0.068	0.000	0.000	0.000
9	A	25	SER	0	-0.009	0.002	8.734	0.070	0.070	0.000	0.000	0.000
10	A	26	LEU	0	0.007	0.001	10.871	0.030	0.030	0.000	0.000	0.000
11	A	27	LYS	1	0.830	0.914	12.637	0.056	0.056	0.000	0.000	0.000
12	A	28	THR	0	-0.015	-0.026	14.248	-0.003	-0.003	0.000	0.000	0.000
13	A	29	TRP	0	0.003	0.021	14.619	0.003	0.003	0.000	0.000	0.000
14	A	30	ILE	0	-0.003	-0.014	16.384	-0.008	-0.008	0.000	0.000	0.000
15	A	31	GLU	-1	-0.997	-0.992	18.722	-0.006	-0.006	0.000	0.000	0.000
16	A	32	ASP	-1	-0.875	-0.930	19.512	0.069	0.069	0.000	0.000	0.000
17	A	33	SER	0	-0.150	-0.069	20.940	0.002	0.002	0.000	0.000	0.000
18	A	34	LEU	0	0.035	-0.003	22.531	-0.010	-0.010	0.000	0.000	0.000
19	A	35	ASP	-1	-0.834	-0.919	25.855	0.031	0.031	0.000	0.000	0.000
20	A	36	LEU	0	-0.082	-0.034	27.936	-0.003	-0.003	0.000	0.000	0.000
21	A	37	PHE	0	0.006	-0.017	23.657	0.000	0.000	0.000	0.000	0.000
22	A	38	LYS	1	0.923	0.965	22.956	-0.032	-0.032	0.000	0.000	0.000
23	A	39	ASN	0	0.010	0.002	23.765	-0.009	-0.009	0.000	0.000	0.000
24	A	40	ASP	-1	-0.838	-0.922	24.206	0.030	0.030	0.000	0.000	0.000
25	A	41	LEU	0	-0.038	-0.019	18.766	0.000	0.000	0.000	0.000	0.000
26	A	42	LEU	0	0.016	0.010	19.690	-0.006	-0.006	0.000	0.000	0.000
27	A	43	PRO	0	-0.041	-0.016	20.656	-0.013	-0.013	0.000	0.000	0.000
28	A	44	LEU	0	0.017	0.008	15.172	-0.012	-0.012	0.000	0.000	0.000
29	A	45	LEU	0	0.033	0.001	15.142	-0.015	-0.015	0.000	0.000	0.000
30	A	46	TYR	0	0.006	0.010	17.086	-0.028	-0.028	0.000	0.000	0.000
31	A	47	PRO	0	0.019	0.001	18.328	-0.020	-0.020	0.000	0.000	0.000
32	A	48	LEU	0	-0.001	0.013	10.854	-0.021	-0.021	0.000	0.000	0.000
33	A	49	PHE	0	-0.014	-0.003	14.012	-0.047	-0.047	0.000	0.000	0.000
34	A	50	ILE	0	0.003	0.019	15.841	-0.035	-0.035	0.000	0.000	0.000
35	A	51	HIS	0	0.016	-0.002	14.163	-0.038	-0.038	0.000	0.000	0.000
36	A	52	ILE	0	0.004	0.007	10.416	-0.048	-0.048	0.000	0.000	0.000
37	A	53	TYR	0	-0.044	-0.021	12.925	-0.054	-0.054	0.000	0.000	0.000
38	A	54	PHE	0	0.002	-0.024	16.094	-0.002	-0.002	0.000	0.000	0.000
39	A	55	ASP	-1	-0.823	-0.881	12.068	-0.340	-0.340	0.000	0.000	0.000
40	A	56	LEU	0	-0.058	-0.024	10.991	-0.039	-0.039	0.000	0.000	0.000
41	A	57	ILE	0	0.003	0.018	14.249	0.017	0.017	0.000	0.000	0.000
42	A	58	GLN	0	-0.034	-0.010	15.543	0.047	0.047	0.000	0.000	0.000
43	A	59	GLN	0	-0.079	-0.045	10.220	-0.043	-0.043	0.000	0.000	0.000
44	A	60	ASN	0	-0.049	-0.023	15.591	0.013	0.013	0.000	0.000	0.000
45	A	61	LYS	1	0.908	0.963	11.677	0.568	0.568	0.000	0.000	0.000
46	A	62	THR	0	0.036	0.009	16.832	-0.007	-0.007	0.000	0.000	0.000
47	A	63	ASP	-1	-0.901	-0.955	19.156	-0.197	-0.197	0.000	0.000	0.000
48	A	64	GLU	-1	-0.902	-0.957	12.446	-0.600	-0.600	0.000	0.000	0.000
49	A	65	ALA	0	-0.021	-0.010	15.957	0.000	0.000	0.000	0.000	0.000
50	A	66	LYS	1	0.941	0.963	16.956	0.188	0.188	0.000	0.000	0.000
51	A	67	GLU	-1	-0.926	-0.955	17.070	-0.218	-0.218	0.000	0.000	0.000
52	A	68	PHE	0	-0.045	-0.019	12.753	0.017	0.017	0.000	0.000	0.000
53	A	69	PHE	0	-0.030	-0.027	16.286	0.032	0.032	0.000	0.000	0.000
54	A	70	GLU	-1	-0.875	-0.964	19.168	-0.100	-0.100	0.000	0.000	0.000
55	A	71	LYS	1	0.884	0.972	15.911	0.228	0.228	0.000	0.000	0.000
56	A	72	TYR	0	-0.013	-0.019	13.394	0.038	0.038	0.000	0.000	0.000
57	A	73	ARG	1	0.856	0.944	19.008	0.115	0.115	0.000	0.000	0.000
58	A	74	GLY	0	-0.041	-0.016	21.998	0.010	0.010	0.000	0.000	0.000
59	A	75	ASP	-1	-0.808	-0.896	18.992	-0.068	-0.068	0.000	0.000	0.000
60	A	76	HIS	1	0.832	0.914	18.324	0.098	0.098	0.000	0.000	0.000
61	A	77	TYR	0	0.031	0.024	23.756	-0.009	-0.009	0.000	0.000	0.000
62	A	78	ASN	0	-0.013	-0.028	26.349	0.000	0.000	0.000	0.000	0.000
63	A	79	LYS	1	0.967	0.985	24.978	0.042	0.042	0.000	0.000	0.000
64	A	80	SER	0	0.027	0.024	27.376	-0.005	-0.005	0.000	0.000	0.000
65	A	81	GLU	-1	-0.942	-0.960	28.773	-0.047	-0.047	0.000	0.000	0.000
66	A	82	GLU	-1	-0.869	-0.949	26.641	-0.053	-0.053	0.000	0.000	0.000
67	A	83	ILE	0	-0.041	-0.012	22.849	-0.009	-0.009	0.000	0.000	0.000
68	A	84	LYS	1	0.971	0.978	25.772	0.058	0.058	0.000	0.000	0.000
69	A	85	GLN	0	-0.011	-0.003	28.520	0.001	0.001	0.000	0.000	0.000
70	A	86	PHE	0	0.007	-0.025	23.106	-0.004	-0.004	0.000	0.000	0.000
71	A	87	GLU	-1	-0.896	-0.936	24.615	-0.097	-0.097	0.000	0.000	0.000
72	A	88	SER	0	-0.079	-0.023	25.862	-0.006	-0.006	0.000	0.000	0.000
73	A	89	ILE	0	-0.039	-0.010	23.358	0.001	0.001	0.000	0.000	0.000
74	A	90	TYR	0	0.028	0.013	22.831	-0.012	-0.012	0.000	0.000	0.000
75	A	91	THR	0	0.007	-0.010	22.090	-0.017	-0.017	0.000	0.000	0.000
76	A	92	VAL	0	0.086	0.023	20.987	0.005	0.005	0.000	0.000	0.000
77	A	93	GLN	0	-0.013	-0.012	23.320	0.006	0.006	0.000	0.000	0.000
78	A	94	HIS	0	0.031	0.026	25.628	-0.001	-0.001	0.000	0.000	0.000
79	A	95	ILE	0	0.019	0.026	20.619	0.008	0.008	0.000	0.000	0.000
80	A	96	HIS	0	-0.079	-0.047	24.168	0.013	0.013	0.000	0.000	0.000
81	A	97	GLU	-1	-0.895	-0.929	27.439	-0.079	-0.079	0.000	0.000	0.000
82	A	98	ASN	0	-0.035	-0.021	28.044	0.012	0.012	0.000	0.000	0.000
83	A	99	ASN	0	0.067	0.011	28.007	-0.008	-0.008	0.000	0.000	0.000
84	A	100	PHE	0	0.003	0.001	26.229	0.003	0.003	0.000	0.000	0.000
85	A	101	ALA	0	0.027	0.015	24.166	-0.002	-0.002	0.000	0.000	0.000
86	A	102	TYR	0	0.006	0.000	23.671	-0.006	-0.006	0.000	0.000	0.000
87	A	103	THR	0	-0.030	-0.033	24.664	0.001	0.001	0.000	0.000	0.000
88	A	104	PHE	0	-0.019	-0.007	19.151	0.006	0.006	0.000	0.000	0.000
89	A	105	LYS	1	0.915	0.972	19.099	0.132	0.132	0.000	0.000	0.000
90	A	106	ASN	0	-0.067	-0.030	20.327	-0.009	-0.009	0.000	0.000	0.000
91	A	107	SER	0	-0.018	0.005	22.953	0.012	0.012	0.000	0.000	0.000
92	A	108	LYS	1	0.869	0.938	20.749	0.010	0.010	0.000	0.000	0.000
93	A	109	TYR	0	0.027	0.019	20.951	-0.002	-0.002	0.000	0.000	0.000
94	A	110	HIS	0	0.017	0.015	22.230	0.004	0.004	0.000	0.000	0.000
95	A	111	LEU	0	-0.042	-0.015	19.758	-0.003	-0.003	0.000	0.000	0.000
96	A	112	SER	0	-0.038	-0.022	24.173	0.003	0.003	0.000	0.000	0.000
97	A	113	MET	0	0.007	0.020	19.238	0.004	0.004	0.000	0.000	0.000
98	A	114	GLY	0	0.032	0.027	25.314	0.000	0.000	0.000	0.000	0.000
99	A	115	ARG	1	0.952	0.955	25.250	-0.059	-0.059	0.000	0.000	0.000
100	A	116	TYR	0	0.000	-0.002	24.817	0.007	0.007	0.000	0.000	0.000
101	A	117	ALA	0	0.054	0.042	22.754	0.010	0.010	0.000	0.000	0.000
102	A	118	PHE	0	0.028	0.005	19.827	0.011	0.011	0.000	0.000	0.000
103	A	119	ASP	-1	-0.888	-0.936	19.701	0.141	0.141	0.000	0.000	0.000
104	A	120	LEU	0	0.004	-0.008	19.500	0.018	0.018	0.000	0.000	0.000
105	A	121	LEU	0	-0.011	-0.006	15.125	0.022	0.022	0.000	0.000	0.000
106	A	122	ILE	0	-0.034	-0.021	15.128	0.028	0.028	0.000	0.000	0.000
107	A	123	ASN	0	0.037	0.020	14.794	0.048	0.048	0.000	0.000	0.000
108	A	124	PHE	0	-0.007	0.002	11.819	0.062	0.062	0.000	0.000	0.000
109	A	125	LEU	0	-0.042	-0.040	10.247	0.077	0.077	0.000	0.000	0.000
110	A	126	GLU	-1	-0.952	-0.982	9.974	0.403	0.403	0.000	0.000	0.000
111	A	127	GLU	-1	-0.985	-0.971	11.791	0.376	0.376	0.000	0.000	0.000
112	A	128	ARG	1	0.894	0.952	8.754	-0.377	-0.377	0.000	0.000	0.000
113	A	129	ASN	0	-0.008	0.002	6.914	0.272	0.272	0.000	0.000	0.000
114	A	130	LEU	0	0.011	0.012	5.372	0.583	0.583	0.000	0.000	0.000
115	A	131	THR	0	-0.015	-0.032	4.225	-0.458	-0.447	0.000	-0.010	0.000
116	A	132	TYR	0	-0.086	-0.087	5.434	-0.242	-0.242	0.000	0.000	0.000
117	A	133	ILE	0	0.039	0.013	6.970	-0.072	-0.072	0.000	0.000	0.000
118	A	134	LEU	0	0.061	0.031	9.408	-0.040	-0.040	0.000	0.000	0.000
119	A	135	LYS	1	0.925	0.983	9.312	0.233	0.233	0.000	0.000	0.000
120	A	136	ILE	0	-0.003	-0.001	11.008	-0.009	-0.009	0.000	0.000	0.000
121	A	137	LEU	0	-0.006	-0.002	13.305	-0.004	-0.004	0.000	0.000	0.000
122	A	138	ASN	0	0.006	0.005	14.136	-0.012	-0.012	0.000	0.000	0.000
123	A	139	GLN	0	-0.038	-0.030	15.278	-0.029	-0.029	0.000	0.000	0.000
124	A	140	HIS	0	-0.004	0.000	14.984	0.008	0.008	0.000	0.000	0.000
125	A	141	LEU	0	-0.066	-0.019	16.197	-0.003	-0.003	0.000	0.000	0.000
126	A	142	ASP	-1	-0.934	-0.959	19.560	0.014	0.014	0.000	0.000	0.000
127	A	143	ILE	0	0.018	0.000	18.503	-0.002	-0.002	0.000	0.000	0.000
128	A	144	LYS	1	0.984	0.993	23.044	-0.019	-0.019	0.000	0.000	0.000
129	A	145	VAL	0	0.012	0.002	23.733	-0.001	-0.001	0.000	0.000	0.000
130	A	146	TYR	0	-0.059	-0.030	26.450	-0.002	-0.002	0.000	0.000	0.000
131	A	147	VAL	0	0.011	-0.007	29.205	0.005	0.005	0.000	0.000	0.000
132	A	148	GLY	0	0.001	-0.005	31.251	-0.004	-0.004	0.000	0.000	0.000
133	A	149	NME	0	-0.013	0.005	33.170	0.003	0.003	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:17:ACE )