FMO DATABASE

FMODB ID: 49KVN

Calculation Name: 5D0Q-G-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D0Q

Chain ID: G

ChEMBL ID:

UniProt ID: P0A940

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	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	85
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-376698.533488
FMO2-HF: Nuclear repulsion	345099.562933
FMO2-HF: Total energy	-31598.970555
FMO2-MP2: Total energy	-31688.754371

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(G:29:SER)

Summations of interaction energy for fragment #1(G:29: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.
-7.06	-2.525	1.34	-2.46	-3.414	-0.005

Interaction energy analysis for fragmet #1(G:29:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.036 / q_NPA : 0.009

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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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	G	31	TYR	0	0.066	0.009	2.408	-5.139	-2.582	1.245	-1.706	-2.096	-0.008
4	G	32	LYS	1	0.936	0.972	3.084	1.304	2.128	0.086	-0.196	-0.714	0.000
5	G	33	ARG	1	0.903	0.966	3.388	-4.360	-3.206	0.009	-0.558	-0.604	0.003
6	G	34	GLN	0	0.060	0.052	7.653	0.321	0.321	0.000	0.000	0.000	0.000
7	G	35	VAL	0	0.065	0.034	10.254	-0.062	-0.062	0.000	0.000	0.000	0.000
8	G	36	SER	0	-0.038	-0.023	11.950	0.148	0.148	0.000	0.000	0.000	0.000
9	G	37	GLY	0	0.052	0.024	13.249	-0.110	-0.110	0.000	0.000	0.000	0.000
10	G	38	ASP	-1	-0.863	-0.924	14.522	0.653	0.653	0.000	0.000	0.000	0.000
11	G	39	GLU	-1	-0.795	-0.906	14.764	0.978	0.978	0.000	0.000	0.000	0.000
12	G	40	ALA	0	0.012	0.017	18.479	-0.034	-0.034	0.000	0.000	0.000	0.000
13	G	41	TYR	0	-0.021	-0.013	17.636	-0.036	-0.036	0.000	0.000	0.000	0.000
14	G	42	LEU	0	-0.040	-0.026	19.071	-0.023	-0.023	0.000	0.000	0.000	0.000
15	G	43	GLU	-1	-0.956	-0.968	22.690	0.365	0.365	0.000	0.000	0.000	0.000
16	G	44	ALA	0	-0.033	-0.006	25.292	-0.023	-0.023	0.000	0.000	0.000	0.000
17	G	45	ALA	0	0.001	-0.003	28.092	-0.005	-0.005	0.000	0.000	0.000	0.000
18	G	46	PRO	0	-0.002	0.001	31.739	-0.001	-0.001	0.000	0.000	0.000	0.000
19	G	47	LEU	0	0.010	0.000	32.714	-0.009	-0.009	0.000	0.000	0.000	0.000
20	G	48	ALA	0	-0.056	-0.027	35.377	-0.006	-0.006	0.000	0.000	0.000	0.000
21	G	49	GLU	-1	-0.840	-0.931	38.609	0.110	0.110	0.000	0.000	0.000	0.000
22	G	50	LEU	0	-0.060	-0.016	41.381	-0.001	-0.001	0.000	0.000	0.000	0.000
23	G	51	HIS	0	-0.018	-0.013	43.904	-0.007	-0.007	0.000	0.000	0.000	0.000
24	G	52	ALA	0	-0.003	0.000	48.149	-0.001	-0.001	0.000	0.000	0.000	0.000
25	G	53	PRO	0	-0.007	-0.011	51.467	-0.001	-0.001	0.000	0.000	0.000	0.000
26	G	54	ALA	0	0.017	0.004	54.405	-0.001	-0.001	0.000	0.000	0.000	0.000
27	G	55	GLY	0	-0.024	-0.010	57.782	-0.001	-0.001	0.000	0.000	0.000	0.000
28	G	56	MET	0	-0.038	-0.006	54.538	0.000	0.000	0.000	0.000	0.000	0.000
29	G	57	ILE	0	0.008	0.002	51.938	0.001	0.001	0.000	0.000	0.000	0.000
30	G	58	LEU	0	0.015	0.003	48.711	-0.001	-0.001	0.000	0.000	0.000	0.000
31	G	59	PRO	0	0.008	-0.010	48.204	-0.001	-0.001	0.000	0.000	0.000	0.000
32	G	60	VAL	0	0.013	0.015	45.170	0.004	0.004	0.000	0.000	0.000	0.000
33	G	61	THR	0	0.006	0.003	40.218	-0.003	-0.003	0.000	0.000	0.000	0.000
34	G	62	SER	0	-0.053	-0.022	43.266	-0.002	-0.002	0.000	0.000	0.000	0.000
35	G	63	GLY	0	-0.015	-0.014	43.009	-0.003	-0.003	0.000	0.000	0.000	0.000
36	G	64	ASP	-1	-0.909	-0.945	37.643	0.100	0.100	0.000	0.000	0.000	0.000
37	G	65	TYR	0	-0.051	-0.040	34.736	0.003	0.003	0.000	0.000	0.000	0.000
38	G	66	ALA	0	0.032	0.032	36.042	0.006	0.006	0.000	0.000	0.000	0.000
39	G	67	ILE	0	-0.024	-0.014	31.134	0.004	0.004	0.000	0.000	0.000	0.000
40	G	68	PRO	0	-0.024	-0.010	33.708	-0.002	-0.002	0.000	0.000	0.000	0.000
41	G	69	VAL	0	0.027	0.023	33.358	0.010	0.010	0.000	0.000	0.000	0.000
42	G	70	THR	0	0.002	-0.010	29.961	-0.002	-0.002	0.000	0.000	0.000	0.000
43	G	71	ASN	0	0.003	-0.010	30.308	0.000	0.000	0.000	0.000	0.000	0.000
44	G	72	GLY	0	0.000	0.045	27.180	0.013	0.013	0.000	0.000	0.000	0.000
45	G	73	SER	0	0.000	-0.039	24.562	-0.007	-0.007	0.000	0.000	0.000	0.000
46	G	74	GLY	0	-0.023	-0.012	21.593	-0.018	-0.018	0.000	0.000	0.000	0.000
47	G	75	ALA	0	-0.032	-0.004	16.253	0.013	0.013	0.000	0.000	0.000	0.000
48	G	76	VAL	0	0.051	0.023	17.995	-0.024	-0.024	0.000	0.000	0.000	0.000
49	G	77	GLY	0	0.068	0.037	16.560	0.056	0.056	0.000	0.000	0.000	0.000
50	G	78	LYS	1	0.678	0.805	10.760	-0.976	-0.976	0.000	0.000	0.000	0.000
51	G	79	ALA	0	-0.025	-0.007	11.611	0.101	0.101	0.000	0.000	0.000	0.000
52	G	80	LEU	0	-0.021	-0.002	13.495	-0.051	-0.051	0.000	0.000	0.000	0.000
53	G	81	ASP	-1	-0.792	-0.886	10.750	0.464	0.464	0.000	0.000	0.000	0.000
54	G	82	ILE	0	0.018	0.011	11.323	-0.106	-0.106	0.000	0.000	0.000	0.000
55	G	83	ARG	1	0.790	0.878	8.596	-0.218	-0.218	0.000	0.000	0.000	0.000
56	G	84	PRO	0	0.045	0.029	12.714	0.010	0.010	0.000	0.000	0.000	0.000
57	G	85	PRO	0	-0.016	-0.007	15.778	-0.029	-0.029	0.000	0.000	0.000	0.000
58	G	86	ALA	0	-0.028	-0.012	17.211	-0.005	-0.005	0.000	0.000	0.000	0.000
59	G	87	GLN	0	0.091	0.035	19.020	-0.012	-0.012	0.000	0.000	0.000	0.000
60	G	88	PRO	0	-0.054	-0.015	21.075	-0.012	-0.012	0.000	0.000	0.000	0.000
61	G	189	ALA	0	0.032	0.017	17.746	-0.004	-0.004	0.000	0.000	0.000	0.000
62	G	190	ASP	-1	-0.823	-0.887	16.790	0.215	0.215	0.000	0.000	0.000	0.000
63	G	191	ALA	0	0.057	0.011	19.593	-0.019	-0.019	0.000	0.000	0.000	0.000
64	G	192	ALA	0	0.019	0.020	18.690	-0.024	-0.024	0.000	0.000	0.000	0.000
65	G	193	SER	0	-0.062	-0.076	15.171	-0.018	-0.018	0.000	0.000	0.000	0.000
66	G	194	MET	0	-0.016	-0.006	16.668	-0.044	-0.044	0.000	0.000	0.000	0.000
67	G	195	GLN	0	0.000	0.005	19.449	-0.025	-0.025	0.000	0.000	0.000	0.000
68	G	196	ARG	1	0.870	0.936	13.009	-0.206	-0.206	0.000	0.000	0.000	0.000
69	G	197	TYR	0	0.005	-0.015	9.804	0.022	0.022	0.000	0.000	0.000	0.000
70	G	198	SER	0	0.002	0.008	16.479	-0.032	-0.032	0.000	0.000	0.000	0.000
71	G	199	THR	0	-0.015	-0.011	18.732	-0.011	-0.011	0.000	0.000	0.000	0.000
72	G	200	GLU	-1	-0.972	-0.973	12.886	-0.349	-0.349	0.000	0.000	0.000	0.000
73	G	201	MET	0	-0.029	-0.016	17.145	-0.017	-0.017	0.000	0.000	0.000	0.000
74	G	202	MET	0	0.060	0.034	19.970	-0.003	-0.003	0.000	0.000	0.000	0.000
75	G	203	ASN	0	0.016	0.008	17.742	0.021	0.021	0.000	0.000	0.000	0.000
76	G	204	VAL	0	-0.021	-0.006	18.603	-0.006	-0.006	0.000	0.000	0.000	0.000
77	G	205	ILE	0	-0.011	-0.009	21.296	0.004	0.004	0.000	0.000	0.000	0.000
78	G	206	SER	0	-0.046	-0.030	24.174	0.011	0.011	0.000	0.000	0.000	0.000
79	G	207	ALA	0	0.003	-0.003	22.786	0.006	0.006	0.000	0.000	0.000	0.000
80	G	208	GLY	0	-0.011	-0.004	24.801	-0.003	-0.003	0.000	0.000	0.000	0.000
81	G	209	LEU	0	-0.013	0.006	26.273	0.004	0.004	0.000	0.000	0.000	0.000
82	G	210	ASP	-1	-0.892	-0.949	28.010	-0.133	-0.133	0.000	0.000	0.000	0.000
83	G	211	LYS	1	0.848	0.917	26.333	0.179	0.179	0.000	0.000	0.000	0.000
84	G	212	SER	0	-0.069	-0.042	29.165	-0.009	-0.009	0.000	0.000	0.000	0.000
85	G	213	ALA	0	-0.030	0.016	32.267	0.009	0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(G:29:SER)