FMO DATABASE

FMODB ID: 39M9L

Calculation Name: 4J4F-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4J4F

Chain ID: A

ChEMBL ID:

UniProt ID: P81180

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:

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	99
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-567412.968779
FMO2-HF: Nuclear repulsion	528188.108361
FMO2-HF: Total energy	-39224.860418
FMO2-MP2: Total energy	-39336.953658

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:1:LEU)

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

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.
-22.189	-23.011	8.295	-3.564	-3.909	0.031

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.051 / 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	3	LYS	1	0.899	0.930	2.142	-22.727	-23.643	8.296	-3.561	-3.819	0.031
4	A	4	PHE	0	0.076	0.040	6.373	0.071	0.071	0.000	0.000	0.000	0.000
5	A	5	SER	0	0.014	0.008	9.050	0.054	0.054	0.000	0.000	0.000	0.000
6	A	6	GLN	0	-0.027	-0.017	7.451	0.394	0.394	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.016	0.013	10.135	-0.027	-0.027	0.000	0.000	0.000	0.000
8	A	8	CYS	0	-0.116	-0.042	12.439	-0.070	-0.070	0.000	0.000	0.000	0.000
9	A	9	TYR	0	0.036	0.022	14.803	0.044	0.044	0.000	0.000	0.000	0.000
10	A	10	ASN	0	0.002	-0.016	18.169	-0.014	-0.014	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.046	-0.020	15.871	-0.004	-0.004	0.000	0.000	0.000	0.000
12	A	12	ALA	0	0.002	0.007	18.012	0.023	0.023	0.000	0.000	0.000	0.000
13	A	13	ILE	0	0.010	-0.009	15.804	-0.024	-0.024	0.000	0.000	0.000	0.000
14	A	14	GLN	0	0.034	0.022	19.594	0.019	0.019	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.006	0.003	21.744	-0.014	-0.014	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.032	-0.032	18.338	0.015	0.015	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.010	-0.004	17.265	-0.027	-0.027	0.000	0.000	0.000	0.000
18	A	18	LEU	0	0.002	0.018	12.341	0.025	0.025	0.000	0.000	0.000	0.000
19	A	19	THR	0	0.003	-0.003	16.428	-0.029	-0.029	0.000	0.000	0.000	0.000
20	A	20	SER	0	0.023	0.010	14.405	0.044	0.044	0.000	0.000	0.000	0.000
21	A	21	THR	0	-0.007	0.004	16.955	-0.023	-0.023	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.830	-0.904	14.332	0.001	0.001	0.000	0.000	0.000	0.000
23	A	24	ARG	1	0.868	0.934	14.446	0.104	0.104	0.000	0.000	0.000	0.000
24	A	25	THR	0	0.010	-0.018	13.317	0.017	0.017	0.000	0.000	0.000	0.000
25	A	26	ASN	0	-0.042	-0.005	15.734	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	27	GLY	0	0.055	0.044	18.589	0.015	0.015	0.000	0.000	0.000	0.000
27	A	28	GLY	0	-0.010	-0.005	20.293	-0.013	-0.013	0.000	0.000	0.000	0.000
28	A	29	TYR	0	-0.032	-0.052	17.325	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	30	ASN	0	-0.019	-0.020	17.352	0.000	0.000	0.000	0.000	0.000	0.000
30	A	31	THR	0	0.015	0.018	17.678	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	32	SER	0	-0.060	-0.005	15.469	-0.025	-0.025	0.000	0.000	0.000	0.000
32	A	33	SER	0	0.043	-0.013	17.012	0.019	0.019	0.000	0.000	0.000	0.000
33	A	34	ILE	0	-0.020	-0.010	11.072	-0.031	-0.031	0.000	0.000	0.000	0.000
34	A	35	ASP	-1	-0.790	-0.877	15.309	-0.154	-0.154	0.000	0.000	0.000	0.000
35	A	36	LEU	0	0.003	-0.010	11.864	-0.039	-0.039	0.000	0.000	0.000	0.000
36	A	37	ASN	0	-0.007	-0.007	14.591	0.005	0.005	0.000	0.000	0.000	0.000
37	A	38	SER	0	-0.028	0.005	15.054	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	39	VAL	0	-0.039	-0.024	10.374	-0.033	-0.033	0.000	0.000	0.000	0.000
39	A	40	ILE	0	-0.053	-0.023	11.067	-0.012	-0.012	0.000	0.000	0.000	0.000
40	A	41	GLU	-1	-0.834	-0.908	13.725	-0.122	-0.122	0.000	0.000	0.000	0.000
41	A	42	ASN	0	-0.030	-0.036	16.705	0.029	0.029	0.000	0.000	0.000	0.000
42	A	43	VAL	0	0.023	0.017	17.187	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	44	ASP	-1	-0.902	-0.956	19.984	0.011	0.011	0.000	0.000	0.000	0.000
44	A	45	GLY	0	-0.008	0.009	22.806	0.009	0.009	0.000	0.000	0.000	0.000
45	A	46	SER	0	-0.029	-0.012	18.950	0.016	0.016	0.000	0.000	0.000	0.000
46	A	47	LEU	0	0.019	0.008	15.758	-0.011	-0.011	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.844	0.920	13.386	-0.019	-0.019	0.000	0.000	0.000	0.000
48	A	49	TRP	0	-0.022	-0.012	8.007	-0.098	-0.098	0.000	0.000	0.000	0.000
49	A	50	GLN	0	-0.027	-0.007	10.708	0.023	0.023	0.000	0.000	0.000	0.000
50	A	51	GLY	0	-0.023	-0.002	10.385	-0.051	-0.051	0.000	0.000	0.000	0.000
51	A	52	SER	0	-0.015	-0.016	12.220	-0.052	-0.052	0.000	0.000	0.000	0.000
52	A	53	ASN	0	0.004	-0.009	14.175	0.034	0.034	0.000	0.000	0.000	0.000
53	A	54	PHE	0	0.064	0.015	17.831	-0.009	-0.009	0.000	0.000	0.000	0.000
54	A	55	ILE	0	-0.016	-0.010	19.020	0.001	0.001	0.000	0.000	0.000	0.000
55	A	56	GLU	-1	-0.884	-0.924	17.556	-0.215	-0.215	0.000	0.000	0.000	0.000
56	A	57	THR	0	-0.069	-0.043	13.587	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	58	CYS	0	-0.066	-0.026	16.066	-0.009	-0.009	0.000	0.000	0.000	0.000
58	A	59	ARG	1	0.876	0.926	19.077	0.101	0.101	0.000	0.000	0.000	0.000
59	A	60	ASN	0	-0.039	-0.046	22.353	0.002	0.002	0.000	0.000	0.000	0.000
60	A	61	THR	0	-0.008	0.012	23.494	0.004	0.004	0.000	0.000	0.000	0.000
61	A	62	GLN	0	-0.055	-0.030	25.834	0.005	0.005	0.000	0.000	0.000	0.000
62	A	63	LEU	0	0.020	0.017	28.581	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	64	ALA	0	-0.019	-0.013	30.000	0.001	0.001	0.000	0.000	0.000	0.000
64	A	65	GLY	0	0.017	0.004	31.880	0.002	0.002	0.000	0.000	0.000	0.000
65	A	66	SER	0	-0.018	-0.017	34.858	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	67	SER	0	-0.003	-0.020	32.891	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.809	-0.878	28.506	-0.013	-0.013	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.001	0.014	24.478	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	70	ALA	0	-0.003	-0.013	25.185	0.003	0.003	0.000	0.000	0.000	0.000
70	A	71	ALA	0	0.024	0.007	21.765	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	72	GLU	-1	-0.808	-0.870	20.472	-0.067	-0.067	0.000	0.000	0.000	0.000
72	A	74	LYS	1	0.825	0.913	11.916	0.308	0.308	0.000	0.000	0.000	0.000
73	A	75	THR	0	0.002	-0.005	10.582	-0.025	-0.025	0.000	0.000	0.000	0.000
74	A	76	ARG	1	0.999	0.978	4.513	0.440	0.534	-0.001	-0.003	-0.090	0.000
75	A	77	ALA	0	-0.009	0.000	7.086	-0.150	-0.150	0.000	0.000	0.000	0.000
76	A	78	GLN	0	0.014	0.014	8.206	0.112	0.112	0.000	0.000	0.000	0.000
77	A	79	GLN	0	0.064	0.043	11.264	0.026	0.026	0.000	0.000	0.000	0.000
78	A	80	PHE	0	-0.001	0.003	13.871	-0.016	-0.016	0.000	0.000	0.000	0.000
79	A	81	VAL	0	-0.005	-0.001	15.534	0.017	0.017	0.000	0.000	0.000	0.000
80	A	82	SER	0	0.019	0.005	17.936	-0.007	-0.007	0.000	0.000	0.000	0.000
81	A	83	THR	0	-0.051	-0.025	18.728	0.013	0.013	0.000	0.000	0.000	0.000
82	A	84	LYS	1	0.839	0.891	21.141	0.010	0.010	0.000	0.000	0.000	0.000
83	A	85	ILE	0	-0.001	0.013	22.033	0.003	0.003	0.000	0.000	0.000	0.000
84	A	86	ASN	0	0.007	-0.011	24.707	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	87	LEU	0	0.002	-0.002	27.698	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	88	ASP	-1	-0.822	-0.898	29.734	-0.016	-0.016	0.000	0.000	0.000	0.000
87	A	89	ASP	-1	-0.908	-0.929	27.169	-0.005	-0.005	0.000	0.000	0.000	0.000
88	A	90	HIS	1	0.842	0.911	26.303	0.021	0.021	0.000	0.000	0.000	0.000
89	A	91	ILE	0	-0.027	0.010	28.965	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	92	ALA	0	0.041	0.025	32.242	0.003	0.003	0.000	0.000	0.000	0.000
91	A	93	ASN	0	-0.002	-0.008	35.996	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	94	ILE	0	-0.021	-0.016	38.144	0.003	0.003	0.000	0.000	0.000	0.000
93	A	95	ASP	-1	-0.919	-0.964	40.939	-0.020	-0.020	0.000	0.000	0.000	0.000
94	A	96	GLY	0	-0.001	0.009	43.191	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	97	THR	0	-0.056	-0.022	38.395	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	98	LEU	0	-0.020	-0.006	35.189	0.001	0.001	0.000	0.000	0.000	0.000
97	A	99	LYS	1	0.828	0.891	34.257	0.028	0.028	0.000	0.000	0.000	0.000
98	A	100	TYR	0	0.013	0.010	26.575	0.002	0.002	0.000	0.000	0.000	0.000
99	A	101	GLU	-1	-0.872	-0.927	30.433	-0.026	-0.026	0.000	0.000	0.000	0.000

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