FMO DATABASE

FMODB ID: N3M5Q

Calculation Name: 2ODM-A-Xray311

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2ODM

Chain ID: A

ChEMBL ID:

UniProt ID: Q7A161

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	85
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-545491.585123
FMO2-HF: Nuclear repulsion	511942.974238
FMO2-HF: Total energy	-33548.610885
FMO2-MP2: Total energy	-33645.201034

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:4:ACE )

Summations of interaction energy for fragment #1(A:4:ACE )

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.
1.049	2.746	-0.004	-0.803	-0.89	-0.001

Interaction energy analysis for fragmet #1(A:4:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / q_NPA : 0.002

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	A	6	THR	0	0.032	0.014	3.843	0.065	1.534	-0.004	-0.757	-0.708	-0.001
4	A	7	MET	0	0.017	0.000	4.215	0.004	0.155	0.000	-0.022	-0.129	0.000
5	A	8	LYS	1	0.939	0.984	5.141	1.393	1.470	0.000	-0.024	-0.053	0.000
6	A	9	ASN	0	0.018	0.016	7.245	0.275	0.275	0.000	0.000	0.000	0.000
7	A	10	ALA	0	0.012	0.000	9.156	0.112	0.112	0.000	0.000	0.000	0.000
8	A	11	ALA	0	0.013	0.015	9.644	0.074	0.074	0.000	0.000	0.000	0.000
9	A	12	LEU	0	0.034	0.007	11.230	0.063	0.063	0.000	0.000	0.000	0.000
10	A	13	LYS	1	0.884	0.945	13.177	0.385	0.385	0.000	0.000	0.000	0.000
11	A	14	GLN	0	-0.033	-0.001	14.450	0.030	0.030	0.000	0.000	0.000	0.000
12	A	15	LEU	0	0.035	0.015	14.674	0.017	0.017	0.000	0.000	0.000	0.000
13	A	16	THR	0	-0.033	-0.024	17.276	0.022	0.022	0.000	0.000	0.000	0.000
14	A	17	LYS	1	0.973	0.998	19.030	0.090	0.090	0.000	0.000	0.000	0.000
15	A	18	ASP	-1	-0.768	-0.870	19.515	-0.077	-0.077	0.000	0.000	0.000	0.000
16	A	19	ALA	0	-0.014	-0.018	21.439	0.009	0.009	0.000	0.000	0.000	0.000
17	A	20	ASP	-1	-0.921	-0.969	23.260	-0.109	-0.109	0.000	0.000	0.000	0.000
18	A	21	GLU	-1	-0.972	-0.979	25.012	-0.049	-0.049	0.000	0.000	0.000	0.000
19	A	22	ILE	0	0.020	0.010	24.916	0.006	0.006	0.000	0.000	0.000	0.000
20	A	23	LEU	0	-0.026	-0.029	27.365	0.003	0.003	0.000	0.000	0.000	0.000
21	A	24	HIS	0	-0.028	-0.003	29.200	0.001	0.001	0.000	0.000	0.000	0.000
22	A	25	LEU	0	-0.013	0.006	31.086	0.005	0.005	0.000	0.000	0.000	0.000
23	A	26	ILE	0	0.000	0.000	30.338	0.003	0.003	0.000	0.000	0.000	0.000
24	A	27	LYS	1	0.954	0.957	30.702	0.079	0.079	0.000	0.000	0.000	0.000
25	A	28	VAL	0	0.009	0.019	34.928	0.003	0.003	0.000	0.000	0.000	0.000
26	A	29	GLN	0	-0.005	0.015	36.900	0.004	0.004	0.000	0.000	0.000	0.000
27	A	30	LEU	0	-0.007	0.003	36.080	0.002	0.002	0.000	0.000	0.000	0.000
28	A	31	ASP	-1	-0.956	-0.971	37.881	-0.048	-0.048	0.000	0.000	0.000	0.000
29	A	32	ASN	0	-0.067	-0.046	40.727	0.004	0.004	0.000	0.000	0.000	0.000
30	A	33	LEU	0	0.025	0.038	43.423	0.001	0.001	0.000	0.000	0.000	0.000
31	A	34	THR	0	-0.101	-0.082	42.604	0.001	0.001	0.000	0.000	0.000	0.000
32	A	35	LEU	0	-0.042	-0.016	42.381	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	36	PRO	0	-0.033	-0.017	41.445	0.002	0.002	0.000	0.000	0.000	0.000
34	A	37	SER	0	0.110	0.027	41.660	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	38	CYS	0	-0.117	0.021	41.634	0.000	0.000	0.000	0.000	0.000	0.000
36	A	39	PRO	0	-0.031	-0.033	43.516	0.000	0.000	0.000	0.000	0.000	0.000
37	A	40	LEU	0	0.087	0.007	41.744	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	41	TYR	0	-0.011	-0.011	36.278	0.001	0.001	0.000	0.000	0.000	0.000
39	A	42	GLU	-1	-0.906	-0.960	37.212	-0.039	-0.039	0.000	0.000	0.000	0.000
40	A	43	GLU	-1	-0.925	-0.951	36.018	-0.026	-0.026	0.000	0.000	0.000	0.000
41	A	44	VAL	0	-0.019	-0.013	34.072	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	45	LEU	0	0.002	-0.017	32.274	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	46	ASP	-1	-0.832	-0.900	31.079	-0.050	-0.050	0.000	0.000	0.000	0.000
44	A	47	THR	0	-0.068	-0.033	30.437	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	48	GLN	0	-0.054	-0.028	28.264	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	49	MET	0	0.011	0.016	26.584	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	50	PHE	0	-0.012	-0.006	25.810	-0.007	-0.007	0.000	0.000	0.000	0.000
48	A	51	GLY	0	0.003	-0.011	24.783	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	52	LEU	0	0.038	0.023	20.699	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	53	GLN	0	0.027	0.004	20.812	-0.012	-0.012	0.000	0.000	0.000	0.000
51	A	54	LYS	1	0.871	0.946	20.781	0.050	0.050	0.000	0.000	0.000	0.000
52	A	55	GLH	0	-0.071	-0.054	17.840	0.002	0.002	0.000	0.000	0.000	0.000
53	A	56	VAL	0	0.004	0.006	16.383	-0.025	-0.025	0.000	0.000	0.000	0.000
54	A	57	ASP	-1	-0.887	-0.948	16.200	-0.134	-0.134	0.000	0.000	0.000	0.000
55	A	58	PHE	0	-0.075	-0.034	13.727	-0.006	-0.006	0.000	0.000	0.000	0.000
56	A	59	ALA	0	0.030	0.007	12.214	0.003	0.003	0.000	0.000	0.000	0.000
57	A	60	VAL	0	-0.026	-0.016	11.590	-0.064	-0.064	0.000	0.000	0.000	0.000
58	A	61	LYS	1	0.910	0.946	12.725	0.046	0.046	0.000	0.000	0.000	0.000
59	A	62	LEU	0	-0.060	-0.016	9.427	0.016	0.016	0.000	0.000	0.000	0.000
60	A	63	GLY	0	0.006	0.016	8.302	-0.008	-0.008	0.000	0.000	0.000	0.000
61	A	64	LEU	0	-0.067	-0.034	6.250	-0.337	-0.337	0.000	0.000	0.000	0.000
62	A	65	VAL	0	-0.004	-0.011	8.287	-0.159	-0.159	0.000	0.000	0.000	0.000
63	A	66	ASP	-1	-0.837	-0.913	11.304	-0.617	-0.617	0.000	0.000	0.000	0.000
64	A	67	ARG	1	0.942	0.950	13.131	0.267	0.267	0.000	0.000	0.000	0.000
65	A	68	GLU	-1	-0.930	-0.971	16.363	-0.162	-0.162	0.000	0.000	0.000	0.000
66	A	69	ASP	-1	-0.833	-0.913	14.213	-0.407	-0.407	0.000	0.000	0.000	0.000
67	A	70	GLY	0	-0.003	-0.009	16.722	0.029	0.029	0.000	0.000	0.000	0.000
68	A	71	LYS	1	0.931	0.955	18.067	0.178	0.178	0.000	0.000	0.000	0.000
69	A	72	GLN	0	0.004	0.010	20.392	0.026	0.026	0.000	0.000	0.000	0.000
70	A	73	ILE	0	-0.039	-0.013	17.185	0.014	0.014	0.000	0.000	0.000	0.000
71	A	74	MET	0	-0.030	0.003	21.572	0.012	0.012	0.000	0.000	0.000	0.000
72	A	75	LEU	0	0.054	0.020	24.026	0.011	0.011	0.000	0.000	0.000	0.000
73	A	76	ARG	1	0.885	0.955	23.757	0.133	0.133	0.000	0.000	0.000	0.000
74	A	77	LEU	0	-0.020	-0.013	25.050	0.008	0.008	0.000	0.000	0.000	0.000
75	A	78	GLU	-1	-0.846	-0.929	27.361	-0.087	-0.087	0.000	0.000	0.000	0.000
76	A	79	LYS	1	0.915	0.968	29.951	0.082	0.082	0.000	0.000	0.000	0.000
77	A	80	GLU	-1	-0.898	-0.957	31.119	-0.070	-0.070	0.000	0.000	0.000	0.000
78	A	81	LEU	0	0.026	-0.004	31.321	0.004	0.004	0.000	0.000	0.000	0.000
79	A	82	SER	0	-0.039	-0.011	33.853	0.005	0.005	0.000	0.000	0.000	0.000
80	A	83	LYS	1	0.792	0.885	34.939	0.070	0.070	0.000	0.000	0.000	0.000
81	A	84	LEU	0	0.013	0.011	36.536	0.002	0.002	0.000	0.000	0.000	0.000
82	A	85	HIS	0	-0.028	0.006	36.443	0.003	0.003	0.000	0.000	0.000	0.000
83	A	86	GLU	-1	-0.935	-0.980	40.489	-0.044	-0.044	0.000	0.000	0.000	0.000
84	A	87	ALA	0	-0.102	-0.046	43.459	0.001	0.001	0.000	0.000	0.000	0.000
85	A	88	NME	0	0.066	0.038	43.588	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:ACE )