FMO DATABASE

FMODB ID: 431ZN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-920037.048846
FMO2-HF: Nuclear repulsion	874732.890806
FMO2-HF: Total energy	-45304.15804
FMO2-MP2: Total energy	-45439.583712

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.
-54.599	-79.061	47.9	-13.846	-9.593	-0.03

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 : -0.944 / q_NPA : -0.983

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	0.027	0.025	2.817	-8.910	-5.998	0.076	-1.255	-1.734	0.007
4	A	134	ILE	0	-0.041	-0.037	4.536	-3.786	-3.655	-0.001	-0.014	-0.116	0.000
5	A	135	ARG	1	0.938	0.955	6.164	-28.617	-28.617	0.000	0.000	0.000	0.000
6	A	136	GLU	-1	-0.842	-0.920	1.750	62.345	32.934	47.681	-11.634	-6.636	-0.046
7	A	137	LEU	0	-0.008	0.007	5.870	-2.588	-2.588	0.000	0.000	0.000	0.000
8	A	138	GLY	0	-0.011	-0.016	8.646	-1.988	-1.988	0.000	0.000	0.000	0.000
9	A	139	ILE	0	0.002	-0.006	7.393	-1.595	-1.595	0.000	0.000	0.000	0.000
10	A	140	GLY	0	0.013	0.019	9.746	-1.335	-1.335	0.000	0.000	0.000	0.000
11	A	141	LEU	0	-0.006	-0.013	11.396	-1.363	-1.363	0.000	0.000	0.000	0.000
12	A	142	ASN	0	-0.013	-0.008	13.756	-1.552	-1.552	0.000	0.000	0.000	0.000
13	A	143	PHE	0	0.064	0.025	15.594	-0.919	-0.919	0.000	0.000	0.000	0.000
14	A	144	LEU	0	-0.007	0.004	17.532	-0.828	-0.828	0.000	0.000	0.000	0.000
15	A	145	LYS	1	0.902	0.965	17.035	-14.674	-14.674	0.000	0.000	0.000	0.000
16	A	146	VAL	0	-0.024	-0.016	19.246	-0.535	-0.535	0.000	0.000	0.000	0.000
17	A	147	SER	0	-0.055	-0.025	21.631	-0.567	-0.567	0.000	0.000	0.000	0.000
18	A	148	GLY	0	0.022	0.016	23.508	-0.425	-0.425	0.000	0.000	0.000	0.000
19	A	149	MET	0	-0.034	0.006	22.966	-0.185	-0.185	0.000	0.000	0.000	0.000
20	A	150	SER	0	0.012	0.002	23.230	0.485	0.485	0.000	0.000	0.000	0.000
21	A	151	TYR	0	0.092	0.011	20.101	0.288	0.288	0.000	0.000	0.000	0.000
22	A	152	LYS	1	0.888	0.951	21.391	-9.579	-9.579	0.000	0.000	0.000	0.000
23	A	153	ASP	-1	-0.830	-0.921	23.761	10.546	10.546	0.000	0.000	0.000	0.000
24	A	154	ILE	0	0.002	0.002	17.996	0.154	0.154	0.000	0.000	0.000	0.000
25	A	155	ALA	0	-0.044	-0.025	18.988	0.348	0.348	0.000	0.000	0.000	0.000
26	A	156	LYS	1	0.950	0.983	20.067	-10.620	-10.620	0.000	0.000	0.000	0.000
27	A	157	LYS	1	0.923	0.967	21.283	-11.633	-11.633	0.000	0.000	0.000	0.000
28	A	158	GLU	-1	-0.869	-0.934	16.579	15.201	15.201	0.000	0.000	0.000	0.000
29	A	159	ASN	0	-0.057	-0.011	17.786	0.111	0.111	0.000	0.000	0.000	0.000
30	A	160	LEU	0	0.003	0.004	14.413	0.834	0.834	0.000	0.000	0.000	0.000
31	A	161	SER	0	0.024	0.002	17.729	-0.665	-0.665	0.000	0.000	0.000	0.000
32	A	162	ARG	1	1.048	0.989	18.392	-10.919	-10.919	0.000	0.000	0.000	0.000
33	A	163	ALA	0	-0.008	0.002	19.272	0.130	0.130	0.000	0.000	0.000	0.000
34	A	164	LYS	1	0.947	0.973	11.732	-20.985	-20.985	0.000	0.000	0.000	0.000
35	A	165	VAL	0	0.075	0.048	14.433	0.868	0.868	0.000	0.000	0.000	0.000
36	A	166	THR	0	-0.017	-0.003	15.719	0.159	0.159	0.000	0.000	0.000	0.000
37	A	167	ARG	1	0.933	0.954	14.143	-17.220	-17.220	0.000	0.000	0.000	0.000
38	A	168	ALA	0	0.034	0.032	11.415	0.903	0.903	0.000	0.000	0.000	0.000
39	A	169	PHE	0	0.021	-0.005	11.938	0.630	0.630	0.000	0.000	0.000	0.000
40	A	170	GLN	0	-0.045	-0.007	14.573	0.306	0.306	0.000	0.000	0.000	0.000
41	A	171	ALA	0	0.030	0.016	9.827	-0.054	-0.054	0.000	0.000	0.000	0.000
42	A	172	ALA	0	-0.028	-0.014	10.642	0.677	0.677	0.000	0.000	0.000	0.000
43	A	173	SER	0	-0.075	-0.037	11.517	-0.706	-0.706	0.000	0.000	0.000	0.000
44	A	174	VAL	0	-0.030	0.003	12.482	-0.936	-0.936	0.000	0.000	0.000	0.000
45	A	175	PRO	0	0.048	0.034	12.991	1.315	1.315	0.000	0.000	0.000	0.000
46	A	176	GLN	0	0.042	0.005	9.380	0.787	0.787	0.000	0.000	0.000	0.000
47	A	177	GLU	-1	-0.900	-0.959	13.104	15.958	15.958	0.000	0.000	0.000	0.000
48	A	178	ILE	0	0.019	0.009	15.695	0.041	0.041	0.000	0.000	0.000	0.000
49	A	179	ILE	0	-0.029	-0.020	9.391	0.402	0.402	0.000	0.000	0.000	0.000
50	A	180	SER	0	-0.046	-0.030	12.064	1.849	1.849	0.000	0.000	0.000	0.000
51	A	181	LEU	0	-0.059	-0.009	13.724	-0.576	-0.576	0.000	0.000	0.000	0.000
52	A	182	PHE	0	-0.053	-0.022	11.468	-0.892	-0.892	0.000	0.000	0.000	0.000
53	A	183	PRO	0	0.046	0.029	12.300	0.730	0.730	0.000	0.000	0.000	0.000
54	A	184	ILE	0	0.025	0.007	7.128	1.862	1.862	0.000	0.000	0.000	0.000
55	A	185	ALA	0	0.011	-0.001	5.871	-1.708	-1.708	0.000	0.000	0.000	0.000
56	A	186	SER	0	-0.005	0.005	3.014	-8.765	-6.891	0.145	-0.934	-1.085	0.009
57	A	187	GLU	-1	-0.844	-0.924	4.811	27.834	27.866	-0.001	-0.009	-0.022	0.000
58	A	188	LEU	0	-0.105	-0.038	7.997	-4.990	-4.990	0.000	0.000	0.000	0.000
59	A	189	ASN	0	0.035	0.020	8.706	1.568	1.568	0.000	0.000	0.000	0.000
60	A	190	PHE	0	0.009	-0.043	9.290	-1.582	-1.582	0.000	0.000	0.000	0.000
61	A	191	ASN	0	-0.032	-0.021	12.726	-1.588	-1.588	0.000	0.000	0.000	0.000
62	A	192	ASP	-1	-0.741	-0.866	12.727	21.133	21.133	0.000	0.000	0.000	0.000
63	A	193	TYR	0	0.049	0.018	7.099	-1.840	-1.840	0.000	0.000	0.000	0.000
64	A	194	LYS	1	0.919	0.975	13.863	-15.907	-15.907	0.000	0.000	0.000	0.000
65	A	195	ILE	0	-0.051	-0.026	17.174	-1.135	-1.135	0.000	0.000	0.000	0.000
66	A	196	LEU	0	0.058	0.029	13.754	-0.878	-0.878	0.000	0.000	0.000	0.000
67	A	197	PHE	0	-0.016	-0.004	16.330	-0.844	-0.844	0.000	0.000	0.000	0.000
68	A	198	ASN	0	-0.071	-0.058	17.871	-1.002	-1.002	0.000	0.000	0.000	0.000
69	A	199	TYR	0	0.009	0.016	20.078	-0.690	-0.690	0.000	0.000	0.000	0.000
70	A	200	TYR	0	0.076	0.027	19.051	-0.411	-0.411	0.000	0.000	0.000	0.000
71	A	201	LYS	1	0.951	0.986	21.027	-12.604	-12.604	0.000	0.000	0.000	0.000
72	A	202	GLY	0	-0.057	-0.034	22.841	-0.568	-0.568	0.000	0.000	0.000	0.000
73	A	203	LEU	0	0.041	0.028	22.442	-0.287	-0.287	0.000	0.000	0.000	0.000
74	A	204	GLU	-1	-0.893	-0.949	22.175	12.620	12.620	0.000	0.000	0.000	0.000
75	A	205	LYS	1	0.853	0.932	25.750	-10.087	-10.087	0.000	0.000	0.000	0.000
76	A	206	ALA	0	-0.025	-0.005	28.565	-0.408	-0.408	0.000	0.000	0.000	0.000
77	A	207	ASN	0	-0.068	-0.036	28.851	-0.232	-0.232	0.000	0.000	0.000	0.000
78	A	208	GLU	-1	-0.886	-0.932	27.653	10.406	10.406	0.000	0.000	0.000	0.000
79	A	209	SER	0	-0.022	-0.015	25.773	0.398	0.398	0.000	0.000	0.000	0.000
80	A	210	LEU	0	0.062	0.004	19.412	0.042	0.042	0.000	0.000	0.000	0.000
81	A	211	SER	0	0.006	0.002	23.558	0.072	0.072	0.000	0.000	0.000	0.000
82	A	212	SER	0	-0.031	-0.015	25.666	-0.136	-0.136	0.000	0.000	0.000	0.000
83	A	213	THR	0	0.064	0.039	24.442	-0.198	-0.198	0.000	0.000	0.000	0.000
84	A	214	LEU	0	-0.058	-0.045	19.838	0.184	0.184	0.000	0.000	0.000	0.000
85	A	215	PRO	0	-0.067	-0.033	23.917	0.335	0.335	0.000	0.000	0.000	0.000
86	A	216	ILE	0	0.102	0.057	26.111	0.070	0.070	0.000	0.000	0.000	0.000
87	A	217	LEU	0	0.022	0.022	22.288	0.209	0.209	0.000	0.000	0.000	0.000
88	A	218	LYS	1	0.910	0.942	20.805	-14.543	-14.543	0.000	0.000	0.000	0.000
89	A	219	GLU	-1	-0.971	-0.994	22.476	11.160	11.160	0.000	0.000	0.000	0.000
90	A	220	GLU	-1	-0.857	-0.937	25.158	11.706	11.706	0.000	0.000	0.000	0.000
91	A	221	ILE	0	-0.074	-0.038	18.744	0.207	0.207	0.000	0.000	0.000	0.000
92	A	222	LYS	1	0.834	0.924	22.068	-13.293	-13.293	0.000	0.000	0.000	0.000
93	A	223	ASP	-1	-0.922	-0.949	23.903	11.905	11.905	0.000	0.000	0.000	0.000
94	A	224	LEU	0	-0.001	0.002	20.321	-0.070	-0.070	0.000	0.000	0.000	0.000
95	A	225	ASP	-1	-0.811	-0.913	23.012	13.580	13.580	0.000	0.000	0.000	0.000
96	A	226	THR	0	-0.064	-0.014	20.745	1.254	1.254	0.000	0.000	0.000	0.000
97	A	227	ASN	0	0.022	-0.023	17.633	-1.010	-1.010	0.000	0.000	0.000	0.000
98	A	228	LEU	0	-0.082	-0.030	20.815	0.262	0.262	0.000	0.000	0.000	0.000
99	A	229	PRO	0	-0.067	-0.009	19.196	0.051	0.051	0.000	0.000	0.000	0.000
100	A	230	PRO	0	-0.011	-0.006	16.183	0.518	0.518	0.000	0.000	0.000	0.000
101	A	231	ASP	-1	-0.820	-0.921	13.241	21.789	21.789	0.000	0.000	0.000	0.000
102	A	232	ILE	0	-0.076	-0.055	15.003	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	233	TYR	0	0.109	0.065	15.555	0.126	0.126	0.000	0.000	0.000	0.000
104	A	234	LYS	1	0.899	0.954	12.091	-24.372	-24.372	0.000	0.000	0.000	0.000
105	A	235	LYS	1	0.898	0.936	15.357	-18.537	-18.537	0.000	0.000	0.000	0.000
106	A	236	GLU	-1	-0.876	-0.936	18.186	13.504	13.504	0.000	0.000	0.000	0.000
107	A	237	ILE	0	0.058	0.038	15.796	-0.597	-0.597	0.000	0.000	0.000	0.000
108	A	238	LEU	0	-0.076	-0.047	15.411	-0.574	-0.574	0.000	0.000	0.000	0.000
109	A	239	ASN	0	-0.087	-0.043	18.982	-0.729	-0.729	0.000	0.000	0.000	0.000
110	A	240	ILE	0	0.017	0.003	21.799	-0.647	-0.647	0.000	0.000	0.000	0.000
111	A	241	ILE	0	0.002	0.013	18.098	-0.421	-0.421	0.000	0.000	0.000	0.000
112	A	242	LYS	1	0.865	0.927	22.443	-12.120	-12.120	0.000	0.000	0.000	0.000
113	A	243	LYS	1	0.933	0.964	24.672	-11.989	-11.989	0.000	0.000	0.000	0.000
114	A	244	SER	0	0.051	0.046	25.637	-0.546	-0.546	0.000	0.000	0.000	0.000
115	A	245	LYS	1	0.914	0.964	25.590	-12.162	-12.162	0.000	0.000	0.000	0.000
116	A	246	ASN	0	-0.022	0.007	27.848	-0.338	-0.338	0.000	0.000	0.000	0.000

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