FMO DATABASE

FMODB ID: G53G1

Calculation Name: 1M8U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1M8U

Chain ID: A

ChEMBL ID:

UniProt ID: P23005

Base Structure: X-ray

Registration Date: 2023-09-24

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	173
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-2049349.56041
FMO2-HF: Nuclear repulsion	1974582.504567
FMO2-HF: Total energy	-74767.055843
FMO2-MP2: Total energy	-74982.694577

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:GLY)

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

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.
-3.398	0.591	5.515	-4.591	-4.911	-0.025

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.014

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	ILE	0	-0.025	0.000	3.796	0.946	2.002	-0.017	-0.476	-0.563	0.000
4	A	4	THR	0	0.062	0.036	6.831	-0.057	-0.057	0.000	0.000	0.000	0.000
5	A	5	PHE	0	-0.008	-0.023	9.735	0.124	0.124	0.000	0.000	0.000	0.000
6	A	6	TYR	0	0.031	0.015	13.334	-0.005	-0.005	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.841	-0.943	16.939	-0.206	-0.206	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.859	-0.918	20.178	-0.134	-0.134	0.000	0.000	0.000	0.000
9	A	9	ARG	0	0.114	0.113	20.373	-0.013	-0.013	0.000	0.000	0.000	0.000
10	A	10	GLY	0	-0.046	-0.025	20.656	0.005	0.005	0.000	0.000	0.000	0.000
11	A	11	PHE	0	-0.060	-0.037	14.708	0.016	0.016	0.000	0.000	0.000	0.000
12	A	12	GLN	0	-0.029	0.004	18.506	0.009	0.009	0.000	0.000	0.000	0.000
13	A	13	GLY	0	0.061	0.027	20.758	-0.016	-0.016	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.896	0.958	19.330	0.254	0.254	0.000	0.000	0.000	0.000
15	A	15	HIS	0	0.007	-0.003	15.237	-0.039	-0.039	0.000	0.000	0.000	0.000
16	A	16	TYR	0	-0.027	-0.019	11.566	0.020	0.020	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.921	-0.954	8.722	-0.830	-0.830	0.000	0.000	0.000	0.000
18	A	18	CYS	0	-0.076	-0.030	7.774	0.050	0.050	0.000	0.000	0.000	0.000
19	A	19	SER	0	0.028	0.002	3.866	-0.642	-0.488	0.000	-0.064	-0.091	0.000
20	A	20	SER	0	-0.017	-0.004	3.948	-0.642	-0.449	0.000	-0.092	-0.101	0.000
21	A	21	ASP	-1	-0.806	-0.902	6.335	-0.579	-0.579	0.000	0.000	0.000	0.000
22	A	22	HIS	0	0.000	0.002	8.886	0.147	0.147	0.000	0.000	0.000	0.000
23	A	23	SER	0	-0.009	-0.002	11.896	0.032	0.032	0.000	0.000	0.000	0.000
24	A	24	ASN	0	0.076	0.009	15.168	0.054	0.054	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.009	0.004	11.764	-0.020	-0.020	0.000	0.000	0.000	0.000
26	A	26	GLN	0	-0.002	-0.004	15.909	0.026	0.026	0.000	0.000	0.000	0.000
27	A	27	PRO	0	-0.054	-0.025	18.142	0.017	0.017	0.000	0.000	0.000	0.000
28	A	28	TYR	0	-0.031	-0.005	15.249	0.003	0.003	0.000	0.000	0.000	0.000
29	A	29	PHE	0	-0.044	-0.022	13.739	0.000	0.000	0.000	0.000	0.000	0.000
30	A	30	SER	0	-0.056	-0.015	19.192	0.007	0.007	0.000	0.000	0.000	0.000
31	A	31	ARG	1	0.886	0.968	20.762	0.185	0.185	0.000	0.000	0.000	0.000
32	A	32	CYS	0	-0.066	-0.022	15.015	-0.031	-0.031	0.000	0.000	0.000	0.000
33	A	33	ASN	0	-0.049	-0.050	18.376	0.029	0.029	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.040	-0.017	17.209	0.023	0.023	0.000	0.000	0.000	0.000
35	A	35	ILE	0	-0.012	-0.005	10.839	-0.041	-0.041	0.000	0.000	0.000	0.000
36	A	36	ARG	1	0.935	0.983	10.554	0.251	0.251	0.000	0.000	0.000	0.000
37	A	37	VAL	0	-0.047	-0.009	5.721	-0.189	-0.189	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.859	-0.936	6.010	-0.074	-0.074	0.000	0.000	0.000	0.000
39	A	39	SER	0	-0.082	-0.057	2.602	0.780	1.480	1.442	-1.130	-1.012	-0.010
40	A	40	GLY	0	0.038	0.024	2.622	-1.654	-0.927	1.934	-1.565	-1.095	-0.012
41	A	41	CYS	0	-0.064	-0.006	3.600	-0.617	-0.742	0.014	0.065	0.047	0.000
42	A	42	TRP	0	0.029	-0.003	2.692	-0.329	0.225	0.467	-0.270	-0.751	-0.001
43	A	43	MET	0	-0.049	0.002	7.581	0.090	0.090	0.000	0.000	0.000	0.000
44	A	44	ILE	0	-0.013	-0.001	10.774	-0.092	-0.092	0.000	0.000	0.000	0.000
45	A	45	TYR	0	0.046	0.012	12.543	0.052	0.052	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.833	-0.912	16.101	-0.165	-0.165	0.000	0.000	0.000	0.000
47	A	47	GLN	0	0.009	0.009	19.348	-0.011	-0.011	0.000	0.000	0.000	0.000
48	A	48	PRO	0	0.020	0.012	18.039	-0.024	-0.024	0.000	0.000	0.000	0.000
49	A	49	ASN	0	-0.030	-0.032	17.420	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	50	PHE	0	-0.055	-0.023	12.201	0.031	0.031	0.000	0.000	0.000	0.000
51	A	51	GLN	0	-0.018	0.008	16.542	0.042	0.042	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.015	0.002	19.614	-0.012	-0.012	0.000	0.000	0.000	0.000
53	A	53	PRO	0	-0.011	-0.009	20.220	0.000	0.000	0.000	0.000	0.000	0.000
54	A	54	GLN	0	0.074	0.041	16.009	-0.024	-0.024	0.000	0.000	0.000	0.000
55	A	55	TYR	0	-0.020	-0.012	15.145	0.024	0.024	0.000	0.000	0.000	0.000
56	A	56	PHE	0	0.017	-0.003	10.839	-0.032	-0.032	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.063	-0.022	9.641	0.005	0.005	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.902	0.941	8.831	-0.170	-0.170	0.000	0.000	0.000	0.000
59	A	59	ARG	1	0.875	0.925	5.842	-1.367	-1.367	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.002	0.006	8.659	0.027	0.027	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.855	-0.932	11.503	-0.157	-0.157	0.000	0.000	0.000	0.000
62	A	62	TYR	0	-0.010	-0.002	11.291	0.040	0.040	0.000	0.000	0.000	0.000
63	A	63	PRO	0	-0.004	-0.015	15.710	-0.033	-0.033	0.000	0.000	0.000	0.000
64	A	64	ASH	0	0.016	-0.070	18.824	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	65	TYR	0	0.109	0.049	18.639	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	66	GLN	0	-0.001	-0.003	19.664	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	67	GLN	0	-0.055	-0.005	17.435	0.016	0.016	0.000	0.000	0.000	0.000
68	A	68	TRP	0	-0.026	0.001	15.413	0.010	0.010	0.000	0.000	0.000	0.000
69	A	69	MET	0	-0.100	-0.058	17.216	0.005	0.005	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.021	0.012	19.931	0.001	0.001	0.000	0.000	0.000	0.000
71	A	71	LEU	0	-0.035	-0.026	20.513	0.013	0.013	0.000	0.000	0.000	0.000
72	A	72	ASN	0	-0.025	-0.020	22.147	-0.007	-0.007	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.829	-0.904	20.531	-0.169	-0.169	0.000	0.000	0.000	0.000
74	A	74	SER	0	-0.025	-0.009	20.585	-0.017	-0.017	0.000	0.000	0.000	0.000
75	A	75	ILE	0	-0.003	-0.001	13.980	0.003	0.003	0.000	0.000	0.000	0.000
76	A	76	ARG	1	0.904	0.939	17.009	0.174	0.174	0.000	0.000	0.000	0.000
77	A	77	SER	0	-0.038	-0.016	13.948	-0.007	-0.007	0.000	0.000	0.000	0.000
78	A	78	CYS	0	-0.008	0.009	8.733	0.009	0.009	0.000	0.000	0.000	0.000
79	A	79	ARG	1	0.916	0.963	8.973	0.206	0.206	0.000	0.000	0.000	0.000
80	A	80	LEU	0	0.010	0.014	2.587	-0.651	0.079	1.675	-1.059	-1.345	-0.002
81	A	81	ILE	0	-0.071	-0.053	5.742	0.033	0.033	0.000	0.000	0.000	0.000
82	A	82	PRO	0	-0.030	-0.015	7.136	0.131	0.131	0.000	0.000	0.000	0.000
83	A	83	HIS	0	0.046	0.035	7.473	0.099	0.099	0.000	0.000	0.000	0.000
84	A	84	THR	0	-0.045	-0.033	9.154	-0.062	-0.062	0.000	0.000	0.000	0.000
85	A	85	SER	0	0.002	-0.004	12.833	0.036	0.036	0.000	0.000	0.000	0.000
86	A	87	SER	0	-0.069	-0.058	15.177	0.008	0.008	0.000	0.000	0.000	0.000
87	A	88	HIS	0	0.004	-0.001	13.710	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	89	ARG	1	0.840	0.913	18.783	-0.081	-0.081	0.000	0.000	0.000	0.000
89	A	90	LEU	0	-0.025	0.004	21.494	-0.008	-0.008	0.000	0.000	0.000	0.000
90	A	91	ARG	1	0.868	0.942	24.237	-0.032	-0.032	0.000	0.000	0.000	0.000
91	A	92	ILE	0	0.006	0.003	26.468	-0.006	-0.006	0.000	0.000	0.000	0.000
92	A	93	TYR	0	0.013	0.000	29.184	0.003	0.003	0.000	0.000	0.000	0.000
93	A	94	GLU	-1	-0.834	-0.922	32.468	0.007	0.007	0.000	0.000	0.000	0.000
94	A	95	ARG	1	0.934	0.968	35.322	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	96	GLU	-1	-0.830	-0.900	33.624	-0.016	-0.016	0.000	0.000	0.000	0.000
96	A	97	ASP	-1	-0.874	-0.942	33.496	-0.011	-0.011	0.000	0.000	0.000	0.000
97	A	98	TYR	0	-0.102	-0.073	28.096	0.001	0.001	0.000	0.000	0.000	0.000
98	A	99	ARG	1	0.924	0.977	33.760	0.000	0.000	0.000	0.000	0.000	0.000
99	A	100	GLY	0	-0.021	-0.021	36.347	0.000	0.000	0.000	0.000	0.000	0.000
100	A	101	GLN	0	-0.023	-0.012	37.429	0.004	0.004	0.000	0.000	0.000	0.000
101	A	102	MET	0	-0.010	0.002	31.844	0.000	0.000	0.000	0.000	0.000	0.000
102	A	103	VAL	0	-0.024	-0.001	29.855	0.002	0.002	0.000	0.000	0.000	0.000
103	A	104	GLU	-1	-0.778	-0.890	27.516	0.050	0.050	0.000	0.000	0.000	0.000
104	A	105	ILE	0	-0.061	-0.029	24.274	0.003	0.003	0.000	0.000	0.000	0.000
105	A	106	THR	0	0.001	-0.027	22.590	0.001	0.001	0.000	0.000	0.000	0.000
106	A	107	GLU	-1	-0.902	-0.937	21.275	0.158	0.158	0.000	0.000	0.000	0.000
107	A	108	ASP	-1	-0.860	-0.922	18.777	0.118	0.118	0.000	0.000	0.000	0.000
108	A	109	CYS	0	-0.029	0.000	21.643	-0.005	-0.005	0.000	0.000	0.000	0.000
109	A	110	SER	0	0.011	0.000	24.279	-0.006	-0.006	0.000	0.000	0.000	0.000
110	A	111	SER	0	0.006	-0.040	25.460	-0.008	-0.008	0.000	0.000	0.000	0.000
111	A	112	LEU	0	-0.020	-0.025	25.664	0.002	0.002	0.000	0.000	0.000	0.000
112	A	113	HIS	1	0.787	0.887	29.271	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	114	GLU	-1	-0.852	-0.896	32.216	0.017	0.017	0.000	0.000	0.000	0.000
114	A	115	ARG	1	0.892	0.951	29.490	-0.043	-0.043	0.000	0.000	0.000	0.000
115	A	116	PHE	0	0.012	0.007	28.319	0.005	0.005	0.000	0.000	0.000	0.000
116	A	117	HIS	0	0.036	0.013	34.340	-0.003	-0.003	0.000	0.000	0.000	0.000
117	A	118	PHE	0	-0.017	0.014	32.727	-0.002	-0.002	0.000	0.000	0.000	0.000
118	A	119	SER	0	0.053	0.015	35.493	0.001	0.001	0.000	0.000	0.000	0.000
119	A	120	GLU	-1	-0.869	-0.900	34.962	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	121	ILE	0	-0.029	-0.038	29.216	0.003	0.003	0.000	0.000	0.000	0.000
121	A	122	HIS	0	-0.077	-0.049	31.765	-0.005	-0.005	0.000	0.000	0.000	0.000
122	A	123	SER	0	-0.039	-0.024	29.507	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	124	PHE	0	-0.014	-0.005	25.189	0.006	0.006	0.000	0.000	0.000	0.000
124	A	125	HIS	0	0.040	0.017	26.162	-0.004	-0.004	0.000	0.000	0.000	0.000
125	A	126	VAL	0	-0.018	0.008	19.356	0.009	0.009	0.000	0.000	0.000	0.000
126	A	127	LEU	0	0.014	0.007	22.421	-0.005	-0.005	0.000	0.000	0.000	0.000
127	A	128	GLU	-1	-0.824	-0.885	19.161	0.099	0.099	0.000	0.000	0.000	0.000
128	A	129	GLY	0	0.062	0.028	15.356	0.004	0.004	0.000	0.000	0.000	0.000
129	A	130	TRP	0	0.017	0.002	12.779	-0.046	-0.046	0.000	0.000	0.000	0.000
130	A	131	TRP	0	0.013	-0.014	14.858	0.039	0.039	0.000	0.000	0.000	0.000
131	A	132	VAL	0	0.001	0.008	14.423	-0.024	-0.024	0.000	0.000	0.000	0.000
132	A	133	LEU	0	0.014	0.011	17.224	0.014	0.014	0.000	0.000	0.000	0.000
133	A	134	TYR	0	-0.004	-0.008	16.725	-0.003	-0.003	0.000	0.000	0.000	0.000
134	A	135	GLU	-1	-0.746	-0.861	22.419	-0.033	-0.033	0.000	0.000	0.000	0.000
135	A	136	MET	0	-0.042	-0.027	25.366	0.004	0.004	0.000	0.000	0.000	0.000
136	A	137	PRO	0	0.038	0.023	25.495	0.002	0.002	0.000	0.000	0.000	0.000
137	A	138	ASN	0	-0.072	-0.049	24.658	0.003	0.003	0.000	0.000	0.000	0.000
138	A	139	TYR	0	-0.018	-0.014	19.885	0.002	0.002	0.000	0.000	0.000	0.000
139	A	140	ARG	1	0.987	0.996	21.314	-0.006	-0.006	0.000	0.000	0.000	0.000
140	A	141	GLY	0	0.045	0.020	23.435	0.003	0.003	0.000	0.000	0.000	0.000
141	A	142	ARG	1	0.823	0.893	22.371	0.045	0.045	0.000	0.000	0.000	0.000
142	A	143	GLN	0	0.051	0.023	16.688	0.013	0.013	0.000	0.000	0.000	0.000
143	A	144	TYR	0	0.023	0.006	19.415	-0.016	-0.016	0.000	0.000	0.000	0.000
144	A	145	LEU	0	-0.042	-0.019	12.592	0.017	0.017	0.000	0.000	0.000	0.000
145	A	146	LEU	0	-0.011	-0.001	16.660	-0.007	-0.007	0.000	0.000	0.000	0.000
146	A	147	ARG	1	0.969	0.995	15.878	0.115	0.115	0.000	0.000	0.000	0.000
147	A	148	PRO	0	0.006	-0.009	16.444	-0.003	-0.003	0.000	0.000	0.000	0.000
148	A	149	GLY	0	0.001	0.006	19.632	-0.013	-0.013	0.000	0.000	0.000	0.000
149	A	150	ASP	-1	-0.878	-0.920	22.911	0.003	0.003	0.000	0.000	0.000	0.000
150	A	151	TYR	0	-0.005	-0.016	20.179	-0.011	-0.011	0.000	0.000	0.000	0.000
151	A	152	ARG	1	0.918	0.953	26.678	0.011	0.011	0.000	0.000	0.000	0.000
152	A	153	ARG	1	0.905	0.925	29.393	0.021	0.021	0.000	0.000	0.000	0.000
153	A	154	TYR	0	0.080	0.014	28.070	-0.003	-0.003	0.000	0.000	0.000	0.000
154	A	155	HIS	0	-0.019	0.007	27.270	-0.004	-0.004	0.000	0.000	0.000	0.000
155	A	156	GLU	-1	-0.937	-0.969	26.323	-0.045	-0.045	0.000	0.000	0.000	0.000
156	A	157	TRP	0	-0.048	-0.009	22.568	0.000	0.000	0.000	0.000	0.000	0.000
157	A	158	GLY	0	-0.028	-0.013	22.625	-0.006	-0.006	0.000	0.000	0.000	0.000
158	A	159	ALA	0	-0.043	0.001	24.339	-0.006	-0.006	0.000	0.000	0.000	0.000
159	A	160	VAL	0	0.004	-0.005	26.463	0.002	0.002	0.000	0.000	0.000	0.000
160	A	161	ASP	-1	-0.846	-0.924	29.042	-0.029	-0.029	0.000	0.000	0.000	0.000
161	A	162	ALA	0	0.040	0.012	29.306	-0.001	-0.001	0.000	0.000	0.000	0.000
162	A	163	ARG	1	0.855	0.933	29.599	0.022	0.022	0.000	0.000	0.000	0.000
163	A	164	VAL	0	-0.008	0.002	26.486	-0.003	-0.003	0.000	0.000	0.000	0.000
164	A	165	GLY	0	0.003	-0.017	26.200	0.002	0.002	0.000	0.000	0.000	0.000
165	A	166	SER	0	-0.078	-0.032	23.495	0.007	0.007	0.000	0.000	0.000	0.000
166	A	167	LEU	0	0.013	0.019	20.591	-0.008	-0.008	0.000	0.000	0.000	0.000
167	A	168	ARG	1	0.886	0.964	15.657	-0.049	-0.049	0.000	0.000	0.000	0.000
168	A	169	ARG	1	0.958	0.985	16.155	-0.188	-0.188	0.000	0.000	0.000	0.000
169	A	170	ALA	0	-0.060	-0.020	10.925	0.012	0.012	0.000	0.000	0.000	0.000
170	A	171	VAL	0	0.002	-0.003	11.106	0.025	0.025	0.000	0.000	0.000	0.000
171	A	172	ASP	-1	-0.749	-0.896	5.788	1.427	1.427	0.000	0.000	0.000	0.000
172	A	173	PHE	0	-0.020	-0.012	8.868	-0.048	-0.048	0.000	0.000	0.000	0.000
173	A	174	TYR	0	0.027	0.025	8.370	0.216	0.216	0.000	0.000	0.000	0.000

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