FMO DATABASE

FMODB ID: 53V2Z

Calculation Name: 3P5J-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3P5J

Chain ID: C

ChEMBL ID:

UniProt ID: Q9CWY8

Base Structure: X-ray

Registration Date: 2023-06-19

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

Total energy (hartree)

FMO2-HF: Electronic energy	-753685.547583
FMO2-HF: Nuclear repulsion	711274.249075
FMO2-HF: Total energy	-42411.298508
FMO2-MP2: Total energy	-42537.180028

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(C:14:ILE)

Summations of interaction energy for fragment #1(C:14:ILE)

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.
-10.735	-3.388	7.688	-4.987	-10.046	-0.019

Interaction energy analysis for fragmet #1(C:14:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : 0.008

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	C	16	LEU	0	0.021	-0.012	3.659	-0.753	1.954	-0.008	-1.488	-1.211	0.005
4	C	17	ARG	1	0.936	0.979	5.858	0.471	0.471	0.000	0.000	0.000	0.000
5	C	18	PRO	0	0.100	0.028	9.673	0.116	0.116	0.000	0.000	0.000	0.000
6	C	19	GLY	0	-0.031	-0.012	11.944	0.081	0.081	0.000	0.000	0.000	0.000
7	C	20	SER	0	0.025	0.019	10.303	0.042	0.042	0.000	0.000	0.000	0.000
8	C	21	LEU	0	0.031	0.021	9.180	0.046	0.046	0.000	0.000	0.000	0.000
9	C	22	ARG	1	0.923	0.959	13.088	0.348	0.348	0.000	0.000	0.000	0.000
10	C	23	GLY	0	0.006	0.004	15.519	0.032	0.032	0.000	0.000	0.000	0.000
11	C	24	ALA	0	-0.021	0.012	14.031	0.035	0.035	0.000	0.000	0.000	0.000
12	C	25	ALA	0	0.042	0.035	16.081	-0.005	-0.005	0.000	0.000	0.000	0.000
13	C	26	PRO	0	0.017	0.006	18.727	-0.002	-0.002	0.000	0.000	0.000	0.000
14	C	27	ALA	0	-0.001	0.002	18.377	0.020	0.020	0.000	0.000	0.000	0.000
15	C	28	LYS	1	0.792	0.900	20.397	0.043	0.043	0.000	0.000	0.000	0.000
16	C	29	LEU	0	0.013	0.008	16.874	0.016	0.016	0.000	0.000	0.000	0.000
17	C	30	HIS	0	0.040	0.010	21.286	-0.006	-0.006	0.000	0.000	0.000	0.000
18	C	31	LEU	0	-0.014	-0.001	20.503	0.006	0.006	0.000	0.000	0.000	0.000
19	C	32	LEU	0	0.021	0.011	23.213	-0.004	-0.004	0.000	0.000	0.000	0.000
20	C	33	PRO	0	-0.002	0.010	24.658	0.001	0.001	0.000	0.000	0.000	0.000
21	C	34	CYS	0	-0.067	-0.048	25.888	0.002	0.002	0.000	0.000	0.000	0.000
22	C	35	ASP	-1	-0.836	-0.906	20.776	0.106	0.106	0.000	0.000	0.000	0.000
23	C	36	VAL	0	-0.077	-0.051	21.862	-0.003	-0.003	0.000	0.000	0.000	0.000
24	C	37	LEU	0	0.024	0.011	21.028	0.012	0.012	0.000	0.000	0.000	0.000
25	C	38	VAL	0	-0.038	-0.012	19.754	0.022	0.022	0.000	0.000	0.000	0.000
26	C	39	SER	0	0.019	0.013	16.147	-0.016	-0.016	0.000	0.000	0.000	0.000
27	C	40	ARG	1	0.898	0.934	18.054	-0.103	-0.103	0.000	0.000	0.000	0.000
28	C	41	PRO	0	0.037	0.028	19.623	-0.019	-0.019	0.000	0.000	0.000	0.000
29	C	42	ALA	0	0.039	0.015	21.923	0.002	0.002	0.000	0.000	0.000	0.000
30	C	43	PRO	0	0.019	0.010	25.149	-0.006	-0.006	0.000	0.000	0.000	0.000
31	C	44	VAL	0	0.055	0.028	24.299	-0.004	-0.004	0.000	0.000	0.000	0.000
32	C	45	ASP	-1	-0.807	-0.892	27.358	0.001	0.001	0.000	0.000	0.000	0.000
33	C	46	ARG	1	0.875	0.940	29.961	-0.045	-0.045	0.000	0.000	0.000	0.000
34	C	47	PHE	0	-0.062	-0.043	30.534	0.005	0.005	0.000	0.000	0.000	0.000
35	C	48	PHE	0	0.005	0.023	28.692	-0.001	-0.001	0.000	0.000	0.000	0.000
36	C	49	THR	0	0.027	-0.017	29.135	-0.004	-0.004	0.000	0.000	0.000	0.000
37	C	50	PRO	0	0.000	0.002	31.629	-0.004	-0.004	0.000	0.000	0.000	0.000
38	C	51	ALA	0	-0.029	-0.003	34.404	-0.001	-0.001	0.000	0.000	0.000	0.000
39	C	52	VAL	0	-0.013	0.008	31.152	-0.001	-0.001	0.000	0.000	0.000	0.000
40	C	53	ARG	1	0.770	0.878	34.577	0.005	0.005	0.000	0.000	0.000	0.000
41	C	54	HIS	0	0.054	0.014	34.227	-0.003	-0.003	0.000	0.000	0.000	0.000
42	C	55	ASP	-1	-0.831	-0.880	38.120	-0.021	-0.021	0.000	0.000	0.000	0.000
43	C	56	ALA	0	0.012	0.004	39.630	-0.003	-0.003	0.000	0.000	0.000	0.000
44	C	57	ASP	-1	-0.899	-0.924	39.072	-0.030	-0.030	0.000	0.000	0.000	0.000
45	C	58	GLY	0	0.012	0.020	35.602	0.000	0.000	0.000	0.000	0.000	0.000
46	C	59	LEU	0	-0.023	-0.013	31.238	0.002	0.002	0.000	0.000	0.000	0.000
47	C	60	GLN	0	0.028	0.017	35.125	0.001	0.001	0.000	0.000	0.000	0.000
48	C	61	ALA	0	0.016	0.010	32.681	0.000	0.000	0.000	0.000	0.000	0.000
49	C	62	SER	0	-0.039	-0.012	34.030	0.002	0.002	0.000	0.000	0.000	0.000
50	C	63	PHE	0	0.040	0.005	27.108	0.003	0.003	0.000	0.000	0.000	0.000
51	C	64	ARG	1	0.893	0.939	28.765	-0.068	-0.068	0.000	0.000	0.000	0.000
52	C	65	GLY	0	0.048	0.034	33.478	0.001	0.001	0.000	0.000	0.000	0.000
53	C	66	ARG	1	0.854	0.917	34.342	-0.021	-0.021	0.000	0.000	0.000	0.000
54	C	67	GLY	0	0.046	0.019	35.266	0.000	0.000	0.000	0.000	0.000	0.000
55	C	68	LEU	0	-0.055	-0.029	30.460	0.001	0.001	0.000	0.000	0.000	0.000
56	C	69	ARG	1	0.811	0.847	33.818	0.020	0.020	0.000	0.000	0.000	0.000
57	C	70	GLY	0	0.018	-0.010	31.402	0.001	0.001	0.000	0.000	0.000	0.000
58	C	71	GLU	-1	-0.849	-0.916	30.226	-0.064	-0.064	0.000	0.000	0.000	0.000
59	C	72	GLU	-1	-0.741	-0.836	26.516	-0.067	-0.067	0.000	0.000	0.000	0.000
60	C	73	VAL	0	-0.010	-0.006	24.885	-0.004	-0.004	0.000	0.000	0.000	0.000
61	C	74	ALA	0	0.006	-0.003	24.752	-0.004	-0.004	0.000	0.000	0.000	0.000
62	C	75	VAL	0	-0.028	-0.014	19.412	-0.001	-0.001	0.000	0.000	0.000	0.000
63	C	76	PRO	0	0.001	0.006	20.225	0.007	0.007	0.000	0.000	0.000	0.000
64	C	77	PRO	0	0.035	0.014	22.652	-0.015	-0.015	0.000	0.000	0.000	0.000
65	C	78	GLY	0	0.009	0.000	22.857	-0.008	-0.008	0.000	0.000	0.000	0.000
66	C	79	PHE	0	-0.054	-0.019	16.095	-0.045	-0.045	0.000	0.000	0.000	0.000
67	C	80	ALA	0	0.002	-0.006	16.949	0.032	0.032	0.000	0.000	0.000	0.000
68	C	81	GLY	0	0.014	0.018	15.765	-0.040	-0.040	0.000	0.000	0.000	0.000
69	C	82	PHE	0	-0.014	-0.026	11.998	-0.001	-0.001	0.000	0.000	0.000	0.000
70	C	83	VAL	0	0.004	0.018	12.439	0.005	0.005	0.000	0.000	0.000	0.000
71	C	84	MET	0	-0.016	-0.022	6.449	-0.065	-0.065	0.000	0.000	0.000	0.000
72	C	85	VAL	0	0.016	0.015	8.000	0.090	0.090	0.000	0.000	0.000	0.000
73	C	86	THR	0	-0.018	-0.003	4.485	0.018	0.178	-0.001	-0.008	-0.151	0.000
74	C	120	ARG	1	0.988	1.000	2.226	-5.995	-4.690	3.076	-0.922	-3.459	0.005
75	C	121	LEU	0	-0.020	-0.017	2.500	-3.952	-1.520	2.286	-2.172	-2.546	-0.023
76	C	122	ILE	0	0.027	-0.008	2.377	-0.422	0.276	2.331	-0.388	-2.639	-0.006
77	C	123	GLY	0	0.032	0.025	4.074	-0.542	-0.497	0.004	-0.009	-0.040	0.000
78	C	124	ALA	0	-0.007	-0.007	7.658	0.082	0.082	0.000	0.000	0.000	0.000
79	C	125	THR	0	-0.040	-0.038	10.288	0.011	0.011	0.000	0.000	0.000	0.000
80	C	126	GLY	0	0.023	0.019	13.261	0.025	0.025	0.000	0.000	0.000	0.000
81	C	127	SER	0	-0.034	-0.033	14.657	-0.037	-0.037	0.000	0.000	0.000	0.000
82	C	128	PHE	0	-0.013	-0.004	15.377	0.027	0.027	0.000	0.000	0.000	0.000
83	C	129	SER	0	0.063	0.021	19.377	-0.026	-0.026	0.000	0.000	0.000	0.000
84	C	130	HIS	0	-0.054	-0.038	22.133	-0.005	-0.005	0.000	0.000	0.000	0.000
85	C	131	PHE	0	-0.029	-0.006	21.489	0.003	0.003	0.000	0.000	0.000	0.000
86	C	132	THR	0	-0.008	-0.009	23.622	0.000	0.000	0.000	0.000	0.000	0.000
87	C	133	LEU	0	-0.020	0.004	24.851	0.007	0.007	0.000	0.000	0.000	0.000
88	C	134	TRP	0	-0.013	-0.026	26.621	0.003	0.003	0.000	0.000	0.000	0.000
89	C	135	GLY	0	0.022	0.001	28.262	0.000	0.000	0.000	0.000	0.000	0.000
90	C	136	LEU	0	-0.030	-0.019	31.005	0.002	0.002	0.000	0.000	0.000	0.000
91	C	137	GLU	-1	-0.826	-0.898	33.477	0.008	0.008	0.000	0.000	0.000	0.000
92	C	138	THR	0	-0.043	-0.017	35.418	-0.002	-0.002	0.000	0.000	0.000	0.000
93	C	139	VAL	0	0.046	0.024	32.547	0.002	0.002	0.000	0.000	0.000	0.000
94	C	140	PRO	0	-0.045	-0.023	28.866	0.000	0.000	0.000	0.000	0.000	0.000
95	C	141	GLY	0	0.062	0.042	31.412	-0.005	-0.005	0.000	0.000	0.000	0.000
96	C	142	PRO	0	0.062	0.011	31.110	-0.002	-0.002	0.000	0.000	0.000	0.000
97	C	143	ASP	-1	-0.824	-0.891	30.323	-0.066	-0.066	0.000	0.000	0.000	0.000
98	C	144	ALA	0	-0.015	0.000	27.814	0.004	0.004	0.000	0.000	0.000	0.000
99	C	145	LYS	1	0.946	0.945	23.532	0.025	0.025	0.000	0.000	0.000	0.000
100	C	146	VAL	0	0.021	0.018	22.152	-0.011	-0.011	0.000	0.000	0.000	0.000
101	C	147	HIS	0	0.037	0.017	23.368	-0.025	-0.025	0.000	0.000	0.000	0.000
102	C	148	ARG	1	0.791	0.886	25.250	0.059	0.059	0.000	0.000	0.000	0.000
103	C	149	ALA	0	-0.035	-0.015	19.811	-0.013	-0.013	0.000	0.000	0.000	0.000
104	C	150	LEU	0	-0.006	-0.009	20.812	-0.028	-0.028	0.000	0.000	0.000	0.000
105	C	151	GLY	0	0.050	0.030	22.469	-0.012	-0.012	0.000	0.000	0.000	0.000
106	C	152	TRP	0	-0.014	-0.004	17.191	0.002	0.002	0.000	0.000	0.000	0.000
107	C	153	PRO	0	0.005	-0.005	18.601	-0.010	-0.010	0.000	0.000	0.000	0.000
108	C	154	SER	0	0.015	0.009	20.774	-0.010	-0.010	0.000	0.000	0.000	0.000
109	C	155	LEU	0	-0.023	0.001	23.951	0.007	0.007	0.000	0.000	0.000	0.000
110	C	156	ALA	0	-0.008	-0.012	19.568	-0.001	-0.001	0.000	0.000	0.000	0.000
111	C	157	ALA	0	0.001	-0.006	21.704	-0.015	-0.015	0.000	0.000	0.000	0.000
112	C	158	ALA	0	-0.010	0.003	22.916	0.003	0.003	0.000	0.000	0.000	0.000
113	C	159	ILE	0	-0.055	-0.030	22.606	0.007	0.007	0.000	0.000	0.000	0.000
114	C	160	HIS	0	-0.040	-0.019	18.913	-0.001	-0.001	0.000	0.000	0.000	0.000
115	C	161	ALA	0	-0.011	0.013	22.403	-0.022	-0.022	0.000	0.000	0.000	0.000
116	C	162	GLN	0	-0.026	-0.009	22.056	0.032	0.032	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:14:ILE)