FMO DATABASE

FMODB ID: G6K31

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1259912.398885
FMO2-HF: Nuclear repulsion	1202376.519736
FMO2-HF: Total energy	-57535.879149
FMO2-MP2: Total energy	-57704.991597

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.
-15.582	-10.534	12.077	-6.32	-10.805	-0.064

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 : -0.045 / q_NPA : -0.021

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	-0.925	-0.960	3.801	-0.458	0.885	-0.017	-0.513	-0.813	0.002
4	A	4	LYS	1	0.816	0.866	5.591	0.632	0.632	0.000	0.000	0.000	0.000
5	A	5	GLY	0	0.001	0.001	8.307	0.153	0.153	0.000	0.000	0.000	0.000
6	A	6	LYS	1	0.842	0.932	8.593	1.092	1.092	0.000	0.000	0.000	0.000
7	A	7	MET	0	0.007	0.014	10.542	-0.058	-0.058	0.000	0.000	0.000	0.000
8	A	8	VAL	0	0.016	0.008	8.269	-0.107	-0.107	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.779	0.888	11.389	0.780	0.780	0.000	0.000	0.000	0.000
10	A	10	ILE	0	0.016	0.008	10.944	-0.103	-0.103	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.050	-0.052	13.477	0.150	0.150	0.000	0.000	0.000	0.000
12	A	12	TYR	0	-0.006	-0.017	14.776	-0.070	-0.070	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.806	-0.860	17.092	-0.291	-0.291	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.053	0.012	19.378	-0.008	-0.008	0.000	0.000	0.000	0.000
15	A	15	TYR	0	-0.022	-0.031	21.121	0.034	0.034	0.000	0.000	0.000	0.000
16	A	16	VAL	0	0.036	0.011	23.319	0.004	0.004	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.830	-0.897	26.106	-0.076	-0.076	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.001	-0.007	26.893	0.006	0.006	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.862	0.929	27.886	0.089	0.089	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.024	0.024	23.431	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	21	PHE	0	-0.040	-0.030	22.196	0.012	0.012	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.858	-0.937	21.865	-0.309	-0.309	0.000	0.000	0.000	0.000
23	A	23	THR	0	-0.005	-0.023	21.696	-0.008	-0.008	0.000	0.000	0.000	0.000
24	A	24	THR	0	0.060	0.056	18.431	0.016	0.016	0.000	0.000	0.000	0.000
25	A	25	ASN	0	-0.006	0.002	21.456	0.018	0.018	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.782	-0.897	23.071	-0.184	-0.184	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.843	-0.920	26.366	-0.167	-0.167	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.046	-0.009	23.029	0.019	0.019	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.056	0.023	26.599	0.016	0.016	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.746	0.852	28.229	0.194	0.194	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.800	0.906	28.230	0.160	0.160	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.878	-0.940	27.606	-0.135	-0.135	0.000	0.000	0.000	0.000
33	A	33	GLY	0	-0.044	-0.004	30.725	0.007	0.007	0.000	0.000	0.000	0.000
34	A	34	ILE	0	-0.054	-0.033	26.712	0.005	0.005	0.000	0.000	0.000	0.000
35	A	35	TYR	0	-0.038	-0.012	30.074	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	36	ASN	0	0.029	0.006	30.509	0.018	0.018	0.000	0.000	0.000	0.000
37	A	37	PRO	0	0.005	-0.004	31.384	-0.010	-0.010	0.000	0.000	0.000	0.000
38	A	38	ALA	0	-0.036	-0.011	33.123	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	39	MET	0	-0.068	-0.022	26.041	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	40	ILE	0	-0.019	-0.008	25.432	0.008	0.008	0.000	0.000	0.000	0.000
41	A	41	TYR	0	0.005	0.006	24.284	-0.009	-0.009	0.000	0.000	0.000	0.000
42	A	42	GLY	0	-0.002	-0.008	21.592	0.004	0.004	0.000	0.000	0.000	0.000
43	A	43	PRO	0	-0.031	-0.029	16.225	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	44	VAL	0	0.008	0.010	16.945	0.042	0.042	0.000	0.000	0.000	0.000
45	A	45	ALA	0	-0.025	-0.010	15.698	-0.094	-0.094	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.002	0.004	11.119	0.088	0.088	0.000	0.000	0.000	0.000
47	A	47	PHE	0	-0.007	0.002	12.912	-0.051	-0.051	0.000	0.000	0.000	0.000
48	A	48	ALA	0	0.023	0.004	7.817	0.070	0.070	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.048	0.011	9.535	0.081	0.081	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.851	-0.905	10.254	-0.451	-0.451	0.000	0.000	0.000	0.000
51	A	51	GLY	0	-0.033	-0.006	13.758	0.085	0.085	0.000	0.000	0.000	0.000
52	A	52	GLN	0	-0.054	-0.026	15.612	0.034	0.034	0.000	0.000	0.000	0.000
53	A	53	VAL	0	-0.005	0.000	13.204	0.040	0.040	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.017	-0.007	16.287	0.029	0.029	0.000	0.000	0.000	0.000
55	A	55	PRO	0	0.032	0.012	14.129	-0.059	-0.059	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.035	-0.004	12.188	-0.044	-0.044	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.040	-0.016	11.569	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.778	-0.900	10.338	-1.040	-1.040	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.859	-0.906	7.804	-0.345	-0.345	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.006	0.007	6.428	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	61	ILE	0	0.032	-0.004	6.143	-0.093	-0.093	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.032	-0.010	3.950	-1.304	-0.992	0.000	-0.070	-0.242	0.000
63	A	63	GLU	-1	-0.909	-0.949	2.526	-4.514	-2.571	6.943	-4.371	-4.516	-0.029
64	A	64	MET	0	-0.118	-0.033	3.117	0.055	0.474	0.828	0.907	-2.153	-0.013
65	A	65	ASP	-1	-0.873	-0.924	2.225	-9.687	-8.667	4.304	-2.409	-2.915	-0.024
66	A	66	VAL	0	-0.017	-0.029	3.258	1.673	1.684	0.019	0.136	-0.166	0.000
67	A	67	GLY	0	-0.050	-0.026	6.354	0.354	0.354	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.824	-0.887	5.688	-1.353	-1.353	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.846	-0.933	8.294	-0.519	-0.519	0.000	0.000	0.000	0.000
70	A	70	ARG	1	0.789	0.875	5.734	0.276	0.276	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.859	-0.931	12.139	-0.211	-0.211	0.000	0.000	0.000	0.000
72	A	72	VAL	0	-0.016	-0.007	11.914	0.053	0.053	0.000	0.000	0.000	0.000
73	A	73	VAL	0	0.009	0.006	14.862	-0.020	-0.020	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.026	0.003	13.732	0.027	0.027	0.000	0.000	0.000	0.000
75	A	75	PRO	0	0.055	0.030	16.628	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	76	PRO	0	0.043	0.014	19.352	-0.020	-0.020	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.893	-0.947	18.745	-0.042	-0.042	0.000	0.000	0.000	0.000
78	A	78	LYS	1	0.809	0.877	12.123	0.046	0.046	0.000	0.000	0.000	0.000
79	A	79	ALA	0	0.042	0.031	16.635	-0.045	-0.045	0.000	0.000	0.000	0.000
80	A	80	PHE	0	0.028	0.006	19.341	-0.012	-0.012	0.000	0.000	0.000	0.000
81	A	81	GLY	0	0.026	0.026	21.902	0.008	0.008	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.881	0.917	22.424	0.025	0.025	0.000	0.000	0.000	0.000
83	A	83	ARG	1	0.787	0.882	25.424	0.077	0.077	0.000	0.000	0.000	0.000
84	A	84	ASP	-1	-0.784	-0.857	28.524	-0.054	-0.054	0.000	0.000	0.000	0.000
85	A	85	PRO	0	0.069	0.019	30.197	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	86	SER	0	-0.056	-0.029	31.726	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.847	0.901	27.923	0.089	0.089	0.000	0.000	0.000	0.000
88	A	88	ILE	0	-0.028	-0.004	33.974	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	89	LYS	1	0.941	0.977	36.001	0.070	0.070	0.000	0.000	0.000	0.000
90	A	90	LEU	0	-0.013	-0.005	39.907	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	91	ILE	0	0.019	0.008	41.606	0.000	0.000	0.000	0.000	0.000	0.000
92	A	92	PRO	0	0.021	0.008	45.659	0.001	0.001	0.000	0.000	0.000	0.000
93	A	93	LEU	0	0.042	0.013	49.349	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	94	SER	0	0.024	-0.002	50.818	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.789	-0.879	48.115	-0.049	-0.049	0.000	0.000	0.000	0.000
96	A	96	PHE	0	0.000	-0.008	43.835	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	97	THR	0	-0.037	-0.019	49.650	0.000	0.000	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.841	0.914	51.190	0.048	0.048	0.000	0.000	0.000	0.000
99	A	99	ARG	1	0.903	0.954	45.249	0.061	0.061	0.000	0.000	0.000	0.000
100	A	100	GLY	0	0.021	0.026	50.967	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	101	ILE	0	-0.018	0.001	46.193	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	102	LYS	1	0.952	0.967	50.107	0.047	0.047	0.000	0.000	0.000	0.000
103	A	103	PRO	0	-0.004	0.006	47.341	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	104	ILE	0	0.008	-0.013	46.609	0.003	0.003	0.000	0.000	0.000	0.000
105	A	105	LYS	1	0.963	0.975	44.146	0.040	0.040	0.000	0.000	0.000	0.000
106	A	106	GLY	0	0.002	0.002	41.429	0.000	0.000	0.000	0.000	0.000	0.000
107	A	107	LEU	0	-0.016	0.002	41.175	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	108	THR	0	0.027	0.004	37.023	0.003	0.003	0.000	0.000	0.000	0.000
109	A	109	ILE	0	-0.047	-0.022	39.987	0.001	0.001	0.000	0.000	0.000	0.000
110	A	110	THR	0	0.032	0.015	37.858	-0.006	-0.006	0.000	0.000	0.000	0.000
111	A	111	ILE	0	-0.067	-0.028	39.174	0.005	0.005	0.000	0.000	0.000	0.000
112	A	112	ASP	-1	-0.882	-0.936	38.722	-0.078	-0.078	0.000	0.000	0.000	0.000
113	A	113	GLY	0	0.006	-0.002	37.151	-0.004	-0.004	0.000	0.000	0.000	0.000
114	A	114	ILE	0	-0.023	-0.017	33.451	-0.008	-0.008	0.000	0.000	0.000	0.000
115	A	115	PRO	0	0.005	0.007	33.141	0.008	0.008	0.000	0.000	0.000	0.000
116	A	116	GLY	0	0.027	0.003	34.936	0.000	0.000	0.000	0.000	0.000	0.000
117	A	117	LYS	1	0.879	0.947	35.775	0.089	0.089	0.000	0.000	0.000	0.000
118	A	118	ILE	0	-0.046	-0.014	38.436	0.005	0.005	0.000	0.000	0.000	0.000
119	A	119	VAL	0	0.032	0.013	38.688	0.001	0.001	0.000	0.000	0.000	0.000
120	A	120	SER	0	-0.068	-0.049	41.418	0.002	0.002	0.000	0.000	0.000	0.000
121	A	121	ILE	0	0.020	0.015	45.099	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	122	ASN	0	-0.001	0.000	48.073	0.000	0.000	0.000	0.000	0.000	0.000
123	A	123	SER	0	0.029	0.009	50.723	0.001	0.001	0.000	0.000	0.000	0.000
124	A	124	GLY	0	0.033	0.010	52.687	0.001	0.001	0.000	0.000	0.000	0.000
125	A	125	ARG	1	0.922	0.978	47.867	0.026	0.026	0.000	0.000	0.000	0.000
126	A	126	VAL	0	0.017	0.008	44.454	0.001	0.001	0.000	0.000	0.000	0.000
127	A	127	LEU	0	0.010	0.019	40.594	0.000	0.000	0.000	0.000	0.000	0.000
128	A	128	VAL	0	-0.011	-0.006	38.660	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	129	ASP	-1	-0.743	-0.858	33.923	-0.072	-0.072	0.000	0.000	0.000	0.000
130	A	130	PHE	0	-0.020	-0.025	34.343	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	131	ASN	0	-0.081	-0.044	29.820	-0.011	-0.011	0.000	0.000	0.000	0.000
132	A	132	HIS	0	0.101	0.061	26.423	0.011	0.011	0.000	0.000	0.000	0.000
133	A	133	GLU	-1	-0.855	-0.928	29.060	-0.101	-0.101	0.000	0.000	0.000	0.000
134	A	134	LEU	0	-0.001	-0.003	25.657	0.013	0.013	0.000	0.000	0.000	0.000
135	A	135	ALA	0	0.006	0.012	25.907	0.001	0.001	0.000	0.000	0.000	0.000
136	A	136	GLY	0	-0.085	-0.060	25.696	0.009	0.009	0.000	0.000	0.000	0.000
137	A	137	LYS	1	0.799	0.886	25.747	0.093	0.093	0.000	0.000	0.000	0.000
138	A	138	GLU	-1	-0.963	-0.967	21.319	-0.046	-0.046	0.000	0.000	0.000	0.000
139	A	139	VAL	0	-0.030	-0.017	19.519	-0.006	-0.006	0.000	0.000	0.000	0.000
140	A	140	LYS	1	0.843	0.923	19.016	0.179	0.179	0.000	0.000	0.000	0.000
141	A	141	TYR	0	0.001	0.001	16.157	0.006	0.006	0.000	0.000	0.000	0.000
142	A	142	ARG	1	0.772	0.883	15.672	0.450	0.450	0.000	0.000	0.000	0.000
143	A	143	ILE	0	0.001	-0.019	11.058	0.018	0.018	0.000	0.000	0.000	0.000
144	A	144	LYS	1	0.872	0.928	10.913	0.648	0.648	0.000	0.000	0.000	0.000
145	A	145	ILE	0	0.016	0.027	5.696	0.177	0.177	0.000	0.000	0.000	0.000
146	A	146	GLU	-1	-0.814	-0.865	9.585	-0.664	-0.664	0.000	0.000	0.000	0.000
147	A	147	GLU	-1	-0.830	-0.912	10.917	-0.572	-0.572	0.000	0.000	0.000	0.000
148	A	148	VAL	0	0.022	0.001	6.764	-0.160	-0.160	0.000	0.000	0.000	0.000
149	A	149	VAL	0	-0.064	-0.023	10.232	0.181	0.181	0.000	0.000	0.000	0.000
150	A	150	ASP	-1	-0.943	-0.976	10.611	-0.574	-0.574	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

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