FMO DATABASE

FMODB ID: 49KLN

Calculation Name: 4ODB-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ODB

Chain ID: D

ChEMBL ID:

UniProt ID: Q9Y624

Base Structure: X-ray

Registration Date: 2023-06-26

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	101
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-757076.56389
FMO2-HF: Nuclear repulsion	716783.39553
FMO2-HF: Total energy	-40293.16836
FMO2-MP2: Total energy	-40409.458547

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(D:28:SER)

Summations of interaction energy for fragment #1(D:28: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.
-2.916	-0.539	0.016	-1.215	-1.178	-0.002

Interaction energy analysis for fragmet #1(D:28:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : -0.014

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	D	30	THR	0	-0.051	-0.027	3.862	-0.300	1.225	-0.017	-0.847	-0.661	0.001
4	D	31	VAL	0	0.049	0.016	6.538	0.023	0.023	0.000	0.000	0.000	0.000
5	D	32	HIS	0	-0.032	-0.014	9.771	0.068	0.068	0.000	0.000	0.000	0.000
6	D	33	SER	0	0.021	0.006	12.509	-0.003	-0.003	0.000	0.000	0.000	0.000
7	D	34	SER	0	-0.031	-0.023	16.334	-0.006	-0.006	0.000	0.000	0.000	0.000
8	D	35	GLU	-1	-0.921	-0.965	18.804	-0.030	-0.030	0.000	0.000	0.000	0.000
9	D	36	PRO	0	-0.021	-0.009	18.231	0.004	0.004	0.000	0.000	0.000	0.000
10	D	37	GLU	-1	-0.962	-0.983	20.040	-0.004	-0.004	0.000	0.000	0.000	0.000
11	D	38	VAL	0	0.038	0.028	23.831	-0.003	-0.003	0.000	0.000	0.000	0.000
12	D	39	ARG	1	0.943	0.978	26.428	0.016	0.016	0.000	0.000	0.000	0.000
13	D	40	ILE	0	0.018	0.002	29.385	-0.001	-0.001	0.000	0.000	0.000	0.000
14	D	41	PRO	0	-0.030	-0.006	32.405	0.001	0.001	0.000	0.000	0.000	0.000
15	D	42	GLU	-1	-0.875	-0.953	35.775	-0.010	-0.010	0.000	0.000	0.000	0.000
16	D	43	ASN	0	-0.050	-0.030	37.286	0.000	0.000	0.000	0.000	0.000	0.000
17	D	44	ASN	0	-0.009	0.008	35.098	0.000	0.000	0.000	0.000	0.000	0.000
18	D	45	PRO	0	0.012	0.002	32.567	0.000	0.000	0.000	0.000	0.000	0.000
19	D	46	VAL	0	0.012	0.006	27.238	0.000	0.000	0.000	0.000	0.000	0.000
20	D	47	LYS	1	0.900	0.966	22.329	0.051	0.051	0.000	0.000	0.000	0.000
21	D	48	LEU	0	0.011	0.025	22.263	0.000	0.000	0.000	0.000	0.000	0.000
22	D	49	SER	0	-0.007	-0.023	19.547	-0.004	-0.004	0.000	0.000	0.000	0.000
23	D	50	CYS	0	-0.094	-0.042	15.553	-0.011	-0.011	0.000	0.000	0.000	0.000
24	D	51	ALA	0	0.017	0.018	14.272	-0.006	-0.006	0.000	0.000	0.000	0.000
25	D	52	TYR	0	0.009	-0.005	10.394	0.012	0.012	0.000	0.000	0.000	0.000
26	D	53	SER	0	-0.031	-0.033	9.083	0.044	0.044	0.000	0.000	0.000	0.000
27	D	54	GLY	0	0.051	0.022	5.691	-0.233	-0.233	0.000	0.000	0.000	0.000
28	D	55	PHE	0	-0.045	-0.018	5.257	-0.073	-0.073	0.000	0.000	0.000	0.000
29	D	56	SER	0	-0.057	-0.026	7.137	0.270	0.270	0.000	0.000	0.000	0.000
30	D	57	SER	0	-0.075	-0.058	9.276	0.103	0.103	0.000	0.000	0.000	0.000
31	D	58	PRO	0	-0.010	0.005	10.523	-0.045	-0.045	0.000	0.000	0.000	0.000
32	D	59	ARG	1	0.925	0.970	11.850	0.231	0.231	0.000	0.000	0.000	0.000
33	D	60	VAL	0	0.001	-0.004	13.668	0.004	0.004	0.000	0.000	0.000	0.000
34	D	61	GLU	-1	-0.957	-0.984	15.881	-0.027	-0.027	0.000	0.000	0.000	0.000
35	D	62	TRP	0	0.012	-0.002	17.548	0.011	0.011	0.000	0.000	0.000	0.000
36	D	63	LYS	1	0.930	0.960	19.443	-0.003	-0.003	0.000	0.000	0.000	0.000
37	D	64	PHE	0	0.005	0.015	22.248	0.003	0.003	0.000	0.000	0.000	0.000
38	D	65	ASP	-1	-0.847	-0.940	22.925	0.013	0.013	0.000	0.000	0.000	0.000
39	D	66	GLN	0	-0.073	-0.031	26.087	0.000	0.000	0.000	0.000	0.000	0.000
40	D	67	GLY	0	-0.029	-0.018	29.039	-0.001	-0.001	0.000	0.000	0.000	0.000
41	D	68	ASP	-1	-0.918	-0.951	29.395	0.007	0.007	0.000	0.000	0.000	0.000
42	D	69	THR	0	-0.027	-0.021	29.442	0.001	0.001	0.000	0.000	0.000	0.000
43	D	70	THR	0	0.013	0.021	24.021	0.000	0.000	0.000	0.000	0.000	0.000
44	D	71	ARG	1	0.884	0.931	26.477	0.011	0.011	0.000	0.000	0.000	0.000
45	D	72	LEU	0	-0.001	0.002	22.072	0.000	0.000	0.000	0.000	0.000	0.000
46	D	73	VAL	0	0.009	0.017	24.021	-0.001	-0.001	0.000	0.000	0.000	0.000
47	D	74	CYS	0	-0.071	-0.023	21.429	-0.004	-0.004	0.000	0.000	0.000	0.000
48	D	75	TYR	0	0.082	0.028	20.308	0.002	0.002	0.000	0.000	0.000	0.000
49	D	76	ASN	0	-0.004	-0.011	18.914	-0.007	-0.007	0.000	0.000	0.000	0.000
50	D	77	ASN	0	0.005	0.014	17.092	0.000	0.000	0.000	0.000	0.000	0.000
51	D	78	LYS	1	0.966	0.994	20.670	0.053	0.053	0.000	0.000	0.000	0.000
52	D	79	ILE	0	0.026	0.015	24.024	0.000	0.000	0.000	0.000	0.000	0.000
53	D	80	THR	0	-0.065	-0.039	25.940	0.000	0.000	0.000	0.000	0.000	0.000
54	D	81	ALA	0	0.104	0.044	28.302	0.001	0.001	0.000	0.000	0.000	0.000
55	D	82	SER	0	-0.067	-0.026	30.956	0.001	0.001	0.000	0.000	0.000	0.000
56	D	83	TYR	0	0.029	0.009	28.949	0.002	0.002	0.000	0.000	0.000	0.000
57	D	84	GLU	-1	-0.919	-0.961	30.823	-0.026	-0.026	0.000	0.000	0.000	0.000
58	D	85	ASP	-1	-0.914	-0.948	31.848	-0.020	-0.020	0.000	0.000	0.000	0.000
59	D	86	ARG	1	0.809	0.879	32.553	0.017	0.017	0.000	0.000	0.000	0.000
60	D	87	VAL	0	-0.013	0.010	26.559	0.000	0.000	0.000	0.000	0.000	0.000
61	D	88	THR	0	-0.037	-0.019	27.810	-0.001	-0.001	0.000	0.000	0.000	0.000
62	D	89	PHE	0	0.074	0.018	18.300	0.000	0.000	0.000	0.000	0.000	0.000
63	D	90	LEU	0	-0.016	-0.002	22.364	0.001	0.001	0.000	0.000	0.000	0.000
64	D	91	PRO	0	0.015	0.009	17.209	0.001	0.001	0.000	0.000	0.000	0.000
65	D	92	THR	0	0.055	0.026	17.478	-0.002	-0.002	0.000	0.000	0.000	0.000
66	D	93	GLY	0	-0.012	-0.007	19.430	0.002	0.002	0.000	0.000	0.000	0.000
67	D	94	ILE	0	-0.029	0.004	21.006	0.000	0.000	0.000	0.000	0.000	0.000
68	D	95	THR	0	0.018	-0.003	23.959	0.002	0.002	0.000	0.000	0.000	0.000
69	D	96	PHE	0	0.008	0.003	26.339	0.000	0.000	0.000	0.000	0.000	0.000
70	D	97	LYS	1	0.882	0.941	30.349	0.025	0.025	0.000	0.000	0.000	0.000
71	D	98	SER	0	-0.028	-0.016	34.023	0.001	0.001	0.000	0.000	0.000	0.000
72	D	99	VAL	0	0.026	0.017	30.911	-0.001	-0.001	0.000	0.000	0.000	0.000
73	D	100	THR	0	0.018	0.002	34.332	0.001	0.001	0.000	0.000	0.000	0.000
74	D	101	ARG	1	0.975	0.979	34.674	0.008	0.008	0.000	0.000	0.000	0.000
75	D	102	GLU	-1	-0.897	-0.931	34.929	-0.007	-0.007	0.000	0.000	0.000	0.000
76	D	103	ASP	-1	-0.803	-0.882	30.834	-0.013	-0.013	0.000	0.000	0.000	0.000
77	D	104	THR	0	-0.027	-0.011	29.764	-0.001	-0.001	0.000	0.000	0.000	0.000
78	D	105	GLY	0	0.042	0.009	27.914	0.001	0.001	0.000	0.000	0.000	0.000
79	D	106	THR	0	-0.053	-0.027	21.436	-0.001	-0.001	0.000	0.000	0.000	0.000
80	D	107	TYR	0	0.010	0.015	22.402	-0.001	-0.001	0.000	0.000	0.000	0.000
81	D	108	THR	0	-0.008	-0.005	17.084	0.002	0.002	0.000	0.000	0.000	0.000
82	D	110	MET	0	0.019	0.001	12.448	0.026	0.026	0.000	0.000	0.000	0.000
83	D	111	VAL	0	-0.027	-0.009	10.443	-0.033	-0.033	0.000	0.000	0.000	0.000
84	D	112	SER	0	-0.007	-0.018	9.342	0.070	0.070	0.000	0.000	0.000	0.000
85	D	113	GLU	-1	-0.756	-0.864	6.502	-0.935	-0.935	0.000	0.000	0.000	0.000
86	D	114	GLU	-1	-0.921	-0.956	9.036	-0.107	-0.107	0.000	0.000	0.000	0.000
87	D	115	GLY	0	-0.011	-0.012	10.555	-0.063	-0.063	0.000	0.000	0.000	0.000
88	D	116	GLY	0	-0.052	-0.025	10.165	0.016	0.016	0.000	0.000	0.000	0.000
89	D	117	ASN	0	0.029	0.022	6.274	0.164	0.164	0.000	0.000	0.000	0.000
90	D	118	SER	0	-0.031	-0.020	3.420	-2.575	-1.757	0.034	-0.367	-0.485	-0.003
91	D	119	TYR	0	-0.007	-0.014	5.211	-0.010	0.024	-0.001	-0.001	-0.032	0.000
92	D	120	GLY	0	0.011	0.014	7.047	0.456	0.456	0.000	0.000	0.000	0.000
93	D	121	GLU	-1	-0.926	-0.969	8.926	-0.016	-0.016	0.000	0.000	0.000	0.000
94	D	122	VAL	0	0.006	-0.003	11.569	0.004	0.004	0.000	0.000	0.000	0.000
95	D	123	LYS	1	0.889	0.950	14.391	-0.050	-0.050	0.000	0.000	0.000	0.000
96	D	124	VAL	0	0.006	0.011	18.041	-0.005	-0.005	0.000	0.000	0.000	0.000
97	D	125	LYS	1	0.915	0.963	20.757	-0.005	-0.005	0.000	0.000	0.000	0.000
98	D	126	LEU	0	0.032	0.021	23.993	-0.003	-0.003	0.000	0.000	0.000	0.000
99	D	127	ILE	0	-0.009	-0.028	27.061	0.002	0.002	0.000	0.000	0.000	0.000
100	D	128	VAL	0	0.024	0.021	30.441	-0.001	-0.001	0.000	0.000	0.000	0.000
101	D	129	LEU	0	-0.054	-0.019	33.477	0.001	0.001	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(D:28:SER)