FMO DATABASE

FMODB ID: N92QQ

Calculation Name: 4J2C-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4J2C

Chain ID: A

ChEMBL ID:

UniProt ID: O43752

Base Structure: X-ray

Registration Date: 2023-06-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	108
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-805404.744301
FMO2-HF: Nuclear repulsion	761469.499404
FMO2-HF: Total energy	-43935.244898
FMO2-MP2: Total energy	-44063.351038

3D Structure Molmil

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:1:GLY)

Summations of interaction energy for fragment #1(A:1: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.
-0.518	0.296	0.001	-0.381	-0.433	0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.017

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	3	MET	0	-0.023	-0.015	3.840	-0.711	0.103	0.001	-0.381	-0.433	0.001
4	A	4	GLU	-1	-0.921	-0.953	6.517	0.183	0.183	0.000	0.000	0.000	0.000
5	A	5	ASP	-1	-0.777	-0.878	10.088	-0.393	-0.393	0.000	0.000	0.000	0.000
6	A	6	PRO	0	0.033	0.009	12.691	0.073	0.073	0.000	0.000	0.000	0.000
7	A	7	PHE	0	0.022	0.013	15.300	0.049	0.049	0.000	0.000	0.000	0.000
8	A	8	PHE	0	-0.012	-0.016	15.176	0.029	0.029	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.005	0.016	16.714	0.020	0.020	0.000	0.000	0.000	0.000
10	A	10	VAL	0	0.044	0.019	18.831	0.015	0.015	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.932	0.984	21.371	0.082	0.082	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.006	0.005	22.973	0.011	0.011	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.826	-0.895	22.896	-0.055	-0.055	0.000	0.000	0.000	0.000
14	A	14	VAL	0	0.057	0.030	25.391	0.008	0.008	0.000	0.000	0.000	0.000
15	A	15	GLN	0	-0.033	-0.028	27.429	0.005	0.005	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.788	0.889	26.507	0.061	0.061	0.000	0.000	0.000	0.000
17	A	17	ALA	0	0.042	0.026	29.548	0.005	0.005	0.000	0.000	0.000	0.000
18	A	18	VAL	0	0.016	0.001	31.364	0.003	0.003	0.000	0.000	0.000	0.000
19	A	19	ASN	0	-0.005	-0.006	33.081	0.002	0.002	0.000	0.000	0.000	0.000
20	A	20	THR	0	-0.051	-0.024	33.351	0.005	0.005	0.000	0.000	0.000	0.000
21	A	21	ALA	0	-0.004	-0.004	35.456	0.002	0.002	0.000	0.000	0.000	0.000
22	A	22	GLN	0	0.025	-0.007	37.319	0.003	0.003	0.000	0.000	0.000	0.000
23	A	23	GLY	0	0.005	0.014	38.945	0.002	0.002	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.012	-0.016	38.741	0.002	0.002	0.000	0.000	0.000	0.000
25	A	25	PHE	0	0.036	0.007	41.397	0.001	0.001	0.000	0.000	0.000	0.000
26	A	26	GLN	0	-0.067	-0.021	43.253	0.001	0.001	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.820	0.879	44.832	0.019	0.019	0.000	0.000	0.000	0.000
28	A	28	TRP	0	0.012	-0.008	45.235	0.001	0.001	0.000	0.000	0.000	0.000
29	A	29	THR	0	-0.005	-0.014	46.954	0.001	0.001	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.870	-0.920	48.592	-0.017	-0.017	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.070	-0.017	48.359	0.001	0.001	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.020	-0.024	49.861	0.001	0.001	0.000	0.000	0.000	0.000
33	A	33	GLN	0	-0.058	-0.009	53.015	0.000	0.000	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.814	-0.889	55.273	-0.013	-0.013	0.000	0.000	0.000	0.000
35	A	35	PRO	0	-0.006	-0.015	56.674	0.000	0.000	0.000	0.000	0.000	0.000
36	A	36	SER	0	-0.089	-0.045	58.405	0.000	0.000	0.000	0.000	0.000	0.000
37	A	37	THR	0	-0.061	-0.037	54.368	0.001	0.001	0.000	0.000	0.000	0.000
38	A	38	ALA	0	-0.012	-0.002	53.614	0.000	0.000	0.000	0.000	0.000	0.000
39	A	39	THR	0	-0.023	-0.006	52.920	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.858	0.889	52.193	0.022	0.022	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.861	-0.912	50.465	-0.022	-0.022	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.820	-0.894	48.247	-0.020	-0.020	0.000	0.000	0.000	0.000
43	A	43	ILE	0	0.036	0.034	47.589	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	44	ASP	-1	-0.847	-0.904	47.336	-0.029	-0.029	0.000	0.000	0.000	0.000
45	A	45	TRP	0	-0.008	0.003	40.672	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	46	THR	0	0.002	-0.010	43.093	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	47	THR	0	-0.026	-0.034	42.668	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	48	ASN	0	-0.090	-0.061	41.616	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.813	-0.905	37.299	-0.047	-0.047	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.040	0.012	37.626	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.950	0.960	37.779	0.041	0.041	0.000	0.000	0.000	0.000
52	A	52	ASN	0	-0.065	-0.033	34.409	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	53	ASN	0	-0.015	-0.017	33.289	-0.005	-0.005	0.000	0.000	0.000	0.000
54	A	54	LEU	0	0.000	-0.012	32.803	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	55	ARG	1	0.896	0.952	32.570	0.057	0.057	0.000	0.000	0.000	0.000
56	A	56	SER	0	-0.064	-0.026	27.937	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	57	ILE	0	0.006	0.000	29.091	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.824	-0.900	29.598	-0.074	-0.074	0.000	0.000	0.000	0.000
59	A	59	TRP	0	-0.010	0.010	23.848	0.003	0.003	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.832	-0.909	25.068	-0.124	-0.124	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.081	-0.052	24.972	-0.011	-0.011	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.935	-0.955	26.875	-0.111	-0.111	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.825	-0.907	21.619	-0.199	-0.199	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.021	-0.019	20.920	-0.021	-0.021	0.000	0.000	0.000	0.000
65	A	65	ASP	-1	-0.790	-0.879	22.327	-0.133	-0.133	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.902	-0.937	21.950	-0.196	-0.196	0.000	0.000	0.000	0.000
67	A	67	THR	0	-0.094	-0.066	17.936	-0.023	-0.023	0.000	0.000	0.000	0.000
68	A	68	ILE	0	-0.010	-0.008	19.162	-0.016	-0.016	0.000	0.000	0.000	0.000
69	A	69	SER	0	-0.006	-0.005	21.600	0.002	0.002	0.000	0.000	0.000	0.000
70	A	70	ILE	0	-0.032	-0.023	16.459	-0.010	-0.010	0.000	0.000	0.000	0.000
71	A	71	VAL	0	-0.046	-0.023	16.474	-0.025	-0.025	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.828	-0.911	18.430	-0.126	-0.126	0.000	0.000	0.000	0.000
73	A	73	ALA	0	-0.012	0.009	20.245	0.012	0.012	0.000	0.000	0.000	0.000
74	A	74	ASN	0	-0.079	-0.045	15.198	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	75	PRO	0	0.086	0.050	16.325	-0.041	-0.041	0.000	0.000	0.000	0.000
76	A	76	ARG	1	0.901	0.948	13.986	0.149	0.149	0.000	0.000	0.000	0.000
77	A	77	LYS	1	0.910	0.965	9.983	0.805	0.805	0.000	0.000	0.000	0.000
78	A	78	PHE	0	0.031	0.005	11.298	-0.124	-0.124	0.000	0.000	0.000	0.000
79	A	79	ASN	0	-0.094	-0.042	13.531	0.041	0.041	0.000	0.000	0.000	0.000
80	A	80	LEU	0	0.051	0.044	15.229	0.038	0.038	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.804	-0.889	17.742	-0.030	-0.030	0.000	0.000	0.000	0.000
82	A	82	ALA	0	0.025	0.015	21.052	-0.014	-0.014	0.000	0.000	0.000	0.000
83	A	83	THR	0	-0.016	-0.016	24.121	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.847	-0.899	19.458	-0.122	-0.122	0.000	0.000	0.000	0.000
85	A	85	LEU	0	0.038	0.026	20.830	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	86	SER	0	-0.019	-0.031	23.057	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	87	ILE	0	-0.042	-0.022	25.595	0.002	0.002	0.000	0.000	0.000	0.000
88	A	88	ARG	1	0.695	0.817	16.895	0.188	0.188	0.000	0.000	0.000	0.000
89	A	89	LYS	1	0.885	0.917	24.817	0.118	0.118	0.000	0.000	0.000	0.000
90	A	90	ALA	0	-0.013	0.008	27.514	0.004	0.004	0.000	0.000	0.000	0.000
91	A	91	PHE	0	0.012	0.012	25.606	0.006	0.006	0.000	0.000	0.000	0.000
92	A	92	ILE	0	0.050	0.044	24.516	0.005	0.005	0.000	0.000	0.000	0.000
93	A	93	THR	0	-0.037	-0.029	28.885	0.004	0.004	0.000	0.000	0.000	0.000
94	A	94	SER	0	-0.050	-0.044	32.145	0.004	0.004	0.000	0.000	0.000	0.000
95	A	95	THR	0	-0.019	-0.024	30.504	0.005	0.005	0.000	0.000	0.000	0.000
96	A	96	ARG	1	0.818	0.877	28.767	0.107	0.107	0.000	0.000	0.000	0.000
97	A	97	GLN	0	-0.057	-0.030	33.898	0.000	0.000	0.000	0.000	0.000	0.000
98	A	98	VAL	0	0.016	0.009	35.653	0.003	0.003	0.000	0.000	0.000	0.000
99	A	99	VAL	0	-0.006	-0.007	33.603	0.003	0.003	0.000	0.000	0.000	0.000
100	A	100	ARG	1	0.860	0.929	36.906	0.053	0.053	0.000	0.000	0.000	0.000
101	A	101	ASP	-1	-0.846	-0.909	39.507	-0.039	-0.039	0.000	0.000	0.000	0.000
102	A	102	MET	0	-0.031	-0.005	37.081	0.003	0.003	0.000	0.000	0.000	0.000
103	A	103	LYS	1	0.826	0.889	37.283	0.064	0.064	0.000	0.000	0.000	0.000
104	A	104	ASP	-1	-0.844	-0.909	42.116	-0.044	-0.044	0.000	0.000	0.000	0.000
105	A	105	GLN	0	-0.050	-0.032	45.008	0.002	0.002	0.000	0.000	0.000	0.000
106	A	106	MET	0	-0.066	-0.017	43.145	0.001	0.001	0.000	0.000	0.000	0.000
107	A	107	SER	0	-0.070	-0.037	44.480	0.001	0.001	0.000	0.000	0.000	0.000
108	A	108	THR	0	-0.116	-0.049	47.158	0.002	0.002	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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