FMO DATABASE

FMODB ID: 727YK

Calculation Name: 4X38-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4X38

Chain ID: A

ChEMBL ID:

UniProt ID: O73909

Base Structure: X-ray

Registration Date: 2023-09-19

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	159
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1560487.411456
FMO2-HF: Nuclear repulsion	1497991.052033
FMO2-HF: Total energy	-62496.359423
FMO2-MP2: Total energy	-62676.720869

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:3:ALA)

Summations of interaction energy for fragment #1(A:3:ALA)

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.
-12.332	-6.742	2.151	-3.797	-3.942	-0.032

Interaction energy analysis for fragmet #1(A:3:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.040 / q_NPA : -0.015

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	5	ARG	1	0.854	0.922	3.882	-2.067	-0.579	-0.017	-0.789	-0.681	0.001
4	A	6	TYR	0	-0.008	-0.016	6.568	-0.131	-0.131	0.000	0.000	0.000	0.000
5	A	7	THR	0	-0.093	-0.049	9.973	0.174	0.174	0.000	0.000	0.000	0.000
6	A	8	ARG	1	0.921	0.947	12.841	0.128	0.128	0.000	0.000	0.000	0.000
7	A	9	SER	0	0.052	0.044	15.180	-0.066	-0.066	0.000	0.000	0.000	0.000
8	A	10	GLN	0	0.002	0.022	17.681	0.032	0.032	0.000	0.000	0.000	0.000
9	A	11	SER	0	-0.037	-0.020	20.505	-0.015	-0.015	0.000	0.000	0.000	0.000
10	A	12	PHE	0	-0.019	-0.018	20.054	0.013	0.013	0.000	0.000	0.000	0.000
11	A	13	ASP	-1	-0.813	-0.881	24.261	-0.100	-0.100	0.000	0.000	0.000	0.000
12	A	14	ILE	0	0.000	-0.008	22.711	-0.005	-0.005	0.000	0.000	0.000	0.000
13	A	15	PHE	0	0.005	0.012	26.568	0.006	0.006	0.000	0.000	0.000	0.000
14	A	16	ASP	-1	-0.711	-0.839	27.491	-0.123	-0.123	0.000	0.000	0.000	0.000
15	A	17	ILE	0	0.001	-0.011	28.444	0.009	0.009	0.000	0.000	0.000	0.000
16	A	18	ASN	0	-0.051	-0.015	30.384	0.007	0.007	0.000	0.000	0.000	0.000
17	A	19	GLN	0	0.001	-0.011	32.393	0.003	0.003	0.000	0.000	0.000	0.000
18	A	20	LYS	1	0.811	0.937	31.164	0.115	0.115	0.000	0.000	0.000	0.000
19	A	21	CYS	0	-0.040	-0.017	29.591	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	22	PHE	0	0.050	0.010	22.666	0.000	0.000	0.000	0.000	0.000	0.000
21	A	23	VAL	0	0.024	0.003	28.381	0.006	0.006	0.000	0.000	0.000	0.000
22	A	24	LEU	0	-0.028	-0.005	25.612	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	25	GLU	-1	-0.883	-0.938	28.976	-0.097	-0.097	0.000	0.000	0.000	0.000
24	A	26	SER	0	0.019	0.002	29.619	0.005	0.005	0.000	0.000	0.000	0.000
25	A	27	PRO	0	0.002	-0.013	26.317	-0.007	-0.007	0.000	0.000	0.000	0.000
26	A	28	THR	0	0.023	0.014	25.024	-0.011	-0.011	0.000	0.000	0.000	0.000
27	A	29	GLN	0	-0.065	-0.027	26.374	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	30	LEU	0	0.016	0.017	23.226	0.007	0.007	0.000	0.000	0.000	0.000
29	A	31	VAL	0	0.023	0.022	26.900	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	32	ALA	0	0.023	0.021	28.383	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	33	LEU	0	-0.020	-0.029	30.201	0.007	0.007	0.000	0.000	0.000	0.000
32	A	34	HIS	0	0.012	0.017	33.659	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	35	LEU	0	-0.011	-0.002	34.093	0.002	0.002	0.000	0.000	0.000	0.000
34	A	36	GLN	0	0.010	-0.009	37.386	0.003	0.003	0.000	0.000	0.000	0.000
35	A	37	GLY	0	0.018	0.012	41.096	0.000	0.000	0.000	0.000	0.000	0.000
36	A	38	PRO	0	0.020	0.023	44.180	0.001	0.001	0.000	0.000	0.000	0.000
37	A	39	SER	0	-0.029	-0.015	40.683	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	40	SER	0	-0.027	-0.022	40.500	0.001	0.001	0.000	0.000	0.000	0.000
39	A	41	SER	0	0.005	0.000	35.920	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	42	GLN	0	-0.008	-0.003	31.508	0.006	0.006	0.000	0.000	0.000	0.000
41	A	43	LYS	1	0.902	0.946	30.139	0.084	0.084	0.000	0.000	0.000	0.000
42	A	44	VAL	0	-0.011	0.006	25.049	0.003	0.003	0.000	0.000	0.000	0.000
43	A	45	ARG	1	0.813	0.891	25.795	0.098	0.098	0.000	0.000	0.000	0.000
44	A	46	LEU	0	0.055	0.024	20.022	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	47	ASN	0	-0.053	-0.044	19.860	0.035	0.035	0.000	0.000	0.000	0.000
46	A	48	ILE	0	0.015	0.016	15.959	-0.025	-0.025	0.000	0.000	0.000	0.000
47	A	49	ALA	0	0.004	0.014	13.284	0.045	0.045	0.000	0.000	0.000	0.000
48	A	50	LEU	0	-0.013	-0.013	12.555	-0.073	-0.073	0.000	0.000	0.000	0.000
49	A	51	TYR	0	0.023	-0.014	7.207	0.053	0.053	0.000	0.000	0.000	0.000
50	A	52	ARG	1	0.920	0.962	8.114	-0.082	-0.082	0.000	0.000	0.000	0.000
51	A	53	PRO	0	0.078	0.048	4.501	-0.130	-0.077	-0.001	-0.070	0.018	0.000
52	A	54	ARG	1	0.927	0.947	4.140	-0.189	-0.061	-0.001	-0.015	-0.111	0.000
53	A	55	GLY	0	0.005	-0.002	5.702	-0.239	-0.239	0.000	0.000	0.000	0.000
54	A	56	PRO	0	0.024	0.040	5.380	0.081	0.081	0.000	0.000	0.000	0.000
55	A	57	ARG	1	0.948	0.947	6.901	-0.714	-0.714	0.000	0.000	0.000	0.000
56	A	58	GLY	0	0.014	-0.001	9.968	-0.016	-0.016	0.000	0.000	0.000	0.000
57	A	59	SER	0	0.001	0.000	9.682	-0.022	-0.022	0.000	0.000	0.000	0.000
58	A	60	ALA	0	-0.013	0.006	8.813	0.016	0.016	0.000	0.000	0.000	0.000
59	A	61	GLY	0	0.034	0.024	8.527	-0.038	-0.038	0.000	0.000	0.000	0.000
60	A	62	THR	0	-0.034	-0.037	9.119	0.040	0.040	0.000	0.000	0.000	0.000
61	A	63	GLY	0	0.020	-0.007	11.341	0.022	0.022	0.000	0.000	0.000	0.000
62	A	64	GLN	0	-0.059	-0.012	11.704	0.009	0.009	0.000	0.000	0.000	0.000
63	A	65	MET	0	-0.004	-0.003	11.900	0.011	0.011	0.000	0.000	0.000	0.000
64	A	66	PRO	0	0.003	0.024	7.351	0.024	0.024	0.000	0.000	0.000	0.000
65	A	67	VAL	0	-0.036	-0.038	9.671	0.070	0.070	0.000	0.000	0.000	0.000
66	A	68	ALA	0	0.085	0.066	11.153	-0.082	-0.082	0.000	0.000	0.000	0.000
67	A	69	LEU	0	-0.024	-0.021	12.666	0.084	0.084	0.000	0.000	0.000	0.000
68	A	70	GLY	0	0.077	0.039	16.371	0.000	0.000	0.000	0.000	0.000	0.000
69	A	71	ILE	0	0.012	0.008	18.681	0.022	0.022	0.000	0.000	0.000	0.000
70	A	72	LYS	1	0.938	0.953	22.309	0.114	0.114	0.000	0.000	0.000	0.000
71	A	73	GLY	0	-0.022	-0.019	23.973	0.009	0.009	0.000	0.000	0.000	0.000
72	A	74	TYR	0	0.021	0.002	24.663	0.012	0.012	0.000	0.000	0.000	0.000
73	A	75	LYS	1	0.858	0.935	21.423	0.113	0.113	0.000	0.000	0.000	0.000
74	A	76	LEU	0	0.095	0.072	20.307	-0.009	-0.009	0.000	0.000	0.000	0.000
75	A	77	TYR	0	-0.053	-0.020	15.261	0.005	0.005	0.000	0.000	0.000	0.000
76	A	78	MET	0	-0.030	-0.006	16.645	0.010	0.010	0.000	0.000	0.000	0.000
77	A	79	SER	0	-0.020	-0.039	14.056	-0.051	-0.051	0.000	0.000	0.000	0.000
78	A	80	CYS	0	-0.048	0.003	13.868	0.068	0.068	0.000	0.000	0.000	0.000
79	A	81	VAL	0	0.020	-0.002	14.196	-0.065	-0.065	0.000	0.000	0.000	0.000
80	A	82	MET	0	-0.016	0.004	16.547	0.027	0.027	0.000	0.000	0.000	0.000
81	A	83	SER	0	-0.003	-0.004	18.990	0.003	0.003	0.000	0.000	0.000	0.000
82	A	84	GLY	0	0.032	0.028	22.407	0.012	0.012	0.000	0.000	0.000	0.000
83	A	85	THR	0	-0.045	-0.037	23.399	-0.006	-0.006	0.000	0.000	0.000	0.000
84	A	86	GLU	-1	-0.924	-0.970	22.793	-0.158	-0.158	0.000	0.000	0.000	0.000
85	A	87	PRO	0	-0.015	0.000	18.263	-0.011	-0.011	0.000	0.000	0.000	0.000
86	A	88	THR	0	-0.005	0.005	19.215	0.028	0.028	0.000	0.000	0.000	0.000
87	A	89	LEU	0	-0.066	-0.015	17.995	-0.035	-0.035	0.000	0.000	0.000	0.000
88	A	90	GLN	0	-0.003	-0.021	17.788	0.052	0.052	0.000	0.000	0.000	0.000
89	A	91	LEU	0	-0.030	-0.015	18.692	-0.027	-0.027	0.000	0.000	0.000	0.000
90	A	92	GLU	-1	-0.730	-0.815	16.140	-0.401	-0.401	0.000	0.000	0.000	0.000
91	A	93	GLU	-1	-0.949	-0.981	18.749	-0.167	-0.167	0.000	0.000	0.000	0.000
92	A	94	ALA	0	-0.034	-0.004	15.035	0.005	0.005	0.000	0.000	0.000	0.000
93	A	95	ASP	-1	-0.895	-0.948	15.054	-0.201	-0.201	0.000	0.000	0.000	0.000
94	A	96	VAL	0	-0.055	-0.040	13.461	-0.057	-0.057	0.000	0.000	0.000	0.000
95	A	97	MET	0	0.034	0.037	9.167	0.033	0.033	0.000	0.000	0.000	0.000
96	A	98	ARG	1	0.919	0.947	9.689	-0.329	-0.329	0.000	0.000	0.000	0.000
97	A	99	ASP	-1	-0.801	-0.887	5.154	1.202	1.202	0.000	0.000	0.000	0.000
98	A	100	ILE	0	0.010	0.011	3.720	-0.278	0.070	0.001	-0.084	-0.266	0.000
99	A	101	ASP	-1	-0.917	-0.973	2.344	-9.985	-6.478	2.157	-3.053	-2.611	-0.032
100	A	102	SER	0	0.036	0.029	3.278	0.975	0.999	0.013	0.214	-0.251	-0.001
101	A	103	VAL	0	0.053	0.010	5.563	-0.244	-0.244	0.000	0.000	0.000	0.000
102	A	104	GLU	-1	-0.803	-0.892	7.351	-0.675	-0.675	0.000	0.000	0.000	0.000
103	A	105	LEU	0	0.015	0.018	6.654	0.062	0.062	0.000	0.000	0.000	0.000
104	A	106	THR	0	-0.049	-0.043	5.049	-0.251	-0.209	-0.001	0.000	-0.040	0.000
105	A	107	ARG	1	0.787	0.860	6.960	0.675	0.675	0.000	0.000	0.000	0.000
106	A	108	PHE	0	-0.022	-0.012	9.857	0.112	0.112	0.000	0.000	0.000	0.000
107	A	109	ILE	0	-0.064	-0.017	6.237	0.056	0.056	0.000	0.000	0.000	0.000
108	A	110	PHE	0	0.025	0.000	9.352	0.073	0.073	0.000	0.000	0.000	0.000
109	A	111	TYR	0	-0.005	-0.006	7.206	-0.108	-0.108	0.000	0.000	0.000	0.000
110	A	112	ARG	1	0.821	0.890	12.209	0.249	0.249	0.000	0.000	0.000	0.000
111	A	113	LEU	0	-0.050	-0.025	14.551	0.015	0.015	0.000	0.000	0.000	0.000
112	A	114	ASP	-1	-0.735	-0.829	17.523	-0.164	-0.164	0.000	0.000	0.000	0.000
113	A	115	SER	0	-0.007	0.000	20.606	0.010	0.010	0.000	0.000	0.000	0.000
114	A	116	PRO	0	0.019	-0.001	23.130	0.004	0.004	0.000	0.000	0.000	0.000
115	A	117	THR	0	0.000	-0.008	25.351	0.002	0.002	0.000	0.000	0.000	0.000
116	A	118	ALA	0	0.034	0.027	27.761	0.003	0.003	0.000	0.000	0.000	0.000
117	A	119	GLY	0	0.036	0.025	25.832	0.001	0.001	0.000	0.000	0.000	0.000
118	A	120	THR	0	-0.079	-0.034	25.475	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	121	THR	0	-0.005	-0.031	19.492	0.005	0.005	0.000	0.000	0.000	0.000
120	A	122	ARG	1	0.892	0.947	19.746	0.178	0.178	0.000	0.000	0.000	0.000
121	A	123	PHE	0	0.019	-0.004	15.980	-0.009	-0.009	0.000	0.000	0.000	0.000
122	A	124	GLU	-1	-0.783	-0.871	13.978	-0.317	-0.317	0.000	0.000	0.000	0.000
123	A	125	SER	0	0.016	0.006	12.900	-0.081	-0.081	0.000	0.000	0.000	0.000
124	A	126	ALA	0	-0.027	-0.025	7.372	0.023	0.023	0.000	0.000	0.000	0.000
125	A	127	ALA	0	-0.001	0.010	9.290	-0.008	-0.008	0.000	0.000	0.000	0.000
126	A	128	PHE	0	-0.043	-0.023	10.554	0.062	0.062	0.000	0.000	0.000	0.000
127	A	129	PRO	0	0.048	0.019	10.964	0.042	0.042	0.000	0.000	0.000	0.000
128	A	130	GLY	0	-0.009	-0.007	13.659	0.034	0.034	0.000	0.000	0.000	0.000
129	A	131	TRP	0	-0.017	-0.011	16.169	0.032	0.032	0.000	0.000	0.000	0.000
130	A	132	PHE	0	-0.033	-0.027	16.529	-0.037	-0.037	0.000	0.000	0.000	0.000
131	A	133	ILE	0	0.016	0.015	16.993	0.016	0.016	0.000	0.000	0.000	0.000
132	A	134	CYS	0	-0.046	-0.006	20.356	0.013	0.013	0.000	0.000	0.000	0.000
133	A	135	THR	0	-0.012	-0.032	24.096	0.000	0.000	0.000	0.000	0.000	0.000
134	A	136	SER	0	0.085	0.043	27.537	0.004	0.004	0.000	0.000	0.000	0.000
135	A	137	LEU	0	0.003	-0.002	30.778	0.001	0.001	0.000	0.000	0.000	0.000
136	A	138	GLN	0	-0.005	0.006	33.553	0.005	0.005	0.000	0.000	0.000	0.000
137	A	139	PRO	0	0.007	-0.010	33.714	-0.006	-0.006	0.000	0.000	0.000	0.000
138	A	140	ARG	1	0.930	0.944	34.004	0.080	0.080	0.000	0.000	0.000	0.000
139	A	141	GLN	0	-0.041	0.007	31.527	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	142	PRO	0	0.058	0.016	27.713	-0.002	-0.002	0.000	0.000	0.000	0.000
141	A	143	VAL	0	-0.074	-0.032	23.054	0.001	0.001	0.000	0.000	0.000	0.000
142	A	144	GLY	0	0.030	0.014	23.368	-0.001	-0.001	0.000	0.000	0.000	0.000
143	A	145	ILE	0	-0.006	-0.017	18.097	-0.014	-0.014	0.000	0.000	0.000	0.000
144	A	146	THR	0	0.002	0.005	21.229	0.015	0.015	0.000	0.000	0.000	0.000
145	A	147	ASN	0	0.069	0.037	21.031	-0.011	-0.011	0.000	0.000	0.000	0.000
146	A	148	GLN	0	-0.008	0.003	21.989	0.017	0.017	0.000	0.000	0.000	0.000
147	A	149	PRO	0	0.007	0.009	21.735	0.007	0.007	0.000	0.000	0.000	0.000
148	A	150	ASP	-1	-0.804	-0.888	24.294	-0.137	-0.137	0.000	0.000	0.000	0.000
149	A	151	GLN	0	-0.032	0.002	27.524	0.010	0.010	0.000	0.000	0.000	0.000
150	A	152	VAL	0	-0.002	-0.013	29.597	-0.002	-0.002	0.000	0.000	0.000	0.000
151	A	153	ASN	0	-0.030	-0.025	26.369	-0.010	-0.010	0.000	0.000	0.000	0.000
152	A	154	ILE	0	-0.028	-0.006	27.362	0.005	0.005	0.000	0.000	0.000	0.000
153	A	155	ALA	0	0.014	0.012	22.554	-0.009	-0.009	0.000	0.000	0.000	0.000
154	A	156	THR	0	-0.037	-0.037	22.908	-0.012	-0.012	0.000	0.000	0.000	0.000
155	A	157	TYR	0	-0.070	-0.063	22.134	0.014	0.014	0.000	0.000	0.000	0.000
156	A	158	LYS	1	0.876	0.933	25.376	0.096	0.096	0.000	0.000	0.000	0.000
157	A	159	LEU	0	0.015	0.012	20.620	-0.002	-0.002	0.000	0.000	0.000	0.000
158	A	160	SER	0	0.023	0.012	25.188	0.011	0.011	0.000	0.000	0.000	0.000
159	A	161	GLY	0	0.000	0.018	25.360	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:ALA)