FMO DATABASE

FMODB ID: 72RNK

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:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
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
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1208781.39729
FMO2-HF: Nuclear repulsion	1154518.257778
FMO2-HF: Total energy	-54263.139512
FMO2-MP2: Total energy	-54415.62724

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.
-3.035	0.005	-0.018	-1.68	-1.343	0.008

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 : 0.065 / q_NPA : 0.031

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	0.889	0.933	3.793	-2.570	0.470	-0.018	-1.680	-1.343	0.008
4	A	139	GLY	0	-0.034	-0.006	6.664	-0.180	-0.180	0.000	0.000	0.000	0.000
5	A	140	VAL	0	0.000	0.009	9.655	-0.123	-0.123	0.000	0.000	0.000	0.000
6	A	141	LYS	1	0.924	0.969	10.984	0.031	0.031	0.000	0.000	0.000	0.000
7	A	142	TYR	0	-0.015	-0.005	14.611	-0.057	-0.057	0.000	0.000	0.000	0.000
8	A	143	TRP	0	0.009	-0.009	17.045	0.048	0.048	0.000	0.000	0.000	0.000
9	A	144	PHE	0	0.037	0.016	19.577	-0.019	-0.019	0.000	0.000	0.000	0.000
10	A	145	CYS	0	-0.025	0.001	23.143	0.002	0.002	0.000	0.000	0.000	0.000
11	A	146	TYR	0	0.025	0.000	26.219	-0.006	-0.006	0.000	0.000	0.000	0.000
12	A	147	SER	0	-0.001	0.012	29.684	0.006	0.006	0.000	0.000	0.000	0.000
13	A	148	THR	0	0.024	0.016	31.215	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	149	LYS	1	0.821	0.896	27.113	-0.054	-0.054	0.000	0.000	0.000	0.000
15	A	151	TYR	0	-0.028	-0.060	22.437	0.015	0.015	0.000	0.000	0.000	0.000
16	A	152	TYR	0	-0.005	-0.004	15.699	-0.020	-0.020	0.000	0.000	0.000	0.000
17	A	153	PHE	0	0.016	0.011	18.867	0.029	0.029	0.000	0.000	0.000	0.000
18	A	154	ILE	0	-0.006	-0.033	13.491	-0.016	-0.016	0.000	0.000	0.000	0.000
19	A	155	MET	0	-0.028	-0.015	15.685	0.027	0.027	0.000	0.000	0.000	0.000
20	A	156	ASN	0	0.040	0.031	11.283	-0.014	-0.014	0.000	0.000	0.000	0.000
21	A	157	LYS	1	0.929	0.963	14.486	-0.045	-0.045	0.000	0.000	0.000	0.000
22	A	158	THR	0	0.008	0.006	13.044	0.049	0.049	0.000	0.000	0.000	0.000
23	A	159	THR	0	0.018	0.019	15.771	-0.037	-0.037	0.000	0.000	0.000	0.000
24	A	160	TRP	0	0.032	0.003	17.963	0.042	0.042	0.000	0.000	0.000	0.000
25	A	161	SER	0	0.018	-0.003	18.513	0.013	0.013	0.000	0.000	0.000	0.000
26	A	162	GLY	0	0.047	0.033	14.773	0.035	0.035	0.000	0.000	0.000	0.000
27	A	163	CYS	0	-0.057	0.001	14.477	0.065	0.065	0.000	0.000	0.000	0.000
28	A	164	LYS	1	0.989	0.983	16.548	-0.257	-0.257	0.000	0.000	0.000	0.000
29	A	165	ALA	0	-0.017	-0.009	13.431	-0.010	-0.010	0.000	0.000	0.000	0.000
30	A	166	ASN	0	-0.004	-0.024	11.080	0.185	0.185	0.000	0.000	0.000	0.000
31	A	167	CYS	0	-0.070	-0.012	12.860	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	168	GLN	0	0.017	0.007	15.554	-0.063	-0.063	0.000	0.000	0.000	0.000
33	A	169	HIS	0	-0.024	0.007	7.595	0.203	0.203	0.000	0.000	0.000	0.000
34	A	170	TYR	0	-0.024	-0.019	10.137	-0.010	-0.010	0.000	0.000	0.000	0.000
35	A	171	GLY	0	0.043	0.025	14.054	-0.057	-0.057	0.000	0.000	0.000	0.000
36	A	172	VAL	0	-0.048	-0.021	17.144	-0.036	-0.036	0.000	0.000	0.000	0.000
37	A	173	PRO	0	0.047	0.018	18.502	0.029	0.029	0.000	0.000	0.000	0.000
38	A	174	ILE	0	-0.001	-0.012	19.913	-0.016	-0.016	0.000	0.000	0.000	0.000
39	A	175	LEU	0	-0.006	-0.005	21.135	-0.013	-0.013	0.000	0.000	0.000	0.000
40	A	176	LYS	1	0.836	0.943	24.244	-0.076	-0.076	0.000	0.000	0.000	0.000
41	A	177	ILE	0	-0.022	-0.008	27.689	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	178	GLU	-1	-0.820	-0.888	30.470	0.063	0.063	0.000	0.000	0.000	0.000
43	A	179	ASP	-1	-0.841	-0.941	33.604	0.032	0.032	0.000	0.000	0.000	0.000
44	A	180	GLU	-1	-0.773	-0.909	34.923	0.037	0.037	0.000	0.000	0.000	0.000
45	A	181	ASP	-1	-0.881	-0.922	36.692	0.017	0.017	0.000	0.000	0.000	0.000
46	A	182	GLU	-1	-0.743	-0.823	29.336	0.051	0.051	0.000	0.000	0.000	0.000
47	A	183	LEU	0	-0.024	-0.014	31.435	0.000	0.000	0.000	0.000	0.000	0.000
48	A	184	LYS	1	0.931	0.951	32.256	-0.027	-0.027	0.000	0.000	0.000	0.000
49	A	185	PHE	0	-0.050	-0.014	28.191	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	186	LEU	0	0.048	0.019	26.547	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	187	GLN	0	-0.053	-0.016	29.064	0.001	0.001	0.000	0.000	0.000	0.000
52	A	188	ARG	1	0.930	0.958	31.278	-0.011	-0.011	0.000	0.000	0.000	0.000
53	A	189	HIS	0	-0.031	0.014	25.201	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	190	VAL	0	-0.001	0.008	25.083	-0.007	-0.007	0.000	0.000	0.000	0.000
55	A	191	ILE	0	0.056	0.040	22.289	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	192	PRO	0	0.003	-0.003	25.828	0.013	0.013	0.000	0.000	0.000	0.000
57	A	193	GLY	0	0.014	0.002	24.430	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	194	ASN	0	-0.034	-0.009	23.919	-0.009	-0.009	0.000	0.000	0.000	0.000
59	A	195	TYR	0	-0.034	-0.039	21.551	0.014	0.014	0.000	0.000	0.000	0.000
60	A	196	TRP	0	-0.016	0.003	19.721	-0.017	-0.017	0.000	0.000	0.000	0.000
61	A	197	ILE	0	0.036	0.009	22.634	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	198	GLY	0	-0.010	-0.001	24.314	0.014	0.014	0.000	0.000	0.000	0.000
63	A	199	LEU	0	-0.022	-0.008	25.041	-0.010	-0.010	0.000	0.000	0.000	0.000
64	A	200	SER	0	-0.015	-0.014	26.106	0.009	0.009	0.000	0.000	0.000	0.000
65	A	201	TYR	0	0.048	0.029	28.242	-0.010	-0.010	0.000	0.000	0.000	0.000
66	A	202	ASP	-1	-0.802	-0.896	29.816	0.146	0.146	0.000	0.000	0.000	0.000
67	A	203	LYS	1	0.943	0.943	27.703	-0.192	-0.192	0.000	0.000	0.000	0.000
68	A	204	LYS	1	0.910	0.956	30.627	-0.140	-0.140	0.000	0.000	0.000	0.000
69	A	205	LYS	1	0.922	0.956	32.835	-0.119	-0.119	0.000	0.000	0.000	0.000
70	A	206	LYS	1	0.886	0.950	35.362	-0.101	-0.101	0.000	0.000	0.000	0.000
71	A	207	GLU	-1	-0.893	-0.931	35.146	0.078	0.078	0.000	0.000	0.000	0.000
72	A	208	TRP	0	-0.027	-0.010	30.066	0.011	0.011	0.000	0.000	0.000	0.000
73	A	209	ALA	0	0.023	0.012	30.318	-0.006	-0.006	0.000	0.000	0.000	0.000
74	A	210	TRP	0	0.029	-0.009	28.596	0.012	0.012	0.000	0.000	0.000	0.000
75	A	211	ILE	0	-0.030	-0.023	22.393	0.007	0.007	0.000	0.000	0.000	0.000
76	A	212	ASP	-1	-0.832	-0.914	26.243	0.100	0.100	0.000	0.000	0.000	0.000
77	A	213	ASN	0	-0.094	-0.039	28.322	-0.007	-0.007	0.000	0.000	0.000	0.000
78	A	214	GLY	0	0.035	0.039	31.421	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	215	PRO	0	0.003	-0.003	33.593	0.004	0.004	0.000	0.000	0.000	0.000
80	A	216	SER	0	0.003	-0.031	33.479	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	217	LYS	1	0.921	0.959	35.577	-0.039	-0.039	0.000	0.000	0.000	0.000
82	A	218	LEU	0	0.025	0.015	33.337	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	219	ASP	-1	-0.770	-0.867	35.608	0.072	0.072	0.000	0.000	0.000	0.000
84	A	220	MET	0	-0.034	-0.020	37.978	0.001	0.001	0.000	0.000	0.000	0.000
85	A	221	LYS	1	0.903	0.942	37.935	-0.042	-0.042	0.000	0.000	0.000	0.000
86	A	222	ILE	0	0.032	0.003	33.677	0.000	0.000	0.000	0.000	0.000	0.000
87	A	223	LYS	1	0.954	0.982	37.874	-0.050	-0.050	0.000	0.000	0.000	0.000
88	A	224	LYS	1	0.910	0.962	40.180	-0.039	-0.039	0.000	0.000	0.000	0.000
89	A	225	MET	0	-0.047	-0.033	36.399	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	226	ASN	0	-0.096	-0.031	39.282	0.002	0.002	0.000	0.000	0.000	0.000
91	A	227	PHE	0	0.054	0.032	33.440	0.000	0.000	0.000	0.000	0.000	0.000
92	A	228	LYS	1	0.956	0.982	36.502	-0.065	-0.065	0.000	0.000	0.000	0.000
93	A	229	SER	0	-0.053	-0.039	32.014	0.007	0.007	0.000	0.000	0.000	0.000
94	A	230	ARG	1	0.932	0.964	32.602	-0.103	-0.103	0.000	0.000	0.000	0.000
95	A	231	GLY	0	-0.040	-0.022	28.710	0.012	0.012	0.000	0.000	0.000	0.000
96	A	232	CYS	0	-0.088	-0.062	23.555	0.006	0.006	0.000	0.000	0.000	0.000
97	A	233	VAL	0	0.087	0.044	27.098	-0.011	-0.011	0.000	0.000	0.000	0.000
98	A	234	PHE	0	-0.043	-0.015	25.543	0.013	0.013	0.000	0.000	0.000	0.000
99	A	235	LEU	0	0.007	0.003	26.547	-0.011	-0.011	0.000	0.000	0.000	0.000
100	A	236	SER	0	0.063	0.024	27.021	0.001	0.001	0.000	0.000	0.000	0.000
101	A	237	LYS	1	0.826	0.884	29.333	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	238	ALA	0	0.003	0.012	31.507	-0.004	-0.004	0.000	0.000	0.000	0.000
103	A	239	ARG	1	0.812	0.890	32.758	-0.053	-0.053	0.000	0.000	0.000	0.000
104	A	240	ILE	0	0.006	0.002	31.077	0.003	0.003	0.000	0.000	0.000	0.000
105	A	241	GLU	-1	-0.817	-0.891	30.916	0.062	0.062	0.000	0.000	0.000	0.000
106	A	242	ASP	-1	-0.788	-0.872	30.510	0.103	0.103	0.000	0.000	0.000	0.000
107	A	243	ILE	0	0.004	0.005	26.707	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	244	ASP	-1	-0.803	-0.908	25.664	0.205	0.205	0.000	0.000	0.000	0.000
109	A	246	ASN	0	-0.047	-0.031	21.148	0.055	0.055	0.000	0.000	0.000	0.000
110	A	247	ILE	0	0.031	0.021	20.923	0.014	0.014	0.000	0.000	0.000	0.000
111	A	248	PRO	0	0.003	-0.007	17.474	0.011	0.011	0.000	0.000	0.000	0.000
112	A	249	TYR	0	-0.017	-0.009	19.308	-0.043	-0.043	0.000	0.000	0.000	0.000
113	A	250	TYR	0	0.006	0.020	17.873	0.031	0.031	0.000	0.000	0.000	0.000
114	A	252	ILE	0	0.039	0.031	19.084	-0.016	-0.016	0.000	0.000	0.000	0.000
115	A	254	GLY	0	0.031	0.006	20.282	-0.026	-0.026	0.000	0.000	0.000	0.000
116	A	255	LYS	1	0.894	0.945	21.168	-0.074	-0.074	0.000	0.000	0.000	0.000
117	A	256	LYS	1	0.879	0.936	24.678	-0.066	-0.066	0.000	0.000	0.000	0.000
118	A	257	LEU	0	0.001	0.005	25.768	0.002	0.002	0.000	0.000	0.000	0.000
119	A	258	ASP	-1	-0.903	-0.946	28.675	0.032	0.032	0.000	0.000	0.000	0.000
120	A	259	LYS	1	0.777	0.861	29.260	0.021	0.021	0.000	0.000	0.000	0.000
121	A	260	PHE	0	-0.016	-0.007	30.534	0.002	0.002	0.000	0.000	0.000	0.000
122	A	261	PRO	0	-0.013	-0.016	26.433	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	262	ASP	-1	-0.793	-0.855	26.350	-0.038	-0.038	0.000	0.000	0.000	0.000

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