FMO DATABASE

FMODB ID: 2J1RR

Calculation Name: 3C8J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3C8J

Chain ID: A

ChEMBL ID:

UniProt ID: Q64329

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	123
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1210394.616456
FMO2-HF: Nuclear repulsion	1156131.043351
FMO2-HF: Total energy	-54263.573105
FMO2-MP2: Total energy	-54416.049994

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:136:THR)

Summations of interaction energy for fragment #1(A:136:THR)

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.
-2.476	0.928	-0.016	-1.98	-1.409	0.009

Interaction energy analysis for fragmet #1(A:136:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.068 / q_NPA : 0.036

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	138	ARG	1	0.836	0.907	3.875	-2.291	1.113	-0.016	-1.980	-1.409	0.009
4	A	139	GLY	0	0.019	0.013	6.902	-0.098	-0.098	0.000	0.000	0.000	0.000
5	A	140	VAL	0	0.008	0.014	9.946	-0.077	-0.077	0.000	0.000	0.000	0.000
6	A	141	LYS	1	0.874	0.943	11.499	0.000	0.000	0.000	0.000	0.000	0.000
7	A	142	TYR	0	-0.015	-0.005	14.857	-0.047	-0.047	0.000	0.000	0.000	0.000
8	A	143	TRP	0	0.004	-0.011	17.538	0.046	0.046	0.000	0.000	0.000	0.000
9	A	144	PHE	0	0.036	0.017	19.787	-0.017	-0.017	0.000	0.000	0.000	0.000
10	A	145	CYS	0	0.000	0.006	23.569	0.001	0.001	0.000	0.000	0.000	0.000
11	A	146	TYR	0	0.023	0.010	26.651	-0.007	-0.007	0.000	0.000	0.000	0.000
12	A	147	SER	0	0.029	0.019	30.224	0.005	0.005	0.000	0.000	0.000	0.000
13	A	148	THR	0	0.020	0.017	31.326	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	149	LYS	1	0.751	0.852	27.571	-0.049	-0.049	0.000	0.000	0.000	0.000
15	A	151	TYR	0	-0.039	-0.059	22.653	0.013	0.013	0.000	0.000	0.000	0.000
16	A	152	TYR	0	0.002	-0.005	16.116	-0.017	-0.017	0.000	0.000	0.000	0.000
17	A	153	PHE	0	0.026	0.011	18.852	0.020	0.020	0.000	0.000	0.000	0.000
18	A	154	ILE	0	-0.003	-0.022	13.944	-0.019	-0.019	0.000	0.000	0.000	0.000
19	A	155	MET	0	0.019	0.005	15.865	0.019	0.019	0.000	0.000	0.000	0.000
20	A	156	ASN	0	0.018	0.017	11.333	-0.041	-0.041	0.000	0.000	0.000	0.000
21	A	157	LYS	1	0.928	0.974	14.518	-0.018	-0.018	0.000	0.000	0.000	0.000
22	A	158	THR	0	-0.034	-0.031	13.576	0.042	0.042	0.000	0.000	0.000	0.000
23	A	159	THR	0	0.059	0.044	16.271	-0.028	-0.028	0.000	0.000	0.000	0.000
24	A	160	TRP	0	0.012	-0.001	18.075	0.042	0.042	0.000	0.000	0.000	0.000
25	A	161	SER	0	0.002	-0.006	18.580	0.013	0.013	0.000	0.000	0.000	0.000
26	A	162	GLY	0	0.047	0.021	14.729	0.035	0.035	0.000	0.000	0.000	0.000
27	A	163	CYS	0	-0.071	-0.008	14.458	0.063	0.063	0.000	0.000	0.000	0.000
28	A	164	LYS	1	0.978	0.984	16.331	-0.225	-0.225	0.000	0.000	0.000	0.000
29	A	165	ALA	0	0.010	0.007	13.380	-0.016	-0.016	0.000	0.000	0.000	0.000
30	A	166	ASN	0	0.015	0.002	10.907	0.216	0.216	0.000	0.000	0.000	0.000
31	A	167	CYS	0	-0.073	-0.015	12.889	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	168	GLN	0	0.003	0.000	15.442	-0.054	-0.054	0.000	0.000	0.000	0.000
33	A	169	HIS	0	-0.031	-0.010	7.522	0.259	0.259	0.000	0.000	0.000	0.000
34	A	170	TYR	0	-0.018	-0.015	9.978	0.009	0.009	0.000	0.000	0.000	0.000
35	A	171	GLY	0	0.060	0.042	14.161	-0.054	-0.054	0.000	0.000	0.000	0.000
36	A	172	VAL	0	-0.052	-0.025	17.260	-0.034	-0.034	0.000	0.000	0.000	0.000
37	A	173	PRO	0	0.065	0.030	18.734	0.026	0.026	0.000	0.000	0.000	0.000
38	A	174	ILE	0	0.005	-0.012	19.921	-0.014	-0.014	0.000	0.000	0.000	0.000
39	A	175	LEU	0	-0.008	-0.015	21.179	-0.011	-0.011	0.000	0.000	0.000	0.000
40	A	176	LYS	1	0.828	0.925	24.263	-0.077	-0.077	0.000	0.000	0.000	0.000
41	A	177	ILE	0	-0.010	0.008	27.614	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	178	GLU	-1	-0.762	-0.847	30.400	0.058	0.058	0.000	0.000	0.000	0.000
43	A	179	ASP	-1	-0.868	-0.947	33.501	0.029	0.029	0.000	0.000	0.000	0.000
44	A	180	GLU	-1	-0.741	-0.894	34.924	0.035	0.035	0.000	0.000	0.000	0.000
45	A	181	ASP	-1	-0.837	-0.897	36.799	0.015	0.015	0.000	0.000	0.000	0.000
46	A	182	GLU	-1	-0.729	-0.820	29.381	0.046	0.046	0.000	0.000	0.000	0.000
47	A	183	LEU	0	-0.029	-0.010	31.628	0.000	0.000	0.000	0.000	0.000	0.000
48	A	184	LYS	1	0.917	0.944	32.787	-0.022	-0.022	0.000	0.000	0.000	0.000
49	A	185	PHE	0	-0.040	0.005	28.005	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	186	LEU	0	0.022	0.012	26.843	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	187	GLN	0	-0.038	-0.025	29.482	0.001	0.001	0.000	0.000	0.000	0.000
52	A	188	ARG	1	0.885	0.935	31.779	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	189	HIS	0	-0.010	0.014	25.388	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	190	VAL	0	0.000	0.013	25.440	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	191	ILE	0	0.068	0.042	22.333	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	192	PRO	0	-0.005	-0.001	26.100	0.013	0.013	0.000	0.000	0.000	0.000
57	A	193	GLY	0	0.014	0.007	24.888	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	194	ASN	0	-0.026	-0.004	24.591	-0.008	-0.008	0.000	0.000	0.000	0.000
59	A	195	TYR	0	-0.034	-0.046	21.748	0.009	0.009	0.000	0.000	0.000	0.000
60	A	196	TRP	0	-0.031	-0.015	19.908	-0.013	-0.013	0.000	0.000	0.000	0.000
61	A	197	ILE	0	0.037	0.012	22.576	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	198	GLY	0	0.006	0.022	24.325	0.012	0.012	0.000	0.000	0.000	0.000
63	A	199	LEU	0	-0.025	-0.014	25.161	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	200	SER	0	-0.012	-0.007	26.391	0.009	0.009	0.000	0.000	0.000	0.000
65	A	201	TYR	0	0.008	0.002	28.517	-0.008	-0.008	0.000	0.000	0.000	0.000
66	A	202	ASP	-1	-0.784	-0.876	30.247	0.135	0.135	0.000	0.000	0.000	0.000
67	A	203	LYS	1	0.896	0.929	27.906	-0.168	-0.168	0.000	0.000	0.000	0.000
68	A	204	LYS	1	0.895	0.956	30.876	-0.127	-0.127	0.000	0.000	0.000	0.000
69	A	205	LYS	1	0.889	0.941	32.567	-0.111	-0.111	0.000	0.000	0.000	0.000
70	A	206	LYS	1	0.917	0.962	35.449	-0.093	-0.093	0.000	0.000	0.000	0.000
71	A	207	GLU	-1	-0.860	-0.911	35.628	0.075	0.075	0.000	0.000	0.000	0.000
72	A	208	TRP	0	-0.027	-0.021	30.315	0.010	0.010	0.000	0.000	0.000	0.000
73	A	209	ALA	0	0.013	0.002	30.880	-0.006	-0.006	0.000	0.000	0.000	0.000
74	A	210	TRP	0	0.014	-0.023	28.613	0.012	0.012	0.000	0.000	0.000	0.000
75	A	211	ILE	0	-0.034	-0.026	22.425	0.006	0.006	0.000	0.000	0.000	0.000
76	A	212	ASP	-1	-0.810	-0.898	26.378	0.095	0.095	0.000	0.000	0.000	0.000
77	A	213	ASN	0	-0.087	-0.048	28.545	-0.008	-0.008	0.000	0.000	0.000	0.000
78	A	214	GLY	0	0.057	0.050	31.477	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	215	PRO	0	0.000	-0.010	33.270	0.004	0.004	0.000	0.000	0.000	0.000
80	A	216	SER	0	-0.018	-0.029	33.509	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	217	LYS	1	0.943	0.961	35.550	-0.036	-0.036	0.000	0.000	0.000	0.000
82	A	218	LEU	0	0.025	0.018	33.173	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	219	ASP	-1	-0.766	-0.860	35.597	0.067	0.067	0.000	0.000	0.000	0.000
84	A	220	MET	0	-0.039	-0.033	38.074	0.001	0.001	0.000	0.000	0.000	0.000
85	A	221	LYS	1	0.840	0.913	38.020	-0.037	-0.037	0.000	0.000	0.000	0.000
86	A	222	ILE	0	0.036	0.002	33.712	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	223	LYS	1	0.936	0.974	37.903	-0.045	-0.045	0.000	0.000	0.000	0.000
88	A	224	LYS	1	0.951	0.981	40.362	-0.034	-0.034	0.000	0.000	0.000	0.000
89	A	225	MET	0	-0.047	-0.018	36.615	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	226	ASN	0	-0.079	-0.034	39.591	0.002	0.002	0.000	0.000	0.000	0.000
91	A	227	PHE	0	0.050	0.023	33.437	0.001	0.001	0.000	0.000	0.000	0.000
92	A	228	LYS	1	0.961	0.979	36.050	-0.057	-0.057	0.000	0.000	0.000	0.000
93	A	229	SER	0	-0.083	-0.044	31.714	0.006	0.006	0.000	0.000	0.000	0.000
94	A	230	ARG	1	0.920	0.949	32.474	-0.092	-0.092	0.000	0.000	0.000	0.000
95	A	231	GLY	0	-0.006	-0.009	28.490	0.012	0.012	0.000	0.000	0.000	0.000
96	A	232	CYS	0	-0.096	-0.051	23.386	0.007	0.007	0.000	0.000	0.000	0.000
97	A	233	VAL	0	0.054	0.028	27.635	-0.009	-0.009	0.000	0.000	0.000	0.000
98	A	234	PHE	0	-0.027	-0.012	25.953	0.013	0.013	0.000	0.000	0.000	0.000
99	A	235	LEU	0	0.004	0.003	26.826	-0.010	-0.010	0.000	0.000	0.000	0.000
100	A	236	SER	0	0.061	0.023	27.301	0.001	0.001	0.000	0.000	0.000	0.000
101	A	237	LYS	1	0.826	0.881	29.489	0.000	0.000	0.000	0.000	0.000	0.000
102	A	238	ALA	0	0.004	0.023	31.683	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	239	ARG	1	0.820	0.893	33.076	-0.045	-0.045	0.000	0.000	0.000	0.000
104	A	240	ILE	0	0.013	0.007	30.944	0.003	0.003	0.000	0.000	0.000	0.000
105	A	241	GLU	-1	-0.821	-0.897	31.262	0.053	0.053	0.000	0.000	0.000	0.000
106	A	242	ASP	-1	-0.771	-0.859	30.543	0.094	0.094	0.000	0.000	0.000	0.000
107	A	243	ILE	0	0.033	0.019	27.008	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	244	ASP	-1	-0.797	-0.900	25.668	0.184	0.184	0.000	0.000	0.000	0.000
109	A	246	ASN	0	-0.046	-0.043	21.103	0.051	0.051	0.000	0.000	0.000	0.000
110	A	247	ILE	0	0.037	0.027	20.839	0.012	0.012	0.000	0.000	0.000	0.000
111	A	248	PRO	0	0.006	-0.008	18.018	0.008	0.008	0.000	0.000	0.000	0.000
112	A	249	TYR	0	-0.014	0.004	19.712	-0.038	-0.038	0.000	0.000	0.000	0.000
113	A	250	TYR	0	0.011	0.016	18.332	0.027	0.027	0.000	0.000	0.000	0.000
114	A	252	ILE	0	0.039	0.027	19.399	-0.022	-0.022	0.000	0.000	0.000	0.000
115	A	254	GLY	0	0.020	-0.003	20.584	-0.023	-0.023	0.000	0.000	0.000	0.000
116	A	255	LYS	1	0.880	0.947	21.278	-0.068	-0.068	0.000	0.000	0.000	0.000
117	A	256	LYS	1	0.860	0.922	24.977	-0.063	-0.063	0.000	0.000	0.000	0.000
118	A	257	LEU	0	0.001	-0.007	26.196	0.003	0.003	0.000	0.000	0.000	0.000
119	A	258	ASP	-1	-0.921	-0.957	28.344	0.031	0.031	0.000	0.000	0.000	0.000
120	A	259	LYS	1	0.784	0.867	29.507	0.017	0.017	0.000	0.000	0.000	0.000
121	A	260	PHE	0	-0.003	0.001	30.630	0.002	0.002	0.000	0.000	0.000	0.000
122	A	261	PRO	0	-0.009	-0.016	26.671	0.000	0.000	0.000	0.000	0.000	0.000
123	A	262	ASP	-1	-0.803	-0.860	26.414	-0.033	-0.033	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:136:THR)