FMO DATABASE

FMODB ID: R5NL8

Calculation Name: 4DUL-B-Xray318

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4DUL

Chain ID: B

ChEMBL ID:

UniProt ID: Q9C932

Base Structure: X-ray

Registration Date: 2021-09-07

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	128
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1084180.723657
FMO2-HF: Nuclear repulsion	1034202.612051
FMO2-HF: Total energy	-49978.111605
FMO2-MP2: Total energy	-50125.382862

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(B:6:ACE )

Summations of interaction energy for fragment #1(B:6: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.
2.019	2.991	-0.005	-0.447	-0.52	-0.001

Interaction energy analysis for fragmet #1(B:6:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / 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

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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	B	8	PRO	0	0.016	0.014	3.844	0.967	1.939	-0.005	-0.447	-0.520	-0.001
4	B	9	LEU	0	0.010	-0.001	6.662	0.409	0.409	0.000	0.000	0.000	0.000
5	B	10	THR	0	0.006	0.007	5.977	0.393	0.393	0.000	0.000	0.000	0.000
6	B	11	GLN	0	-0.022	-0.008	5.673	0.176	0.176	0.000	0.000	0.000	0.000
7	B	12	LEU	0	-0.034	-0.008	9.191	0.119	0.119	0.000	0.000	0.000	0.000
8	B	13	SER	0	-0.043	-0.022	11.945	0.062	0.062	0.000	0.000	0.000	0.000
9	B	14	LEU	0	-0.019	0.000	13.403	0.044	0.044	0.000	0.000	0.000	0.000
10	B	15	PRO	0	0.005	0.014	15.554	-0.006	-0.006	0.000	0.000	0.000	0.000
11	B	16	PRO	0	0.048	-0.005	18.233	-0.021	-0.021	0.000	0.000	0.000	0.000
12	B	17	GLY	0	-0.023	-0.004	19.300	0.021	0.021	0.000	0.000	0.000	0.000
13	B	18	PHE	0	-0.025	0.007	18.212	0.016	0.016	0.000	0.000	0.000	0.000
14	B	19	ARG	1	0.881	0.906	17.154	0.252	0.252	0.000	0.000	0.000	0.000
15	B	20	PHE	0	0.009	0.004	16.114	0.014	0.014	0.000	0.000	0.000	0.000
16	B	21	TYR	0	-0.039	-0.014	18.171	0.005	0.005	0.000	0.000	0.000	0.000
17	B	22	PRO	0	-0.001	0.019	19.943	0.020	0.020	0.000	0.000	0.000	0.000
18	B	23	THR	0	0.014	-0.021	22.588	0.008	0.008	0.000	0.000	0.000	0.000
19	B	24	ASP	-1	-0.879	-0.968	25.836	-0.113	-0.113	0.000	0.000	0.000	0.000
20	B	25	GLU	-1	-0.866	-0.942	27.663	-0.089	-0.089	0.000	0.000	0.000	0.000
21	B	26	GLU	-1	-0.817	-0.894	23.607	-0.137	-0.137	0.000	0.000	0.000	0.000
22	B	27	LEU	0	-0.046	-0.020	21.304	-0.002	-0.002	0.000	0.000	0.000	0.000
23	B	28	MET	0	-0.046	0.060	23.768	0.001	0.001	0.000	0.000	0.000	0.000
24	B	29	VAL	0	0.015	-0.004	26.147	0.004	0.004	0.000	0.000	0.000	0.000
25	B	30	GLN	0	0.011	0.003	22.228	0.005	0.005	0.000	0.000	0.000	0.000
26	B	31	TYR	0	-0.022	-0.010	16.748	-0.003	-0.003	0.000	0.000	0.000	0.000
27	B	32	LEU	0	0.000	0.001	21.385	0.008	0.008	0.000	0.000	0.000	0.000
28	B	33	CYS	0	-0.074	-0.029	23.765	0.011	0.011	0.000	0.000	0.000	0.000
29	B	34	ARG	1	0.905	0.974	19.696	0.087	0.087	0.000	0.000	0.000	0.000
30	B	35	LYN	0	0.069	0.087	19.778	0.007	0.007	0.000	0.000	0.000	0.000
31	B	36	ALA	0	-0.047	-0.009	22.049	0.011	0.011	0.000	0.000	0.000	0.000
32	B	37	ALA	0	-0.006	-0.011	24.054	0.001	0.001	0.000	0.000	0.000	0.000
33	B	38	GLY	0	0.007	-0.046	21.342	0.004	0.004	0.000	0.000	0.000	0.000
34	B	39	TYR	0	-0.133	-0.075	19.000	-0.016	-0.016	0.000	0.000	0.000	0.000
35	B	40	ASP	-1	-0.817	-0.895	15.913	0.031	0.031	0.000	0.000	0.000	0.000
36	B	41	PHE	0	-0.039	-0.023	14.713	-0.017	-0.017	0.000	0.000	0.000	0.000
37	B	42	SER	0	-0.070	-0.036	13.877	-0.007	-0.007	0.000	0.000	0.000	0.000
38	B	43	LEU	0	0.026	0.007	9.640	0.026	0.026	0.000	0.000	0.000	0.000
39	B	44	GLN	0	-0.002	0.011	9.855	-0.049	-0.049	0.000	0.000	0.000	0.000
40	B	45	LEU	0	0.029	0.003	10.422	-0.058	-0.058	0.000	0.000	0.000	0.000
41	B	46	ILE	0	-0.051	-0.017	11.330	-0.074	-0.074	0.000	0.000	0.000	0.000
42	B	47	ALA	0	0.058	0.029	11.495	0.042	0.042	0.000	0.000	0.000	0.000
43	B	48	GLU	-1	-0.915	-0.956	13.576	-0.046	-0.046	0.000	0.000	0.000	0.000
44	B	49	ILE	0	-0.032	-0.028	15.054	-0.001	-0.001	0.000	0.000	0.000	0.000
45	B	50	ASP	-1	-0.836	-0.907	17.732	-0.050	-0.050	0.000	0.000	0.000	0.000
46	B	51	LEU	0	0.003	-0.017	19.393	0.003	0.003	0.000	0.000	0.000	0.000
47	B	52	TYR	0	-0.050	-0.044	21.562	-0.002	-0.002	0.000	0.000	0.000	0.000
48	B	53	LYS	1	0.866	0.955	20.906	0.034	0.034	0.000	0.000	0.000	0.000
49	B	54	PHE	0	0.008	-0.006	17.675	0.000	0.000	0.000	0.000	0.000	0.000
50	B	55	ASP	-1	-0.752	-0.835	22.237	-0.070	-0.070	0.000	0.000	0.000	0.000
51	B	56	PRO	0	-0.039	-0.035	21.605	-0.014	-0.014	0.000	0.000	0.000	0.000
52	B	57	TRP	0	0.005	-0.007	20.404	-0.022	-0.022	0.000	0.000	0.000	0.000
53	B	58	VAL	0	0.015	0.012	17.236	-0.012	-0.012	0.000	0.000	0.000	0.000
54	B	59	LEU	0	-0.017	0.004	15.599	-0.025	-0.025	0.000	0.000	0.000	0.000
55	B	60	PRO	0	0.008	0.011	14.328	-0.037	-0.037	0.000	0.000	0.000	0.000
56	B	61	ASN	0	-0.011	-0.006	11.739	-0.099	-0.099	0.000	0.000	0.000	0.000
57	B	62	LYS	1	0.910	0.946	9.564	0.112	0.112	0.000	0.000	0.000	0.000
58	B	63	ALA	0	-0.018	0.017	11.293	0.034	0.034	0.000	0.000	0.000	0.000
59	B	64	LEU	0	-0.042	-0.007	7.483	-0.088	-0.088	0.000	0.000	0.000	0.000
60	B	65	PHE	0	0.030	0.013	7.322	-0.458	-0.458	0.000	0.000	0.000	0.000
61	B	66	GLY	0	0.034	0.018	9.870	0.187	0.187	0.000	0.000	0.000	0.000
62	B	67	GLU	-1	-0.910	-0.926	13.147	-0.397	-0.397	0.000	0.000	0.000	0.000
63	B	68	LYS	1	0.937	0.940	15.613	0.256	0.256	0.000	0.000	0.000	0.000
64	B	69	GLU	-1	-0.908	-0.949	17.622	-0.210	-0.210	0.000	0.000	0.000	0.000
65	B	70	TRP	0	-0.033	-0.024	13.646	0.012	0.012	0.000	0.000	0.000	0.000
66	B	71	TYR	0	0.038	0.025	15.744	0.063	0.063	0.000	0.000	0.000	0.000
67	B	72	PHE	0	-0.014	-0.013	13.981	-0.029	-0.029	0.000	0.000	0.000	0.000
68	B	73	PHE	0	0.076	0.034	16.960	0.017	0.017	0.000	0.000	0.000	0.000
69	B	74	SER	0	-0.031	-0.026	18.953	0.004	0.004	0.000	0.000	0.000	0.000
70	B	75	NME	0	0.035	0.029	21.713	0.007	0.007	0.000	0.000	0.000	0.000
71	B	86	ACE	0	0.027	0.004	36.041	0.001	0.001	0.000	0.000	0.000	0.000
72	B	87	ASN	0	-0.033	-0.040	34.019	-0.005	-0.005	0.000	0.000	0.000	0.000
73	B	88	ARG	1	0.924	1.002	26.133	0.059	0.059	0.000	0.000	0.000	0.000
74	B	89	VAL	0	0.097	0.057	28.558	-0.005	-0.005	0.000	0.000	0.000	0.000
75	B	90	ALA	0	-0.103	-0.059	26.097	-0.006	-0.006	0.000	0.000	0.000	0.000
76	B	91	GLY	0	-0.017	-0.011	25.165	0.007	0.007	0.000	0.000	0.000	0.000
77	B	92	SER	0	-0.044	-0.051	26.107	0.006	0.006	0.000	0.000	0.000	0.000
78	B	93	GLY	0	0.041	-0.007	28.714	0.003	0.003	0.000	0.000	0.000	0.000
79	B	94	TYR	0	-0.053	-0.013	30.058	0.002	0.002	0.000	0.000	0.000	0.000
80	B	95	TRP	0	0.017	0.003	24.053	-0.006	-0.006	0.000	0.000	0.000	0.000
81	B	96	LYS	1	0.941	0.964	30.450	0.062	0.062	0.000	0.000	0.000	0.000
82	B	97	ALA	0	0.041	0.024	32.798	-0.005	-0.005	0.000	0.000	0.000	0.000
83	B	98	THR	0	-0.073	-0.039	32.806	0.004	0.004	0.000	0.000	0.000	0.000
84	B	99	GLY	0	0.033	0.011	35.398	0.003	0.003	0.000	0.000	0.000	0.000
85	B	100	THR	0	-0.038	-0.029	36.736	0.005	0.005	0.000	0.000	0.000	0.000
86	B	101	ASP	-1	-0.823	-0.855	33.800	-0.075	-0.075	0.000	0.000	0.000	0.000
87	B	102	LYS	1	0.850	0.948	31.606	0.091	0.091	0.000	0.000	0.000	0.000
88	B	103	ILE	0	0.004	-0.013	34.356	-0.003	-0.003	0.000	0.000	0.000	0.000
89	B	104	ILE	0	0.025	0.017	30.459	-0.002	-0.002	0.000	0.000	0.000	0.000
90	B	105	SER	0	-0.044	-0.039	33.721	0.005	0.005	0.000	0.000	0.000	0.000
91	B	106	THR	0	0.007	0.001	31.510	-0.004	-0.004	0.000	0.000	0.000	0.000
92	B	107	GLU	-1	-0.843	-0.923	33.859	-0.048	-0.048	0.000	0.000	0.000	0.000
93	B	108	GLY	0	-0.029	-0.001	36.410	0.004	0.004	0.000	0.000	0.000	0.000
94	B	109	GLN	0	-0.057	-0.035	37.320	0.002	0.002	0.000	0.000	0.000	0.000
95	B	110	ARG	1	0.941	0.962	35.938	0.037	0.037	0.000	0.000	0.000	0.000
96	B	111	VAL	0	-0.001	-0.037	31.131	0.002	0.002	0.000	0.000	0.000	0.000
97	B	112	GLY	0	0.128	0.046	30.523	-0.002	-0.002	0.000	0.000	0.000	0.000
98	B	113	ILE	0	-0.036	-0.039	30.210	-0.003	-0.003	0.000	0.000	0.000	0.000
99	B	114	LYS	1	0.918	0.977	28.408	0.107	0.107	0.000	0.000	0.000	0.000
100	B	115	LYS	1	0.904	0.925	29.715	0.072	0.072	0.000	0.000	0.000	0.000
101	B	116	ALA	0	-0.016	0.003	29.489	-0.009	-0.009	0.000	0.000	0.000	0.000
102	B	117	LEU	0	-0.039	-0.018	28.657	0.009	0.009	0.000	0.000	0.000	0.000
103	B	118	VAL	0	0.018	0.009	29.533	-0.008	-0.008	0.000	0.000	0.000	0.000
104	B	119	PHE	0	0.053	0.023	27.648	0.003	0.003	0.000	0.000	0.000	0.000
105	B	120	NME	0	0.001	0.004	29.793	0.001	0.001	0.000	0.000	0.000	0.000
106	B	128	ACE	0	0.052	0.019	35.177	0.001	0.001	0.000	0.000	0.000	0.000
107	B	129	LYS	1	0.884	0.939	33.363	0.064	0.064	0.000	0.000	0.000	0.000
108	B	130	THR	0	-0.004	0.019	28.638	-0.004	-0.004	0.000	0.000	0.000	0.000
109	B	131	ASN	0	-0.018	-0.012	27.558	0.002	0.002	0.000	0.000	0.000	0.000
110	B	132	TRP	0	0.076	0.029	20.506	-0.011	-0.011	0.000	0.000	0.000	0.000
111	B	133	ILE	0	-0.001	0.003	25.681	0.012	0.012	0.000	0.000	0.000	0.000
112	B	134	MET	0	0.043	0.021	24.714	-0.016	-0.016	0.000	0.000	0.000	0.000
113	B	135	HIS	0	-0.105	-0.035	24.725	0.003	0.003	0.000	0.000	0.000	0.000
114	B	136	GLU	-1	-0.830	-0.933	24.785	-0.090	-0.090	0.000	0.000	0.000	0.000
115	B	137	TYR	0	-0.039	-0.027	24.987	0.003	0.003	0.000	0.000	0.000	0.000
116	B	138	NME	0	0.035	0.018	26.557	-0.001	-0.001	0.000	0.000	0.000	0.000
117	B	153	ACE	0	-0.037	-0.030	27.121	0.001	0.001	0.000	0.000	0.000	0.000
118	B	154	TRP	0	0.022	0.005	20.764	-0.003	-0.003	0.000	0.000	0.000	0.000
119	B	155	VAL	0	0.018	0.032	23.845	0.000	0.000	0.000	0.000	0.000	0.000
120	B	156	LEU	0	0.014	0.009	19.347	-0.010	-0.010	0.000	0.000	0.000	0.000
121	B	157	CYS	0	-0.036	-0.036	21.091	0.012	0.012	0.000	0.000	0.000	0.000
122	B	158	ARG	1	0.882	0.946	20.209	0.152	0.152	0.000	0.000	0.000	0.000
123	B	159	ILE	0	-0.028	-0.011	19.900	0.025	0.025	0.000	0.000	0.000	0.000
124	B	160	TYR	0	0.033	0.008	20.317	-0.021	-0.021	0.000	0.000	0.000	0.000
125	B	161	LYS	1	0.960	0.997	22.223	0.164	0.164	0.000	0.000	0.000	0.000
126	B	162	LYS	1	0.909	0.941	24.181	0.118	0.118	0.000	0.000	0.000	0.000
127	B	163	GLN	0	-0.036	-0.028	27.601	-0.002	-0.002	0.000	0.000	0.000	0.000
128	B	164	NME	0	0.023	0.035	27.817	-0.005	-0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:6:ACE )