FMO DATABASE

FMODB ID: R1388

Calculation Name: 3K5B-E-Xray312

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K5B

Chain ID: E

ChEMBL ID:

UniProt ID: P74901

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	187
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1332947.405239
FMO2-HF: Nuclear repulsion	1261822.009209
FMO2-HF: Total energy	-71125.39603
FMO2-MP2: Total energy	-71335.37234

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(E:2:ACE )

Summations of interaction energy for fragment #1(E:2:ACE )

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.
1.289	2.072	-0.005	-0.352	-0.426	0

Interaction energy analysis for fragmet #1(E:2:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.034 / q_NPA : 0.007

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].
3	E	4	LEU	0	0.069	0.025	3.855	1.023	1.768	-0.005	-0.348	-0.392
4	E	5	GLU	-1	-0.908	-0.949	7.122	-0.604	-0.604	0.000	0.000	0.000
5	E	6	ALA	0	0.017	-0.006	4.796	0.122	0.160	0.000	-0.004	-0.034
6	E	7	ILE	0	0.011	0.013	5.230	0.236	0.236	0.000	0.000	0.000
7	E	8	LEU	0	0.023	0.011	7.712	0.076	0.076	0.000	0.000	0.000
8	E	9	SER	0	-0.009	-0.023	9.779	0.044	0.044	0.000	0.000	0.000
9	E	10	GLN	0	-0.066	-0.027	8.359	0.128	0.128	0.000	0.000	0.000
10	E	11	GLU	-1	-0.934	-0.965	10.422	0.052	0.052	0.000	0.000	0.000
11	E	12	VAL	0	-0.028	-0.001	13.039	-0.003	-0.003	0.000	0.000	0.000
12	E	13	GLU	-1	-0.908	-0.949	13.699	0.136	0.136	0.000	0.000	0.000
13	E	14	ALA	0	0.016	-0.012	14.807	0.041	0.041	0.000	0.000	0.000
14	E	15	GLU	-1	-0.900	-0.938	16.840	0.017	0.017	0.000	0.000	0.000
15	E	16	ILE	0	-0.095	-0.051	18.104	-0.007	-0.007	0.000	0.000	0.000
16	E	17	GLN	0	0.020	0.002	18.116	0.014	0.014	0.000	0.000	0.000
17	E	18	ALA	0	0.023	0.023	20.990	-0.004	-0.004	0.000	0.000	0.000
18	E	19	LEU	0	0.010	-0.002	22.830	-0.006	-0.006	0.000	0.000	0.000
19	E	20	LEU	0	-0.029	-0.017	22.920	-0.004	-0.004	0.000	0.000	0.000
20	E	21	GLN	0	-0.038	-0.009	22.572	0.013	0.013	0.000	0.000	0.000
21	E	22	GLU	-1	-0.949	-0.977	26.479	0.028	0.028	0.000	0.000	0.000
22	E	23	ALA	0	-0.096	-0.065	28.573	-0.005	-0.005	0.000	0.000	0.000
23	E	24	GLU	-1	-0.906	-0.948	29.697	0.045	0.045	0.000	0.000	0.000
24	E	25	ALA	0	0.002	0.007	30.723	0.001	0.001	0.000	0.000	0.000
25	E	26	LYS	1	0.886	0.940	31.355	-0.034	-0.034	0.000	0.000	0.000
26	E	27	ALA	0	0.022	0.018	34.287	-0.003	-0.003	0.000	0.000	0.000
27	E	28	GLU	-1	-0.941	-0.946	34.603	0.045	0.045	0.000	0.000	0.000
28	E	29	ALA	0	0.028	0.006	36.988	-0.003	-0.003	0.000	0.000	0.000
29	E	30	VAL	0	0.012	-0.005	38.827	-0.002	-0.002	0.000	0.000	0.000
30	E	31	LYS	1	0.839	0.913	40.013	-0.037	-0.037	0.000	0.000	0.000
31	E	32	ARG	1	0.871	0.937	39.883	-0.038	-0.038	0.000	0.000	0.000
32	E	33	GLU	-1	-0.915	-0.940	42.876	0.020	0.020	0.000	0.000	0.000
33	E	34	ALA	0	0.046	0.018	44.523	-0.002	-0.002	0.000	0.000	0.000
34	E	35	GLU	-1	-0.851	-0.920	44.683	0.031	0.031	0.000	0.000	0.000
35	E	36	GLU	-1	-0.945	-1.003	45.037	0.028	0.028	0.000	0.000	0.000
36	E	37	LYS	1	0.921	0.994	48.695	-0.018	-0.018	0.000	0.000	0.000
37	E	38	ALA	0	0.021	-0.007	50.300	-0.001	-0.001	0.000	0.000	0.000
38	E	39	LYS	1	1.010	1.008	51.503	-0.024	-0.024	0.000	0.000	0.000
39	E	40	ALA	0	0.017	0.001	53.166	-0.001	-0.001	0.000	0.000	0.000
40	E	41	LEU	0	-0.101	-0.046	54.573	-0.001	-0.001	0.000	0.000	0.000
41	E	42	LEU	0	-0.005	-0.005	56.293	-0.001	-0.001	0.000	0.000	0.000
42	E	43	GLN	0	0.048	0.036	56.758	-0.001	-0.001	0.000	0.000	0.000
43	E	44	ALA	0	-0.006	-0.003	59.107	-0.001	-0.001	0.000	0.000	0.000
44	E	45	ARG	1	0.948	0.973	60.795	-0.014	-0.014	0.000	0.000	0.000
45	E	46	GLU	-1	-0.878	-0.947	59.500	0.017	0.017	0.000	0.000	0.000
46	E	47	ARG	1	0.901	0.935	60.002	-0.016	-0.016	0.000	0.000	0.000
47	E	48	ALA	0	-0.031	-0.006	65.302	-0.001	-0.001	0.000	0.000	0.000
48	E	49	LEU	0	0.019	0.003	66.003	-0.001	-0.001	0.000	0.000	0.000
49	E	50	GLU	-1	-0.828	-0.903	67.928	0.013	0.013	0.000	0.000	0.000
50	E	51	ALA	0	0.011	0.016	70.109	0.000	0.000	0.000	0.000	0.000
51	E	52	GLN	0	-0.034	-0.038	69.432	0.000	0.000	0.000	0.000	0.000
52	E	53	TYR	0	0.022	0.021	72.783	0.000	0.000	0.000	0.000	0.000
53	E	54	ARG	1	0.846	0.917	71.945	-0.012	-0.012	0.000	0.000	0.000
54	E	55	ALA	0	-0.038	-0.018	75.838	0.000	0.000	0.000	0.000	0.000
55	E	56	ALA	0	-0.001	-0.006	77.221	0.000	0.000	0.000	0.000	0.000
56	E	57	LEU	0	0.052	0.015	77.988	0.000	0.000	0.000	0.000	0.000
57	E	58	ARG	1	1.025	1.028	79.430	-0.009	-0.009	0.000	0.000	0.000
58	E	59	ARG	1	0.887	0.953	81.883	-0.008	-0.008	0.000	0.000	0.000
59	E	60	ALA	0	0.006	-0.013	83.015	0.000	0.000	0.000	0.000	0.000
60	E	61	GLU	-1	-0.901	-0.931	82.470	0.009	0.009	0.000	0.000	0.000
61	E	62	SER	0	0.013	0.004	86.179	0.000	0.000	0.000	0.000	0.000
62	E	63	ALA	0	-0.037	-0.005	87.685	0.000	0.000	0.000	0.000	0.000
63	E	64	GLY	0	0.046	0.018	88.676	0.000	0.000	0.000	0.000	0.000
64	E	65	GLU	-1	-0.900	-0.963	89.633	0.008	0.008	0.000	0.000	0.000
65	E	66	LEU	0	-0.088	-0.053	92.039	0.000	0.000	0.000	0.000	0.000
66	E	67	LEU	0	-0.058	-0.034	92.126	0.000	0.000	0.000	0.000	0.000
67	E	68	VAL	0	0.028	0.035	94.215	0.000	0.000	0.000	0.000	0.000
68	E	69	ALA	0	-0.004	-0.007	96.550	0.000	0.000	0.000	0.000	0.000
69	E	70	THR	0	-0.006	0.008	97.717	0.000	0.000	0.000	0.000	0.000
70	E	71	ALA	0	0.090	0.053	99.253	0.000	0.000	0.000	0.000	0.000
71	E	72	ARG	1	0.929	0.962	100.030	-0.007	-0.007	0.000	0.000	0.000
72	E	73	THR	0	-0.070	-0.047	102.042	0.000	0.000	0.000	0.000	0.000
73	E	74	GLN	0	-0.045	-0.021	103.870	0.000	0.000	0.000	0.000	0.000
74	E	75	ALA	0	0.051	0.037	105.243	0.000	0.000	0.000	0.000	0.000
75	E	76	ARG	1	0.901	0.938	104.529	-0.006	-0.006	0.000	0.000	0.000
76	E	77	GLY	0	-0.002	-0.007	108.142	0.000	0.000	0.000	0.000	0.000
77	E	78	GLU	-1	-0.837	-0.922	108.311	0.005	0.005	0.000	0.000	0.000
78	E	79	VAL	0	0.003	0.013	111.457	0.000	0.000	0.000	0.000	0.000
79	E	80	LEU	0	-0.026	-0.015	111.992	0.000	0.000	0.000	0.000	0.000
80	E	81	GLU	-1	-0.955	-0.988	113.627	0.004	0.004	0.000	0.000	0.000
81	E	82	GLU	-1	-0.852	-0.930	115.879	0.004	0.004	0.000	0.000	0.000
82	E	83	VAL	0	-0.033	-0.022	117.430	0.000	0.000	0.000	0.000	0.000
83	E	84	ARG	1	0.878	0.947	118.759	-0.004	-0.004	0.000	0.000	0.000
84	E	85	ARG	1	0.902	0.961	119.910	-0.004	-0.004	0.000	0.000	0.000
85	E	86	ARG	1	0.923	0.963	121.263	-0.005	-0.005	0.000	0.000	0.000
86	E	87	VAL	0	0.020	0.016	123.086	0.000	0.000	0.000	0.000	0.000
87	E	88	ARG	1	0.989	0.970	121.269	-0.004	-0.004	0.000	0.000	0.000
88	E	89	GLU	-1	-0.977	-0.973	126.174	0.004	0.004	0.000	0.000	0.000
89	E	90	ALA	0	-0.030	-0.012	128.007	0.000	0.000	0.000	0.000	0.000
90	E	91	LEU	0	-0.024	-0.029	129.004	0.000	0.000	0.000	0.000	0.000
91	E	92	GLU	-1	-0.857	-0.925	129.894	0.003	0.003	0.000	0.000	0.000
92	E	93	ALA	0	-0.008	0.003	132.013	0.000	0.000	0.000	0.000	0.000
93	E	94	LEU	0	-0.080	-0.043	133.765	0.000	0.000	0.000	0.000	0.000
94	E	95	PRO	0	0.041	-0.005	135.824	0.000	0.000	0.000	0.000	0.000
95	E	96	GLN	0	-0.038	-0.005	137.450	0.000	0.000	0.000	0.000	0.000
96	E	97	LYS	1	0.914	0.962	135.402	-0.003	-0.003	0.000	0.000	0.000
97	E	98	PRO	0	0.038	0.028	140.627	0.000	0.000	0.000	0.000	0.000
98	E	99	GLU	-1	-0.899	-0.951	139.011	0.003	0.003	0.000	0.000	0.000
99	E	100	TRP	0	0.009	0.010	137.648	0.000	0.000	0.000	0.000	0.000
100	E	101	PRO	0	0.002	-0.010	141.011	0.000	0.000	0.000	0.000	0.000
101	E	102	GLU	-1	-0.942	-0.988	142.665	0.003	0.003	0.000	0.000	0.000
102	E	103	VAL	0	-0.036	-0.005	137.007	0.000	0.000	0.000	0.000	0.000
103	E	104	VAL	0	0.020	0.010	140.041	0.000	0.000	0.000	0.000	0.000
104	E	105	ARG	1	0.924	0.969	141.359	-0.003	-0.003	0.000	0.000	0.000
105	E	106	LYS	1	0.878	0.947	138.946	-0.003	-0.003	0.000	0.000	0.000
106	E	107	LEU	0	-0.032	-0.018	135.294	0.000	0.000	0.000	0.000	0.000
107	E	108	ALA	0	0.019	0.001	139.215	0.000	0.000	0.000	0.000	0.000
108	E	109	LEU	0	-0.021	-0.009	142.025	0.000	0.000	0.000	0.000	0.000
109	E	110	GLU	-1	-0.831	-0.914	136.143	0.003	0.003	0.000	0.000	0.000
110	E	111	ALA	0	-0.048	-0.024	139.441	0.000	0.000	0.000	0.000	0.000
111	E	112	LEU	0	-0.063	-0.032	140.415	0.000	0.000	0.000	0.000	0.000
112	E	113	GLU	-1	-0.979	-0.971	141.131	0.003	0.003	0.000	0.000	0.000
113	E	114	ALA	0	-0.053	-0.017	137.573	0.000	0.000	0.000	0.000	0.000
114	E	115	LEU	0	-0.044	-0.035	135.161	0.000	0.000	0.000	0.000	0.000
115	E	116	PRO	0	-0.041	-0.021	138.619	0.000	0.000	0.000	0.000	0.000
116	E	117	GLY	0	0.054	0.051	141.727	0.000	0.000	0.000	0.000	0.000
117	E	118	ALA	0	0.016	-0.002	145.198	0.000	0.000	0.000	0.000	0.000
118	E	119	LYS	1	0.912	0.956	147.088	-0.002	-0.002	0.000	0.000	0.000
119	E	120	ALA	0	-0.048	-0.016	146.570	0.000	0.000	0.000	0.000	0.000
120	E	121	LEU	0	-0.021	0.013	142.064	0.000	0.000	0.000	0.000	0.000
121	E	122	VAL	0	-0.011	0.001	141.617	0.000	0.000	0.000	0.000	0.000
122	E	123	ALA	0	0.064	0.014	141.289	0.000	0.000	0.000	0.000	0.000
123	E	124	ASN	0	0.039	0.031	138.898	0.000	0.000	0.000	0.000	0.000
124	E	125	PRO	0	0.051	0.011	142.388	0.000	0.000	0.000	0.000	0.000
125	E	126	GLU	-1	-0.934	-0.983	143.373	0.003	0.003	0.000	0.000	0.000
126	E	127	ASP	-1	-0.874	-0.952	141.454	0.003	0.003	0.000	0.000	0.000
127	E	128	LEU	0	-0.040	-0.005	144.656	0.000	0.000	0.000	0.000	0.000
128	E	129	PRO	0	-0.018	-0.002	147.821	0.000	0.000	0.000	0.000	0.000
129	E	130	HIS	0	-0.067	-0.020	145.364	0.000	0.000	0.000	0.000	0.000
130	E	131	LEU	0	-0.026	-0.011	144.373	0.000	0.000	0.000	0.000	0.000
131	E	132	GLU	-1	-0.731	-0.862	148.362	0.002	0.002	0.000	0.000	0.000
132	E	133	ALA	0	-0.058	-0.032	150.522	0.000	0.000	0.000	0.000	0.000
133	E	134	MET	0	0.042	0.003	149.289	0.000	0.000	0.000	0.000	0.000
134	E	135	ALA	0	-0.030	0.014	151.224	0.000	0.000	0.000	0.000	0.000
135	E	136	ARG	1	0.836	0.884	152.447	-0.002	-0.002	0.000	0.000	0.000
136	E	137	GLU	-1	-0.898	-0.923	153.159	0.002	0.002	0.000	0.000	0.000
137	E	138	ARG	1	0.798	0.887	153.558	-0.002	-0.002	0.000	0.000	0.000
138	E	139	GLY	0	0.045	0.036	150.633	0.000	0.000	0.000	0.000	0.000
139	E	140	VAL	0	-0.079	-0.043	150.528	0.000	0.000	0.000	0.000	0.000
140	E	141	GLU	-1	-0.780	-0.900	145.508	0.003	0.003	0.000	0.000	0.000
141	E	142	LEU	0	-0.065	-0.043	145.528	0.000	0.000	0.000	0.000	0.000
142	E	143	GLN	0	0.030	0.010	147.274	0.000	0.000	0.000	0.000	0.000
143	E	144	ALA	0	-0.029	-0.022	145.985	0.000	0.000	0.000	0.000	0.000
144	E	145	GLU	-1	-0.890	-0.956	139.949	0.003	0.003	0.000	0.000	0.000
145	E	146	PRO	0	-0.058	-0.025	139.416	0.000	0.000	0.000	0.000	0.000
146	E	147	ALA	0	-0.007	0.003	136.377	0.000	0.000	0.000	0.000	0.000
147	E	148	LEU	0	-0.007	-0.002	136.100	0.000	0.000	0.000	0.000	0.000
148	E	149	ARG	1	0.833	0.920	130.983	-0.003	-0.003	0.000	0.000	0.000
149	E	150	LEU	0	0.004	0.000	132.714	0.000	0.000	0.000	0.000	0.000
150	E	151	GLY	0	-0.006	-0.013	135.046	0.000	0.000	0.000	0.000	0.000
151	E	152	VAL	0	0.022	0.029	136.753	0.000	0.000	0.000	0.000	0.000
152	E	153	ARG	1	0.833	0.914	136.562	-0.003	-0.003	0.000	0.000	0.000
153	E	154	ALA	0	0.061	0.021	139.209	0.000	0.000	0.000	0.000	0.000
154	E	155	VAL	0	-0.080	-0.041	140.640	0.000	0.000	0.000	0.000	0.000
155	E	156	GLY	0	0.058	0.018	142.286	0.000	0.000	0.000	0.000	0.000
156	E	157	ALA	0	0.002	-0.002	143.672	0.000	0.000	0.000	0.000	0.000
157	E	158	GLU	-1	-0.873	-0.937	145.486	0.002	0.002	0.000	0.000	0.000
158	E	159	GLY	0	-0.029	-0.004	143.010	0.000	0.000	0.000	0.000	0.000
159	E	160	LYS	1	0.928	0.931	139.522	-0.002	-0.002	0.000	0.000	0.000
160	E	161	THR	0	-0.003	0.026	138.736	0.000	0.000	0.000	0.000	0.000
161	E	162	GLN	0	-0.049	-0.039	135.920	0.000	0.000	0.000	0.000	0.000
162	E	163	VAL	0	0.046	0.039	135.923	0.000	0.000	0.000	0.000	0.000
163	E	164	GLU	-1	-0.858	-0.918	133.552	0.003	0.003	0.000	0.000	0.000
164	E	165	ASN	0	-0.021	-0.012	134.006	0.000	0.000	0.000	0.000	0.000
165	E	166	SER	0	0.078	0.019	132.159	0.000	0.000	0.000	0.000	0.000
166	E	167	LEU	0	0.049	0.023	131.748	0.000	0.000	0.000	0.000	0.000
167	E	168	LEU	0	0.028	0.018	128.257	0.000	0.000	0.000	0.000	0.000
168	E	169	ALA	0	0.057	0.027	127.231	0.000	0.000	0.000	0.000	0.000
169	E	170	ARG	1	0.899	0.945	127.150	-0.003	-0.003	0.000	0.000	0.000
170	E	171	MET	0	-0.033	0.014	124.474	0.000	0.000	0.000	0.000	0.000
171	E	172	ASP	-1	-0.855	-0.943	122.811	0.004	0.004	0.000	0.000	0.000
172	E	173	ARG	1	0.847	0.935	122.204	-0.003	-0.003	0.000	0.000	0.000
173	E	174	ALA	0	0.023	-0.012	122.628	0.000	0.000	0.000	0.000	0.000
174	E	175	TRP	0	-0.030	-0.019	116.330	0.000	0.000	0.000	0.000	0.000
175	E	176	ASP	-1	-0.919	-0.952	116.238	0.004	0.004	0.000	0.000	0.000
176	E	177	ALA	0	-0.028	0.008	117.802	0.000	0.000	0.000	0.000	0.000
177	E	178	MET	0	-0.032	-0.028	118.855	0.000	0.000	0.000	0.000	0.000
178	E	179	SER	0	0.041	0.025	114.397	0.000	0.000	0.000	0.000	0.000
179	E	180	SER	0	0.017	0.006	113.412	0.000	0.000	0.000	0.000	0.000
180	E	181	LYS	1	0.944	0.972	114.380	-0.005	-0.005	0.000	0.000	0.000
181	E	182	VAL	0	0.050	0.028	116.205	0.000	0.000	0.000	0.000	0.000
182	E	183	ALA	0	0.038	0.008	111.800	0.000	0.000	0.000	0.000	0.000
183	E	184	GLN	0	-0.065	-0.046	113.129	0.000	0.000	0.000	0.000	0.000
184	E	185	ALA	0	-0.023	-0.008	114.153	0.000	0.000	0.000	0.000	0.000
185	E	186	LEU	0	-0.065	-0.016	113.724	0.000	0.000	0.000	0.000	0.000
186	E	187	TRP	0	-0.091	-0.051	109.354	0.000	0.000	0.000	0.000	0.000
187	E	188	GLY	-1	-0.923	-0.944	110.130	0.006	0.006	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:2:ACE )