FMO DATABASE

FMODB ID: 76JZK

Calculation Name: 3R0A-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3R0A

Chain ID: A

ChEMBL ID:

UniProt ID: Q8PXX2

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	120
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-969177.748777
FMO2-HF: Nuclear repulsion	920193.01387
FMO2-HF: Total energy	-48984.734907
FMO2-MP2: Total energy	-49127.615862

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:-2:SER)

Summations of interaction energy for fragment #1(A:-2:SER)

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.
-11.169	-3.964	3.698	-4.473	-6.43	-0.01

Interaction energy analysis for fragmet #1(A:-2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / 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	A	0	ALA	0	0.020	0.023	2.884	-2.732	0.496	0.092	-1.467	-1.853	0.000
4	A	1	MET	0	-0.013	0.011	4.383	2.016	2.234	-0.001	-0.024	-0.194	0.000
5	A	2	ILE	0	-0.035	-0.016	6.879	-0.200	-0.200	0.000	0.000	0.000	0.000
6	A	3	ASP	-1	-0.838	-0.925	9.221	0.718	0.718	0.000	0.000	0.000	0.000
7	A	4	PHE	0	-0.032	-0.021	12.790	-0.012	-0.012	0.000	0.000	0.000	0.000
8	A	5	ALA	0	-0.005	-0.009	14.680	-0.013	-0.013	0.000	0.000	0.000	0.000
9	A	6	CYS	0	-0.002	0.008	17.500	-0.045	-0.045	0.000	0.000	0.000	0.000
10	A	7	LYS	1	0.929	0.968	16.266	-0.548	-0.548	0.000	0.000	0.000	0.000
11	A	8	GLU	-1	-0.837	-0.924	11.894	1.230	1.230	0.000	0.000	0.000	0.000
12	A	9	PHE	0	-0.054	-0.024	9.817	-0.048	-0.048	0.000	0.000	0.000	0.000
13	A	10	LYS	1	0.955	0.966	5.657	-1.690	-1.690	0.000	0.000	0.000	0.000
14	A	11	VAL	0	0.031	0.010	2.659	-1.202	-0.282	0.383	-0.415	-0.888	0.003
15	A	12	GLU	-1	-0.817	-0.919	2.545	-4.835	-2.186	3.226	-2.525	-3.349	-0.013
16	A	13	ASP	-1	-0.853	-0.925	4.561	0.537	0.569	0.000	-0.025	-0.007	0.000
17	A	14	VAL	0	0.058	0.042	7.661	-0.571	-0.571	0.000	0.000	0.000	0.000
18	A	15	ILE	0	0.020	0.006	4.232	-0.611	-0.541	-0.001	-0.005	-0.064	0.000
19	A	16	LYS	1	0.821	0.911	7.849	-2.242	-2.242	0.000	0.000	0.000	0.000
20	A	17	CYS	0	-0.003	0.016	10.070	-0.282	-0.282	0.000	0.000	0.000	0.000
21	A	18	ALA	0	0.033	0.025	11.640	-0.151	-0.151	0.000	0.000	0.000	0.000
22	A	19	LEU	0	0.021	-0.016	10.273	-0.145	-0.145	0.000	0.000	0.000	0.000
23	A	20	ASN	0	-0.031	0.006	13.399	-0.071	-0.071	0.000	0.000	0.000	0.000
24	A	21	LEU	0	-0.042	-0.009	10.151	-0.097	-0.097	0.000	0.000	0.000	0.000
25	A	22	THR	0	0.041	-0.014	12.467	0.113	0.113	0.000	0.000	0.000	0.000
26	A	23	LYS	1	0.974	0.969	10.264	-0.227	-0.227	0.000	0.000	0.000	0.000
27	A	24	ALA	0	0.017	0.019	11.204	-0.068	-0.068	0.000	0.000	0.000	0.000
28	A	25	ASP	-1	-0.696	-0.808	13.073	0.236	0.236	0.000	0.000	0.000	0.000
29	A	26	LEU	0	0.027	0.022	5.680	-0.083	-0.083	0.000	0.000	0.000	0.000
30	A	27	ASN	0	0.009	-0.003	8.212	-0.097	-0.097	0.000	0.000	0.000	0.000
31	A	28	VAL	0	0.034	0.029	10.104	-0.141	-0.141	0.000	0.000	0.000	0.000
32	A	29	MET	0	0.009	0.007	8.395	-0.052	-0.052	0.000	0.000	0.000	0.000
33	A	30	LYS	1	0.793	0.879	4.379	-0.280	-0.192	-0.001	-0.012	-0.075	0.000
34	A	31	SER	0	-0.001	-0.005	9.128	-0.146	-0.146	0.000	0.000	0.000	0.000
35	A	32	PHE	0	-0.008	-0.005	12.410	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	33	LEU	0	-0.026	-0.024	8.067	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	34	ASN	0	-0.025	-0.014	8.487	-0.251	-0.251	0.000	0.000	0.000	0.000
38	A	35	GLU	-1	-0.850	-0.911	10.986	-0.446	-0.446	0.000	0.000	0.000	0.000
39	A	36	PRO	0	-0.008	0.004	13.403	0.074	0.074	0.000	0.000	0.000	0.000
40	A	37	ASP	-1	-0.858	-0.934	15.444	-0.258	-0.258	0.000	0.000	0.000	0.000
41	A	38	ARG	1	0.795	0.907	15.685	0.409	0.409	0.000	0.000	0.000	0.000
42	A	39	TRP	0	-0.002	0.003	19.541	0.011	0.011	0.000	0.000	0.000	0.000
43	A	40	ILE	0	-0.039	-0.025	19.065	-0.011	-0.011	0.000	0.000	0.000	0.000
44	A	41	ASP	-1	-0.768	-0.874	22.331	-0.099	-0.099	0.000	0.000	0.000	0.000
45	A	42	THR	0	0.032	-0.011	22.009	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	43	ASP	-1	-0.865	-0.925	22.426	-0.052	-0.052	0.000	0.000	0.000	0.000
47	A	44	ALA	0	-0.005	-0.003	23.690	-0.007	-0.007	0.000	0.000	0.000	0.000
48	A	45	LEU	0	0.001	0.005	16.204	-0.023	-0.023	0.000	0.000	0.000	0.000
49	A	46	SER	0	-0.067	-0.038	18.929	-0.011	-0.011	0.000	0.000	0.000	0.000
50	A	47	LYS	1	0.970	0.976	20.329	0.107	0.107	0.000	0.000	0.000	0.000
51	A	48	SER	0	-0.016	0.005	17.881	-0.016	-0.016	0.000	0.000	0.000	0.000
52	A	49	LEU	0	-0.025	-0.016	12.723	-0.029	-0.029	0.000	0.000	0.000	0.000
53	A	50	LYS	1	0.854	0.927	16.290	0.272	0.272	0.000	0.000	0.000	0.000
54	A	51	LEU	0	-0.029	-0.005	15.014	0.034	0.034	0.000	0.000	0.000	0.000
55	A	52	ASP	-1	-0.750	-0.858	19.460	0.028	0.028	0.000	0.000	0.000	0.000
56	A	53	VAL	0	0.059	0.022	21.653	0.008	0.008	0.000	0.000	0.000	0.000
57	A	54	SER	0	0.019	0.011	23.412	0.006	0.006	0.000	0.000	0.000	0.000
58	A	55	THR	0	-0.078	-0.062	18.314	0.028	0.028	0.000	0.000	0.000	0.000
59	A	56	VAL	0	0.006	0.011	17.881	0.017	0.017	0.000	0.000	0.000	0.000
60	A	57	GLN	0	0.030	0.025	19.667	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	58	ARG	1	0.883	0.926	21.344	-0.114	-0.114	0.000	0.000	0.000	0.000
62	A	59	SER	0	-0.039	-0.037	16.224	0.010	0.010	0.000	0.000	0.000	0.000
63	A	60	VAL	0	-0.009	-0.007	17.767	0.009	0.009	0.000	0.000	0.000	0.000
64	A	61	LYS	1	0.812	0.896	19.370	-0.096	-0.096	0.000	0.000	0.000	0.000
65	A	62	LYS	1	0.842	0.906	16.396	-0.321	-0.321	0.000	0.000	0.000	0.000
66	A	63	LEU	0	-0.013	-0.015	13.282	0.015	0.015	0.000	0.000	0.000	0.000
67	A	64	HIS	0	-0.012	-0.003	17.194	-0.011	-0.011	0.000	0.000	0.000	0.000
68	A	65	GLU	-1	-0.785	-0.875	20.506	0.096	0.096	0.000	0.000	0.000	0.000
69	A	66	LYS	1	0.822	0.916	16.281	-0.346	-0.346	0.000	0.000	0.000	0.000
70	A	67	GLU	-1	-0.894	-0.924	18.312	0.038	0.038	0.000	0.000	0.000	0.000
71	A	68	ILE	0	-0.007	-0.010	13.170	-0.015	-0.015	0.000	0.000	0.000	0.000
72	A	69	LEU	0	-0.037	-0.026	15.991	-0.055	-0.055	0.000	0.000	0.000	0.000
73	A	70	GLN	0	0.020	0.030	18.649	0.013	0.013	0.000	0.000	0.000	0.000
74	A	71	ARG	1	0.866	0.913	22.050	-0.012	-0.012	0.000	0.000	0.000	0.000
75	A	72	SER	0	0.025	0.022	24.845	0.004	0.004	0.000	0.000	0.000	0.000
76	A	73	GLN	0	-0.002	-0.017	27.837	0.004	0.004	0.000	0.000	0.000	0.000
77	A	74	GLN	0	0.003	0.019	29.038	-0.012	-0.012	0.000	0.000	0.000	0.000
78	A	75	ASN	0	0.012	-0.015	31.252	0.006	0.006	0.000	0.000	0.000	0.000
79	A	76	LEU	0	-0.006	-0.006	32.910	-0.007	-0.007	0.000	0.000	0.000	0.000
80	A	77	ASP	-1	-0.877	-0.940	36.632	-0.057	-0.057	0.000	0.000	0.000	0.000
81	A	78	GLY	0	-0.044	-0.015	39.813	0.003	0.003	0.000	0.000	0.000	0.000
82	A	79	GLY	0	-0.005	0.005	40.941	0.004	0.004	0.000	0.000	0.000	0.000
83	A	80	GLY	0	0.007	0.015	37.766	0.004	0.004	0.000	0.000	0.000	0.000
84	A	81	TYR	0	-0.048	-0.036	31.663	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	82	VAL	0	0.030	0.027	29.080	0.005	0.005	0.000	0.000	0.000	0.000
86	A	83	TYR	0	-0.020	-0.020	26.722	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	84	ILE	0	-0.025	-0.004	24.678	-0.005	-0.005	0.000	0.000	0.000	0.000
88	A	85	TYR	0	-0.005	-0.026	20.549	0.020	0.020	0.000	0.000	0.000	0.000
89	A	86	LYS	1	0.878	0.938	18.932	0.219	0.219	0.000	0.000	0.000	0.000
90	A	87	ILE	0	-0.062	-0.010	13.176	0.032	0.032	0.000	0.000	0.000	0.000
91	A	88	TYR	0	0.004	-0.009	16.615	-0.023	-0.023	0.000	0.000	0.000	0.000
92	A	89	SER	0	0.026	0.013	16.453	-0.042	-0.042	0.000	0.000	0.000	0.000
93	A	90	LYS	1	1.016	0.984	12.682	0.614	0.614	0.000	0.000	0.000	0.000
94	A	91	ASN	0	0.015	0.002	13.746	-0.037	-0.037	0.000	0.000	0.000	0.000
95	A	92	GLN	0	0.025	0.039	16.418	0.043	0.043	0.000	0.000	0.000	0.000
96	A	93	ILE	0	0.002	0.000	10.919	0.050	0.050	0.000	0.000	0.000	0.000
97	A	94	ARG	1	0.915	0.952	10.577	0.444	0.444	0.000	0.000	0.000	0.000
98	A	95	ASN	0	0.010	0.004	13.276	0.079	0.079	0.000	0.000	0.000	0.000
99	A	96	ILE	0	0.016	0.018	14.952	0.040	0.040	0.000	0.000	0.000	0.000
100	A	97	ILE	0	-0.004	-0.006	8.959	0.052	0.052	0.000	0.000	0.000	0.000
101	A	98	GLN	0	0.019	0.011	13.056	0.091	0.091	0.000	0.000	0.000	0.000
102	A	99	LYS	1	0.958	0.974	14.847	-0.133	-0.133	0.000	0.000	0.000	0.000
103	A	100	ILE	0	-0.014	0.017	15.156	0.001	0.001	0.000	0.000	0.000	0.000
104	A	101	VAL	0	0.023	0.019	12.217	0.012	0.012	0.000	0.000	0.000	0.000
105	A	102	GLN	0	-0.097	-0.053	15.567	0.003	0.003	0.000	0.000	0.000	0.000
106	A	103	SER	0	-0.022	-0.023	18.906	-0.011	-0.011	0.000	0.000	0.000	0.000
107	A	104	TRP	0	-0.009	-0.022	12.515	0.026	0.026	0.000	0.000	0.000	0.000
108	A	105	ALA	0	0.014	0.017	19.403	-0.009	-0.009	0.000	0.000	0.000	0.000
109	A	106	ASP	-1	-0.819	-0.906	21.054	0.218	0.218	0.000	0.000	0.000	0.000
110	A	107	ARG	1	0.800	0.879	22.826	-0.334	-0.334	0.000	0.000	0.000	0.000
111	A	108	LEU	0	-0.016	-0.013	21.296	-0.011	-0.011	0.000	0.000	0.000	0.000
112	A	109	GLY	0	0.028	0.013	24.403	-0.014	-0.014	0.000	0.000	0.000	0.000
113	A	110	GLN	0	-0.058	-0.040	26.897	-0.032	-0.032	0.000	0.000	0.000	0.000
114	A	111	GLU	-1	-0.781	-0.871	25.990	0.258	0.258	0.000	0.000	0.000	0.000
115	A	112	LEU	0	-0.029	-0.014	26.566	-0.007	-0.007	0.000	0.000	0.000	0.000
116	A	113	LYS	1	0.794	0.897	29.885	-0.177	-0.177	0.000	0.000	0.000	0.000
117	A	114	GLU	-1	-0.876	-0.925	32.247	0.152	0.152	0.000	0.000	0.000	0.000
118	A	115	TRP	0	-0.052	-0.009	31.744	0.003	0.003	0.000	0.000	0.000	0.000
119	A	116	GLU	-1	-0.952	-0.979	33.645	0.137	0.137	0.000	0.000	0.000	0.000
120	A	117	ASN	0	-0.095	-0.041	36.470	-0.014	-0.014	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-2:SER)