FMO DATABASE

FMODB ID: 6YV8Z

Calculation Name: 2JLJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2JLJ

Chain ID: A

ChEMBL ID:

UniProt ID: P69986

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	115
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-978439.827026
FMO2-HF: Nuclear repulsion	933009.022644
FMO2-HF: Total energy	-45430.804383
FMO2-MP2: Total energy	-45566.746658

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:230:GLY)

Summations of interaction energy for fragment #1(A:230:GLY)

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.
2.82	3.03	4.217	-2.457	-1.97	-0.003

Interaction energy analysis for fragmet #1(A:230:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / q_NPA : -0.022

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	232	PRO	0	0.075	0.021	3.779	-1.220	-0.119	-0.001	-0.592	-0.508	0.002
4	A	233	GLU	-1	-0.822	-0.909	6.494	-0.422	-0.422	0.000	0.000	0.000	0.000
5	A	234	ILE	0	-0.021	0.003	2.153	1.261	0.006	4.201	-1.762	-1.184	-0.005
6	A	235	LYS	1	0.934	0.963	3.391	2.796	3.116	0.018	-0.098	-0.240	0.000
7	A	236	SER	0	-0.037	-0.017	5.480	0.230	0.230	0.000	0.000	0.000	0.000
8	A	237	LYS	1	0.989	0.994	8.210	-0.085	-0.085	0.000	0.000	0.000	0.000
9	A	238	ARG	1	0.932	0.967	4.730	0.169	0.213	-0.001	-0.005	-0.038	0.000
10	A	239	ARG	1	0.951	0.984	8.766	0.629	0.629	0.000	0.000	0.000	0.000
11	A	240	GLN	0	0.019	0.016	11.036	0.023	0.023	0.000	0.000	0.000	0.000
12	A	241	PHE	0	-0.002	-0.007	11.884	0.023	0.023	0.000	0.000	0.000	0.000
13	A	242	HIS	0	0.020	-0.005	10.639	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	243	GLN	0	-0.028	-0.014	14.287	-0.019	-0.019	0.000	0.000	0.000	0.000
15	A	244	GLU	-1	-0.953	-0.983	16.621	-0.051	-0.051	0.000	0.000	0.000	0.000
16	A	245	ILE	0	-0.065	-0.012	16.288	0.010	0.010	0.000	0.000	0.000	0.000
17	A	246	GLN	0	-0.091	-0.039	18.874	0.007	0.007	0.000	0.000	0.000	0.000
18	A	247	SER	0	0.017	0.003	20.499	0.003	0.003	0.000	0.000	0.000	0.000
19	A	248	ARG	1	0.866	0.944	23.031	0.060	0.060	0.000	0.000	0.000	0.000
20	A	249	ASN	0	0.024	0.023	25.882	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	250	MET	0	0.015	0.003	27.713	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	251	ARG	1	0.830	0.902	28.759	0.042	0.042	0.000	0.000	0.000	0.000
23	A	252	GLU	-1	-0.826	-0.911	27.870	-0.048	-0.048	0.000	0.000	0.000	0.000
24	A	253	ASN	0	-0.007	-0.027	23.341	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	254	VAL	0	-0.013	0.006	26.524	-0.006	-0.006	0.000	0.000	0.000	0.000
26	A	255	LYS	1	0.998	1.002	28.739	0.044	0.044	0.000	0.000	0.000	0.000
27	A	256	ARG	1	0.742	0.874	21.078	0.089	0.089	0.000	0.000	0.000	0.000
28	A	257	SER	0	-0.055	-0.029	25.608	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	258	SER	0	0.014	0.005	26.359	0.006	0.006	0.000	0.000	0.000	0.000
30	A	259	VAL	0	-0.004	-0.001	25.947	0.004	0.004	0.000	0.000	0.000	0.000
31	A	260	VAL	0	0.004	0.009	26.046	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	261	VAL	0	0.015	0.012	23.376	0.006	0.006	0.000	0.000	0.000	0.000
33	A	262	ALA	0	-0.006	-0.014	24.893	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	263	ALA	0	-0.004	-0.007	25.934	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	264	ALA	0	-0.072	-0.071	27.641	0.002	0.002	0.000	0.000	0.000	0.000
36	A	265	THR	0	-0.040	-0.036	30.878	0.000	0.000	0.000	0.000	0.000	0.000
37	A	266	HIS	0	0.079	0.082	26.284	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	267	ILE	0	0.007	0.009	21.792	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	268	ALA	0	-0.019	-0.010	24.469	0.007	0.007	0.000	0.000	0.000	0.000
40	A	269	ILE	0	-0.015	-0.003	19.326	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	270	GLY	0	0.014	0.020	22.270	0.007	0.007	0.000	0.000	0.000	0.000
42	A	271	ILE	0	0.023	0.006	20.147	-0.017	-0.017	0.000	0.000	0.000	0.000
43	A	272	LEU	0	0.018	0.006	22.074	0.014	0.014	0.000	0.000	0.000	0.000
44	A	273	TYR	0	-0.012	-0.014	22.586	-0.012	-0.012	0.000	0.000	0.000	0.000
45	A	274	LYS	1	0.981	1.014	24.842	0.074	0.074	0.000	0.000	0.000	0.000
46	A	275	ARG	1	0.978	0.968	24.561	0.086	0.086	0.000	0.000	0.000	0.000
47	A	276	GLY	0	-0.015	-0.008	26.802	0.005	0.005	0.000	0.000	0.000	0.000
48	A	277	GLU	-1	-0.894	-0.935	26.314	-0.055	-0.055	0.000	0.000	0.000	0.000
49	A	278	THR	0	-0.031	-0.018	21.742	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	279	PRO	0	-0.026	-0.008	19.006	0.000	0.000	0.000	0.000	0.000	0.000
51	A	280	LEU	0	-0.022	-0.018	16.100	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	281	PRO	0	0.011	-0.001	19.632	0.010	0.010	0.000	0.000	0.000	0.000
53	A	282	LEU	0	0.012	0.022	17.430	-0.025	-0.025	0.000	0.000	0.000	0.000
54	A	283	VAL	0	0.023	0.012	16.403	0.013	0.013	0.000	0.000	0.000	0.000
55	A	284	THR	0	-0.032	-0.023	18.235	0.001	0.001	0.000	0.000	0.000	0.000
56	A	285	PHE	0	0.030	0.013	20.608	0.010	0.010	0.000	0.000	0.000	0.000
57	A	286	LYS	1	0.812	0.888	14.141	0.264	0.264	0.000	0.000	0.000	0.000
58	A	287	TYR	0	0.020	0.028	20.992	0.010	0.010	0.000	0.000	0.000	0.000
59	A	288	THR	0	0.015	-0.010	22.706	-0.009	-0.009	0.000	0.000	0.000	0.000
60	A	289	ASP	-1	-0.817	-0.901	25.553	-0.088	-0.088	0.000	0.000	0.000	0.000
61	A	290	ALA	0	-0.001	-0.007	28.858	0.001	0.001	0.000	0.000	0.000	0.000
62	A	291	GLN	0	0.015	0.007	26.018	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	292	VAL	0	-0.011	-0.007	27.334	0.002	0.002	0.000	0.000	0.000	0.000
64	A	293	GLN	0	-0.002	-0.008	29.799	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	294	THR	0	-0.013	-0.004	31.951	0.005	0.005	0.000	0.000	0.000	0.000
66	A	295	VAL	0	0.019	0.005	27.672	0.002	0.002	0.000	0.000	0.000	0.000
67	A	296	ARG	1	0.919	0.962	30.994	0.085	0.085	0.000	0.000	0.000	0.000
68	A	297	LYS	1	0.982	1.006	33.538	0.049	0.049	0.000	0.000	0.000	0.000
69	A	298	ILE	0	-0.003	-0.014	32.127	0.002	0.002	0.000	0.000	0.000	0.000
70	A	299	ALA	0	-0.022	-0.019	31.786	0.002	0.002	0.000	0.000	0.000	0.000
71	A	300	GLU	-1	-0.937	-0.957	33.647	-0.057	-0.057	0.000	0.000	0.000	0.000
72	A	301	GLU	-1	-0.901	-0.957	37.292	-0.043	-0.043	0.000	0.000	0.000	0.000
73	A	302	GLU	-1	-0.905	-0.956	34.117	-0.045	-0.045	0.000	0.000	0.000	0.000
74	A	303	GLY	0	-0.012	0.022	35.790	0.000	0.000	0.000	0.000	0.000	0.000
75	A	304	VAL	0	-0.062	-0.022	29.671	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	305	PRO	0	0.022	0.018	31.537	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	306	ILE	0	0.015	-0.010	29.637	-0.007	-0.007	0.000	0.000	0.000	0.000
78	A	307	LEU	0	-0.018	0.005	27.480	0.004	0.004	0.000	0.000	0.000	0.000
79	A	308	GLN	0	0.048	0.030	28.869	-0.007	-0.007	0.000	0.000	0.000	0.000
80	A	309	ARG	1	0.947	0.958	25.730	0.116	0.116	0.000	0.000	0.000	0.000
81	A	310	ILE	0	0.031	0.016	25.140	-0.010	-0.010	0.000	0.000	0.000	0.000
82	A	311	PRO	0	0.023	0.005	23.280	-0.010	-0.010	0.000	0.000	0.000	0.000
83	A	312	LEU	0	0.059	0.040	19.766	-0.017	-0.017	0.000	0.000	0.000	0.000
84	A	313	ALA	0	0.017	0.012	20.186	-0.018	-0.018	0.000	0.000	0.000	0.000
85	A	314	ARG	1	0.960	0.958	20.297	0.150	0.150	0.000	0.000	0.000	0.000
86	A	315	ALA	0	0.051	0.044	16.905	-0.017	-0.017	0.000	0.000	0.000	0.000
87	A	316	LEU	0	0.010	-0.005	15.573	-0.045	-0.045	0.000	0.000	0.000	0.000
88	A	317	TYR	0	0.001	0.006	15.756	-0.011	-0.011	0.000	0.000	0.000	0.000
89	A	318	TRP	0	-0.005	0.000	14.649	0.001	0.001	0.000	0.000	0.000	0.000
90	A	319	ASP	-1	-0.910	-0.943	11.379	-0.610	-0.610	0.000	0.000	0.000	0.000
91	A	320	ALA	0	-0.073	-0.036	10.736	-0.071	-0.071	0.000	0.000	0.000	0.000
92	A	321	LEU	0	-0.026	-0.015	8.060	0.001	0.001	0.000	0.000	0.000	0.000
93	A	322	VAL	0	0.035	0.020	12.213	0.006	0.006	0.000	0.000	0.000	0.000
94	A	323	ASP	-1	-0.786	-0.882	14.651	-0.095	-0.095	0.000	0.000	0.000	0.000
95	A	324	HIS	0	-0.084	-0.048	11.329	0.017	0.017	0.000	0.000	0.000	0.000
96	A	325	TYR	0	0.002	-0.011	14.217	0.006	0.006	0.000	0.000	0.000	0.000
97	A	326	ILE	0	-0.013	-0.004	13.417	-0.042	-0.042	0.000	0.000	0.000	0.000
98	A	327	PRO	0	0.004	-0.002	11.545	-0.020	-0.020	0.000	0.000	0.000	0.000
99	A	328	ALA	0	0.046	0.013	11.999	0.051	0.051	0.000	0.000	0.000	0.000
100	A	329	GLU	-1	-0.936	-0.960	13.320	-0.410	-0.410	0.000	0.000	0.000	0.000
101	A	330	GLN	0	0.012	-0.007	15.227	0.075	0.075	0.000	0.000	0.000	0.000
102	A	331	ILE	0	0.002	0.008	16.076	0.035	0.035	0.000	0.000	0.000	0.000
103	A	332	GLU	-1	-0.917	-0.950	19.096	-0.147	-0.147	0.000	0.000	0.000	0.000
104	A	333	ALA	0	0.053	0.021	21.541	0.017	0.017	0.000	0.000	0.000	0.000
105	A	334	THR	0	-0.017	-0.025	19.976	0.016	0.016	0.000	0.000	0.000	0.000
106	A	335	ALA	0	0.006	-0.002	22.593	0.017	0.017	0.000	0.000	0.000	0.000
107	A	336	GLU	-1	-0.986	-0.989	24.757	-0.110	-0.110	0.000	0.000	0.000	0.000
108	A	337	VAL	0	-0.032	-0.022	25.486	0.012	0.012	0.000	0.000	0.000	0.000
109	A	338	LEU	0	0.005	-0.008	23.806	0.009	0.009	0.000	0.000	0.000	0.000
110	A	339	ARG	1	0.979	1.000	27.356	0.118	0.118	0.000	0.000	0.000	0.000
111	A	340	TRP	0	-0.067	-0.031	30.507	0.006	0.006	0.000	0.000	0.000	0.000
112	A	341	LEU	0	0.001	-0.012	28.972	0.004	0.004	0.000	0.000	0.000	0.000
113	A	342	GLU	-1	-0.964	-0.971	31.780	-0.071	-0.071	0.000	0.000	0.000	0.000
114	A	343	ARG	1	0.878	0.944	33.277	0.084	0.084	0.000	0.000	0.000	0.000
115	A	344	GLN	0	-0.035	0.006	34.631	0.007	0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:230:GLY)