FMO DATABASE

FMODB ID: V5R21

Calculation Name: 2P23-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2P23

Chain ID: A

ChEMBL ID:

UniProt ID: O95750

Base Structure: X-ray

Registration Date: 2023-06-21

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	135
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1252425.891355
FMO2-HF: Nuclear repulsion	1197766.3968
FMO2-HF: Total energy	-54659.494555
FMO2-MP2: Total energy	-54815.584897

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:40:ASP)

Summations of interaction energy for fragment #1(A:40:ASP)

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.
-45.474	-43.632	0.062	-0.815	-1.088	0.002

Interaction energy analysis for fragmet #1(A:40:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.906 / q_NPA : -0.966

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	42	ILE	0	-0.006	0.006	3.904	-2.348	-1.031	-0.009	-0.647	-0.661	0.002
4	A	43	ARG	1	0.818	0.880	5.526	-34.359	-34.359	0.000	0.000	0.000	0.000
5	A	44	LEU	0	0.050	0.045	8.624	-1.365	-1.365	0.000	0.000	0.000	0.000
6	A	45	ARG	1	0.860	0.924	10.546	-23.504	-23.504	0.000	0.000	0.000	0.000
7	A	46	HIS	0	0.083	0.051	14.190	-1.015	-1.015	0.000	0.000	0.000	0.000
8	A	47	LEU	0	0.003	0.007	14.213	0.035	0.035	0.000	0.000	0.000	0.000
9	A	48	TYR	0	0.003	0.010	17.770	-0.831	-0.831	0.000	0.000	0.000	0.000
10	A	49	THR	0	0.025	-0.019	20.549	0.171	0.171	0.000	0.000	0.000	0.000
11	A	50	SER	0	-0.010	-0.005	23.304	-0.464	-0.464	0.000	0.000	0.000	0.000
12	A	51	GLY	0	0.021	0.008	27.103	0.130	0.130	0.000	0.000	0.000	0.000
13	A	52	PRO	0	0.005	-0.004	30.052	0.036	0.036	0.000	0.000	0.000	0.000
14	A	53	HIS	0	0.033	0.013	32.163	0.114	0.114	0.000	0.000	0.000	0.000
15	A	54	GLY	0	0.055	0.052	30.590	-0.154	-0.154	0.000	0.000	0.000	0.000
16	A	55	LEU	0	0.014	-0.014	30.763	0.268	0.268	0.000	0.000	0.000	0.000
17	A	56	SER	0	-0.073	-0.029	30.077	-0.116	-0.116	0.000	0.000	0.000	0.000
18	A	57	SER	0	0.005	0.005	27.664	0.398	0.398	0.000	0.000	0.000	0.000
19	A	58	CYS	0	-0.025	0.006	25.668	-0.254	-0.254	0.000	0.000	0.000	0.000
20	A	59	PHE	0	0.044	0.027	21.056	0.493	0.493	0.000	0.000	0.000	0.000
21	A	60	LEU	0	-0.023	-0.003	18.697	-0.496	-0.496	0.000	0.000	0.000	0.000
22	A	61	ARG	1	0.840	0.891	20.755	-10.167	-10.167	0.000	0.000	0.000	0.000
23	A	62	ILE	0	0.011	0.002	18.680	-0.249	-0.249	0.000	0.000	0.000	0.000
24	A	63	ARG	1	0.814	0.904	22.899	-9.851	-9.851	0.000	0.000	0.000	0.000
25	A	64	ALA	0	0.061	0.013	25.457	0.170	0.170	0.000	0.000	0.000	0.000
26	A	65	ASP	-1	-0.799	-0.879	26.793	10.000	10.000	0.000	0.000	0.000	0.000
27	A	66	GLY	0	0.021	0.002	25.506	-0.102	-0.102	0.000	0.000	0.000	0.000
28	A	67	VAL	0	-0.064	-0.023	26.122	0.158	0.158	0.000	0.000	0.000	0.000
29	A	68	VAL	0	-0.003	0.003	22.482	0.281	0.281	0.000	0.000	0.000	0.000
30	A	69	ASP	-1	-0.805	-0.866	25.344	10.226	10.226	0.000	0.000	0.000	0.000
31	A	70	CYS	0	0.004	-0.002	25.205	0.392	0.392	0.000	0.000	0.000	0.000
32	A	71	ALA	0	0.006	0.024	24.967	-0.443	-0.443	0.000	0.000	0.000	0.000
33	A	72	ARG	1	0.852	0.900	26.576	-9.393	-9.393	0.000	0.000	0.000	0.000
34	A	73	GLY	0	0.019	0.006	26.126	-0.084	-0.084	0.000	0.000	0.000	0.000
35	A	74	GLN	0	-0.001	0.003	19.625	-0.113	-0.113	0.000	0.000	0.000	0.000
36	A	75	SER	0	0.002	-0.002	22.869	-0.551	-0.551	0.000	0.000	0.000	0.000
37	A	76	ALA	0	0.089	0.028	22.291	0.509	0.509	0.000	0.000	0.000	0.000
38	A	77	HIS	0	-0.009	-0.018	21.886	0.387	0.387	0.000	0.000	0.000	0.000
39	A	78	SER	0	-0.020	-0.020	20.979	-0.194	-0.194	0.000	0.000	0.000	0.000
40	A	79	LEU	0	-0.005	0.036	16.357	0.471	0.471	0.000	0.000	0.000	0.000
41	A	80	LEU	0	-0.033	-0.027	14.798	-0.273	-0.273	0.000	0.000	0.000	0.000
42	A	81	GLU	-1	-0.757	-0.861	10.645	21.830	21.830	0.000	0.000	0.000	0.000
43	A	82	ILE	0	-0.026	-0.010	8.479	-0.720	-0.720	0.000	0.000	0.000	0.000
44	A	83	LYS	1	0.902	0.923	6.075	-22.016	-22.016	0.000	0.000	0.000	0.000
45	A	84	ALA	0	0.020	0.016	2.928	-2.867	-2.389	0.072	-0.166	-0.383	0.000
46	A	85	VAL	0	-0.019	-0.013	5.070	-0.536	-0.489	-0.001	-0.002	-0.044	0.000
47	A	86	ALA	0	0.028	0.012	6.821	-0.636	-0.636	0.000	0.000	0.000	0.000
48	A	87	LEU	0	-0.012	-0.006	6.603	1.939	1.939	0.000	0.000	0.000	0.000
49	A	88	ARG	1	0.834	0.907	6.771	-17.595	-17.595	0.000	0.000	0.000	0.000
50	A	89	THR	0	-0.011	-0.013	8.340	-1.636	-1.636	0.000	0.000	0.000	0.000
51	A	90	VAL	0	-0.025	-0.021	6.886	2.603	2.603	0.000	0.000	0.000	0.000
52	A	91	ALA	0	0.050	0.040	9.013	-2.495	-2.495	0.000	0.000	0.000	0.000
53	A	92	ILE	0	-0.014	-0.020	10.495	1.071	1.071	0.000	0.000	0.000	0.000
54	A	93	LYS	1	0.853	0.933	13.221	-19.517	-19.517	0.000	0.000	0.000	0.000
55	A	94	GLY	0	0.011	0.020	15.445	0.505	0.505	0.000	0.000	0.000	0.000
56	A	95	VAL	0	0.000	-0.012	15.865	-0.221	-0.221	0.000	0.000	0.000	0.000
57	A	96	HIS	0	-0.013	-0.001	18.326	-0.238	-0.238	0.000	0.000	0.000	0.000
58	A	97	SER	0	-0.040	-0.043	21.786	-0.198	-0.198	0.000	0.000	0.000	0.000
59	A	98	VAL	0	-0.002	-0.001	18.399	-0.272	-0.272	0.000	0.000	0.000	0.000
60	A	99	ARG	1	0.805	0.926	19.063	-11.043	-11.043	0.000	0.000	0.000	0.000
61	A	100	TYR	0	0.032	0.005	13.240	0.925	0.925	0.000	0.000	0.000	0.000
62	A	101	LEU	0	-0.014	-0.016	16.622	-0.984	-0.984	0.000	0.000	0.000	0.000
63	A	102	CYS	0	-0.110	-0.028	16.179	0.210	0.210	0.000	0.000	0.000	0.000
64	A	103	MET	0	-0.051	-0.014	19.884	-0.509	-0.509	0.000	0.000	0.000	0.000
65	A	104	GLY	0	0.064	0.031	22.274	-0.029	-0.029	0.000	0.000	0.000	0.000
66	A	105	ALA	0	0.017	-0.003	25.731	0.079	0.079	0.000	0.000	0.000	0.000
67	A	106	ASP	-1	-0.920	-0.958	28.771	9.535	9.535	0.000	0.000	0.000	0.000
68	A	107	GLY	0	0.085	0.032	24.864	0.075	0.075	0.000	0.000	0.000	0.000
69	A	108	LYS	1	0.873	0.940	24.826	-9.587	-9.587	0.000	0.000	0.000	0.000
70	A	109	MET	0	0.005	0.027	19.900	0.177	0.177	0.000	0.000	0.000	0.000
71	A	110	GLN	0	-0.043	-0.032	22.957	-0.705	-0.705	0.000	0.000	0.000	0.000
72	A	111	GLY	0	0.052	0.023	21.511	0.607	0.607	0.000	0.000	0.000	0.000
73	A	112	LEU	0	-0.011	-0.009	20.881	-0.741	-0.741	0.000	0.000	0.000	0.000
74	A	113	LEU	0	0.031	0.001	20.300	0.543	0.543	0.000	0.000	0.000	0.000
75	A	114	GLN	0	-0.032	-0.016	19.651	0.208	0.208	0.000	0.000	0.000	0.000
76	A	115	TYR	0	-0.035	-0.039	12.248	-0.145	-0.145	0.000	0.000	0.000	0.000
77	A	116	SER	0	0.049	0.004	17.328	-0.164	-0.164	0.000	0.000	0.000	0.000
78	A	117	GLU	-1	-0.839	-0.904	12.645	19.788	19.788	0.000	0.000	0.000	0.000
79	A	118	GLU	-1	-0.838	-0.904	15.806	13.183	13.183	0.000	0.000	0.000	0.000
80	A	119	ASP	-1	-0.816	-0.896	18.601	12.437	12.437	0.000	0.000	0.000	0.000
81	A	121	ALA	0	0.030	0.028	12.086	1.027	1.027	0.000	0.000	0.000	0.000
82	A	122	PHE	0	-0.047	-0.035	12.674	-1.283	-1.283	0.000	0.000	0.000	0.000
83	A	123	GLU	-1	-0.760	-0.844	11.887	24.138	24.138	0.000	0.000	0.000	0.000
84	A	124	GLU	-1	-0.766	-0.826	8.752	26.378	26.378	0.000	0.000	0.000	0.000
85	A	125	GLU	-1	-0.834	-0.907	12.008	17.555	17.555	0.000	0.000	0.000	0.000
86	A	126	ILE	0	0.029	0.029	13.778	-0.964	-0.964	0.000	0.000	0.000	0.000
87	A	127	ARG	1	0.842	0.928	15.333	-15.656	-15.656	0.000	0.000	0.000	0.000
88	A	128	PRO	0	-0.003	-0.015	19.184	0.196	0.196	0.000	0.000	0.000	0.000
89	A	129	ASP	-1	-0.810	-0.894	21.965	13.588	13.588	0.000	0.000	0.000	0.000
90	A	130	GLY	0	0.004	0.000	18.565	-0.219	-0.219	0.000	0.000	0.000	0.000
91	A	131	TYR	0	-0.086	-0.025	17.436	0.687	0.687	0.000	0.000	0.000	0.000
92	A	132	ASN	0	-0.006	-0.018	11.743	-0.374	-0.374	0.000	0.000	0.000	0.000
93	A	133	VAL	0	-0.033	-0.014	15.895	-1.088	-1.088	0.000	0.000	0.000	0.000
94	A	134	TYR	0	0.009	-0.026	11.531	0.291	0.291	0.000	0.000	0.000	0.000
95	A	135	ARG	1	0.863	0.920	15.861	-16.161	-16.161	0.000	0.000	0.000	0.000
96	A	136	SER	0	0.058	0.046	16.414	0.670	0.670	0.000	0.000	0.000	0.000
97	A	137	GLU	-1	-0.895	-0.962	17.291	15.734	15.734	0.000	0.000	0.000	0.000
98	A	138	LYS	1	0.778	0.871	20.015	-13.057	-13.057	0.000	0.000	0.000	0.000
99	A	139	HIS	0	-0.022	-0.036	21.795	-1.003	-1.003	0.000	0.000	0.000	0.000
100	A	140	ARG	1	0.858	0.939	22.737	-11.836	-11.836	0.000	0.000	0.000	0.000
101	A	141	LEU	0	0.001	0.023	22.375	-0.430	-0.430	0.000	0.000	0.000	0.000
102	A	142	PRO	0	-0.012	0.002	19.950	0.635	0.635	0.000	0.000	0.000	0.000
103	A	143	VAL	0	0.033	0.003	17.417	-0.716	-0.716	0.000	0.000	0.000	0.000
104	A	144	SER	0	-0.001	-0.013	20.467	-0.258	-0.258	0.000	0.000	0.000	0.000
105	A	145	LEU	0	0.026	0.005	23.321	-0.210	-0.210	0.000	0.000	0.000	0.000
106	A	146	SER	0	-0.043	-0.011	26.033	-0.574	-0.574	0.000	0.000	0.000	0.000
107	A	147	SER	0	0.019	-0.019	29.078	-0.048	-0.048	0.000	0.000	0.000	0.000
108	A	148	ALA	0	0.056	0.005	32.236	0.081	0.081	0.000	0.000	0.000	0.000
109	A	149	LYS	1	0.954	0.972	33.823	-7.690	-7.690	0.000	0.000	0.000	0.000
110	A	150	GLN	0	0.050	0.046	31.866	-0.050	-0.050	0.000	0.000	0.000	0.000
111	A	151	ARG	1	0.814	0.899	26.027	-10.843	-10.843	0.000	0.000	0.000	0.000
112	A	152	GLN	0	0.034	0.025	31.470	0.073	0.073	0.000	0.000	0.000	0.000
113	A	153	LEU	0	-0.014	-0.010	31.704	-0.087	-0.087	0.000	0.000	0.000	0.000
114	A	154	TYR	0	0.020	0.001	24.680	0.021	0.021	0.000	0.000	0.000	0.000
115	A	155	LYS	1	0.914	0.944	30.187	-9.259	-9.259	0.000	0.000	0.000	0.000
116	A	156	ASN	0	-0.012	0.007	33.158	-0.131	-0.131	0.000	0.000	0.000	0.000
117	A	157	ARG	1	0.890	0.927	33.274	-8.622	-8.622	0.000	0.000	0.000	0.000
118	A	158	GLY	0	0.037	0.046	30.266	0.053	0.053	0.000	0.000	0.000	0.000
119	A	159	PHE	0	-0.018	-0.009	27.321	0.354	0.354	0.000	0.000	0.000	0.000
120	A	160	LEU	0	0.026	0.010	25.343	-0.361	-0.361	0.000	0.000	0.000	0.000
121	A	161	PRO	0	-0.012	0.009	26.395	0.340	0.340	0.000	0.000	0.000	0.000
122	A	162	LEU	0	-0.004	0.009	25.118	0.099	0.099	0.000	0.000	0.000	0.000
123	A	163	SER	0	0.009	-0.022	22.181	0.219	0.219	0.000	0.000	0.000	0.000
124	A	164	HIS	0	-0.024	-0.006	20.095	0.632	0.632	0.000	0.000	0.000	0.000
125	A	165	PHE	0	-0.023	-0.020	17.390	-0.719	-0.719	0.000	0.000	0.000	0.000
126	A	166	LEU	0	0.063	0.038	16.394	0.927	0.927	0.000	0.000	0.000	0.000
127	A	167	PRO	0	-0.010	-0.016	12.336	-0.633	-0.633	0.000	0.000	0.000	0.000
128	A	168	MET	0	-0.007	0.011	14.306	0.712	0.712	0.000	0.000	0.000	0.000
129	A	169	LEU	0	0.043	0.008	13.504	0.684	0.684	0.000	0.000	0.000	0.000
130	A	170	PRO	0	-0.007	0.015	15.580	-0.880	-0.880	0.000	0.000	0.000	0.000
131	A	171	MET	0	-0.046	-0.035	18.531	0.002	0.002	0.000	0.000	0.000	0.000
132	A	172	VAL	0	-0.007	0.001	20.891	-0.600	-0.600	0.000	0.000	0.000	0.000
133	A	173	PRO	0	-0.038	-0.025	18.686	0.541	0.541	0.000	0.000	0.000	0.000
134	A	174	GLU	-1	-0.888	-0.948	17.663	13.990	13.990	0.000	0.000	0.000	0.000
135	A	175	GLU	-1	-1.007	-0.989	14.508	17.877	17.877	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:40:ASP)