FMO DATABASE

FMODB ID: J38L9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-490094.157263
FMO2-HF: Nuclear repulsion	455966.667526
FMO2-HF: Total energy	-34127.489737
FMO2-MP2: Total energy	-34221.912881

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.
-398.484	-391.635	35.646	-20.6	-21.894	-0.223

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 : 0.768 / q_NPA : 0.880

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	0.004	-0.013	3.812	1.187	2.819	-0.023	-0.790	-0.819	0.000
4	A	5	VAL	0	-0.022	0.003	6.391	0.859	0.859	0.000	0.000	0.000	0.000
5	A	6	GLU	-1	-0.838	-0.912	9.147	-14.354	-14.354	0.000	0.000	0.000	0.000
6	A	7	VAL	0	0.003	-0.005	12.731	0.114	0.114	0.000	0.000	0.000	0.000
7	A	8	ARG	1	0.804	0.900	15.671	14.069	14.069	0.000	0.000	0.000	0.000
8	A	9	ILE	0	0.024	0.011	19.138	0.033	0.033	0.000	0.000	0.000	0.000
9	A	10	ARG	1	0.936	0.973	22.025	11.279	11.279	0.000	0.000	0.000	0.000
10	A	11	LEU	0	-0.017	0.002	25.679	-0.039	-0.039	0.000	0.000	0.000	0.000
11	A	12	LYS	1	0.856	0.957	28.648	10.364	10.364	0.000	0.000	0.000	0.000
12	A	13	LYS	1	1.001	0.981	30.781	8.231	8.231	0.000	0.000	0.000	0.000
13	A	14	GLY	0	-0.059	-0.029	33.846	0.051	0.051	0.000	0.000	0.000	0.000
14	A	15	MET	0	-0.038	-0.005	32.322	0.270	0.270	0.000	0.000	0.000	0.000
15	A	16	LEU	0	-0.003	-0.003	34.797	0.016	0.016	0.000	0.000	0.000	0.000
16	A	17	ASN	0	0.066	0.020	30.304	-0.136	-0.136	0.000	0.000	0.000	0.000
17	A	18	PRO	0	-0.006	-0.011	33.233	0.154	0.154	0.000	0.000	0.000	0.000
18	A	19	GLU	-1	-0.868	-0.917	30.432	-8.471	-8.471	0.000	0.000	0.000	0.000
19	A	20	ALA	0	0.017	0.016	32.518	0.163	0.163	0.000	0.000	0.000	0.000
20	A	21	ALA	0	0.013	0.001	33.993	0.194	0.194	0.000	0.000	0.000	0.000
21	A	22	THR	0	-0.081	-0.057	36.061	0.300	0.300	0.000	0.000	0.000	0.000
22	A	23	ILE	0	-0.018	-0.017	31.906	0.185	0.185	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.816	-0.872	36.418	-7.352	-7.352	0.000	0.000	0.000	0.000
24	A	25	ARG	1	0.969	0.985	38.682	6.761	6.761	0.000	0.000	0.000	0.000
25	A	26	ALA	0	-0.037	-0.020	39.001	0.177	0.177	0.000	0.000	0.000	0.000
26	A	27	LEU	0	0.020	0.001	36.246	0.141	0.141	0.000	0.000	0.000	0.000
27	A	28	ALA	0	0.087	0.053	40.681	0.143	0.143	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.108	-0.055	43.899	0.178	0.178	0.000	0.000	0.000	0.000
29	A	30	LEU	0	-0.108	-0.046	40.520	0.124	0.124	0.000	0.000	0.000	0.000
30	A	31	GLY	0	-0.037	-0.011	44.479	0.056	0.056	0.000	0.000	0.000	0.000
31	A	32	TYR	0	-0.117	-0.059	40.885	-0.009	-0.009	0.000	0.000	0.000	0.000
32	A	33	GLU	-1	-0.917	-0.959	42.536	-6.399	-6.399	0.000	0.000	0.000	0.000
33	A	34	VAL	0	-0.078	-0.041	37.658	-0.062	-0.062	0.000	0.000	0.000	0.000
34	A	35	GLU	-1	-0.910	-0.957	39.252	-6.738	-6.738	0.000	0.000	0.000	0.000
35	A	36	ASP	-1	-1.005	-1.002	36.144	-7.745	-7.745	0.000	0.000	0.000	0.000
36	A	37	THR	0	-0.060	-0.045	33.659	-0.281	-0.281	0.000	0.000	0.000	0.000
37	A	38	ASP	-1	-0.883	-0.959	29.692	-9.520	-9.520	0.000	0.000	0.000	0.000
38	A	39	THR	0	-0.046	-0.023	27.738	0.076	0.076	0.000	0.000	0.000	0.000
39	A	40	THR	0	-0.077	-0.040	22.113	-0.097	-0.097	0.000	0.000	0.000	0.000
40	A	41	ASP	-1	-0.908	-0.930	21.683	-11.191	-11.191	0.000	0.000	0.000	0.000
41	A	42	VAL	0	-0.020	-0.027	16.223	-0.317	-0.317	0.000	0.000	0.000	0.000
42	A	43	ILE	0	-0.020	0.001	13.966	0.041	0.041	0.000	0.000	0.000	0.000
43	A	44	THR	0	0.003	0.000	11.314	-0.516	-0.516	0.000	0.000	0.000	0.000
44	A	45	PHE	0	-0.032	-0.027	8.259	0.521	0.521	0.000	0.000	0.000	0.000
45	A	46	THR	0	0.003	0.002	2.747	-0.452	0.118	0.205	-0.260	-0.514	0.001
46	A	47	MET	0	-0.018	0.003	3.612	2.249	2.592	0.000	-0.080	-0.263	0.000
47	A	48	ASP	-1	-0.879	-0.945	1.723	-136.520	-134.057	19.164	-10.983	-10.644	-0.137
48	A	49	GLU	-1	-0.806	-0.909	1.794	-40.993	-41.187	4.322	-1.444	-2.683	-0.008
49	A	50	ASP	-1	-0.929	-0.954	1.780	-103.124	-103.667	11.586	-6.109	-4.934	-0.083
50	A	51	SER	0	-0.084	-0.052	4.030	6.885	7.012	-0.001	-0.016	-0.110	0.000
51	A	52	LEU	0	0.052	0.018	6.396	-0.884	-0.884	0.000	0.000	0.000	0.000
52	A	53	GLU	-1	-0.916	-0.957	7.674	-20.519	-20.519	0.000	0.000	0.000	0.000
53	A	54	ALA	0	-0.022	-0.011	7.928	2.500	2.500	0.000	0.000	0.000	0.000
54	A	55	VAL	0	0.040	0.014	5.582	1.743	1.743	0.000	0.000	0.000	0.000
55	A	56	GLU	-1	-0.925	-0.954	8.802	-19.678	-19.678	0.000	0.000	0.000	0.000
56	A	57	ARG	1	0.910	0.949	11.984	20.784	20.784	0.000	0.000	0.000	0.000
57	A	58	GLU	-1	-0.927	-0.957	10.522	-27.555	-27.555	0.000	0.000	0.000	0.000
58	A	59	VAL	0	0.008	-0.014	10.276	1.509	1.509	0.000	0.000	0.000	0.000
59	A	60	GLU	-1	-0.793	-0.861	12.956	-13.815	-13.815	0.000	0.000	0.000	0.000
60	A	61	ASP	-1	-0.858	-0.907	15.743	-15.614	-15.614	0.000	0.000	0.000	0.000
61	A	62	MET	0	-0.021	-0.019	10.676	1.294	1.294	0.000	0.000	0.000	0.000
62	A	63	CYS	0	-0.045	-0.019	16.200	0.900	0.900	0.000	0.000	0.000	0.000
63	A	64	GLN	0	-0.056	-0.031	18.819	1.404	1.404	0.000	0.000	0.000	0.000
64	A	65	ARG	1	0.768	0.868	18.988	16.715	16.715	0.000	0.000	0.000	0.000
65	A	66	LEU	0	-0.091	-0.041	18.068	0.144	0.144	0.000	0.000	0.000	0.000
66	A	67	LEU	0	0.008	-0.005	15.025	0.528	0.528	0.000	0.000	0.000	0.000
67	A	68	CYS	0	-0.057	-0.006	19.745	0.483	0.483	0.000	0.000	0.000	0.000
68	A	69	ASN	0	0.048	0.020	22.925	-0.102	-0.102	0.000	0.000	0.000	0.000
69	A	70	PRO	0	0.110	0.057	23.620	0.466	0.466	0.000	0.000	0.000	0.000
70	A	71	VAL	0	-0.065	-0.029	26.227	0.347	0.347	0.000	0.000	0.000	0.000
71	A	72	ILE	0	-0.038	-0.034	28.982	0.358	0.358	0.000	0.000	0.000	0.000
72	A	73	HIS	0	0.017	0.016	24.878	0.068	0.068	0.000	0.000	0.000	0.000
73	A	74	ASP	-1	-0.859	-0.937	25.595	-10.568	-10.568	0.000	0.000	0.000	0.000
74	A	75	TYR	0	-0.100	-0.099	18.931	0.323	0.323	0.000	0.000	0.000	0.000
75	A	76	ASP	-1	-0.915	-0.952	19.153	-12.751	-12.751	0.000	0.000	0.000	0.000
76	A	77	VAL	0	0.032	0.001	13.477	-0.342	-0.342	0.000	0.000	0.000	0.000
77	A	78	SER	0	-0.071	-0.018	13.694	0.089	0.089	0.000	0.000	0.000	0.000
78	A	79	ILE	0	0.046	0.006	7.395	-0.698	-0.698	0.000	0.000	0.000	0.000
79	A	80	ASN	0	-0.039	-0.011	8.654	1.316	1.316	0.000	0.000	0.000	0.000
80	A	81	GLU	-1	-0.905	-0.950	4.127	-38.189	-37.997	-0.001	-0.024	-0.168	0.000
81	A	82	MET	0	-0.096	-0.041	2.949	0.755	3.014	0.394	-0.894	-1.759	0.004

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