FMO DATABASE

FMODB ID: 2293R

Calculation Name: 3JRZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3JRZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q84B82

Base Structure: X-ray

Registration Date: 2023-06-19

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	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	104
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-805925.39606
FMO2-HF: Nuclear repulsion	764996.958586
FMO2-HF: Total energy	-40928.437474
FMO2-MP2: Total energy	-41048.508538

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:2:SER)

Summations of interaction energy for fragment #1(A:2:SER)

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.
-15.138	-6.59	4.123	-5.942	-6.728	-0.043

Interaction energy analysis for fragmet #1(A:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : 0.001

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

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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	4	PHE	0	-0.044	-0.045	3.721	-0.592	1.416	0.011	-0.908	-1.111	0.004
4	A	5	THR	0	-0.013	-0.007	2.110	2.417	4.858	1.529	-1.732	-2.237	-0.016
5	A	6	LEU	0	-0.033	-0.021	4.493	0.112	0.195	-0.001	-0.026	-0.056	0.000
6	A	7	TYR	0	0.019	-0.008	3.446	-1.097	-0.677	0.020	-0.165	-0.276	-0.001
7	A	8	LYS	1	0.855	0.927	8.962	0.424	0.424	0.000	0.000	0.000	0.000
8	A	9	ASN	0	-0.034	-0.021	12.647	0.019	0.019	0.000	0.000	0.000	0.000
9	A	10	LYS	1	0.841	0.888	13.900	0.479	0.479	0.000	0.000	0.000	0.000
10	A	11	ASP	-1	-0.854	-0.888	17.053	-0.406	-0.406	0.000	0.000	0.000	0.000
11	A	12	LYS	1	0.950	0.952	19.102	0.279	0.279	0.000	0.000	0.000	0.000
12	A	13	SER	0	-0.054	-0.021	22.478	0.025	0.025	0.000	0.000	0.000	0.000
13	A	14	SER	0	-0.008	-0.034	19.480	-0.010	-0.010	0.000	0.000	0.000	0.000
14	A	15	ALA	0	0.011	0.021	18.842	-0.018	-0.018	0.000	0.000	0.000	0.000
15	A	16	LYS	1	0.951	0.962	19.844	0.263	0.263	0.000	0.000	0.000	0.000
16	A	17	THR	0	-0.009	0.003	22.063	0.030	0.030	0.000	0.000	0.000	0.000
17	A	18	TYR	0	-0.021	-0.004	17.165	-0.011	-0.011	0.000	0.000	0.000	0.000
18	A	19	PRO	0	0.042	0.034	17.037	-0.051	-0.051	0.000	0.000	0.000	0.000
19	A	20	TYR	0	0.035	0.013	12.154	0.047	0.047	0.000	0.000	0.000	0.000
20	A	21	PHE	0	-0.029	-0.002	10.427	0.101	0.101	0.000	0.000	0.000	0.000
21	A	22	VAL	0	0.017	0.014	7.744	-0.171	-0.171	0.000	0.000	0.000	0.000
22	A	23	ASP	-1	-0.838	-0.920	3.961	-6.990	-6.741	0.000	-0.067	-0.183	0.000
23	A	24	VAL	0	0.018	-0.001	6.745	-0.582	-0.582	0.000	0.000	0.000	0.000
24	A	25	GLN	0	-0.009	0.012	7.288	0.827	0.827	0.000	0.000	0.000	0.000
25	A	26	SER	0	0.008	0.008	5.926	-0.810	-0.810	0.000	0.000	0.000	0.000
26	A	27	ASP	-1	-0.680	-0.845	2.428	-10.758	-7.677	2.567	-3.026	-2.621	-0.030
27	A	28	LEU	0	-0.072	-0.033	5.195	0.683	0.714	-0.001	-0.002	-0.027	0.000
28	A	29	LEU	0	-0.068	-0.041	8.091	0.265	0.265	0.000	0.000	0.000	0.000
29	A	30	ASP	-1	-0.842	-0.919	4.513	-2.109	-1.913	-0.001	-0.016	-0.179	0.000
30	A	31	ASN	0	-0.104	-0.052	7.576	0.130	0.130	0.000	0.000	0.000	0.000
31	A	32	LEU	0	0.004	0.025	10.691	0.089	0.089	0.000	0.000	0.000	0.000
32	A	33	ASN	0	-0.013	-0.020	10.313	-0.072	-0.072	0.000	0.000	0.000	0.000
33	A	34	THR	0	-0.026	-0.013	11.417	0.048	0.048	0.000	0.000	0.000	0.000
34	A	35	ARG	1	0.862	0.935	4.619	2.694	2.733	-0.001	0.000	-0.038	0.000
35	A	36	LEU	0	0.012	0.010	9.046	0.242	0.242	0.000	0.000	0.000	0.000
36	A	37	VAL	0	0.009	0.003	8.596	-0.496	-0.496	0.000	0.000	0.000	0.000
37	A	38	ILE	0	0.008	0.000	10.926	0.340	0.340	0.000	0.000	0.000	0.000
38	A	39	PRO	0	-0.009	0.012	12.735	-0.121	-0.121	0.000	0.000	0.000	0.000
39	A	40	LEU	0	0.010	0.004	12.946	0.036	0.036	0.000	0.000	0.000	0.000
40	A	41	THR	0	-0.044	-0.039	16.239	0.055	0.055	0.000	0.000	0.000	0.000
41	A	42	PRO	0	0.046	0.021	19.824	-0.006	-0.006	0.000	0.000	0.000	0.000
42	A	43	ILE	0	0.046	0.020	21.809	0.007	0.007	0.000	0.000	0.000	0.000
43	A	44	GLU	-1	-0.917	-0.966	23.875	-0.278	-0.278	0.000	0.000	0.000	0.000
44	A	45	LEU	0	-0.081	-0.035	23.728	0.021	0.021	0.000	0.000	0.000	0.000
45	A	46	LEU	0	-0.063	-0.022	23.205	0.004	0.004	0.000	0.000	0.000	0.000
46	A	47	ASP	-1	-0.776	-0.861	26.924	-0.214	-0.214	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.791	0.874	30.223	0.232	0.232	0.000	0.000	0.000	0.000
48	A	49	LYS	1	0.850	0.907	24.771	0.356	0.356	0.000	0.000	0.000	0.000
49	A	50	ALA	0	0.046	0.036	27.822	0.014	0.014	0.000	0.000	0.000	0.000
50	A	51	PRO	0	0.008	0.004	24.182	-0.030	-0.030	0.000	0.000	0.000	0.000
51	A	52	SER	0	-0.053	-0.061	20.980	0.024	0.024	0.000	0.000	0.000	0.000
52	A	53	HIS	0	-0.024	0.008	22.815	0.008	0.008	0.000	0.000	0.000	0.000
53	A	54	LEU	0	0.064	0.028	21.594	-0.035	-0.035	0.000	0.000	0.000	0.000
54	A	55	CYS	0	-0.049	-0.008	20.203	-0.057	-0.057	0.000	0.000	0.000	0.000
55	A	56	PRO	0	0.063	0.042	16.954	0.065	0.065	0.000	0.000	0.000	0.000
56	A	57	THR	0	-0.013	-0.007	19.242	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	58	ILE	0	-0.024	0.000	14.168	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	59	HIS	1	0.820	0.876	17.180	0.378	0.378	0.000	0.000	0.000	0.000
59	A	60	ILE	0	-0.019	0.001	13.082	-0.008	-0.008	0.000	0.000	0.000	0.000
60	A	61	ASP	-1	-0.862	-0.925	15.869	-0.074	-0.074	0.000	0.000	0.000	0.000
61	A	62	GLU	-1	-0.889	-0.949	14.127	-0.399	-0.399	0.000	0.000	0.000	0.000
62	A	63	GLY	0	-0.016	-0.014	17.418	0.006	0.006	0.000	0.000	0.000	0.000
63	A	64	ASP	-1	-0.855	-0.897	18.875	-0.327	-0.327	0.000	0.000	0.000	0.000
64	A	65	PHE	0	-0.023	-0.020	17.152	-0.010	-0.010	0.000	0.000	0.000	0.000
65	A	66	ILE	0	0.006	0.003	19.437	0.007	0.007	0.000	0.000	0.000	0.000
66	A	67	MET	0	0.010	0.009	13.291	-0.073	-0.073	0.000	0.000	0.000	0.000
67	A	68	LEU	0	-0.022	-0.018	17.364	0.068	0.068	0.000	0.000	0.000	0.000
68	A	69	THR	0	0.038	-0.020	17.134	-0.076	-0.076	0.000	0.000	0.000	0.000
69	A	70	GLN	0	0.039	0.010	18.210	-0.073	-0.073	0.000	0.000	0.000	0.000
70	A	71	GLN	0	-0.088	-0.041	19.069	0.031	0.031	0.000	0.000	0.000	0.000
71	A	72	MET	0	-0.029	0.007	14.071	-0.090	-0.090	0.000	0.000	0.000	0.000
72	A	73	THR	0	-0.010	-0.005	14.653	0.125	0.125	0.000	0.000	0.000	0.000
73	A	74	SER	0	0.005	0.015	13.124	-0.238	-0.238	0.000	0.000	0.000	0.000
74	A	75	VAL	0	0.010	0.006	10.814	0.182	0.182	0.000	0.000	0.000	0.000
75	A	76	PRO	0	0.022	-0.002	11.741	-0.121	-0.121	0.000	0.000	0.000	0.000
76	A	77	VAL	0	0.058	0.018	6.944	0.015	0.015	0.000	0.000	0.000	0.000
77	A	78	LYS	1	0.900	0.943	9.316	0.447	0.447	0.000	0.000	0.000	0.000
78	A	79	ILE	0	-0.032	-0.014	10.999	0.114	0.114	0.000	0.000	0.000	0.000
79	A	80	LEU	0	-0.009	0.027	6.352	0.052	0.052	0.000	0.000	0.000	0.000
80	A	81	SER	0	-0.004	-0.008	9.252	0.262	0.262	0.000	0.000	0.000	0.000
81	A	82	GLU	-1	-0.810	-0.893	10.260	-0.364	-0.364	0.000	0.000	0.000	0.000
82	A	83	PRO	0	0.020	0.012	5.982	-0.197	-0.197	0.000	0.000	0.000	0.000
83	A	84	VAL	0	-0.033	-0.020	7.821	0.286	0.286	0.000	0.000	0.000	0.000
84	A	85	ASN	0	0.040	0.023	8.835	0.222	0.222	0.000	0.000	0.000	0.000
85	A	86	GLU	-1	-0.839	-0.895	5.211	-1.254	-1.254	0.000	0.000	0.000	0.000
86	A	87	LEU	0	0.002	-0.002	7.120	0.477	0.477	0.000	0.000	0.000	0.000
87	A	88	SER	0	-0.032	-0.029	6.337	0.150	0.150	0.000	0.000	0.000	0.000
88	A	89	THR	0	-0.075	-0.043	8.288	0.162	0.162	0.000	0.000	0.000	0.000
89	A	90	PHE	0	0.029	0.004	11.398	0.094	0.094	0.000	0.000	0.000	0.000
90	A	91	ARG	1	0.977	0.994	9.798	0.393	0.393	0.000	0.000	0.000	0.000
91	A	92	ASN	0	-0.014	-0.016	11.722	-0.059	-0.059	0.000	0.000	0.000	0.000
92	A	93	GLU	-1	-0.833	-0.895	15.168	-0.533	-0.533	0.000	0.000	0.000	0.000
93	A	94	ILE	0	0.002	-0.001	11.026	-0.007	-0.007	0.000	0.000	0.000	0.000
94	A	95	ILE	0	-0.013	-0.016	11.256	-0.011	-0.011	0.000	0.000	0.000	0.000
95	A	96	ALA	0	0.017	0.011	14.866	0.058	0.058	0.000	0.000	0.000	0.000
96	A	97	ALA	0	0.008	0.018	17.579	0.051	0.051	0.000	0.000	0.000	0.000
97	A	98	ILE	0	-0.036	-0.030	13.331	0.021	0.021	0.000	0.000	0.000	0.000
98	A	99	ASP	-1	-0.901	-0.949	17.855	-0.441	-0.441	0.000	0.000	0.000	0.000
99	A	100	PHE	0	-0.009	0.012	20.158	0.057	0.057	0.000	0.000	0.000	0.000
100	A	101	LEU	0	-0.075	-0.038	19.599	0.040	0.040	0.000	0.000	0.000	0.000
101	A	102	ILE	0	-0.083	-0.042	18.871	0.028	0.028	0.000	0.000	0.000	0.000
102	A	103	THR	0	-0.054	-0.041	22.784	0.047	0.047	0.000	0.000	0.000	0.000
103	A	104	GLY	0	-0.021	0.022	25.195	0.038	0.038	0.000	0.000	0.000	0.000
104	A	105	ILE	0	-0.016	-0.021	26.320	-0.004	-0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)