FMO DATABASE

FMODB ID: 52Z9Z

Calculation Name: 3EXZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EXZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q2RSA1

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	146
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1219434.178522
FMO2-HF: Nuclear repulsion	1164879.694406
FMO2-HF: Total energy	-54554.484116
FMO2-MP2: Total energy	-54716.400767

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:15:GLY)

Summations of interaction energy for fragment #1(A:15: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.
-7.742	-6.346	7.733	-4.462	-4.668	-0.042

Interaction energy analysis for fragmet #1(A:15:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : 0.005

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	17	PHE	0	-0.011	-0.016	3.864	0.802	2.055	-0.014	-0.672	-0.566	0.002
4	A	18	LEU	0	-0.034	-0.029	7.109	0.131	0.131	0.000	0.000	0.000	0.000
5	A	19	GLU	-1	-0.805	-0.901	10.688	-1.119	-1.119	0.000	0.000	0.000	0.000
6	A	20	ASP	-1	-0.814	-0.860	6.307	-3.409	-3.409	0.000	0.000	0.000	0.000
7	A	21	LEU	0	-0.004	0.007	7.627	-0.001	-0.001	0.000	0.000	0.000	0.000
8	A	22	ALA	0	-0.006	-0.014	10.941	0.163	0.163	0.000	0.000	0.000	0.000
9	A	23	VAL	0	-0.055	-0.031	14.350	-0.002	-0.002	0.000	0.000	0.000	0.000
10	A	24	GLY	0	0.000	0.001	16.612	0.035	0.035	0.000	0.000	0.000	0.000
11	A	25	ASP	-1	-0.838	-0.908	11.393	-0.972	-0.972	0.000	0.000	0.000	0.000
12	A	26	ARG	1	0.877	0.926	12.603	0.391	0.391	0.000	0.000	0.000	0.000
13	A	27	PHE	0	-0.001	0.004	6.917	-0.123	-0.123	0.000	0.000	0.000	0.000
14	A	28	ASP	-1	-0.753	-0.861	10.701	0.066	0.066	0.000	0.000	0.000	0.000
15	A	29	SER	0	-0.016	-0.013	10.759	0.029	0.029	0.000	0.000	0.000	0.000
16	A	30	ALA	0	-0.003	0.001	12.346	-0.005	-0.005	0.000	0.000	0.000	0.000
17	A	31	ARG	1	0.838	0.897	14.203	-0.175	-0.175	0.000	0.000	0.000	0.000
18	A	32	HIS	0	-0.010	0.002	17.794	0.083	0.083	0.000	0.000	0.000	0.000
19	A	33	ARG	1	0.799	0.902	19.795	-0.149	-0.149	0.000	0.000	0.000	0.000
20	A	34	VAL	0	-0.030	-0.008	23.623	0.010	0.010	0.000	0.000	0.000	0.000
21	A	35	GLU	-1	-0.782	-0.894	25.789	0.101	0.101	0.000	0.000	0.000	0.000
22	A	36	ALA	0	0.039	0.011	29.178	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	37	ALA	0	-0.004	0.001	31.544	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	38	ALA	0	0.009	0.003	26.567	0.001	0.001	0.000	0.000	0.000	0.000
25	A	39	ILE	0	-0.009	0.001	28.521	0.000	0.000	0.000	0.000	0.000	0.000
26	A	40	LYS	1	0.827	0.904	29.908	-0.064	-0.064	0.000	0.000	0.000	0.000
27	A	41	ALA	0	-0.034	-0.005	29.540	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	42	PHE	0	0.042	0.018	24.673	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	43	ALA	0	0.015	0.001	29.026	-0.006	-0.006	0.000	0.000	0.000	0.000
30	A	44	GLY	0	-0.032	-0.022	32.138	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	45	GLU	-1	-0.984	-0.977	29.036	0.105	0.105	0.000	0.000	0.000	0.000
32	A	46	PHE	0	-0.064	-0.038	27.037	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	47	ASP	-1	-0.824	-0.875	30.566	0.016	0.016	0.000	0.000	0.000	0.000
34	A	48	PRO	0	0.042	0.037	32.563	0.001	0.001	0.000	0.000	0.000	0.000
35	A	49	GLN	0	-0.055	-0.050	34.312	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	50	PRO	0	0.061	0.007	36.986	0.003	0.003	0.000	0.000	0.000	0.000
37	A	51	PHE	0	0.007	0.004	35.287	0.003	0.003	0.000	0.000	0.000	0.000
38	A	52	HIS	0	-0.048	-0.027	32.452	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	53	LEU	0	-0.008	-0.009	34.175	0.008	0.008	0.000	0.000	0.000	0.000
40	A	54	ASP	-1	-0.850	-0.930	36.949	0.043	0.043	0.000	0.000	0.000	0.000
41	A	55	GLU	-1	-0.827	-0.908	38.274	0.052	0.052	0.000	0.000	0.000	0.000
42	A	56	GLU	-1	-0.869	-0.902	39.674	0.026	0.026	0.000	0.000	0.000	0.000
43	A	57	ALA	0	0.006	-0.016	41.876	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	58	ALA	0	-0.019	-0.005	38.006	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	59	ARG	1	0.854	0.934	40.032	-0.038	-0.038	0.000	0.000	0.000	0.000
46	A	60	HIS	0	-0.074	-0.030	42.425	-0.005	-0.005	0.000	0.000	0.000	0.000
47	A	61	SER	0	-0.025	-0.030	39.838	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	62	LEU	0	0.015	-0.006	38.879	0.000	0.000	0.000	0.000	0.000	0.000
49	A	63	PHE	0	0.009	0.015	32.851	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	64	GLY	0	0.000	0.016	37.242	0.002	0.002	0.000	0.000	0.000	0.000
51	A	65	GLY	0	-0.005	-0.004	38.472	0.002	0.002	0.000	0.000	0.000	0.000
52	A	66	LEU	0	-0.032	-0.024	33.566	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	67	ALA	0	-0.004	0.014	31.880	0.000	0.000	0.000	0.000	0.000	0.000
54	A	68	ALA	0	-0.004	0.002	27.515	0.003	0.003	0.000	0.000	0.000	0.000
55	A	69	SER	0	-0.035	-0.033	28.549	-0.008	-0.008	0.000	0.000	0.000	0.000
56	A	70	GLY	0	0.066	0.018	26.798	0.005	0.005	0.000	0.000	0.000	0.000
57	A	71	TRP	0	0.027	0.000	24.892	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	72	HIS	0	0.022	0.017	23.806	0.000	0.000	0.000	0.000	0.000	0.000
59	A	73	THR	0	-0.007	0.002	22.342	0.018	0.018	0.000	0.000	0.000	0.000
60	A	74	ALA	0	0.030	0.025	20.549	0.007	0.007	0.000	0.000	0.000	0.000
61	A	75	ALA	0	-0.014	-0.005	19.082	0.003	0.003	0.000	0.000	0.000	0.000
62	A	76	ILE	0	-0.028	-0.011	18.294	0.036	0.036	0.000	0.000	0.000	0.000
63	A	77	THR	0	0.006	-0.001	16.064	0.035	0.035	0.000	0.000	0.000	0.000
64	A	78	MET	0	-0.008	0.001	13.166	-0.012	-0.012	0.000	0.000	0.000	0.000
65	A	79	ARG	1	0.917	0.949	13.362	-0.314	-0.314	0.000	0.000	0.000	0.000
66	A	80	LEU	0	0.010	0.013	12.567	0.095	0.095	0.000	0.000	0.000	0.000
67	A	81	LEU	0	0.013	0.014	10.628	0.064	0.064	0.000	0.000	0.000	0.000
68	A	82	VAL	0	-0.008	-0.006	8.751	0.016	0.016	0.000	0.000	0.000	0.000
69	A	83	THR	0	-0.042	-0.025	8.151	0.267	0.267	0.000	0.000	0.000	0.000
70	A	84	SER	0	-0.088	-0.046	7.744	0.246	0.246	0.000	0.000	0.000	0.000
71	A	85	GLY	0	0.014	0.008	7.693	-0.132	-0.132	0.000	0.000	0.000	0.000
72	A	86	LEU	0	-0.014	-0.017	7.261	-0.191	-0.191	0.000	0.000	0.000	0.000
73	A	87	PRO	0	0.019	0.035	2.678	-0.819	-0.021	0.443	-0.495	-0.746	0.000
74	A	88	LEU	0	0.015	0.004	1.987	-8.678	-9.668	6.297	-3.080	-2.228	-0.043
75	A	89	ALA	0	-0.009	-0.013	2.547	1.012	1.522	0.926	-0.500	-0.936	-0.001
76	A	90	GLN	0	-0.045	-0.027	3.198	0.883	0.708	0.081	0.285	-0.192	0.000
77	A	91	GLY	0	0.008	0.023	6.390	0.144	0.144	0.000	0.000	0.000	0.000
78	A	92	ILE	0	-0.002	-0.012	8.397	-0.298	-0.298	0.000	0.000	0.000	0.000
79	A	93	ILE	0	0.025	0.013	10.941	0.097	0.097	0.000	0.000	0.000	0.000
80	A	94	GLY	0	0.008	0.004	13.910	-0.060	-0.060	0.000	0.000	0.000	0.000
81	A	95	ALA	0	-0.036	-0.017	16.469	0.037	0.037	0.000	0.000	0.000	0.000
82	A	96	GLY	0	0.006	-0.001	19.440	0.030	0.030	0.000	0.000	0.000	0.000
83	A	97	THR	0	-0.055	-0.042	19.705	-0.044	-0.044	0.000	0.000	0.000	0.000
84	A	98	GLU	-1	-0.802	-0.845	21.475	-0.118	-0.118	0.000	0.000	0.000	0.000
85	A	99	LEU	0	-0.042	-0.014	21.885	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	100	SER	0	0.001	-0.006	24.308	0.009	0.009	0.000	0.000	0.000	0.000
87	A	101	TRP	0	-0.004	-0.009	24.347	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	102	PRO	0	-0.045	-0.011	26.343	0.005	0.005	0.000	0.000	0.000	0.000
89	A	103	ASN	0	-0.017	-0.006	28.199	0.005	0.005	0.000	0.000	0.000	0.000
90	A	104	PRO	0	0.002	-0.007	28.543	0.003	0.003	0.000	0.000	0.000	0.000
91	A	105	THR	0	0.055	0.015	25.462	0.000	0.000	0.000	0.000	0.000	0.000
92	A	106	ARG	1	0.813	0.894	28.083	-0.025	-0.025	0.000	0.000	0.000	0.000
93	A	107	PRO	0	-0.030	-0.024	28.767	0.009	0.009	0.000	0.000	0.000	0.000
94	A	108	GLY	0	0.005	0.004	29.210	-0.007	-0.007	0.000	0.000	0.000	0.000
95	A	109	ASP	-1	-0.810	-0.892	25.408	0.049	0.049	0.000	0.000	0.000	0.000
96	A	110	GLU	-1	-0.895	-0.958	22.794	0.167	0.167	0.000	0.000	0.000	0.000
97	A	111	LEU	0	-0.023	-0.011	20.470	-0.015	-0.015	0.000	0.000	0.000	0.000
98	A	112	HIS	0	-0.066	-0.050	16.609	0.068	0.068	0.000	0.000	0.000	0.000
99	A	113	VAL	0	-0.005	-0.012	14.286	-0.024	-0.024	0.000	0.000	0.000	0.000
100	A	114	GLU	-1	-0.821	-0.874	14.028	-0.114	-0.114	0.000	0.000	0.000	0.000
101	A	115	THR	0	-0.024	-0.012	12.127	0.003	0.003	0.000	0.000	0.000	0.000
102	A	116	THR	0	-0.008	-0.007	13.587	-0.050	-0.050	0.000	0.000	0.000	0.000
103	A	117	VAL	0	-0.011	0.004	11.698	0.036	0.036	0.000	0.000	0.000	0.000
104	A	118	LEU	0	0.005	-0.002	14.702	0.032	0.032	0.000	0.000	0.000	0.000
105	A	119	ALA	0	-0.017	-0.019	17.361	0.036	0.036	0.000	0.000	0.000	0.000
106	A	120	ILE	0	0.033	0.032	13.815	-0.026	-0.026	0.000	0.000	0.000	0.000
107	A	121	THR	0	-0.027	-0.005	17.185	0.054	0.054	0.000	0.000	0.000	0.000
108	A	122	PRO	0	0.042	0.026	18.290	0.004	0.004	0.000	0.000	0.000	0.000
109	A	123	SER	0	0.031	0.026	19.225	0.066	0.066	0.000	0.000	0.000	0.000
110	A	124	LYS	1	0.853	0.898	21.306	0.316	0.316	0.000	0.000	0.000	0.000
111	A	125	SER	0	0.018	0.024	24.648	0.007	0.007	0.000	0.000	0.000	0.000
112	A	126	ARG	1	0.860	0.899	19.571	0.276	0.276	0.000	0.000	0.000	0.000
113	A	127	PRO	0	0.035	0.025	19.498	-0.031	-0.031	0.000	0.000	0.000	0.000
114	A	128	ASP	-1	-0.774	-0.848	15.993	-0.394	-0.394	0.000	0.000	0.000	0.000
115	A	129	ARG	1	0.863	0.919	14.458	0.265	0.265	0.000	0.000	0.000	0.000
116	A	130	ALA	0	0.002	-0.007	14.534	0.080	0.080	0.000	0.000	0.000	0.000
117	A	131	ILE	0	-0.003	0.011	14.998	-0.037	-0.037	0.000	0.000	0.000	0.000
118	A	132	VAL	0	0.028	0.012	11.850	0.038	0.038	0.000	0.000	0.000	0.000
119	A	133	THR	0	-0.040	-0.013	14.841	0.065	0.065	0.000	0.000	0.000	0.000
120	A	134	CYS	0	-0.003	0.002	12.715	-0.083	-0.083	0.000	0.000	0.000	0.000
121	A	135	GLN	0	-0.006	-0.025	15.188	0.055	0.055	0.000	0.000	0.000	0.000
122	A	136	SER	0	0.006	-0.015	14.087	-0.035	-0.035	0.000	0.000	0.000	0.000
123	A	137	ASP	-1	-0.764	-0.848	16.659	-0.117	-0.117	0.000	0.000	0.000	0.000
124	A	138	THR	0	-0.033	-0.022	18.600	0.005	0.005	0.000	0.000	0.000	0.000
125	A	139	LEU	0	-0.006	0.009	19.914	-0.005	-0.005	0.000	0.000	0.000	0.000
126	A	140	ASN	0	0.037	0.004	21.544	0.015	0.015	0.000	0.000	0.000	0.000
127	A	141	GLN	0	0.043	0.016	24.089	-0.013	-0.013	0.000	0.000	0.000	0.000
128	A	142	ARG	1	0.730	0.825	25.478	-0.020	-0.020	0.000	0.000	0.000	0.000
129	A	143	GLY	0	0.005	0.013	24.763	-0.007	-0.007	0.000	0.000	0.000	0.000
130	A	144	GLU	-1	-0.804	-0.848	25.832	-0.007	-0.007	0.000	0.000	0.000	0.000
131	A	145	VAL	0	0.042	0.006	23.234	0.007	0.007	0.000	0.000	0.000	0.000
132	A	146	VAL	0	0.002	0.013	23.505	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	147	GLN	0	-0.024	-0.028	19.898	0.015	0.015	0.000	0.000	0.000	0.000
134	A	148	ARG	1	0.810	0.887	21.469	0.147	0.147	0.000	0.000	0.000	0.000
135	A	149	SER	0	-0.026	-0.026	18.840	0.012	0.012	0.000	0.000	0.000	0.000
136	A	150	THR	0	-0.036	-0.021	18.666	-0.039	-0.039	0.000	0.000	0.000	0.000
137	A	151	ALA	0	0.053	0.036	16.089	0.012	0.012	0.000	0.000	0.000	0.000
138	A	152	LYS	1	0.875	0.917	17.150	0.253	0.253	0.000	0.000	0.000	0.000
139	A	153	VAL	0	0.030	0.017	11.300	0.054	0.054	0.000	0.000	0.000	0.000
140	A	154	VAL	0	-0.051	-0.022	14.369	-0.057	-0.057	0.000	0.000	0.000	0.000
141	A	155	VAL	0	0.023	0.014	8.847	-0.009	-0.009	0.000	0.000	0.000	0.000
142	A	156	PHE	0	0.007	-0.012	10.750	0.106	0.106	0.000	0.000	0.000	0.000
143	A	157	ARG	1	0.870	0.924	9.934	0.448	0.448	0.000	0.000	0.000	0.000
144	A	158	ARG	1	0.823	0.883	6.788	2.267	2.267	0.000	0.000	0.000	0.000
145	A	159	PRO	0	-0.021	-0.020	10.000	0.124	0.124	0.000	0.000	0.000	0.000
146	A	160	LEU	0	0.004	0.017	12.595	-0.007	-0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:15:GLY)