FMO DATABASE

FMODB ID: M35YZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1514148.730465
FMO2-HF: Nuclear repulsion	1448406.567374
FMO2-HF: Total energy	-65742.163091
FMO2-MP2: Total energy	-65933.802645

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.
1.54	5.099	-0.006	-1.87	-1.683	0.009

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 : 0.081 / q_NPA : 0.036

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	-0.036	-0.025	3.162	-0.185	3.341	-0.004	-1.836	-1.686	0.009
4	A	24	GLY	0	0.060	0.026	4.396	-0.840	-0.897	-0.001	-0.024	0.082	0.000
5	A	25	SER	0	0.055	0.007	7.149	0.079	0.079	0.000	0.000	0.000	0.000
6	A	26	GLY	0	0.013	0.021	8.747	0.247	0.247	0.000	0.000	0.000	0.000
7	A	27	GLY	0	0.024	0.007	9.261	0.180	0.180	0.000	0.000	0.000	0.000
8	A	28	LEU	0	0.014	0.001	4.132	0.332	0.422	-0.001	-0.010	-0.079	0.000
9	A	29	PHE	0	0.003	0.009	8.192	0.293	0.293	0.000	0.000	0.000	0.000
10	A	30	PHE	0	0.024	0.001	11.771	0.142	0.142	0.000	0.000	0.000	0.000
11	A	31	ASN	0	-0.010	-0.016	9.274	0.096	0.096	0.000	0.000	0.000	0.000
12	A	32	ALA	0	0.050	0.037	11.358	0.099	0.099	0.000	0.000	0.000	0.000
13	A	33	LEU	0	-0.023	-0.014	12.901	0.056	0.056	0.000	0.000	0.000	0.000
14	A	34	LYS	1	0.877	0.941	15.487	0.178	0.178	0.000	0.000	0.000	0.000
15	A	35	ASN	0	0.104	0.049	14.219	-0.028	-0.028	0.000	0.000	0.000	0.000
16	A	36	CYS	0	-0.015	0.015	16.736	0.016	0.016	0.000	0.000	0.000	0.000
17	A	37	LYS	1	0.942	0.959	18.590	0.097	0.097	0.000	0.000	0.000	0.000
18	A	38	GLU	-1	-0.928	-0.952	19.435	0.115	0.115	0.000	0.000	0.000	0.000
19	A	39	ASN	0	0.001	-0.022	17.960	0.008	0.008	0.000	0.000	0.000	0.000
20	A	40	PHE	0	-0.041	-0.018	21.982	0.001	0.001	0.000	0.000	0.000	0.000
21	A	41	THR	0	0.004	0.001	24.433	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	42	VAL	0	0.011	0.026	24.386	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	43	LEU	0	0.036	0.015	25.574	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	44	GLN	0	-0.021	-0.002	28.139	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	45	THR	0	-0.075	-0.045	29.825	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	46	ILE	0	0.017	0.004	30.395	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	47	ARG	1	0.946	0.982	32.132	-0.035	-0.035	0.000	0.000	0.000	0.000
28	A	48	GLN	0	-0.015	-0.006	33.888	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	49	GLN	0	0.100	0.053	34.670	0.003	0.003	0.000	0.000	0.000	0.000
30	A	50	GLN	0	0.013	0.024	35.782	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	51	SER	0	-0.102	-0.054	37.973	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	52	THR	0	0.036	0.010	40.047	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	53	LEU	0	0.029	0.023	40.946	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	54	ASN	0	0.070	0.084	40.219	0.001	0.001	0.000	0.000	0.000	0.000
35	A	55	GLY	0	-0.007	0.010	43.607	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	56	SER	0	-0.036	-0.035	45.801	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	57	TRP	0	0.019	0.008	45.299	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	58	VAL	0	0.030	0.014	46.948	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	59	ALA	0	0.004	0.008	49.456	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	60	LEU	0	0.010	0.012	50.108	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	61	LEU	0	0.023	0.017	49.936	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	62	GLN	0	-0.046	-0.020	53.029	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	63	THR	0	-0.012	0.006	55.522	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	64	ARG	1	0.860	0.897	56.301	-0.036	-0.036	0.000	0.000	0.000	0.000
45	A	65	ASN	0	-0.061	-0.029	57.762	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	66	THR	0	-0.024	-0.024	59.275	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	67	LEU	0	0.043	0.022	60.982	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	68	ASN	0	0.013	0.002	61.090	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	69	ARG	1	0.917	0.968	61.665	-0.021	-0.021	0.000	0.000	0.000	0.000
50	A	70	ALA	0	0.014	0.006	65.475	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	71	GLY	0	0.059	0.031	67.239	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	72	ILE	0	-0.009	-0.013	66.439	0.000	0.000	0.000	0.000	0.000	0.000
53	A	73	ARG	1	0.782	0.871	69.613	-0.016	-0.016	0.000	0.000	0.000	0.000
54	A	74	TYR	0	0.059	0.028	71.525	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	75	MET	0	-0.010	-0.023	70.625	0.000	0.000	0.000	0.000	0.000	0.000
56	A	76	MET	0	-0.091	-0.029	72.174	0.000	0.000	0.000	0.000	0.000	0.000
57	A	77	ASP	-1	-0.808	-0.890	75.347	0.015	0.015	0.000	0.000	0.000	0.000
58	A	78	GLN	0	-0.090	-0.021	77.335	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	79	ASN	0	-0.027	-0.016	79.424	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	80	ASN	0	-0.043	-0.029	80.986	0.000	0.000	0.000	0.000	0.000	0.000
61	A	81	ILE	0	0.007	0.026	77.046	0.000	0.000	0.000	0.000	0.000	0.000
62	A	82	GLY	0	0.020	0.014	74.452	0.000	0.000	0.000	0.000	0.000	0.000
63	A	83	SER	0	-0.037	-0.027	73.229	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	84	GLY	0	-0.008	-0.009	69.824	0.001	0.001	0.000	0.000	0.000	0.000
65	A	85	SER	0	0.016	0.006	66.906	0.000	0.000	0.000	0.000	0.000	0.000
66	A	86	THR	0	0.003	0.012	69.224	0.001	0.001	0.000	0.000	0.000	0.000
67	A	87	VAL	0	0.100	0.048	69.477	0.000	0.000	0.000	0.000	0.000	0.000
68	A	88	ALA	0	0.021	0.005	69.015	0.000	0.000	0.000	0.000	0.000	0.000
69	A	89	GLU	-1	-0.865	-0.943	67.570	0.012	0.012	0.000	0.000	0.000	0.000
70	A	90	LEU	0	-0.051	-0.033	64.596	0.000	0.000	0.000	0.000	0.000	0.000
71	A	91	MET	0	-0.005	0.012	64.298	0.001	0.001	0.000	0.000	0.000	0.000
72	A	92	GLU	-1	-0.889	-0.952	64.218	0.012	0.012	0.000	0.000	0.000	0.000
73	A	93	SER	0	-0.004	-0.010	60.653	0.000	0.000	0.000	0.000	0.000	0.000
74	A	94	ALA	0	-0.004	-0.001	59.992	0.001	0.001	0.000	0.000	0.000	0.000
75	A	95	SER	0	0.011	0.008	59.394	0.001	0.001	0.000	0.000	0.000	0.000
76	A	96	ILE	0	-0.055	-0.019	57.558	0.000	0.000	0.000	0.000	0.000	0.000
77	A	97	SER	0	-0.035	-0.036	55.595	0.000	0.000	0.000	0.000	0.000	0.000
78	A	98	LEU	0	0.024	0.016	54.610	0.001	0.001	0.000	0.000	0.000	0.000
79	A	99	LYS	1	0.988	0.994	54.674	-0.012	-0.012	0.000	0.000	0.000	0.000
80	A	100	GLN	0	-0.019	-0.012	50.598	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	101	ALA	0	0.005	0.014	50.516	0.001	0.001	0.000	0.000	0.000	0.000
82	A	102	GLU	-1	-0.818	-0.899	49.895	0.020	0.020	0.000	0.000	0.000	0.000
83	A	103	LYS	1	0.914	0.965	49.200	-0.011	-0.011	0.000	0.000	0.000	0.000
84	A	104	ASN	0	0.000	-0.011	45.916	0.000	0.000	0.000	0.000	0.000	0.000
85	A	105	TRP	0	0.005	0.003	45.361	0.003	0.003	0.000	0.000	0.000	0.000
86	A	106	ALA	0	0.008	0.008	45.882	0.001	0.001	0.000	0.000	0.000	0.000
87	A	107	ASP	-1	-0.935	-0.969	43.184	0.015	0.015	0.000	0.000	0.000	0.000
88	A	108	TYR	0	-0.077	-0.048	39.716	0.000	0.000	0.000	0.000	0.000	0.000
89	A	109	GLU	-1	-0.903	-0.967	40.944	0.031	0.031	0.000	0.000	0.000	0.000
90	A	110	ALA	0	-0.065	-0.020	41.961	0.000	0.000	0.000	0.000	0.000	0.000
91	A	111	LEU	0	-0.087	-0.024	37.108	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	112	PRO	0	-0.017	-0.012	34.131	0.003	0.003	0.000	0.000	0.000	0.000
93	A	113	ARG	1	0.973	0.985	34.415	-0.040	-0.040	0.000	0.000	0.000	0.000
94	A	114	ASP	-1	-0.768	-0.852	27.793	0.093	0.093	0.000	0.000	0.000	0.000
95	A	115	PRO	0	-0.014	-0.025	27.908	0.002	0.002	0.000	0.000	0.000	0.000
96	A	116	ARG	1	0.823	0.885	24.316	-0.131	-0.131	0.000	0.000	0.000	0.000
97	A	117	GLN	0	-0.043	-0.018	30.066	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	118	SER	0	0.028	0.021	33.329	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	119	THR	0	0.006	-0.021	36.047	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	120	ALA	0	0.022	0.014	38.737	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	121	ALA	0	0.045	0.011	38.806	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	122	ALA	0	-0.006	0.005	39.312	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	123	ALA	0	0.000	-0.005	41.184	-0.004	-0.004	0.000	0.000	0.000	0.000
104	A	124	GLU	-1	-0.747	-0.820	43.867	0.049	0.049	0.000	0.000	0.000	0.000
105	A	125	ILE	0	-0.009	-0.007	42.641	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	126	LYS	1	0.922	0.975	45.158	-0.033	-0.033	0.000	0.000	0.000	0.000
107	A	127	ARG	1	0.791	0.860	47.041	-0.049	-0.049	0.000	0.000	0.000	0.000
108	A	128	ASN	0	-0.033	-0.035	48.245	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	129	TYR	0	0.023	0.021	48.234	-0.002	-0.002	0.000	0.000	0.000	0.000
110	A	130	ASP	-1	-0.904	-0.959	50.188	0.028	0.028	0.000	0.000	0.000	0.000
111	A	131	ILE	0	-0.058	-0.019	52.973	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	132	TYR	0	0.023	0.000	51.885	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	133	HIS	1	0.833	0.892	53.240	-0.026	-0.026	0.000	0.000	0.000	0.000
114	A	134	ASN	0	-0.017	-0.022	55.097	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	135	ALA	0	0.031	0.040	57.928	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	136	LEU	0	0.033	0.008	55.865	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	137	ALA	0	-0.009	-0.010	59.355	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	138	GLU	-1	-0.887	-0.946	61.006	0.022	0.022	0.000	0.000	0.000	0.000
119	A	139	LEU	0	-0.034	-0.003	61.678	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	140	ILE	0	-0.027	-0.020	61.052	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	141	GLN	0	-0.010	-0.009	65.028	0.000	0.000	0.000	0.000	0.000	0.000
122	A	142	LEU	0	-0.029	-0.016	66.876	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	143	LEU	0	-0.005	-0.010	67.116	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	144	GLY	0	-0.032	-0.011	69.352	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	145	ALA	0	-0.049	-0.013	71.074	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	146	GLY	0	0.011	0.011	73.196	0.000	0.000	0.000	0.000	0.000	0.000
127	A	147	LYS	1	0.874	0.958	71.300	-0.018	-0.018	0.000	0.000	0.000	0.000
128	A	148	ILE	0	0.006	-0.011	71.945	0.001	0.001	0.000	0.000	0.000	0.000
129	A	149	ASN	0	0.022	-0.007	71.642	0.001	0.001	0.000	0.000	0.000	0.000
130	A	150	GLU	-1	-0.880	-0.927	69.075	0.022	0.022	0.000	0.000	0.000	0.000
131	A	151	PHE	0	-0.069	-0.047	66.067	0.001	0.001	0.000	0.000	0.000	0.000
132	A	152	PHE	0	-0.076	-0.052	67.141	0.001	0.001	0.000	0.000	0.000	0.000
133	A	153	ASP	-1	-0.896	-0.933	67.714	0.025	0.025	0.000	0.000	0.000	0.000
134	A	154	GLN	0	-0.020	0.027	61.864	0.002	0.002	0.000	0.000	0.000	0.000
135	A	155	PRO	0	0.020	0.017	61.513	0.001	0.001	0.000	0.000	0.000	0.000
136	A	156	THR	0	-0.028	-0.059	58.488	0.001	0.001	0.000	0.000	0.000	0.000
137	A	157	GLN	0	-0.012	0.013	55.155	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	158	GLY	0	0.051	0.028	56.063	0.002	0.002	0.000	0.000	0.000	0.000
139	A	159	TYR	0	0.011	-0.006	54.904	0.002	0.002	0.000	0.000	0.000	0.000
140	A	160	GLN	0	0.062	0.054	52.585	-0.001	-0.001	0.000	0.000	0.000	0.000
141	A	161	ASP	-1	-0.857	-0.929	51.568	0.049	0.049	0.000	0.000	0.000	0.000
142	A	162	GLY	0	-0.077	-0.026	50.289	0.003	0.003	0.000	0.000	0.000	0.000
143	A	163	PHE	0	0.024	0.001	46.264	0.002	0.002	0.000	0.000	0.000	0.000
144	A	164	GLU	-1	-0.909	-0.957	46.948	0.056	0.056	0.000	0.000	0.000	0.000
145	A	165	LYS	1	0.891	0.947	45.614	-0.055	-0.055	0.000	0.000	0.000	0.000
146	A	166	GLN	0	-0.002	-0.015	43.717	0.006	0.006	0.000	0.000	0.000	0.000
147	A	167	TYR	0	-0.062	-0.081	42.172	0.003	0.003	0.000	0.000	0.000	0.000
148	A	168	VAL	0	0.032	0.008	41.126	0.003	0.003	0.000	0.000	0.000	0.000
149	A	169	ALA	0	0.028	0.024	39.559	0.005	0.005	0.000	0.000	0.000	0.000
150	A	170	TYR	0	-0.016	-0.010	37.234	0.005	0.005	0.000	0.000	0.000	0.000
151	A	171	MET	0	-0.006	-0.015	36.552	0.003	0.003	0.000	0.000	0.000	0.000
152	A	172	GLU	-1	-0.931	-0.936	35.017	0.116	0.116	0.000	0.000	0.000	0.000
153	A	173	GLN	0	-0.009	-0.009	33.246	0.011	0.011	0.000	0.000	0.000	0.000
154	A	174	ASN	0	0.001	-0.030	31.831	0.011	0.011	0.000	0.000	0.000	0.000
155	A	175	ASP	-1	-0.857	-0.914	30.850	0.107	0.107	0.000	0.000	0.000	0.000
156	A	176	ARG	1	0.955	0.982	27.994	-0.162	-0.162	0.000	0.000	0.000	0.000
157	A	177	LEU	0	-0.062	-0.036	27.114	0.016	0.016	0.000	0.000	0.000	0.000
158	A	178	HIS	0	-0.041	-0.028	25.981	-0.001	-0.001	0.000	0.000	0.000	0.000
159	A	179	ASP	-1	-0.827	-0.916	25.333	0.177	0.177	0.000	0.000	0.000	0.000
160	A	180	ILE	0	-0.104	-0.042	21.592	0.026	0.026	0.000	0.000	0.000	0.000
161	A	181	ALA	0	0.028	0.015	21.091	0.024	0.024	0.000	0.000	0.000	0.000
162	A	182	VAL	0	-0.026	-0.009	20.759	0.006	0.006	0.000	0.000	0.000	0.000
163	A	183	SER	0	-0.053	-0.041	19.558	0.022	0.022	0.000	0.000	0.000	0.000
164	A	184	ASP	-1	-0.899	-0.945	16.039	0.376	0.376	0.000	0.000	0.000	0.000
165	A	185	ASN	0	-0.078	-0.039	15.750	0.000	0.000	0.000	0.000	0.000	0.000
166	A	186	ASN	0	-0.058	-0.026	16.479	-0.037	-0.037	0.000	0.000	0.000	0.000
167	A	187	ALA	0	-0.056	-0.006	11.243	0.043	0.043	0.000	0.000	0.000	0.000

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