FMO DATABASE

FMODB ID: 22YQR

Calculation Name: 2D4U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D4U

Chain ID: A

ChEMBL ID:

UniProt ID: P02942

Base Structure: X-ray

Registration Date: 2023-06-20

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	167
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1517364.113216
FMO2-HF: Nuclear repulsion	1451620.291116
FMO2-HF: Total energy	-65743.8221
FMO2-MP2: Total energy	-65935.238834

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:21:GLY)

Summations of interaction energy for fragment #1(A:21:GLY)

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.
3.187	5.197	-0.002	-1.079	-0.929	0.003

Interaction energy analysis for fragmet #1(A:21:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.083 / q_NPA : 0.041

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	23	LEU	0	-0.001	-0.010	3.649	1.300	3.192	0.000	-1.048	-0.844	0.003
4	A	24	GLY	0	0.048	0.030	4.550	-0.569	-0.565	-0.001	-0.012	0.010	0.000
5	A	25	SER	0	0.053	0.001	7.249	0.187	0.187	0.000	0.000	0.000	0.000
6	A	26	GLY	0	0.019	0.020	8.579	0.240	0.240	0.000	0.000	0.000	0.000
7	A	27	GLY	0	0.019	0.009	9.532	0.183	0.183	0.000	0.000	0.000	0.000
8	A	28	LEU	0	-0.001	-0.001	3.967	0.293	0.407	-0.001	-0.019	-0.095	0.000
9	A	29	PHE	0	0.016	0.012	8.054	0.276	0.276	0.000	0.000	0.000	0.000
10	A	30	PHE	0	-0.008	-0.003	11.590	0.128	0.128	0.000	0.000	0.000	0.000
11	A	31	ASN	0	-0.012	-0.012	10.089	0.054	0.054	0.000	0.000	0.000	0.000
12	A	32	ALA	0	0.051	0.030	11.151	0.096	0.096	0.000	0.000	0.000	0.000
13	A	33	LEU	0	-0.031	-0.010	12.778	0.049	0.049	0.000	0.000	0.000	0.000
14	A	34	LYS	1	0.931	0.962	15.100	0.080	0.080	0.000	0.000	0.000	0.000
15	A	35	ASN	0	-0.004	-0.021	14.298	-0.033	-0.033	0.000	0.000	0.000	0.000
16	A	36	CYS	0	-0.008	0.011	16.466	0.003	0.003	0.000	0.000	0.000	0.000
17	A	37	LYS	1	0.963	0.975	18.361	0.061	0.061	0.000	0.000	0.000	0.000
18	A	38	GLU	-1	-0.936	-0.950	19.882	0.122	0.122	0.000	0.000	0.000	0.000
19	A	39	ASN	0	0.017	-0.024	17.835	0.000	0.000	0.000	0.000	0.000	0.000
20	A	40	PHE	0	-0.024	-0.007	21.915	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	41	THR	0	-0.028	-0.027	24.349	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	42	VAL	0	0.000	0.011	24.239	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	43	LEU	0	0.033	0.021	24.456	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	44	GLN	0	-0.033	-0.015	27.849	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	45	THR	0	-0.056	-0.035	29.716	-0.006	-0.006	0.000	0.000	0.000	0.000
26	A	46	ILE	0	0.008	0.007	29.741	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	47	ARG	1	0.951	0.975	31.897	-0.044	-0.044	0.000	0.000	0.000	0.000
28	A	48	GLN	0	0.027	0.031	33.709	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	49	GLN	0	0.047	0.042	34.343	0.003	0.003	0.000	0.000	0.000	0.000
30	A	50	GLN	0	-0.001	0.005	34.566	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	51	SER	0	-0.062	-0.053	37.605	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	52	THR	0	-0.008	-0.013	39.683	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	53	LEU	0	0.020	0.021	40.424	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	54	ASN	0	0.032	0.015	39.920	0.000	0.000	0.000	0.000	0.000	0.000
35	A	55	GLY	0	0.002	0.010	43.413	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	56	SER	0	-0.048	-0.046	45.638	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	57	TRP	0	-0.004	-0.003	45.245	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	58	VAL	0	0.024	0.001	46.690	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	59	ALA	0	-0.033	-0.006	49.208	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	60	LEU	0	0.026	0.012	49.868	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	61	LEU	0	-0.012	0.005	49.803	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	62	GLN	0	-0.022	-0.010	53.226	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	63	THR	0	-0.026	-0.006	55.416	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	64	ARG	1	0.896	0.927	56.090	-0.039	-0.039	0.000	0.000	0.000	0.000
45	A	65	ASN	0	-0.029	-0.015	57.336	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	66	THR	0	-0.039	-0.041	59.053	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	67	LEU	0	0.029	0.017	60.448	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	68	ASN	0	0.016	0.007	60.590	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	69	ARG	1	0.911	0.964	60.746	-0.025	-0.025	0.000	0.000	0.000	0.000
50	A	70	ALA	0	0.007	0.006	65.199	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	71	GLY	0	0.066	0.028	66.910	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	72	ILE	0	-0.019	-0.022	65.702	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	73	ARG	1	0.743	0.852	69.162	-0.018	-0.018	0.000	0.000	0.000	0.000
54	A	74	TYR	0	0.054	0.011	71.038	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	75	MET	0	-0.024	-0.018	70.119	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	76	MET	0	-0.066	-0.016	72.224	0.000	0.000	0.000	0.000	0.000	0.000
57	A	77	ASP	-1	-0.769	-0.867	74.544	0.016	0.016	0.000	0.000	0.000	0.000
58	A	78	GLN	0	-0.068	-0.026	76.869	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	79	ASN	0	-0.038	-0.009	78.750	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	80	ASN	0	-0.061	-0.032	80.958	0.000	0.000	0.000	0.000	0.000	0.000
61	A	81	ILE	0	0.000	0.014	77.410	0.000	0.000	0.000	0.000	0.000	0.000
62	A	82	GLY	0	0.045	0.022	74.246	0.000	0.000	0.000	0.000	0.000	0.000
63	A	83	SER	0	-0.064	-0.039	72.653	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	84	GLY	0	0.016	0.005	69.357	0.001	0.001	0.000	0.000	0.000	0.000
65	A	85	SER	0	0.006	-0.006	66.898	0.000	0.000	0.000	0.000	0.000	0.000
66	A	86	THR	0	0.006	0.005	69.191	0.001	0.001	0.000	0.000	0.000	0.000
67	A	87	VAL	0	0.059	0.021	69.430	0.000	0.000	0.000	0.000	0.000	0.000
68	A	88	ALA	0	0.022	0.015	68.771	0.000	0.000	0.000	0.000	0.000	0.000
69	A	89	GLU	-1	-0.854	-0.923	67.179	0.015	0.015	0.000	0.000	0.000	0.000
70	A	90	LEU	0	-0.045	-0.016	64.766	0.000	0.000	0.000	0.000	0.000	0.000
71	A	91	MET	0	0.050	0.038	63.956	0.001	0.001	0.000	0.000	0.000	0.000
72	A	92	GLU	-1	-0.781	-0.881	62.779	0.016	0.016	0.000	0.000	0.000	0.000
73	A	93	SER	0	0.001	-0.004	60.487	0.000	0.000	0.000	0.000	0.000	0.000
74	A	94	ALA	0	-0.008	-0.003	59.715	0.001	0.001	0.000	0.000	0.000	0.000
75	A	95	SER	0	0.020	0.005	58.935	0.001	0.001	0.000	0.000	0.000	0.000
76	A	96	ILE	0	-0.064	-0.029	57.143	0.000	0.000	0.000	0.000	0.000	0.000
77	A	97	SER	0	-0.058	-0.026	55.164	0.001	0.001	0.000	0.000	0.000	0.000
78	A	98	LEU	0	0.059	0.026	54.201	0.001	0.001	0.000	0.000	0.000	0.000
79	A	99	LYS	1	0.867	0.934	54.369	-0.015	-0.015	0.000	0.000	0.000	0.000
80	A	100	GLN	0	-0.036	-0.017	50.867	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	101	ALA	0	0.033	0.015	50.256	0.001	0.001	0.000	0.000	0.000	0.000
82	A	102	GLU	-1	-0.830	-0.882	49.784	0.023	0.023	0.000	0.000	0.000	0.000
83	A	103	LYS	1	0.926	0.972	48.447	-0.014	-0.014	0.000	0.000	0.000	0.000
84	A	104	ASN	0	-0.006	-0.009	45.738	0.001	0.001	0.000	0.000	0.000	0.000
85	A	105	TRP	0	-0.006	-0.012	45.054	0.004	0.004	0.000	0.000	0.000	0.000
86	A	106	ALA	0	-0.008	-0.003	45.625	0.001	0.001	0.000	0.000	0.000	0.000
87	A	107	ASP	-1	-0.931	-0.977	43.271	0.020	0.020	0.000	0.000	0.000	0.000
88	A	108	TYR	0	-0.049	-0.027	39.411	0.000	0.000	0.000	0.000	0.000	0.000
89	A	109	GLU	-1	-0.818	-0.899	40.859	0.036	0.036	0.000	0.000	0.000	0.000
90	A	110	ALA	0	-0.020	0.000	41.751	0.001	0.001	0.000	0.000	0.000	0.000
91	A	111	LEU	0	-0.049	-0.002	36.687	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	112	PRO	0	-0.021	-0.018	33.747	0.002	0.002	0.000	0.000	0.000	0.000
93	A	113	ARG	1	0.891	0.931	34.068	-0.040	-0.040	0.000	0.000	0.000	0.000
94	A	114	ASP	-1	-0.737	-0.830	27.749	0.106	0.106	0.000	0.000	0.000	0.000
95	A	115	PRO	0	-0.020	-0.029	28.301	0.002	0.002	0.000	0.000	0.000	0.000
96	A	116	ARG	1	0.818	0.891	22.986	-0.138	-0.138	0.000	0.000	0.000	0.000
97	A	117	GLN	0	-0.036	-0.019	29.876	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	118	SER	0	0.021	0.013	33.361	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	119	THR	0	0.030	0.000	36.211	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	120	ALA	0	0.013	0.013	38.827	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	121	ALA	0	0.041	0.017	38.774	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	122	ALA	0	0.005	0.000	39.464	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	123	ALA	0	-0.003	0.000	41.357	-0.004	-0.004	0.000	0.000	0.000	0.000
104	A	124	GLU	-1	-0.754	-0.847	44.030	0.052	0.052	0.000	0.000	0.000	0.000
105	A	125	ILE	0	-0.015	0.007	42.102	-0.003	-0.003	0.000	0.000	0.000	0.000
106	A	126	LYS	1	0.818	0.902	45.199	-0.036	-0.036	0.000	0.000	0.000	0.000
107	A	127	ARG	1	0.832	0.904	47.068	-0.051	-0.051	0.000	0.000	0.000	0.000
108	A	128	ASN	0	-0.061	-0.059	47.967	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	129	TYR	0	0.011	0.017	48.085	-0.002	-0.002	0.000	0.000	0.000	0.000
110	A	130	ASP	-1	-0.855	-0.925	50.096	0.031	0.031	0.000	0.000	0.000	0.000
111	A	131	ILE	0	-0.048	-0.019	52.713	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	132	TYR	0	0.040	0.013	51.812	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	133	HIS	1	0.835	0.880	53.077	-0.028	-0.028	0.000	0.000	0.000	0.000
114	A	134	ASN	0	-0.007	-0.005	54.976	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	135	ALA	0	0.041	0.036	57.858	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	136	LEU	0	0.019	0.007	55.369	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	137	ALA	0	-0.008	-0.009	59.100	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	138	GLU	-1	-0.872	-0.917	60.792	0.025	0.025	0.000	0.000	0.000	0.000
119	A	139	LEU	0	-0.010	0.003	61.494	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	140	ILE	0	-0.022	-0.011	60.630	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	141	GLN	0	-0.032	-0.019	64.794	0.000	0.000	0.000	0.000	0.000	0.000
122	A	142	LEU	0	-0.019	-0.008	66.817	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	143	LEU	0	-0.016	-0.007	67.261	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	144	GLY	0	-0.003	-0.008	68.950	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	145	ALA	0	-0.057	-0.019	70.649	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	146	GLY	0	0.008	0.005	72.950	0.000	0.000	0.000	0.000	0.000	0.000
127	A	147	LYS	1	0.766	0.885	71.038	-0.020	-0.020	0.000	0.000	0.000	0.000
128	A	148	ILE	0	-0.004	-0.017	71.775	0.001	0.001	0.000	0.000	0.000	0.000
129	A	149	ASN	0	0.002	-0.001	71.419	0.001	0.001	0.000	0.000	0.000	0.000
130	A	150	GLU	-1	-0.740	-0.865	69.107	0.023	0.023	0.000	0.000	0.000	0.000
131	A	151	PHE	0	-0.072	-0.034	65.739	0.001	0.001	0.000	0.000	0.000	0.000
132	A	152	PHE	0	-0.037	-0.028	66.615	0.001	0.001	0.000	0.000	0.000	0.000
133	A	153	ASP	-1	-0.924	-0.951	67.307	0.026	0.026	0.000	0.000	0.000	0.000
134	A	154	GLN	0	-0.047	-0.014	61.733	0.002	0.002	0.000	0.000	0.000	0.000
135	A	155	PRO	0	0.012	0.016	61.513	0.001	0.001	0.000	0.000	0.000	0.000
136	A	156	THR	0	-0.033	-0.066	58.388	0.002	0.002	0.000	0.000	0.000	0.000
137	A	157	GLN	0	-0.042	-0.015	54.981	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	158	GLY	0	0.049	0.031	55.708	0.002	0.002	0.000	0.000	0.000	0.000
139	A	159	TYR	0	-0.007	-0.009	54.692	0.002	0.002	0.000	0.000	0.000	0.000
140	A	160	GLN	0	-0.003	0.012	51.916	-0.001	-0.001	0.000	0.000	0.000	0.000
141	A	161	ASP	-1	-0.828	-0.906	51.123	0.050	0.050	0.000	0.000	0.000	0.000
142	A	162	GLY	0	-0.045	-0.012	50.232	0.004	0.004	0.000	0.000	0.000	0.000
143	A	163	PHE	0	0.009	-0.003	45.980	0.003	0.003	0.000	0.000	0.000	0.000
144	A	164	GLU	-1	-0.832	-0.922	46.673	0.057	0.057	0.000	0.000	0.000	0.000
145	A	165	LYS	1	0.874	0.929	45.456	-0.056	-0.056	0.000	0.000	0.000	0.000
146	A	166	GLN	0	0.001	-0.018	43.668	0.008	0.008	0.000	0.000	0.000	0.000
147	A	167	TYR	0	-0.045	-0.034	42.195	0.004	0.004	0.000	0.000	0.000	0.000
148	A	168	VAL	0	0.018	0.007	40.933	0.003	0.003	0.000	0.000	0.000	0.000
149	A	169	ALA	0	-0.010	0.000	39.369	0.006	0.006	0.000	0.000	0.000	0.000
150	A	170	TYR	0	0.003	-0.007	36.947	0.005	0.005	0.000	0.000	0.000	0.000
151	A	171	MET	0	-0.020	-0.005	36.456	0.003	0.003	0.000	0.000	0.000	0.000
152	A	172	GLU	-1	-0.819	-0.870	34.135	0.138	0.138	0.000	0.000	0.000	0.000
153	A	173	GLN	0	0.020	0.006	33.186	0.009	0.009	0.000	0.000	0.000	0.000
154	A	174	ASN	0	-0.004	-0.011	31.642	0.009	0.009	0.000	0.000	0.000	0.000
155	A	175	ASP	-1	-0.875	-0.938	30.720	0.109	0.109	0.000	0.000	0.000	0.000
156	A	176	ARG	1	0.827	0.892	28.729	-0.144	-0.144	0.000	0.000	0.000	0.000
157	A	177	LEU	0	-0.043	-0.029	27.130	0.016	0.016	0.000	0.000	0.000	0.000
158	A	178	HIS	0	-0.040	-0.034	25.950	-0.001	-0.001	0.000	0.000	0.000	0.000
159	A	179	ASP	-1	-0.843	-0.911	25.102	0.189	0.189	0.000	0.000	0.000	0.000
160	A	180	ILE	0	-0.059	-0.010	21.903	0.031	0.031	0.000	0.000	0.000	0.000
161	A	181	ALA	0	0.014	0.010	21.088	0.027	0.027	0.000	0.000	0.000	0.000
162	A	182	VAL	0	-0.026	-0.022	20.670	0.006	0.006	0.000	0.000	0.000	0.000
163	A	183	SER	0	-0.062	-0.050	19.671	0.024	0.024	0.000	0.000	0.000	0.000
164	A	184	ASP	-1	-0.855	-0.892	15.843	0.384	0.384	0.000	0.000	0.000	0.000
165	A	185	ASN	0	-0.046	-0.026	15.656	0.001	0.001	0.000	0.000	0.000	0.000
166	A	186	ASN	0	-0.047	-0.016	16.578	-0.042	-0.042	0.000	0.000	0.000	0.000
167	A	187	ALA	0	-0.061	-0.014	10.591	0.049	0.049	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:21:GLY)