FMO DATABASE

FMODB ID: 76KZK

Calculation Name: 3C9G-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3C9G

Chain ID: A

ChEMBL ID:

UniProt ID: O28876

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:

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	131
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1217437.907011
FMO2-HF: Nuclear repulsion	1165187.665124
FMO2-HF: Total energy	-52250.241887
FMO2-MP2: Total energy	-52406.222829

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:187:LYS)

Summations of interaction energy for fragment #1(A:187:LYS)

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.
5.295	9.828	0.069	-2.182	-2.417	-0.002

Interaction energy analysis for fragmet #1(A:187:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.986 / q_NPA : 0.981

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	189	VAL	0	0.027	0.018	3.825	3.161	6.366	-0.043	-1.819	-1.342	-0.003
4	A	190	GLU	-1	-0.837	-0.912	7.419	-29.339	-29.339	0.000	0.000	0.000	0.000
5	A	191	ILE	0	0.013	0.028	9.527	2.270	2.270	0.000	0.000	0.000	0.000
6	A	192	GLU	-1	-0.780	-0.869	13.147	-19.333	-19.333	0.000	0.000	0.000	0.000
7	A	193	ILE	0	-0.029	-0.014	15.905	0.889	0.889	0.000	0.000	0.000	0.000
8	A	194	ARG	1	0.784	0.863	19.291	12.866	12.866	0.000	0.000	0.000	0.000
9	A	195	THR	0	-0.012	-0.021	22.571	0.362	0.362	0.000	0.000	0.000	0.000
10	A	196	LYS	1	0.863	0.916	26.221	10.097	10.097	0.000	0.000	0.000	0.000
11	A	197	ILE	0	-0.011	0.005	27.934	0.040	0.040	0.000	0.000	0.000	0.000
12	A	198	HIS	0	0.017	0.018	31.374	-0.001	-0.001	0.000	0.000	0.000	0.000
13	A	199	PRO	0	0.076	0.026	34.968	-0.020	-0.020	0.000	0.000	0.000	0.000
14	A	200	THR	0	-0.013	-0.002	37.825	0.068	0.068	0.000	0.000	0.000	0.000
15	A	201	GLU	-1	-0.836	-0.905	32.891	-9.805	-9.805	0.000	0.000	0.000	0.000
16	A	202	SER	0	-0.040	-0.021	34.248	-0.027	-0.027	0.000	0.000	0.000	0.000
17	A	203	GLU	-1	-0.823	-0.928	28.807	-10.997	-10.997	0.000	0.000	0.000	0.000
18	A	204	ASP	-1	-0.832	-0.904	29.210	-10.796	-10.796	0.000	0.000	0.000	0.000
19	A	205	LYS	1	0.939	0.957	29.036	8.861	8.861	0.000	0.000	0.000	0.000
20	A	206	VAL	0	0.052	0.036	27.010	-0.264	-0.264	0.000	0.000	0.000	0.000
21	A	207	LEU	0	0.056	0.024	24.269	-0.482	-0.482	0.000	0.000	0.000	0.000
22	A	208	LYS	1	0.822	0.904	24.191	10.063	10.063	0.000	0.000	0.000	0.000
23	A	209	ALA	0	0.006	0.006	25.092	-0.306	-0.306	0.000	0.000	0.000	0.000
24	A	210	ILE	0	-0.006	-0.003	20.734	-0.360	-0.360	0.000	0.000	0.000	0.000
25	A	211	ARG	1	0.880	0.923	19.536	14.779	14.779	0.000	0.000	0.000	0.000
26	A	212	ASN	0	-0.091	-0.032	21.158	-0.456	-0.456	0.000	0.000	0.000	0.000
27	A	213	ILE	0	-0.082	-0.045	19.878	0.061	0.061	0.000	0.000	0.000	0.000
28	A	214	PHE	0	-0.008	-0.023	15.600	-0.763	-0.763	0.000	0.000	0.000	0.000
29	A	215	PRO	0	0.025	-0.004	16.895	0.083	0.083	0.000	0.000	0.000	0.000
30	A	216	ASP	-1	-0.875	-0.927	12.317	-23.341	-23.341	0.000	0.000	0.000	0.000
31	A	217	ALA	0	-0.015	0.002	14.660	-1.119	-1.119	0.000	0.000	0.000	0.000
32	A	218	GLU	-1	-0.903	-0.933	14.895	-18.359	-18.359	0.000	0.000	0.000	0.000
33	A	219	ILE	0	-0.072	-0.066	16.983	0.000	0.000	0.000	0.000	0.000	0.000
34	A	220	GLU	-1	-0.908	-0.935	20.122	-15.090	-15.090	0.000	0.000	0.000	0.000
35	A	221	ILE	0	-0.047	-0.046	22.726	-0.031	-0.031	0.000	0.000	0.000	0.000
36	A	222	SER	0	-0.039	-0.033	26.301	0.104	0.104	0.000	0.000	0.000	0.000
37	A	223	GLU	-1	-0.909	-0.957	28.238	-9.249	-9.249	0.000	0.000	0.000	0.000
38	A	224	GLU	-1	-0.855	-0.911	30.438	-10.229	-10.229	0.000	0.000	0.000	0.000
39	A	225	GLY	0	-0.011	0.007	30.600	0.198	0.198	0.000	0.000	0.000	0.000
40	A	226	GLU	-1	-0.824	-0.876	26.891	-11.203	-11.203	0.000	0.000	0.000	0.000
41	A	227	VAL	0	0.000	-0.002	22.976	-0.242	-0.242	0.000	0.000	0.000	0.000
42	A	228	TYR	0	0.026	0.007	20.419	-0.217	-0.217	0.000	0.000	0.000	0.000
43	A	229	GLY	0	0.038	0.015	18.517	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	230	ARG	1	0.772	0.884	12.623	20.827	20.827	0.000	0.000	0.000	0.000
45	A	231	ALA	0	0.030	0.016	13.329	0.263	0.263	0.000	0.000	0.000	0.000
46	A	232	TYR	0	-0.031	-0.037	7.950	-3.018	-3.018	0.000	0.000	0.000	0.000
47	A	233	SER	0	-0.034	-0.011	10.288	-0.201	-0.201	0.000	0.000	0.000	0.000
48	A	234	LEU	0	0.015	-0.010	10.462	1.856	1.856	0.000	0.000	0.000	0.000
49	A	235	ASP	-1	-0.900	-0.935	13.103	-21.803	-21.803	0.000	0.000	0.000	0.000
50	A	236	ARG	1	0.884	0.947	15.640	15.220	15.220	0.000	0.000	0.000	0.000
51	A	237	PHE	0	0.067	0.015	16.365	0.907	0.907	0.000	0.000	0.000	0.000
52	A	238	ARG	1	0.861	0.935	14.284	20.094	20.094	0.000	0.000	0.000	0.000
53	A	239	GLU	-1	-0.815	-0.890	18.692	-13.617	-13.617	0.000	0.000	0.000	0.000
54	A	240	LEU	0	-0.013	-0.005	21.500	0.807	0.807	0.000	0.000	0.000	0.000
55	A	241	LEU	0	0.019	0.023	19.472	0.641	0.641	0.000	0.000	0.000	0.000
56	A	242	ARG	0	-0.020	0.001	17.716	-0.082	-0.082	0.000	0.000	0.000	0.000
57	A	243	LYS	1	0.816	0.884	23.980	13.388	13.388	0.000	0.000	0.000	0.000
58	A	244	GLN	0	-0.018	0.003	26.689	0.537	0.537	0.000	0.000	0.000	0.000
59	A	245	ARG	1	0.896	0.943	27.617	10.700	10.700	0.000	0.000	0.000	0.000
60	A	246	ILE	0	0.028	0.023	25.827	0.311	0.311	0.000	0.000	0.000	0.000
61	A	247	LEU	0	0.032	0.002	21.314	-0.463	-0.463	0.000	0.000	0.000	0.000
62	A	248	ASP	-1	-0.849	-0.921	23.526	-10.842	-10.842	0.000	0.000	0.000	0.000
63	A	249	THR	0	0.019	0.012	25.697	-0.020	-0.020	0.000	0.000	0.000	0.000
64	A	250	ALA	0	-0.009	0.012	21.262	-0.151	-0.151	0.000	0.000	0.000	0.000
65	A	251	ARG	1	0.770	0.847	19.004	12.663	12.663	0.000	0.000	0.000	0.000
66	A	252	SER	0	-0.038	-0.034	21.441	-0.118	-0.118	0.000	0.000	0.000	0.000
67	A	253	GLU	-1	-0.802	-0.883	23.028	-11.164	-11.164	0.000	0.000	0.000	0.000
68	A	254	ILE	0	-0.042	-0.025	16.557	-0.377	-0.377	0.000	0.000	0.000	0.000
69	A	255	LEU	0	-0.066	-0.042	19.140	-0.368	-0.368	0.000	0.000	0.000	0.000
70	A	256	LYS	1	0.817	0.892	20.782	10.740	10.740	0.000	0.000	0.000	0.000
71	A	257	GLY	0	0.072	0.049	21.238	0.278	0.278	0.000	0.000	0.000	0.000
72	A	258	ARG	1	0.877	0.953	16.079	13.865	13.865	0.000	0.000	0.000	0.000
73	A	259	ASN	0	0.050	0.027	17.615	0.962	0.962	0.000	0.000	0.000	0.000
74	A	260	GLY	0	0.016	0.011	16.485	0.264	0.264	0.000	0.000	0.000	0.000
75	A	261	LYS	1	0.835	0.922	8.702	21.273	21.273	0.000	0.000	0.000	0.000
76	A	262	GLU	-1	-0.920	-0.966	12.056	-18.370	-18.370	0.000	0.000	0.000	0.000
77	A	263	VAL	0	-0.027	-0.011	14.475	0.798	0.798	0.000	0.000	0.000	0.000
78	A	264	THR	0	-0.029	-0.019	16.290	-0.722	-0.722	0.000	0.000	0.000	0.000
79	A	265	ILE	0	0.012	0.018	19.101	0.536	0.536	0.000	0.000	0.000	0.000
80	A	266	TYR	0	-0.028	-0.053	21.467	-0.515	-0.515	0.000	0.000	0.000	0.000
81	A	267	LEU	0	-0.012	0.003	21.354	0.308	0.308	0.000	0.000	0.000	0.000
82	A	268	ASN	0	0.039	0.008	25.352	0.113	0.113	0.000	0.000	0.000	0.000
83	A	269	LYS	1	0.871	0.937	28.029	10.164	10.164	0.000	0.000	0.000	0.000
84	A	270	GLN	0	0.024	0.015	29.037	0.007	0.007	0.000	0.000	0.000	0.000
85	A	271	THR	0	-0.017	-0.006	29.450	0.077	0.077	0.000	0.000	0.000	0.000
86	A	272	ALA	0	0.046	0.039	26.032	-0.044	-0.044	0.000	0.000	0.000	0.000
87	A	273	THR	0	0.000	-0.008	27.463	-0.252	-0.252	0.000	0.000	0.000	0.000
88	A	274	VAL	0	-0.058	-0.028	29.893	0.070	0.070	0.000	0.000	0.000	0.000
89	A	275	SER	0	-0.082	-0.045	25.445	-0.079	-0.079	0.000	0.000	0.000	0.000
90	A	276	ARG	1	0.968	0.993	26.763	9.395	9.395	0.000	0.000	0.000	0.000
91	A	277	ILE	0	0.000	0.005	23.197	-0.037	-0.037	0.000	0.000	0.000	0.000
92	A	278	ASN	0	-0.023	-0.021	26.437	0.294	0.294	0.000	0.000	0.000	0.000
93	A	279	PHE	0	0.023	0.013	21.520	-0.227	-0.227	0.000	0.000	0.000	0.000
94	A	280	CYS	0	-0.064	-0.036	26.785	0.353	0.353	0.000	0.000	0.000	0.000
95	A	281	ASP	-1	-0.869	-0.923	27.797	-9.772	-9.772	0.000	0.000	0.000	0.000
96	A	282	GLU	-1	-0.844	-0.917	27.271	-10.930	-10.930	0.000	0.000	0.000	0.000
97	A	283	ASN	0	-0.053	-0.027	29.635	0.054	0.054	0.000	0.000	0.000	0.000
98	A	284	ALA	0	-0.011	0.009	31.387	0.242	0.242	0.000	0.000	0.000	0.000
99	A	285	VAL	0	0.047	0.008	33.313	-0.113	-0.113	0.000	0.000	0.000	0.000
100	A	286	LEU	0	-0.055	-0.036	34.540	-0.117	-0.117	0.000	0.000	0.000	0.000
101	A	287	SER	0	0.033	0.009	30.019	-0.180	-0.180	0.000	0.000	0.000	0.000
102	A	288	PRO	0	0.007	0.023	27.447	-0.138	-0.138	0.000	0.000	0.000	0.000
103	A	289	ILE	0	-0.010	0.010	22.424	-0.147	-0.147	0.000	0.000	0.000	0.000
104	A	290	LYS	1	0.935	0.964	19.277	14.661	14.661	0.000	0.000	0.000	0.000
105	A	291	VAL	0	-0.018	-0.015	17.032	-0.517	-0.517	0.000	0.000	0.000	0.000
106	A	292	THR	0	0.028	0.018	15.147	0.644	0.644	0.000	0.000	0.000	0.000
107	A	293	PHE	0	-0.005	0.004	12.116	-1.145	-1.145	0.000	0.000	0.000	0.000
108	A	294	ARG	1	0.859	0.903	9.321	24.142	24.142	0.000	0.000	0.000	0.000
109	A	295	LEU	0	-0.026	0.002	7.796	-2.982	-2.982	0.000	0.000	0.000	0.000
110	A	296	ASN	0	-0.049	-0.041	4.562	4.513	4.693	0.000	-0.025	-0.154	0.000
111	A	297	ASN	0	-0.004	-0.008	3.097	0.942	1.682	0.106	-0.268	-0.577	0.001
112	A	298	ILE	0	-0.001	0.004	3.661	-2.215	-1.807	0.006	-0.070	-0.344	0.000
113	A	299	PRO	0	0.033	0.020	6.083	1.090	1.090	0.000	0.000	0.000	0.000
114	A	300	PHE	0	0.102	0.031	9.836	-0.283	-0.283	0.000	0.000	0.000	0.000
115	A	301	SER	0	-0.006	-0.004	12.355	0.376	0.376	0.000	0.000	0.000	0.000
116	A	302	ARG	1	0.961	0.982	9.153	21.595	21.595	0.000	0.000	0.000	0.000
117	A	303	PHE	0	0.010	0.007	10.112	-0.344	-0.344	0.000	0.000	0.000	0.000
118	A	304	LEU	0	0.011	0.006	11.718	0.020	0.020	0.000	0.000	0.000	0.000
119	A	305	ASP	-1	-0.782	-0.880	15.476	-14.361	-14.361	0.000	0.000	0.000	0.000
120	A	306	TYR	0	-0.047	-0.015	11.500	0.139	0.139	0.000	0.000	0.000	0.000
121	A	307	ILE	0	-0.027	-0.014	13.159	-0.055	-0.055	0.000	0.000	0.000	0.000
122	A	308	ALA	0	-0.007	-0.003	16.105	0.632	0.632	0.000	0.000	0.000	0.000
123	A	309	PRO	0	0.018	0.026	18.196	0.343	0.343	0.000	0.000	0.000	0.000
124	A	310	GLU	-1	-0.827	-0.898	20.094	-11.286	-11.286	0.000	0.000	0.000	0.000
125	A	311	THR	0	0.017	-0.015	23.457	-0.075	-0.075	0.000	0.000	0.000	0.000
126	A	312	LYS	1	0.869	0.946	25.629	9.649	9.649	0.000	0.000	0.000	0.000
127	A	313	ASP	-1	-0.832	-0.908	23.050	-10.986	-10.986	0.000	0.000	0.000	0.000
128	A	314	GLY	0	-0.048	-0.020	21.130	-0.418	-0.418	0.000	0.000	0.000	0.000
129	A	315	ARG	1	0.886	0.931	18.084	15.691	15.691	0.000	0.000	0.000	0.000
130	A	316	PRO	0	-0.030	0.001	13.718	-0.183	-0.183	0.000	0.000	0.000	0.000
131	A	317	VAL	0	0.018	0.005	10.422	-0.304	-0.304	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:187:LYS)