FMO DATABASE

FMODB ID: 5JQZZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1052872.995528
FMO2-HF: Nuclear repulsion	1003025.10379
FMO2-HF: Total energy	-49847.891738
FMO2-MP2: Total energy	-49988.06314

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.
28.178	41.809	9.284	-8.662	-14.25	-0.076

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 : 1.020 / q_NPA : 1.026

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	3	PHE	0	-0.043	-0.009	2.351	-12.336	-7.295	2.978	-2.645	-5.374	-0.017
4	A	4	THR	0	0.082	0.048	4.410	6.016	6.141	0.000	-0.019	-0.105	0.000
5	A	5	ARG	1	0.869	0.910	7.385	18.190	18.190	0.000	0.000	0.000	0.000
6	A	119	CYS	0	-0.018	-0.007	9.813	-1.283	-1.283	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.026	0.029	5.770	-0.356	-0.356	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.002	-0.002	6.228	-3.219	-3.219	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.029	0.005	7.096	0.871	0.871	0.000	0.000	0.000	0.000
10	A	10	HIS	0	-0.032	0.002	7.085	-0.403	-0.403	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.796	-0.915	3.766	-54.348	-54.055	0.000	-0.054	-0.239	0.000
12	A	12	LEU	0	-0.010	-0.022	6.896	3.083	3.083	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.854	0.921	10.093	22.919	22.919	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.867	0.948	5.788	46.237	46.237	0.000	0.000	0.000	0.000
15	A	15	HIS	0	-0.076	-0.043	7.261	2.827	2.827	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.002	-0.011	11.878	1.252	1.252	0.000	0.000	0.000	0.000
17	A	17	PHE	0	-0.102	-0.045	12.258	0.947	0.947	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.867	-0.931	15.475	-15.016	-15.016	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.771	-0.881	17.038	-18.890	-18.890	0.000	0.000	0.000	0.000
20	A	20	ASN	0	0.001	0.005	18.725	-0.189	-0.189	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.026	-0.033	19.205	0.472	0.472	0.000	0.000	0.000	0.000
22	A	22	MET	0	-0.005	0.013	13.673	-1.022	-1.022	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.924	0.940	16.114	13.851	13.851	0.000	0.000	0.000	0.000
24	A	24	ASN	0	0.055	0.033	17.762	-0.029	-0.029	0.000	0.000	0.000	0.000
25	A	25	TRP	0	0.033	0.024	14.310	-0.514	-0.514	0.000	0.000	0.000	0.000
26	A	26	VAL	0	0.013	0.015	12.344	-1.112	-1.112	0.000	0.000	0.000	0.000
27	A	27	CYS	0	-0.084	-0.012	13.956	-0.814	-0.814	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.010	0.003	15.101	0.047	0.047	0.000	0.000	0.000	0.000
29	A	29	VAL	0	0.012	0.000	9.385	-0.103	-0.103	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.812	-0.894	11.551	-23.056	-23.056	0.000	0.000	0.000	0.000
31	A	31	HIS	0	-0.042	-0.035	12.740	0.928	0.928	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.884	-0.928	13.592	-16.087	-16.087	0.000	0.000	0.000	0.000
33	A	33	SER	0	-0.032	-0.050	8.481	-0.576	-0.576	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.032	-0.005	8.555	-0.826	-0.826	0.000	0.000	0.000	0.000
35	A	35	ARG	1	0.775	0.863	6.666	27.100	27.100	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.813	-0.903	3.261	-44.792	-43.878	0.025	-0.455	-0.483	-0.003
37	A	37	THR	0	-0.036	-0.036	2.258	-1.713	0.074	2.704	-1.731	-2.760	-0.014
38	A	38	SER	0	-0.020	-0.004	3.344	5.711	6.293	0.021	-0.133	-0.470	0.000
39	A	39	LYS	1	0.971	1.005	4.790	24.562	24.615	-0.001	-0.003	-0.048	0.000
40	A	40	THR	0	-0.010	-0.016	7.532	0.689	0.689	0.000	0.000	0.000	0.000
41	A	41	ASN	0	0.005	0.015	10.976	0.568	0.568	0.000	0.000	0.000	0.000
42	A	42	THR	0	-0.008	-0.006	14.286	0.257	0.257	0.000	0.000	0.000	0.000
43	A	43	ASN	0	-0.032	-0.018	17.725	0.246	0.246	0.000	0.000	0.000	0.000
44	A	44	ARG	1	1.004	0.984	20.714	10.846	10.846	0.000	0.000	0.000	0.000
45	A	45	ASN	0	-0.008	0.025	23.536	-0.095	-0.095	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.059	0.035	23.099	0.199	0.199	0.000	0.000	0.000	0.000
47	A	47	SER	0	-0.126	-0.078	20.666	-0.337	-0.337	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.960	0.966	15.318	14.019	14.019	0.000	0.000	0.000	0.000
49	A	49	ASP	-1	-0.817	-0.887	14.537	-15.219	-15.219	0.000	0.000	0.000	0.000
50	A	50	TYR	0	-0.047	-0.059	10.805	-0.435	-0.435	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.079	0.055	7.364	0.058	0.058	0.000	0.000	0.000	0.000
52	A	52	LEU	0	0.001	0.015	6.159	1.622	1.622	0.000	0.000	0.000	0.000
53	A	53	PHE	0	-0.025	-0.007	8.558	1.345	1.345	0.000	0.000	0.000	0.000
54	A	54	GLN	0	-0.018	-0.002	10.353	2.755	2.755	0.000	0.000	0.000	0.000
55	A	55	ILE	0	0.002	0.010	12.990	1.501	1.501	0.000	0.000	0.000	0.000
56	A	56	ASN	0	-0.006	-0.029	15.063	0.624	0.624	0.000	0.000	0.000	0.000
57	A	57	ASP	-1	-0.740	-0.889	17.842	-14.101	-14.101	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.858	0.936	19.272	11.058	11.058	0.000	0.000	0.000	0.000
59	A	59	TYR	0	0.013	-0.015	21.954	0.492	0.492	0.000	0.000	0.000	0.000
60	A	60	TRP	0	0.090	0.036	18.389	0.147	0.147	0.000	0.000	0.000	0.000
61	A	61	CYS	0	0.031	0.034	14.210	-1.081	-1.081	0.000	0.000	0.000	0.000
62	A	62	SER	0	-0.038	-0.023	18.421	0.349	0.349	0.000	0.000	0.000	0.000
63	A	63	LYS	1	0.977	0.978	17.931	12.018	12.018	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.009	0.017	19.022	0.136	0.136	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.032	0.009	19.294	-0.651	-0.651	0.000	0.000	0.000	0.000
66	A	66	SER	0	0.045	0.026	20.935	-0.154	-0.154	0.000	0.000	0.000	0.000
67	A	67	PRO	0	-0.028	-0.008	19.766	-0.195	-0.195	0.000	0.000	0.000	0.000
68	A	68	GLY	0	0.044	0.020	20.589	0.691	0.691	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.848	0.940	21.068	11.776	11.776	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.747	-0.854	23.096	-12.046	-12.046	0.000	0.000	0.000	0.000
71	A	71	CYS	0	-0.142	-0.052	15.118	1.622	1.622	0.000	0.000	0.000	0.000
72	A	72	ASN	0	-0.047	-0.013	20.013	-0.327	-0.327	0.000	0.000	0.000	0.000
73	A	73	VAL	0	0.012	0.009	15.240	-0.391	-0.391	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.934	0.973	15.744	16.417	16.417	0.000	0.000	0.000	0.000
75	A	76	SER	0	0.065	0.021	11.693	-0.687	-0.687	0.000	0.000	0.000	0.000
76	A	77	ASP	-1	-0.938	-0.971	10.384	-21.101	-21.101	0.000	0.000	0.000	0.000
77	A	78	LEU	0	-0.119	-0.059	9.841	-1.498	-1.498	0.000	0.000	0.000	0.000
78	A	79	LEU	0	-0.023	-0.007	6.648	-0.562	-0.562	0.000	0.000	0.000	0.000
79	A	80	THR	0	-0.017	0.003	5.354	0.364	0.364	0.000	0.000	0.000	0.000
80	A	81	ASP	-1	-0.867	-0.941	2.375	-60.435	-56.253	3.526	-3.380	-4.328	-0.039
81	A	82	ASP	-1	-0.928	-0.946	3.436	-44.715	-44.061	0.031	-0.242	-0.443	-0.003
82	A	83	ILE	0	0.062	0.014	4.858	4.964	4.964	0.000	0.000	0.000	0.000
83	A	84	THR	0	-0.001	0.012	7.462	5.075	5.075	0.000	0.000	0.000	0.000
84	A	85	LYS	1	0.941	0.956	10.496	23.182	23.182	0.000	0.000	0.000	0.000
85	A	86	ALA	0	0.067	0.028	9.798	1.842	1.842	0.000	0.000	0.000	0.000
86	A	87	ALA	0	0.013	0.011	10.718	1.790	1.790	0.000	0.000	0.000	0.000
87	A	88	LYS	1	0.908	0.954	12.468	21.273	21.273	0.000	0.000	0.000	0.000
88	A	90	ALA	0	0.080	0.040	14.194	1.212	1.212	0.000	0.000	0.000	0.000
89	A	91	LYS	1	0.925	0.956	14.759	21.375	21.375	0.000	0.000	0.000	0.000
90	A	92	LYS	1	0.863	0.940	18.168	14.470	14.470	0.000	0.000	0.000	0.000
91	A	93	ILE	0	0.008	0.005	17.633	0.831	0.831	0.000	0.000	0.000	0.000
92	A	94	TYR	0	0.030	0.023	19.741	0.855	0.855	0.000	0.000	0.000	0.000
93	A	95	LYS	1	0.915	0.965	21.531	12.883	12.883	0.000	0.000	0.000	0.000
94	A	96	ARG	1	0.806	0.895	23.977	12.417	12.417	0.000	0.000	0.000	0.000
95	A	97	HIS	0	0.007	-0.001	24.089	0.407	0.407	0.000	0.000	0.000	0.000
96	A	98	ARG	1	0.964	0.992	24.142	12.315	12.315	0.000	0.000	0.000	0.000
97	A	99	PHE	0	0.035	-0.015	18.731	-0.474	-0.474	0.000	0.000	0.000	0.000
98	A	100	ASP	-1	-0.886	-0.932	22.578	-11.921	-11.921	0.000	0.000	0.000	0.000
99	A	101	ALA	0	-0.080	-0.044	21.605	0.240	0.240	0.000	0.000	0.000	0.000
100	A	102	TRP	0	-0.035	-0.017	15.784	0.132	0.132	0.000	0.000	0.000	0.000
101	A	103	TYR	0	-0.002	0.007	20.282	0.400	0.400	0.000	0.000	0.000	0.000
102	A	104	GLY	0	0.050	0.013	18.226	0.433	0.433	0.000	0.000	0.000	0.000
103	A	105	TRP	0	0.006	-0.021	19.310	0.230	0.230	0.000	0.000	0.000	0.000
104	A	106	LYS	1	0.945	0.960	20.751	12.457	12.457	0.000	0.000	0.000	0.000
105	A	107	ASN	0	-0.065	-0.039	23.101	0.074	0.074	0.000	0.000	0.000	0.000
106	A	108	HIS	1	0.921	0.964	20.628	13.836	13.836	0.000	0.000	0.000	0.000
107	A	110	GLN	0	0.015	0.019	22.447	0.330	0.330	0.000	0.000	0.000	0.000
108	A	111	GLY	0	0.014	0.025	25.690	0.379	0.379	0.000	0.000	0.000	0.000
109	A	112	SER	0	0.002	-0.010	24.672	-0.190	-0.190	0.000	0.000	0.000	0.000
110	A	113	LEU	0	0.002	0.006	20.545	-0.575	-0.575	0.000	0.000	0.000	0.000
111	A	114	PRO	0	-0.008	-0.009	16.674	0.270	0.270	0.000	0.000	0.000	0.000
112	A	115	ASP	-1	-0.813	-0.851	18.703	-15.190	-15.190	0.000	0.000	0.000	0.000
113	A	116	ILE	0	-0.016	-0.040	14.737	-0.936	-0.936	0.000	0.000	0.000	0.000
114	A	117	SER	0	-0.041	-0.051	16.765	-0.586	-0.586	0.000	0.000	0.000	0.000
115	A	118	SER	0	0.014	0.012	16.206	0.280	0.280	0.000	0.000	0.000	0.000

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