FMO DATABASE

FMODB ID: YY5G2

Calculation Name: 3W3C-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3W3C

Chain ID: A

ChEMBL ID:

UniProt ID: P0A247

Base Structure: X-ray

Registration Date: 2023-06-20

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	116
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-923209.720176
FMO2-HF: Nuclear repulsion	877904.364035
FMO2-HF: Total energy	-45305.356141
FMO2-MP2: Total energy	-45440.750025

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:131:GLU)

Summations of interaction energy for fragment #1(A:131:GLU)

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.
-123.208	-136.957	43.118	-18.298	-11.068	0.051

Interaction energy analysis for fragmet #1(A:131:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.857 / q_NPA : -0.898

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	133	SER	0	-0.022	-0.037	2.973	-4.721	-1.542	0.045	-1.566	-1.657	0.007
4	A	134	ILE	0	-0.076	-0.058	4.717	-3.797	-3.673	-0.001	-0.015	-0.108	0.000
5	A	135	ARG	1	0.902	0.941	6.168	-29.849	-29.849	0.000	0.000	0.000	0.000
6	A	136	GLU	-1	-0.698	-0.803	1.970	32.621	24.659	16.993	-4.907	-4.123	-0.055
7	A	137	LEU	0	0.004	0.013	6.267	-2.200	-2.200	0.000	0.000	0.000	0.000
8	A	138	GLY	0	-0.016	-0.014	9.179	-1.573	-1.573	0.000	0.000	0.000	0.000
9	A	139	ILE	0	-0.001	-0.011	7.828	-1.342	-1.342	0.000	0.000	0.000	0.000
10	A	140	GLY	0	0.004	0.009	9.838	-1.053	-1.053	0.000	0.000	0.000	0.000
11	A	141	LEU	0	-0.012	-0.020	11.195	-1.153	-1.153	0.000	0.000	0.000	0.000
12	A	142	ASN	0	-0.031	-0.009	13.888	-1.450	-1.450	0.000	0.000	0.000	0.000
13	A	143	PHE	0	0.080	0.026	15.439	-0.784	-0.784	0.000	0.000	0.000	0.000
14	A	144	LEU	0	-0.001	0.014	17.771	-0.718	-0.718	0.000	0.000	0.000	0.000
15	A	145	LYS	1	0.881	0.957	17.105	-14.387	-14.387	0.000	0.000	0.000	0.000
16	A	146	VAL	0	0.002	-0.003	19.617	-0.437	-0.437	0.000	0.000	0.000	0.000
17	A	147	SER	0	-0.046	-0.027	22.000	-0.521	-0.521	0.000	0.000	0.000	0.000
18	A	148	GLY	0	0.031	0.020	24.007	-0.398	-0.398	0.000	0.000	0.000	0.000
19	A	149	MET	0	-0.024	0.025	22.997	-0.100	-0.100	0.000	0.000	0.000	0.000
20	A	150	SER	0	0.014	-0.021	23.276	0.510	0.510	0.000	0.000	0.000	0.000
21	A	151	TYR	0	0.093	0.013	20.195	0.251	0.251	0.000	0.000	0.000	0.000
22	A	152	LYS	1	0.806	0.891	21.405	-9.461	-9.461	0.000	0.000	0.000	0.000
23	A	153	ASP	-1	-0.777	-0.853	23.950	10.184	10.184	0.000	0.000	0.000	0.000
24	A	154	ILE	0	0.031	0.032	18.068	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	155	ALA	0	-0.039	-0.017	19.304	0.168	0.168	0.000	0.000	0.000	0.000
26	A	156	LYS	1	0.939	0.965	20.363	-10.169	-10.169	0.000	0.000	0.000	0.000
27	A	157	LYS	1	0.833	0.915	21.067	-11.751	-11.751	0.000	0.000	0.000	0.000
28	A	158	GLU	-1	-0.840	-0.936	16.266	13.672	13.672	0.000	0.000	0.000	0.000
29	A	159	ASN	0	-0.045	-0.012	17.394	0.050	0.050	0.000	0.000	0.000	0.000
30	A	160	LEU	0	0.011	0.016	14.416	0.712	0.712	0.000	0.000	0.000	0.000
31	A	161	SER	0	0.043	0.011	18.170	-0.527	-0.527	0.000	0.000	0.000	0.000
32	A	162	ARG	1	1.035	0.996	18.540	-10.597	-10.597	0.000	0.000	0.000	0.000
33	A	163	ALA	0	0.027	0.028	19.421	0.240	0.240	0.000	0.000	0.000	0.000
34	A	164	LYS	1	0.938	0.994	11.327	-20.330	-20.330	0.000	0.000	0.000	0.000
35	A	165	VAL	0	0.072	0.032	14.694	0.770	0.770	0.000	0.000	0.000	0.000
36	A	166	THR	0	-0.027	-0.024	15.831	0.090	0.090	0.000	0.000	0.000	0.000
37	A	167	ARG	1	0.906	0.937	14.098	-16.955	-16.955	0.000	0.000	0.000	0.000
38	A	168	ALA	0	0.034	0.030	11.422	0.960	0.960	0.000	0.000	0.000	0.000
39	A	169	PHE	0	0.030	0.000	12.007	0.577	0.577	0.000	0.000	0.000	0.000
40	A	170	GLN	0	-0.053	-0.007	14.684	0.418	0.418	0.000	0.000	0.000	0.000
41	A	171	ALA	0	0.044	0.016	9.894	0.061	0.061	0.000	0.000	0.000	0.000
42	A	172	ALA	0	-0.026	-0.014	10.767	0.887	0.887	0.000	0.000	0.000	0.000
43	A	173	SER	0	-0.068	-0.037	11.654	-0.508	-0.508	0.000	0.000	0.000	0.000
44	A	174	VAL	0	-0.011	0.007	12.411	-0.957	-0.957	0.000	0.000	0.000	0.000
45	A	175	PRO	0	0.038	0.028	12.935	1.423	1.423	0.000	0.000	0.000	0.000
46	A	176	GLN	0	0.062	0.026	9.503	0.964	0.964	0.000	0.000	0.000	0.000
47	A	177	GLU	-1	-0.834	-0.899	13.047	16.724	16.724	0.000	0.000	0.000	0.000
48	A	178	ILE	0	0.033	0.014	15.285	0.091	0.091	0.000	0.000	0.000	0.000
49	A	179	ILE	0	-0.015	-0.016	9.038	0.443	0.443	0.000	0.000	0.000	0.000
50	A	180	SER	0	-0.054	-0.046	11.192	2.199	2.199	0.000	0.000	0.000	0.000
51	A	181	LEU	0	-0.029	0.002	12.898	-0.935	-0.935	0.000	0.000	0.000	0.000
52	A	182	PHE	0	-0.035	-0.016	10.466	-1.003	-1.003	0.000	0.000	0.000	0.000
53	A	183	PRO	0	0.033	0.022	10.846	1.405	1.405	0.000	0.000	0.000	0.000
54	A	184	ILE	0	0.031	0.009	5.843	2.179	2.179	0.000	0.000	0.000	0.000
55	A	185	ALA	0	0.004	-0.002	4.766	-2.973	-2.983	-0.001	-0.008	0.019	0.000
56	A	186	SER	0	-0.031	-0.058	1.545	-37.707	-47.269	26.047	-11.527	-4.958	0.096
57	A	187	GLU	-1	-0.830	-0.894	3.737	21.136	21.618	0.035	-0.275	-0.241	0.003
58	A	188	LEU	0	-0.057	-0.007	7.104	-6.356	-6.356	0.000	0.000	0.000	0.000
59	A	189	ASN	0	0.014	-0.004	8.379	0.386	0.386	0.000	0.000	0.000	0.000
60	A	190	PHE	0	-0.011	-0.039	8.805	-1.702	-1.702	0.000	0.000	0.000	0.000
61	A	191	ASN	0	0.001	0.001	12.320	-2.033	-2.033	0.000	0.000	0.000	0.000
62	A	192	ASP	-1	-0.736	-0.861	11.987	22.921	22.921	0.000	0.000	0.000	0.000
63	A	193	TYR	0	0.050	0.016	6.748	-3.034	-3.034	0.000	0.000	0.000	0.000
64	A	194	LYS	1	0.881	0.945	13.304	-16.679	-16.679	0.000	0.000	0.000	0.000
65	A	195	ILE	0	-0.025	-0.012	16.729	-1.334	-1.334	0.000	0.000	0.000	0.000
66	A	196	LEU	0	0.044	0.026	12.826	-0.930	-0.930	0.000	0.000	0.000	0.000
67	A	197	PHE	0	-0.001	0.000	16.075	-0.970	-0.970	0.000	0.000	0.000	0.000
68	A	198	ASN	0	-0.083	-0.067	17.654	-1.423	-1.423	0.000	0.000	0.000	0.000
69	A	199	TYR	0	0.001	0.007	20.063	-0.471	-0.471	0.000	0.000	0.000	0.000
70	A	200	TYR	0	0.010	-0.020	18.768	-0.312	-0.312	0.000	0.000	0.000	0.000
71	A	201	LYS	1	0.928	0.959	20.943	-13.173	-13.173	0.000	0.000	0.000	0.000
72	A	202	GLY	0	-0.063	-0.025	22.802	-0.599	-0.599	0.000	0.000	0.000	0.000
73	A	203	LEU	0	0.053	0.028	22.558	-0.334	-0.334	0.000	0.000	0.000	0.000
74	A	204	GLU	-1	-0.875	-0.920	22.097	12.788	12.788	0.000	0.000	0.000	0.000
75	A	205	LYS	1	0.867	0.936	25.664	-10.191	-10.191	0.000	0.000	0.000	0.000
76	A	206	ALA	0	-0.011	0.000	28.480	-0.434	-0.434	0.000	0.000	0.000	0.000
77	A	207	ASN	0	-0.075	-0.043	28.578	-0.419	-0.419	0.000	0.000	0.000	0.000
78	A	208	GLU	-1	-0.892	-0.926	27.518	10.792	10.792	0.000	0.000	0.000	0.000
79	A	209	SER	0	0.021	0.016	25.767	0.535	0.535	0.000	0.000	0.000	0.000
80	A	210	LEU	0	0.034	0.005	19.219	0.057	0.057	0.000	0.000	0.000	0.000
81	A	211	SER	0	0.034	0.007	23.330	0.154	0.154	0.000	0.000	0.000	0.000
82	A	212	SER	0	-0.046	-0.026	25.320	-0.264	-0.264	0.000	0.000	0.000	0.000
83	A	213	THR	0	0.013	0.006	24.627	-0.256	-0.256	0.000	0.000	0.000	0.000
84	A	214	LEU	0	-0.020	-0.026	19.015	0.213	0.213	0.000	0.000	0.000	0.000
85	A	215	PRO	0	-0.062	-0.027	22.628	0.454	0.454	0.000	0.000	0.000	0.000
86	A	216	ILE	0	0.115	0.061	24.788	0.195	0.195	0.000	0.000	0.000	0.000
87	A	217	LEU	0	0.022	0.011	20.944	0.236	0.236	0.000	0.000	0.000	0.000
88	A	218	LYS	1	0.845	0.916	20.054	-15.136	-15.136	0.000	0.000	0.000	0.000
89	A	219	GLU	-1	-0.971	-0.974	21.363	11.620	11.620	0.000	0.000	0.000	0.000
90	A	220	GLU	-1	-0.731	-0.856	24.015	12.174	12.174	0.000	0.000	0.000	0.000
91	A	221	ILE	0	-0.073	-0.045	17.776	0.155	0.155	0.000	0.000	0.000	0.000
92	A	222	LYS	1	0.809	0.891	20.728	-13.114	-13.114	0.000	0.000	0.000	0.000
93	A	223	ASP	-1	-0.937	-0.958	23.065	12.084	12.084	0.000	0.000	0.000	0.000
94	A	224	LEU	0	-0.036	-0.009	19.384	-0.087	-0.087	0.000	0.000	0.000	0.000
95	A	225	ASP	-1	-0.833	-0.925	22.177	14.463	14.463	0.000	0.000	0.000	0.000
96	A	226	THR	0	-0.004	0.001	19.668	1.283	1.283	0.000	0.000	0.000	0.000
97	A	227	ASN	0	-0.032	-0.045	17.639	-0.342	-0.342	0.000	0.000	0.000	0.000
98	A	228	LEU	0	-0.047	-0.003	19.621	0.402	0.402	0.000	0.000	0.000	0.000
99	A	229	PRO	0	-0.058	-0.010	18.752	0.179	0.179	0.000	0.000	0.000	0.000
100	A	230	PRO	0	0.032	0.018	15.570	0.859	0.859	0.000	0.000	0.000	0.000
101	A	231	ASP	-1	-0.765	-0.892	13.099	20.831	20.831	0.000	0.000	0.000	0.000
102	A	232	ILE	0	-0.094	-0.044	14.119	-0.100	-0.100	0.000	0.000	0.000	0.000
103	A	233	TYR	0	0.122	0.070	14.644	0.474	0.474	0.000	0.000	0.000	0.000
104	A	234	LYS	1	0.798	0.894	11.043	-27.716	-27.716	0.000	0.000	0.000	0.000
105	A	235	LYS	1	0.772	0.859	14.402	-20.614	-20.614	0.000	0.000	0.000	0.000
106	A	236	GLU	-1	-0.865	-0.937	17.402	14.649	14.649	0.000	0.000	0.000	0.000
107	A	237	ILE	0	0.057	0.034	14.818	-0.799	-0.799	0.000	0.000	0.000	0.000
108	A	238	LEU	0	-0.067	-0.035	14.375	-0.745	-0.745	0.000	0.000	0.000	0.000
109	A	239	ASN	0	-0.023	-0.016	18.187	-1.071	-1.071	0.000	0.000	0.000	0.000
110	A	240	ILE	0	0.043	0.025	20.838	-0.760	-0.760	0.000	0.000	0.000	0.000
111	A	241	ILE	0	-0.005	0.000	17.175	-0.590	-0.590	0.000	0.000	0.000	0.000
112	A	242	LYS	1	0.832	0.911	21.410	-13.202	-13.202	0.000	0.000	0.000	0.000
113	A	243	LYS	1	0.798	0.897	23.551	-12.704	-12.704	0.000	0.000	0.000	0.000
114	A	244	SER	0	0.043	0.042	24.195	-0.277	-0.277	0.000	0.000	0.000	0.000
115	A	245	LYS	1	0.951	0.985	24.865	-12.684	-12.684	0.000	0.000	0.000	0.000
116	A	246	ASN	0	-0.055	-0.018	27.269	-0.634	-0.634	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:131:GLU)