FMO DATABASE

FMODB ID: MVY9Z

Calculation Name: 4U3H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4U3H

Chain ID: A

ChEMBL ID:

UniProt ID:

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:

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	100
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-672121.052292
FMO2-HF: Nuclear repulsion	634790.794933
FMO2-HF: Total energy	-37330.257359
FMO2-MP2: Total energy	-37441.00746

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:MET)

Summations of interaction energy for fragment #1(A: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.
-7.283	-4.025	2.737	-1.025	-4.97	-0.017

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / q_NPA : 0.003

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	HIS	0	-0.008	-0.009	2.556	-8.216	-4.992	2.718	-1.209	-4.733	-0.017
4	A	4	HIS	0	0.025	0.012	3.404	0.674	0.708	0.019	0.184	-0.237	0.000
5	A	5	HIS	0	0.025	0.016	6.462	0.126	0.126	0.000	0.000	0.000	0.000
6	A	6	HIS	0	0.007	0.009	8.815	0.043	0.043	0.000	0.000	0.000	0.000
7	A	7	HIS	0	0.039	0.007	12.058	0.086	0.086	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.042	-0.020	15.369	0.031	0.031	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.025	0.023	17.658	0.013	0.013	0.000	0.000	0.000	0.000
10	A	10	PRO	0	0.022	0.011	21.068	0.001	0.001	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.891	0.951	19.131	0.194	0.194	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.066	0.033	24.973	0.010	0.010	0.000	0.000	0.000	0.000
13	A	13	SER	0	-0.057	-0.018	24.069	0.003	0.003	0.000	0.000	0.000	0.000
14	A	14	PRO	0	-0.008	0.001	25.553	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	15	SER	0	-0.004	-0.002	22.840	-0.015	-0.015	0.000	0.000	0.000	0.000
16	A	16	PRO	0	0.006	-0.009	19.544	0.009	0.009	0.000	0.000	0.000	0.000
17	A	17	PRO	0	-0.007	-0.004	22.502	0.009	0.009	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.022	0.027	24.323	-0.011	-0.011	0.000	0.000	0.000	0.000
19	A	19	ASN	0	-0.055	-0.049	25.273	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.019	0.012	22.888	0.011	0.011	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.788	0.874	24.674	0.090	0.090	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.007	-0.001	26.253	0.001	0.001	0.000	0.000	0.000	0.000
23	A	23	THR	0	-0.052	-0.043	28.987	0.003	0.003	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.822	-0.894	32.728	-0.053	-0.053	0.000	0.000	0.000	0.000
25	A	25	VAL	0	-0.004	0.009	30.237	-0.007	-0.007	0.000	0.000	0.000	0.000
26	A	26	THR	0	-0.010	-0.008	33.373	0.006	0.006	0.000	0.000	0.000	0.000
27	A	27	SER	0	0.004	-0.009	34.204	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	28	THR	0	0.001	-0.008	35.500	0.000	0.000	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.001	0.018	34.652	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	30	VAL	0	0.014	0.006	28.672	0.001	0.001	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.047	-0.024	32.161	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.010	0.001	26.962	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	33	SER	0	0.013	-0.016	29.611	0.007	0.007	0.000	0.000	0.000	0.000
34	A	34	TRP	0	-0.047	-0.024	28.092	-0.011	-0.011	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.754	-0.848	29.116	-0.090	-0.090	0.000	0.000	0.000	0.000
36	A	36	PRO	0	-0.008	-0.001	29.145	-0.009	-0.009	0.000	0.000	0.000	0.000
37	A	37	PRO	0	-0.016	0.000	26.243	0.001	0.001	0.000	0.000	0.000	0.000
38	A	38	PRO	0	-0.011	-0.009	26.964	0.007	0.007	0.000	0.000	0.000	0.000
39	A	39	GLY	0	0.006	-0.001	29.044	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	40	PRO	0	-0.029	-0.009	31.646	0.003	0.003	0.000	0.000	0.000	0.000
41	A	41	ILE	0	0.019	0.000	29.687	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	42	THR	0	-0.062	-0.047	32.687	0.004	0.004	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.022	0.000	32.401	0.006	0.006	0.000	0.000	0.000	0.000
44	A	44	TYR	0	-0.032	-0.011	28.327	-0.010	-0.010	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.813	0.897	25.982	0.143	0.143	0.000	0.000	0.000	0.000
46	A	46	VAL	0	0.002	-0.003	27.267	-0.009	-0.009	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.870	-0.954	22.812	-0.182	-0.182	0.000	0.000	0.000	0.000
48	A	48	TYR	0	-0.005	-0.029	24.860	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	49	ARG	1	0.832	0.907	17.630	0.195	0.195	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.740	-0.841	24.696	-0.065	-0.065	0.000	0.000	0.000	0.000
51	A	51	ALA	0	-0.002	-0.017	20.676	-0.011	-0.011	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.015	-0.003	19.221	0.012	0.012	0.000	0.000	0.000	0.000
53	A	53	GLY	0	-0.027	-0.006	20.185	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.875	-0.927	22.550	-0.160	-0.160	0.000	0.000	0.000	0.000
55	A	55	TRP	0	-0.082	-0.052	19.507	0.006	0.006	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.914	0.973	25.552	0.089	0.089	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.813	-0.899	27.406	-0.129	-0.129	0.000	0.000	0.000	0.000
58	A	58	VAL	0	-0.021	-0.001	29.279	0.008	0.008	0.000	0.000	0.000	0.000
59	A	59	THR	0	-0.012	-0.016	31.199	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	60	VAL	0	-0.041	-0.006	32.101	0.007	0.007	0.000	0.000	0.000	0.000
61	A	61	PRO	0	0.058	0.009	33.957	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.029	0.020	33.767	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	63	SER	0	-0.027	-0.023	34.541	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.882	-0.925	34.194	-0.073	-0.073	0.000	0.000	0.000	0.000
65	A	65	THR	0	-0.032	-0.029	32.984	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	66	SER	0	-0.029	-0.016	32.957	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	67	TYR	0	0.011	0.011	32.284	0.001	0.001	0.000	0.000	0.000	0.000
68	A	68	THR	0	0.003	-0.005	32.843	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	69	VAL	0	0.004	0.014	30.273	0.002	0.002	0.000	0.000	0.000	0.000
70	A	70	THR	0	-0.003	-0.017	33.550	0.003	0.003	0.000	0.000	0.000	0.000
71	A	71	GLY	0	-0.007	0.002	35.348	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	72	LEU	0	-0.057	-0.012	30.731	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.836	0.891	29.882	0.059	0.059	0.000	0.000	0.000	0.000
74	A	74	PRO	0	0.045	0.023	32.590	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	75	GLY	0	-0.014	0.015	31.903	0.001	0.001	0.000	0.000	0.000	0.000
76	A	76	THR	0	-0.064	-0.023	27.892	0.003	0.003	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.821	-0.884	23.405	-0.066	-0.066	0.000	0.000	0.000	0.000
78	A	78	TYR	0	-0.044	-0.047	24.974	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.782	-0.864	18.038	-0.246	-0.246	0.000	0.000	0.000	0.000
80	A	80	PHE	0	0.035	-0.005	22.123	0.008	0.008	0.000	0.000	0.000	0.000
81	A	81	ARG	1	0.778	0.881	17.412	0.240	0.240	0.000	0.000	0.000	0.000
82	A	82	VAL	0	0.021	0.026	22.711	0.014	0.014	0.000	0.000	0.000	0.000
83	A	83	ARG	1	0.841	0.926	21.182	0.192	0.192	0.000	0.000	0.000	0.000
84	A	84	ALA	0	0.067	0.036	24.633	0.013	0.013	0.000	0.000	0.000	0.000
85	A	85	VAL	0	0.006	-0.005	26.368	-0.011	-0.011	0.000	0.000	0.000	0.000
86	A	86	ASN	0	0.023	-0.003	29.009	0.006	0.006	0.000	0.000	0.000	0.000
87	A	87	GLY	0	0.008	-0.003	31.156	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	88	ALA	0	-0.029	0.002	29.062	0.003	0.003	0.000	0.000	0.000	0.000
89	A	89	GLY	0	-0.004	-0.008	27.060	-0.006	-0.006	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.831	-0.893	24.103	-0.154	-0.154	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.070	0.043	22.826	-0.011	-0.011	0.000	0.000	0.000	0.000
92	A	92	PRO	0	-0.043	-0.029	17.486	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	93	PRO	0	0.002	0.015	17.628	0.018	0.018	0.000	0.000	0.000	0.000
94	A	94	SER	0	0.007	0.018	18.532	-0.033	-0.033	0.000	0.000	0.000	0.000
95	A	95	SER	0	-0.008	-0.029	17.808	0.007	0.007	0.000	0.000	0.000	0.000
96	A	96	VAL	0	0.014	0.016	19.798	-0.004	-0.004	0.000	0.000	0.000	0.000
97	A	97	SER	0	-0.050	-0.033	19.912	-0.011	-0.011	0.000	0.000	0.000	0.000
98	A	98	VAL	0	-0.015	0.003	22.233	0.006	0.006	0.000	0.000	0.000	0.000
99	A	99	THR	0	-0.013	-0.020	25.746	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	100	THR	0	-0.043	-0.032	27.957	0.006	0.006	0.000	0.000	0.000	0.000

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