FMO DATABASE

FMODB ID: N1R9Q

Calculation Name: 1GTD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1GTD

Chain ID: A

ChEMBL ID:

UniProt ID: O26271

Base Structure: X-ray

Registration Date: 2023-06-21

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	81
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-490259.260562
FMO2-HF: Nuclear repulsion	456132.295497
FMO2-HF: Total energy	-34126.965064
FMO2-MP2: Total energy	-34221.445232

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:2:LYS)

Summations of interaction energy for fragment #1(A:2:LYS)

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.
-319.157	-303.202	6.037	-9.526	-12.467	-0.075

Interaction energy analysis for fragmet #1(A:2:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.908 / q_NPA : 0.964

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	4	MET	0	-0.005	-0.014	3.812	1.606	3.265	-0.024	-0.794	-0.841	0.000
4	A	5	VAL	0	-0.017	0.002	6.393	0.594	0.594	0.000	0.000	0.000	0.000
5	A	6	GLU	-1	-0.928	-0.979	9.161	-14.510	-14.510	0.000	0.000	0.000	0.000
6	A	7	VAL	0	0.003	0.001	12.744	0.107	0.107	0.000	0.000	0.000	0.000
7	A	8	ARG	1	0.913	0.966	15.683	13.536	13.536	0.000	0.000	0.000	0.000
8	A	9	ILE	0	0.029	0.020	19.114	0.052	0.052	0.000	0.000	0.000	0.000
9	A	10	ARG	1	0.944	0.976	22.035	10.700	10.700	0.000	0.000	0.000	0.000
10	A	11	LEU	0	-0.009	0.004	25.690	-0.047	-0.047	0.000	0.000	0.000	0.000
11	A	12	LYS	1	0.891	0.969	28.941	10.104	10.104	0.000	0.000	0.000	0.000
12	A	13	LYS	1	1.004	0.988	30.793	8.197	8.197	0.000	0.000	0.000	0.000
13	A	14	GLY	0	-0.065	-0.033	33.858	0.055	0.055	0.000	0.000	0.000	0.000
14	A	15	MET	0	-0.037	-0.006	32.599	0.277	0.277	0.000	0.000	0.000	0.000
15	A	16	LEU	0	0.007	0.001	34.742	0.002	0.002	0.000	0.000	0.000	0.000
16	A	17	ASN	0	0.084	0.035	30.430	-0.122	-0.122	0.000	0.000	0.000	0.000
17	A	18	PRO	0	-0.010	-0.015	33.199	0.156	0.156	0.000	0.000	0.000	0.000
18	A	19	GLU	-1	-0.857	-0.891	30.552	-8.266	-8.266	0.000	0.000	0.000	0.000
19	A	20	ALA	0	0.000	0.012	32.614	0.140	0.140	0.000	0.000	0.000	0.000
20	A	21	ALA	0	0.000	-0.005	34.001	0.182	0.182	0.000	0.000	0.000	0.000
21	A	22	THR	0	-0.075	-0.077	36.033	0.284	0.284	0.000	0.000	0.000	0.000
22	A	23	ILE	0	-0.012	-0.012	31.938	0.178	0.178	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.811	-0.861	36.424	-7.269	-7.269	0.000	0.000	0.000	0.000
24	A	25	ARG	1	0.968	0.984	38.690	6.690	6.690	0.000	0.000	0.000	0.000
25	A	26	ALA	0	-0.039	-0.022	39.004	0.175	0.175	0.000	0.000	0.000	0.000
26	A	27	LEU	0	0.023	0.002	36.298	0.139	0.139	0.000	0.000	0.000	0.000
27	A	28	ALA	0	0.085	0.052	40.688	0.139	0.139	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.110	-0.058	43.907	0.176	0.176	0.000	0.000	0.000	0.000
29	A	30	LEU	0	-0.107	-0.046	40.522	0.122	0.122	0.000	0.000	0.000	0.000
30	A	31	GLY	0	-0.035	-0.009	44.484	0.054	0.054	0.000	0.000	0.000	0.000
31	A	32	TYR	0	-0.116	-0.058	40.918	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	33	GLU	-1	-0.931	-0.970	42.545	-6.394	-6.394	0.000	0.000	0.000	0.000
33	A	34	VAL	0	-0.082	-0.038	37.933	-0.068	-0.068	0.000	0.000	0.000	0.000
34	A	35	GLU	-1	-0.880	-0.943	39.253	-6.726	-6.726	0.000	0.000	0.000	0.000
35	A	36	ASP	-1	-1.015	-1.007	36.237	-7.687	-7.687	0.000	0.000	0.000	0.000
36	A	37	THR	0	-0.061	-0.053	33.711	-0.286	-0.286	0.000	0.000	0.000	0.000
37	A	38	ASP	-1	-0.870	-0.952	30.309	-9.362	-9.362	0.000	0.000	0.000	0.000
38	A	39	THR	0	-0.066	-0.040	27.543	0.058	0.058	0.000	0.000	0.000	0.000
39	A	40	THR	0	-0.085	-0.050	22.096	-0.057	-0.057	0.000	0.000	0.000	0.000
40	A	41	ASP	-1	-0.908	-0.932	21.494	-11.056	-11.056	0.000	0.000	0.000	0.000
41	A	42	VAL	0	-0.019	-0.026	16.150	-0.260	-0.260	0.000	0.000	0.000	0.000
42	A	43	ILE	0	-0.024	-0.001	13.984	0.079	0.079	0.000	0.000	0.000	0.000
43	A	44	THR	0	0.004	0.002	11.322	-0.488	-0.488	0.000	0.000	0.000	0.000
44	A	45	PHE	0	-0.051	-0.043	8.089	0.627	0.627	0.000	0.000	0.000	0.000
45	A	46	THR	0	0.011	0.012	2.856	-0.234	0.271	0.138	-0.208	-0.435	0.001
46	A	47	MET	0	-0.023	0.000	3.624	2.608	2.918	0.000	-0.075	-0.235	0.000
47	A	48	ASP	-1	-0.930	-0.968	2.232	-70.962	-65.524	2.170	-3.638	-3.971	-0.035
48	A	49	GLU	-1	-0.855	-0.949	2.043	-36.710	-35.871	1.501	-0.608	-1.732	-0.009
49	A	50	ASP	-1	-0.987	-0.987	2.595	-86.332	-81.961	1.808	-3.138	-3.041	-0.038
50	A	51	SER	0	-0.063	-0.051	4.421	3.309	3.405	-0.001	-0.005	-0.090	0.000
51	A	52	LEU	0	0.042	0.018	6.428	-0.396	-0.396	0.000	0.000	0.000	0.000
52	A	53	GLU	-1	-0.935	-0.968	7.653	-20.778	-20.778	0.000	0.000	0.000	0.000
53	A	54	ALA	0	0.000	0.004	8.467	2.502	2.502	0.000	0.000	0.000	0.000
54	A	55	VAL	0	0.059	0.025	5.624	2.013	2.013	0.000	0.000	0.000	0.000
55	A	56	GLU	-1	-0.927	-0.957	8.859	-19.948	-19.948	0.000	0.000	0.000	0.000
56	A	57	ARG	1	0.921	0.954	11.938	20.390	20.390	0.000	0.000	0.000	0.000
57	A	58	GLU	-1	-0.903	-0.952	10.081	-26.904	-26.904	0.000	0.000	0.000	0.000
58	A	59	VAL	0	-0.012	-0.017	10.446	1.456	1.456	0.000	0.000	0.000	0.000
59	A	60	GLU	-1	-0.799	-0.879	13.009	-13.713	-13.713	0.000	0.000	0.000	0.000
60	A	61	ASP	-1	-0.883	-0.945	15.797	-15.012	-15.012	0.000	0.000	0.000	0.000
61	A	62	MET	0	-0.046	-0.031	10.703	1.312	1.312	0.000	0.000	0.000	0.000
62	A	63	CYS	0	-0.036	-0.018	16.327	0.873	0.873	0.000	0.000	0.000	0.000
63	A	64	GLN	0	-0.048	-0.032	18.825	1.427	1.427	0.000	0.000	0.000	0.000
64	A	65	ARG	1	0.785	0.909	19.635	15.834	15.834	0.000	0.000	0.000	0.000
65	A	66	LEU	0	-0.091	-0.048	18.058	0.167	0.167	0.000	0.000	0.000	0.000
66	A	67	LEU	0	0.008	-0.001	15.068	0.488	0.488	0.000	0.000	0.000	0.000
67	A	68	CYS	0	-0.057	-0.006	19.749	0.439	0.439	0.000	0.000	0.000	0.000
68	A	69	ASN	0	0.026	0.015	22.931	-0.069	-0.069	0.000	0.000	0.000	0.000
69	A	70	PRO	0	0.124	0.057	24.129	0.427	0.427	0.000	0.000	0.000	0.000
70	A	71	VAL	0	-0.065	-0.028	26.259	0.322	0.322	0.000	0.000	0.000	0.000
71	A	72	ILE	0	-0.052	-0.042	28.907	0.352	0.352	0.000	0.000	0.000	0.000
72	A	73	HIS	0	0.017	0.019	24.913	0.033	0.033	0.000	0.000	0.000	0.000
73	A	74	ASP	-1	-0.883	-0.945	25.607	-10.517	-10.517	0.000	0.000	0.000	0.000
74	A	75	TYR	0	-0.088	-0.076	19.271	0.303	0.303	0.000	0.000	0.000	0.000
75	A	76	ASP	-1	-0.937	-0.955	19.136	-12.841	-12.841	0.000	0.000	0.000	0.000
76	A	77	VAL	0	0.025	-0.006	13.509	-0.282	-0.282	0.000	0.000	0.000	0.000
77	A	78	SER	0	-0.061	-0.013	13.015	0.355	0.355	0.000	0.000	0.000	0.000
78	A	79	ILE	0	0.029	0.001	7.391	-0.575	-0.575	0.000	0.000	0.000	0.000
79	A	80	ASN	0	-0.018	-0.006	8.655	0.957	0.957	0.000	0.000	0.000	0.000
80	A	81	GLU	-1	-0.924	-0.958	4.186	-41.155	-40.960	-0.001	-0.022	-0.173	0.000
81	A	82	MET	0	-0.106	-0.050	2.939	-0.123	2.419	0.446	-1.038	-1.949	0.006

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:LYS)