FMO DATABASE

FMODB ID: QY7RY

Calculation Name: 4P4H-I-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4P4H

Chain ID: I

ChEMBL ID:

UniProt ID: O95786

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	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	97
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-770664.514007
FMO2-HF: Nuclear repulsion	730342.770798
FMO2-HF: Total energy	-40321.743209
FMO2-MP2: Total energy	-40437.044735

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(I:1:MET)

Summations of interaction energy for fragment #1(I:1:MET)

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.
-16.046	-8.254	2.948	-3.522	-7.218	-0.022

Interaction energy analysis for fragmet #1(I:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : -0.021

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	I	3	PHE	0	0.014	0.012	3.526	-3.234	-0.036	0.297	-1.422	-2.073	0.000
4	I	4	ALA	0	0.030	0.009	3.737	-2.448	-1.747	0.097	-0.204	-0.594	0.002
5	I	5	GLU	-1	-0.856	-0.931	4.589	-0.369	-0.074	-0.001	-0.038	-0.256	0.000
6	I	6	ASP	-1	-0.843	-0.915	6.882	0.631	0.631	0.000	0.000	0.000	0.000
7	I	7	LYS	1	0.826	0.913	8.418	-0.743	-0.743	0.000	0.000	0.000	0.000
8	I	8	THR	0	0.011	0.009	8.158	-0.205	-0.205	0.000	0.000	0.000	0.000
9	I	9	TYR	0	0.070	0.033	10.730	-0.070	-0.070	0.000	0.000	0.000	0.000
10	I	10	LYS	1	0.968	0.974	13.139	-0.346	-0.346	0.000	0.000	0.000	0.000
11	I	11	TYR	0	-0.102	-0.055	13.706	-0.030	-0.030	0.000	0.000	0.000	0.000
12	I	12	ILE	0	0.008	0.012	13.408	-0.023	-0.023	0.000	0.000	0.000	0.000
13	I	13	CYS	0	-0.051	-0.019	16.665	-0.014	-0.014	0.000	0.000	0.000	0.000
14	I	14	ARG	1	0.892	0.950	15.533	-0.134	-0.134	0.000	0.000	0.000	0.000
15	I	15	ASN	0	0.033	0.011	18.977	-0.002	-0.002	0.000	0.000	0.000	0.000
16	I	16	PHE	0	0.044	0.038	20.724	-0.012	-0.012	0.000	0.000	0.000	0.000
17	I	17	SER	0	-0.020	-0.032	21.602	-0.002	-0.002	0.000	0.000	0.000	0.000
18	I	18	ASN	0	-0.011	-0.006	20.821	0.001	0.001	0.000	0.000	0.000	0.000
19	I	19	PHE	0	0.025	0.012	16.431	-0.006	-0.006	0.000	0.000	0.000	0.000
20	I	20	CYS	0	-0.055	-0.032	21.858	0.002	0.002	0.000	0.000	0.000	0.000
21	I	21	ASN	0	0.024	-0.006	24.873	0.001	0.001	0.000	0.000	0.000	0.000
22	I	22	VAL	0	0.002	0.023	20.396	-0.003	-0.003	0.000	0.000	0.000	0.000
23	I	23	LYS	1	0.927	0.952	23.671	-0.015	-0.015	0.000	0.000	0.000	0.000
24	I	24	VAL	0	0.059	0.013	23.138	0.000	0.000	0.000	0.000	0.000	0.000
25	I	25	VAL	0	0.034	0.004	24.211	0.003	0.003	0.000	0.000	0.000	0.000
26	I	26	LYS	1	0.911	0.954	25.828	-0.014	-0.014	0.000	0.000	0.000	0.000
27	I	27	ILE	0	0.056	0.026	18.267	-0.003	-0.003	0.000	0.000	0.000	0.000
28	I	28	LEU	0	-0.024	-0.006	20.513	0.007	0.007	0.000	0.000	0.000	0.000
29	I	29	PRO	0	-0.048	-0.021	20.464	0.010	0.010	0.000	0.000	0.000	0.000
30	I	30	TYR	0	-0.037	-0.006	19.335	-0.001	-0.001	0.000	0.000	0.000	0.000
31	I	31	LEU	0	-0.004	0.008	15.139	0.008	0.008	0.000	0.000	0.000	0.000
32	I	32	PRO	0	0.030	0.011	14.683	0.006	0.006	0.000	0.000	0.000	0.000
33	I	33	CYS	0	0.006	0.016	11.848	-0.002	-0.002	0.000	0.000	0.000	0.000
34	I	34	LEU	0	-0.069	-0.021	13.733	0.006	0.006	0.000	0.000	0.000	0.000
35	I	35	THR	0	0.012	0.017	16.528	-0.020	-0.020	0.000	0.000	0.000	0.000
36	I	36	ALA	0	0.079	0.026	18.580	-0.006	-0.006	0.000	0.000	0.000	0.000
37	I	37	ARG	1	0.987	0.995	21.542	-0.110	-0.110	0.000	0.000	0.000	0.000
38	I	38	ASP	-1	-0.765	-0.894	17.488	0.163	0.163	0.000	0.000	0.000	0.000
39	I	39	GLN	0	0.027	0.001	19.926	-0.016	-0.016	0.000	0.000	0.000	0.000
40	I	40	ASP	-1	-0.919	-0.951	22.865	0.070	0.070	0.000	0.000	0.000	0.000
41	I	41	ARG	1	0.893	0.931	20.074	-0.138	-0.138	0.000	0.000	0.000	0.000
42	I	42	LEU	0	-0.021	-0.022	20.183	-0.004	-0.004	0.000	0.000	0.000	0.000
43	I	43	ARG	1	0.912	0.964	24.221	-0.070	-0.070	0.000	0.000	0.000	0.000
44	I	44	ALA	0	0.049	0.033	27.337	-0.005	-0.005	0.000	0.000	0.000	0.000
45	I	45	THR	0	-0.040	-0.020	26.835	-0.002	-0.002	0.000	0.000	0.000	0.000
46	I	46	CYS	0	-0.072	-0.039	27.388	-0.004	-0.004	0.000	0.000	0.000	0.000
47	I	47	THR	0	-0.069	-0.013	29.278	-0.006	-0.006	0.000	0.000	0.000	0.000
48	I	48	LEU	0	-0.002	-0.026	32.739	-0.001	-0.001	0.000	0.000	0.000	0.000
49	I	49	SER	0	0.010	0.019	30.619	-0.001	-0.001	0.000	0.000	0.000	0.000
50	I	50	GLY	0	0.059	0.060	32.344	-0.001	-0.001	0.000	0.000	0.000	0.000
51	I	51	ASN	0	0.020	-0.005	26.485	0.006	0.006	0.000	0.000	0.000	0.000
52	I	52	ARG	1	0.907	0.950	26.854	-0.034	-0.034	0.000	0.000	0.000	0.000
53	I	53	ASP	-1	-0.834	-0.901	27.226	0.059	0.059	0.000	0.000	0.000	0.000
54	I	54	THR	0	0.002	-0.011	24.665	0.008	0.008	0.000	0.000	0.000	0.000
55	I	55	LEU	0	-0.068	-0.022	22.357	0.010	0.010	0.000	0.000	0.000	0.000
56	I	56	TRP	0	0.040	0.014	21.563	0.012	0.012	0.000	0.000	0.000	0.000
57	I	57	HIS	0	0.027	0.015	21.217	0.022	0.022	0.000	0.000	0.000	0.000
58	I	58	LEU	0	-0.011	-0.006	18.860	0.013	0.013	0.000	0.000	0.000	0.000
59	I	59	PHE	0	0.024	-0.003	16.813	0.014	0.014	0.000	0.000	0.000	0.000
60	I	60	ASN	0	0.019	0.033	15.997	0.025	0.025	0.000	0.000	0.000	0.000
61	I	61	THR	0	-0.026	-0.008	16.752	0.016	0.016	0.000	0.000	0.000	0.000
62	I	62	LEU	0	0.028	0.008	13.470	0.013	0.013	0.000	0.000	0.000	0.000
63	I	63	GLN	0	-0.032	0.005	11.392	0.056	0.056	0.000	0.000	0.000	0.000
64	I	64	ARG	1	0.867	0.922	11.025	-0.192	-0.192	0.000	0.000	0.000	0.000
65	I	65	ARG	1	0.770	0.877	11.115	-0.208	-0.208	0.000	0.000	0.000	0.000
66	I	66	PRO	0	0.033	0.011	6.709	0.008	0.008	0.000	0.000	0.000	0.000
67	I	67	GLY	0	0.073	0.034	5.418	0.011	0.011	0.000	0.000	0.000	0.000
68	I	68	TRP	0	-0.013	0.009	6.298	-0.165	-0.165	0.000	0.000	0.000	0.000
69	I	69	VAL	0	0.041	0.022	6.760	-0.069	-0.069	0.000	0.000	0.000	0.000
70	I	70	GLU	-1	-0.852	-0.938	6.016	-0.356	-0.356	0.000	0.000	0.000	0.000
71	I	71	TYR	0	-0.017	-0.020	8.832	-0.105	-0.105	0.000	0.000	0.000	0.000
72	I	72	PHE	0	-0.034	-0.024	11.492	-0.052	-0.052	0.000	0.000	0.000	0.000
73	I	73	ILE	0	0.062	0.033	10.153	-0.028	-0.028	0.000	0.000	0.000	0.000
74	I	74	ALA	0	-0.041	-0.041	13.533	-0.009	-0.009	0.000	0.000	0.000	0.000
75	I	75	ALA	0	0.049	0.059	15.582	0.005	0.005	0.000	0.000	0.000	0.000
76	I	76	LEU	0	-0.038	-0.025	16.023	-0.011	-0.011	0.000	0.000	0.000	0.000
77	I	77	ARG	1	0.878	0.919	14.655	0.139	0.139	0.000	0.000	0.000	0.000
78	I	78	GLY	0	0.040	0.038	19.478	-0.004	-0.004	0.000	0.000	0.000	0.000
79	I	79	CYS	0	-0.102	-0.048	21.450	0.005	0.005	0.000	0.000	0.000	0.000
80	I	80	LYS	1	0.908	0.942	22.870	0.022	0.022	0.000	0.000	0.000	0.000
81	I	81	LEU	0	-0.003	-0.008	21.173	0.001	0.001	0.000	0.000	0.000	0.000
82	I	82	VAL	0	-0.013	-0.016	20.227	0.000	0.000	0.000	0.000	0.000	0.000
83	I	83	ASP	-1	-0.825	-0.896	19.981	-0.077	-0.077	0.000	0.000	0.000	0.000
84	I	84	LEU	0	0.012	0.012	18.592	-0.008	-0.008	0.000	0.000	0.000	0.000
85	I	85	ALA	0	-0.066	-0.041	16.415	-0.004	-0.004	0.000	0.000	0.000	0.000
86	I	86	ASP	-1	-0.823	-0.900	15.153	-0.168	-0.168	0.000	0.000	0.000	0.000
87	I	87	GLU	-1	-0.842	-0.901	15.581	-0.055	-0.055	0.000	0.000	0.000	0.000
88	I	88	VAL	0	-0.060	-0.051	11.598	-0.006	-0.006	0.000	0.000	0.000	0.000
89	I	89	ALA	0	0.011	-0.005	10.995	-0.022	-0.022	0.000	0.000	0.000	0.000
90	I	90	SER	0	-0.014	0.009	10.704	-0.128	-0.128	0.000	0.000	0.000	0.000
91	I	91	VAL	0	-0.007	0.003	11.557	-0.052	-0.052	0.000	0.000	0.000	0.000
92	I	92	TYR	0	-0.025	0.007	3.276	-1.411	-0.586	0.045	-0.320	-0.550	-0.003
93	I	93	GLN	0	0.036	0.005	6.147	0.087	0.087	0.000	0.000	0.000	0.000
94	I	94	SER	0	-0.084	-0.053	7.878	-0.086	-0.086	0.000	0.000	0.000	0.000
95	I	95	TYR	0	-0.036	-0.037	6.921	0.085	0.085	0.000	0.000	0.000	0.000
96	I	96	GLN	0	0.000	-0.002	2.342	-5.912	-3.626	2.379	-1.468	-3.198	-0.021
97	I	97	PRO	0	-0.009	0.020	2.815	-0.349	0.138	0.131	-0.070	-0.547	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(I:1:MET)