FMO DATABASE

FMODB ID: 98MN2

Calculation Name: 3PU2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PU2

Chain ID: A

ChEMBL ID:

UniProt ID: Q3J4M4

Base Structure: X-ray

Registration Date: 2023-09-21

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	154
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1449242.849297
FMO2-HF: Nuclear repulsion	1389576.680889
FMO2-HF: Total energy	-59666.168407
FMO2-MP2: Total energy	-59839.496211

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:16:GLU)

Summations of interaction energy for fragment #1(A:16: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.
51.295	52.995	12.285	-6.815	-7.168	0.062

Interaction energy analysis for fragmet #1(A:16:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.924 / q_NPA : -0.964

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	18	GLN	0	-0.017	0.000	3.680	-3.354	-1.575	-0.019	-0.691	-1.069	0.001
4	A	19	ILE	0	0.004	0.000	6.487	-1.624	-1.624	0.000	0.000	0.000	0.000
5	A	20	GLY	0	-0.006	0.004	9.386	-0.420	-0.420	0.000	0.000	0.000	0.000
6	A	21	PRO	0	-0.048	-0.031	12.577	-0.136	-0.136	0.000	0.000	0.000	0.000
7	A	22	GLY	0	0.017	0.021	16.042	-0.268	-0.268	0.000	0.000	0.000	0.000
8	A	23	SER	0	-0.017	-0.032	17.872	-0.764	-0.764	0.000	0.000	0.000	0.000
9	A	24	ALA	0	0.012	-0.003	20.465	0.442	0.442	0.000	0.000	0.000	0.000
10	A	25	THR	0	0.037	0.022	22.665	-0.037	-0.037	0.000	0.000	0.000	0.000
11	A	26	ARG	1	0.795	0.899	18.568	-14.552	-14.552	0.000	0.000	0.000	0.000
12	A	27	LEU	0	-0.014	0.002	14.461	0.298	0.298	0.000	0.000	0.000	0.000
13	A	28	GLU	-1	-0.840	-0.926	13.823	16.101	16.101	0.000	0.000	0.000	0.000
14	A	29	PHE	0	0.027	0.007	8.674	1.290	1.290	0.000	0.000	0.000	0.000
15	A	30	ARG	1	0.832	0.907	8.043	-25.096	-25.096	0.000	0.000	0.000	0.000
16	A	31	ARG	1	0.723	0.814	3.094	-46.871	-45.873	0.180	-0.348	-0.830	-0.001
17	A	32	HIS	0	-0.002	0.012	4.572	-4.141	-3.954	-0.001	-0.014	-0.171	0.000
18	A	33	PHE	0	0.052	0.015	5.701	2.911	2.911	0.000	0.000	0.000	0.000
19	A	34	ALA	0	0.028	0.020	8.376	-1.868	-1.868	0.000	0.000	0.000	0.000
20	A	35	ALA	0	0.019	0.007	10.918	-0.916	-0.916	0.000	0.000	0.000	0.000
21	A	36	THR	0	-0.019	-0.014	14.028	0.310	0.310	0.000	0.000	0.000	0.000
22	A	37	PRO	0	0.059	0.032	15.837	0.196	0.196	0.000	0.000	0.000	0.000
23	A	38	GLU	-1	-0.860	-0.926	16.804	13.699	13.699	0.000	0.000	0.000	0.000
24	A	39	GLN	0	-0.005	-0.006	16.682	0.084	0.084	0.000	0.000	0.000	0.000
25	A	40	LEU	0	0.033	0.020	11.383	0.047	0.047	0.000	0.000	0.000	0.000
26	A	41	TRP	0	0.050	0.016	15.282	0.154	0.154	0.000	0.000	0.000	0.000
27	A	42	ALA	0	-0.029	-0.007	18.124	-0.328	-0.328	0.000	0.000	0.000	0.000
28	A	43	ALA	0	-0.005	-0.008	15.264	-0.359	-0.359	0.000	0.000	0.000	0.000
29	A	44	LEU	0	-0.003	-0.012	12.984	0.066	0.066	0.000	0.000	0.000	0.000
30	A	45	THR	0	-0.032	-0.022	16.886	-0.606	-0.606	0.000	0.000	0.000	0.000
31	A	46	SER	0	0.016	0.019	20.507	-0.837	-0.837	0.000	0.000	0.000	0.000
32	A	47	PRO	0	0.022	-0.007	21.762	0.525	0.525	0.000	0.000	0.000	0.000
33	A	48	ALA	0	-0.040	-0.016	24.020	0.022	0.022	0.000	0.000	0.000	0.000
34	A	49	LEU	0	-0.021	-0.016	18.864	0.125	0.125	0.000	0.000	0.000	0.000
35	A	50	LEU	0	0.011	0.011	17.112	0.762	0.762	0.000	0.000	0.000	0.000
36	A	51	PRO	0	0.020	-0.009	17.774	0.845	0.845	0.000	0.000	0.000	0.000
37	A	52	ALA	0	-0.061	-0.022	18.266	0.298	0.298	0.000	0.000	0.000	0.000
38	A	53	TRP	0	-0.014	-0.026	11.578	1.233	1.233	0.000	0.000	0.000	0.000
39	A	54	LEU	0	0.011	0.023	13.585	1.532	1.532	0.000	0.000	0.000	0.000
40	A	55	PHE	0	-0.048	-0.007	14.537	-1.420	-1.420	0.000	0.000	0.000	0.000
41	A	56	ALA	0	0.086	0.062	13.993	1.476	1.476	0.000	0.000	0.000	0.000
42	A	57	ARG	1	0.967	0.957	13.945	-21.222	-21.222	0.000	0.000	0.000	0.000
43	A	58	GLY	0	-0.044	-0.022	15.877	-0.702	-0.702	0.000	0.000	0.000	0.000
44	A	59	TRP	0	-0.016	-0.007	18.671	-1.176	-1.176	0.000	0.000	0.000	0.000
45	A	60	PRO	0	0.046	0.033	19.415	0.601	0.601	0.000	0.000	0.000	0.000
46	A	61	MET	0	0.018	0.013	19.147	-0.590	-0.590	0.000	0.000	0.000	0.000
47	A	62	THR	0	-0.035	-0.021	21.949	-0.186	-0.186	0.000	0.000	0.000	0.000
48	A	63	GLU	-1	-0.905	-0.949	25.316	10.160	10.160	0.000	0.000	0.000	0.000
49	A	64	CYS	0	-0.030	-0.012	22.024	0.499	0.499	0.000	0.000	0.000	0.000
50	A	65	VAL	0	-0.002	0.014	25.294	-0.226	-0.226	0.000	0.000	0.000	0.000
51	A	66	PHE	0	0.067	0.017	20.946	0.227	0.227	0.000	0.000	0.000	0.000
52	A	67	GLU	-1	-0.858	-0.908	25.683	9.682	9.682	0.000	0.000	0.000	0.000
53	A	68	PRO	0	0.007	0.001	23.676	-0.077	-0.077	0.000	0.000	0.000	0.000
54	A	69	HIS	0	-0.022	-0.015	25.682	-0.109	-0.109	0.000	0.000	0.000	0.000
55	A	70	LYS	1	0.959	0.967	28.754	-9.318	-9.318	0.000	0.000	0.000	0.000
56	A	71	GLY	0	-0.010	0.000	30.477	-0.257	-0.257	0.000	0.000	0.000	0.000
57	A	72	GLY	0	-0.011	0.019	29.181	-0.170	-0.170	0.000	0.000	0.000	0.000
58	A	73	LEU	0	-0.040	-0.032	29.392	0.086	0.086	0.000	0.000	0.000	0.000
59	A	74	ILE	0	0.003	0.007	23.088	0.154	0.154	0.000	0.000	0.000	0.000
60	A	75	ARG	1	0.873	0.936	26.353	-10.999	-10.999	0.000	0.000	0.000	0.000
61	A	76	GLN	0	0.025	0.007	19.767	0.311	0.311	0.000	0.000	0.000	0.000
62	A	77	VAL	0	-0.010	0.003	24.398	-0.181	-0.181	0.000	0.000	0.000	0.000
63	A	78	TRP	0	-0.021	-0.008	18.568	-0.088	-0.088	0.000	0.000	0.000	0.000
64	A	79	THR	0	-0.022	-0.024	23.290	-0.605	-0.605	0.000	0.000	0.000	0.000
65	A	80	GLY	0	0.033	0.025	23.192	0.497	0.497	0.000	0.000	0.000	0.000
66	A	81	PRO	0	-0.034	-0.027	22.858	-0.549	-0.549	0.000	0.000	0.000	0.000
67	A	82	GLU	-1	-0.990	-1.014	25.914	10.647	10.647	0.000	0.000	0.000	0.000
68	A	83	GLY	0	-0.021	0.001	28.342	-0.420	-0.420	0.000	0.000	0.000	0.000
69	A	84	ARG	1	0.940	0.983	24.881	-12.148	-12.148	0.000	0.000	0.000	0.000
70	A	85	THR	0	0.004	-0.008	26.590	0.345	0.345	0.000	0.000	0.000	0.000
71	A	86	ARG	1	0.855	0.934	18.127	-16.121	-16.121	0.000	0.000	0.000	0.000
72	A	87	GLY	0	0.011	-0.004	24.522	0.277	0.277	0.000	0.000	0.000	0.000
73	A	88	LEU	0	0.000	0.035	20.794	-0.122	-0.122	0.000	0.000	0.000	0.000
74	A	89	THR	0	-0.027	-0.029	25.145	-0.216	-0.216	0.000	0.000	0.000	0.000
75	A	90	GLY	0	0.076	0.040	25.818	0.254	0.254	0.000	0.000	0.000	0.000
76	A	91	ARG	1	0.842	0.923	26.873	-9.803	-9.803	0.000	0.000	0.000	0.000
77	A	92	VAL	0	0.050	0.029	24.764	0.306	0.306	0.000	0.000	0.000	0.000
78	A	93	ILE	0	-0.056	-0.038	26.315	-0.541	-0.541	0.000	0.000	0.000	0.000
79	A	94	LEU	0	-0.078	-0.057	24.762	-0.540	-0.540	0.000	0.000	0.000	0.000
80	A	95	ALA	0	0.021	0.006	24.492	0.465	0.465	0.000	0.000	0.000	0.000
81	A	96	GLU	-1	-0.894	-0.921	23.936	11.049	11.049	0.000	0.000	0.000	0.000
82	A	97	PRO	0	-0.006	0.049	22.605	0.439	0.439	0.000	0.000	0.000	0.000
83	A	98	PRO	0	0.006	-0.024	19.447	-0.499	-0.499	0.000	0.000	0.000	0.000
84	A	99	HIS	1	0.938	0.955	18.756	-11.661	-11.661	0.000	0.000	0.000	0.000
85	A	100	ARG	1	0.885	0.934	18.886	-11.457	-11.457	0.000	0.000	0.000	0.000
86	A	101	LEU	0	0.010	0.012	19.831	-0.645	-0.645	0.000	0.000	0.000	0.000
87	A	102	ILE	0	0.002	0.008	20.477	0.426	0.426	0.000	0.000	0.000	0.000
88	A	103	HIS	0	-0.018	-0.003	20.184	-0.288	-0.288	0.000	0.000	0.000	0.000
89	A	104	SER	0	-0.031	-0.009	23.373	0.394	0.394	0.000	0.000	0.000	0.000
90	A	105	GLU	-1	-0.840	-0.922	19.493	15.568	15.568	0.000	0.000	0.000	0.000
91	A	106	LEU	0	-0.013	-0.013	23.885	-0.132	-0.132	0.000	0.000	0.000	0.000
92	A	107	TYR	0	-0.037	-0.023	18.915	-0.045	-0.045	0.000	0.000	0.000	0.000
93	A	108	ASP	-1	-0.919	-0.964	25.190	10.386	10.386	0.000	0.000	0.000	0.000
94	A	109	GLU	-1	-0.902	-0.943	21.334	14.406	14.406	0.000	0.000	0.000	0.000
95	A	110	ASP	-1	-0.894	-0.957	24.202	11.747	11.747	0.000	0.000	0.000	0.000
96	A	111	TRP	0	0.010	-0.009	20.483	0.571	0.571	0.000	0.000	0.000	0.000
97	A	112	THR	0	-0.109	-0.040	24.657	-0.557	-0.557	0.000	0.000	0.000	0.000
98	A	113	GLY	0	0.033	0.012	23.460	0.599	0.599	0.000	0.000	0.000	0.000
99	A	114	GLY	0	-0.032	-0.014	25.220	-0.477	-0.477	0.000	0.000	0.000	0.000
100	A	115	GLU	-1	-0.945	-0.956	25.448	10.869	10.869	0.000	0.000	0.000	0.000
101	A	116	THR	0	-0.037	-0.013	21.495	0.263	0.263	0.000	0.000	0.000	0.000
102	A	117	LEU	0	-0.020	-0.014	22.999	-0.272	-0.272	0.000	0.000	0.000	0.000
103	A	118	VAL	0	0.048	0.030	17.409	0.454	0.454	0.000	0.000	0.000	0.000
104	A	119	THR	0	-0.059	-0.040	18.646	-0.793	-0.793	0.000	0.000	0.000	0.000
105	A	120	LEU	0	0.025	0.017	14.376	0.949	0.949	0.000	0.000	0.000	0.000
106	A	121	GLN	0	-0.034	-0.043	15.364	-1.626	-1.626	0.000	0.000	0.000	0.000
107	A	122	LEU	0	-0.016	0.003	14.128	1.093	1.093	0.000	0.000	0.000	0.000
108	A	123	LEU	0	-0.027	-0.016	13.523	-1.295	-1.295	0.000	0.000	0.000	0.000
109	A	124	PRO	0	0.004	-0.010	13.898	0.994	0.994	0.000	0.000	0.000	0.000
110	A	125	VAL	0	-0.033	-0.004	10.299	-0.534	-0.534	0.000	0.000	0.000	0.000
111	A	126	GLU	-1	-0.947	-0.979	13.227	16.758	16.758	0.000	0.000	0.000	0.000
112	A	127	GLY	0	0.018	0.008	11.006	1.271	1.271	0.000	0.000	0.000	0.000
113	A	128	GLY	0	-0.031	-0.023	12.035	0.241	0.241	0.000	0.000	0.000	0.000
114	A	129	THR	0	-0.051	-0.038	11.171	-1.738	-1.738	0.000	0.000	0.000	0.000
115	A	130	GLU	-1	-0.868	-0.914	8.408	24.738	24.738	0.000	0.000	0.000	0.000
116	A	131	LEU	0	-0.019	-0.017	9.116	-2.086	-2.086	0.000	0.000	0.000	0.000
117	A	132	ALA	0	0.003	0.001	9.826	1.628	1.628	0.000	0.000	0.000	0.000
118	A	133	MET	0	0.016	0.000	12.039	-0.722	-0.722	0.000	0.000	0.000	0.000
119	A	134	ALA	0	-0.006	-0.010	13.716	0.467	0.467	0.000	0.000	0.000	0.000
120	A	135	VAL	0	0.016	0.020	15.799	-0.492	-0.492	0.000	0.000	0.000	0.000
121	A	136	ASP	-1	-0.861	-0.914	18.376	13.533	13.533	0.000	0.000	0.000	0.000
122	A	137	TYR	0	0.039	-0.020	17.399	0.019	0.019	0.000	0.000	0.000	0.000
123	A	138	ALA	0	0.010	0.006	23.222	-0.321	-0.321	0.000	0.000	0.000	0.000
124	A	139	THR	0	-0.038	-0.044	26.491	-0.149	-0.149	0.000	0.000	0.000	0.000
125	A	140	PRO	0	-0.019	-0.027	24.628	0.407	0.407	0.000	0.000	0.000	0.000
126	A	141	GLU	-1	-0.782	-0.881	24.069	11.026	11.026	0.000	0.000	0.000	0.000
127	A	142	ALA	0	-0.045	-0.013	24.338	0.266	0.266	0.000	0.000	0.000	0.000
128	A	143	ARG	1	0.887	0.961	18.649	-14.688	-14.688	0.000	0.000	0.000	0.000
129	A	144	ASP	-1	-0.932	-0.964	19.632	13.832	13.832	0.000	0.000	0.000	0.000
130	A	145	ALA	0	-0.021	-0.008	20.216	0.669	0.669	0.000	0.000	0.000	0.000
131	A	146	VAL	0	0.018	0.004	16.701	0.552	0.552	0.000	0.000	0.000	0.000
132	A	147	ALA	0	-0.024	-0.005	15.641	1.158	1.158	0.000	0.000	0.000	0.000
133	A	148	ALA	0	-0.077	-0.026	15.619	1.007	1.007	0.000	0.000	0.000	0.000
134	A	149	SER	0	0.042	0.032	16.363	-0.556	-0.556	0.000	0.000	0.000	0.000
135	A	150	ALA	0	-0.025	0.006	12.908	1.141	1.141	0.000	0.000	0.000	0.000
136	A	151	MET	0	0.074	0.019	12.529	1.677	1.677	0.000	0.000	0.000	0.000
137	A	152	ALA	0	0.042	0.007	8.682	1.226	1.226	0.000	0.000	0.000	0.000
138	A	153	THR	0	-0.066	-0.038	7.728	3.723	3.723	0.000	0.000	0.000	0.000
139	A	154	GLU	-1	-0.906	-0.965	8.417	23.262	23.262	0.000	0.000	0.000	0.000
140	A	155	MET	0	-0.014	0.012	8.946	-0.752	-0.752	0.000	0.000	0.000	0.000
141	A	156	GLU	-1	-0.781	-0.875	3.193	63.019	65.124	0.282	-0.952	-1.434	-0.001
142	A	157	GLU	-1	-0.957	-0.987	6.179	29.528	29.528	0.000	0.000	0.000	0.000
143	A	158	ALA	0	0.035	0.025	7.817	-1.233	-1.233	0.000	0.000	0.000	0.000
144	A	159	TYR	0	0.005	-0.018	5.984	-2.724	-2.724	0.000	0.000	0.000	0.000
145	A	160	ARG	1	0.928	0.970	1.742	-96.166	-99.535	11.843	-4.810	-3.664	0.063
146	A	161	HIS	0	-0.051	-0.020	7.162	-2.026	-2.026	0.000	0.000	0.000	0.000
147	A	162	LEU	0	-0.019	-0.009	9.899	-2.081	-2.081	0.000	0.000	0.000	0.000
148	A	163	ASP	-1	-0.823	-0.893	6.228	38.544	38.544	0.000	0.000	0.000	0.000
149	A	164	VAL	0	-0.042	-0.029	9.837	-2.229	-2.229	0.000	0.000	0.000	0.000
150	A	165	MET	0	-0.016	0.007	12.536	-1.978	-1.978	0.000	0.000	0.000	0.000
151	A	166	LEU	0	-0.029	-0.019	10.901	-1.467	-1.467	0.000	0.000	0.000	0.000
152	A	167	ALA	0	0.002	0.005	13.100	-1.230	-1.230	0.000	0.000	0.000	0.000
153	A	168	ALA	0	-0.057	-0.015	14.941	-1.095	-1.095	0.000	0.000	0.000	0.000
154	A	169	LEU	0	-0.107	-0.043	17.462	-1.554	-1.554	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:16:GLU)