FMO DATABASE

FMODB ID: 7G97K

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	OptHSide
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	-1515128.238113
FMO2-HF: Nuclear repulsion	1449384.873304
FMO2-HF: Total energy	-65743.364809
FMO2-MP2: Total energy	-65934.909312

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.
1.451	5.041	-0.006	-1.89	-1.693	0.01

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 : 0.037

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	-0.041	-0.022	3.161	-0.199	3.355	-0.004	-1.855	-1.695	0.010
4	A	24	GLY	0	0.065	0.027	4.429	-0.810	-0.870	-0.001	-0.023	0.084	0.000
5	A	25	SER	0	0.062	0.008	7.181	0.066	0.066	0.000	0.000	0.000	0.000
6	A	26	GLY	0	0.008	0.018	8.772	0.245	0.245	0.000	0.000	0.000	0.000
7	A	27	GLY	0	0.022	0.003	9.279	0.176	0.176	0.000	0.000	0.000	0.000
8	A	28	LEU	0	0.015	0.004	4.057	0.312	0.408	-0.001	-0.012	-0.082	0.000
9	A	29	PHE	0	0.002	0.006	8.183	0.293	0.293	0.000	0.000	0.000	0.000
10	A	30	PHE	0	0.005	-0.003	11.766	0.138	0.138	0.000	0.000	0.000	0.000
11	A	31	ASN	0	-0.016	-0.014	10.054	0.088	0.088	0.000	0.000	0.000	0.000
12	A	32	ALA	0	0.051	0.029	11.284	0.105	0.105	0.000	0.000	0.000	0.000
13	A	33	LEU	0	-0.021	-0.010	12.874	0.060	0.060	0.000	0.000	0.000	0.000
14	A	34	LYS	1	0.910	0.954	15.353	0.155	0.155	0.000	0.000	0.000	0.000
15	A	35	ASN	0	0.021	-0.006	14.738	-0.029	-0.029	0.000	0.000	0.000	0.000
16	A	36	CYS	0	-0.010	0.017	16.711	0.012	0.012	0.000	0.000	0.000	0.000
17	A	37	LYS	1	0.965	0.975	18.556	0.101	0.101	0.000	0.000	0.000	0.000
18	A	38	GLU	-1	-0.944	-0.952	19.703	0.093	0.093	0.000	0.000	0.000	0.000
19	A	39	ASN	0	0.005	-0.037	17.929	0.011	0.011	0.000	0.000	0.000	0.000
20	A	40	PHE	0	-0.039	-0.017	21.941	0.002	0.002	0.000	0.000	0.000	0.000
21	A	41	THR	0	-0.016	-0.021	24.397	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	42	VAL	0	0.017	0.026	24.436	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	43	LEU	0	0.040	0.023	25.080	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	44	GLN	0	-0.035	-0.011	28.097	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	45	THR	0	-0.061	-0.042	29.732	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	46	ILE	0	0.007	0.000	30.088	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	47	ARG	1	0.935	0.968	32.098	-0.031	-0.031	0.000	0.000	0.000	0.000
28	A	48	GLN	0	0.007	0.009	33.846	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	49	GLN	0	0.077	0.055	34.820	0.004	0.004	0.000	0.000	0.000	0.000
30	A	50	GLN	0	0.005	0.017	35.218	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	51	SER	0	-0.069	-0.044	37.928	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	52	THR	0	0.022	-0.001	40.005	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	53	LEU	0	0.008	0.017	40.702	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	54	ASN	0	0.033	0.024	40.128	0.001	0.001	0.000	0.000	0.000	0.000
35	A	55	GLY	0	0.007	0.015	43.562	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	56	SER	0	-0.040	-0.045	45.759	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	57	TRP	0	0.007	0.005	45.550	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	58	VAL	0	0.029	0.009	46.934	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	59	ALA	0	0.009	0.013	49.411	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	60	LEU	0	0.008	0.016	50.222	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	61	LEU	0	0.004	0.007	49.972	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	62	GLN	0	-0.035	-0.011	53.100	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	63	THR	0	-0.012	0.007	55.477	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	64	ARG	1	0.880	0.917	56.279	-0.035	-0.035	0.000	0.000	0.000	0.000
45	A	65	ASN	0	-0.045	-0.022	57.690	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	66	THR	0	-0.025	-0.033	59.155	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	67	LEU	0	0.035	0.018	60.658	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	68	ASN	0	0.010	0.003	60.875	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	69	ARG	1	0.918	0.967	61.553	-0.020	-0.020	0.000	0.000	0.000	0.000
50	A	70	ALA	0	0.011	0.006	65.430	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	71	GLY	0	0.064	0.031	67.191	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	72	ILE	0	-0.016	-0.015	66.183	0.000	0.000	0.000	0.000	0.000	0.000
53	A	73	ARG	1	0.787	0.876	69.568	-0.015	-0.015	0.000	0.000	0.000	0.000
54	A	74	TYR	0	0.041	0.015	71.480	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	75	MET	0	-0.020	-0.019	70.452	0.000	0.000	0.000	0.000	0.000	0.000
56	A	76	MET	0	-0.086	-0.029	71.953	0.000	0.000	0.000	0.000	0.000	0.000
57	A	77	ASP	-1	-0.804	-0.889	75.041	0.014	0.014	0.000	0.000	0.000	0.000
58	A	78	GLN	0	-0.055	-0.009	77.323	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	79	ASN	0	-0.044	-0.018	79.377	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	80	ASN	0	-0.049	-0.036	80.968	0.000	0.000	0.000	0.000	0.000	0.000
61	A	81	ILE	0	0.011	0.032	77.241	0.000	0.000	0.000	0.000	0.000	0.000
62	A	82	GLY	0	0.024	0.012	74.409	0.000	0.000	0.000	0.000	0.000	0.000
63	A	83	SER	0	-0.049	-0.035	73.163	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	84	GLY	0	0.005	0.000	69.783	0.001	0.001	0.000	0.000	0.000	0.000
65	A	85	SER	0	0.008	0.000	66.859	0.000	0.000	0.000	0.000	0.000	0.000
66	A	86	THR	0	0.006	-0.007	69.183	0.001	0.001	0.000	0.000	0.000	0.000
67	A	87	VAL	0	0.083	0.044	69.435	0.000	0.000	0.000	0.000	0.000	0.000
68	A	88	ALA	0	0.028	0.009	68.973	0.000	0.000	0.000	0.000	0.000	0.000
69	A	89	GLU	-1	-0.851	-0.919	67.464	0.012	0.012	0.000	0.000	0.000	0.000
70	A	90	LEU	0	-0.063	-0.036	64.745	0.000	0.000	0.000	0.000	0.000	0.000
71	A	91	MET	0	0.005	0.015	64.256	0.001	0.001	0.000	0.000	0.000	0.000
72	A	92	GLU	-1	-0.851	-0.938	63.533	0.011	0.011	0.000	0.000	0.000	0.000
73	A	93	SER	0	-0.014	-0.010	60.474	0.000	0.000	0.000	0.000	0.000	0.000
74	A	94	ALA	0	0.005	0.003	59.951	0.001	0.001	0.000	0.000	0.000	0.000
75	A	95	SER	0	0.010	0.002	59.351	0.001	0.001	0.000	0.000	0.000	0.000
76	A	96	ILE	0	-0.073	-0.031	57.506	0.000	0.000	0.000	0.000	0.000	0.000
77	A	97	SER	0	-0.021	-0.028	55.546	0.000	0.000	0.000	0.000	0.000	0.000
78	A	98	LEU	0	0.015	0.011	54.568	0.001	0.001	0.000	0.000	0.000	0.000
79	A	99	LYS	1	0.950	0.985	54.631	-0.011	-0.011	0.000	0.000	0.000	0.000
80	A	100	GLN	0	-0.021	-0.011	50.692	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	101	ALA	0	0.019	0.017	50.460	0.001	0.001	0.000	0.000	0.000	0.000
82	A	102	GLU	-1	-0.815	-0.883	49.852	0.018	0.018	0.000	0.000	0.000	0.000
83	A	103	LYS	1	0.918	0.965	48.890	-0.009	-0.009	0.000	0.000	0.000	0.000
84	A	104	ASN	0	-0.011	-0.019	45.914	0.001	0.001	0.000	0.000	0.000	0.000
85	A	105	TRP	0	-0.016	-0.018	45.319	0.003	0.003	0.000	0.000	0.000	0.000
86	A	106	ALA	0	-0.001	0.001	45.838	0.001	0.001	0.000	0.000	0.000	0.000
87	A	107	ASP	-1	-0.935	-0.966	43.217	0.012	0.012	0.000	0.000	0.000	0.000
88	A	108	TYR	0	-0.064	-0.045	39.572	0.000	0.000	0.000	0.000	0.000	0.000
89	A	109	GLU	-1	-0.827	-0.904	40.901	0.029	0.029	0.000	0.000	0.000	0.000
90	A	110	ALA	0	-0.056	-0.014	41.962	0.000	0.000	0.000	0.000	0.000	0.000
91	A	111	LEU	0	-0.072	-0.015	36.976	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	112	PRO	0	-0.017	-0.013	34.026	0.003	0.003	0.000	0.000	0.000	0.000
93	A	113	ARG	1	0.958	0.972	34.415	-0.035	-0.035	0.000	0.000	0.000	0.000
94	A	114	ASP	-1	-0.758	-0.845	27.923	0.086	0.086	0.000	0.000	0.000	0.000
95	A	115	PRO	0	-0.018	-0.031	28.319	0.003	0.003	0.000	0.000	0.000	0.000
96	A	116	ARG	1	0.817	0.885	23.492	-0.121	-0.121	0.000	0.000	0.000	0.000
97	A	117	GLN	0	-0.043	-0.019	30.066	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	118	SER	0	0.035	0.020	33.329	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	119	THR	0	0.017	-0.015	36.047	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	120	ALA	0	0.007	0.008	38.737	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	121	ALA	0	0.048	0.018	38.783	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	122	ALA	0	0.003	0.004	39.269	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	123	ALA	0	-0.003	-0.002	41.185	-0.004	-0.004	0.000	0.000	0.000	0.000
104	A	124	GLU	-1	-0.749	-0.842	43.859	0.047	0.047	0.000	0.000	0.000	0.000
105	A	125	ILE	0	-0.001	0.016	42.300	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	126	LYS	1	0.874	0.933	45.158	-0.030	-0.030	0.000	0.000	0.000	0.000
107	A	127	ARG	1	0.846	0.907	47.041	-0.046	-0.046	0.000	0.000	0.000	0.000
108	A	128	ASN	0	-0.074	-0.066	48.023	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	129	TYR	0	0.017	0.018	48.213	-0.002	-0.002	0.000	0.000	0.000	0.000
110	A	130	ASP	-1	-0.908	-0.963	50.189	0.026	0.026	0.000	0.000	0.000	0.000
111	A	131	ILE	0	-0.052	-0.018	52.973	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	132	TYR	0	0.034	0.007	51.909	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	133	HIS	1	0.835	0.888	53.162	-0.024	-0.024	0.000	0.000	0.000	0.000
114	A	134	ASN	0	-0.012	-0.016	55.049	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	135	ALA	0	0.037	0.041	57.910	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	136	LEU	0	0.035	0.012	55.963	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	137	ALA	0	-0.006	-0.006	59.306	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	138	GLU	-1	-0.880	-0.930	60.959	0.022	0.022	0.000	0.000	0.000	0.000
119	A	139	LEU	0	-0.025	-0.003	61.617	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	140	ILE	0	-0.023	-0.017	60.871	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	141	GLN	0	-0.033	-0.017	64.982	0.000	0.000	0.000	0.000	0.000	0.000
122	A	142	LEU	0	-0.017	-0.015	66.789	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	143	LEU	0	0.003	-0.003	67.090	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	144	GLY	0	-0.022	-0.009	69.309	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	145	ALA	0	-0.052	-0.016	71.029	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	146	GLY	0	0.008	0.010	73.148	0.000	0.000	0.000	0.000	0.000	0.000
127	A	147	LYS	1	0.804	0.917	71.052	-0.017	-0.017	0.000	0.000	0.000	0.000
128	A	148	ILE	0	0.003	-0.009	71.896	0.001	0.001	0.000	0.000	0.000	0.000
129	A	149	ASN	0	0.023	-0.002	71.592	0.001	0.001	0.000	0.000	0.000	0.000
130	A	150	GLU	-1	-0.800	-0.888	69.212	0.020	0.020	0.000	0.000	0.000	0.000
131	A	151	PHE	0	-0.081	-0.048	65.854	0.001	0.001	0.000	0.000	0.000	0.000
132	A	152	PHE	0	-0.055	-0.047	67.091	0.001	0.001	0.000	0.000	0.000	0.000
133	A	153	ASP	-1	-0.908	-0.937	67.663	0.024	0.024	0.000	0.000	0.000	0.000
134	A	154	GLN	0	-0.059	-0.012	61.750	0.002	0.002	0.000	0.000	0.000	0.000
135	A	155	PRO	0	0.021	0.016	61.683	0.001	0.001	0.000	0.000	0.000	0.000
136	A	156	THR	0	-0.022	-0.051	58.267	0.001	0.001	0.000	0.000	0.000	0.000
137	A	157	GLN	0	-0.040	-0.014	55.198	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	158	GLY	0	0.060	0.034	56.010	0.002	0.002	0.000	0.000	0.000	0.000
139	A	159	TYR	0	0.002	-0.012	54.904	0.002	0.002	0.000	0.000	0.000	0.000
140	A	160	GLN	0	0.018	0.037	52.312	-0.001	-0.001	0.000	0.000	0.000	0.000
141	A	161	ASP	-1	-0.837	-0.912	51.516	0.046	0.046	0.000	0.000	0.000	0.000
142	A	162	GLY	0	-0.070	-0.029	50.273	0.003	0.003	0.000	0.000	0.000	0.000
143	A	163	PHE	0	0.025	0.002	46.105	0.002	0.002	0.000	0.000	0.000	0.000
144	A	164	GLU	-1	-0.873	-0.948	46.900	0.052	0.052	0.000	0.000	0.000	0.000
145	A	165	LYS	1	0.884	0.939	45.561	-0.052	-0.052	0.000	0.000	0.000	0.000
146	A	166	GLN	0	-0.009	-0.017	43.807	0.007	0.007	0.000	0.000	0.000	0.000
147	A	167	TYR	0	-0.045	-0.030	42.286	0.004	0.004	0.000	0.000	0.000	0.000
148	A	168	VAL	0	0.032	0.006	41.075	0.003	0.003	0.000	0.000	0.000	0.000
149	A	169	ALA	0	0.020	0.021	39.518	0.005	0.005	0.000	0.000	0.000	0.000
150	A	170	TYR	0	-0.016	-0.010	37.042	0.005	0.005	0.000	0.000	0.000	0.000
151	A	171	MET	0	-0.003	-0.005	36.501	0.003	0.003	0.000	0.000	0.000	0.000
152	A	172	GLU	-1	-0.857	-0.889	34.734	0.124	0.124	0.000	0.000	0.000	0.000
153	A	173	GLN	0	-0.024	-0.021	33.268	0.009	0.009	0.000	0.000	0.000	0.000
154	A	174	ASN	0	0.004	-0.017	31.831	0.010	0.010	0.000	0.000	0.000	0.000
155	A	175	ASP	-1	-0.850	-0.918	30.800	0.101	0.101	0.000	0.000	0.000	0.000
156	A	176	ARG	1	0.865	0.927	28.231	-0.140	-0.140	0.000	0.000	0.000	0.000
157	A	177	LEU	0	-0.046	-0.028	27.118	0.014	0.014	0.000	0.000	0.000	0.000
158	A	178	HIS	0	-0.050	-0.032	25.931	-0.002	-0.002	0.000	0.000	0.000	0.000
159	A	179	ASP	-1	-0.816	-0.909	25.285	0.173	0.173	0.000	0.000	0.000	0.000
160	A	180	ILE	0	-0.098	-0.030	21.641	0.027	0.027	0.000	0.000	0.000	0.000
161	A	181	ALA	0	0.023	0.013	21.040	0.023	0.023	0.000	0.000	0.000	0.000
162	A	182	VAL	0	-0.030	-0.012	20.713	0.005	0.005	0.000	0.000	0.000	0.000
163	A	183	SER	0	-0.046	-0.045	19.596	0.020	0.020	0.000	0.000	0.000	0.000
164	A	184	ASP	-1	-0.855	-0.893	16.051	0.336	0.336	0.000	0.000	0.000	0.000
165	A	185	ASN	0	-0.067	-0.033	15.704	-0.005	-0.005	0.000	0.000	0.000	0.000
166	A	186	ASN	0	-0.056	-0.029	16.440	-0.037	-0.037	0.000	0.000	0.000	0.000
167	A	187	ALA	0	-0.049	-0.001	11.173	0.037	0.037	0.000	0.000	0.000	0.000

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