FMO DATABASE

FMODB ID: VQYR1

Calculation Name: 2GD5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GD5

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y3E7

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	142
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1205317.013299
FMO2-HF: Nuclear repulsion	1146174.148827
FMO2-HF: Total energy	-59142.864472
FMO2-MP2: Total energy	-59308.337915

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:12:PRO)

Summations of interaction energy for fragment #1(A:12:PRO)

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.
-5.66	-0.389	3.609	-3.188	-5.693	0

Interaction energy analysis for fragmet #1(A:12:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.081 / q_NPA : 0.030

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].
3	A	14	GLU	-1	-0.843	-0.915	2.228	-7.966	-3.000	3.601	-3.291	-5.276
4	A	15	LEU	0	0.028	0.016	3.556	-0.027	0.278	0.008	0.103	-0.417
5	A	16	VAL	0	0.055	0.036	5.987	0.319	0.319	0.000	0.000	0.000
6	A	17	ASN	0	-0.016	-0.014	5.974	0.378	0.378	0.000	0.000	0.000
7	A	18	GLU	-1	-0.853	-0.916	6.834	-0.622	-0.622	0.000	0.000	0.000
8	A	19	TRP	0	-0.009	-0.061	8.555	0.161	0.161	0.000	0.000	0.000
9	A	20	SER	0	-0.037	-0.024	10.913	0.139	0.139	0.000	0.000	0.000
10	A	21	LEU	0	0.000	0.008	10.109	0.109	0.109	0.000	0.000	0.000
11	A	22	LYS	1	0.860	0.944	11.013	0.610	0.610	0.000	0.000	0.000
12	A	23	ILE	0	0.046	0.039	14.870	0.058	0.058	0.000	0.000	0.000
13	A	24	ARG	1	0.942	0.958	16.234	0.279	0.279	0.000	0.000	0.000
14	A	25	LYS	1	0.787	0.876	17.107	0.267	0.267	0.000	0.000	0.000
15	A	26	GLU	-1	-0.712	-0.858	18.727	-0.191	-0.191	0.000	0.000	0.000
16	A	27	MET	0	-0.065	-0.037	20.640	0.016	0.016	0.000	0.000	0.000
17	A	28	ARG	1	0.913	0.965	17.660	0.275	0.275	0.000	0.000	0.000
18	A	29	VAL	0	-0.031	0.008	22.772	0.016	0.016	0.000	0.000	0.000
19	A	30	VAL	0	0.076	0.038	25.152	0.012	0.012	0.000	0.000	0.000
20	A	31	ASP	-1	-0.854	-0.905	26.476	-0.132	-0.132	0.000	0.000	0.000
21	A	32	ARG	1	0.925	0.966	26.211	0.130	0.130	0.000	0.000	0.000
22	A	33	GLN	0	-0.029	-0.033	27.954	0.001	0.001	0.000	0.000	0.000
23	A	34	ILE	0	0.014	0.002	30.402	0.008	0.008	0.000	0.000	0.000
24	A	35	ARG	1	0.929	0.956	28.654	0.119	0.119	0.000	0.000	0.000
25	A	36	ASP	-1	-0.822	-0.908	33.264	-0.083	-0.083	0.000	0.000	0.000
26	A	37	ILE	0	0.014	0.009	35.020	0.005	0.005	0.000	0.000	0.000
27	A	38	GLN	0	0.025	0.011	36.603	0.008	0.008	0.000	0.000	0.000
28	A	39	ARG	1	0.821	0.910	35.166	0.081	0.081	0.000	0.000	0.000
29	A	40	GLU	-1	-0.827	-0.889	40.041	-0.052	-0.052	0.000	0.000	0.000
30	A	41	GLU	-1	-0.810	-0.914	41.550	-0.056	-0.056	0.000	0.000	0.000
31	A	42	GLU	-1	-0.907	-0.946	41.912	-0.057	-0.057	0.000	0.000	0.000
32	A	43	LYS	1	0.816	0.890	42.238	0.059	0.059	0.000	0.000	0.000
33	A	44	VAL	0	0.049	0.026	45.589	0.003	0.003	0.000	0.000	0.000
34	A	45	LYS	1	1.010	0.993	47.490	0.052	0.052	0.000	0.000	0.000
35	A	46	ARG	1	0.848	0.922	45.948	0.051	0.051	0.000	0.000	0.000
36	A	47	SER	0	0.025	0.011	50.396	0.002	0.002	0.000	0.000	0.000
37	A	48	VAL	0	0.008	0.003	51.000	0.002	0.002	0.000	0.000	0.000
38	A	49	LYS	1	0.930	0.973	52.989	0.041	0.041	0.000	0.000	0.000
39	A	50	ASP	-1	-0.837	-0.908	55.694	-0.031	-0.031	0.000	0.000	0.000
40	A	51	ALA	0	0.028	0.015	56.423	0.001	0.001	0.000	0.000	0.000
41	A	52	ALA	0	0.016	-0.007	57.724	0.001	0.001	0.000	0.000	0.000
42	A	53	LYS	1	0.844	0.927	57.785	0.034	0.034	0.000	0.000	0.000
43	A	54	LYS	1	0.859	0.929	59.665	0.031	0.031	0.000	0.000	0.000
44	A	55	GLY	0	0.038	0.026	62.696	0.001	0.001	0.000	0.000	0.000
45	A	56	GLN	0	0.003	-0.005	59.592	0.000	0.000	0.000	0.000	0.000
46	A	57	LYS	1	1.014	0.995	59.577	0.025	0.025	0.000	0.000	0.000
47	A	58	ASP	-1	-0.855	-0.931	58.589	-0.029	-0.029	0.000	0.000	0.000
48	A	59	VAL	0	0.003	0.003	55.106	-0.001	-0.001	0.000	0.000	0.000
49	A	60	CYS	0	-0.049	-0.009	54.560	-0.002	-0.002	0.000	0.000	0.000
50	A	61	ILE	0	0.018	0.013	53.747	-0.002	-0.002	0.000	0.000	0.000
51	A	62	VAL	0	0.000	0.001	51.394	-0.002	-0.002	0.000	0.000	0.000
52	A	63	LEU	0	0.068	0.025	50.011	-0.002	-0.002	0.000	0.000	0.000
53	A	64	ALA	0	-0.005	0.001	49.042	-0.002	-0.002	0.000	0.000	0.000
54	A	65	LYS	1	0.940	0.961	48.499	0.034	0.034	0.000	0.000	0.000
55	A	66	GLU	-1	-0.805	-0.873	44.033	-0.053	-0.053	0.000	0.000	0.000
56	A	67	MET	0	0.001	0.012	44.487	-0.003	-0.003	0.000	0.000	0.000
57	A	68	ILE	0	-0.039	-0.020	44.138	-0.003	-0.003	0.000	0.000	0.000
58	A	69	ARG	1	0.819	0.897	41.465	0.048	0.048	0.000	0.000	0.000
59	A	70	SER	0	0.016	0.000	40.375	-0.004	-0.004	0.000	0.000	0.000
60	A	71	ARG	1	0.882	0.929	39.178	0.051	0.051	0.000	0.000	0.000
61	A	72	LYS	1	0.925	0.954	38.699	0.049	0.049	0.000	0.000	0.000
62	A	73	ALA	0	-0.005	0.006	36.432	-0.004	-0.004	0.000	0.000	0.000
63	A	74	VAL	0	0.033	0.012	34.734	-0.006	-0.006	0.000	0.000	0.000
64	A	75	SER	0	-0.044	-0.005	33.884	-0.006	-0.006	0.000	0.000	0.000
65	A	76	LYS	1	0.986	0.977	32.205	0.074	0.074	0.000	0.000	0.000
66	A	77	LEU	0	0.029	0.027	29.738	-0.007	-0.007	0.000	0.000	0.000
67	A	78	TYR	0	0.039	0.010	29.321	-0.008	-0.008	0.000	0.000	0.000
68	A	79	ALA	0	-0.042	-0.010	29.461	-0.006	-0.006	0.000	0.000	0.000
69	A	80	SER	0	0.071	0.017	26.313	-0.006	-0.006	0.000	0.000	0.000
70	A	81	LYS	1	0.803	0.899	25.225	0.132	0.132	0.000	0.000	0.000
71	A	82	ALA	0	0.024	0.006	24.667	-0.014	-0.014	0.000	0.000	0.000
72	A	83	HIS	0	0.038	0.030	24.828	-0.014	-0.014	0.000	0.000	0.000
73	A	84	MET	0	0.016	0.000	21.130	-0.017	-0.017	0.000	0.000	0.000
74	A	85	ASN	0	-0.011	-0.014	20.299	-0.039	-0.039	0.000	0.000	0.000
75	A	86	SER	0	-0.034	-0.004	20.882	-0.014	-0.014	0.000	0.000	0.000
76	A	87	VAL	0	0.016	-0.004	16.711	-0.009	-0.009	0.000	0.000	0.000
77	A	88	LEU	0	-0.013	0.007	15.192	-0.031	-0.031	0.000	0.000	0.000
78	A	89	MET	0	0.001	-0.005	16.128	-0.030	-0.030	0.000	0.000	0.000
79	A	90	GLY	0	0.036	0.016	17.371	0.006	0.006	0.000	0.000	0.000
80	A	91	MET	0	0.004	-0.002	12.374	-0.032	-0.032	0.000	0.000	0.000
81	A	92	LYS	1	0.947	0.963	12.484	0.203	0.203	0.000	0.000	0.000
82	A	93	ASN	0	-0.014	-0.007	13.971	0.010	0.010	0.000	0.000	0.000
83	A	94	GLN	0	0.000	-0.007	11.418	0.020	0.020	0.000	0.000	0.000
84	A	95	LEU	0	0.017	0.014	8.373	0.011	0.011	0.000	0.000	0.000
85	A	96	ALA	0	0.001	0.013	10.937	0.041	0.041	0.000	0.000	0.000
86	A	97	VAL	0	0.002	-0.007	13.400	0.030	0.030	0.000	0.000	0.000
87	A	98	LEU	0	-0.045	-0.019	7.494	0.015	0.015	0.000	0.000	0.000
88	A	99	ARG	1	0.872	0.922	9.468	0.117	0.117	0.000	0.000	0.000
89	A	100	VAL	0	-0.037	-0.012	11.971	0.027	0.027	0.000	0.000	0.000
90	A	101	ALA	0	0.100	0.079	13.892	0.019	0.019	0.000	0.000	0.000
91	A	102	GLY	0	0.010	-0.001	9.718	0.034	0.034	0.000	0.000	0.000
92	A	103	SER	0	-0.053	-0.031	9.838	0.055	0.055	0.000	0.000	0.000
93	A	104	LEU	0	-0.031	-0.005	8.601	-0.051	-0.051	0.000	0.000	0.000
94	A	105	GLN	0	0.036	0.031	12.694	0.045	0.045	0.000	0.000	0.000
95	A	106	LYS	1	0.852	0.911	16.460	0.052	0.052	0.000	0.000	0.000
96	A	107	SER	0	0.012	0.023	18.109	0.021	0.021	0.000	0.000	0.000
97	A	108	THR	0	0.069	0.016	19.787	-0.005	-0.005	0.000	0.000	0.000
98	A	109	GLU	-1	-0.799	-0.879	21.557	-0.121	-0.121	0.000	0.000	0.000
99	A	110	VAL	0	-0.046	-0.020	16.904	0.001	0.001	0.000	0.000	0.000
100	A	111	MET	0	0.038	0.036	19.737	-0.012	-0.012	0.000	0.000	0.000
101	A	112	LYS	1	0.817	0.880	21.896	0.118	0.118	0.000	0.000	0.000
102	A	113	ALA	0	0.007	0.014	22.217	0.006	0.006	0.000	0.000	0.000
103	A	114	MET	0	0.052	0.022	17.563	-0.002	-0.002	0.000	0.000	0.000
104	A	115	GLN	0	0.034	0.032	21.832	0.013	0.013	0.000	0.000	0.000
105	A	116	SER	0	-0.054	-0.046	25.124	0.008	0.008	0.000	0.000	0.000
106	A	117	LEU	0	0.013	-0.006	21.537	0.004	0.004	0.000	0.000	0.000
107	A	118	VAL	0	-0.075	-0.023	22.606	0.002	0.002	0.000	0.000	0.000
108	A	119	LYS	1	0.857	0.921	24.985	0.106	0.106	0.000	0.000	0.000
109	A	120	ILE	0	-0.042	0.005	26.238	0.008	0.008	0.000	0.000	0.000
110	A	121	PRO	0	-0.039	-0.037	28.301	-0.002	-0.002	0.000	0.000	0.000
111	A	122	GLU	-1	-0.792	-0.884	27.672	-0.119	-0.119	0.000	0.000	0.000
112	A	123	ILE	0	-0.036	-0.009	21.150	0.001	0.001	0.000	0.000	0.000
113	A	124	GLN	0	0.059	0.026	24.082	0.002	0.002	0.000	0.000	0.000
114	A	125	ALA	0	-0.014	-0.003	23.045	-0.002	-0.002	0.000	0.000	0.000
115	A	126	THR	0	0.067	0.023	18.239	-0.007	-0.007	0.000	0.000	0.000
116	A	127	MET	0	0.027	0.017	18.740	-0.018	-0.018	0.000	0.000	0.000
117	A	128	ARG	1	0.898	0.937	19.670	0.100	0.100	0.000	0.000	0.000
118	A	129	GLU	-1	-0.957	-0.976	15.676	-0.201	-0.201	0.000	0.000	0.000
119	A	130	LEU	0	0.004	-0.011	13.215	-0.025	-0.025	0.000	0.000	0.000
120	A	131	SER	0	0.023	0.006	15.018	-0.021	-0.021	0.000	0.000	0.000
121	A	132	LYS	1	0.935	0.984	16.009	0.116	0.116	0.000	0.000	0.000
122	A	133	GLU	-1	-0.799	-0.885	10.307	-0.560	-0.560	0.000	0.000	0.000
123	A	134	MET	0	-0.036	-0.013	11.802	-0.020	-0.020	0.000	0.000	0.000
124	A	135	MET	0	-0.006	-0.011	13.483	0.015	0.015	0.000	0.000	0.000
125	A	136	LYS	1	0.921	0.958	11.769	0.067	0.067	0.000	0.000	0.000
126	A	137	ALA	0	-0.029	-0.008	9.742	0.021	0.021	0.000	0.000	0.000
127	A	138	GLY	0	0.012	0.027	11.144	0.028	0.028	0.000	0.000	0.000
128	A	139	ILE	0	-0.058	-0.049	13.254	0.012	0.012	0.000	0.000	0.000
129	A	140	ILE	0	-0.035	-0.022	16.025	0.007	0.007	0.000	0.000	0.000
130	A	141	GLU	-1	-0.817	-0.896	18.688	-0.056	-0.056	0.000	0.000	0.000
131	A	161	ALA	0	0.036	0.006	23.274	-0.003	-0.003	0.000	0.000	0.000
132	A	162	GLU	-1	-0.887	-0.964	24.700	0.000	0.000	0.000	0.000	0.000
133	A	163	MET	0	0.020	0.015	20.810	0.007	0.007	0.000	0.000	0.000
134	A	164	GLU	-1	-0.921	-0.976	19.443	-0.046	-0.046	0.000	0.000	0.000
135	A	165	ILE	0	-0.004	0.014	21.174	0.004	0.004	0.000	0.000	0.000
136	A	166	ASP	-1	-0.878	-0.919	22.426	0.046	0.046	0.000	0.000	0.000
137	A	167	ARG	1	0.795	0.866	15.462	0.034	0.034	0.000	0.000	0.000
138	A	168	ILE	0	0.002	-0.017	17.623	0.010	0.010	0.000	0.000	0.000
139	A	169	LEU	0	-0.036	0.008	18.820	0.004	0.004	0.000	0.000	0.000
140	A	170	PHE	0	-0.093	-0.049	15.833	0.022	0.022	0.000	0.000	0.000
141	A	171	GLU	-1	-0.949	-0.975	15.710	0.020	0.020	0.000	0.000	0.000
142	A	172	ILE	0	-0.081	-0.024	16.748	0.004	0.004	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:12:PRO)