FMO DATABASE

FMODB ID: 6Y6QZ

Calculation Name: 2G2D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2G2D

Chain ID: A

ChEMBL ID:

UniProt ID: P9WP99

Base Structure: X-ray

Registration Date: 2023-09-21

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	160
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1435405.434925
FMO2-HF: Nuclear repulsion	1376166.23286
FMO2-HF: Total energy	-59239.202065
FMO2-MP2: Total energy	-59415.291952

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:29:THR)

Summations of interaction energy for fragment #1(A:29:THR)

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.
-2.283	0.691	0.17	-1.246	-1.898	0

Interaction energy analysis for fragmet #1(A:29:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : 0.003

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	31	ALA	0	0.046	0.023	3.736	-2.703	-1.117	0.006	-0.811	-0.781	0.003
4	A	32	ARG	1	0.836	0.921	5.788	0.861	0.861	0.000	0.000	0.000	0.000
5	A	33	LEU	0	-0.012	-0.007	3.190	-0.297	0.374	0.027	-0.195	-0.503	-0.001
6	A	34	VAL	0	-0.036	-0.007	2.774	-0.324	0.346	0.138	-0.237	-0.571	-0.002
7	A	35	ALA	0	0.044	0.024	5.095	0.640	0.687	-0.001	-0.003	-0.043	0.000
8	A	36	TYR	0	-0.022	-0.006	8.080	0.288	0.288	0.000	0.000	0.000	0.000
9	A	37	ALA	0	0.014	0.006	7.306	0.207	0.207	0.000	0.000	0.000	0.000
10	A	38	ASP	-1	-0.796	-0.858	9.033	-0.796	-0.796	0.000	0.000	0.000	0.000
11	A	39	CYS	0	-0.053	-0.028	10.977	0.129	0.129	0.000	0.000	0.000	0.000
12	A	40	ASP	-1	-0.910	-0.947	12.498	-0.087	-0.087	0.000	0.000	0.000	0.000
13	A	41	GLU	-1	-0.828	-0.875	12.883	-0.231	-0.231	0.000	0.000	0.000	0.000
14	A	42	ALA	0	-0.020	-0.022	14.687	0.043	0.043	0.000	0.000	0.000	0.000
15	A	43	ASN	0	-0.003	-0.006	16.685	0.050	0.050	0.000	0.000	0.000	0.000
16	A	44	ALA	0	0.018	0.008	17.637	0.028	0.028	0.000	0.000	0.000	0.000
17	A	45	ALA	0	-0.027	-0.010	18.826	0.022	0.022	0.000	0.000	0.000	0.000
18	A	46	ILE	0	0.022	0.006	20.696	0.015	0.015	0.000	0.000	0.000	0.000
19	A	47	GLY	0	0.028	0.020	22.260	0.014	0.014	0.000	0.000	0.000	0.000
20	A	48	ALA	0	-0.033	-0.019	23.188	0.014	0.014	0.000	0.000	0.000	0.000
21	A	49	ALA	0	-0.019	-0.017	24.895	0.009	0.009	0.000	0.000	0.000	0.000
22	A	50	LEU	0	-0.023	-0.008	26.193	0.008	0.008	0.000	0.000	0.000	0.000
23	A	51	ALA	0	-0.022	-0.016	27.553	0.007	0.007	0.000	0.000	0.000	0.000
24	A	52	LEU	0	-0.062	-0.039	26.944	0.008	0.008	0.000	0.000	0.000	0.000
25	A	53	GLY	0	0.002	0.003	30.221	0.001	0.001	0.000	0.000	0.000	0.000
26	A	54	HIS	0	-0.117	-0.045	31.622	0.001	0.001	0.000	0.000	0.000	0.000
27	A	55	PRO	0	0.039	0.029	31.043	0.001	0.001	0.000	0.000	0.000	0.000
28	A	56	ASP	-1	-0.795	-0.892	34.306	-0.059	-0.059	0.000	0.000	0.000	0.000
29	A	57	THR	0	0.017	-0.006	35.424	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	58	GLN	0	0.010	0.034	35.480	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	59	ILE	0	0.034	0.009	31.638	-0.005	-0.005	0.000	0.000	0.000	0.000
32	A	60	THR	0	-0.028	-0.026	31.266	-0.007	-0.007	0.000	0.000	0.000	0.000
33	A	61	ASP	-1	-0.818	-0.908	30.605	-0.059	-0.059	0.000	0.000	0.000	0.000
34	A	62	VAL	0	-0.029	0.002	29.399	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	63	LEU	0	0.015	0.002	26.481	-0.011	-0.011	0.000	0.000	0.000	0.000
36	A	64	ARG	1	0.841	0.901	25.906	0.049	0.049	0.000	0.000	0.000	0.000
37	A	65	GLN	0	-0.053	-0.027	26.268	0.007	0.007	0.000	0.000	0.000	0.000
38	A	66	ILE	0	0.006	0.000	22.735	-0.009	-0.009	0.000	0.000	0.000	0.000
39	A	67	GLN	0	-0.027	-0.016	21.662	-0.007	-0.007	0.000	0.000	0.000	0.000
40	A	68	ASN	0	-0.044	-0.003	21.275	0.004	0.004	0.000	0.000	0.000	0.000
41	A	69	ASP	-1	-0.712	-0.796	21.497	-0.147	-0.147	0.000	0.000	0.000	0.000
42	A	70	LEU	0	0.002	0.001	17.199	-0.027	-0.027	0.000	0.000	0.000	0.000
43	A	71	PHE	0	-0.035	0.003	16.899	-0.036	-0.036	0.000	0.000	0.000	0.000
44	A	72	ASP	-1	-0.785	-0.889	17.013	-0.139	-0.139	0.000	0.000	0.000	0.000
45	A	73	ALA	0	-0.022	-0.020	16.784	-0.014	-0.014	0.000	0.000	0.000	0.000
46	A	74	GLY	0	0.041	0.023	13.136	-0.066	-0.066	0.000	0.000	0.000	0.000
47	A	75	ALA	0	0.020	0.005	12.755	-0.041	-0.041	0.000	0.000	0.000	0.000
48	A	76	ASP	-1	-0.814	-0.891	14.385	-0.270	-0.270	0.000	0.000	0.000	0.000
49	A	77	LEU	0	-0.012	-0.018	11.180	-0.010	-0.010	0.000	0.000	0.000	0.000
50	A	78	SER	0	-0.055	-0.031	9.582	-0.081	-0.081	0.000	0.000	0.000	0.000
51	A	79	THR	0	-0.036	-0.015	10.632	0.134	0.134	0.000	0.000	0.000	0.000
52	A	80	PRO	0	0.009	0.010	11.886	-0.059	-0.059	0.000	0.000	0.000	0.000
53	A	81	ILE	0	-0.041	-0.019	14.037	0.044	0.044	0.000	0.000	0.000	0.000
54	A	82	VAL	0	-0.039	-0.022	17.645	0.023	0.023	0.000	0.000	0.000	0.000
55	A	83	GLU	-1	-0.799	-0.900	20.153	-0.067	-0.067	0.000	0.000	0.000	0.000
56	A	84	ASN	0	-0.114	-0.059	23.886	0.020	0.020	0.000	0.000	0.000	0.000
57	A	85	PRO	0	0.000	0.014	22.758	0.017	0.017	0.000	0.000	0.000	0.000
58	A	86	LYS	1	0.877	0.925	24.696	-0.021	-0.021	0.000	0.000	0.000	0.000
59	A	87	HIS	0	0.018	0.015	20.239	0.018	0.018	0.000	0.000	0.000	0.000
60	A	88	PRO	0	0.033	0.000	24.831	-0.009	-0.009	0.000	0.000	0.000	0.000
61	A	89	PRO	0	-0.026	0.001	22.098	0.002	0.002	0.000	0.000	0.000	0.000
62	A	90	LEU	0	-0.001	0.003	19.008	-0.007	-0.007	0.000	0.000	0.000	0.000
63	A	91	ARG	1	0.771	0.864	15.575	0.186	0.186	0.000	0.000	0.000	0.000
64	A	92	ILE	0	-0.020	0.002	19.323	0.016	0.016	0.000	0.000	0.000	0.000
65	A	93	ALA	0	0.019	0.007	21.675	-0.007	-0.007	0.000	0.000	0.000	0.000
66	A	94	GLN	0	-0.003	-0.032	25.151	-0.020	-0.020	0.000	0.000	0.000	0.000
67	A	95	SER	0	0.021	0.016	26.884	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	96	TYR	0	-0.092	-0.065	23.826	0.006	0.006	0.000	0.000	0.000	0.000
69	A	97	ILE	0	-0.018	-0.016	22.915	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	98	ASP	-1	-0.816	-0.904	26.339	-0.127	-0.127	0.000	0.000	0.000	0.000
71	A	99	ARG	1	0.769	0.865	26.312	0.130	0.130	0.000	0.000	0.000	0.000
72	A	100	LEU	0	-0.006	0.006	23.669	0.006	0.006	0.000	0.000	0.000	0.000
73	A	101	GLU	-1	-0.806	-0.877	28.389	-0.155	-0.155	0.000	0.000	0.000	0.000
74	A	102	GLY	0	0.017	0.008	30.692	0.007	0.007	0.000	0.000	0.000	0.000
75	A	103	TRP	0	0.011	-0.015	27.703	0.004	0.004	0.000	0.000	0.000	0.000
76	A	104	CYS	0	-0.053	-0.022	29.557	0.001	0.001	0.000	0.000	0.000	0.000
77	A	105	ASP	-1	-0.868	-0.939	32.247	-0.103	-0.103	0.000	0.000	0.000	0.000
78	A	106	ALA	0	-0.077	-0.035	35.803	0.006	0.006	0.000	0.000	0.000	0.000
79	A	107	TYR	0	-0.045	-0.043	33.150	0.004	0.004	0.000	0.000	0.000	0.000
80	A	108	ASN	0	0.000	-0.017	34.753	0.004	0.004	0.000	0.000	0.000	0.000
81	A	109	ALA	0	-0.028	-0.011	36.667	0.003	0.003	0.000	0.000	0.000	0.000
82	A	110	GLY	0	-0.023	0.001	39.589	0.005	0.005	0.000	0.000	0.000	0.000
83	A	111	LEU	0	-0.039	-0.006	35.627	0.002	0.002	0.000	0.000	0.000	0.000
84	A	112	PRO	0	-0.010	0.008	40.196	0.000	0.000	0.000	0.000	0.000	0.000
85	A	113	ALA	0	0.031	0.004	40.137	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	114	LEU	0	-0.014	-0.001	34.926	0.002	0.002	0.000	0.000	0.000	0.000
87	A	115	LYS	1	0.951	0.973	39.389	0.062	0.062	0.000	0.000	0.000	0.000
88	A	116	SER	0	-0.051	-0.048	38.453	0.001	0.001	0.000	0.000	0.000	0.000
89	A	117	PHE	0	0.038	0.023	32.995	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	118	VAL	0	0.029	0.015	31.686	0.005	0.005	0.000	0.000	0.000	0.000
91	A	119	LEU	0	-0.048	-0.025	31.001	-0.008	-0.008	0.000	0.000	0.000	0.000
92	A	120	PRO	0	-0.025	-0.018	26.951	0.002	0.002	0.000	0.000	0.000	0.000
93	A	121	GLY	0	0.012	-0.002	29.082	0.004	0.004	0.000	0.000	0.000	0.000
94	A	122	GLY	0	-0.003	-0.007	31.598	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	123	SER	0	0.012	0.012	34.716	0.004	0.004	0.000	0.000	0.000	0.000
96	A	124	PRO	0	0.035	-0.003	32.251	-0.006	-0.006	0.000	0.000	0.000	0.000
97	A	125	LEU	0	0.061	0.039	29.993	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	126	SER	0	0.046	-0.004	29.598	-0.009	-0.009	0.000	0.000	0.000	0.000
99	A	127	ALA	0	-0.058	-0.016	29.074	-0.010	-0.010	0.000	0.000	0.000	0.000
100	A	128	LEU	0	0.004	0.007	25.990	-0.011	-0.011	0.000	0.000	0.000	0.000
101	A	129	LEU	0	0.020	0.019	24.800	-0.014	-0.014	0.000	0.000	0.000	0.000
102	A	130	HIS	0	0.034	0.021	24.849	-0.029	-0.029	0.000	0.000	0.000	0.000
103	A	131	VAL	0	-0.008	0.001	21.462	-0.017	-0.017	0.000	0.000	0.000	0.000
104	A	132	ALA	0	0.059	0.037	20.583	-0.025	-0.025	0.000	0.000	0.000	0.000
105	A	133	ARG	1	0.871	0.943	20.018	0.141	0.141	0.000	0.000	0.000	0.000
106	A	134	THR	0	-0.117	-0.073	19.865	-0.025	-0.025	0.000	0.000	0.000	0.000
107	A	135	VAL	0	0.011	0.013	14.954	-0.039	-0.039	0.000	0.000	0.000	0.000
108	A	136	VAL	0	0.034	0.021	15.553	-0.066	-0.066	0.000	0.000	0.000	0.000
109	A	137	ARG	1	0.864	0.897	16.775	0.263	0.263	0.000	0.000	0.000	0.000
110	A	138	ARG	1	0.677	0.810	11.336	0.423	0.423	0.000	0.000	0.000	0.000
111	A	139	ALA	0	0.065	0.020	12.142	-0.100	-0.100	0.000	0.000	0.000	0.000
112	A	140	GLU	-1	-0.799	-0.866	13.017	-0.422	-0.422	0.000	0.000	0.000	0.000
113	A	141	ARG	1	0.883	0.938	13.546	0.470	0.470	0.000	0.000	0.000	0.000
114	A	142	SER	0	-0.016	-0.035	8.421	-0.005	-0.005	0.000	0.000	0.000	0.000
115	A	143	ALA	0	0.026	0.009	10.041	-0.158	-0.158	0.000	0.000	0.000	0.000
116	A	144	TRP	0	-0.032	-0.028	12.333	0.037	0.037	0.000	0.000	0.000	0.000
117	A	145	ALA	0	0.036	0.024	9.891	0.012	0.012	0.000	0.000	0.000	0.000
118	A	146	ALA	0	-0.024	-0.015	9.282	-0.125	-0.125	0.000	0.000	0.000	0.000
119	A	147	VAL	0	-0.023	-0.013	10.457	0.110	0.110	0.000	0.000	0.000	0.000
120	A	148	ASP	-1	-0.927	-0.972	13.128	-0.600	-0.600	0.000	0.000	0.000	0.000
121	A	149	ALA	0	-0.077	-0.035	9.403	0.041	0.041	0.000	0.000	0.000	0.000
122	A	150	HIS	0	-0.064	-0.037	8.075	0.345	0.345	0.000	0.000	0.000	0.000
123	A	151	PRO	0	0.018	0.022	13.408	0.054	0.054	0.000	0.000	0.000	0.000
124	A	152	GLU	-1	-0.925	-0.966	17.054	-0.207	-0.207	0.000	0.000	0.000	0.000
125	A	153	GLY	0	-0.018	-0.014	15.289	0.048	0.048	0.000	0.000	0.000	0.000
126	A	154	VAL	0	0.015	0.006	11.615	0.005	0.005	0.000	0.000	0.000	0.000
127	A	155	SER	0	0.044	0.042	14.934	0.022	0.022	0.000	0.000	0.000	0.000
128	A	156	VAL	0	0.043	0.006	16.770	-0.045	-0.045	0.000	0.000	0.000	0.000
129	A	157	LEU	0	-0.042	-0.006	19.026	0.008	0.008	0.000	0.000	0.000	0.000
130	A	158	PRO	0	0.056	0.023	15.871	0.010	0.010	0.000	0.000	0.000	0.000
131	A	159	ALA	0	0.050	0.029	15.968	0.004	0.004	0.000	0.000	0.000	0.000
132	A	160	LYS	1	0.891	0.947	17.307	0.299	0.299	0.000	0.000	0.000	0.000
133	A	161	TYR	0	0.007	-0.028	19.833	0.015	0.015	0.000	0.000	0.000	0.000
134	A	162	LEU	0	0.019	-0.005	14.828	0.019	0.019	0.000	0.000	0.000	0.000
135	A	163	ASN	0	-0.054	-0.034	19.122	0.039	0.039	0.000	0.000	0.000	0.000
136	A	164	ARG	1	0.850	0.917	21.190	0.216	0.216	0.000	0.000	0.000	0.000
137	A	165	LEU	0	0.015	0.024	20.236	0.019	0.019	0.000	0.000	0.000	0.000
138	A	166	SER	0	-0.074	-0.044	21.347	0.016	0.016	0.000	0.000	0.000	0.000
139	A	167	ASP	-1	-0.866	-0.941	23.283	-0.182	-0.182	0.000	0.000	0.000	0.000
140	A	168	LEU	0	0.024	0.004	26.526	0.015	0.015	0.000	0.000	0.000	0.000
141	A	169	LEU	0	0.014	-0.001	22.592	0.013	0.013	0.000	0.000	0.000	0.000
142	A	170	PHE	0	-0.037	-0.005	26.716	0.012	0.012	0.000	0.000	0.000	0.000
143	A	171	ILE	0	-0.023	-0.006	28.657	0.011	0.011	0.000	0.000	0.000	0.000
144	A	172	LEU	0	0.033	0.006	28.911	0.009	0.009	0.000	0.000	0.000	0.000
145	A	173	SER	0	-0.053	-0.046	28.598	0.007	0.007	0.000	0.000	0.000	0.000
146	A	174	ARG	1	0.776	0.874	31.181	0.098	0.098	0.000	0.000	0.000	0.000
147	A	175	VAL	0	-0.011	0.000	34.319	0.006	0.006	0.000	0.000	0.000	0.000
148	A	176	ALA	0	-0.018	0.006	33.061	0.006	0.006	0.000	0.000	0.000	0.000
149	A	177	ASN	0	-0.037	-0.002	33.871	0.007	0.007	0.000	0.000	0.000	0.000
150	A	178	PRO	0	0.017	0.018	37.151	0.000	0.000	0.000	0.000	0.000	0.000
151	A	179	ASP	-1	-0.924	-0.963	40.773	-0.050	-0.050	0.000	0.000	0.000	0.000
152	A	180	GLY	0	-0.049	-0.021	40.441	0.001	0.001	0.000	0.000	0.000	0.000
153	A	181	ASP	-1	-0.805	-0.886	35.206	-0.091	-0.091	0.000	0.000	0.000	0.000
154	A	182	VAL	0	-0.007	-0.001	34.228	0.004	0.004	0.000	0.000	0.000	0.000
155	A	183	LEU	0	-0.037	-0.014	35.080	-0.006	-0.006	0.000	0.000	0.000	0.000
156	A	184	TRP	0	0.040	0.012	34.346	0.005	0.005	0.000	0.000	0.000	0.000
157	A	185	ARG	1	0.944	0.975	36.573	0.066	0.066	0.000	0.000	0.000	0.000
158	A	186	PRO	0	0.020	0.012	38.815	-0.002	-0.002	0.000	0.000	0.000	0.000
159	A	187	GLY	0	-0.001	0.007	40.038	0.003	0.003	0.000	0.000	0.000	0.000
160	A	188	GLY	0	-0.015	0.009	41.018	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:29:THR)