FMO DATABASE

FMODB ID: N9MQQ

Calculation Name: 3MEX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MEX

Chain ID: A

ChEMBL ID:

UniProt ID: P52003

Base Structure: X-ray

Registration Date: 2023-09-20

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	142
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1225665.878894
FMO2-HF: Nuclear repulsion	1167570.718902
FMO2-HF: Total energy	-58095.159992
FMO2-MP2: Total energy	-58262.168707

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.
-6.229	-0.998	2.724	-2.812	-5.143	-0.012

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 : 0.021 / q_NPA : 0.018

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	TYR	0	0.028	0.003	2.589	-4.822	0.371	2.725	-2.810	-5.108	-0.012
4	A	4	PRO	0	-0.028	-0.007	5.375	0.125	0.163	-0.001	-0.002	-0.035	0.000
5	A	5	VAL	0	0.022	0.008	9.203	-0.150	-0.150	0.000	0.000	0.000	0.000
6	A	6	ASN	0	-0.014	-0.020	11.361	0.189	0.189	0.000	0.000	0.000	0.000
7	A	7	PRO	0	0.020	0.001	14.217	-0.017	-0.017	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.828	-0.903	17.513	-0.332	-0.332	0.000	0.000	0.000	0.000
9	A	9	LEU	0	-0.031	-0.016	13.850	0.018	0.018	0.000	0.000	0.000	0.000
10	A	10	MET	0	0.021	0.013	17.667	0.012	0.012	0.000	0.000	0.000	0.000
11	A	11	PRO	0	-0.001	-0.012	19.612	0.023	0.023	0.000	0.000	0.000	0.000
12	A	12	ALA	0	0.023	0.022	20.389	0.020	0.020	0.000	0.000	0.000	0.000
13	A	13	LEU	0	0.024	0.013	17.377	0.022	0.022	0.000	0.000	0.000	0.000
14	A	14	MET	0	-0.010	-0.015	21.074	0.023	0.023	0.000	0.000	0.000	0.000
15	A	15	ALA	0	-0.004	0.007	23.906	0.027	0.027	0.000	0.000	0.000	0.000
16	A	16	VAL	0	0.032	0.021	23.510	0.021	0.021	0.000	0.000	0.000	0.000
17	A	17	PHE	0	-0.006	0.001	23.768	0.023	0.023	0.000	0.000	0.000	0.000
18	A	18	GLN	0	0.008	-0.012	25.691	0.019	0.019	0.000	0.000	0.000	0.000
19	A	19	HIS	0	0.028	0.035	28.760	0.021	0.021	0.000	0.000	0.000	0.000
20	A	20	VAL	0	0.048	0.018	26.595	0.016	0.016	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.882	0.938	29.487	0.159	0.159	0.000	0.000	0.000	0.000
22	A	22	THR	0	-0.048	-0.040	31.174	0.016	0.016	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.725	0.836	32.915	0.148	0.148	0.000	0.000	0.000	0.000
24	A	24	ILE	0	0.049	0.019	30.569	0.010	0.010	0.000	0.000	0.000	0.000
25	A	25	GLN	0	0.006	-0.004	34.600	0.003	0.003	0.000	0.000	0.000	0.000
26	A	26	SER	0	-0.006	0.011	36.918	0.007	0.007	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.716	-0.823	36.853	-0.107	-0.107	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.028	-0.018	35.835	0.005	0.005	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.890	-0.933	39.953	-0.078	-0.078	0.000	0.000	0.000	0.000
30	A	30	CYS	0	-0.051	-0.028	42.663	0.005	0.005	0.000	0.000	0.000	0.000
31	A	31	GLN	0	-0.071	-0.036	40.427	0.007	0.007	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.884	0.938	44.349	0.068	0.068	0.000	0.000	0.000	0.000
33	A	33	LEU	0	0.011	0.009	40.101	0.003	0.003	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.890	-0.922	42.953	-0.068	-0.068	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.025	0.007	38.219	0.000	0.000	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.034	-0.049	36.727	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	37	PRO	0	0.034	-0.005	31.906	0.000	0.000	0.000	0.000	0.000	0.000
38	A	38	PRO	0	0.010	-0.001	31.992	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.753	-0.831	33.009	-0.085	-0.085	0.000	0.000	0.000	0.000
40	A	40	VAL	0	0.055	0.029	32.426	0.002	0.002	0.000	0.000	0.000	0.000
41	A	41	HIS	0	-0.025	-0.013	29.074	0.003	0.003	0.000	0.000	0.000	0.000
42	A	42	VAL	0	-0.033	-0.016	30.781	0.000	0.000	0.000	0.000	0.000	0.000
43	A	43	LEU	0	0.006	0.000	32.925	0.004	0.004	0.000	0.000	0.000	0.000
44	A	44	LYS	1	0.836	0.910	27.390	0.164	0.164	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.026	-0.021	26.515	0.002	0.002	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.066	-0.034	30.139	0.006	0.006	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.800	-0.876	33.331	-0.085	-0.085	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.864	-0.917	27.210	-0.156	-0.156	0.000	0.000	0.000	0.000
49	A	49	GLN	0	-0.043	-0.021	26.821	0.009	0.009	0.000	0.000	0.000	0.000
50	A	50	ARG	1	0.845	0.895	30.365	0.086	0.086	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.046	0.038	34.104	0.005	0.005	0.000	0.000	0.000	0.000
52	A	52	LEU	0	-0.039	-0.003	30.256	0.006	0.006	0.000	0.000	0.000	0.000
53	A	53	ASN	0	-0.004	-0.010	32.713	0.006	0.006	0.000	0.000	0.000	0.000
54	A	54	LEU	0	0.011	0.002	33.329	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	55	GLN	0	-0.006	-0.023	32.423	-0.008	-0.008	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.791	-0.891	29.183	-0.061	-0.061	0.000	0.000	0.000	0.000
57	A	57	LEU	0	0.021	0.026	28.156	-0.012	-0.012	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.056	0.018	26.144	0.005	0.005	0.000	0.000	0.000	0.000
59	A	59	ARG	1	0.806	0.893	23.821	0.094	0.094	0.000	0.000	0.000	0.000
60	A	60	GLN	0	-0.006	0.010	20.024	0.014	0.014	0.000	0.000	0.000	0.000
61	A	61	MET	0	0.004	0.006	21.555	-0.018	-0.018	0.000	0.000	0.000	0.000
62	A	62	CYS	0	0.005	0.006	23.791	0.015	0.015	0.000	0.000	0.000	0.000
63	A	63	ARG	1	0.932	0.959	26.305	0.083	0.083	0.000	0.000	0.000	0.000
64	A	64	ASP	-1	-0.816	-0.908	29.357	-0.048	-0.048	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.885	0.921	28.845	0.065	0.065	0.000	0.000	0.000	0.000
66	A	66	ALA	0	0.006	0.011	34.201	0.001	0.001	0.000	0.000	0.000	0.000
67	A	67	LEU	0	0.011	0.012	34.662	0.000	0.000	0.000	0.000	0.000	0.000
68	A	68	ILE	0	0.018	0.018	31.015	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	69	THR	0	0.008	0.000	35.442	0.000	0.000	0.000	0.000	0.000	0.000
70	A	70	ARG	1	0.884	0.938	38.596	0.047	0.047	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.831	0.889	36.159	0.080	0.080	0.000	0.000	0.000	0.000
72	A	72	ILE	0	0.017	0.013	35.743	0.000	0.000	0.000	0.000	0.000	0.000
73	A	73	ARG	1	0.917	0.960	39.407	0.042	0.042	0.000	0.000	0.000	0.000
74	A	74	GLU	-1	-0.872	-0.901	41.483	-0.067	-0.067	0.000	0.000	0.000	0.000
75	A	75	LEU	0	0.037	0.003	37.535	0.001	0.001	0.000	0.000	0.000	0.000
76	A	76	GLU	-1	-0.779	-0.852	42.033	-0.046	-0.046	0.000	0.000	0.000	0.000
77	A	77	GLY	0	-0.048	-0.018	44.376	0.002	0.002	0.000	0.000	0.000	0.000
78	A	78	ARG	1	0.768	0.859	41.601	0.071	0.071	0.000	0.000	0.000	0.000
79	A	79	ASN	0	-0.015	-0.003	46.140	0.000	0.000	0.000	0.000	0.000	0.000
80	A	80	LEU	0	0.042	0.049	41.354	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	81	VAL	0	-0.022	-0.022	38.688	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	82	ARG	1	0.884	0.937	41.430	0.052	0.052	0.000	0.000	0.000	0.000
83	A	83	ARG	1	0.755	0.834	41.109	0.041	0.041	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.826	-0.890	41.562	-0.036	-0.036	0.000	0.000	0.000	0.000
85	A	85	ARG	1	0.844	0.912	41.633	0.021	0.021	0.000	0.000	0.000	0.000
86	A	86	ASN	0	0.038	0.031	36.762	0.003	0.003	0.000	0.000	0.000	0.000
87	A	87	PRO	0	0.013	0.000	40.913	0.003	0.003	0.000	0.000	0.000	0.000
88	A	88	SER	0	-0.073	-0.039	38.200	0.003	0.003	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.806	-0.897	38.135	-0.014	-0.014	0.000	0.000	0.000	0.000
90	A	90	GLN	0	0.069	0.033	40.429	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	91	ARG	1	0.873	0.951	38.716	0.009	0.009	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.034	-0.027	37.570	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	93	PHE	0	-0.024	-0.026	38.690	0.002	0.002	0.000	0.000	0.000	0.000
94	A	94	GLN	0	-0.011	-0.008	36.712	0.000	0.000	0.000	0.000	0.000	0.000
95	A	95	LEU	0	-0.020	-0.007	35.421	0.002	0.002	0.000	0.000	0.000	0.000
96	A	96	PHE	0	0.016	-0.003	37.020	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	97	LEU	0	0.032	0.023	36.579	0.001	0.001	0.000	0.000	0.000	0.000
98	A	98	THR	0	-0.044	-0.034	40.086	0.003	0.003	0.000	0.000	0.000	0.000
99	A	99	ASP	-1	-0.863	-0.946	42.682	-0.056	-0.056	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.894	-0.931	44.149	-0.059	-0.059	0.000	0.000	0.000	0.000
101	A	101	GLY	0	0.033	0.004	41.510	-0.004	-0.004	0.000	0.000	0.000	0.000
102	A	102	LEU	0	-0.031	-0.009	38.152	-0.006	-0.006	0.000	0.000	0.000	0.000
103	A	103	ALA	0	-0.035	-0.012	39.753	-0.005	-0.005	0.000	0.000	0.000	0.000
104	A	104	ILE	0	0.030	0.009	39.728	-0.005	-0.005	0.000	0.000	0.000	0.000
105	A	105	HIS	0	-0.043	-0.031	32.733	-0.012	-0.012	0.000	0.000	0.000	0.000
106	A	106	GLN	0	0.013	-0.005	36.182	-0.007	-0.007	0.000	0.000	0.000	0.000
107	A	107	HIS	0	-0.020	-0.010	37.312	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	108	ALA	0	0.008	-0.006	35.439	-0.005	-0.005	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.833	-0.904	30.925	-0.158	-0.158	0.000	0.000	0.000	0.000
110	A	110	ALA	0	-0.007	0.002	33.136	-0.009	-0.009	0.000	0.000	0.000	0.000
111	A	111	ILE	0	-0.043	-0.022	34.820	-0.005	-0.005	0.000	0.000	0.000	0.000
112	A	112	MET	0	-0.026	-0.015	29.195	-0.011	-0.011	0.000	0.000	0.000	0.000
113	A	113	SER	0	-0.025	-0.006	30.462	-0.014	-0.014	0.000	0.000	0.000	0.000
114	A	114	ARG	1	0.841	0.895	31.280	0.113	0.113	0.000	0.000	0.000	0.000
115	A	115	VAL	0	-0.049	-0.015	30.292	-0.004	-0.004	0.000	0.000	0.000	0.000
116	A	116	HIS	0	-0.067	-0.045	25.650	-0.026	-0.026	0.000	0.000	0.000	0.000
117	A	117	ASP	-1	-0.849	-0.921	28.879	-0.175	-0.175	0.000	0.000	0.000	0.000
118	A	118	GLU	-1	-0.841	-0.912	31.224	-0.143	-0.143	0.000	0.000	0.000	0.000
119	A	119	LEU	0	-0.062	-0.019	26.461	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	120	PHE	0	-0.014	-0.017	23.500	-0.016	-0.016	0.000	0.000	0.000	0.000
121	A	121	ALA	0	0.014	0.012	27.906	-0.002	-0.002	0.000	0.000	0.000	0.000
122	A	122	PRO	0	-0.072	-0.037	30.102	0.005	0.005	0.000	0.000	0.000	0.000
123	A	123	LEU	0	-0.011	0.023	24.410	-0.004	-0.004	0.000	0.000	0.000	0.000
124	A	124	THR	0	-0.013	-0.041	26.658	0.008	0.008	0.000	0.000	0.000	0.000
125	A	125	PRO	0	0.035	-0.004	26.165	-0.018	-0.018	0.000	0.000	0.000	0.000
126	A	126	VAL	0	0.010	0.015	22.525	-0.015	-0.015	0.000	0.000	0.000	0.000
127	A	127	GLU	-1	-0.813	-0.858	21.894	-0.296	-0.296	0.000	0.000	0.000	0.000
128	A	128	GLN	0	-0.030	-0.023	21.563	-0.037	-0.037	0.000	0.000	0.000	0.000
129	A	129	ALA	0	0.014	0.007	20.997	-0.026	-0.026	0.000	0.000	0.000	0.000
130	A	130	THR	0	-0.043	-0.034	16.893	-0.046	-0.046	0.000	0.000	0.000	0.000
131	A	131	LEU	0	-0.017	-0.010	16.817	-0.078	-0.078	0.000	0.000	0.000	0.000
132	A	132	VAL	0	0.026	0.011	17.068	-0.052	-0.052	0.000	0.000	0.000	0.000
133	A	133	HIS	0	0.031	0.023	11.832	-0.001	-0.001	0.000	0.000	0.000	0.000
134	A	134	LEU	0	-0.041	-0.030	12.248	-0.128	-0.128	0.000	0.000	0.000	0.000
135	A	135	LEU	0	-0.020	0.004	12.376	-0.133	-0.133	0.000	0.000	0.000	0.000
136	A	136	ASP	-1	-0.831	-0.913	12.970	-0.568	-0.568	0.000	0.000	0.000	0.000
137	A	137	GLN	0	-0.091	-0.047	7.532	0.132	0.132	0.000	0.000	0.000	0.000
138	A	138	SER	0	-0.106	-0.053	8.155	-0.289	-0.289	0.000	0.000	0.000	0.000
139	A	139	LEU	0	0.006	-0.004	9.910	-0.029	-0.029	0.000	0.000	0.000	0.000
140	A	140	ALA	0	0.000	-0.010	9.176	0.071	0.071	0.000	0.000	0.000	0.000
141	A	141	ALA	0	-0.033	0.000	6.129	0.084	0.084	0.000	0.000	0.000	0.000
142	A	142	GLN	0	-0.123	-0.054	7.489	0.098	0.098	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:MET)