FMO DATABASE

FMODB ID: VQZ41

Calculation Name: 1GD6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1GD6

Chain ID: A

ChEMBL ID:

UniProt ID: P48816

Base Structure: X-ray

Registration Date: 2023-09-23

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	115
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1052787.04889
FMO2-HF: Nuclear repulsion	1002938.13511
FMO2-HF: Total energy	-49848.913781
FMO2-MP2: Total energy	-49989.124394

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:1:LYS)

Summations of interaction energy for fragment #1(A:1: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.
1.276	6.794	30.088	-14.088	-21.518	-0.154

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.948 / q_NPA : 0.997

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

Sort

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	3	PHE	0	-0.001	0.014	2.441	-7.582	-5.493	6.245	-2.755	-5.579	-0.014
4	A	4	THR	0	0.070	0.031	4.949	4.494	4.548	-0.001	-0.003	-0.049	0.000
5	A	5	ARG	1	0.838	0.880	8.340	16.820	16.820	0.000	0.000	0.000	0.000
6	A	119	CYS	0	-0.033	-0.003	10.628	-1.531	-1.531	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.036	0.028	6.722	-0.133	-0.133	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.005	-0.004	6.659	-3.531	-3.531	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.043	0.010	7.573	0.289	0.289	0.000	0.000	0.000	0.000
10	A	10	HIS	0	-0.017	0.006	8.119	-1.128	-1.128	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.754	-0.874	3.751	-58.545	-58.033	0.001	-0.232	-0.281	-0.001
12	A	12	LEU	0	-0.041	-0.027	7.236	1.931	1.931	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.825	0.866	10.594	21.846	21.846	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.839	0.913	5.174	48.681	48.681	0.000	0.000	0.000	0.000
15	A	15	HIS	0	-0.076	-0.042	6.352	2.120	2.120	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.022	0.019	11.441	1.274	1.274	0.000	0.000	0.000	0.000
17	A	17	PHE	0	-0.099	-0.058	11.214	0.774	0.774	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.871	-0.932	15.656	-15.002	-15.002	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.736	-0.841	16.862	-18.700	-18.700	0.000	0.000	0.000	0.000
20	A	20	ASN	0	-0.002	-0.009	18.971	-0.366	-0.366	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.026	-0.012	19.794	0.511	0.511	0.000	0.000	0.000	0.000
22	A	22	MET	0	-0.006	0.012	14.090	-1.067	-1.067	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.886	0.920	16.355	13.538	13.538	0.000	0.000	0.000	0.000
24	A	24	ASN	0	0.068	0.038	18.539	-0.019	-0.019	0.000	0.000	0.000	0.000
25	A	25	TRP	0	0.017	0.010	14.285	-0.625	-0.625	0.000	0.000	0.000	0.000
26	A	26	VAL	0	0.020	0.006	12.605	-1.233	-1.233	0.000	0.000	0.000	0.000
27	A	27	CYS	0	-0.103	-0.013	14.207	-0.592	-0.592	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.033	0.026	14.733	0.144	0.144	0.000	0.000	0.000	0.000
29	A	29	VAL	0	-0.012	-0.001	9.404	-0.136	-0.136	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.777	-0.855	11.715	-21.547	-21.547	0.000	0.000	0.000	0.000
31	A	31	HIS	0	-0.038	-0.034	13.121	0.825	0.825	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.849	-0.923	13.768	-16.041	-16.041	0.000	0.000	0.000	0.000
33	A	33	SER	0	-0.029	-0.031	8.658	-0.797	-0.797	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.018	0.000	8.836	-0.896	-0.896	0.000	0.000	0.000	0.000
35	A	35	ARG	1	0.781	0.870	7.206	24.967	24.967	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.779	-0.862	3.452	-41.492	-40.973	0.013	-0.228	-0.305	-0.001
37	A	37	THR	0	-0.034	-0.041	2.154	0.062	1.156	5.262	-2.371	-3.985	-0.022
38	A	38	SER	0	-0.022	-0.027	3.017	4.485	5.500	0.105	-0.365	-0.756	0.000
39	A	39	LYS	1	0.838	0.918	4.430	28.324	28.410	-0.001	-0.014	-0.072	0.000
40	A	40	THR	0	-0.013	-0.011	7.552	0.340	0.340	0.000	0.000	0.000	0.000
41	A	41	ASN	0	0.043	0.026	11.037	0.733	0.733	0.000	0.000	0.000	0.000
42	A	42	THR	0	-0.070	-0.048	14.562	0.240	0.240	0.000	0.000	0.000	0.000
43	A	43	ASN	0	-0.016	-0.001	18.118	0.574	0.574	0.000	0.000	0.000	0.000
44	A	44	ARG	1	0.989	0.979	21.154	10.790	10.790	0.000	0.000	0.000	0.000
45	A	45	ASN	0	0.029	0.036	23.451	-0.014	-0.014	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.038	0.024	23.120	0.102	0.102	0.000	0.000	0.000	0.000
47	A	47	SER	0	-0.116	-0.068	20.901	-0.535	-0.535	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.932	0.954	15.532	14.051	14.051	0.000	0.000	0.000	0.000
49	A	49	ASP	-1	-0.789	-0.857	14.541	-15.242	-15.242	0.000	0.000	0.000	0.000
50	A	50	TYR	0	0.022	-0.030	10.872	-0.232	-0.232	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.102	0.067	7.506	0.188	0.188	0.000	0.000	0.000	0.000
52	A	52	LEU	0	-0.038	-0.008	5.477	2.015	2.015	0.000	0.000	0.000	0.000
53	A	53	PHE	0	0.010	0.001	8.977	1.514	1.514	0.000	0.000	0.000	0.000
54	A	54	GLN	0	-0.021	-0.020	10.229	2.896	2.896	0.000	0.000	0.000	0.000
55	A	55	ILE	0	0.011	0.015	12.749	1.550	1.550	0.000	0.000	0.000	0.000
56	A	56	ASN	0	0.014	-0.013	15.108	0.498	0.498	0.000	0.000	0.000	0.000
57	A	57	ASP	-1	-0.739	-0.872	17.841	-14.230	-14.230	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.852	0.933	19.051	11.494	11.494	0.000	0.000	0.000	0.000
59	A	59	TYR	0	0.059	0.025	21.905	0.480	0.480	0.000	0.000	0.000	0.000
60	A	60	TRP	0	0.063	0.029	18.555	0.083	0.083	0.000	0.000	0.000	0.000
61	A	61	CYS	0	-0.023	-0.017	14.521	-1.434	-1.434	0.000	0.000	0.000	0.000
62	A	62	SER	0	-0.017	-0.027	18.701	0.564	0.564	0.000	0.000	0.000	0.000
63	A	63	LYS	1	0.874	0.916	17.415	13.023	13.023	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.026	0.024	18.956	0.277	0.277	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.028	0.006	19.564	-0.661	-0.661	0.000	0.000	0.000	0.000
66	A	66	SER	0	0.023	0.018	20.813	-0.370	-0.370	0.000	0.000	0.000	0.000
67	A	67	PRO	0	-0.018	0.011	19.632	-0.320	-0.320	0.000	0.000	0.000	0.000
68	A	68	GLY	0	0.059	0.027	21.049	0.844	0.844	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.815	0.911	21.463	12.504	12.504	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.736	-0.839	23.352	-12.532	-12.532	0.000	0.000	0.000	0.000
71	A	71	CYS	0	-0.148	-0.063	14.368	1.739	1.739	0.000	0.000	0.000	0.000
72	A	72	ASN	0	-0.019	-0.001	18.965	-0.418	-0.418	0.000	0.000	0.000	0.000
73	A	73	VAL	0	-0.001	0.004	14.753	-0.520	-0.520	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.910	0.966	15.745	18.693	18.693	0.000	0.000	0.000	0.000
75	A	76	SER	0	0.069	0.013	11.873	-0.600	-0.600	0.000	0.000	0.000	0.000
76	A	77	ASP	-1	-0.846	-0.886	10.430	-22.662	-22.662	0.000	0.000	0.000	0.000
77	A	78	LEU	0	-0.054	-0.037	10.057	-1.311	-1.311	0.000	0.000	0.000	0.000
78	A	79	LEU	0	-0.034	-0.002	6.390	-0.802	-0.802	0.000	0.000	0.000	0.000
79	A	80	THR	0	-0.026	-0.009	4.952	0.813	0.933	-0.001	-0.005	-0.113	0.000
80	A	81	ASP	-1	-0.821	-0.924	2.158	-72.794	-68.291	6.369	-5.042	-5.830	-0.045
81	A	82	ASP	-1	-0.840	-0.893	1.780	-80.941	-85.617	12.097	-3.048	-4.373	-0.071
82	A	83	ILE	0	0.038	0.020	4.064	7.467	7.669	-0.001	-0.025	-0.175	0.000
83	A	84	THR	0	0.017	-0.009	6.432	7.170	7.170	0.000	0.000	0.000	0.000
84	A	85	LYS	1	0.829	0.926	9.349	27.188	27.188	0.000	0.000	0.000	0.000
85	A	86	ALA	0	0.086	0.032	9.357	2.155	2.155	0.000	0.000	0.000	0.000
86	A	87	ALA	0	0.020	0.013	9.561	2.218	2.218	0.000	0.000	0.000	0.000
87	A	88	LYS	1	0.880	0.935	11.461	24.415	24.415	0.000	0.000	0.000	0.000
88	A	90	ALA	0	0.070	0.033	14.025	1.361	1.361	0.000	0.000	0.000	0.000
89	A	91	LYS	1	0.883	0.938	13.858	22.953	22.953	0.000	0.000	0.000	0.000
90	A	92	LYS	1	0.861	0.929	17.709	15.276	15.276	0.000	0.000	0.000	0.000
91	A	93	ILE	0	0.003	-0.001	17.434	0.896	0.896	0.000	0.000	0.000	0.000
92	A	94	TYR	0	0.028	0.019	19.625	0.961	0.961	0.000	0.000	0.000	0.000
93	A	95	LYS	1	0.920	0.964	21.326	13.303	13.303	0.000	0.000	0.000	0.000
94	A	96	ARG	1	0.833	0.907	23.578	12.709	12.709	0.000	0.000	0.000	0.000
95	A	97	HIS	0	0.005	-0.008	23.766	0.357	0.357	0.000	0.000	0.000	0.000
96	A	98	ARG	1	0.913	0.972	24.190	12.695	12.695	0.000	0.000	0.000	0.000
97	A	99	PHE	0	0.047	-0.008	18.489	-0.460	-0.460	0.000	0.000	0.000	0.000
98	A	100	ASP	-1	-0.809	-0.892	22.696	-11.756	-11.756	0.000	0.000	0.000	0.000
99	A	101	ALA	0	-0.064	-0.024	21.579	0.357	0.357	0.000	0.000	0.000	0.000
100	A	102	TRP	0	-0.064	-0.026	16.118	0.039	0.039	0.000	0.000	0.000	0.000
101	A	103	TYR	0	0.040	0.023	20.210	0.462	0.462	0.000	0.000	0.000	0.000
102	A	104	GLY	0	0.040	0.011	18.392	0.464	0.464	0.000	0.000	0.000	0.000
103	A	105	TRP	0	0.002	-0.032	19.480	0.209	0.209	0.000	0.000	0.000	0.000
104	A	106	LYS	1	0.830	0.902	20.776	12.209	12.209	0.000	0.000	0.000	0.000
105	A	107	ASN	0	-0.036	-0.023	23.027	0.196	0.196	0.000	0.000	0.000	0.000
106	A	108	HIS	1	0.882	0.951	20.807	13.762	13.762	0.000	0.000	0.000	0.000
107	A	110	GLN	0	0.010	0.003	22.755	0.316	0.316	0.000	0.000	0.000	0.000
108	A	111	GLY	0	0.048	0.024	25.674	0.526	0.526	0.000	0.000	0.000	0.000
109	A	112	SER	0	-0.035	-0.008	25.307	-0.259	-0.259	0.000	0.000	0.000	0.000
110	A	113	LEU	0	0.029	0.012	20.928	-0.441	-0.441	0.000	0.000	0.000	0.000
111	A	114	PRO	0	0.010	0.009	16.988	0.321	0.321	0.000	0.000	0.000	0.000
112	A	115	ASP	-1	-0.768	-0.841	19.138	-14.626	-14.626	0.000	0.000	0.000	0.000
113	A	116	ILE	0	-0.021	-0.036	15.399	-1.061	-1.061	0.000	0.000	0.000	0.000
114	A	117	SER	0	-0.015	-0.022	17.467	-0.642	-0.642	0.000	0.000	0.000	0.000
115	A	118	SER	0	0.005	0.003	17.698	0.027	0.027	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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