FMO DATABASE

FMODB ID: 3Q29L

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

Total energy (hartree)

FMO2-HF: Electronic energy	-490789.051938
FMO2-HF: Nuclear repulsion	456661.313448
FMO2-HF: Total energy	-34127.73849
FMO2-MP2: Total energy	-34222.159516

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.
-428.739	-426.493	46.49	-22.562	-26.173	-0.259

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 : 0.751 / q_NPA : 0.865

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	0.000	0.000	3.881	1.155	2.646	-0.018	-0.731	-0.742	0.000
4	A	5	VAL	0	-0.007	0.007	6.715	0.700	0.700	0.000	0.000	0.000	0.000
5	A	6	GLU	-1	-0.831	-0.903	9.086	-14.126	-14.126	0.000	0.000	0.000	0.000
6	A	7	VAL	0	0.001	0.006	12.745	-0.131	-0.131	0.000	0.000	0.000	0.000
7	A	8	ARG	1	0.808	0.881	15.568	14.106	14.106	0.000	0.000	0.000	0.000
8	A	9	ILE	0	0.028	0.009	19.194	-0.098	-0.098	0.000	0.000	0.000	0.000
9	A	10	ARG	1	0.864	0.919	22.178	11.585	11.585	0.000	0.000	0.000	0.000
10	A	11	LEU	0	-0.013	-0.002	25.868	-0.073	-0.073	0.000	0.000	0.000	0.000
11	A	12	LYS	1	0.840	0.936	28.524	10.507	10.507	0.000	0.000	0.000	0.000
12	A	13	LYS	1	0.985	0.977	31.085	8.267	8.267	0.000	0.000	0.000	0.000
13	A	14	GLY	0	-0.025	-0.015	34.028	0.151	0.151	0.000	0.000	0.000	0.000
14	A	15	MET	0	-0.058	-0.013	32.357	0.268	0.268	0.000	0.000	0.000	0.000
15	A	16	LEU	0	-0.008	-0.005	35.125	0.048	0.048	0.000	0.000	0.000	0.000
16	A	17	ASN	0	0.057	0.007	30.372	-0.129	-0.129	0.000	0.000	0.000	0.000
17	A	18	PRO	0	-0.016	-0.019	33.203	0.173	0.173	0.000	0.000	0.000	0.000
18	A	19	GLU	-1	-0.878	-0.922	30.581	-8.478	-8.478	0.000	0.000	0.000	0.000
19	A	20	ALA	0	0.016	0.021	32.616	0.159	0.159	0.000	0.000	0.000	0.000
20	A	21	ALA	0	0.047	0.021	34.136	0.194	0.194	0.000	0.000	0.000	0.000
21	A	22	THR	0	-0.081	-0.053	36.321	0.307	0.307	0.000	0.000	0.000	0.000
22	A	23	ILE	0	-0.008	-0.010	32.141	0.180	0.180	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.823	-0.879	36.610	-7.371	-7.371	0.000	0.000	0.000	0.000
24	A	25	ARG	1	0.950	0.971	38.918	6.793	6.793	0.000	0.000	0.000	0.000
25	A	26	ALA	0	-0.042	-0.028	39.133	0.186	0.186	0.000	0.000	0.000	0.000
26	A	27	LEU	0	-0.002	-0.001	36.497	0.128	0.128	0.000	0.000	0.000	0.000
27	A	28	ALA	0	0.085	0.053	40.917	0.141	0.141	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.097	-0.056	44.218	0.175	0.175	0.000	0.000	0.000	0.000
29	A	30	LEU	0	-0.076	-0.028	41.018	0.118	0.118	0.000	0.000	0.000	0.000
30	A	31	GLY	0	-0.052	-0.019	44.858	0.042	0.042	0.000	0.000	0.000	0.000
31	A	32	TYR	0	-0.113	-0.059	41.183	0.003	0.003	0.000	0.000	0.000	0.000
32	A	33	GLU	-1	-0.909	-0.959	42.251	-6.422	-6.422	0.000	0.000	0.000	0.000
33	A	34	VAL	0	-0.087	-0.047	38.248	-0.088	-0.088	0.000	0.000	0.000	0.000
34	A	35	GLU	-1	-0.910	-0.955	39.321	-6.696	-6.696	0.000	0.000	0.000	0.000
35	A	36	ASP	-1	-0.996	-0.994	36.342	-7.767	-7.767	0.000	0.000	0.000	0.000
36	A	37	THR	0	-0.081	-0.051	34.000	-0.288	-0.288	0.000	0.000	0.000	0.000
37	A	38	ASP	-1	-0.860	-0.942	29.944	-9.473	-9.473	0.000	0.000	0.000	0.000
38	A	39	THR	0	-0.065	-0.031	27.733	0.049	0.049	0.000	0.000	0.000	0.000
39	A	40	THR	0	-0.043	-0.039	22.352	-0.112	-0.112	0.000	0.000	0.000	0.000
40	A	41	ASP	-1	-0.915	-0.925	22.098	-11.195	-11.195	0.000	0.000	0.000	0.000
41	A	42	VAL	0	-0.034	-0.037	16.765	-0.313	-0.313	0.000	0.000	0.000	0.000
42	A	43	ILE	0	-0.025	-0.005	13.920	0.110	0.110	0.000	0.000	0.000	0.000
43	A	44	THR	0	0.003	0.001	11.797	-0.548	-0.548	0.000	0.000	0.000	0.000
44	A	45	PHE	0	-0.025	-0.021	7.949	0.532	0.532	0.000	0.000	0.000	0.000
45	A	46	THR	0	0.000	-0.006	3.046	-0.800	-0.105	0.155	-0.347	-0.504	0.002
46	A	47	MET	0	-0.019	0.003	3.879	2.156	2.575	-0.001	-0.145	-0.273	0.000
47	A	48	ASP	-1	-0.871	-0.941	1.746	-138.057	-137.946	23.545	-11.467	-12.189	-0.149
48	A	49	GLU	-1	-0.753	-0.873	1.853	-44.741	-43.647	3.188	-1.547	-2.735	-0.007
49	A	50	ASP	-1	-0.928	-0.958	1.822	-136.054	-139.399	19.463	-7.983	-8.134	-0.105
50	A	51	SER	0	-0.113	-0.062	3.242	12.683	12.769	0.017	0.120	-0.223	-0.001
51	A	52	LEU	0	0.047	0.021	6.229	-1.781	-1.781	0.000	0.000	0.000	0.000
52	A	53	GLU	-1	-0.901	-0.950	7.658	-21.414	-21.414	0.000	0.000	0.000	0.000
53	A	54	ALA	0	-0.008	-0.008	7.994	2.513	2.513	0.000	0.000	0.000	0.000
54	A	55	VAL	0	0.039	0.018	5.216	1.816	1.816	0.000	0.000	0.000	0.000
55	A	56	GLU	-1	-0.915	-0.966	8.616	-20.332	-20.332	0.000	0.000	0.000	0.000
56	A	57	ARG	1	0.889	0.942	11.795	21.870	21.870	0.000	0.000	0.000	0.000
57	A	58	GLU	-1	-0.941	-0.968	10.661	-27.692	-27.692	0.000	0.000	0.000	0.000
58	A	59	VAL	0	-0.002	-0.005	10.269	1.356	1.356	0.000	0.000	0.000	0.000
59	A	60	GLU	-1	-0.764	-0.839	13.053	-13.785	-13.785	0.000	0.000	0.000	0.000
60	A	61	ASP	-1	-0.869	-0.913	16.033	-16.049	-16.049	0.000	0.000	0.000	0.000
61	A	62	MET	0	-0.009	-0.018	10.660	1.245	1.245	0.000	0.000	0.000	0.000
62	A	63	CYS	0	-0.042	-0.015	16.185	0.997	0.997	0.000	0.000	0.000	0.000
63	A	64	GLN	0	-0.063	-0.042	18.695	1.394	1.394	0.000	0.000	0.000	0.000
64	A	65	ARG	1	0.763	0.867	18.582	16.960	16.960	0.000	0.000	0.000	0.000
65	A	66	LEU	0	-0.081	-0.036	17.620	0.005	0.005	0.000	0.000	0.000	0.000
66	A	67	LEU	0	0.008	-0.003	14.833	0.562	0.562	0.000	0.000	0.000	0.000
67	A	68	CYS	0	-0.067	-0.022	19.524	0.520	0.520	0.000	0.000	0.000	0.000
68	A	69	ASN	0	0.044	0.017	22.710	-0.070	-0.070	0.000	0.000	0.000	0.000
69	A	70	PRO	0	0.097	0.049	23.261	0.538	0.538	0.000	0.000	0.000	0.000
70	A	71	VAL	0	-0.053	-0.012	25.965	0.325	0.325	0.000	0.000	0.000	0.000
71	A	72	ILE	0	-0.040	-0.030	29.006	0.332	0.332	0.000	0.000	0.000	0.000
72	A	73	HIS	0	0.038	0.021	24.891	0.072	0.072	0.000	0.000	0.000	0.000
73	A	74	ASP	-1	-0.876	-0.939	25.669	-10.519	-10.519	0.000	0.000	0.000	0.000
74	A	75	TYR	0	-0.074	-0.089	19.035	0.330	0.330	0.000	0.000	0.000	0.000
75	A	76	ASP	-1	-0.849	-0.892	19.586	-12.365	-12.365	0.000	0.000	0.000	0.000
76	A	77	VAL	0	0.011	-0.004	13.686	-0.292	-0.292	0.000	0.000	0.000	0.000
77	A	78	SER	0	-0.049	-0.010	13.577	0.185	0.185	0.000	0.000	0.000	0.000
78	A	79	ILE	0	0.050	0.014	7.329	-0.633	-0.633	0.000	0.000	0.000	0.000
79	A	80	ASN	0	-0.064	-0.027	8.341	1.337	1.337	0.000	0.000	0.000	0.000
80	A	81	GLU	-1	-0.899	-0.952	3.871	-36.995	-36.756	0.000	-0.037	-0.202	0.000
81	A	82	MET	0	-0.099	-0.023	2.980	2.875	4.331	0.141	-0.425	-1.171	0.001

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