FMO DATABASE

FMODB ID: 9G6Z2

Calculation Name: 5B3D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5B3D

Chain ID: A

ChEMBL ID:

UniProt ID: P0A1J7

Base Structure: X-ray

Registration Date: 2023-06-20

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	114
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-737041.19031
FMO2-HF: Nuclear repulsion	690798.230508
FMO2-HF: Total energy	-46242.959802
FMO2-MP2: Total energy	-46378.466725

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:THR)

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

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.
-27.668	-25.929	10.966	-6.892	-5.813	-0.06

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.028 / q_NPA : -0.029

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	4	LEU	0	0.008	-0.001	3.609	-1.534	0.786	0.013	-1.040	-1.294	0.003
4	A	5	SER	0	-0.010	-0.002	3.637	-0.617	0.094	0.014	-0.246	-0.478	0.001
5	A	6	GLU	-1	-0.771	-0.874	1.781	-26.257	-27.549	10.939	-5.606	-4.041	-0.064
6	A	7	ILE	0	-0.042	-0.014	5.539	0.492	0.492	0.000	0.000	0.000	0.000
7	A	8	LEU	0	0.036	0.018	8.274	0.155	0.155	0.000	0.000	0.000	0.000
8	A	9	ASP	-1	-0.832	-0.900	7.185	0.252	0.252	0.000	0.000	0.000	0.000
9	A	10	GLN	0	-0.001	0.003	9.012	-0.262	-0.262	0.000	0.000	0.000	0.000
10	A	11	MET	0	-0.019	-0.014	11.400	0.086	0.086	0.000	0.000	0.000	0.000
11	A	12	THR	0	-0.007	-0.022	12.764	0.034	0.034	0.000	0.000	0.000	0.000
12	A	13	THR	0	-0.046	-0.019	13.257	0.031	0.031	0.000	0.000	0.000	0.000
13	A	14	VAL	0	0.039	0.012	15.712	0.020	0.020	0.000	0.000	0.000	0.000
14	A	15	LEU	0	-0.003	-0.002	17.031	0.022	0.022	0.000	0.000	0.000	0.000
15	A	16	ASN	0	-0.027	-0.006	17.847	0.030	0.030	0.000	0.000	0.000	0.000
16	A	17	ASP	-1	-0.888	-0.930	19.487	-0.122	-0.122	0.000	0.000	0.000	0.000
17	A	18	LEU	0	-0.028	-0.025	21.042	0.008	0.008	0.000	0.000	0.000	0.000
18	A	19	LYS	1	0.803	0.886	23.357	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	20	THR	0	0.005	-0.005	24.437	0.007	0.007	0.000	0.000	0.000	0.000
20	A	21	VAL	0	-0.034	-0.020	25.969	0.002	0.002	0.000	0.000	0.000	0.000
21	A	22	MET	0	0.016	0.001	27.462	0.003	0.003	0.000	0.000	0.000	0.000
22	A	23	ASP	-1	-0.799	-0.863	29.169	0.008	0.008	0.000	0.000	0.000	0.000
23	A	24	ALA	0	-0.005	-0.004	30.915	0.002	0.002	0.000	0.000	0.000	0.000
24	A	25	GLU	-1	-0.926	-0.967	31.600	-0.029	-0.029	0.000	0.000	0.000	0.000
25	A	26	GLN	0	0.024	0.009	33.558	0.003	0.003	0.000	0.000	0.000	0.000
26	A	27	GLN	0	-0.033	-0.011	35.051	0.001	0.001	0.000	0.000	0.000	0.000
27	A	28	GLN	0	-0.054	-0.039	36.329	0.001	0.001	0.000	0.000	0.000	0.000
28	A	29	LEU	0	0.006	0.005	36.520	0.001	0.001	0.000	0.000	0.000	0.000
29	A	30	SER	0	-0.059	-0.022	39.069	0.004	0.004	0.000	0.000	0.000	0.000
30	A	31	VAL	0	-0.004	-0.021	41.466	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	32	GLY	0	0.002	0.015	45.240	0.002	0.002	0.000	0.000	0.000	0.000
32	A	33	GLN	0	-0.079	-0.043	41.616	0.003	0.003	0.000	0.000	0.000	0.000
33	A	34	ILE	0	0.021	0.000	44.658	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	35	ASN	0	-0.038	-0.017	40.743	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	36	GLY	0	0.052	0.041	41.814	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	37	SER	0	0.005	0.014	40.538	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	38	GLN	0	0.033	-0.003	42.235	0.003	0.003	0.000	0.000	0.000	0.000
38	A	39	LEU	0	0.034	0.028	41.397	0.001	0.001	0.000	0.000	0.000	0.000
39	A	40	GLN	0	-0.012	0.020	43.890	0.001	0.001	0.000	0.000	0.000	0.000
40	A	41	ARG	1	0.864	0.923	43.835	0.018	0.018	0.000	0.000	0.000	0.000
41	A	42	ILE	0	0.037	0.020	46.200	0.001	0.001	0.000	0.000	0.000	0.000
42	A	43	THR	0	-0.029	-0.021	46.815	0.000	0.000	0.000	0.000	0.000	0.000
43	A	44	GLU	-1	-0.803	-0.906	48.778	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	45	GLU	-1	-0.935	-0.948	51.696	-0.014	-0.014	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.907	0.947	50.843	0.015	0.015	0.000	0.000	0.000	0.000
46	A	47	SER	0	-0.040	-0.040	52.870	0.001	0.001	0.000	0.000	0.000	0.000
47	A	48	SER	0	0.000	-0.011	55.080	0.001	0.001	0.000	0.000	0.000	0.000
48	A	49	LEU	0	0.017	0.015	56.544	0.000	0.000	0.000	0.000	0.000	0.000
49	A	50	LEU	0	-0.029	-0.020	55.635	0.000	0.000	0.000	0.000	0.000	0.000
50	A	51	ALA	0	0.010	0.010	59.243	0.000	0.000	0.000	0.000	0.000	0.000
51	A	52	THR	0	-0.035	-0.025	61.121	0.001	0.001	0.000	0.000	0.000	0.000
52	A	53	LEU	0	-0.032	-0.020	61.793	0.000	0.000	0.000	0.000	0.000	0.000
53	A	54	ASP	-1	-0.886	-0.931	63.022	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	55	TYR	0	0.007	-0.001	64.885	0.000	0.000	0.000	0.000	0.000	0.000
55	A	56	LEU	0	0.005	-0.004	66.521	0.000	0.000	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.761	-0.823	67.488	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	58	GLN	0	-0.080	-0.061	66.796	0.001	0.001	0.000	0.000	0.000	0.000
58	A	59	GLN	0	0.019	0.013	70.896	0.001	0.001	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.833	0.888	71.521	0.007	0.007	0.000	0.000	0.000	0.000
60	A	61	ARG	1	0.839	0.895	69.743	0.005	0.005	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.026	-0.003	74.994	0.000	0.000	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-0.916	-0.954	77.139	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	64	GLN	0	-0.095	-0.044	77.037	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	65	ASN	0	-0.051	-0.024	80.174	0.000	0.000	0.000	0.000	0.000	0.000
65	A	66	ALA	0	0.017	0.027	82.238	0.000	0.000	0.000	0.000	0.000	0.000
66	A	67	GLN	0	-0.011	-0.017	84.132	0.000	0.000	0.000	0.000	0.000	0.000
67	A	68	ARG	1	0.934	0.969	84.583	0.006	0.006	0.000	0.000	0.000	0.000
68	A	69	SER	0	0.009	-0.022	83.540	0.000	0.000	0.000	0.000	0.000	0.000
69	A	70	ALA	0	-0.082	-0.023	86.298	0.000	0.000	0.000	0.000	0.000	0.000
70	A	71	ASN	0	-0.029	-0.012	83.182	0.000	0.000	0.000	0.000	0.000	0.000
71	A	72	ASP	-1	-0.755	-0.883	80.906	-0.008	-0.008	0.000	0.000	0.000	0.000
72	A	73	ASP	-1	-0.788	-0.854	77.317	-0.010	-0.010	0.000	0.000	0.000	0.000
73	A	74	ILE	0	-0.004	-0.008	77.248	0.000	0.000	0.000	0.000	0.000	0.000
74	A	75	ALA	0	0.004	-0.007	76.136	0.000	0.000	0.000	0.000	0.000	0.000
75	A	76	GLU	-1	-0.922	-0.945	74.833	-0.012	-0.012	0.000	0.000	0.000	0.000
76	A	77	ARG	1	0.787	0.851	72.750	0.008	0.008	0.000	0.000	0.000	0.000
77	A	78	TRP	0	-0.001	-0.004	70.021	0.000	0.000	0.000	0.000	0.000	0.000
78	A	79	GLN	0	-0.016	-0.010	70.125	0.000	0.000	0.000	0.000	0.000	0.000
79	A	80	ALA	0	0.018	0.017	68.909	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	81	ILE	0	0.016	-0.004	67.149	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	82	THR	0	-0.052	-0.018	66.172	0.000	0.000	0.000	0.000	0.000	0.000
82	A	83	GLU	-1	-0.817	-0.907	65.373	-0.015	-0.015	0.000	0.000	0.000	0.000
83	A	84	LYS	1	0.869	0.942	62.546	0.014	0.014	0.000	0.000	0.000	0.000
84	A	85	THR	0	-0.008	-0.023	61.377	0.000	0.000	0.000	0.000	0.000	0.000
85	A	86	GLN	0	-0.038	-0.014	61.038	0.001	0.001	0.000	0.000	0.000	0.000
86	A	87	HIS	0	0.016	0.010	56.343	0.000	0.000	0.000	0.000	0.000	0.000
87	A	88	LEU	0	0.001	-0.010	56.756	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	89	ARG	1	0.838	0.921	56.270	0.013	0.013	0.000	0.000	0.000	0.000
89	A	90	ASP	-1	-0.793	-0.884	55.927	-0.017	-0.017	0.000	0.000	0.000	0.000
90	A	91	LEU	0	0.006	0.006	51.362	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	92	ASN	0	-0.002	0.006	51.744	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	93	GLN	0	-0.001	0.001	51.364	0.000	0.000	0.000	0.000	0.000	0.000
93	A	94	HIS	0	0.014	0.009	47.203	0.001	0.001	0.000	0.000	0.000	0.000
94	A	95	ASN	0	-0.049	-0.054	47.258	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	96	GLY	0	0.015	0.024	46.505	0.000	0.000	0.000	0.000	0.000	0.000
96	A	97	TRP	0	0.034	0.017	46.053	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	98	LEU	0	-0.063	-0.021	43.043	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	99	LEU	0	-0.020	-0.011	41.828	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	100	GLU	-1	-0.906	-0.963	41.529	-0.016	-0.016	0.000	0.000	0.000	0.000
100	A	101	GLY	0	0.021	0.007	40.121	0.000	0.000	0.000	0.000	0.000	0.000
101	A	102	GLN	0	-0.028	-0.018	36.709	-0.005	-0.005	0.000	0.000	0.000	0.000
102	A	103	ILE	0	0.006	0.012	36.632	0.000	0.000	0.000	0.000	0.000	0.000
103	A	104	GLU	-1	-0.785	-0.867	36.396	-0.041	-0.041	0.000	0.000	0.000	0.000
104	A	105	ARG	1	0.827	0.893	33.178	0.042	0.042	0.000	0.000	0.000	0.000
105	A	106	ASN	0	-0.048	-0.015	32.291	0.002	0.002	0.000	0.000	0.000	0.000
106	A	107	GLN	0	0.005	-0.009	32.223	0.001	0.001	0.000	0.000	0.000	0.000
107	A	108	GLN	0	-0.071	-0.037	30.475	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	109	ALA	0	0.009	0.008	27.945	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	110	LEU	0	0.007	0.001	27.483	0.003	0.003	0.000	0.000	0.000	0.000
110	A	111	GLU	-1	-0.850	-0.923	28.157	0.009	0.009	0.000	0.000	0.000	0.000
111	A	112	VAL	0	-0.059	-0.018	23.040	0.003	0.003	0.000	0.000	0.000	0.000
112	A	113	LEU	0	-0.008	-0.001	23.432	0.003	0.003	0.000	0.000	0.000	0.000
113	A	114	LYS	1	0.780	0.905	24.222	0.008	0.008	0.000	0.000	0.000	0.000
114	A	115	PRO	0	-0.060	-0.036	21.950	0.007	0.007	0.000	0.000	0.000	0.000

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