FMO DATABASE

FMODB ID: 76GRK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1429169.468707
FMO2-HF: Nuclear repulsion	1369930.900968
FMO2-HF: Total energy	-59238.567739
FMO2-MP2: Total energy	-59414.729089

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.
-5.403	-2.216	0.387	-1.394	-2.179	0.001

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 : -0.011 / q_NPA : -0.022

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	0.053	0.017	3.633	-3.442	-1.889	0.008	-0.774	-0.786	0.003
4	A	32	ARG	1	0.903	0.952	5.945	-0.374	-0.374	0.000	0.000	0.000	0.000
5	A	33	LEU	0	-0.036	-0.017	3.164	-0.710	0.076	0.034	-0.269	-0.551	0.001
6	A	34	VAL	0	-0.019	-0.004	2.467	-1.195	-0.412	0.346	-0.343	-0.786	-0.003
7	A	35	ALA	0	0.029	0.018	4.865	0.388	0.453	-0.001	-0.008	-0.056	0.000
8	A	36	TYR	0	-0.054	-0.017	8.118	0.156	0.156	0.000	0.000	0.000	0.000
9	A	37	ALA	0	0.021	0.004	7.102	0.076	0.076	0.000	0.000	0.000	0.000
10	A	38	ASP	-1	-0.821	-0.895	8.813	-1.260	-1.260	0.000	0.000	0.000	0.000
11	A	39	CYS	0	-0.049	-0.025	10.630	0.113	0.113	0.000	0.000	0.000	0.000
12	A	40	ASP	-1	-0.926	-0.947	12.199	-0.042	-0.042	0.000	0.000	0.000	0.000
13	A	41	GLU	-1	-0.830	-0.901	12.199	-0.622	-0.622	0.000	0.000	0.000	0.000
14	A	42	ALA	0	-0.031	-0.043	14.317	0.037	0.037	0.000	0.000	0.000	0.000
15	A	43	ASN	0	0.010	-0.008	16.463	0.031	0.031	0.000	0.000	0.000	0.000
16	A	44	ALA	0	0.018	0.010	17.372	0.028	0.028	0.000	0.000	0.000	0.000
17	A	45	ALA	0	-0.024	-0.008	18.683	0.016	0.016	0.000	0.000	0.000	0.000
18	A	46	ILE	0	0.004	0.000	20.573	0.016	0.016	0.000	0.000	0.000	0.000
19	A	47	GLY	0	0.025	0.012	22.084	0.017	0.017	0.000	0.000	0.000	0.000
20	A	48	ALA	0	-0.024	-0.009	23.114	0.014	0.014	0.000	0.000	0.000	0.000
21	A	49	ALA	0	-0.006	-0.001	24.884	0.010	0.010	0.000	0.000	0.000	0.000
22	A	50	LEU	0	-0.034	-0.017	26.039	0.011	0.011	0.000	0.000	0.000	0.000
23	A	51	ALA	0	-0.037	-0.012	27.524	0.009	0.009	0.000	0.000	0.000	0.000
24	A	52	LEU	0	-0.065	-0.047	27.125	0.006	0.006	0.000	0.000	0.000	0.000
25	A	53	GLY	0	-0.010	-0.008	30.194	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	54	HIS	0	-0.100	-0.033	31.706	0.004	0.004	0.000	0.000	0.000	0.000
27	A	55	PRO	0	0.029	0.021	31.193	0.001	0.001	0.000	0.000	0.000	0.000
28	A	56	ASP	-1	-0.813	-0.894	34.277	-0.057	-0.057	0.000	0.000	0.000	0.000
29	A	57	THR	0	0.022	-0.006	35.546	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	58	GLN	0	0.016	0.029	35.799	0.000	0.000	0.000	0.000	0.000	0.000
31	A	59	ILE	0	0.018	-0.002	31.644	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	60	THR	0	-0.034	-0.037	31.417	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	61	ASP	-1	-0.909	-0.964	30.740	-0.035	-0.035	0.000	0.000	0.000	0.000
34	A	62	VAL	0	-0.020	0.006	29.249	0.001	0.001	0.000	0.000	0.000	0.000
35	A	63	LEU	0	0.011	-0.011	26.407	-0.005	-0.005	0.000	0.000	0.000	0.000
36	A	64	ARG	1	0.933	0.964	26.061	0.023	0.023	0.000	0.000	0.000	0.000
37	A	65	GLN	0	-0.054	-0.017	26.456	0.011	0.011	0.000	0.000	0.000	0.000
38	A	66	ILE	0	0.011	0.002	22.647	0.001	0.001	0.000	0.000	0.000	0.000
39	A	67	GLN	0	-0.049	-0.024	21.859	0.006	0.006	0.000	0.000	0.000	0.000
40	A	68	ASN	0	-0.059	-0.026	21.444	0.011	0.011	0.000	0.000	0.000	0.000
41	A	69	ASP	-1	-0.683	-0.827	22.169	-0.046	-0.046	0.000	0.000	0.000	0.000
42	A	70	LEU	0	-0.015	-0.013	17.477	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	71	PHE	0	-0.053	-0.003	17.094	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	72	ASP	-1	-0.787	-0.879	17.422	0.052	0.052	0.000	0.000	0.000	0.000
45	A	73	ALA	0	-0.033	-0.024	16.606	0.016	0.016	0.000	0.000	0.000	0.000
46	A	74	GLY	0	0.034	0.016	13.329	-0.018	-0.018	0.000	0.000	0.000	0.000
47	A	75	ALA	0	0.027	0.001	13.299	0.062	0.062	0.000	0.000	0.000	0.000
48	A	76	ASP	-1	-0.849	-0.912	15.311	0.080	0.080	0.000	0.000	0.000	0.000
49	A	77	LEU	0	0.000	-0.021	11.235	0.026	0.026	0.000	0.000	0.000	0.000
50	A	78	SER	0	-0.063	-0.026	10.472	0.062	0.062	0.000	0.000	0.000	0.000
51	A	79	THR	0	-0.040	-0.015	11.508	0.222	0.222	0.000	0.000	0.000	0.000
52	A	80	PRO	0	-0.014	0.002	12.372	-0.113	-0.113	0.000	0.000	0.000	0.000
53	A	81	ILE	0	-0.025	-0.023	14.704	0.001	0.001	0.000	0.000	0.000	0.000
54	A	82	VAL	0	-0.039	-0.014	18.356	0.026	0.026	0.000	0.000	0.000	0.000
55	A	83	GLU	-1	-0.875	-0.947	20.627	0.083	0.083	0.000	0.000	0.000	0.000
56	A	84	ASN	0	-0.075	-0.033	24.250	0.006	0.006	0.000	0.000	0.000	0.000
57	A	85	PRO	0	-0.009	0.011	23.044	0.014	0.014	0.000	0.000	0.000	0.000
58	A	86	LYS	1	0.950	0.959	24.902	-0.242	-0.242	0.000	0.000	0.000	0.000
59	A	87	HIS	0	-0.029	0.003	20.928	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	88	PRO	0	0.025	-0.002	25.504	-0.008	-0.008	0.000	0.000	0.000	0.000
61	A	89	PRO	0	-0.029	-0.009	22.836	0.018	0.018	0.000	0.000	0.000	0.000
62	A	90	LEU	0	0.032	0.027	19.873	-0.012	-0.012	0.000	0.000	0.000	0.000
63	A	91	ARG	1	0.772	0.866	16.479	-0.147	-0.147	0.000	0.000	0.000	0.000
64	A	92	ILE	0	0.011	0.030	19.354	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	93	ALA	0	-0.008	-0.010	21.828	0.003	0.003	0.000	0.000	0.000	0.000
66	A	94	GLN	0	-0.022	-0.039	25.225	-0.015	-0.015	0.000	0.000	0.000	0.000
67	A	95	SER	0	0.014	0.004	27.176	-0.009	-0.009	0.000	0.000	0.000	0.000
68	A	96	TYR	0	-0.078	-0.065	23.469	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	97	ILE	0	-0.017	-0.019	22.978	-0.011	-0.011	0.000	0.000	0.000	0.000
70	A	98	ASP	-1	-0.807	-0.888	26.578	-0.068	-0.068	0.000	0.000	0.000	0.000
71	A	99	ARG	1	0.806	0.911	26.485	0.054	0.054	0.000	0.000	0.000	0.000
72	A	100	LEU	0	-0.027	-0.013	24.046	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	101	GLU	-1	-0.852	-0.929	28.680	-0.114	-0.114	0.000	0.000	0.000	0.000
74	A	102	GLY	0	0.035	0.029	30.752	0.002	0.002	0.000	0.000	0.000	0.000
75	A	103	TRP	0	0.006	-0.017	28.149	0.001	0.001	0.000	0.000	0.000	0.000
76	A	104	CYS	0	-0.032	-0.009	29.523	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	105	ASP	-1	-0.891	-0.943	32.354	-0.091	-0.091	0.000	0.000	0.000	0.000
78	A	106	ALA	0	-0.074	-0.043	35.834	0.003	0.003	0.000	0.000	0.000	0.000
79	A	107	TYR	0	-0.027	-0.030	33.667	0.002	0.002	0.000	0.000	0.000	0.000
80	A	108	ASN	0	-0.003	-0.017	34.918	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	109	ALA	0	-0.015	0.007	36.703	0.001	0.001	0.000	0.000	0.000	0.000
82	A	110	GLY	0	-0.035	-0.008	40.076	0.003	0.003	0.000	0.000	0.000	0.000
83	A	111	LEU	0	-0.025	-0.004	35.992	0.000	0.000	0.000	0.000	0.000	0.000
84	A	112	PRO	0	-0.007	0.009	40.429	0.000	0.000	0.000	0.000	0.000	0.000
85	A	113	ALA	0	0.031	0.005	40.221	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	114	LEU	0	-0.017	-0.003	34.629	0.001	0.001	0.000	0.000	0.000	0.000
87	A	115	LYS	1	0.951	0.983	39.320	0.095	0.095	0.000	0.000	0.000	0.000
88	A	116	SER	0	-0.037	-0.032	38.505	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	117	PHE	0	0.028	0.013	32.736	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	118	VAL	0	0.029	0.012	31.572	0.004	0.004	0.000	0.000	0.000	0.000
91	A	119	LEU	0	-0.063	-0.036	31.101	-0.013	-0.013	0.000	0.000	0.000	0.000
92	A	120	PRO	0	-0.037	-0.031	26.951	0.007	0.007	0.000	0.000	0.000	0.000
93	A	121	GLY	0	0.032	0.012	29.427	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	122	GLY	0	0.001	0.004	31.409	0.003	0.003	0.000	0.000	0.000	0.000
95	A	123	SER	0	0.023	0.018	34.728	0.000	0.000	0.000	0.000	0.000	0.000
96	A	124	PRO	0	0.028	-0.004	32.391	-0.009	-0.009	0.000	0.000	0.000	0.000
97	A	125	LEU	0	0.073	0.042	30.027	-0.010	-0.010	0.000	0.000	0.000	0.000
98	A	126	SER	0	0.049	0.015	29.835	-0.008	-0.008	0.000	0.000	0.000	0.000
99	A	127	ALA	0	-0.059	-0.027	29.261	-0.015	-0.015	0.000	0.000	0.000	0.000
100	A	128	LEU	0	-0.004	-0.001	26.287	-0.020	-0.020	0.000	0.000	0.000	0.000
101	A	129	LEU	0	0.032	0.025	25.080	-0.016	-0.016	0.000	0.000	0.000	0.000
102	A	130	HIS	0	0.064	0.045	25.025	-0.035	-0.035	0.000	0.000	0.000	0.000
103	A	131	VAL	0	-0.016	0.002	21.341	-0.027	-0.027	0.000	0.000	0.000	0.000
104	A	132	ALA	0	0.068	0.032	20.712	-0.036	-0.036	0.000	0.000	0.000	0.000
105	A	133	ARG	1	0.873	0.934	20.281	0.211	0.211	0.000	0.000	0.000	0.000
106	A	134	THR	0	-0.137	-0.085	20.252	-0.033	-0.033	0.000	0.000	0.000	0.000
107	A	135	VAL	0	0.015	0.020	15.189	-0.052	-0.052	0.000	0.000	0.000	0.000
108	A	136	VAL	0	0.060	0.028	15.800	-0.062	-0.062	0.000	0.000	0.000	0.000
109	A	137	ARG	1	0.946	0.973	16.767	0.317	0.317	0.000	0.000	0.000	0.000
110	A	138	ARG	1	0.741	0.866	11.625	0.726	0.726	0.000	0.000	0.000	0.000
111	A	139	ALA	0	0.067	0.029	12.190	-0.114	-0.114	0.000	0.000	0.000	0.000
112	A	140	GLU	-1	-0.852	-0.913	12.933	-0.393	-0.393	0.000	0.000	0.000	0.000
113	A	141	ARG	1	0.892	0.946	13.269	0.689	0.689	0.000	0.000	0.000	0.000
114	A	142	SER	0	0.002	-0.007	8.476	0.040	0.040	0.000	0.000	0.000	0.000
115	A	143	ALA	0	0.028	0.019	10.217	-0.038	-0.038	0.000	0.000	0.000	0.000
116	A	144	TRP	0	-0.056	-0.051	12.443	0.091	0.091	0.000	0.000	0.000	0.000
117	A	145	ALA	0	0.024	0.021	9.810	0.033	0.033	0.000	0.000	0.000	0.000
118	A	146	ALA	0	-0.020	-0.011	9.679	-0.024	-0.024	0.000	0.000	0.000	0.000
119	A	147	VAL	0	-0.040	-0.025	10.630	0.139	0.139	0.000	0.000	0.000	0.000
120	A	148	ASP	-1	-0.928	-0.970	13.329	-0.450	-0.450	0.000	0.000	0.000	0.000
121	A	149	ALA	0	-0.079	-0.027	9.971	0.037	0.037	0.000	0.000	0.000	0.000
122	A	150	HIS	0	-0.068	-0.037	8.690	0.206	0.206	0.000	0.000	0.000	0.000
123	A	151	PRO	0	0.024	0.009	13.889	0.043	0.043	0.000	0.000	0.000	0.000
124	A	152	GLU	-1	-0.913	-0.952	17.414	0.005	0.005	0.000	0.000	0.000	0.000
125	A	153	GLY	0	-0.038	-0.014	15.713	0.044	0.044	0.000	0.000	0.000	0.000
126	A	154	VAL	0	0.005	0.001	12.387	0.073	0.073	0.000	0.000	0.000	0.000
127	A	155	SER	0	0.070	0.050	15.501	-0.033	-0.033	0.000	0.000	0.000	0.000
128	A	156	VAL	0	0.061	0.009	16.815	-0.040	-0.040	0.000	0.000	0.000	0.000
129	A	157	LEU	0	-0.049	-0.026	18.951	-0.025	-0.025	0.000	0.000	0.000	0.000
130	A	158	PRO	0	0.054	0.033	15.746	-0.018	-0.018	0.000	0.000	0.000	0.000
131	A	159	ALA	0	0.050	0.024	16.104	-0.021	-0.021	0.000	0.000	0.000	0.000
132	A	160	LYS	1	0.920	0.956	17.364	0.165	0.165	0.000	0.000	0.000	0.000
133	A	161	TYR	0	0.027	0.000	19.849	0.000	0.000	0.000	0.000	0.000	0.000
134	A	162	LEU	0	0.008	-0.009	15.081	0.005	0.005	0.000	0.000	0.000	0.000
135	A	163	ASN	0	-0.099	-0.045	19.381	0.025	0.025	0.000	0.000	0.000	0.000
136	A	164	ARG	1	0.910	0.950	21.420	0.172	0.172	0.000	0.000	0.000	0.000
137	A	165	LEU	0	0.013	0.018	20.287	0.008	0.008	0.000	0.000	0.000	0.000
138	A	166	SER	0	-0.064	-0.032	21.365	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	167	ASP	-1	-0.867	-0.935	23.306	-0.192	-0.192	0.000	0.000	0.000	0.000
140	A	168	LEU	0	0.020	0.001	26.498	0.012	0.012	0.000	0.000	0.000	0.000
141	A	169	LEU	0	0.001	-0.004	22.733	0.008	0.008	0.000	0.000	0.000	0.000
142	A	170	PHE	0	-0.046	-0.017	26.856	0.004	0.004	0.000	0.000	0.000	0.000
143	A	171	ILE	0	-0.004	0.001	28.658	0.008	0.008	0.000	0.000	0.000	0.000
144	A	172	LEU	0	0.033	0.007	28.593	0.007	0.007	0.000	0.000	0.000	0.000
145	A	173	SER	0	-0.044	-0.022	28.615	0.004	0.004	0.000	0.000	0.000	0.000
146	A	174	ARG	1	0.818	0.919	31.246	0.118	0.118	0.000	0.000	0.000	0.000
147	A	175	VAL	0	-0.015	0.004	34.326	0.006	0.006	0.000	0.000	0.000	0.000
148	A	176	ALA	0	-0.030	-0.012	33.233	0.007	0.007	0.000	0.000	0.000	0.000
149	A	177	ASN	0	-0.047	-0.013	34.067	0.004	0.004	0.000	0.000	0.000	0.000
150	A	178	PRO	0	0.019	0.015	37.121	0.000	0.000	0.000	0.000	0.000	0.000
151	A	179	ASP	-1	-0.940	-0.970	40.700	-0.072	-0.072	0.000	0.000	0.000	0.000
152	A	180	GLY	0	-0.051	-0.015	40.246	0.000	0.000	0.000	0.000	0.000	0.000
153	A	181	ASP	-1	-0.843	-0.934	35.282	-0.122	-0.122	0.000	0.000	0.000	0.000
154	A	182	VAL	0	0.011	0.010	34.269	0.005	0.005	0.000	0.000	0.000	0.000
155	A	183	LEU	0	-0.037	-0.023	35.144	-0.006	-0.006	0.000	0.000	0.000	0.000
156	A	184	TRP	0	0.046	0.019	34.543	0.004	0.004	0.000	0.000	0.000	0.000
157	A	185	ARG	1	0.929	0.962	36.497	0.115	0.115	0.000	0.000	0.000	0.000
158	A	186	PRO	0	0.012	0.008	39.035	-0.005	-0.005	0.000	0.000	0.000	0.000
159	A	187	GLY	0	0.004	0.009	39.556	0.003	0.003	0.000	0.000	0.000	0.000
160	A	188	GLY	0	-0.006	0.009	40.733	0.005	0.005	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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