FMO DATABASE

FMODB ID: 2NGVR

Calculation Name: 5J45-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5J45

Chain ID: A

ChEMBL ID:

UniProt ID: Q8T0Q4

Base Structure: X-ray

Registration Date: 2023-09-23

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	OptH
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	112
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-687234.921755
FMO2-HF: Nuclear repulsion	641546.306577
FMO2-HF: Total energy	-45688.615178
FMO2-MP2: Total energy	-45818.897976

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:18:THR)

Summations of interaction energy for fragment #1(A:18: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.
-20.742	-23.452	17.25	-7.44	-7.101	0.032

Interaction energy analysis for fragmet #1(A:18:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.079 / q_NPA : 0.041

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	20	GLU	-1	-0.917	-0.977	1.742	-18.924	-22.777	17.205	-7.153	-6.199	0.029
4	A	21	ALA	0	-0.038	-0.004	3.389	-2.492	-1.500	0.046	-0.273	-0.765	0.003
5	A	22	ILE	0	0.033	0.004	4.846	0.059	0.210	-0.001	-0.014	-0.137	0.000
6	A	23	GLN	0	-0.037	-0.023	6.840	0.103	0.103	0.000	0.000	0.000	0.000
7	A	24	LYS	1	0.966	0.984	7.529	0.793	0.793	0.000	0.000	0.000	0.000
8	A	25	LEU	0	-0.003	0.034	8.007	0.055	0.055	0.000	0.000	0.000	0.000
9	A	26	ARG	1	1.042	1.021	10.967	-0.157	-0.157	0.000	0.000	0.000	0.000
10	A	27	GLU	-1	-0.919	-0.950	12.060	-0.560	-0.560	0.000	0.000	0.000	0.000
11	A	28	THR	0	-0.065	-0.057	12.678	0.022	0.022	0.000	0.000	0.000	0.000
12	A	29	GLU	-1	-0.897	-0.963	14.916	-0.014	-0.014	0.000	0.000	0.000	0.000
13	A	30	ASN	0	-0.032	-0.005	16.814	0.027	0.027	0.000	0.000	0.000	0.000
14	A	31	MET	0	-0.041	-0.016	18.139	0.023	0.023	0.000	0.000	0.000	0.000
15	A	32	LEU	0	0.000	-0.015	18.722	0.012	0.012	0.000	0.000	0.000	0.000
16	A	33	ILE	0	0.103	0.047	20.972	0.010	0.010	0.000	0.000	0.000	0.000
17	A	34	LYS	1	0.997	1.017	23.094	0.105	0.105	0.000	0.000	0.000	0.000
18	A	35	LYS	1	0.840	0.923	23.458	0.127	0.127	0.000	0.000	0.000	0.000
19	A	36	GLN	0	0.008	0.007	25.116	0.008	0.008	0.000	0.000	0.000	0.000
20	A	37	GLU	-1	-0.860	-0.931	26.994	-0.046	-0.046	0.000	0.000	0.000	0.000
21	A	38	PHE	0	-0.129	-0.061	28.576	0.003	0.003	0.000	0.000	0.000	0.000
22	A	39	LEU	0	-0.045	-0.027	28.670	0.004	0.004	0.000	0.000	0.000	0.000
23	A	40	GLU	-1	-0.870	-0.938	30.561	-0.032	-0.032	0.000	0.000	0.000	0.000
24	A	41	ALA	0	-0.009	0.007	33.058	0.004	0.004	0.000	0.000	0.000	0.000
25	A	42	LYS	1	0.957	0.961	34.477	0.054	0.054	0.000	0.000	0.000	0.000
26	A	43	ILE	0	-0.008	0.003	34.247	0.003	0.003	0.000	0.000	0.000	0.000
27	A	44	GLU	-1	-0.834	-0.939	37.484	-0.020	-0.020	0.000	0.000	0.000	0.000
28	A	45	ASP	-1	-0.929	-0.937	39.050	-0.037	-0.037	0.000	0.000	0.000	0.000
29	A	46	GLU	-1	-0.935	-0.997	39.527	-0.035	-0.035	0.000	0.000	0.000	0.000
30	A	47	LEU	0	-0.062	-0.020	41.678	0.002	0.002	0.000	0.000	0.000	0.000
31	A	48	ASN	0	0.055	0.018	43.396	0.004	0.004	0.000	0.000	0.000	0.000
32	A	49	ILE	0	-0.043	-0.007	43.663	0.002	0.002	0.000	0.000	0.000	0.000
33	A	50	ALA	0	0.000	-0.003	46.222	0.001	0.001	0.000	0.000	0.000	0.000
34	A	51	ARG	1	0.894	0.947	44.126	0.020	0.020	0.000	0.000	0.000	0.000
35	A	52	LYS	1	0.958	0.985	48.146	0.024	0.024	0.000	0.000	0.000	0.000
36	A	53	ASN	0	-0.103	-0.065	50.230	0.000	0.000	0.000	0.000	0.000	0.000
37	A	54	ALA	0	0.025	0.033	51.801	0.000	0.000	0.000	0.000	0.000	0.000
38	A	55	SER	0	-0.019	-0.019	53.157	0.000	0.000	0.000	0.000	0.000	0.000
39	A	56	LYS	1	1.006	1.011	55.766	0.020	0.020	0.000	0.000	0.000	0.000
40	A	57	ASN	0	-0.021	-0.023	54.019	0.000	0.000	0.000	0.000	0.000	0.000
41	A	58	LYS	1	1.060	1.025	53.453	0.014	0.014	0.000	0.000	0.000	0.000
42	A	59	ARG	1	1.014	1.017	51.199	0.025	0.025	0.000	0.000	0.000	0.000
43	A	60	VAL	0	0.000	-0.006	48.981	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	61	ALA	0	0.042	0.026	48.470	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	62	LEU	0	0.014	-0.007	47.938	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	63	GLN	0	-0.091	-0.048	46.145	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	64	ALA	0	0.022	0.036	44.004	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	65	LEU	0	0.037	0.013	42.809	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	66	LYS	1	0.913	0.965	42.784	0.025	0.025	0.000	0.000	0.000	0.000
50	A	67	LYS	1	0.915	0.953	39.189	0.037	0.037	0.000	0.000	0.000	0.000
51	A	68	LYS	1	0.915	0.948	38.389	0.022	0.022	0.000	0.000	0.000	0.000
52	A	69	LYS	1	0.973	0.997	37.825	0.022	0.022	0.000	0.000	0.000	0.000
53	A	70	ARG	1	0.923	0.950	36.476	0.040	0.040	0.000	0.000	0.000	0.000
54	A	71	LEU	0	0.015	0.016	33.960	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	72	GLU	-1	-0.776	-0.886	32.853	-0.029	-0.029	0.000	0.000	0.000	0.000
56	A	73	LYS	1	0.906	0.964	32.432	0.038	0.038	0.000	0.000	0.000	0.000
57	A	74	GLN	0	-0.047	-0.040	29.708	0.000	0.000	0.000	0.000	0.000	0.000
58	A	75	LEU	0	0.045	0.026	28.324	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	76	GLN	0	0.041	0.035	28.136	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	77	GLN	0	-0.023	-0.004	26.377	0.006	0.006	0.000	0.000	0.000	0.000
61	A	78	ILE	0	-0.017	0.005	23.772	-0.010	-0.010	0.000	0.000	0.000	0.000
62	A	79	ASP	-1	-0.808	-0.906	23.272	-0.047	-0.047	0.000	0.000	0.000	0.000
63	A	80	GLY	0	-0.038	-0.025	23.502	0.001	0.001	0.000	0.000	0.000	0.000
64	A	81	THR	0	-0.058	-0.048	19.395	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	82	LEU	0	0.016	0.005	18.983	-0.018	-0.018	0.000	0.000	0.000	0.000
66	A	83	SER	0	0.022	0.024	18.797	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	84	THR	0	-0.038	-0.026	16.987	0.007	0.007	0.000	0.000	0.000	0.000
68	A	85	ILE	0	-0.067	-0.041	13.916	-0.019	-0.019	0.000	0.000	0.000	0.000
69	A	86	GLU	-1	-0.894	-0.950	14.309	-0.037	-0.037	0.000	0.000	0.000	0.000
70	A	87	MET	0	0.040	0.016	15.451	0.017	0.017	0.000	0.000	0.000	0.000
71	A	88	GLN	0	-0.039	-0.019	11.661	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	89	ARG	1	0.924	0.960	10.852	-0.118	-0.118	0.000	0.000	0.000	0.000
73	A	90	GLU	-1	-0.889	-0.953	11.758	0.119	0.119	0.000	0.000	0.000	0.000
74	A	91	ALA	0	-0.017	0.002	12.370	0.040	0.040	0.000	0.000	0.000	0.000
75	A	92	LEU	0	-0.031	-0.028	5.841	-0.017	-0.017	0.000	0.000	0.000	0.000
76	A	93	GLU	-1	-0.892	-0.952	9.215	0.411	0.411	0.000	0.000	0.000	0.000
77	A	94	SER	0	0.006	0.007	11.361	0.073	0.073	0.000	0.000	0.000	0.000
78	A	95	ALA	0	0.000	0.021	9.322	0.049	0.049	0.000	0.000	0.000	0.000
79	A	96	ASN	0	-0.056	-0.005	6.126	-0.050	-0.050	0.000	0.000	0.000	0.000
80	A	97	THR	0	0.035	0.021	8.846	0.071	0.071	0.000	0.000	0.000	0.000
81	A	98	ASN	0	-0.039	-0.048	12.325	-0.038	-0.038	0.000	0.000	0.000	0.000
82	A	99	THR	0	-0.022	-0.012	7.711	-0.015	-0.015	0.000	0.000	0.000	0.000
83	A	100	ALA	0	0.006	0.008	10.727	-0.017	-0.017	0.000	0.000	0.000	0.000
84	A	101	VAL	0	0.030	0.004	12.564	-0.058	-0.058	0.000	0.000	0.000	0.000
85	A	102	LEU	0	0.020	-0.010	14.522	-0.038	-0.038	0.000	0.000	0.000	0.000
86	A	103	THR	0	-0.053	-0.016	12.213	-0.040	-0.040	0.000	0.000	0.000	0.000
87	A	104	THR	0	-0.021	-0.011	15.492	-0.046	-0.046	0.000	0.000	0.000	0.000
88	A	105	MET	0	0.011	0.007	18.047	-0.032	-0.032	0.000	0.000	0.000	0.000
89	A	106	LYS	1	0.971	0.981	18.228	-0.235	-0.235	0.000	0.000	0.000	0.000
90	A	107	ASN	0	-0.033	-0.003	18.892	-0.025	-0.025	0.000	0.000	0.000	0.000
91	A	108	ALA	0	0.045	0.026	20.756	-0.018	-0.018	0.000	0.000	0.000	0.000
92	A	109	ALA	0	-0.006	-0.003	23.516	-0.015	-0.015	0.000	0.000	0.000	0.000
93	A	110	ASP	-1	-0.938	-0.969	22.120	0.153	0.153	0.000	0.000	0.000	0.000
94	A	111	ALA	0	-0.033	-0.020	24.968	-0.013	-0.013	0.000	0.000	0.000	0.000
95	A	112	LEU	0	-0.014	-0.017	26.863	-0.009	-0.009	0.000	0.000	0.000	0.000
96	A	113	LYS	1	0.975	0.989	27.623	-0.119	-0.119	0.000	0.000	0.000	0.000
97	A	114	ARG	1	0.970	0.980	28.974	-0.095	-0.095	0.000	0.000	0.000	0.000
98	A	115	ALA	0	-0.030	0.005	31.001	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	116	HIS	0	-0.004	-0.034	33.100	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	117	GLN	0	0.015	0.013	31.317	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	118	ASN	0	-0.008	-0.015	33.773	-0.005	-0.005	0.000	0.000	0.000	0.000
102	A	119	MET	0	-0.007	0.014	36.848	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	120	ASP	-1	-0.904	-0.953	38.061	0.061	0.061	0.000	0.000	0.000	0.000
104	A	121	VAL	0	-0.089	-0.053	37.697	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	122	ASP	-1	-0.902	-0.949	40.769	0.051	0.051	0.000	0.000	0.000	0.000
106	A	123	LYS	1	0.915	0.960	43.117	-0.049	-0.049	0.000	0.000	0.000	0.000
107	A	124	VAL	0	-0.015	-0.018	43.032	-0.002	-0.002	0.000	0.000	0.000	0.000
108	A	125	HIS	0	-0.020	-0.005	44.615	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	126	ASP	-1	-0.872	-0.927	46.387	0.039	0.039	0.000	0.000	0.000	0.000
110	A	127	MET	0	-0.151	-0.070	48.435	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	128	MET	0	-0.067	-0.029	48.432	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	129	ASP	-1	-1.006	-0.983	51.496	0.030	0.030	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:18:THR)