FMO DATABASE

FMODB ID: 17G1Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1258354.119981
FMO2-HF: Nuclear repulsion	1200819.089161
FMO2-HF: Total energy	-57535.03082
FMO2-MP2: Total energy	-57704.081486

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.
-16.459	-10.15	13.194	-7.467	-12.035	-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 : -0.014 / q_NPA : 0.009

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	-0.987	-0.994	3.801	-1.100	1.198	-0.022	-1.099	-1.178	0.007
4	A	4	LYS	1	0.854	0.901	5.562	0.280	0.280	0.000	0.000	0.000	0.000
5	A	5	GLY	0	-0.005	-0.003	8.500	0.069	0.069	0.000	0.000	0.000	0.000
6	A	6	LYS	1	0.893	0.953	8.328	1.482	1.482	0.000	0.000	0.000	0.000
7	A	7	MET	0	-0.003	0.004	10.509	0.009	0.009	0.000	0.000	0.000	0.000
8	A	8	VAL	0	0.031	0.014	8.233	-0.186	-0.186	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.907	0.972	11.678	0.904	0.904	0.000	0.000	0.000	0.000
10	A	10	ILE	0	0.032	0.019	11.248	-0.137	-0.137	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.057	-0.061	13.723	0.152	0.152	0.000	0.000	0.000	0.000
12	A	12	TYR	0	-0.018	-0.021	14.780	-0.054	-0.054	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.801	-0.863	17.028	-0.290	-0.290	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.037	0.012	19.270	0.009	0.009	0.000	0.000	0.000	0.000
15	A	15	TYR	0	-0.007	-0.021	20.968	0.007	0.007	0.000	0.000	0.000	0.000
16	A	16	VAL	0	0.028	0.005	23.333	0.015	0.015	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.902	-0.955	26.119	-0.014	-0.014	0.000	0.000	0.000	0.000
18	A	18	GLY	0	-0.020	-0.017	26.854	0.000	0.000	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.891	0.944	27.795	0.042	0.042	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.027	0.025	23.223	0.001	0.001	0.000	0.000	0.000	0.000
21	A	21	PHE	0	-0.050	-0.035	22.293	0.007	0.007	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.866	-0.942	22.381	-0.249	-0.249	0.000	0.000	0.000	0.000
23	A	23	THR	0	-0.020	-0.022	21.640	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	24	THR	0	0.071	0.058	18.661	0.015	0.015	0.000	0.000	0.000	0.000
25	A	25	ASN	0	-0.004	0.005	21.554	0.008	0.008	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.840	-0.939	23.160	-0.194	-0.194	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.923	-0.968	26.491	-0.182	-0.182	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.058	-0.021	22.864	0.023	0.023	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.058	0.025	26.563	0.021	0.021	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.862	0.934	28.202	0.193	0.193	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.879	0.960	27.868	0.158	0.158	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.945	-0.984	27.307	-0.109	-0.109	0.000	0.000	0.000	0.000
33	A	33	GLY	0	-0.056	-0.008	30.574	0.010	0.010	0.000	0.000	0.000	0.000
34	A	34	ILE	0	-0.043	-0.024	26.617	0.007	0.007	0.000	0.000	0.000	0.000
35	A	35	TYR	0	-0.010	-0.003	30.216	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	36	ASN	0	0.031	0.007	30.612	0.015	0.015	0.000	0.000	0.000	0.000
37	A	37	PRO	0	-0.009	-0.011	31.521	-0.012	-0.012	0.000	0.000	0.000	0.000
38	A	38	ALA	0	-0.037	-0.015	33.141	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	39	MET	0	-0.058	-0.014	26.412	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	40	ILE	0	-0.030	-0.014	25.976	0.005	0.005	0.000	0.000	0.000	0.000
41	A	41	TYR	0	0.009	0.009	24.485	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	42	GLY	0	-0.006	-0.010	21.875	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	43	PRO	0	-0.028	-0.025	16.641	0.009	0.009	0.000	0.000	0.000	0.000
44	A	44	VAL	0	0.008	0.010	17.150	0.040	0.040	0.000	0.000	0.000	0.000
45	A	45	ALA	0	-0.031	-0.017	15.832	-0.098	-0.098	0.000	0.000	0.000	0.000
46	A	46	ILE	0	0.002	0.010	10.957	0.102	0.102	0.000	0.000	0.000	0.000
47	A	47	PHE	0	-0.007	-0.001	12.914	-0.087	-0.087	0.000	0.000	0.000	0.000
48	A	48	ALA	0	0.027	0.005	7.817	0.109	0.109	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.045	0.018	9.864	0.097	0.097	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.899	-0.942	10.617	-0.274	-0.274	0.000	0.000	0.000	0.000
51	A	51	GLY	0	-0.029	-0.002	14.120	0.052	0.052	0.000	0.000	0.000	0.000
52	A	52	GLN	0	-0.051	-0.022	15.803	0.016	0.016	0.000	0.000	0.000	0.000
53	A	53	VAL	0	-0.013	-0.005	13.184	0.018	0.018	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.028	-0.011	16.482	0.039	0.039	0.000	0.000	0.000	0.000
55	A	55	PRO	0	0.035	0.015	14.488	-0.032	-0.032	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.031	-0.003	12.512	0.004	0.004	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.045	-0.014	11.838	0.039	0.039	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.788	-0.908	10.346	-0.646	-0.646	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.876	-0.920	8.139	0.135	0.135	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.002	0.006	6.729	0.197	0.197	0.000	0.000	0.000	0.000
61	A	61	ILE	0	0.027	-0.007	6.153	0.044	0.044	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.037	-0.017	4.314	-1.319	-1.063	-0.001	-0.049	-0.205	0.000
63	A	63	GLU	-1	-0.933	-0.970	2.537	-1.225	0.846	5.972	-4.015	-4.028	-0.021
64	A	64	MET	0	-0.116	-0.028	3.135	0.760	1.374	0.805	0.844	-2.262	-0.014
65	A	65	ASP	-1	-0.850	-0.913	2.296	-14.707	-13.770	6.427	-3.166	-4.197	-0.033
66	A	66	VAL	0	-0.016	-0.034	3.478	2.207	2.340	0.013	0.018	-0.165	0.000
67	A	67	GLY	0	-0.044	-0.024	6.719	0.300	0.300	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.824	-0.905	5.233	-0.917	-0.917	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.877	-0.939	8.231	-0.459	-0.459	0.000	0.000	0.000	0.000
70	A	70	ARG	1	0.834	0.922	6.140	-0.590	-0.590	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.894	-0.954	11.690	-0.124	-0.124	0.000	0.000	0.000	0.000
72	A	72	VAL	0	-0.010	-0.005	11.805	0.091	0.091	0.000	0.000	0.000	0.000
73	A	73	VAL	0	0.008	0.004	14.875	-0.052	-0.052	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.029	-0.008	14.248	0.051	0.051	0.000	0.000	0.000	0.000
75	A	75	PRO	0	0.067	0.039	16.742	-0.024	-0.024	0.000	0.000	0.000	0.000
76	A	76	PRO	0	0.039	0.010	19.556	-0.016	-0.016	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.976	-1.004	18.706	0.100	0.100	0.000	0.000	0.000	0.000
78	A	78	LYS	1	0.817	0.888	12.961	-0.236	-0.236	0.000	0.000	0.000	0.000
79	A	79	ALA	0	0.054	0.038	16.911	-0.034	-0.034	0.000	0.000	0.000	0.000
80	A	80	PHE	0	0.029	0.004	19.615	-0.014	-0.014	0.000	0.000	0.000	0.000
81	A	81	GLY	0	0.019	0.023	22.169	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.975	0.974	22.681	-0.097	-0.097	0.000	0.000	0.000	0.000
83	A	83	ARG	1	0.808	0.903	25.650	0.007	0.007	0.000	0.000	0.000	0.000
84	A	84	ASP	-1	-0.828	-0.906	28.839	0.021	0.021	0.000	0.000	0.000	0.000
85	A	85	PRO	0	0.055	0.014	30.442	-0.007	-0.007	0.000	0.000	0.000	0.000
86	A	86	SER	0	-0.049	-0.019	31.961	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.920	0.957	27.894	0.023	0.023	0.000	0.000	0.000	0.000
88	A	88	ILE	0	-0.029	-0.003	34.261	-0.006	-0.006	0.000	0.000	0.000	0.000
89	A	89	LYS	1	0.952	0.980	36.578	0.024	0.024	0.000	0.000	0.000	0.000
90	A	90	LEU	0	-0.020	-0.011	40.189	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	91	ILE	0	0.021	0.011	41.964	0.000	0.000	0.000	0.000	0.000	0.000
92	A	92	PRO	0	0.018	0.007	45.962	0.000	0.000	0.000	0.000	0.000	0.000
93	A	93	LEU	0	0.038	0.010	49.667	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	94	SER	0	-0.012	-0.013	51.129	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.748	-0.876	48.598	-0.027	-0.027	0.000	0.000	0.000	0.000
96	A	96	PHE	0	-0.033	-0.025	44.260	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	97	THR	0	-0.056	-0.029	49.989	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.896	0.957	51.734	0.027	0.027	0.000	0.000	0.000	0.000
99	A	99	ARG	1	0.904	0.956	45.480	0.038	0.038	0.000	0.000	0.000	0.000
100	A	100	GLY	0	0.028	0.028	51.183	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	101	ILE	0	-0.026	-0.004	46.479	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	102	LYS	1	0.960	0.968	50.326	0.030	0.030	0.000	0.000	0.000	0.000
103	A	103	PRO	0	-0.006	0.008	47.638	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	104	ILE	0	0.010	-0.010	46.922	0.002	0.002	0.000	0.000	0.000	0.000
105	A	105	LYS	1	0.981	0.982	44.387	0.012	0.012	0.000	0.000	0.000	0.000
106	A	106	GLY	0	-0.016	-0.008	41.715	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	107	LEU	0	-0.011	0.003	41.343	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	108	THR	0	0.020	0.009	37.055	0.003	0.003	0.000	0.000	0.000	0.000
109	A	109	ILE	0	-0.048	-0.026	40.115	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	110	THR	0	0.030	0.012	38.207	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	111	ILE	0	-0.058	-0.026	39.526	0.002	0.002	0.000	0.000	0.000	0.000
112	A	112	ASP	-1	-0.895	-0.940	39.088	-0.047	-0.047	0.000	0.000	0.000	0.000
113	A	113	GLY	0	0.006	-0.003	37.518	-0.003	-0.003	0.000	0.000	0.000	0.000
114	A	114	ILE	0	-0.025	-0.018	33.806	-0.006	-0.006	0.000	0.000	0.000	0.000
115	A	115	PRO	0	0.012	0.012	33.352	0.006	0.006	0.000	0.000	0.000	0.000
116	A	116	GLY	0	0.033	0.005	35.277	0.003	0.003	0.000	0.000	0.000	0.000
117	A	117	LYS	1	0.961	0.997	36.731	0.035	0.035	0.000	0.000	0.000	0.000
118	A	118	ILE	0	-0.042	-0.015	38.744	0.005	0.005	0.000	0.000	0.000	0.000
119	A	119	VAL	0	0.013	0.008	39.004	0.000	0.000	0.000	0.000	0.000	0.000
120	A	120	SER	0	-0.041	-0.033	41.684	0.001	0.001	0.000	0.000	0.000	0.000
121	A	121	ILE	0	0.013	0.011	45.360	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	122	ASN	0	-0.009	-0.009	48.625	0.001	0.001	0.000	0.000	0.000	0.000
123	A	123	SER	0	0.026	0.004	50.979	0.001	0.001	0.000	0.000	0.000	0.000
124	A	124	GLY	0	0.028	0.014	52.970	0.001	0.001	0.000	0.000	0.000	0.000
125	A	125	ARG	1	0.928	0.980	48.104	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	126	VAL	0	0.017	0.008	44.675	0.001	0.001	0.000	0.000	0.000	0.000
127	A	127	LEU	0	0.009	0.016	40.806	0.000	0.000	0.000	0.000	0.000	0.000
128	A	128	VAL	0	-0.009	-0.007	38.985	-0.002	-0.002	0.000	0.000	0.000	0.000
129	A	129	ASP	-1	-0.766	-0.873	34.131	-0.014	-0.014	0.000	0.000	0.000	0.000
130	A	130	PHE	0	-0.014	-0.025	34.641	-0.004	-0.004	0.000	0.000	0.000	0.000
131	A	131	ASN	0	-0.093	-0.051	30.149	-0.004	-0.004	0.000	0.000	0.000	0.000
132	A	132	HIS	0	0.103	0.062	26.543	0.009	0.009	0.000	0.000	0.000	0.000
133	A	133	GLU	-1	-0.936	-0.972	29.376	-0.066	-0.066	0.000	0.000	0.000	0.000
134	A	134	LEU	0	-0.002	-0.007	25.571	0.012	0.012	0.000	0.000	0.000	0.000
135	A	135	ALA	0	-0.005	0.006	26.171	0.008	0.008	0.000	0.000	0.000	0.000
136	A	136	GLY	0	-0.097	-0.071	25.932	0.003	0.003	0.000	0.000	0.000	0.000
137	A	137	LYS	1	0.868	0.944	25.980	0.018	0.018	0.000	0.000	0.000	0.000
138	A	138	GLU	-1	-0.941	-0.956	21.416	0.082	0.082	0.000	0.000	0.000	0.000
139	A	139	VAL	0	-0.037	-0.015	19.665	-0.018	-0.018	0.000	0.000	0.000	0.000
140	A	140	LYS	1	0.878	0.945	18.357	0.080	0.080	0.000	0.000	0.000	0.000
141	A	141	TYR	0	0.028	0.004	16.203	-0.007	-0.007	0.000	0.000	0.000	0.000
142	A	142	ARG	1	0.780	0.877	15.321	0.476	0.476	0.000	0.000	0.000	0.000
143	A	143	ILE	0	0.006	-0.010	10.900	0.003	0.003	0.000	0.000	0.000	0.000
144	A	144	LYS	1	0.935	0.973	10.865	0.804	0.804	0.000	0.000	0.000	0.000
145	A	145	ILE	0	-0.006	0.017	5.797	0.213	0.213	0.000	0.000	0.000	0.000
146	A	146	GLU	-1	-0.876	-0.911	9.837	-0.880	-0.880	0.000	0.000	0.000	0.000
147	A	147	GLU	-1	-0.950	-0.990	11.164	-0.848	-0.848	0.000	0.000	0.000	0.000
148	A	148	VAL	0	0.009	-0.002	6.939	-0.117	-0.117	0.000	0.000	0.000	0.000
149	A	149	VAL	0	-0.066	-0.021	10.331	0.152	0.152	0.000	0.000	0.000	0.000
150	A	150	ASP	-1	-0.919	-0.957	10.264	-0.808	-0.808	0.000	0.000	0.000	0.000

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