FMO DATABASE

FMODB ID: 89Q4Y

Calculation Name: 3CM1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CM1

Chain ID: A

ChEMBL ID:

UniProt ID: Q47N25

Base Structure: X-ray

Registration Date: 2023-09-23

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	137
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1150072.576243
FMO2-HF: Nuclear repulsion	1097134.944851
FMO2-HF: Total energy	-52937.631392
FMO2-MP2: Total energy	-53093.184039

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.
-8.387	-3.949	9.046	-3.823	-9.661	-0.021

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 : 0.010 / q_NPA : 0.019

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	SER	0	-0.003	-0.005	3.195	-3.432	-0.769	0.080	-1.466	-1.278	0.001
4	A	4	SER	0	0.114	0.058	5.406	0.445	0.445	0.000	0.000	0.000	0.000
5	A	5	GLY	0	0.025	0.031	6.187	0.309	0.309	0.000	0.000	0.000	0.000
6	A	6	THR	0	-0.079	-0.039	7.066	0.273	0.273	0.000	0.000	0.000	0.000
7	A	7	SER	0	0.025	0.007	9.494	0.024	0.024	0.000	0.000	0.000	0.000
8	A	8	ILE	0	-0.041	-0.011	12.260	0.048	0.048	0.000	0.000	0.000	0.000
9	A	9	THR	0	0.022	-0.005	15.069	-0.011	-0.011	0.000	0.000	0.000	0.000
10	A	10	CYS	0	-0.088	-0.025	18.701	0.031	0.031	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.902	-0.949	21.492	-0.125	-0.125	0.000	0.000	0.000	0.000
12	A	12	VAL	0	-0.012	-0.013	24.105	0.021	0.021	0.000	0.000	0.000	0.000
13	A	13	GLY	0	-0.020	0.006	26.872	-0.009	-0.009	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.003	-0.014	28.010	0.010	0.010	0.000	0.000	0.000	0.000
15	A	15	GLN	0	-0.008	-0.012	31.861	0.002	0.002	0.000	0.000	0.000	0.000
16	A	16	LEU	0	0.033	0.026	34.246	0.002	0.002	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.060	-0.040	35.989	0.002	0.002	0.000	0.000	0.000	0.000
18	A	18	VAL	0	0.013	-0.010	38.352	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	19	PRO	0	0.000	-0.004	40.656	0.002	0.002	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.904	-0.936	43.587	-0.012	-0.012	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.884	0.941	42.106	0.029	0.029	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.003	0.013	44.166	0.002	0.002	0.000	0.000	0.000	0.000
23	A	23	PRO	0	-0.017	-0.025	39.334	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	24	VAL	0	-0.008	0.008	38.264	0.000	0.000	0.000	0.000	0.000	0.000
25	A	25	PRO	0	-0.025	-0.004	36.378	0.000	0.000	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.010	-0.008	31.057	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	27	VAL	0	0.026	0.016	28.753	0.008	0.008	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.004	-0.004	26.202	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.832	0.907	20.874	0.248	0.248	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.003	-0.004	20.172	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.828	-0.913	17.021	-0.325	-0.325	0.000	0.000	0.000	0.000
32	A	32	TYR	0	0.009	-0.014	9.320	0.028	0.028	0.000	0.000	0.000	0.000
33	A	33	SER	0	0.032	0.014	11.138	-0.042	-0.042	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.004	-0.006	5.541	0.098	0.098	0.000	0.000	0.000	0.000
35	A	35	ASH	0	-0.040	-0.042	6.784	-0.245	-0.245	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.850	-0.916	8.750	-0.461	-0.461	0.000	0.000	0.000	0.000
37	A	37	PRO	0	0.030	0.033	6.873	0.259	0.259	0.000	0.000	0.000	0.000
38	A	38	TYR	0	0.036	0.018	9.028	0.190	0.190	0.000	0.000	0.000	0.000
39	A	39	ALA	0	-0.025	0.012	12.205	0.106	0.106	0.000	0.000	0.000	0.000
40	A	40	ILE	0	-0.026	-0.011	14.051	0.005	0.005	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.843	0.919	13.775	0.463	0.463	0.000	0.000	0.000	0.000
42	A	42	ALA	0	-0.018	-0.029	19.298	0.022	0.022	0.000	0.000	0.000	0.000
43	A	43	ALA	0	0.003	0.018	22.705	0.000	0.000	0.000	0.000	0.000	0.000
44	A	44	PHE	0	-0.012	-0.010	25.469	0.015	0.015	0.000	0.000	0.000	0.000
45	A	45	HIS	1	0.917	0.948	28.847	0.098	0.098	0.000	0.000	0.000	0.000
46	A	46	VAL	0	-0.014	-0.015	32.029	0.008	0.008	0.000	0.000	0.000	0.000
47	A	47	GLY	0	-0.006	0.010	35.550	0.000	0.000	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.962	-0.978	35.445	-0.080	-0.080	0.000	0.000	0.000	0.000
49	A	49	ASP	-1	-0.917	-0.953	34.672	-0.090	-0.090	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.921	-0.972	31.329	-0.154	-0.154	0.000	0.000	0.000	0.000
51	A	51	PRO	0	-0.055	-0.036	27.734	0.007	0.007	0.000	0.000	0.000	0.000
52	A	52	VAL	0	-0.019	0.011	29.026	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.896	-0.958	21.513	-0.261	-0.261	0.000	0.000	0.000	0.000
54	A	54	TRP	0	-0.057	-0.030	24.291	0.009	0.009	0.000	0.000	0.000	0.000
55	A	55	ILE	0	0.032	0.014	16.926	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	56	PHE	0	-0.027	-0.011	19.572	0.013	0.013	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.099	0.053	16.827	-0.018	-0.018	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.812	0.874	9.897	-0.288	-0.288	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.922	-0.981	16.219	0.123	0.123	0.000	0.000	0.000	0.000
60	A	60	LEU	0	0.071	0.055	17.668	0.026	0.026	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.024	-0.020	19.940	0.012	0.012	0.000	0.000	0.000	0.000
62	A	62	THR	0	-0.005	0.008	18.301	0.016	0.016	0.000	0.000	0.000	0.000
63	A	63	VAL	0	0.002	0.007	20.505	0.019	0.019	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.059	0.025	23.009	0.001	0.001	0.000	0.000	0.000	0.000
65	A	65	ILE	0	-0.025	-0.006	22.594	-0.007	-0.007	0.000	0.000	0.000	0.000
66	A	66	ILE	0	-0.067	-0.030	24.562	0.002	0.002	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.893	0.927	26.029	-0.157	-0.157	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.877	-0.922	27.861	0.028	0.028	0.000	0.000	0.000	0.000
69	A	69	THR	0	0.022	0.014	24.619	0.004	0.004	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.001	-0.017	26.590	-0.007	-0.007	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.918	-0.948	21.181	-0.083	-0.083	0.000	0.000	0.000	0.000
72	A	72	GLY	0	-0.007	0.001	25.715	-0.012	-0.012	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.890	-0.945	28.159	-0.063	-0.063	0.000	0.000	0.000	0.000
74	A	74	VAL	0	-0.002	0.014	24.787	0.007	0.007	0.000	0.000	0.000	0.000
75	A	75	ARG	1	0.859	0.913	27.718	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	76	ILE	0	-0.011	-0.007	23.830	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	77	TRP	0	0.034	0.010	28.057	0.008	0.008	0.000	0.000	0.000	0.000
78	A	78	PRO	0	0.000	0.032	29.550	-0.008	-0.008	0.000	0.000	0.000	0.000
79	A	79	SER	0	-0.033	-0.025	31.132	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	80	GLN	0	-0.036	-0.017	33.785	0.013	0.013	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.777	-0.880	36.349	0.026	0.026	0.000	0.000	0.000	0.000
82	A	82	GLY	0	0.019	0.010	38.218	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	83	LYS	1	0.943	0.949	36.492	-0.061	-0.061	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.891	-0.938	32.445	0.069	0.069	0.000	0.000	0.000	0.000
85	A	85	ARG	1	0.857	0.940	29.148	-0.111	-0.111	0.000	0.000	0.000	0.000
86	A	86	MET	0	-0.040	0.002	30.861	0.000	0.000	0.000	0.000	0.000	0.000
87	A	87	VAL	0	0.005	-0.008	26.191	0.009	0.009	0.000	0.000	0.000	0.000
88	A	88	ASN	0	-0.063	-0.023	29.572	-0.016	-0.016	0.000	0.000	0.000	0.000
89	A	89	ILE	0	0.071	0.041	25.304	0.005	0.005	0.000	0.000	0.000	0.000
90	A	90	ALA	0	-0.022	-0.009	29.228	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	91	LEU	0	0.035	0.039	29.311	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.059	-0.040	31.309	0.008	0.008	0.000	0.000	0.000	0.000
93	A	93	SER	0	0.067	0.019	33.428	-0.008	-0.008	0.000	0.000	0.000	0.000
94	A	94	PRO	0	0.006	-0.010	36.196	0.006	0.006	0.000	0.000	0.000	0.000
95	A	95	PHE	0	-0.072	-0.035	38.864	0.004	0.004	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.015	0.026	39.825	0.001	0.001	0.000	0.000	0.000	0.000
97	A	97	GLN	0	-0.036	-0.011	35.458	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	98	ALA	0	0.009	0.014	34.980	0.004	0.004	0.000	0.000	0.000	0.000
99	A	99	ARG	1	0.894	0.934	33.478	-0.007	-0.007	0.000	0.000	0.000	0.000
100	A	100	PHE	0	0.025	0.007	29.248	0.002	0.002	0.000	0.000	0.000	0.000
101	A	101	HIS	1	0.777	0.873	32.088	-0.011	-0.011	0.000	0.000	0.000	0.000
102	A	102	ALA	0	0.079	0.034	28.604	-0.007	-0.007	0.000	0.000	0.000	0.000
103	A	103	GLN	0	0.000	-0.013	29.240	0.006	0.006	0.000	0.000	0.000	0.000
104	A	104	VAL	0	0.021	0.002	25.404	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	105	ALA	0	-0.010	0.005	24.899	0.007	0.007	0.000	0.000	0.000	0.000
106	A	106	PRO	0	0.028	0.011	23.410	0.016	0.016	0.000	0.000	0.000	0.000
107	A	107	LEU	0	0.053	0.031	22.156	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	108	SER	0	-0.006	-0.013	20.534	0.012	0.012	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.858	-0.909	18.857	0.205	0.205	0.000	0.000	0.000	0.000
110	A	110	PHE	0	-0.006	-0.008	16.744	0.031	0.031	0.000	0.000	0.000	0.000
111	A	111	LEU	0	0.022	0.006	16.056	0.005	0.005	0.000	0.000	0.000	0.000
112	A	112	HIS	0	-0.060	-0.021	13.927	0.061	0.061	0.000	0.000	0.000	0.000
113	A	113	ARG	1	0.893	0.929	12.884	-0.019	-0.019	0.000	0.000	0.000	0.000
114	A	114	THR	0	-0.080	-0.033	11.392	0.026	0.026	0.000	0.000	0.000	0.000
115	A	115	TYR	0	-0.053	-0.064	10.120	0.043	0.043	0.000	0.000	0.000	0.000
116	A	116	GLU	-1	-0.919	-0.947	9.016	0.753	0.753	0.000	0.000	0.000	0.000
117	A	117	LEU	0	-0.070	-0.019	6.613	0.251	0.251	0.000	0.000	0.000	0.000
118	A	118	VAL	0	0.025	0.005	5.223	0.812	0.812	0.000	0.000	0.000	0.000
119	A	119	PRO	0	0.036	0.027	6.280	-0.586	-0.586	0.000	0.000	0.000	0.000
120	A	120	ALA	0	-0.019	-0.015	9.055	-0.115	-0.115	0.000	0.000	0.000	0.000
121	A	121	GLY	0	-0.075	-0.037	10.759	0.167	0.167	0.000	0.000	0.000	0.000
122	A	122	GLN	0	-0.012	-0.013	5.816	0.937	0.937	0.000	0.000	0.000	0.000
123	A	123	GLU	-1	-0.771	-0.880	5.022	-0.250	-0.154	-0.001	-0.001	-0.094	0.000
124	A	124	SER	0	-0.009	-0.011	5.949	-0.548	-0.548	0.000	0.000	0.000	0.000
125	A	125	ASP	-1	-0.869	-0.921	2.476	0.199	0.269	1.809	-0.514	-1.365	-0.003
126	A	126	TYR	0	-0.004	-0.025	2.934	-4.269	-2.453	5.390	-1.567	-5.639	-0.017
127	A	127	ILE	0	-0.016	0.001	3.971	0.531	0.604	0.003	-0.019	-0.056	0.000
128	A	128	ASP	-1	-0.911	-0.959	5.939	-0.912	-0.912	0.000	0.000	0.000	0.000
129	A	129	ILE	0	-0.010	0.001	2.453	-0.109	-0.389	1.765	-0.256	-1.229	-0.002
130	A	130	ASP	-1	-0.906	-0.960	6.514	-1.359	-1.359	0.000	0.000	0.000	0.000
131	A	131	ALA	0	-0.058	-0.028	9.373	0.264	0.264	0.000	0.000	0.000	0.000
132	A	132	GLU	-1	-0.890	-0.951	7.673	-1.536	-1.536	0.000	0.000	0.000	0.000
133	A	133	ILE	0	-0.061	-0.020	8.607	0.202	0.202	0.000	0.000	0.000	0.000
134	A	134	ALA	0	-0.012	-0.012	12.118	0.161	0.161	0.000	0.000	0.000	0.000
135	A	135	GLU	-1	-1.014	-1.001	14.170	-0.595	-0.595	0.000	0.000	0.000	0.000
136	A	136	HIS	0	-0.131	-0.065	13.530	0.127	0.127	0.000	0.000	0.000	0.000
137	A	137	LEU	0	-0.094	-0.031	16.511	0.096	0.096	0.000	0.000	0.000	0.000

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