FMO DATABASE

FMODB ID: 52QNZ

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	OptHSide
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	-757941.354483
FMO2-HF: Nuclear repulsion	717647.546678
FMO2-HF: Total energy	-40293.807805
FMO2-MP2: Total energy	-40410.118976

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.
-0.549	1.779	0.059	-1.166	-1.218	-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 : 0.018 / q_NPA : -0.004

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

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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	-0.035	-0.019	3.869	1.129	2.620	-0.018	-0.831	-0.642	0.001
4	D	31	VAL	0	0.039	0.016	6.614	-0.011	-0.011	0.000	0.000	0.000	0.000
5	D	32	HIS	0	-0.037	-0.017	9.853	0.183	0.183	0.000	0.000	0.000	0.000
6	D	33	SER	0	0.024	-0.001	12.582	-0.001	-0.001	0.000	0.000	0.000	0.000
7	D	34	SER	0	-0.036	-0.021	16.405	-0.005	-0.005	0.000	0.000	0.000	0.000
8	D	35	GLU	-1	-0.930	-0.966	18.869	-0.143	-0.143	0.000	0.000	0.000	0.000
9	D	36	PRO	0	-0.014	-0.010	18.219	0.013	0.013	0.000	0.000	0.000	0.000
10	D	37	GLU	-1	-0.894	-0.933	20.104	-0.049	-0.049	0.000	0.000	0.000	0.000
11	D	38	VAL	0	0.044	0.029	23.895	-0.007	-0.007	0.000	0.000	0.000	0.000
12	D	39	ARG	1	0.937	0.970	26.498	0.080	0.080	0.000	0.000	0.000	0.000
13	D	40	ILE	0	0.015	0.008	29.814	-0.005	-0.005	0.000	0.000	0.000	0.000
14	D	41	PRO	0	0.001	0.008	32.478	0.005	0.005	0.000	0.000	0.000	0.000
15	D	42	GLU	-1	-0.787	-0.903	35.851	-0.041	-0.041	0.000	0.000	0.000	0.000
16	D	43	ASN	0	-0.056	-0.028	37.352	0.002	0.002	0.000	0.000	0.000	0.000
17	D	44	ASN	0	-0.015	0.005	35.120	0.002	0.002	0.000	0.000	0.000	0.000
18	D	45	PRO	0	0.002	-0.005	32.792	0.000	0.000	0.000	0.000	0.000	0.000
19	D	46	VAL	0	0.010	0.006	27.326	-0.002	-0.002	0.000	0.000	0.000	0.000
20	D	47	LYS	1	0.887	0.966	22.667	0.203	0.203	0.000	0.000	0.000	0.000
21	D	48	LEU	0	0.012	0.030	22.379	-0.005	-0.005	0.000	0.000	0.000	0.000
22	D	49	SER	0	0.000	-0.020	19.580	-0.002	-0.002	0.000	0.000	0.000	0.000
23	D	50	CYS	0	-0.118	-0.047	15.485	-0.012	-0.012	0.000	0.000	0.000	0.000
24	D	51	ALA	0	0.021	0.021	14.432	-0.012	-0.012	0.000	0.000	0.000	0.000
25	D	52	TYR	0	0.023	-0.003	10.337	0.034	0.034	0.000	0.000	0.000	0.000
26	D	53	SER	0	-0.049	-0.033	8.953	0.030	0.030	0.000	0.000	0.000	0.000
27	D	54	GLY	0	0.062	0.025	4.931	-0.510	-0.510	0.000	0.000	0.000	0.000
28	D	55	PHE	0	-0.054	-0.021	4.835	-0.695	-0.647	-0.001	-0.003	-0.043	0.000
29	D	56	SER	0	-0.041	-0.035	7.286	0.204	0.204	0.000	0.000	0.000	0.000
30	D	57	SER	0	-0.086	-0.056	9.297	0.081	0.081	0.000	0.000	0.000	0.000
31	D	58	PRO	0	0.000	0.008	10.671	0.060	0.060	0.000	0.000	0.000	0.000
32	D	59	ARG	1	0.841	0.900	12.068	0.078	0.078	0.000	0.000	0.000	0.000
33	D	60	VAL	0	0.002	0.002	13.590	0.005	0.005	0.000	0.000	0.000	0.000
34	D	61	GLU	-1	-0.874	-0.934	15.804	0.053	0.053	0.000	0.000	0.000	0.000
35	D	62	TRP	0	0.022	0.004	17.534	-0.001	-0.001	0.000	0.000	0.000	0.000
36	D	63	LYS	1	0.844	0.905	19.025	-0.033	-0.033	0.000	0.000	0.000	0.000
37	D	64	PHE	0	-0.014	0.002	22.270	-0.005	-0.005	0.000	0.000	0.000	0.000
38	D	65	ASP	-1	-0.813	-0.907	22.732	0.021	0.021	0.000	0.000	0.000	0.000
39	D	66	GLN	0	-0.081	-0.053	26.160	-0.004	-0.004	0.000	0.000	0.000	0.000
40	D	67	GLY	0	-0.022	-0.012	29.110	0.002	0.002	0.000	0.000	0.000	0.000
41	D	68	ASP	-1	-0.926	-0.953	29.457	0.020	0.020	0.000	0.000	0.000	0.000
42	D	69	THR	0	-0.028	-0.019	29.533	0.005	0.005	0.000	0.000	0.000	0.000
43	D	70	THR	0	0.007	0.006	24.125	-0.002	-0.002	0.000	0.000	0.000	0.000
44	D	71	ARG	1	0.857	0.918	26.500	0.019	0.019	0.000	0.000	0.000	0.000
45	D	72	LEU	0	-0.005	0.000	22.128	-0.004	-0.004	0.000	0.000	0.000	0.000
46	D	73	VAL	0	0.011	0.025	23.983	-0.002	-0.002	0.000	0.000	0.000	0.000
47	D	74	CYS	0	-0.067	-0.031	21.362	-0.013	-0.013	0.000	0.000	0.000	0.000
48	D	75	TYR	0	0.084	0.036	20.263	0.009	0.009	0.000	0.000	0.000	0.000
49	D	76	ASN	0	0.003	-0.009	18.821	-0.003	-0.003	0.000	0.000	0.000	0.000
50	D	77	ASN	0	0.012	0.018	17.049	-0.003	-0.003	0.000	0.000	0.000	0.000
51	D	78	LYS	1	0.966	0.983	20.560	0.043	0.043	0.000	0.000	0.000	0.000
52	D	79	ILE	0	0.000	0.012	23.950	0.003	0.003	0.000	0.000	0.000	0.000
53	D	80	THR	0	-0.057	-0.039	25.882	0.005	0.005	0.000	0.000	0.000	0.000
54	D	81	ALA	0	0.117	0.050	28.252	-0.003	-0.003	0.000	0.000	0.000	0.000
55	D	82	SER	0	-0.083	-0.031	30.467	0.000	0.000	0.000	0.000	0.000	0.000
56	D	83	TYR	0	0.027	-0.001	28.774	0.002	0.002	0.000	0.000	0.000	0.000
57	D	84	GLU	-1	-0.916	-0.958	30.752	-0.047	-0.047	0.000	0.000	0.000	0.000
58	D	85	ASP	-1	-0.878	-0.935	31.779	-0.053	-0.053	0.000	0.000	0.000	0.000
59	D	86	ARG	1	0.780	0.865	32.370	0.046	0.046	0.000	0.000	0.000	0.000
60	D	87	VAL	0	-0.001	0.016	26.508	-0.006	-0.006	0.000	0.000	0.000	0.000
61	D	88	THR	0	-0.025	-0.006	27.718	-0.001	-0.001	0.000	0.000	0.000	0.000
62	D	89	PHE	0	0.071	0.018	18.292	-0.004	-0.004	0.000	0.000	0.000	0.000
63	D	90	LEU	0	-0.027	-0.010	22.250	0.001	0.001	0.000	0.000	0.000	0.000
64	D	91	PRO	0	0.016	0.009	16.844	0.002	0.002	0.000	0.000	0.000	0.000
65	D	92	THR	0	0.056	0.027	17.370	-0.011	-0.011	0.000	0.000	0.000	0.000
66	D	93	GLY	0	0.023	0.011	19.512	-0.002	-0.002	0.000	0.000	0.000	0.000
67	D	94	ILE	0	-0.036	0.000	20.941	0.008	0.008	0.000	0.000	0.000	0.000
68	D	95	THR	0	0.009	-0.010	23.893	-0.003	-0.003	0.000	0.000	0.000	0.000
69	D	96	PHE	0	-0.007	0.001	26.139	0.007	0.007	0.000	0.000	0.000	0.000
70	D	97	LYS	1	0.836	0.902	30.331	0.069	0.069	0.000	0.000	0.000	0.000
71	D	98	SER	0	-0.008	-0.011	33.982	0.002	0.002	0.000	0.000	0.000	0.000
72	D	99	VAL	0	0.001	0.007	31.022	-0.001	-0.001	0.000	0.000	0.000	0.000
73	D	100	THR	0	0.009	-0.003	34.414	0.003	0.003	0.000	0.000	0.000	0.000
74	D	101	ARG	1	0.914	0.930	34.753	0.034	0.034	0.000	0.000	0.000	0.000
75	D	102	GLU	-1	-0.897	-0.931	35.005	-0.023	-0.023	0.000	0.000	0.000	0.000
76	D	103	ASP	-1	-0.791	-0.856	30.949	-0.046	-0.046	0.000	0.000	0.000	0.000
77	D	104	THR	0	-0.003	0.006	29.842	-0.007	-0.007	0.000	0.000	0.000	0.000
78	D	105	GLY	0	0.043	0.013	27.986	0.007	0.007	0.000	0.000	0.000	0.000
79	D	106	THR	0	-0.026	-0.008	21.627	-0.012	-0.012	0.000	0.000	0.000	0.000
80	D	107	TYR	0	-0.019	-0.015	22.481	0.007	0.007	0.000	0.000	0.000	0.000
81	D	108	THR	0	-0.001	0.009	17.264	-0.014	-0.014	0.000	0.000	0.000	0.000
82	D	110	MET	0	0.004	-0.007	12.448	0.025	0.025	0.000	0.000	0.000	0.000
83	D	111	VAL	0	-0.019	-0.007	10.371	-0.032	-0.032	0.000	0.000	0.000	0.000
84	D	112	SER	0	0.001	-0.014	9.311	0.104	0.104	0.000	0.000	0.000	0.000
85	D	113	GLU	-1	-0.765	-0.853	7.107	-0.923	-0.923	0.000	0.000	0.000	0.000
86	D	114	GLU	-1	-0.839	-0.898	9.228	0.081	0.081	0.000	0.000	0.000	0.000
87	D	115	GLY	0	-0.019	-0.015	11.270	0.028	0.028	0.000	0.000	0.000	0.000
88	D	116	GLY	0	-0.043	-0.021	10.135	0.072	0.072	0.000	0.000	0.000	0.000
89	D	117	ASN	0	0.031	0.022	6.713	-0.160	-0.160	0.000	0.000	0.000	0.000
90	D	118	SER	0	-0.025	-0.017	3.194	-0.425	0.334	0.079	-0.331	-0.506	-0.003
91	D	119	TYR	0	-0.007	-0.014	5.205	-0.408	-0.378	-0.001	-0.001	-0.027	0.000
92	D	120	GLY	0	0.013	0.012	7.131	0.431	0.431	0.000	0.000	0.000	0.000
93	D	121	GLU	-1	-0.872	-0.933	8.973	0.000	0.000	0.000	0.000	0.000	0.000
94	D	122	VAL	0	0.013	-0.001	11.644	-0.035	-0.035	0.000	0.000	0.000	0.000
95	D	123	LYS	1	0.856	0.921	14.467	-0.031	-0.031	0.000	0.000	0.000	0.000
96	D	124	VAL	0	-0.011	0.002	18.113	-0.015	-0.015	0.000	0.000	0.000	0.000
97	D	125	LYS	1	0.849	0.915	20.830	0.066	0.066	0.000	0.000	0.000	0.000
98	D	126	LEU	0	0.025	0.018	24.063	-0.010	-0.010	0.000	0.000	0.000	0.000
99	D	127	ILE	0	-0.020	-0.025	27.134	0.010	0.010	0.000	0.000	0.000	0.000
100	D	128	VAL	0	0.030	0.024	30.511	-0.005	-0.005	0.000	0.000	0.000	0.000
101	D	129	LEU	0	-0.047	-0.018	33.551	0.004	0.004	0.000	0.000	0.000	0.000

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