FMO DATABASE

FMODB ID: YVRY2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1204684.464838
FMO2-HF: Nuclear repulsion	1145543.281218
FMO2-HF: Total energy	-59141.18362
FMO2-MP2: Total energy	-59306.768619

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.
-4.161	0.571	1.808	-2.291	-4.248	0.004

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 : 0.088 / 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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	14	GLU	-1	-0.873	-0.942	2.107	-6.307	-1.953	1.809	-2.282	-3.880	0.004
4	A	15	LEU	0	0.029	0.020	3.941	-0.211	0.167	-0.001	-0.009	-0.368	0.000
5	A	16	VAL	0	0.058	0.038	6.114	0.296	0.296	0.000	0.000	0.000	0.000
6	A	17	ASN	0	-0.005	-0.002	6.242	0.378	0.378	0.000	0.000	0.000	0.000
7	A	18	GLU	-1	-0.863	-0.918	7.157	-0.821	-0.821	0.000	0.000	0.000	0.000
8	A	19	TRP	0	0.038	-0.026	8.705	0.162	0.162	0.000	0.000	0.000	0.000
9	A	20	SER	0	-0.023	-0.012	11.000	0.142	0.142	0.000	0.000	0.000	0.000
10	A	21	LEU	0	-0.010	0.005	10.006	0.113	0.113	0.000	0.000	0.000	0.000
11	A	22	LYS	1	0.886	0.956	11.423	0.646	0.646	0.000	0.000	0.000	0.000
12	A	23	ILE	0	0.070	0.056	15.036	0.057	0.057	0.000	0.000	0.000	0.000
13	A	24	ARG	1	0.945	0.952	16.343	0.294	0.294	0.000	0.000	0.000	0.000
14	A	25	LYS	1	0.885	0.922	16.165	0.354	0.354	0.000	0.000	0.000	0.000
15	A	26	GLU	-1	-0.764	-0.905	18.902	-0.192	-0.192	0.000	0.000	0.000	0.000
16	A	27	MET	0	-0.077	-0.040	20.773	0.018	0.018	0.000	0.000	0.000	0.000
17	A	28	ARG	1	0.925	0.978	17.826	0.289	0.289	0.000	0.000	0.000	0.000
18	A	29	VAL	0	-0.009	0.019	23.164	0.016	0.016	0.000	0.000	0.000	0.000
19	A	30	VAL	0	0.078	0.036	25.301	0.014	0.014	0.000	0.000	0.000	0.000
20	A	31	ASP	-1	-0.922	-0.962	26.504	-0.138	-0.138	0.000	0.000	0.000	0.000
21	A	32	ARG	1	0.889	0.950	25.763	0.149	0.149	0.000	0.000	0.000	0.000
22	A	33	GLN	0	-0.040	-0.045	28.426	0.002	0.002	0.000	0.000	0.000	0.000
23	A	34	ILE	0	0.019	-0.001	30.832	0.009	0.009	0.000	0.000	0.000	0.000
24	A	35	ARG	1	0.904	0.942	29.177	0.124	0.124	0.000	0.000	0.000	0.000
25	A	36	ASP	-1	-0.905	-0.953	33.432	-0.093	-0.093	0.000	0.000	0.000	0.000
26	A	37	ILE	0	-0.004	-0.006	35.430	0.005	0.005	0.000	0.000	0.000	0.000
27	A	38	GLN	0	0.028	0.011	36.628	0.008	0.008	0.000	0.000	0.000	0.000
28	A	39	ARG	1	0.946	0.978	35.185	0.088	0.088	0.000	0.000	0.000	0.000
29	A	40	GLU	-1	-0.913	-0.955	40.190	-0.056	-0.056	0.000	0.000	0.000	0.000
30	A	41	GLU	-1	-0.912	-0.977	40.842	-0.063	-0.063	0.000	0.000	0.000	0.000
31	A	42	GLU	-1	-0.957	-0.972	41.238	-0.064	-0.064	0.000	0.000	0.000	0.000
32	A	43	LYS	1	0.899	0.950	42.962	0.065	0.065	0.000	0.000	0.000	0.000
33	A	44	VAL	0	0.062	0.040	45.482	0.003	0.003	0.000	0.000	0.000	0.000
34	A	45	LYS	1	1.012	0.994	47.625	0.053	0.053	0.000	0.000	0.000	0.000
35	A	46	ARG	1	0.884	0.936	46.456	0.054	0.054	0.000	0.000	0.000	0.000
36	A	47	SER	0	0.056	0.031	50.573	0.002	0.002	0.000	0.000	0.000	0.000
37	A	48	VAL	0	0.003	-0.006	51.083	0.002	0.002	0.000	0.000	0.000	0.000
38	A	49	LYS	1	0.884	0.949	52.690	0.044	0.044	0.000	0.000	0.000	0.000
39	A	50	ASP	-1	-0.914	-0.951	55.847	-0.036	-0.036	0.000	0.000	0.000	0.000
40	A	51	ALA	0	0.003	-0.005	56.643	0.001	0.001	0.000	0.000	0.000	0.000
41	A	52	ALA	0	0.009	-0.012	57.873	0.001	0.001	0.000	0.000	0.000	0.000
42	A	53	LYS	1	0.919	0.966	59.222	0.035	0.035	0.000	0.000	0.000	0.000
43	A	54	LYS	1	0.919	0.973	60.333	0.033	0.033	0.000	0.000	0.000	0.000
44	A	55	GLY	0	0.037	0.026	62.858	0.001	0.001	0.000	0.000	0.000	0.000
45	A	56	GLN	0	-0.001	-0.007	58.998	0.001	0.001	0.000	0.000	0.000	0.000
46	A	57	LYS	1	1.001	0.980	59.736	0.026	0.026	0.000	0.000	0.000	0.000
47	A	58	ASP	-1	-0.850	-0.928	58.747	-0.032	-0.032	0.000	0.000	0.000	0.000
48	A	59	VAL	0	0.000	0.003	55.191	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	60	CYS	0	-0.042	0.002	54.724	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	61	ILE	0	0.028	0.021	53.902	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	62	VAL	0	0.003	0.003	51.321	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	63	LEU	0	0.063	0.024	50.095	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	64	ALA	0	-0.003	-0.001	49.198	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	65	LYS	1	0.927	0.948	48.647	0.037	0.037	0.000	0.000	0.000	0.000
55	A	66	GLU	-1	-0.878	-0.942	44.148	-0.058	-0.058	0.000	0.000	0.000	0.000
56	A	67	MET	0	0.032	0.018	44.645	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	68	ILE	0	-0.058	-0.016	44.357	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	69	ARG	1	0.873	0.950	41.560	0.052	0.052	0.000	0.000	0.000	0.000
59	A	70	SER	0	0.014	0.015	40.545	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	71	ARG	1	1.007	1.006	39.320	0.052	0.052	0.000	0.000	0.000	0.000
61	A	72	LYS	1	0.917	0.947	38.828	0.052	0.052	0.000	0.000	0.000	0.000
62	A	73	ALA	0	-0.005	0.008	36.580	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	74	VAL	0	0.051	0.023	34.738	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	75	SER	0	-0.048	-0.012	34.007	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	76	LYS	1	0.985	0.979	32.287	0.078	0.078	0.000	0.000	0.000	0.000
66	A	77	LEU	0	0.041	0.036	29.817	-0.007	-0.007	0.000	0.000	0.000	0.000
67	A	78	TYR	0	0.036	0.007	29.443	-0.009	-0.009	0.000	0.000	0.000	0.000
68	A	79	ALA	0	-0.054	-0.015	29.556	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	80	SER	0	0.057	0.009	26.643	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	81	LYS	1	0.876	0.961	25.332	0.132	0.132	0.000	0.000	0.000	0.000
71	A	82	ALA	0	0.010	0.003	24.752	-0.013	-0.013	0.000	0.000	0.000	0.000
72	A	83	HIS	0	0.031	0.035	24.942	-0.011	-0.011	0.000	0.000	0.000	0.000
73	A	84	MET	0	0.020	0.003	21.237	-0.017	-0.017	0.000	0.000	0.000	0.000
74	A	85	ASN	0	-0.024	-0.021	20.370	-0.033	-0.033	0.000	0.000	0.000	0.000
75	A	86	SER	0	-0.040	-0.004	21.223	-0.013	-0.013	0.000	0.000	0.000	0.000
76	A	87	VAL	0	0.035	0.005	16.857	-0.007	-0.007	0.000	0.000	0.000	0.000
77	A	88	LEU	0	-0.016	0.001	15.383	-0.028	-0.028	0.000	0.000	0.000	0.000
78	A	89	MET	0	-0.016	-0.010	16.657	-0.026	-0.026	0.000	0.000	0.000	0.000
79	A	90	GLY	0	0.038	0.019	17.678	0.010	0.010	0.000	0.000	0.000	0.000
80	A	91	MET	0	0.002	-0.004	12.803	-0.028	-0.028	0.000	0.000	0.000	0.000
81	A	92	LYS	1	0.945	0.966	12.795	0.197	0.197	0.000	0.000	0.000	0.000
82	A	93	ASN	0	-0.005	-0.009	14.146	0.014	0.014	0.000	0.000	0.000	0.000
83	A	94	GLN	0	0.040	0.010	11.217	0.026	0.026	0.000	0.000	0.000	0.000
84	A	95	LEU	0	-0.011	0.005	8.706	0.017	0.017	0.000	0.000	0.000	0.000
85	A	96	ALA	0	0.004	0.013	10.879	0.053	0.053	0.000	0.000	0.000	0.000
86	A	97	VAL	0	0.015	0.005	12.800	0.034	0.034	0.000	0.000	0.000	0.000
87	A	98	LEU	0	-0.071	-0.031	6.951	0.027	0.027	0.000	0.000	0.000	0.000
88	A	99	ARG	1	0.880	0.929	8.911	0.027	0.027	0.000	0.000	0.000	0.000
89	A	100	VAL	0	-0.042	-0.013	11.918	0.020	0.020	0.000	0.000	0.000	0.000
90	A	101	ALA	0	0.100	0.080	14.122	0.019	0.019	0.000	0.000	0.000	0.000
91	A	102	GLY	0	-0.001	-0.009	9.926	0.045	0.045	0.000	0.000	0.000	0.000
92	A	103	SER	0	-0.055	-0.034	10.152	0.058	0.058	0.000	0.000	0.000	0.000
93	A	104	LEU	0	-0.029	-0.005	8.829	-0.057	-0.057	0.000	0.000	0.000	0.000
94	A	105	GLN	0	0.084	0.031	12.553	0.032	0.032	0.000	0.000	0.000	0.000
95	A	106	LYS	1	0.908	0.958	16.292	0.044	0.044	0.000	0.000	0.000	0.000
96	A	107	SER	0	0.026	0.041	17.916	0.019	0.019	0.000	0.000	0.000	0.000
97	A	108	THR	0	0.069	0.008	19.637	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	109	GLU	-1	-0.857	-0.933	21.544	-0.120	-0.120	0.000	0.000	0.000	0.000
99	A	110	VAL	0	-0.123	-0.052	17.193	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	111	MET	0	0.035	0.021	19.786	-0.013	-0.013	0.000	0.000	0.000	0.000
101	A	112	LYS	1	0.940	0.964	21.929	0.098	0.098	0.000	0.000	0.000	0.000
102	A	113	ALA	0	0.017	0.020	22.266	0.005	0.005	0.000	0.000	0.000	0.000
103	A	114	MET	0	0.043	0.016	17.424	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	115	GLN	0	-0.018	0.005	21.958	0.009	0.009	0.000	0.000	0.000	0.000
105	A	116	SER	0	-0.079	-0.080	25.121	0.007	0.007	0.000	0.000	0.000	0.000
106	A	117	LEU	0	0.021	0.000	21.877	0.004	0.004	0.000	0.000	0.000	0.000
107	A	118	VAL	0	-0.056	-0.013	22.553	0.000	0.000	0.000	0.000	0.000	0.000
108	A	119	LYS	1	0.916	0.966	25.031	0.105	0.105	0.000	0.000	0.000	0.000
109	A	120	ILE	0	-0.045	0.004	26.238	0.010	0.010	0.000	0.000	0.000	0.000
110	A	121	PRO	0	-0.025	-0.033	28.492	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	122	GLU	-1	-0.781	-0.887	27.845	-0.131	-0.131	0.000	0.000	0.000	0.000
112	A	123	ILE	0	-0.042	0.006	21.680	0.002	0.002	0.000	0.000	0.000	0.000
113	A	124	GLN	0	0.043	0.014	24.315	0.000	0.000	0.000	0.000	0.000	0.000
114	A	125	ALA	0	0.003	0.005	23.034	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	126	THR	0	0.063	0.034	18.691	-0.011	-0.011	0.000	0.000	0.000	0.000
116	A	127	MET	0	0.030	0.008	18.747	-0.018	-0.018	0.000	0.000	0.000	0.000
117	A	128	ARG	1	0.896	0.949	19.646	0.115	0.115	0.000	0.000	0.000	0.000
118	A	129	GLU	-1	-0.962	-0.979	15.713	-0.224	-0.224	0.000	0.000	0.000	0.000
119	A	130	LEU	0	0.005	-0.013	13.594	-0.030	-0.030	0.000	0.000	0.000	0.000
120	A	131	SER	0	-0.007	-0.005	15.015	-0.022	-0.022	0.000	0.000	0.000	0.000
121	A	132	LYS	1	0.962	0.997	16.215	0.138	0.138	0.000	0.000	0.000	0.000
122	A	133	GLU	-1	-0.891	-0.947	10.452	-0.549	-0.549	0.000	0.000	0.000	0.000
123	A	134	MET	0	-0.040	-0.016	11.807	-0.015	-0.015	0.000	0.000	0.000	0.000
124	A	135	MET	0	-0.028	-0.008	13.505	0.021	0.021	0.000	0.000	0.000	0.000
125	A	136	LYS	1	0.947	0.962	11.701	0.068	0.068	0.000	0.000	0.000	0.000
126	A	137	ALA	0	-0.034	-0.012	9.774	0.025	0.025	0.000	0.000	0.000	0.000
127	A	138	GLY	0	0.008	0.024	11.158	0.038	0.038	0.000	0.000	0.000	0.000
128	A	139	ILE	0	-0.070	-0.055	13.222	0.016	0.016	0.000	0.000	0.000	0.000
129	A	140	ILE	0	-0.004	-0.002	16.035	0.006	0.006	0.000	0.000	0.000	0.000
130	A	141	GLU	-1	-0.908	-0.958	18.696	-0.044	-0.044	0.000	0.000	0.000	0.000
131	A	161	ALA	0	0.018	-0.011	23.409	-0.003	-0.003	0.000	0.000	0.000	0.000
132	A	162	GLU	-1	-0.906	-0.972	24.894	0.021	0.021	0.000	0.000	0.000	0.000
133	A	163	MET	0	0.025	0.029	20.721	0.007	0.007	0.000	0.000	0.000	0.000
134	A	164	GLU	-1	-1.000	-1.021	19.697	-0.007	-0.007	0.000	0.000	0.000	0.000
135	A	165	ILE	0	0.035	0.019	21.464	0.007	0.007	0.000	0.000	0.000	0.000
136	A	166	ASP	-1	-0.897	-0.929	22.820	0.064	0.064	0.000	0.000	0.000	0.000
137	A	167	ARG	1	0.865	0.927	16.445	-0.008	-0.008	0.000	0.000	0.000	0.000
138	A	168	ILE	0	0.003	-0.013	18.041	0.015	0.015	0.000	0.000	0.000	0.000
139	A	169	LEU	0	-0.036	0.009	19.209	0.007	0.007	0.000	0.000	0.000	0.000
140	A	170	PHE	0	-0.110	-0.054	16.291	0.021	0.021	0.000	0.000	0.000	0.000
141	A	171	GLU	-1	-0.929	-0.965	16.168	0.073	0.073	0.000	0.000	0.000	0.000
142	A	172	ILE	0	-0.090	-0.028	17.170	0.003	0.003	0.000	0.000	0.000	0.000

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