FMO DATABASE

FMODB ID: 85ZYY

Calculation Name: 3PR9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PR9

Chain ID: A

ChEMBL ID:

UniProt ID: Q58235

Base Structure: X-ray

Registration Date: 2023-09-20

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	150
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1259875.904953
FMO2-HF: Nuclear repulsion	1202339.836406
FMO2-HF: Total energy	-57536.068547
FMO2-MP2: Total energy	-57705.141038

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:1:MET)

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

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.
-14.477	-11.958	15.484	-7.191	-10.811	-0.061

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.035 / q_NPA : -0.005

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	3	GLU	-1	-0.903	-0.954	3.889	-1.900	0.082	-0.014	-0.988	-0.980	0.004
4	A	4	LYS	1	0.802	0.863	5.981	1.017	1.017	0.000	0.000	0.000	0.000
5	A	5	GLY	0	0.010	0.012	8.320	0.139	0.139	0.000	0.000	0.000	0.000
6	A	6	LYS	1	0.831	0.933	8.753	2.021	2.021	0.000	0.000	0.000	0.000
7	A	7	MET	0	0.010	0.010	10.832	0.056	0.056	0.000	0.000	0.000	0.000
8	A	8	VAL	0	0.007	0.002	8.660	-0.234	-0.234	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.768	0.876	11.573	1.096	1.096	0.000	0.000	0.000	0.000
10	A	10	ILE	0	0.021	0.014	10.514	-0.131	-0.131	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.054	-0.063	13.036	0.137	0.137	0.000	0.000	0.000	0.000
12	A	12	TYR	0	0.000	-0.012	14.120	-0.022	-0.022	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.792	-0.838	16.486	-0.157	-0.157	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.058	0.017	18.988	0.030	0.030	0.000	0.000	0.000	0.000
15	A	15	TYR	0	-0.011	-0.029	20.329	0.008	0.008	0.000	0.000	0.000	0.000
16	A	16	VAL	0	0.022	0.007	23.065	0.019	0.019	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.822	-0.885	25.909	0.048	0.048	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.009	0.008	26.875	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.836	0.907	27.576	-0.042	-0.042	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.039	0.029	22.963	0.006	0.006	0.000	0.000	0.000	0.000
21	A	21	PHE	0	-0.058	-0.037	22.153	0.002	0.002	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.810	-0.895	21.007	-0.223	-0.223	0.000	0.000	0.000	0.000
23	A	23	THR	0	0.002	-0.025	20.907	0.010	0.010	0.000	0.000	0.000	0.000
24	A	24	THR	0	0.021	0.039	17.717	0.012	0.012	0.000	0.000	0.000	0.000
25	A	25	ASN	0	0.007	0.001	20.720	-0.011	-0.011	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.762	-0.873	22.782	-0.162	-0.162	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.824	-0.910	26.264	-0.138	-0.138	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.044	-0.003	22.438	0.020	0.020	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.033	0.008	26.181	0.019	0.019	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.734	0.848	27.750	0.170	0.170	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.765	0.877	28.024	0.054	0.054	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.823	-0.901	27.121	-0.032	-0.032	0.000	0.000	0.000	0.000
33	A	33	GLY	0	-0.044	-0.011	30.300	0.007	0.007	0.000	0.000	0.000	0.000
34	A	34	ILE	0	-0.056	-0.028	26.250	0.003	0.003	0.000	0.000	0.000	0.000
35	A	35	TYR	0	-0.062	-0.035	29.838	-0.005	-0.005	0.000	0.000	0.000	0.000
36	A	36	ASN	0	0.027	0.008	30.156	0.012	0.012	0.000	0.000	0.000	0.000
37	A	37	PRO	0	0.012	-0.008	31.033	-0.014	-0.014	0.000	0.000	0.000	0.000
38	A	38	ALA	0	-0.038	-0.006	32.688	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	39	MET	0	-0.062	-0.019	26.121	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	40	ILE	0	-0.024	-0.015	25.171	0.005	0.005	0.000	0.000	0.000	0.000
41	A	41	TYR	0	0.024	0.013	23.852	-0.013	-0.013	0.000	0.000	0.000	0.000
42	A	42	GLY	0	0.009	0.006	21.591	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	43	PRO	0	-0.038	-0.030	16.147	0.002	0.002	0.000	0.000	0.000	0.000
44	A	44	VAL	0	0.020	0.025	16.917	0.007	0.007	0.000	0.000	0.000	0.000
45	A	45	ALA	0	-0.012	-0.008	15.559	-0.106	-0.106	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.028	-0.015	10.958	0.111	0.111	0.000	0.000	0.000	0.000
47	A	47	PHE	0	0.001	0.005	12.958	-0.098	-0.098	0.000	0.000	0.000	0.000
48	A	48	ALA	0	0.036	0.020	7.807	0.149	0.149	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.046	0.003	9.359	-0.035	-0.035	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.857	-0.908	10.097	-0.658	-0.658	0.000	0.000	0.000	0.000
51	A	51	GLY	0	-0.040	-0.008	13.652	0.099	0.099	0.000	0.000	0.000	0.000
52	A	52	GLN	0	-0.051	-0.027	15.224	0.017	0.017	0.000	0.000	0.000	0.000
53	A	53	VAL	0	-0.002	0.002	13.144	0.038	0.038	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.011	-0.002	16.367	0.034	0.034	0.000	0.000	0.000	0.000
55	A	55	PRO	0	0.026	0.007	14.212	-0.024	-0.024	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.034	0.009	11.994	-0.031	-0.031	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.038	-0.016	11.392	0.112	0.112	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.756	-0.891	10.178	-0.985	-0.985	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.861	-0.909	7.734	0.062	0.062	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.007	0.003	6.415	0.135	0.135	0.000	0.000	0.000	0.000
61	A	61	ILE	0	0.029	0.000	6.020	0.216	0.216	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.037	-0.011	3.985	-1.574	-1.261	0.000	-0.077	-0.236	0.000
63	A	63	GLU	-1	-0.915	-0.952	2.517	-3.080	-1.368	7.954	-5.015	-4.651	-0.028
64	A	64	MET	0	-0.101	-0.023	3.157	3.408	2.903	0.359	1.871	-1.725	-0.007
65	A	65	ASP	-1	-0.851	-0.916	2.031	-13.134	-14.061	7.148	-3.289	-2.930	-0.030
66	A	66	VAL	0	-0.039	-0.035	3.147	1.814	1.633	0.038	0.309	-0.167	0.000
67	A	67	GLY	0	-0.022	-0.009	6.439	0.535	0.535	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.831	-0.888	5.143	1.051	1.176	-0.001	-0.002	-0.122	0.000
69	A	69	GLU	-1	-0.858	-0.938	8.016	-0.381	-0.381	0.000	0.000	0.000	0.000
70	A	70	ARG	1	0.777	0.873	5.710	-2.094	-2.094	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.836	-0.910	11.626	0.046	0.046	0.000	0.000	0.000	0.000
72	A	72	VAL	0	-0.005	-0.005	11.672	0.148	0.148	0.000	0.000	0.000	0.000
73	A	73	VAL	0	-0.003	-0.003	14.600	-0.100	-0.100	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.006	0.012	13.464	0.069	0.069	0.000	0.000	0.000	0.000
75	A	75	PRO	0	0.045	0.028	16.603	-0.044	-0.044	0.000	0.000	0.000	0.000
76	A	76	PRO	0	0.037	0.004	19.121	-0.020	-0.020	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.879	-0.941	18.363	0.148	0.148	0.000	0.000	0.000	0.000
78	A	78	LYS	1	0.805	0.879	11.907	-0.335	-0.335	0.000	0.000	0.000	0.000
79	A	79	ALA	0	0.051	0.033	16.502	-0.030	-0.030	0.000	0.000	0.000	0.000
80	A	80	PHE	0	0.019	0.004	19.385	-0.026	-0.026	0.000	0.000	0.000	0.000
81	A	81	GLY	0	0.045	0.033	21.778	-0.008	-0.008	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.872	0.909	22.255	-0.142	-0.142	0.000	0.000	0.000	0.000
83	A	83	ARG	1	0.776	0.884	25.377	-0.021	-0.021	0.000	0.000	0.000	0.000
84	A	84	ASP	-1	-0.786	-0.857	28.122	0.009	0.009	0.000	0.000	0.000	0.000
85	A	85	PRO	0	0.061	0.013	29.872	-0.009	-0.009	0.000	0.000	0.000	0.000
86	A	86	SER	0	-0.050	-0.017	31.432	-0.007	-0.007	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.845	0.896	27.605	0.016	0.016	0.000	0.000	0.000	0.000
88	A	88	ILE	0	-0.035	-0.006	33.862	-0.005	-0.005	0.000	0.000	0.000	0.000
89	A	89	LYS	1	0.940	0.975	35.808	0.031	0.031	0.000	0.000	0.000	0.000
90	A	90	LEU	0	-0.015	-0.007	39.806	0.000	0.000	0.000	0.000	0.000	0.000
91	A	91	ILE	0	0.025	0.014	41.542	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	92	PRO	0	0.019	0.002	45.539	0.002	0.002	0.000	0.000	0.000	0.000
93	A	93	LEU	0	0.047	0.014	49.186	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	94	SER	0	0.005	0.000	50.892	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.766	-0.864	47.718	-0.036	-0.036	0.000	0.000	0.000	0.000
96	A	96	PHE	0	0.004	0.007	43.656	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	97	THR	0	-0.001	-0.018	49.333	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.821	0.907	50.859	0.034	0.034	0.000	0.000	0.000	0.000
99	A	99	ARG	1	0.857	0.923	45.042	0.040	0.040	0.000	0.000	0.000	0.000
100	A	100	GLY	0	0.031	0.024	51.012	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	101	ILE	0	-0.028	-0.002	46.081	0.000	0.000	0.000	0.000	0.000	0.000
102	A	102	LYS	1	0.952	0.970	50.056	0.024	0.024	0.000	0.000	0.000	0.000
103	A	103	PRO	0	0.003	0.011	47.113	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	104	ILE	0	0.014	-0.017	46.420	0.003	0.003	0.000	0.000	0.000	0.000
105	A	105	LYS	1	0.942	0.969	44.123	-0.008	-0.008	0.000	0.000	0.000	0.000
106	A	106	GLY	0	0.010	0.004	41.279	0.001	0.001	0.000	0.000	0.000	0.000
107	A	107	LEU	0	-0.013	-0.001	40.903	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	108	THR	0	0.033	0.010	36.666	0.005	0.005	0.000	0.000	0.000	0.000
109	A	109	ILE	0	-0.026	-0.007	39.612	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	110	THR	0	-0.001	-0.021	37.927	-0.005	-0.005	0.000	0.000	0.000	0.000
111	A	111	ILE	0	-0.063	-0.025	39.055	0.004	0.004	0.000	0.000	0.000	0.000
112	A	112	ASP	-1	-0.892	-0.946	38.756	-0.061	-0.061	0.000	0.000	0.000	0.000
113	A	113	GLY	0	0.012	0.013	37.032	-0.005	-0.005	0.000	0.000	0.000	0.000
114	A	114	ILE	0	-0.014	-0.003	33.339	-0.006	-0.006	0.000	0.000	0.000	0.000
115	A	115	PRO	0	0.012	0.005	33.042	0.008	0.008	0.000	0.000	0.000	0.000
116	A	116	GLY	0	0.049	0.016	34.708	0.002	0.002	0.000	0.000	0.000	0.000
117	A	117	LYS	1	0.833	0.912	36.061	0.024	0.024	0.000	0.000	0.000	0.000
118	A	118	ILE	0	-0.041	-0.008	38.299	0.006	0.006	0.000	0.000	0.000	0.000
119	A	119	VAL	0	0.047	0.027	38.390	0.002	0.002	0.000	0.000	0.000	0.000
120	A	120	SER	0	-0.074	-0.058	41.151	0.003	0.003	0.000	0.000	0.000	0.000
121	A	121	ILE	0	0.031	0.020	44.893	-0.003	-0.003	0.000	0.000	0.000	0.000
122	A	122	ASN	0	-0.006	0.001	47.717	0.002	0.002	0.000	0.000	0.000	0.000
123	A	123	SER	0	0.027	0.011	50.567	0.000	0.000	0.000	0.000	0.000	0.000
124	A	124	GLY	0	0.041	0.024	53.043	0.000	0.000	0.000	0.000	0.000	0.000
125	A	125	ARG	1	0.921	0.973	47.897	-0.007	-0.007	0.000	0.000	0.000	0.000
126	A	126	VAL	0	0.008	0.002	44.451	0.001	0.001	0.000	0.000	0.000	0.000
127	A	127	LEU	0	0.002	0.015	40.679	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	128	VAL	0	-0.008	-0.016	38.570	0.000	0.000	0.000	0.000	0.000	0.000
129	A	129	ASP	-1	-0.751	-0.852	33.610	-0.002	-0.002	0.000	0.000	0.000	0.000
130	A	130	PHE	0	0.001	-0.006	34.188	-0.004	-0.004	0.000	0.000	0.000	0.000
131	A	131	ASN	0	-0.065	-0.055	29.389	-0.009	-0.009	0.000	0.000	0.000	0.000
132	A	132	HIS	0	0.088	0.055	26.441	0.012	0.012	0.000	0.000	0.000	0.000
133	A	133	GLU	-1	-0.857	-0.925	28.999	-0.026	-0.026	0.000	0.000	0.000	0.000
134	A	134	LEU	0	0.005	0.001	25.489	0.014	0.014	0.000	0.000	0.000	0.000
135	A	135	ALA	0	0.006	0.016	25.858	0.015	0.015	0.000	0.000	0.000	0.000
136	A	136	GLY	0	-0.089	-0.063	25.687	0.004	0.004	0.000	0.000	0.000	0.000
137	A	137	LYS	1	0.782	0.884	25.888	-0.031	-0.031	0.000	0.000	0.000	0.000
138	A	138	GLU	-1	-0.950	-0.969	21.099	0.219	0.219	0.000	0.000	0.000	0.000
139	A	139	VAL	0	-0.029	-0.019	19.240	-0.029	-0.029	0.000	0.000	0.000	0.000
140	A	140	LYS	1	0.818	0.909	18.868	-0.103	-0.103	0.000	0.000	0.000	0.000
141	A	141	TYR	0	-0.030	-0.040	15.994	-0.030	-0.030	0.000	0.000	0.000	0.000
142	A	142	ARG	1	0.767	0.864	15.258	0.314	0.314	0.000	0.000	0.000	0.000
143	A	143	ILE	0	-0.004	-0.027	10.663	-0.039	-0.039	0.000	0.000	0.000	0.000
144	A	144	LYS	1	0.862	0.922	10.346	0.695	0.695	0.000	0.000	0.000	0.000
145	A	145	ILE	0	0.017	0.025	5.193	0.085	0.085	0.000	0.000	0.000	0.000
146	A	146	GLU	-1	-0.826	-0.877	9.297	-0.564	-0.564	0.000	0.000	0.000	0.000
147	A	147	GLU	-1	-0.831	-0.906	11.103	-0.890	-0.890	0.000	0.000	0.000	0.000
148	A	148	VAL	0	0.014	-0.003	6.834	-0.133	-0.133	0.000	0.000	0.000	0.000
149	A	149	VAL	0	-0.040	-0.012	10.308	0.185	0.185	0.000	0.000	0.000	0.000
150	A	150	ASP	-1	-0.955	-0.979	10.655	-1.272	-1.272	0.000	0.000	0.000	0.000

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