FMO DATABASE

FMODB ID: 7GNJK

Calculation Name: 1U9P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1U9P

Chain ID: A

ChEMBL ID:

UniProt ID: P03050

Base Structure: X-ray

Registration Date: 2023-03-13

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	OptHSide
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	101
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-779603.040841
FMO2-HF: Nuclear repulsion	739336.34756
FMO2-HF: Total energy	-40266.69328
FMO2-MP2: Total energy	-40384.379559

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:7:MET)

Summations of interaction energy for fragment #1(A:7: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.
-8.892	-1.47	5.177	-3.943	-8.656	-0.028

Interaction energy analysis for fragmet #1(A:7:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : 0.002

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	9	GLN	0	0.048	0.011	3.602	-1.878	0.308	0.006	-1.145	-1.047	0.005
4	A	10	PHE	0	0.005	0.005	6.344	0.584	0.584	0.000	0.000	0.000	0.000
5	A	11	ASN	0	-0.044	-0.030	9.285	-0.021	-0.021	0.000	0.000	0.000	0.000
6	A	12	LEU	0	0.021	0.021	12.380	0.126	0.126	0.000	0.000	0.000	0.000
7	A	13	ARG	1	0.934	0.954	13.999	0.510	0.510	0.000	0.000	0.000	0.000
8	A	14	TRP	0	0.002	-0.001	16.446	0.038	0.038	0.000	0.000	0.000	0.000
9	A	15	PRO	0	0.001	-0.004	19.787	-0.001	-0.001	0.000	0.000	0.000	0.000
10	A	16	GLY	0	0.036	0.017	23.014	-0.001	-0.001	0.000	0.000	0.000	0.000
11	A	17	GLY	0	-0.020	0.001	24.877	0.003	0.003	0.000	0.000	0.000	0.000
12	A	18	GLY	0	0.033	0.028	22.410	0.006	0.006	0.000	0.000	0.000	0.000
13	A	19	PRO	0	-0.050	-0.026	18.678	-0.026	-0.026	0.000	0.000	0.000	0.000
14	A	20	GLN	0	0.046	0.017	16.103	-0.017	-0.017	0.000	0.000	0.000	0.000
15	A	21	PHE	0	0.007	0.011	12.161	-0.013	-0.013	0.000	0.000	0.000	0.000
16	A	22	ASN	0	0.002	-0.005	8.306	-0.259	-0.259	0.000	0.000	0.000	0.000
17	A	23	LEU	0	-0.004	0.001	7.406	-0.134	-0.134	0.000	0.000	0.000	0.000
18	A	24	ARG	1	0.910	0.961	2.942	1.976	2.863	0.175	-0.236	-0.826	0.000
19	A	25	TRP	0	0.027	0.017	2.531	-2.500	-0.900	1.786	-1.105	-2.281	-0.013
20	A	26	PRO	0	0.091	0.033	2.443	-4.233	-1.698	3.139	-1.939	-3.735	-0.019
21	A	27	ARG	1	0.949	0.955	3.432	-5.706	-5.492	0.071	0.482	-0.767	-0.001
22	A	28	GLU	-1	-0.825	-0.917	5.792	2.617	2.617	0.000	0.000	0.000	0.000
23	A	29	VAL	0	-0.001	0.007	7.168	-0.280	-0.280	0.000	0.000	0.000	0.000
24	A	30	LEU	0	-0.009	-0.013	6.920	-0.336	-0.336	0.000	0.000	0.000	0.000
25	A	31	ASP	-1	-0.808	-0.900	8.759	-0.136	-0.136	0.000	0.000	0.000	0.000
26	A	32	LEU	0	-0.018	0.012	11.177	-0.076	-0.076	0.000	0.000	0.000	0.000
27	A	33	VAL	0	-0.022	-0.025	11.251	-0.080	-0.080	0.000	0.000	0.000	0.000
28	A	34	ARG	1	0.816	0.895	9.009	0.386	0.386	0.000	0.000	0.000	0.000
29	A	35	LYS	1	0.992	1.006	14.931	-0.202	-0.202	0.000	0.000	0.000	0.000
30	A	36	VAL	0	-0.003	0.001	16.950	-0.010	-0.010	0.000	0.000	0.000	0.000
31	A	37	ALA	0	-0.037	-0.022	17.378	-0.019	-0.019	0.000	0.000	0.000	0.000
32	A	38	GLU	-1	-0.971	-0.979	19.187	-0.045	-0.045	0.000	0.000	0.000	0.000
33	A	39	GLU	-1	-0.809	-0.885	21.184	0.104	0.104	0.000	0.000	0.000	0.000
34	A	40	ASN	0	-0.058	-0.028	21.463	0.006	0.006	0.000	0.000	0.000	0.000
35	A	41	GLY	0	0.001	0.018	23.955	-0.009	-0.009	0.000	0.000	0.000	0.000
36	A	42	ARG	1	0.833	0.908	21.358	0.024	0.024	0.000	0.000	0.000	0.000
37	A	43	SER	0	0.042	0.018	19.472	-0.008	-0.008	0.000	0.000	0.000	0.000
38	A	44	VAL	0	0.084	0.020	12.831	0.015	0.015	0.000	0.000	0.000	0.000
39	A	45	ASN	0	-0.040	-0.033	15.761	-0.049	-0.049	0.000	0.000	0.000	0.000
40	A	46	SER	0	-0.007	0.002	16.935	0.016	0.016	0.000	0.000	0.000	0.000
41	A	47	GLU	-1	-0.699	-0.830	17.060	0.013	0.013	0.000	0.000	0.000	0.000
42	A	48	ILE	0	-0.021	-0.008	11.989	0.029	0.029	0.000	0.000	0.000	0.000
43	A	49	TYR	0	0.024	0.009	16.007	0.022	0.022	0.000	0.000	0.000	0.000
44	A	50	GLN	0	0.003	-0.002	18.920	0.036	0.036	0.000	0.000	0.000	0.000
45	A	51	ARG	1	0.839	0.894	16.528	-0.078	-0.078	0.000	0.000	0.000	0.000
46	A	52	VAL	0	-0.016	0.000	15.634	0.020	0.020	0.000	0.000	0.000	0.000
47	A	53	MET	0	-0.030	0.006	18.385	0.018	0.018	0.000	0.000	0.000	0.000
48	A	54	GLU	-1	-0.833	-0.928	22.044	0.020	0.020	0.000	0.000	0.000	0.000
49	A	55	SER	0	-0.081	-0.044	19.023	0.015	0.015	0.000	0.000	0.000	0.000
50	A	56	PHE	0	0.049	0.010	18.737	0.008	0.008	0.000	0.000	0.000	0.000
51	A	57	LYS	1	0.848	0.917	23.022	0.012	0.012	0.000	0.000	0.000	0.000
52	A	58	LYS	1	0.918	0.964	23.087	-0.105	-0.105	0.000	0.000	0.000	0.000
53	A	59	GLU	-1	-0.828	-0.876	21.146	0.013	0.013	0.000	0.000	0.000	0.000
54	A	60	GLY	0	0.016	0.009	25.429	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	61	ARG	1	0.848	0.908	21.563	0.012	0.012	0.000	0.000	0.000	0.000
56	A	62	ILE	0	-0.033	-0.014	24.467	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	63	GLY	0	0.012	0.012	28.253	0.001	0.001	0.000	0.000	0.000	0.000
58	A	64	GLY	0	0.002	0.002	31.580	-0.008	-0.008	0.000	0.000	0.000	0.000
59	A	65	THR	0	-0.020	-0.023	31.099	0.004	0.004	0.000	0.000	0.000	0.000
60	A	66	GLY	0	0.007	0.010	34.215	0.001	0.001	0.000	0.000	0.000	0.000
61	A	67	GLY	0	-0.007	-0.016	34.278	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	68	SER	0	-0.014	-0.006	33.490	0.005	0.005	0.000	0.000	0.000	0.000
63	A	69	GLY	0	0.029	0.029	29.934	-0.009	-0.009	0.000	0.000	0.000	0.000
64	A	70	GLY	0	0.040	0.005	28.655	0.002	0.002	0.000	0.000	0.000	0.000
65	A	71	GLY	0	-0.008	-0.004	24.544	-0.016	-0.016	0.000	0.000	0.000	0.000
66	A	72	ARG	1	0.826	0.884	23.967	0.187	0.187	0.000	0.000	0.000	0.000
67	A	73	GLU	-1	-0.803	-0.887	25.226	-0.097	-0.097	0.000	0.000	0.000	0.000
68	A	74	VAL	0	0.034	0.013	20.687	0.001	0.001	0.000	0.000	0.000	0.000
69	A	75	LEU	0	-0.053	-0.020	19.441	-0.013	-0.013	0.000	0.000	0.000	0.000
70	A	76	ASP	-1	-0.792	-0.887	20.943	-0.205	-0.205	0.000	0.000	0.000	0.000
71	A	77	LEU	0	0.002	0.014	22.449	0.003	0.003	0.000	0.000	0.000	0.000
72	A	78	VAL	0	-0.032	-0.013	16.873	0.004	0.004	0.000	0.000	0.000	0.000
73	A	79	ARG	1	0.890	0.937	17.962	0.322	0.322	0.000	0.000	0.000	0.000
74	A	80	LYS	1	0.929	0.964	19.426	0.076	0.076	0.000	0.000	0.000	0.000
75	A	81	VAL	0	0.022	0.011	18.275	0.009	0.009	0.000	0.000	0.000	0.000
76	A	82	ALA	0	-0.058	-0.025	15.098	0.014	0.014	0.000	0.000	0.000	0.000
77	A	83	GLU	-1	-0.944	-0.965	16.674	-0.157	-0.157	0.000	0.000	0.000	0.000
78	A	84	GLU	-1	-0.865	-0.919	19.042	-0.047	-0.047	0.000	0.000	0.000	0.000
79	A	85	ASN	0	-0.084	-0.049	16.052	0.040	0.040	0.000	0.000	0.000	0.000
80	A	86	GLY	0	0.016	0.028	16.361	0.022	0.022	0.000	0.000	0.000	0.000
81	A	87	ARG	1	0.818	0.911	11.668	-0.036	-0.036	0.000	0.000	0.000	0.000
82	A	88	SER	0	0.053	0.028	9.545	0.005	0.005	0.000	0.000	0.000	0.000
83	A	89	VAL	0	0.093	0.011	12.301	0.030	0.030	0.000	0.000	0.000	0.000
84	A	90	ASN	0	-0.055	-0.031	8.866	0.181	0.181	0.000	0.000	0.000	0.000
85	A	91	SER	0	-0.005	0.006	8.183	0.064	0.064	0.000	0.000	0.000	0.000
86	A	92	GLU	-1	-0.699	-0.840	9.135	0.102	0.102	0.000	0.000	0.000	0.000
87	A	93	ILE	0	-0.032	-0.022	11.791	0.077	0.077	0.000	0.000	0.000	0.000
88	A	94	TYR	0	-0.001	-0.003	6.674	0.242	0.242	0.000	0.000	0.000	0.000
89	A	95	GLN	0	-0.013	-0.011	9.714	0.208	0.208	0.000	0.000	0.000	0.000
90	A	96	ARG	1	0.779	0.853	11.611	0.082	0.082	0.000	0.000	0.000	0.000
91	A	97	VAL	0	0.003	0.015	12.120	0.018	0.018	0.000	0.000	0.000	0.000
92	A	98	MET	0	0.012	0.023	9.285	0.051	0.051	0.000	0.000	0.000	0.000
93	A	99	GLU	-1	-0.812	-0.891	12.787	0.377	0.377	0.000	0.000	0.000	0.000
94	A	100	SER	0	-0.069	-0.041	15.985	-0.021	-0.021	0.000	0.000	0.000	0.000
95	A	101	PHE	0	0.080	0.021	12.403	-0.014	-0.014	0.000	0.000	0.000	0.000
96	A	102	LYS	1	0.858	0.921	14.118	-0.530	-0.530	0.000	0.000	0.000	0.000
97	A	103	LYS	1	0.835	0.908	17.943	-0.261	-0.261	0.000	0.000	0.000	0.000
98	A	104	GLU	-1	-0.787	-0.851	20.232	0.128	0.128	0.000	0.000	0.000	0.000
99	A	105	GLY	0	-0.004	0.014	20.794	-0.010	-0.010	0.000	0.000	0.000	0.000
100	A	106	ARG	1	0.754	0.840	17.648	-0.159	-0.159	0.000	0.000	0.000	0.000
101	A	107	ILE	0	-0.052	-0.013	12.873	0.048	0.048	0.000	0.000	0.000	0.000

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Graph

Overview

Highlights

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:7:MET)