FMO DATABASE

FMODB ID: 4JY8N

Calculation Name: 3CFU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CFU

Chain ID: A

ChEMBL ID:

UniProt ID: O34725

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	151
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1444237.163917
FMO2-HF: Nuclear repulsion	1384359.61009
FMO2-HF: Total energy	-59877.553827
FMO2-MP2: Total energy	-60052.675224

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:63:MET)

Summations of interaction energy for fragment #1(A:63:MET)

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.
-17.515	-12.521	8.271	-3.875	-9.393	-0.017

Interaction energy analysis for fragmet #1(A:63:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.034 / q_NPA : -0.032

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	65	LYS	1	0.895	0.953	3.736	-1.998	-0.555	0.014	-0.585	-0.873	0.000
4	A	66	ILE	0	0.009	0.005	5.932	-0.461	-0.461	0.000	0.000	0.000	0.000
5	A	67	GLY	0	-0.013	-0.003	9.340	0.124	0.124	0.000	0.000	0.000	0.000
6	A	68	GLU	-1	-0.903	-0.942	6.888	-2.631	-2.631	0.000	0.000	0.000	0.000
7	A	69	THR	0	-0.028	-0.009	10.405	-0.095	-0.095	0.000	0.000	0.000	0.000
8	A	70	PHE	0	-0.041	-0.019	7.940	-0.248	-0.248	0.000	0.000	0.000	0.000
9	A	71	LYS	1	0.973	0.989	10.765	1.075	1.075	0.000	0.000	0.000	0.000
10	A	72	ALA	0	-0.018	-0.007	10.341	-0.246	-0.246	0.000	0.000	0.000	0.000
11	A	73	GLY	0	0.047	0.045	12.056	0.130	0.130	0.000	0.000	0.000	0.000
12	A	74	HIS	0	-0.037	-0.032	15.266	0.017	0.017	0.000	0.000	0.000	0.000
13	A	75	THR	0	-0.014	-0.011	15.092	0.054	0.054	0.000	0.000	0.000	0.000
14	A	76	ASN	0	-0.003	0.007	14.207	-0.203	-0.203	0.000	0.000	0.000	0.000
15	A	77	PHE	0	0.008	-0.021	9.578	0.132	0.132	0.000	0.000	0.000	0.000
16	A	78	THR	0	0.019	0.007	11.219	-0.170	-0.170	0.000	0.000	0.000	0.000
17	A	79	VAL	0	0.047	0.033	8.664	0.094	0.094	0.000	0.000	0.000	0.000
18	A	80	ASN	0	-0.046	-0.028	11.664	0.014	0.014	0.000	0.000	0.000	0.000
19	A	81	LYS	1	0.950	0.958	14.302	0.150	0.150	0.000	0.000	0.000	0.000
20	A	82	VAL	0	-0.004	-0.001	11.378	-0.059	-0.059	0.000	0.000	0.000	0.000
21	A	83	ASP	-1	-0.921	-0.940	14.709	0.077	0.077	0.000	0.000	0.000	0.000
22	A	84	ARG	1	0.938	0.959	16.457	-0.284	-0.284	0.000	0.000	0.000	0.000
23	A	85	VAL	0	0.016	0.026	19.371	0.000	0.000	0.000	0.000	0.000	0.000
24	A	86	GLN	0	-0.039	-0.043	22.171	0.036	0.036	0.000	0.000	0.000	0.000
25	A	87	LYS	1	0.795	0.914	24.774	-0.050	-0.050	0.000	0.000	0.000	0.000
26	A	88	GLY	0	0.015	-0.010	27.630	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	89	GLU	-1	-0.854	-0.919	27.548	0.032	0.032	0.000	0.000	0.000	0.000
28	A	90	TYR	0	-0.029	-0.006	23.374	-0.014	-0.014	0.000	0.000	0.000	0.000
29	A	91	MET	0	-0.007	-0.013	24.901	0.003	0.003	0.000	0.000	0.000	0.000
30	A	92	ASN	0	0.075	0.024	22.476	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	93	VAL	0	-0.049	-0.005	20.918	0.005	0.005	0.000	0.000	0.000	0.000
32	A	94	GLY	0	-0.004	-0.011	22.870	-0.022	-0.022	0.000	0.000	0.000	0.000
33	A	95	GLY	0	-0.042	-0.014	24.280	0.003	0.003	0.000	0.000	0.000	0.000
34	A	96	ALA	0	0.055	0.021	26.562	0.007	0.007	0.000	0.000	0.000	0.000
35	A	97	VAL	0	0.008	-0.004	28.427	0.006	0.006	0.000	0.000	0.000	0.000
36	A	98	ASN	0	-0.061	-0.021	31.200	0.000	0.000	0.000	0.000	0.000	0.000
37	A	99	GLU	-1	-0.817	-0.903	32.101	-0.027	-0.027	0.000	0.000	0.000	0.000
38	A	100	GLU	-1	-0.942	-0.953	26.425	-0.009	-0.009	0.000	0.000	0.000	0.000
39	A	101	THR	0	-0.031	-0.023	30.759	0.003	0.003	0.000	0.000	0.000	0.000
40	A	102	LYS	1	0.797	0.869	33.154	0.022	0.022	0.000	0.000	0.000	0.000
41	A	103	THR	0	-0.024	-0.017	31.431	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	104	ILE	0	0.031	0.049	26.145	0.007	0.007	0.000	0.000	0.000	0.000
43	A	105	LYS	1	0.814	0.900	28.362	-0.083	-0.083	0.000	0.000	0.000	0.000
44	A	106	ASP	-1	-0.751	-0.892	25.518	0.068	0.068	0.000	0.000	0.000	0.000
45	A	107	ASP	-1	-0.920	-0.949	20.959	0.114	0.114	0.000	0.000	0.000	0.000
46	A	108	GLU	-1	-0.806	-0.903	20.509	0.247	0.247	0.000	0.000	0.000	0.000
47	A	109	GLU	-1	-0.895	-0.949	18.159	0.273	0.273	0.000	0.000	0.000	0.000
48	A	110	ARG	1	0.886	0.955	18.547	0.011	0.011	0.000	0.000	0.000	0.000
49	A	111	LEU	0	0.028	0.011	12.180	0.008	0.008	0.000	0.000	0.000	0.000
50	A	112	ILE	0	-0.027	-0.009	16.307	-0.049	-0.049	0.000	0.000	0.000	0.000
51	A	113	ILE	0	0.005	0.009	10.691	0.018	0.018	0.000	0.000	0.000	0.000
52	A	114	GLU	-1	-0.887	-0.936	14.589	-0.222	-0.222	0.000	0.000	0.000	0.000
53	A	115	VAL	0	0.008	0.003	12.572	-0.031	-0.031	0.000	0.000	0.000	0.000
54	A	116	THR	0	-0.006	-0.019	14.914	0.087	0.087	0.000	0.000	0.000	0.000
55	A	117	MET	0	-0.019	0.004	15.411	-0.092	-0.092	0.000	0.000	0.000	0.000
56	A	118	GLU	-1	-0.894	-0.970	17.446	-0.440	-0.440	0.000	0.000	0.000	0.000
57	A	119	ASN	0	0.005	0.009	18.684	-0.102	-0.102	0.000	0.000	0.000	0.000
58	A	120	ILE	0	-0.052	-0.017	17.195	0.037	0.037	0.000	0.000	0.000	0.000
59	A	121	GLY	0	0.030	0.015	21.328	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	122	GLU	-1	-0.969	-0.977	23.020	-0.266	-0.266	0.000	0.000	0.000	0.000
61	A	123	ASP	-1	-0.827	-0.902	25.446	-0.322	-0.322	0.000	0.000	0.000	0.000
62	A	124	SER	0	-0.086	-0.052	25.385	-0.026	-0.026	0.000	0.000	0.000	0.000
63	A	125	ILE	0	0.041	0.033	20.097	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	126	SER	0	-0.052	-0.024	24.233	0.035	0.035	0.000	0.000	0.000	0.000
65	A	127	TYR	0	0.026	0.024	20.189	-0.012	-0.012	0.000	0.000	0.000	0.000
66	A	128	ASN	0	0.014	-0.012	20.146	0.050	0.050	0.000	0.000	0.000	0.000
67	A	129	PHE	0	0.053	0.013	18.416	-0.049	-0.049	0.000	0.000	0.000	0.000
68	A	130	ILE	0	-0.017	-0.007	17.284	-0.028	-0.028	0.000	0.000	0.000	0.000
69	A	131	GLY	0	0.000	0.016	16.005	-0.021	-0.021	0.000	0.000	0.000	0.000
70	A	132	PHE	0	-0.078	-0.049	12.110	-0.134	-0.134	0.000	0.000	0.000	0.000
71	A	133	ASP	-1	-0.783	-0.890	11.230	-0.372	-0.372	0.000	0.000	0.000	0.000
72	A	134	LEU	0	-0.060	-0.010	8.884	-0.175	-0.175	0.000	0.000	0.000	0.000
73	A	135	ARG	1	0.927	0.980	6.821	0.928	0.928	0.000	0.000	0.000	0.000
74	A	136	ASP	-1	-0.860	-0.933	7.706	0.290	0.290	0.000	0.000	0.000	0.000
75	A	137	LYS	1	0.955	0.967	7.417	-1.133	-1.133	0.000	0.000	0.000	0.000
76	A	138	ASN	0	-0.095	-0.073	8.481	0.195	0.195	0.000	0.000	0.000	0.000
77	A	139	ASP	-1	-0.914	-0.960	7.611	-0.439	-0.439	0.000	0.000	0.000	0.000
78	A	140	GLN	0	-0.016	0.007	9.160	-0.100	-0.100	0.000	0.000	0.000	0.000
79	A	141	SER	0	0.014	-0.003	11.441	0.024	0.024	0.000	0.000	0.000	0.000
80	A	142	VAL	0	-0.076	-0.026	12.096	0.081	0.081	0.000	0.000	0.000	0.000
81	A	143	ARG	1	0.953	0.969	14.479	-0.039	-0.039	0.000	0.000	0.000	0.000
82	A	144	PRO	0	0.051	0.039	17.127	0.022	0.022	0.000	0.000	0.000	0.000
83	A	145	VAL	0	-0.001	-0.014	18.013	0.025	0.025	0.000	0.000	0.000	0.000
84	A	146	PHE	0	-0.072	-0.047	20.433	-0.022	-0.022	0.000	0.000	0.000	0.000
85	A	147	SER	0	0.029	0.018	22.992	0.016	0.016	0.000	0.000	0.000	0.000
86	A	148	ILE	0	-0.071	-0.050	25.352	-0.016	-0.016	0.000	0.000	0.000	0.000
87	A	149	GLU	-1	-0.846	-0.924	26.159	0.000	0.000	0.000	0.000	0.000	0.000
88	A	150	GLU	-1	-0.812	-0.898	22.046	-0.068	-0.068	0.000	0.000	0.000	0.000
89	A	151	LYS	1	0.926	0.945	25.288	0.067	0.067	0.000	0.000	0.000	0.000
90	A	152	GLY	0	-0.021	-0.013	27.726	0.003	0.003	0.000	0.000	0.000	0.000
91	A	153	ARG	1	0.895	0.950	20.789	0.106	0.106	0.000	0.000	0.000	0.000
92	A	154	ILE	0	-0.040	-0.009	21.948	-0.027	-0.027	0.000	0.000	0.000	0.000
93	A	155	LEU	0	0.001	0.023	17.058	0.002	0.002	0.000	0.000	0.000	0.000
94	A	156	MET	0	-0.033	-0.014	20.928	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	157	GLY	0	0.055	0.001	22.567	-0.024	-0.024	0.000	0.000	0.000	0.000
96	A	158	GLY	0	-0.038	-0.002	24.275	0.026	0.026	0.000	0.000	0.000	0.000
97	A	159	THR	0	-0.054	-0.017	25.588	-0.023	-0.023	0.000	0.000	0.000	0.000
98	A	160	LEU	0	0.001	0.009	21.193	0.014	0.014	0.000	0.000	0.000	0.000
99	A	161	VAL	0	-0.010	-0.013	25.187	-0.017	-0.017	0.000	0.000	0.000	0.000
100	A	162	SER	0	0.016	0.009	25.223	-0.007	-0.007	0.000	0.000	0.000	0.000
101	A	163	GLY	0	0.016	0.005	24.378	0.028	0.028	0.000	0.000	0.000	0.000
102	A	164	LYS	1	0.894	0.953	24.992	0.259	0.259	0.000	0.000	0.000	0.000
103	A	165	LYS	1	0.931	0.957	20.242	0.381	0.381	0.000	0.000	0.000	0.000
104	A	166	VAL	0	-0.004	0.007	20.434	0.041	0.041	0.000	0.000	0.000	0.000
105	A	167	THR	0	-0.009	-0.013	18.967	-0.061	-0.061	0.000	0.000	0.000	0.000
106	A	168	GLY	0	0.012	0.019	18.936	0.036	0.036	0.000	0.000	0.000	0.000
107	A	169	VAL	0	-0.065	-0.037	17.648	-0.023	-0.023	0.000	0.000	0.000	0.000
108	A	170	LEU	0	0.014	0.018	12.974	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	171	SER	0	-0.040	-0.029	16.555	0.047	0.047	0.000	0.000	0.000	0.000
110	A	172	TYR	0	0.063	0.033	13.420	-0.027	-0.027	0.000	0.000	0.000	0.000
111	A	173	VAL	0	-0.031	0.006	16.626	0.028	0.028	0.000	0.000	0.000	0.000
112	A	174	ILE	0	-0.021	-0.010	13.009	-0.005	-0.005	0.000	0.000	0.000	0.000
113	A	175	PRO	0	0.072	0.024	15.219	-0.012	-0.012	0.000	0.000	0.000	0.000
114	A	176	LYS	1	0.822	0.902	16.887	-0.178	-0.178	0.000	0.000	0.000	0.000
115	A	177	GLY	0	-0.020	0.000	17.008	0.037	0.037	0.000	0.000	0.000	0.000
116	A	178	GLU	-1	-0.932	-0.967	13.383	0.642	0.642	0.000	0.000	0.000	0.000
117	A	179	GLN	0	0.012	-0.020	11.034	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	180	LYS	1	0.863	0.941	9.293	-0.864	-0.864	0.000	0.000	0.000	0.000
119	A	181	HIS	0	-0.083	-0.042	7.701	0.579	0.579	0.000	0.000	0.000	0.000
120	A	182	TYR	0	0.042	0.025	7.176	-0.064	-0.064	0.000	0.000	0.000	0.000
121	A	183	THR	0	-0.037	-0.022	2.362	-1.109	-0.779	1.907	-0.634	-1.604	-0.007
122	A	184	LEU	0	0.000	0.008	4.837	0.097	0.152	-0.001	-0.007	-0.048	0.000
123	A	185	VAL	0	0.003	-0.006	5.795	-0.713	-0.713	0.000	0.000	0.000	0.000
124	A	186	TYR	0	-0.011	-0.022	7.984	0.308	0.308	0.000	0.000	0.000	0.000
125	A	187	ASN	0	0.069	0.036	10.536	-0.187	-0.187	0.000	0.000	0.000	0.000
126	A	188	PRO	0	-0.034	-0.018	12.239	0.125	0.125	0.000	0.000	0.000	0.000
127	A	189	PHE	0	0.003	0.020	15.280	0.097	0.097	0.000	0.000	0.000	0.000
128	A	190	LEU	0	0.019	0.000	15.823	0.068	0.068	0.000	0.000	0.000	0.000
129	A	191	ALA	0	-0.030	-0.016	16.104	0.060	0.060	0.000	0.000	0.000	0.000
130	A	192	ASP	-1	-0.819	-0.911	18.108	-0.383	-0.383	0.000	0.000	0.000	0.000
131	A	193	THR	0	0.006	-0.009	21.131	0.010	0.010	0.000	0.000	0.000	0.000
132	A	194	ASN	0	-0.046	0.015	24.169	0.055	0.055	0.000	0.000	0.000	0.000
133	A	195	SER	0	0.024	0.002	26.262	-0.015	-0.015	0.000	0.000	0.000	0.000
134	A	196	SER	0	-0.100	-0.068	28.797	0.008	0.008	0.000	0.000	0.000	0.000
135	A	197	ASN	0	0.080	0.044	25.331	0.010	0.010	0.000	0.000	0.000	0.000
136	A	198	THR	0	0.017	0.001	24.320	-0.016	-0.016	0.000	0.000	0.000	0.000
137	A	199	GLU	-1	-0.859	-0.947	24.269	-0.332	-0.332	0.000	0.000	0.000	0.000
138	A	200	GLU	-1	-1.045	-1.017	25.152	-0.313	-0.313	0.000	0.000	0.000	0.000
139	A	201	ARG	1	0.773	0.867	20.823	0.427	0.427	0.000	0.000	0.000	0.000
140	A	202	VAL	0	0.043	0.032	19.983	-0.056	-0.056	0.000	0.000	0.000	0.000
141	A	203	LYS	1	0.889	0.934	18.340	0.421	0.421	0.000	0.000	0.000	0.000
142	A	204	ASP	-1	-0.875	-0.933	15.642	-0.775	-0.775	0.000	0.000	0.000	0.000
143	A	205	ASP	-1	-0.943	-0.968	14.632	-0.758	-0.758	0.000	0.000	0.000	0.000
144	A	206	ILE	0	-0.023	-0.013	9.635	-0.023	-0.023	0.000	0.000	0.000	0.000
145	A	207	ASP	-1	-0.854	-0.928	8.053	-1.124	-1.124	0.000	0.000	0.000	0.000
146	A	208	TYR	0	-0.063	-0.037	6.220	-0.386	-0.386	0.000	0.000	0.000	0.000
147	A	209	LEU	0	-0.002	-0.012	2.236	-0.717	-0.498	2.634	-0.604	-2.249	-0.004
148	A	210	VAL	0	-0.005	-0.008	3.106	-3.125	-1.538	0.159	-0.917	-0.829	-0.008
149	A	211	LYS	1	0.906	0.970	2.428	-7.127	-5.891	3.547	-1.112	-3.671	0.002
150	A	212	LEU	0	0.019	-0.006	3.783	-0.236	-0.112	0.011	-0.016	-0.119	0.000
151	A	213	ASP	-1	-0.880	-0.932	7.252	3.504	3.504	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:63:MET)