FMO DATABASE

FMODB ID: LZK69

Calculation Name: 3DRX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DRX

Chain ID: A

ChEMBL ID:

UniProt ID: Q9NXV2

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	164
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1407798.288447
FMO2-HF: Nuclear repulsion	1340919.797533
FMO2-HF: Total energy	-66878.490914
FMO2-MP2: Total energy	-67072.988171

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:34:ALA)

Summations of interaction energy for fragment #1(A:34:ALA)

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.
-4.363	-0.337	2.932	-2.203	-4.756	-0.007

Interaction energy analysis for fragmet #1(A:34:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : -0.022

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	36	ALA	0	-0.025	-0.010	3.819	-1.001	0.288	-0.011	-0.524	-0.754	0.002
4	A	37	GLN	0	-0.012	-0.013	2.290	-0.506	0.371	2.506	-1.089	-2.294	-0.008
5	A	38	ARG	0	0.067	0.037	4.377	-0.934	-0.937	-0.001	-0.023	0.027	0.000
6	A	39	PRO	0	0.000	-0.010	4.389	-0.978	-0.857	-0.001	-0.010	-0.110	0.000
7	A	40	GLY	0	-0.019	0.009	4.590	0.301	0.367	-0.001	-0.003	-0.062	0.000
8	A	41	SER	0	0.027	0.019	3.467	0.299	0.467	0.007	-0.038	-0.137	0.000
9	A	42	VAL	0	-0.017	-0.008	5.137	-0.090	0.002	-0.001	-0.003	-0.088	0.000
10	A	43	SER	0	0.025	-0.013	2.661	-0.936	-0.163	0.409	-0.396	-0.787	-0.001
11	A	44	LYS	1	0.912	0.968	4.638	0.264	0.400	-0.001	-0.010	-0.125	0.000
12	A	45	TRP	0	0.037	0.019	3.280	-0.953	-0.446	0.026	-0.107	-0.426	0.000
13	A	46	VAL	0	0.003	-0.006	8.142	-0.010	-0.010	0.000	0.000	0.000	0.000
14	A	47	ARG	1	0.870	0.931	11.814	-0.283	-0.283	0.000	0.000	0.000	0.000
15	A	48	LEU	0	0.003	-0.002	14.548	-0.022	-0.022	0.000	0.000	0.000	0.000
16	A	49	ASN	0	0.009	-0.006	17.609	0.004	0.004	0.000	0.000	0.000	0.000
17	A	50	VAL	0	0.007	0.006	20.236	-0.010	-0.010	0.000	0.000	0.000	0.000
18	A	51	GLY	0	0.069	0.030	22.860	0.002	0.002	0.000	0.000	0.000	0.000
19	A	52	GLY	0	-0.011	-0.002	24.647	0.000	0.000	0.000	0.000	0.000	0.000
20	A	53	THR	0	-0.037	-0.019	20.741	0.005	0.005	0.000	0.000	0.000	0.000
21	A	54	TYR	0	-0.083	-0.058	17.125	0.004	0.004	0.000	0.000	0.000	0.000
22	A	55	PHE	0	-0.016	-0.004	15.887	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	56	LEU	0	-0.033	-0.002	8.474	0.001	0.001	0.000	0.000	0.000	0.000
24	A	57	THR	0	0.018	-0.012	9.922	-0.068	-0.068	0.000	0.000	0.000	0.000
25	A	58	THR	0	-0.009	0.004	5.506	0.041	0.041	0.000	0.000	0.000	0.000
26	A	59	ARG	1	0.912	0.937	8.830	-0.079	-0.079	0.000	0.000	0.000	0.000
27	A	60	GLN	0	-0.005	0.009	6.512	-0.022	-0.022	0.000	0.000	0.000	0.000
28	A	61	THR	0	0.015	-0.008	9.644	0.007	0.007	0.000	0.000	0.000	0.000
29	A	62	LEU	0	-0.042	-0.006	11.713	0.018	0.018	0.000	0.000	0.000	0.000
30	A	63	CYS	0	-0.032	0.004	14.265	0.011	0.011	0.000	0.000	0.000	0.000
31	A	64	ARG	1	0.853	0.945	15.234	0.213	0.213	0.000	0.000	0.000	0.000
32	A	65	ASP	-1	-0.797	-0.899	16.563	-0.099	-0.099	0.000	0.000	0.000	0.000
33	A	66	PRO	0	0.003	-0.008	20.131	0.011	0.011	0.000	0.000	0.000	0.000
34	A	67	LYS	1	0.814	0.892	21.835	0.103	0.103	0.000	0.000	0.000	0.000
35	A	68	SER	0	-0.023	-0.013	20.904	0.010	0.010	0.000	0.000	0.000	0.000
36	A	69	PHE	0	0.071	0.018	22.865	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	70	LEU	0	0.011	-0.011	18.232	0.007	0.007	0.000	0.000	0.000	0.000
38	A	71	TYR	0	-0.010	0.012	18.230	0.002	0.002	0.000	0.000	0.000	0.000
39	A	72	ARG	1	0.818	0.916	19.051	-0.010	-0.010	0.000	0.000	0.000	0.000
40	A	73	LEU	0	-0.002	0.010	15.936	0.005	0.005	0.000	0.000	0.000	0.000
41	A	75	GLN	0	-0.041	-0.032	13.974	-0.019	-0.019	0.000	0.000	0.000	0.000
42	A	76	ALA	0	-0.071	-0.064	13.854	0.022	0.022	0.000	0.000	0.000	0.000
43	A	77	ASP	-1	-0.765	-0.876	15.740	-0.016	-0.016	0.000	0.000	0.000	0.000
44	A	78	PRO	0	-0.063	-0.013	19.510	0.007	0.007	0.000	0.000	0.000	0.000
45	A	79	ASP	-1	-0.862	-0.942	22.133	0.017	0.017	0.000	0.000	0.000	0.000
46	A	80	LEU	0	-0.080	-0.039	22.427	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	81	ASP	-1	-0.818	-0.898	24.472	0.008	0.008	0.000	0.000	0.000	0.000
48	A	82	SER	0	-0.096	-0.065	22.185	0.003	0.003	0.000	0.000	0.000	0.000
49	A	83	ASP	-1	-0.889	-0.936	23.121	0.064	0.064	0.000	0.000	0.000	0.000
50	A	84	LYS	1	0.839	0.920	17.265	-0.134	-0.134	0.000	0.000	0.000	0.000
51	A	85	ASP	-1	-0.661	-0.770	21.038	0.160	0.160	0.000	0.000	0.000	0.000
52	A	86	GLU	-1	-0.920	-0.953	22.037	0.168	0.168	0.000	0.000	0.000	0.000
53	A	87	THR	0	-0.042	-0.047	18.890	0.031	0.031	0.000	0.000	0.000	0.000
54	A	88	GLY	0	-0.042	-0.035	17.604	0.038	0.038	0.000	0.000	0.000	0.000
55	A	89	ALA	0	-0.075	-0.034	17.393	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	90	TYR	0	0.038	0.014	15.652	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	91	LEU	0	0.019	0.019	20.041	0.006	0.006	0.000	0.000	0.000	0.000
58	A	92	ILE	0	-0.037	-0.027	20.604	-0.012	-0.012	0.000	0.000	0.000	0.000
59	A	93	ASP	-1	-0.912	-0.940	24.478	0.040	0.040	0.000	0.000	0.000	0.000
60	A	94	ARG	1	0.785	0.859	25.549	-0.010	-0.010	0.000	0.000	0.000	0.000
61	A	95	ASP	-1	-0.789	-0.875	26.788	0.034	0.034	0.000	0.000	0.000	0.000
62	A	96	PRO	0	0.016	0.008	23.138	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	97	THR	0	-0.060	-0.062	23.098	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	98	TYR	0	0.016	0.011	24.785	-0.009	-0.009	0.000	0.000	0.000	0.000
65	A	99	PHE	0	0.014	0.013	17.762	-0.012	-0.012	0.000	0.000	0.000	0.000
66	A	100	GLY	0	0.011	0.019	19.278	-0.010	-0.010	0.000	0.000	0.000	0.000
67	A	101	PRO	0	-0.019	-0.024	19.058	-0.015	-0.015	0.000	0.000	0.000	0.000
68	A	102	VAL	0	0.015	0.017	20.376	-0.018	-0.018	0.000	0.000	0.000	0.000
69	A	103	LEU	0	-0.011	-0.006	13.967	-0.018	-0.018	0.000	0.000	0.000	0.000
70	A	104	ASN	0	0.001	-0.021	15.594	-0.028	-0.028	0.000	0.000	0.000	0.000
71	A	105	TYR	0	0.009	0.029	16.310	-0.032	-0.032	0.000	0.000	0.000	0.000
72	A	106	LEU	0	0.007	0.002	15.200	-0.027	-0.027	0.000	0.000	0.000	0.000
73	A	107	ARG	1	0.867	0.938	11.443	-0.016	-0.016	0.000	0.000	0.000	0.000
74	A	108	HIS	0	-0.008	-0.015	12.806	-0.060	-0.060	0.000	0.000	0.000	0.000
75	A	109	GLY	0	-0.059	-0.015	15.272	-0.011	-0.011	0.000	0.000	0.000	0.000
76	A	110	LYS	1	0.912	0.954	18.629	0.203	0.203	0.000	0.000	0.000	0.000
77	A	111	LEU	0	0.020	0.013	20.357	0.001	0.001	0.000	0.000	0.000	0.000
78	A	112	VAL	0	-0.029	-0.027	21.122	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	113	ILE	0	0.004	-0.004	23.183	0.003	0.003	0.000	0.000	0.000	0.000
80	A	114	ASN	0	-0.005	0.014	24.431	-0.009	-0.009	0.000	0.000	0.000	0.000
81	A	115	LYS	1	0.991	0.973	27.007	0.024	0.024	0.000	0.000	0.000	0.000
82	A	116	ASP	-1	-0.944	-0.955	29.419	0.001	0.001	0.000	0.000	0.000	0.000
83	A	117	LEU	0	-0.005	-0.003	26.258	0.002	0.002	0.000	0.000	0.000	0.000
84	A	118	ALA	0	0.056	0.037	30.373	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	119	GLU	-1	-0.802	-0.904	30.162	-0.029	-0.029	0.000	0.000	0.000	0.000
86	A	120	GLU	-1	-0.808	-0.896	30.868	-0.021	-0.021	0.000	0.000	0.000	0.000
87	A	121	GLY	0	0.025	0.016	30.574	0.000	0.000	0.000	0.000	0.000	0.000
88	A	122	VAL	0	-0.022	-0.026	25.273	0.000	0.000	0.000	0.000	0.000	0.000
89	A	123	LEU	0	-0.058	-0.025	27.397	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	124	GLU	-1	-0.825	-0.915	29.428	-0.010	-0.010	0.000	0.000	0.000	0.000
91	A	125	GLU	-1	-0.762	-0.849	25.248	0.003	0.003	0.000	0.000	0.000	0.000
92	A	126	ALA	0	-0.061	-0.030	25.231	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	127	GLU	-1	-0.846	-0.933	26.310	-0.037	-0.037	0.000	0.000	0.000	0.000
94	A	128	PHE	0	0.015	0.028	25.546	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	129	TYR	0	-0.030	-0.037	22.584	0.000	0.000	0.000	0.000	0.000	0.000
96	A	130	ASN	0	0.014	0.026	24.339	-0.008	-0.008	0.000	0.000	0.000	0.000
97	A	131	ILE	0	0.015	0.015	20.459	-0.009	-0.009	0.000	0.000	0.000	0.000
98	A	132	THR	0	0.064	0.032	24.377	-0.005	-0.005	0.000	0.000	0.000	0.000
99	A	133	SER	0	-0.013	-0.015	23.417	0.000	0.000	0.000	0.000	0.000	0.000
100	A	134	LEU	0	-0.025	-0.015	22.122	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	135	ILE	0	0.038	0.025	25.272	0.004	0.004	0.000	0.000	0.000	0.000
102	A	136	LYS	1	0.844	0.919	28.487	0.073	0.073	0.000	0.000	0.000	0.000
103	A	137	LEU	0	-0.004	-0.008	24.416	0.003	0.003	0.000	0.000	0.000	0.000
104	A	138	VAL	0	0.015	0.006	27.178	0.002	0.002	0.000	0.000	0.000	0.000
105	A	139	LYS	1	0.917	0.956	29.607	0.040	0.040	0.000	0.000	0.000	0.000
106	A	140	ASP	-1	-0.842	-0.891	31.442	-0.057	-0.057	0.000	0.000	0.000	0.000
107	A	141	LYS	1	0.907	0.964	29.054	0.043	0.043	0.000	0.000	0.000	0.000
108	A	142	ILE	0	0.018	0.005	32.227	0.002	0.002	0.000	0.000	0.000	0.000
109	A	143	ARG	1	0.888	0.923	34.827	0.047	0.047	0.000	0.000	0.000	0.000
110	A	144	GLU	-1	-0.931	-0.951	34.252	-0.043	-0.043	0.000	0.000	0.000	0.000
111	A	145	ARG	1	0.754	0.836	35.012	0.025	0.025	0.000	0.000	0.000	0.000
112	A	146	ASP	-1	-0.816	-0.881	37.386	-0.022	-0.022	0.000	0.000	0.000	0.000
113	A	147	SER	0	-0.107	-0.046	40.008	0.002	0.002	0.000	0.000	0.000	0.000
114	A	148	LYS	1	0.833	0.901	36.892	0.039	0.039	0.000	0.000	0.000	0.000
115	A	149	THR	0	-0.047	-0.023	40.380	0.002	0.002	0.000	0.000	0.000	0.000
116	A	150	SER	0	-0.010	-0.009	42.988	0.002	0.002	0.000	0.000	0.000	0.000
117	A	151	GLN	0	-0.006	-0.007	46.019	-0.002	-0.002	0.000	0.000	0.000	0.000
118	A	152	VAL	0	-0.049	-0.033	48.703	0.001	0.001	0.000	0.000	0.000	0.000
119	A	153	PRO	0	0.006	-0.007	52.371	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	154	VAL	0	0.047	0.044	52.546	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	155	LYS	1	0.950	0.984	54.602	0.020	0.020	0.000	0.000	0.000	0.000
122	A	156	HIS	0	0.020	0.008	56.592	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	157	VAL	0	-0.051	-0.019	58.465	0.000	0.000	0.000	0.000	0.000	0.000
124	A	158	TYR	0	0.024	-0.003	60.904	0.000	0.000	0.000	0.000	0.000	0.000
125	A	159	ARG	1	0.896	0.949	62.768	0.019	0.019	0.000	0.000	0.000	0.000
126	A	160	VAL	0	0.033	0.012	66.336	0.000	0.000	0.000	0.000	0.000	0.000
127	A	161	LEU	0	-0.017	0.013	65.613	0.000	0.000	0.000	0.000	0.000	0.000
128	A	162	GLN	0	0.010	0.004	69.796	0.001	0.001	0.000	0.000	0.000	0.000
129	A	163	CYS	0	-0.068	-0.036	72.124	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	164	GLN	0	0.022	0.010	74.284	0.001	0.001	0.000	0.000	0.000	0.000
131	A	165	GLU	-1	-0.895	-0.960	75.729	-0.012	-0.012	0.000	0.000	0.000	0.000
132	A	166	GLU	-1	-0.853	-0.934	75.998	-0.014	-0.014	0.000	0.000	0.000	0.000
133	A	167	GLU	-1	-0.978	-0.975	72.196	-0.016	-0.016	0.000	0.000	0.000	0.000
134	A	168	LEU	0	0.055	0.025	71.337	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	169	THR	0	0.022	-0.010	69.054	0.000	0.000	0.000	0.000	0.000	0.000
136	A	170	GLN	0	-0.003	0.002	68.146	0.000	0.000	0.000	0.000	0.000	0.000
137	A	171	MET	0	0.004	0.016	66.706	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	172	VAL	0	-0.018	-0.018	65.586	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	173	SER	0	-0.012	0.001	63.863	0.000	0.000	0.000	0.000	0.000	0.000
140	A	174	THR	0	-0.137	-0.071	62.028	-0.001	-0.001	0.000	0.000	0.000	0.000
141	A	175	MET	0	-0.026	0.007	60.867	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	176	SER	0	-0.035	-0.028	58.656	-0.001	-0.001	0.000	0.000	0.000	0.000
143	A	177	ASP	-1	-0.940	-0.971	52.537	-0.028	-0.028	0.000	0.000	0.000	0.000
144	A	178	GLY	0	0.079	0.037	54.528	0.000	0.000	0.000	0.000	0.000	0.000
145	A	179	TRP	0	-0.121	-0.073	55.253	0.001	0.001	0.000	0.000	0.000	0.000
146	A	180	LYS	1	0.938	0.976	54.915	0.020	0.020	0.000	0.000	0.000	0.000
147	A	181	PHE	0	0.061	0.011	60.561	0.000	0.000	0.000	0.000	0.000	0.000
148	A	182	GLU	-1	-0.890	-0.910	63.165	-0.014	-0.014	0.000	0.000	0.000	0.000
149	A	183	GLN	0	-0.007	-0.014	66.033	0.001	0.001	0.000	0.000	0.000	0.000
150	A	184	LEU	0	-0.002	0.005	69.718	-0.001	-0.001	0.000	0.000	0.000	0.000
151	A	185	VAL	0	-0.030	-0.021	72.255	0.001	0.001	0.000	0.000	0.000	0.000
152	A	186	SER	0	0.000	0.016	75.656	0.000	0.000	0.000	0.000	0.000	0.000
153	A	187	ILE	0	-0.023	-0.012	78.842	0.000	0.000	0.000	0.000	0.000	0.000
154	A	200	GLU	-1	-0.943	-0.964	78.455	-0.011	-0.011	0.000	0.000	0.000	0.000
155	A	201	PHE	0	0.021	-0.004	74.981	0.000	0.000	0.000	0.000	0.000	0.000
156	A	202	LEU	0	-0.025	-0.010	73.964	-0.001	-0.001	0.000	0.000	0.000	0.000
157	A	203	CYS	0	-0.006	-0.005	67.958	0.000	0.000	0.000	0.000	0.000	0.000
158	A	204	VAL	0	-0.039	-0.006	67.121	-0.001	-0.001	0.000	0.000	0.000	0.000
159	A	205	VAL	0	-0.005	0.003	62.669	0.000	0.000	0.000	0.000	0.000	0.000
160	A	206	SER	0	-0.022	-0.047	61.442	0.000	0.000	0.000	0.000	0.000	0.000
161	A	207	LYS	1	0.905	0.947	53.996	0.023	0.023	0.000	0.000	0.000	0.000
162	A	208	GLU	-1	-0.857	-0.908	52.906	-0.019	-0.019	0.000	0.000	0.000	0.000
163	A	209	LEU	0	-0.062	-0.034	53.233	-0.001	-0.001	0.000	0.000	0.000	0.000
164	A	210	HIS	0	-0.007	0.005	47.844	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:34:ALA)