FMO DATABASE

FMODB ID: 94122

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1409958.706619
FMO2-HF: Nuclear repulsion	1343079.236628
FMO2-HF: Total energy	-66879.469991
FMO2-MP2: Total energy	-67073.896738

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.
-2.794	1.214	3.676	-2.593	-5.091	-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 : -0.018 / q_NPA : -0.024

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	-0.008	0.005	3.885	-0.955	0.513	-0.008	-0.667	-0.793	0.001
4	A	37	GLN	0	0.006	0.005	2.435	-0.530	0.485	1.858	-0.859	-2.014	-0.007
5	A	38	ARG	0	0.083	0.043	4.542	-0.462	-0.466	-0.001	-0.012	0.017	0.000
6	A	39	PRO	0	-0.024	-0.023	4.566	-0.755	-0.659	-0.001	-0.005	-0.090	0.000
7	A	40	GLY	0	0.005	0.025	4.748	0.410	0.474	-0.001	-0.003	-0.059	0.000
8	A	41	SER	0	0.002	-0.005	3.418	0.287	0.475	0.008	-0.044	-0.153	0.000
9	A	42	VAL	0	0.032	0.008	4.986	-0.173	-0.069	-0.001	-0.003	-0.100	0.000
10	A	43	SER	0	-0.035	-0.013	2.247	-0.183	0.027	1.777	-0.801	-1.186	-0.001
11	A	44	LYS	1	0.929	0.958	4.308	0.204	0.383	-0.001	-0.033	-0.145	0.000
12	A	45	TRP	0	0.020	0.007	3.198	-0.886	-0.198	0.046	-0.166	-0.568	0.000
13	A	46	VAL	0	-0.001	-0.001	7.800	-0.011	-0.011	0.000	0.000	0.000	0.000
14	A	47	ARG	1	0.875	0.948	11.572	-0.229	-0.229	0.000	0.000	0.000	0.000
15	A	48	LEU	0	0.015	0.003	14.202	-0.023	-0.023	0.000	0.000	0.000	0.000
16	A	49	ASN	0	-0.017	-0.028	17.363	0.009	0.009	0.000	0.000	0.000	0.000
17	A	50	VAL	0	0.011	0.006	20.084	-0.009	-0.009	0.000	0.000	0.000	0.000
18	A	51	GLY	0	0.083	0.042	22.846	0.003	0.003	0.000	0.000	0.000	0.000
19	A	52	GLY	0	-0.018	0.003	24.959	0.000	0.000	0.000	0.000	0.000	0.000
20	A	53	THR	0	-0.040	-0.016	20.781	0.010	0.010	0.000	0.000	0.000	0.000
21	A	54	TYR	0	-0.072	-0.059	17.029	0.003	0.003	0.000	0.000	0.000	0.000
22	A	55	PHE	0	-0.013	-0.002	15.735	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	56	LEU	0	-0.016	0.001	8.367	0.013	0.013	0.000	0.000	0.000	0.000
24	A	57	THR	0	0.011	-0.005	9.936	-0.069	-0.069	0.000	0.000	0.000	0.000
25	A	58	THR	0	-0.010	-0.001	5.420	0.030	0.030	0.000	0.000	0.000	0.000
26	A	59	ARG	1	0.910	0.933	8.490	0.009	0.009	0.000	0.000	0.000	0.000
27	A	60	GLN	0	0.035	0.014	6.960	0.003	0.003	0.000	0.000	0.000	0.000
28	A	61	THR	0	-0.023	-0.020	9.662	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	62	LEU	0	-0.019	-0.001	11.778	0.020	0.020	0.000	0.000	0.000	0.000
30	A	63	CYS	0	-0.101	-0.020	13.936	0.003	0.003	0.000	0.000	0.000	0.000
31	A	64	ARG	1	0.833	0.925	14.952	0.215	0.215	0.000	0.000	0.000	0.000
32	A	65	ASP	-1	-0.761	-0.874	16.973	-0.094	-0.094	0.000	0.000	0.000	0.000
33	A	66	PRO	0	0.012	0.003	20.657	0.009	0.009	0.000	0.000	0.000	0.000
34	A	67	LYS	1	0.799	0.879	22.179	0.097	0.097	0.000	0.000	0.000	0.000
35	A	68	SER	0	-0.041	-0.012	21.075	0.009	0.009	0.000	0.000	0.000	0.000
36	A	69	PHE	0	0.090	0.031	22.680	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	70	LEU	0	0.019	-0.006	18.319	0.004	0.004	0.000	0.000	0.000	0.000
38	A	71	TYR	0	0.001	0.017	18.334	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	72	ARG	1	0.803	0.907	19.082	0.005	0.005	0.000	0.000	0.000	0.000
40	A	73	LEU	0	-0.002	0.011	15.767	0.007	0.007	0.000	0.000	0.000	0.000
41	A	75	GLN	0	0.019	0.000	14.035	-0.033	-0.033	0.000	0.000	0.000	0.000
42	A	76	ALA	0	-0.094	-0.068	13.806	0.018	0.018	0.000	0.000	0.000	0.000
43	A	77	ASP	-1	-0.811	-0.898	15.737	-0.020	-0.020	0.000	0.000	0.000	0.000
44	A	78	PRO	0	-0.035	-0.020	19.474	0.008	0.008	0.000	0.000	0.000	0.000
45	A	79	ASP	-1	-0.835	-0.907	21.996	0.007	0.007	0.000	0.000	0.000	0.000
46	A	80	LEU	0	-0.082	-0.044	22.407	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	81	ASP	-1	-0.838	-0.906	24.191	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	82	SER	0	-0.099	-0.079	21.910	0.001	0.001	0.000	0.000	0.000	0.000
49	A	83	ASP	-1	-0.870	-0.927	22.444	0.043	0.043	0.000	0.000	0.000	0.000
50	A	84	LYS	1	0.807	0.902	17.426	-0.090	-0.090	0.000	0.000	0.000	0.000
51	A	85	ASP	-1	-0.681	-0.776	20.735	0.129	0.129	0.000	0.000	0.000	0.000
52	A	86	GLU	-1	-0.877	-0.951	21.773	0.135	0.135	0.000	0.000	0.000	0.000
53	A	87	THR	0	-0.079	-0.052	18.340	0.027	0.027	0.000	0.000	0.000	0.000
54	A	88	GLY	0	-0.003	-0.009	17.316	0.031	0.031	0.000	0.000	0.000	0.000
55	A	89	ALA	0	-0.082	-0.035	17.008	-0.008	-0.008	0.000	0.000	0.000	0.000
56	A	90	TYR	0	0.027	0.008	15.639	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	91	LEU	0	0.001	0.003	19.644	0.002	0.002	0.000	0.000	0.000	0.000
58	A	92	ILE	0	-0.038	-0.025	20.197	-0.011	-0.011	0.000	0.000	0.000	0.000
59	A	93	ASP	-1	-0.916	-0.950	24.195	0.028	0.028	0.000	0.000	0.000	0.000
60	A	94	ARG	1	0.743	0.833	25.373	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	95	ASP	-1	-0.792	-0.872	26.585	0.021	0.021	0.000	0.000	0.000	0.000
62	A	96	PRO	0	0.000	-0.008	23.103	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	97	THR	0	-0.071	-0.065	22.856	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	98	TYR	0	0.016	0.008	24.406	-0.008	-0.008	0.000	0.000	0.000	0.000
65	A	99	PHE	0	0.019	0.019	17.547	-0.012	-0.012	0.000	0.000	0.000	0.000
66	A	100	GLY	0	0.023	0.018	19.224	-0.009	-0.009	0.000	0.000	0.000	0.000
67	A	101	PRO	0	-0.022	-0.019	19.033	-0.016	-0.016	0.000	0.000	0.000	0.000
68	A	102	VAL	0	0.010	0.022	20.314	-0.017	-0.017	0.000	0.000	0.000	0.000
69	A	103	LEU	0	0.017	0.007	13.978	-0.019	-0.019	0.000	0.000	0.000	0.000
70	A	104	ASN	0	-0.011	-0.015	15.487	-0.033	-0.033	0.000	0.000	0.000	0.000
71	A	105	TYR	0	-0.002	0.012	16.505	-0.028	-0.028	0.000	0.000	0.000	0.000
72	A	106	LEU	0	-0.011	0.000	15.560	-0.023	-0.023	0.000	0.000	0.000	0.000
73	A	107	ARG	1	0.882	0.940	11.362	0.022	0.022	0.000	0.000	0.000	0.000
74	A	108	HIS	0	-0.019	-0.012	12.984	-0.057	-0.057	0.000	0.000	0.000	0.000
75	A	109	GLY	0	-0.019	0.001	15.260	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	110	LYS	1	0.895	0.937	18.021	0.201	0.201	0.000	0.000	0.000	0.000
77	A	111	LEU	0	0.028	0.021	20.601	0.000	0.000	0.000	0.000	0.000	0.000
78	A	112	VAL	0	-0.030	-0.018	21.099	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	113	ILE	0	0.007	-0.005	23.083	0.002	0.002	0.000	0.000	0.000	0.000
80	A	114	ASN	0	-0.034	-0.013	24.656	-0.007	-0.007	0.000	0.000	0.000	0.000
81	A	115	LYS	1	0.959	0.965	26.998	0.024	0.024	0.000	0.000	0.000	0.000
82	A	116	ASP	-1	-0.870	-0.920	28.750	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	117	LEU	0	-0.017	-0.004	26.234	0.003	0.003	0.000	0.000	0.000	0.000
84	A	118	ALA	0	0.049	0.034	30.293	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	119	GLU	-1	-0.786	-0.896	29.856	-0.031	-0.031	0.000	0.000	0.000	0.000
86	A	120	GLU	-1	-0.803	-0.895	30.572	-0.024	-0.024	0.000	0.000	0.000	0.000
87	A	121	GLY	0	0.020	0.014	30.581	0.000	0.000	0.000	0.000	0.000	0.000
88	A	122	VAL	0	-0.017	-0.017	25.056	0.000	0.000	0.000	0.000	0.000	0.000
89	A	123	LEU	0	-0.043	-0.012	27.065	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	124	GLU	-1	-0.801	-0.887	29.291	-0.015	-0.015	0.000	0.000	0.000	0.000
91	A	125	GLU	-1	-0.742	-0.842	24.912	-0.006	-0.006	0.000	0.000	0.000	0.000
92	A	126	ALA	0	-0.044	-0.023	25.044	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	127	GLU	-1	-0.811	-0.923	26.095	-0.041	-0.041	0.000	0.000	0.000	0.000
94	A	128	PHE	0	0.033	0.035	25.818	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	129	TYR	0	-0.035	-0.046	22.779	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	130	ASN	0	0.009	0.003	24.262	-0.008	-0.008	0.000	0.000	0.000	0.000
97	A	131	ILE	0	-0.006	0.013	20.863	-0.009	-0.009	0.000	0.000	0.000	0.000
98	A	132	THR	0	0.026	-0.002	24.186	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	133	SER	0	-0.007	-0.004	23.410	0.001	0.001	0.000	0.000	0.000	0.000
100	A	134	LEU	0	-0.026	-0.011	22.074	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	135	ILE	0	0.036	0.035	25.280	0.004	0.004	0.000	0.000	0.000	0.000
102	A	136	LYS	1	0.858	0.917	28.685	0.068	0.068	0.000	0.000	0.000	0.000
103	A	137	LEU	0	0.001	0.002	24.661	0.003	0.003	0.000	0.000	0.000	0.000
104	A	138	VAL	0	0.025	0.006	27.014	0.002	0.002	0.000	0.000	0.000	0.000
105	A	139	LYS	1	0.856	0.918	29.545	0.041	0.041	0.000	0.000	0.000	0.000
106	A	140	ASP	-1	-0.841	-0.890	31.635	-0.054	-0.054	0.000	0.000	0.000	0.000
107	A	141	LYS	1	0.834	0.916	29.524	0.043	0.043	0.000	0.000	0.000	0.000
108	A	142	ILE	0	0.042	0.027	32.120	0.002	0.002	0.000	0.000	0.000	0.000
109	A	143	ARG	1	0.886	0.933	34.845	0.045	0.045	0.000	0.000	0.000	0.000
110	A	144	GLU	-1	-0.847	-0.889	33.959	-0.041	-0.041	0.000	0.000	0.000	0.000
111	A	145	ARG	1	0.732	0.819	34.826	0.025	0.025	0.000	0.000	0.000	0.000
112	A	146	ASP	-1	-0.814	-0.883	37.547	-0.024	-0.024	0.000	0.000	0.000	0.000
113	A	147	SER	0	-0.067	-0.056	39.848	0.002	0.002	0.000	0.000	0.000	0.000
114	A	148	LYS	1	0.793	0.882	36.672	0.038	0.038	0.000	0.000	0.000	0.000
115	A	149	THR	0	-0.047	-0.025	40.681	0.002	0.002	0.000	0.000	0.000	0.000
116	A	150	SER	0	-0.035	-0.018	43.363	0.002	0.002	0.000	0.000	0.000	0.000
117	A	151	GLN	0	-0.041	-0.017	46.045	-0.002	-0.002	0.000	0.000	0.000	0.000
118	A	152	VAL	0	-0.021	-0.018	48.830	0.001	0.001	0.000	0.000	0.000	0.000
119	A	153	PRO	0	0.013	-0.001	52.568	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	154	VAL	0	0.036	0.021	52.249	0.000	0.000	0.000	0.000	0.000	0.000
121	A	155	LYS	1	0.954	0.993	54.383	0.018	0.018	0.000	0.000	0.000	0.000
122	A	156	HIS	0	-0.002	-0.006	56.832	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	157	VAL	0	-0.051	-0.019	58.534	0.000	0.000	0.000	0.000	0.000	0.000
124	A	158	TYR	0	0.006	-0.024	60.903	0.000	0.000	0.000	0.000	0.000	0.000
125	A	159	ARG	1	0.893	0.951	63.534	0.018	0.018	0.000	0.000	0.000	0.000
126	A	160	VAL	0	0.022	0.007	66.609	0.000	0.000	0.000	0.000	0.000	0.000
127	A	161	LEU	0	-0.020	0.005	65.895	0.000	0.000	0.000	0.000	0.000	0.000
128	A	162	GLN	0	-0.001	-0.009	70.151	0.001	0.001	0.000	0.000	0.000	0.000
129	A	163	CYS	0	-0.072	-0.029	72.640	0.000	0.000	0.000	0.000	0.000	0.000
130	A	164	GLN	0	0.024	-0.002	74.768	0.000	0.000	0.000	0.000	0.000	0.000
131	A	165	GLU	-1	-0.909	-0.968	75.983	-0.010	-0.010	0.000	0.000	0.000	0.000
132	A	166	GLU	-1	-0.882	-0.935	76.252	-0.012	-0.012	0.000	0.000	0.000	0.000
133	A	167	GLU	-1	-0.907	-0.956	72.666	-0.014	-0.014	0.000	0.000	0.000	0.000
134	A	168	LEU	0	0.012	0.015	71.364	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	169	THR	0	0.022	-0.005	69.638	0.000	0.000	0.000	0.000	0.000	0.000
136	A	170	GLN	0	0.007	0.003	68.219	0.000	0.000	0.000	0.000	0.000	0.000
137	A	171	MET	0	0.002	0.022	66.722	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	172	VAL	0	-0.033	-0.025	65.761	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	173	SER	0	-0.042	-0.018	63.954	0.000	0.000	0.000	0.000	0.000	0.000
140	A	174	THR	0	-0.094	-0.058	62.111	-0.001	-0.001	0.000	0.000	0.000	0.000
141	A	175	MET	0	-0.014	0.006	60.910	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	176	SER	0	-0.056	-0.022	58.292	-0.001	-0.001	0.000	0.000	0.000	0.000
143	A	177	ASP	-1	-0.853	-0.948	52.644	-0.025	-0.025	0.000	0.000	0.000	0.000
144	A	178	GLY	0	0.035	0.028	54.163	0.001	0.001	0.000	0.000	0.000	0.000
145	A	179	TRP	0	-0.109	-0.048	54.838	0.001	0.001	0.000	0.000	0.000	0.000
146	A	180	LYS	1	0.880	0.935	55.206	0.018	0.018	0.000	0.000	0.000	0.000
147	A	181	PHE	0	0.049	0.013	60.551	0.000	0.000	0.000	0.000	0.000	0.000
148	A	182	GLU	-1	-0.846	-0.870	63.247	-0.013	-0.013	0.000	0.000	0.000	0.000
149	A	183	GLN	0	-0.030	-0.028	66.104	0.001	0.001	0.000	0.000	0.000	0.000
150	A	184	LEU	0	-0.007	0.005	69.828	-0.001	-0.001	0.000	0.000	0.000	0.000
151	A	185	VAL	0	-0.019	-0.011	72.447	0.000	0.000	0.000	0.000	0.000	0.000
152	A	186	SER	0	0.036	0.024	75.979	0.000	0.000	0.000	0.000	0.000	0.000
153	A	187	ILE	0	-0.043	-0.017	79.114	0.000	0.000	0.000	0.000	0.000	0.000
154	A	200	GLU	-1	-0.889	-0.934	78.736	-0.010	-0.010	0.000	0.000	0.000	0.000
155	A	201	PHE	0	-0.032	-0.021	75.061	0.000	0.000	0.000	0.000	0.000	0.000
156	A	202	LEU	0	0.001	0.003	74.093	0.000	0.000	0.000	0.000	0.000	0.000
157	A	203	CYS	0	-0.003	-0.014	68.022	0.000	0.000	0.000	0.000	0.000	0.000
158	A	204	VAL	0	-0.034	0.003	67.261	-0.001	-0.001	0.000	0.000	0.000	0.000
159	A	205	VAL	0	-0.008	-0.006	62.631	0.000	0.000	0.000	0.000	0.000	0.000
160	A	206	SER	0	-0.030	-0.048	61.583	0.000	0.000	0.000	0.000	0.000	0.000
161	A	207	LYS	1	0.916	0.940	54.000	0.021	0.021	0.000	0.000	0.000	0.000
162	A	208	GLU	-1	-0.829	-0.891	52.942	-0.018	-0.018	0.000	0.000	0.000	0.000
163	A	209	LEU	0	-0.058	-0.029	53.156	-0.001	-0.001	0.000	0.000	0.000	0.000
164	A	210	HIS	0	0.002	0.005	47.732	-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)