FMO DATABASE

FMODB ID: 5316Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-920656.750488
FMO2-HF: Nuclear repulsion	875351.836871
FMO2-HF: Total energy	-45304.913617
FMO2-MP2: Total energy	-45440.344892

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.
-81.267	-95.954	37.231	-13.156	-9.388	-0.039

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 : -0.943 / q_NPA : -0.987

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

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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	-0.024	-0.032	2.713	-6.460	-1.835	0.117	-2.376	-2.366	0.014
4	A	134	ILE	0	-0.056	-0.052	4.432	-3.752	-3.635	-0.001	-0.016	-0.099	0.000
5	A	135	ARG	1	0.911	0.936	6.179	-29.117	-29.117	0.000	0.000	0.000	0.000
6	A	136	GLU	-1	-0.685	-0.793	1.814	39.582	17.544	36.543	-9.322	-5.183	-0.072
7	A	137	LEU	0	-0.021	0.000	5.906	-2.165	-2.165	0.000	0.000	0.000	0.000
8	A	138	GLY	0	-0.014	-0.015	8.607	-1.667	-1.667	0.000	0.000	0.000	0.000
9	A	139	ILE	0	-0.001	-0.010	7.600	-1.384	-1.384	0.000	0.000	0.000	0.000
10	A	140	GLY	0	0.017	0.022	9.438	-1.161	-1.161	0.000	0.000	0.000	0.000
11	A	141	LEU	0	-0.002	-0.012	10.872	-1.182	-1.182	0.000	0.000	0.000	0.000
12	A	142	ASN	0	-0.021	-0.010	13.493	-1.487	-1.487	0.000	0.000	0.000	0.000
13	A	143	PHE	0	0.070	0.028	15.066	-0.828	-0.828	0.000	0.000	0.000	0.000
14	A	144	LEU	0	-0.005	0.007	17.087	-0.768	-0.768	0.000	0.000	0.000	0.000
15	A	145	LYS	1	0.894	0.963	16.874	-14.362	-14.362	0.000	0.000	0.000	0.000
16	A	146	VAL	0	-0.008	-0.007	19.170	-0.496	-0.496	0.000	0.000	0.000	0.000
17	A	147	SER	0	-0.056	-0.024	21.507	-0.543	-0.543	0.000	0.000	0.000	0.000
18	A	148	GLY	0	0.024	0.017	23.411	-0.409	-0.409	0.000	0.000	0.000	0.000
19	A	149	MET	0	-0.050	-0.004	22.764	-0.211	-0.211	0.000	0.000	0.000	0.000
20	A	150	SER	0	0.005	-0.034	23.239	0.467	0.467	0.000	0.000	0.000	0.000
21	A	151	TYR	0	0.094	0.011	20.005	0.277	0.277	0.000	0.000	0.000	0.000
22	A	152	LYS	1	0.831	0.913	21.360	-9.527	-9.527	0.000	0.000	0.000	0.000
23	A	153	ASP	-1	-0.799	-0.870	23.722	10.261	10.261	0.000	0.000	0.000	0.000
24	A	154	ILE	0	0.026	0.022	17.906	0.104	0.104	0.000	0.000	0.000	0.000
25	A	155	ALA	0	-0.032	-0.020	18.925	0.306	0.306	0.000	0.000	0.000	0.000
26	A	156	LYS	1	0.957	0.985	20.006	-10.344	-10.344	0.000	0.000	0.000	0.000
27	A	157	LYS	1	0.899	0.961	20.737	-11.428	-11.428	0.000	0.000	0.000	0.000
28	A	158	GLU	-1	-0.855	-0.929	16.144	14.159	14.159	0.000	0.000	0.000	0.000
29	A	159	ASN	0	-0.066	-0.016	17.342	0.017	0.017	0.000	0.000	0.000	0.000
30	A	160	LEU	0	0.003	0.005	14.091	0.754	0.754	0.000	0.000	0.000	0.000
31	A	161	SER	0	0.028	-0.001	17.660	-0.562	-0.562	0.000	0.000	0.000	0.000
32	A	162	ARG	1	1.051	0.996	18.323	-10.692	-10.692	0.000	0.000	0.000	0.000
33	A	163	ALA	0	0.010	0.011	19.199	0.158	0.158	0.000	0.000	0.000	0.000
34	A	164	LYS	1	0.944	0.979	11.312	-20.471	-20.471	0.000	0.000	0.000	0.000
35	A	165	VAL	0	0.076	0.047	14.376	0.806	0.806	0.000	0.000	0.000	0.000
36	A	166	THR	0	-0.033	-0.017	15.691	0.147	0.147	0.000	0.000	0.000	0.000
37	A	167	ARG	1	0.925	0.951	14.026	-16.667	-16.667	0.000	0.000	0.000	0.000
38	A	168	ALA	0	0.037	0.035	11.393	0.913	0.913	0.000	0.000	0.000	0.000
39	A	169	PHE	0	0.034	-0.004	11.936	0.638	0.638	0.000	0.000	0.000	0.000
40	A	170	GLN	0	-0.056	-0.001	14.578	0.284	0.284	0.000	0.000	0.000	0.000
41	A	171	ALA	0	0.037	0.015	9.861	0.035	0.035	0.000	0.000	0.000	0.000
42	A	172	ALA	0	-0.025	-0.012	10.692	0.814	0.814	0.000	0.000	0.000	0.000
43	A	173	SER	0	-0.073	-0.043	11.559	-0.611	-0.611	0.000	0.000	0.000	0.000
44	A	174	VAL	0	-0.029	0.001	12.571	-0.894	-0.894	0.000	0.000	0.000	0.000
45	A	175	PRO	0	0.053	0.040	13.061	1.373	1.373	0.000	0.000	0.000	0.000
46	A	176	GLN	0	0.067	0.024	9.526	0.814	0.814	0.000	0.000	0.000	0.000
47	A	177	GLU	-1	-0.842	-0.914	13.203	16.387	16.387	0.000	0.000	0.000	0.000
48	A	178	ILE	0	0.031	0.015	15.801	0.087	0.087	0.000	0.000	0.000	0.000
49	A	179	ILE	0	-0.022	-0.017	9.389	0.446	0.446	0.000	0.000	0.000	0.000
50	A	180	SER	0	-0.053	-0.046	11.590	2.025	2.025	0.000	0.000	0.000	0.000
51	A	181	LEU	0	-0.043	-0.003	13.219	-0.581	-0.581	0.000	0.000	0.000	0.000
52	A	182	PHE	0	-0.053	-0.023	11.067	-0.989	-0.989	0.000	0.000	0.000	0.000
53	A	183	PRO	0	0.045	0.029	11.794	0.951	0.951	0.000	0.000	0.000	0.000
54	A	184	ILE	0	0.043	0.012	6.724	2.095	2.095	0.000	0.000	0.000	0.000
55	A	185	ALA	0	0.008	-0.001	5.411	-2.119	-2.119	0.000	0.000	0.000	0.000
56	A	186	SER	0	0.008	0.010	2.639	-13.074	-10.511	0.573	-1.413	-1.723	0.019
57	A	187	GLU	-1	-0.862	-0.924	4.584	26.679	26.725	-0.001	-0.029	-0.017	0.000
58	A	188	LEU	0	-0.085	-0.014	7.775	-5.470	-5.470	0.000	0.000	0.000	0.000
59	A	189	ASN	0	0.005	-0.004	8.643	0.966	0.966	0.000	0.000	0.000	0.000
60	A	190	PHE	0	0.007	-0.037	9.119	-1.499	-1.499	0.000	0.000	0.000	0.000
61	A	191	ASN	0	0.001	-0.001	12.634	-1.722	-1.722	0.000	0.000	0.000	0.000
62	A	192	ASP	-1	-0.700	-0.840	12.595	21.569	21.569	0.000	0.000	0.000	0.000
63	A	193	TYR	0	0.058	0.027	7.419	-2.075	-2.075	0.000	0.000	0.000	0.000
64	A	194	LYS	1	0.894	0.958	13.838	-16.127	-16.127	0.000	0.000	0.000	0.000
65	A	195	ILE	0	-0.022	-0.005	17.143	-1.146	-1.146	0.000	0.000	0.000	0.000
66	A	196	LEU	0	0.055	0.031	13.585	-0.886	-0.886	0.000	0.000	0.000	0.000
67	A	197	PHE	0	-0.022	-0.009	16.266	-0.886	-0.886	0.000	0.000	0.000	0.000
68	A	198	ASN	0	-0.114	-0.088	17.882	-1.284	-1.284	0.000	0.000	0.000	0.000
69	A	199	TYR	0	0.013	0.020	20.257	-0.426	-0.426	0.000	0.000	0.000	0.000
70	A	200	TYR	0	0.028	-0.016	18.949	-0.291	-0.291	0.000	0.000	0.000	0.000
71	A	201	LYS	1	0.956	0.981	21.068	-12.627	-12.627	0.000	0.000	0.000	0.000
72	A	202	GLY	0	-0.053	-0.026	22.873	-0.569	-0.569	0.000	0.000	0.000	0.000
73	A	203	LEU	0	0.046	0.030	22.583	-0.300	-0.300	0.000	0.000	0.000	0.000
74	A	204	GLU	-1	-0.850	-0.905	22.285	12.565	12.565	0.000	0.000	0.000	0.000
75	A	205	LYS	1	0.848	0.928	25.808	-10.046	-10.046	0.000	0.000	0.000	0.000
76	A	206	ALA	0	-0.033	-0.010	28.614	-0.424	-0.424	0.000	0.000	0.000	0.000
77	A	207	ASN	0	-0.071	-0.037	28.874	-0.324	-0.324	0.000	0.000	0.000	0.000
78	A	208	GLU	-1	-0.878	-0.926	27.660	10.516	10.516	0.000	0.000	0.000	0.000
79	A	209	SER	0	-0.022	-0.010	25.857	0.397	0.397	0.000	0.000	0.000	0.000
80	A	210	LEU	0	0.053	0.012	19.460	0.065	0.065	0.000	0.000	0.000	0.000
81	A	211	SER	0	0.015	0.012	23.642	0.079	0.079	0.000	0.000	0.000	0.000
82	A	212	SER	0	-0.019	-0.020	25.762	-0.115	-0.115	0.000	0.000	0.000	0.000
83	A	213	THR	0	0.031	0.012	24.903	-0.293	-0.293	0.000	0.000	0.000	0.000
84	A	214	LEU	0	-0.034	-0.035	19.597	0.207	0.207	0.000	0.000	0.000	0.000
85	A	215	PRO	0	-0.055	-0.021	23.461	0.347	0.347	0.000	0.000	0.000	0.000
86	A	216	ILE	0	0.095	0.051	25.613	0.068	0.068	0.000	0.000	0.000	0.000
87	A	217	LEU	0	0.033	0.018	21.801	0.173	0.173	0.000	0.000	0.000	0.000
88	A	218	LYS	1	0.866	0.918	20.178	-15.045	-15.045	0.000	0.000	0.000	0.000
89	A	219	GLU	-1	-0.988	-0.985	21.983	11.375	11.375	0.000	0.000	0.000	0.000
90	A	220	GLU	-1	-0.756	-0.869	24.781	11.727	11.727	0.000	0.000	0.000	0.000
91	A	221	ILE	0	-0.073	-0.041	18.388	0.193	0.193	0.000	0.000	0.000	0.000
92	A	222	LYS	1	0.832	0.911	21.612	-13.383	-13.383	0.000	0.000	0.000	0.000
93	A	223	ASP	-1	-0.939	-0.958	23.425	11.941	11.941	0.000	0.000	0.000	0.000
94	A	224	LEU	0	-0.028	0.001	19.829	-0.104	-0.104	0.000	0.000	0.000	0.000
95	A	225	ASP	-1	-0.813	-0.921	22.757	13.820	13.820	0.000	0.000	0.000	0.000
96	A	226	THR	0	-0.034	0.003	20.319	1.282	1.282	0.000	0.000	0.000	0.000
97	A	227	ASN	0	0.006	-0.031	18.121	-0.619	-0.619	0.000	0.000	0.000	0.000
98	A	228	LEU	0	-0.091	-0.030	20.471	0.267	0.267	0.000	0.000	0.000	0.000
99	A	229	PRO	0	-0.055	-0.008	18.935	0.064	0.064	0.000	0.000	0.000	0.000
100	A	230	PRO	0	-0.010	-0.005	15.988	0.581	0.581	0.000	0.000	0.000	0.000
101	A	231	ASP	-1	-0.767	-0.890	13.444	21.142	21.142	0.000	0.000	0.000	0.000
102	A	232	ILE	0	-0.088	-0.066	14.788	0.011	0.011	0.000	0.000	0.000	0.000
103	A	233	TYR	0	0.135	0.081	15.216	0.210	0.210	0.000	0.000	0.000	0.000
104	A	234	LYS	1	0.837	0.897	11.445	-25.319	-25.319	0.000	0.000	0.000	0.000
105	A	235	LYS	1	0.817	0.900	15.045	-19.336	-19.336	0.000	0.000	0.000	0.000
106	A	236	GLU	-1	-0.856	-0.935	17.930	14.012	14.012	0.000	0.000	0.000	0.000
107	A	237	ILE	0	0.051	0.032	15.611	-0.633	-0.633	0.000	0.000	0.000	0.000
108	A	238	LEU	0	-0.076	-0.047	14.894	-0.575	-0.575	0.000	0.000	0.000	0.000
109	A	239	ASN	0	-0.085	-0.042	18.669	-0.846	-0.846	0.000	0.000	0.000	0.000
110	A	240	ILE	0	0.029	0.008	21.449	-0.689	-0.689	0.000	0.000	0.000	0.000
111	A	241	ILE	0	-0.004	0.009	17.878	-0.428	-0.428	0.000	0.000	0.000	0.000
112	A	242	LYS	1	0.877	0.937	22.082	-12.374	-12.374	0.000	0.000	0.000	0.000
113	A	243	LYS	1	0.813	0.895	24.365	-12.330	-12.330	0.000	0.000	0.000	0.000
114	A	244	SER	0	0.041	0.045	25.094	-0.262	-0.262	0.000	0.000	0.000	0.000
115	A	245	LYS	1	0.950	0.974	25.114	-12.348	-12.348	0.000	0.000	0.000	0.000
116	A	246	ASN	0	-0.053	-0.010	27.513	-0.671	-0.671	0.000	0.000	0.000	0.000

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