FMO DATABASE

FMODB ID: 1N94Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1206505.970557
FMO2-HF: Nuclear repulsion	1147362.057992
FMO2-HF: Total energy	-59143.912565
FMO2-MP2: Total energy	-59309.190154

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.
-5.535	-0.759	2.905	-2.912	-4.77	0.005

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 : 0.085 / q_NPA : 0.047

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	14	GLU	-1	-0.863	-0.916	2.077	-6.696	-2.138	2.905	-3.013	-4.451	0.005
4	A	15	LEU	0	0.041	0.026	3.625	-0.081	0.137	0.000	0.101	-0.319	0.000
5	A	16	VAL	0	0.055	0.036	6.088	0.202	0.202	0.000	0.000	0.000	0.000
6	A	17	ASN	0	-0.022	-0.011	6.373	0.213	0.213	0.000	0.000	0.000	0.000
7	A	18	GLU	-1	-0.870	-0.935	7.001	-0.311	-0.311	0.000	0.000	0.000	0.000
8	A	19	TRP	0	-0.003	-0.044	8.709	0.076	0.076	0.000	0.000	0.000	0.000
9	A	20	SER	0	-0.028	-0.027	10.919	0.077	0.077	0.000	0.000	0.000	0.000
10	A	21	LEU	0	-0.027	-0.015	9.946	0.059	0.059	0.000	0.000	0.000	0.000
11	A	22	LYS	1	0.841	0.922	10.995	0.324	0.324	0.000	0.000	0.000	0.000
12	A	23	ILE	0	0.045	0.021	14.779	0.033	0.033	0.000	0.000	0.000	0.000
13	A	24	ARG	1	0.940	0.967	16.200	0.162	0.162	0.000	0.000	0.000	0.000
14	A	25	LYS	1	0.796	0.889	17.265	0.134	0.134	0.000	0.000	0.000	0.000
15	A	26	GLU	-1	-0.702	-0.839	18.895	-0.097	-0.097	0.000	0.000	0.000	0.000
16	A	27	MET	0	-0.060	-0.035	20.714	0.008	0.008	0.000	0.000	0.000	0.000
17	A	28	ARG	1	0.901	0.954	17.621	0.156	0.156	0.000	0.000	0.000	0.000
18	A	29	VAL	0	-0.030	0.005	22.976	0.009	0.009	0.000	0.000	0.000	0.000
19	A	30	VAL	0	0.088	0.044	25.326	0.007	0.007	0.000	0.000	0.000	0.000
20	A	31	ASP	-1	-0.822	-0.900	26.119	-0.082	-0.082	0.000	0.000	0.000	0.000
21	A	32	ARG	1	0.866	0.960	27.137	0.065	0.065	0.000	0.000	0.000	0.000
22	A	33	GLN	0	-0.004	-0.023	28.020	0.000	0.000	0.000	0.000	0.000	0.000
23	A	34	ILE	0	0.023	0.011	30.263	0.004	0.004	0.000	0.000	0.000	0.000
24	A	35	ARG	1	0.887	0.929	28.588	0.068	0.068	0.000	0.000	0.000	0.000
25	A	36	ASP	-1	-0.799	-0.891	33.512	-0.045	-0.045	0.000	0.000	0.000	0.000
26	A	37	ILE	0	0.006	0.007	34.963	0.003	0.003	0.000	0.000	0.000	0.000
27	A	38	GLN	0	-0.005	-0.007	36.628	0.004	0.004	0.000	0.000	0.000	0.000
28	A	39	ARG	1	0.847	0.917	35.501	0.044	0.044	0.000	0.000	0.000	0.000
29	A	40	GLU	-1	-0.807	-0.883	40.429	-0.028	-0.028	0.000	0.000	0.000	0.000
30	A	41	GLU	-1	-0.787	-0.889	41.789	-0.033	-0.033	0.000	0.000	0.000	0.000
31	A	42	GLU	-1	-0.880	-0.930	42.526	-0.032	-0.032	0.000	0.000	0.000	0.000
32	A	43	LYS	1	0.827	0.904	42.853	0.031	0.031	0.000	0.000	0.000	0.000
33	A	44	VAL	0	0.034	0.033	45.800	0.002	0.002	0.000	0.000	0.000	0.000
34	A	45	LYS	1	0.980	0.981	46.967	0.032	0.032	0.000	0.000	0.000	0.000
35	A	46	ARG	1	0.821	0.893	46.317	0.029	0.029	0.000	0.000	0.000	0.000
36	A	47	SER	0	0.029	0.007	50.558	0.001	0.001	0.000	0.000	0.000	0.000
37	A	48	VAL	0	0.005	0.003	51.523	0.001	0.001	0.000	0.000	0.000	0.000
38	A	49	LYS	1	0.953	0.969	53.407	0.024	0.024	0.000	0.000	0.000	0.000
39	A	50	ASP	-1	-0.817	-0.874	55.722	-0.018	-0.018	0.000	0.000	0.000	0.000
40	A	51	ALA	0	0.035	0.022	56.723	0.001	0.001	0.000	0.000	0.000	0.000
41	A	52	ALA	0	-0.001	-0.009	58.018	0.001	0.001	0.000	0.000	0.000	0.000
42	A	53	LYS	1	0.817	0.891	58.140	0.020	0.020	0.000	0.000	0.000	0.000
43	A	54	LYS	1	0.885	0.945	59.893	0.017	0.017	0.000	0.000	0.000	0.000
44	A	55	GLY	0	0.044	0.035	63.088	0.000	0.000	0.000	0.000	0.000	0.000
45	A	56	GLN	0	0.022	-0.001	60.056	0.000	0.000	0.000	0.000	0.000	0.000
46	A	57	LYS	1	0.971	0.975	59.406	0.014	0.014	0.000	0.000	0.000	0.000
47	A	58	ASP	-1	-0.838	-0.913	58.427	-0.017	-0.017	0.000	0.000	0.000	0.000
48	A	59	VAL	0	0.025	0.010	55.467	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	60	CYS	0	-0.058	-0.026	54.598	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	61	ILE	0	0.015	0.004	53.886	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	62	VAL	0	-0.018	-0.008	51.582	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	63	LEU	0	0.031	0.007	50.074	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	64	ALA	0	-0.005	-0.006	49.149	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	65	LYS	1	0.942	0.963	48.650	0.019	0.019	0.000	0.000	0.000	0.000
55	A	66	GLU	-1	-0.777	-0.841	44.561	-0.029	-0.029	0.000	0.000	0.000	0.000
56	A	67	MET	0	-0.013	0.009	44.503	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	68	ILE	0	-0.023	-0.009	43.895	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	69	ARG	1	0.816	0.874	41.501	0.027	0.027	0.000	0.000	0.000	0.000
59	A	70	SER	0	0.008	0.000	40.215	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	71	ARG	1	0.868	0.908	38.997	0.031	0.031	0.000	0.000	0.000	0.000
61	A	72	LYS	1	0.951	0.977	38.663	0.029	0.029	0.000	0.000	0.000	0.000
62	A	73	ALA	0	-0.032	0.002	36.206	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	74	VAL	0	0.040	0.008	34.627	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	75	SER	0	-0.017	-0.002	33.927	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	76	LYS	1	0.954	0.971	32.256	0.043	0.043	0.000	0.000	0.000	0.000
66	A	77	LEU	0	0.031	0.026	29.767	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	78	TYR	0	0.031	0.001	29.141	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	79	ALA	0	-0.011	0.007	29.317	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	80	SER	0	0.046	0.006	26.486	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	81	LYS	1	0.828	0.902	25.113	0.081	0.081	0.000	0.000	0.000	0.000
71	A	82	ALA	0	0.003	0.002	24.634	-0.009	-0.009	0.000	0.000	0.000	0.000
72	A	83	HIS	0	0.031	0.022	24.642	-0.010	-0.010	0.000	0.000	0.000	0.000
73	A	84	MET	0	0.018	0.012	21.084	-0.011	-0.011	0.000	0.000	0.000	0.000
74	A	85	ASN	0	0.003	-0.004	20.070	-0.023	-0.023	0.000	0.000	0.000	0.000
75	A	86	SER	0	-0.011	0.007	20.864	-0.011	-0.011	0.000	0.000	0.000	0.000
76	A	87	VAL	0	0.031	0.008	16.669	-0.009	-0.009	0.000	0.000	0.000	0.000
77	A	88	LEU	0	-0.017	-0.003	15.156	-0.020	-0.020	0.000	0.000	0.000	0.000
78	A	89	MET	0	-0.017	-0.021	16.227	-0.022	-0.022	0.000	0.000	0.000	0.000
79	A	90	GLY	0	0.033	0.019	17.650	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	91	MET	0	-0.012	-0.005	12.288	-0.024	-0.024	0.000	0.000	0.000	0.000
81	A	92	LYS	1	0.960	0.970	12.878	0.141	0.141	0.000	0.000	0.000	0.000
82	A	93	ASN	0	-0.007	0.000	14.464	0.008	0.008	0.000	0.000	0.000	0.000
83	A	94	GLN	0	0.009	-0.006	11.740	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	95	LEU	0	-0.011	-0.001	8.435	-0.010	-0.010	0.000	0.000	0.000	0.000
85	A	96	ALA	0	0.003	0.009	11.078	0.010	0.010	0.000	0.000	0.000	0.000
86	A	97	VAL	0	0.007	-0.002	14.017	0.015	0.015	0.000	0.000	0.000	0.000
87	A	98	LEU	0	-0.026	-0.009	7.450	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	99	ARG	1	0.876	0.934	10.048	0.184	0.184	0.000	0.000	0.000	0.000
89	A	100	VAL	0	-0.016	0.005	12.235	0.020	0.020	0.000	0.000	0.000	0.000
90	A	101	ALA	0	0.094	0.048	13.634	0.012	0.012	0.000	0.000	0.000	0.000
91	A	102	GLY	0	-0.032	-0.004	9.180	0.015	0.015	0.000	0.000	0.000	0.000
92	A	103	SER	0	-0.029	-0.025	9.113	-0.019	-0.019	0.000	0.000	0.000	0.000
93	A	104	LEU	0	-0.026	-0.010	8.602	-0.026	-0.026	0.000	0.000	0.000	0.000
94	A	105	GLN	0	0.045	0.019	12.549	0.034	0.034	0.000	0.000	0.000	0.000
95	A	106	LYS	1	0.828	0.916	16.407	0.059	0.059	0.000	0.000	0.000	0.000
96	A	107	SER	0	0.009	0.005	18.573	0.019	0.019	0.000	0.000	0.000	0.000
97	A	108	THR	0	0.070	0.012	20.445	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	109	GLU	-1	-0.816	-0.882	21.875	-0.086	-0.086	0.000	0.000	0.000	0.000
99	A	110	VAL	0	0.029	0.009	16.915	0.002	0.002	0.000	0.000	0.000	0.000
100	A	111	MET	0	0.037	0.040	19.973	0.001	0.001	0.000	0.000	0.000	0.000
101	A	112	LYS	1	0.801	0.880	21.855	0.089	0.089	0.000	0.000	0.000	0.000
102	A	113	ALA	0	-0.018	0.000	21.949	0.006	0.006	0.000	0.000	0.000	0.000
103	A	114	MET	0	0.041	0.021	18.051	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	115	GLN	0	0.020	0.026	21.984	0.011	0.011	0.000	0.000	0.000	0.000
105	A	116	SER	0	-0.043	-0.044	25.404	0.006	0.006	0.000	0.000	0.000	0.000
106	A	117	LEU	0	0.014	0.006	21.142	0.004	0.004	0.000	0.000	0.000	0.000
107	A	118	VAL	0	-0.052	-0.021	22.641	0.004	0.004	0.000	0.000	0.000	0.000
108	A	119	LYS	1	0.842	0.905	25.131	0.068	0.068	0.000	0.000	0.000	0.000
109	A	120	ILE	0	-0.028	0.013	26.437	0.005	0.005	0.000	0.000	0.000	0.000
110	A	121	PRO	0	-0.020	-0.023	28.547	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	122	GLU	-1	-0.804	-0.892	28.459	-0.060	-0.060	0.000	0.000	0.000	0.000
112	A	123	ILE	0	-0.019	-0.004	21.592	0.000	0.000	0.000	0.000	0.000	0.000
113	A	124	GLN	0	0.045	0.017	24.538	-0.005	-0.005	0.000	0.000	0.000	0.000
114	A	125	ALA	0	-0.032	-0.010	23.340	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	126	THR	0	0.056	0.005	18.421	0.000	0.000	0.000	0.000	0.000	0.000
116	A	127	MET	0	0.005	0.008	18.371	-0.017	-0.017	0.000	0.000	0.000	0.000
117	A	128	ARG	1	0.890	0.934	19.579	0.050	0.050	0.000	0.000	0.000	0.000
118	A	129	GLU	-1	-0.952	-0.963	15.637	-0.092	-0.092	0.000	0.000	0.000	0.000
119	A	130	LEU	0	0.020	0.000	13.579	-0.012	-0.012	0.000	0.000	0.000	0.000
120	A	131	SER	0	0.010	-0.004	15.010	-0.020	-0.020	0.000	0.000	0.000	0.000
121	A	132	LYS	1	0.933	0.980	16.326	0.057	0.057	0.000	0.000	0.000	0.000
122	A	133	GLU	-1	-0.816	-0.895	10.619	-0.303	-0.303	0.000	0.000	0.000	0.000
123	A	134	MET	0	-0.023	-0.007	12.071	-0.016	-0.016	0.000	0.000	0.000	0.000
124	A	135	MET	0	-0.010	0.002	13.714	0.003	0.003	0.000	0.000	0.000	0.000
125	A	136	LYS	1	0.940	0.970	11.969	0.023	0.023	0.000	0.000	0.000	0.000
126	A	137	ALA	0	-0.037	-0.018	10.157	0.004	0.004	0.000	0.000	0.000	0.000
127	A	138	GLY	0	0.025	0.029	11.654	-0.011	-0.011	0.000	0.000	0.000	0.000
128	A	139	ILE	0	-0.050	-0.041	13.056	0.008	0.008	0.000	0.000	0.000	0.000
129	A	140	ILE	0	-0.052	-0.031	16.188	0.010	0.010	0.000	0.000	0.000	0.000
130	A	141	GLU	-1	-0.785	-0.877	18.902	-0.061	-0.061	0.000	0.000	0.000	0.000
131	A	161	ALA	0	0.052	0.020	23.825	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	162	GLU	-1	-0.891	-0.959	24.861	-0.028	-0.028	0.000	0.000	0.000	0.000
133	A	163	MET	0	-0.008	-0.004	21.158	0.003	0.003	0.000	0.000	0.000	0.000
134	A	164	GLU	-1	-0.928	-0.968	19.687	-0.084	-0.084	0.000	0.000	0.000	0.000
135	A	165	ILE	0	0.034	0.013	21.189	-0.003	-0.003	0.000	0.000	0.000	0.000
136	A	166	ASP	-1	-0.869	-0.920	21.917	-0.007	-0.007	0.000	0.000	0.000	0.000
137	A	167	ARG	1	0.756	0.852	15.340	0.091	0.091	0.000	0.000	0.000	0.000
138	A	168	ILE	0	-0.019	-0.011	17.334	-0.002	-0.002	0.000	0.000	0.000	0.000
139	A	169	LEU	0	0.036	0.026	18.695	0.000	0.000	0.000	0.000	0.000	0.000
140	A	170	PHE	0	-0.079	-0.039	15.374	0.011	0.011	0.000	0.000	0.000	0.000
141	A	171	GLU	-1	-0.978	-0.977	15.309	-0.045	-0.045	0.000	0.000	0.000	0.000
142	A	172	ILE	0	-0.099	-0.038	16.835	0.008	0.008	0.000	0.000	0.000	0.000

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