FMO DATABASE

FMODB ID: YV722

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1053663.08071
FMO2-HF: Nuclear repulsion	1003814.458648
FMO2-HF: Total energy	-49848.622062
FMO2-MP2: Total energy	-49988.821439

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.
13.81	24.07	23.579	-13.578	-20.263	-0.122

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 : 0.972 / q_NPA : 1.010

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	-0.011	0.010	2.351	-6.640	-5.611	8.320	-3.083	-6.266	-0.013
4	A	4	THR	0	0.086	0.044	4.765	4.479	4.550	-0.001	-0.007	-0.064	0.000
5	A	5	ARG	1	0.877	0.888	8.230	17.118	17.118	0.000	0.000	0.000	0.000
6	A	119	CYS	0	-0.022	-0.007	10.403	-1.169	-1.169	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.033	0.033	6.580	-0.409	-0.409	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.007	-0.007	6.406	-3.281	-3.281	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.028	0.005	7.317	0.025	0.025	0.000	0.000	0.000	0.000
10	A	10	HIS	0	-0.014	0.010	8.000	-1.096	-1.096	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.782	-0.897	3.559	-60.820	-59.930	0.005	-0.474	-0.421	-0.003
12	A	12	LEU	0	-0.020	-0.014	6.851	2.088	2.088	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.842	0.887	10.070	21.771	21.771	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.872	0.939	4.995	49.009	49.009	0.000	0.000	0.000	0.000
15	A	15	HIS	0	-0.109	-0.066	6.146	1.974	1.974	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.016	-0.004	11.349	1.209	1.209	0.000	0.000	0.000	0.000
17	A	17	PHE	0	-0.115	-0.049	11.231	0.952	0.952	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.862	-0.930	15.306	-14.950	-14.950	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.724	-0.836	16.827	-18.708	-18.708	0.000	0.000	0.000	0.000
20	A	20	ASN	0	-0.010	-0.004	18.799	-0.270	-0.270	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.029	-0.023	19.378	0.454	0.454	0.000	0.000	0.000	0.000
22	A	22	MET	0	-0.010	0.010	14.088	-1.179	-1.179	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.906	0.933	16.134	13.422	13.422	0.000	0.000	0.000	0.000
24	A	24	ASN	0	0.068	0.037	17.927	-0.122	-0.122	0.000	0.000	0.000	0.000
25	A	25	TRP	0	0.030	0.021	14.087	-0.556	-0.556	0.000	0.000	0.000	0.000
26	A	26	VAL	0	0.017	0.014	12.406	-1.151	-1.151	0.000	0.000	0.000	0.000
27	A	27	CYS	0	-0.121	-0.024	14.006	-0.687	-0.687	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.012	0.004	14.878	0.022	0.022	0.000	0.000	0.000	0.000
29	A	29	VAL	0	0.007	-0.005	9.320	-0.149	-0.149	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.783	-0.848	11.727	-21.684	-21.684	0.000	0.000	0.000	0.000
31	A	31	HIS	0	-0.037	-0.034	12.849	0.892	0.892	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.870	-0.923	13.663	-16.127	-16.127	0.000	0.000	0.000	0.000
33	A	33	SER	0	-0.014	-0.033	8.693	-0.602	-0.602	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.017	0.001	8.754	-1.085	-1.085	0.000	0.000	0.000	0.000
35	A	35	ARG	1	0.774	0.866	6.914	25.144	25.144	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.754	-0.849	3.711	-39.565	-39.189	0.002	-0.148	-0.231	-0.001
37	A	37	THR	0	-0.057	-0.050	1.944	-0.510	-1.269	8.247	-3.353	-4.135	-0.018
38	A	38	SER	0	-0.038	-0.025	3.380	3.495	4.273	0.024	-0.235	-0.566	-0.001
39	A	39	LYS	1	0.853	0.935	4.828	27.546	27.609	-0.001	-0.004	-0.058	0.000
40	A	40	THR	0	-0.019	-0.020	7.673	0.516	0.516	0.000	0.000	0.000	0.000
41	A	41	ASN	0	0.008	0.012	11.098	0.753	0.753	0.000	0.000	0.000	0.000
42	A	42	THR	0	-0.024	-0.008	14.414	0.201	0.201	0.000	0.000	0.000	0.000
43	A	43	ASN	0	-0.017	-0.021	17.836	0.519	0.519	0.000	0.000	0.000	0.000
44	A	44	ARG	1	1.002	0.982	20.853	10.869	10.869	0.000	0.000	0.000	0.000
45	A	45	ASN	0	-0.006	0.011	23.522	-0.119	-0.119	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.061	0.039	23.207	0.190	0.190	0.000	0.000	0.000	0.000
47	A	47	SER	0	-0.131	-0.065	20.617	-0.397	-0.397	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.947	0.955	15.397	14.333	14.333	0.000	0.000	0.000	0.000
49	A	49	ASP	-1	-0.807	-0.864	14.539	-15.436	-15.436	0.000	0.000	0.000	0.000
50	A	50	TYR	0	-0.024	-0.063	10.877	-0.361	-0.361	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.098	0.059	7.241	-0.073	-0.073	0.000	0.000	0.000	0.000
52	A	52	LEU	0	-0.015	0.016	5.875	1.798	1.798	0.000	0.000	0.000	0.000
53	A	53	PHE	0	-0.017	-0.008	8.451	1.574	1.574	0.000	0.000	0.000	0.000
54	A	54	GLN	0	-0.017	-0.010	10.312	2.855	2.855	0.000	0.000	0.000	0.000
55	A	55	ILE	0	0.003	0.012	12.666	1.563	1.563	0.000	0.000	0.000	0.000
56	A	56	ASN	0	0.014	-0.020	14.953	0.575	0.575	0.000	0.000	0.000	0.000
57	A	57	ASP	-1	-0.728	-0.860	17.731	-14.364	-14.364	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.887	0.948	19.171	11.390	11.390	0.000	0.000	0.000	0.000
59	A	59	TYR	0	0.043	0.017	21.851	0.499	0.499	0.000	0.000	0.000	0.000
60	A	60	TRP	0	0.092	0.044	18.278	0.160	0.160	0.000	0.000	0.000	0.000
61	A	61	CYS	0	0.014	0.023	14.175	-1.363	-1.363	0.000	0.000	0.000	0.000
62	A	62	SER	0	-0.030	-0.021	18.363	0.374	0.374	0.000	0.000	0.000	0.000
63	A	63	LYS	1	0.907	0.929	17.769	12.852	12.852	0.000	0.000	0.000	0.000
64	A	64	GLY	0	-0.001	0.008	18.964	0.136	0.136	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.037	0.018	19.271	-0.672	-0.672	0.000	0.000	0.000	0.000
66	A	66	SER	0	0.035	0.021	20.930	-0.174	-0.174	0.000	0.000	0.000	0.000
67	A	67	PRO	0	-0.033	-0.009	19.617	-0.236	-0.236	0.000	0.000	0.000	0.000
68	A	68	GLY	0	0.041	0.016	20.565	0.767	0.767	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.817	0.908	21.089	12.221	12.221	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.715	-0.831	23.076	-12.546	-12.546	0.000	0.000	0.000	0.000
71	A	71	CYS	0	-0.138	-0.043	14.068	1.873	1.873	0.000	0.000	0.000	0.000
72	A	72	ASN	0	-0.054	-0.017	19.128	-0.313	-0.313	0.000	0.000	0.000	0.000
73	A	73	VAL	0	0.010	0.007	14.669	-0.526	-0.526	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.901	0.958	15.635	18.769	18.769	0.000	0.000	0.000	0.000
75	A	76	SER	0	0.077	0.030	11.659	-0.744	-0.744	0.000	0.000	0.000	0.000
76	A	77	ASP	-1	-0.861	-0.915	10.378	-22.346	-22.346	0.000	0.000	0.000	0.000
77	A	78	LEU	0	-0.078	-0.044	9.824	-1.917	-1.917	0.000	0.000	0.000	0.000
78	A	79	LEU	0	-0.020	-0.003	6.589	-0.355	-0.355	0.000	0.000	0.000	0.000
79	A	80	THR	0	-0.019	0.004	5.340	1.099	1.099	0.000	0.000	0.000	0.000
80	A	81	ASP	-1	-0.832	-0.922	2.409	-70.272	-65.856	5.233	-4.091	-5.559	-0.043
81	A	82	ASP	-1	-0.863	-0.921	2.288	-70.783	-67.597	1.751	-2.162	-2.775	-0.043
82	A	83	ILE	0	0.034	0.003	3.864	7.953	8.163	-0.001	-0.021	-0.188	0.000
83	A	84	THR	0	0.014	0.002	6.185	7.367	7.367	0.000	0.000	0.000	0.000
84	A	85	LYS	1	0.852	0.909	9.088	26.331	26.331	0.000	0.000	0.000	0.000
85	A	86	ALA	0	0.072	0.033	9.094	2.270	2.270	0.000	0.000	0.000	0.000
86	A	87	ALA	0	0.007	0.011	9.690	2.286	2.286	0.000	0.000	0.000	0.000
87	A	88	LYS	1	0.876	0.929	11.419	25.191	25.191	0.000	0.000	0.000	0.000
88	A	90	ALA	0	0.074	0.037	13.767	1.354	1.354	0.000	0.000	0.000	0.000
89	A	91	LYS	1	0.922	0.954	13.862	22.914	22.914	0.000	0.000	0.000	0.000
90	A	92	LYS	1	0.853	0.927	17.324	15.310	15.310	0.000	0.000	0.000	0.000
91	A	93	ILE	0	0.014	0.010	17.472	0.890	0.890	0.000	0.000	0.000	0.000
92	A	94	TYR	0	0.031	0.025	19.287	0.932	0.932	0.000	0.000	0.000	0.000
93	A	95	LYS	1	0.933	0.970	21.019	13.450	13.450	0.000	0.000	0.000	0.000
94	A	96	ARG	1	0.790	0.883	23.227	12.864	12.864	0.000	0.000	0.000	0.000
95	A	97	HIS	0	0.013	-0.001	23.791	0.364	0.364	0.000	0.000	0.000	0.000
96	A	98	ARG	1	0.921	0.974	23.728	12.717	12.717	0.000	0.000	0.000	0.000
97	A	99	PHE	0	0.047	-0.014	18.444	-0.445	-0.445	0.000	0.000	0.000	0.000
98	A	100	ASP	-1	-0.803	-0.882	22.525	-11.849	-11.849	0.000	0.000	0.000	0.000
99	A	101	ALA	0	-0.069	-0.027	21.506	0.267	0.267	0.000	0.000	0.000	0.000
100	A	102	TRP	0	-0.047	-0.020	15.708	0.083	0.083	0.000	0.000	0.000	0.000
101	A	103	TYR	0	0.035	0.017	20.291	0.377	0.377	0.000	0.000	0.000	0.000
102	A	104	GLY	0	0.043	0.011	18.466	0.436	0.436	0.000	0.000	0.000	0.000
103	A	105	TRP	0	-0.001	-0.024	19.351	0.218	0.218	0.000	0.000	0.000	0.000
104	A	106	LYS	1	0.851	0.900	20.694	12.306	12.306	0.000	0.000	0.000	0.000
105	A	107	ASN	0	-0.056	-0.028	23.307	0.185	0.185	0.000	0.000	0.000	0.000
106	A	108	HIS	1	0.910	0.958	20.742	13.702	13.702	0.000	0.000	0.000	0.000
107	A	110	GLN	0	0.014	0.014	22.468	0.345	0.345	0.000	0.000	0.000	0.000
108	A	111	GLY	0	0.014	0.024	25.767	0.371	0.371	0.000	0.000	0.000	0.000
109	A	112	SER	0	-0.006	-0.008	25.016	-0.230	-0.230	0.000	0.000	0.000	0.000
110	A	113	LEU	0	0.021	0.008	20.746	-0.558	-0.558	0.000	0.000	0.000	0.000
111	A	114	PRO	0	0.002	-0.003	16.885	0.302	0.302	0.000	0.000	0.000	0.000
112	A	115	ASP	-1	-0.816	-0.864	19.194	-14.426	-14.426	0.000	0.000	0.000	0.000
113	A	116	ILE	0	-0.027	-0.040	15.396	-0.820	-0.820	0.000	0.000	0.000	0.000
114	A	117	SER	0	-0.035	-0.040	17.335	-0.629	-0.629	0.000	0.000	0.000	0.000
115	A	118	SER	0	0.010	0.010	17.111	0.253	0.253	0.000	0.000	0.000	0.000

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