FMO DATABASE

FMODB ID: NNLJQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1151731.257699
FMO2-HF: Nuclear repulsion	1098793.247515
FMO2-HF: Total energy	-52938.010184
FMO2-MP2: Total energy	-53093.62027

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.
-9.944	-4.916	11.293	-4.589	-11.732	-0.029

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 : 0.002 / q_NPA : 0.017

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	0.002	0.000	2.830	-3.673	-1.063	0.312	-1.479	-1.442	-0.003
4	A	4	SER	0	0.123	0.074	5.310	0.406	0.550	-0.001	-0.006	-0.137	0.000
5	A	5	GLY	0	-0.001	0.013	6.327	0.351	0.351	0.000	0.000	0.000	0.000
6	A	6	THR	0	-0.074	-0.052	6.972	0.267	0.267	0.000	0.000	0.000	0.000
7	A	7	SER	0	0.041	0.006	9.512	0.030	0.030	0.000	0.000	0.000	0.000
8	A	8	ILE	0	-0.062	-0.015	12.307	0.037	0.037	0.000	0.000	0.000	0.000
9	A	9	THR	0	0.006	-0.017	14.864	-0.006	-0.006	0.000	0.000	0.000	0.000
10	A	10	CYS	0	-0.078	-0.018	18.556	0.030	0.030	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.809	-0.907	21.528	-0.141	-0.141	0.000	0.000	0.000	0.000
12	A	12	VAL	0	-0.036	-0.015	23.945	0.019	0.019	0.000	0.000	0.000	0.000
13	A	13	GLY	0	0.004	0.009	26.744	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.028	-0.020	27.680	0.010	0.010	0.000	0.000	0.000	0.000
15	A	15	GLN	0	-0.014	-0.013	31.964	0.002	0.002	0.000	0.000	0.000	0.000
16	A	16	LEU	0	0.040	0.034	34.153	0.001	0.001	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.066	-0.044	35.841	0.004	0.004	0.000	0.000	0.000	0.000
18	A	18	VAL	0	0.028	0.000	38.246	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	19	PRO	0	-0.007	-0.010	40.871	0.002	0.002	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.906	-0.939	43.590	-0.020	-0.020	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.876	0.938	42.351	0.035	0.035	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.017	0.018	44.278	0.002	0.002	0.000	0.000	0.000	0.000
23	A	23	PRO	0	-0.019	-0.025	39.121	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	24	VAL	0	-0.017	0.003	38.129	0.001	0.001	0.000	0.000	0.000	0.000
25	A	25	PRO	0	-0.031	-0.008	36.556	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.016	-0.011	31.214	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	27	VAL	0	-0.004	0.001	28.792	0.010	0.010	0.000	0.000	0.000	0.000
28	A	28	ALA	0	0.023	0.009	26.358	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.790	0.881	20.466	0.277	0.277	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.004	-0.005	20.413	0.004	0.004	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.827	-0.902	16.915	-0.356	-0.356	0.000	0.000	0.000	0.000
32	A	32	TYR	0	0.003	-0.016	9.183	0.039	0.039	0.000	0.000	0.000	0.000
33	A	33	SER	0	0.033	0.018	10.935	0.047	0.047	0.000	0.000	0.000	0.000
34	A	34	VAL	0	0.006	0.002	5.270	0.084	0.084	0.000	0.000	0.000	0.000
35	A	35	ASH	0	-0.044	-0.038	6.777	-0.172	-0.172	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.855	-0.907	8.714	-0.440	-0.440	0.000	0.000	0.000	0.000
37	A	37	PRO	0	0.011	0.035	6.746	0.265	0.265	0.000	0.000	0.000	0.000
38	A	38	TYR	0	0.036	0.011	8.876	0.197	0.197	0.000	0.000	0.000	0.000
39	A	39	ALA	0	-0.011	0.019	11.922	0.110	0.110	0.000	0.000	0.000	0.000
40	A	40	ILE	0	-0.016	-0.020	13.999	0.014	0.014	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.819	0.892	13.470	0.533	0.533	0.000	0.000	0.000	0.000
42	A	42	ALA	0	-0.004	-0.019	19.279	0.020	0.020	0.000	0.000	0.000	0.000
43	A	43	ALA	0	0.011	0.010	22.796	0.001	0.001	0.000	0.000	0.000	0.000
44	A	44	PHE	0	-0.012	-0.011	25.517	0.011	0.011	0.000	0.000	0.000	0.000
45	A	45	HIS	1	0.880	0.936	28.920	0.115	0.115	0.000	0.000	0.000	0.000
46	A	46	VAL	0	-0.023	-0.018	32.121	0.008	0.008	0.000	0.000	0.000	0.000
47	A	47	GLY	0	-0.014	-0.002	35.346	0.001	0.001	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.952	-0.985	34.942	-0.090	-0.090	0.000	0.000	0.000	0.000
49	A	49	ASP	-1	-0.919	-0.945	34.352	-0.099	-0.099	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.917	-0.969	31.276	-0.165	-0.165	0.000	0.000	0.000	0.000
51	A	51	PRO	0	-0.079	-0.044	27.516	0.006	0.006	0.000	0.000	0.000	0.000
52	A	52	VAL	0	-0.006	0.016	29.292	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.876	-0.940	21.561	-0.269	-0.269	0.000	0.000	0.000	0.000
54	A	54	TRP	0	-0.060	-0.036	24.198	0.011	0.011	0.000	0.000	0.000	0.000
55	A	55	ILE	0	0.015	0.006	16.687	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	56	PHE	0	-0.029	-0.009	19.310	0.017	0.017	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.055	0.032	16.779	-0.021	-0.021	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.774	0.852	9.712	-0.225	-0.225	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.901	-0.961	16.050	0.109	0.109	0.000	0.000	0.000	0.000
60	A	60	LEU	0	0.052	0.046	17.577	0.026	0.026	0.000	0.000	0.000	0.000
61	A	61	LEU	0	0.014	-0.007	20.013	0.012	0.012	0.000	0.000	0.000	0.000
62	A	62	THR	0	-0.008	0.002	17.945	0.027	0.027	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.021	-0.013	20.464	0.021	0.021	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.059	0.023	22.981	0.002	0.002	0.000	0.000	0.000	0.000
65	A	65	ILE	0	-0.006	0.001	22.308	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	66	ILE	0	-0.069	-0.030	24.449	0.005	0.005	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.897	0.935	25.887	-0.136	-0.136	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.835	-0.906	27.814	0.015	0.015	0.000	0.000	0.000	0.000
69	A	69	THR	0	-0.009	-0.004	24.074	0.007	0.007	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.007	-0.008	26.301	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.857	-0.923	20.494	-0.113	-0.113	0.000	0.000	0.000	0.000
72	A	72	GLY	0	0.004	0.004	25.076	-0.013	-0.013	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.900	-0.952	27.824	-0.071	-0.071	0.000	0.000	0.000	0.000
74	A	74	VAL	0	0.011	0.030	24.497	0.008	0.008	0.000	0.000	0.000	0.000
75	A	75	ARG	1	0.851	0.908	27.421	0.012	0.012	0.000	0.000	0.000	0.000
76	A	76	ILE	0	-0.005	0.000	23.639	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	77	TRP	0	0.036	0.007	27.841	0.007	0.007	0.000	0.000	0.000	0.000
78	A	78	PRO	0	-0.003	0.024	29.374	-0.008	-0.008	0.000	0.000	0.000	0.000
79	A	79	SER	0	-0.067	-0.049	30.988	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	80	GLN	0	0.005	0.009	33.456	0.014	0.014	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.762	-0.853	36.022	0.017	0.017	0.000	0.000	0.000	0.000
82	A	82	GLY	0	-0.007	-0.012	37.938	0.000	0.000	0.000	0.000	0.000	0.000
83	A	83	LYS	1	0.943	0.950	36.420	-0.048	-0.048	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.860	-0.922	32.188	0.055	0.055	0.000	0.000	0.000	0.000
85	A	85	ARG	1	0.832	0.928	28.920	-0.093	-0.093	0.000	0.000	0.000	0.000
86	A	86	MET	0	-0.055	0.009	30.227	0.000	0.000	0.000	0.000	0.000	0.000
87	A	87	VAL	0	0.005	-0.001	26.577	0.010	0.010	0.000	0.000	0.000	0.000
88	A	88	ASN	0	-0.059	-0.017	29.879	-0.014	-0.014	0.000	0.000	0.000	0.000
89	A	89	ILE	0	0.071	0.038	25.109	0.006	0.006	0.000	0.000	0.000	0.000
90	A	90	ALA	0	-0.025	-0.015	28.863	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	91	LEU	0	0.023	0.033	28.757	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.050	-0.044	31.082	0.008	0.008	0.000	0.000	0.000	0.000
93	A	93	SER	0	0.064	0.018	33.429	-0.008	-0.008	0.000	0.000	0.000	0.000
94	A	94	PRO	0	-0.014	-0.010	36.215	0.006	0.006	0.000	0.000	0.000	0.000
95	A	95	PHE	0	-0.050	-0.021	38.926	0.004	0.004	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.010	0.015	39.565	0.002	0.002	0.000	0.000	0.000	0.000
97	A	97	GLN	0	-0.046	-0.015	35.152	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	98	ALA	0	0.023	0.023	34.184	0.004	0.004	0.000	0.000	0.000	0.000
99	A	99	ARG	1	0.885	0.928	33.369	0.005	0.005	0.000	0.000	0.000	0.000
100	A	100	PHE	0	0.052	0.030	29.303	0.003	0.003	0.000	0.000	0.000	0.000
101	A	101	HIS	1	0.731	0.843	32.054	0.002	0.002	0.000	0.000	0.000	0.000
102	A	102	ALA	0	0.083	0.033	28.887	-0.007	-0.007	0.000	0.000	0.000	0.000
103	A	103	GLN	0	0.031	-0.017	28.913	0.004	0.004	0.000	0.000	0.000	0.000
104	A	104	VAL	0	0.012	-0.006	24.883	-0.005	-0.005	0.000	0.000	0.000	0.000
105	A	105	ALA	0	-0.017	0.001	24.573	0.004	0.004	0.000	0.000	0.000	0.000
106	A	106	PRO	0	0.029	0.009	23.138	0.012	0.012	0.000	0.000	0.000	0.000
107	A	107	LEU	0	0.032	0.020	21.797	-0.006	-0.006	0.000	0.000	0.000	0.000
108	A	108	SER	0	0.015	0.000	20.283	0.007	0.007	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.864	-0.909	18.369	0.166	0.166	0.000	0.000	0.000	0.000
110	A	110	PHE	0	-0.014	-0.008	16.432	0.023	0.023	0.000	0.000	0.000	0.000
111	A	111	LEU	0	0.024	0.005	15.832	-0.005	-0.005	0.000	0.000	0.000	0.000
112	A	112	HIS	0	-0.049	-0.006	13.732	0.066	0.066	0.000	0.000	0.000	0.000
113	A	113	ARG	1	0.859	0.921	12.764	0.010	0.010	0.000	0.000	0.000	0.000
114	A	114	THR	0	-0.063	-0.039	11.266	-0.003	-0.003	0.000	0.000	0.000	0.000
115	A	115	TYR	0	-0.056	-0.049	9.912	0.045	0.045	0.000	0.000	0.000	0.000
116	A	116	GLU	-1	-0.909	-0.955	8.905	0.618	0.618	0.000	0.000	0.000	0.000
117	A	117	LEU	0	-0.065	-0.015	6.460	0.128	0.128	0.000	0.000	0.000	0.000
118	A	118	VAL	0	0.030	0.011	5.044	0.561	0.746	-0.001	-0.013	-0.170	0.000
119	A	119	PRO	0	0.041	0.032	6.113	-0.573	-0.573	0.000	0.000	0.000	0.000
120	A	120	ALA	0	-0.010	-0.006	8.814	-0.119	-0.119	0.000	0.000	0.000	0.000
121	A	121	GLY	0	-0.090	-0.046	10.386	0.138	0.138	0.000	0.000	0.000	0.000
122	A	122	GLN	0	-0.014	-0.010	5.455	1.133	1.133	0.000	0.000	0.000	0.000
123	A	123	GLU	-1	-0.761	-0.875	4.598	-0.471	-0.341	-0.001	-0.005	-0.124	0.000
124	A	124	SER	0	-0.029	-0.018	5.731	-0.552	-0.552	0.000	0.000	0.000	0.000
125	A	125	ASP	-1	-0.843	-0.925	2.426	0.342	0.432	1.825	-0.525	-1.390	-0.002
126	A	126	TYR	0	-0.030	-0.023	2.846	-5.795	-3.609	7.205	-2.304	-7.088	-0.022
127	A	127	ILE	0	0.012	0.009	3.667	0.704	0.758	0.015	0.024	-0.093	0.000
128	A	128	ASP	-1	-0.907	-0.948	5.851	-0.904	-0.904	0.000	0.000	0.000	0.000
129	A	129	ILE	0	-0.001	0.005	2.368	0.044	-0.327	1.939	-0.281	-1.288	-0.002
130	A	130	ASP	-1	-0.881	-0.957	6.345	-1.515	-1.515	0.000	0.000	0.000	0.000
131	A	131	ALA	0	-0.037	-0.011	8.980	0.284	0.284	0.000	0.000	0.000	0.000
132	A	132	GLU	-1	-0.912	-0.959	7.686	-1.418	-1.418	0.000	0.000	0.000	0.000
133	A	133	ILE	0	-0.056	-0.027	8.448	0.200	0.200	0.000	0.000	0.000	0.000
134	A	134	ALA	0	-0.037	-0.020	11.873	0.155	0.155	0.000	0.000	0.000	0.000
135	A	135	GLU	-1	-0.986	-0.993	14.124	-0.553	-0.553	0.000	0.000	0.000	0.000
136	A	136	HIS	0	-0.121	-0.058	13.531	0.152	0.152	0.000	0.000	0.000	0.000
137	A	137	LEU	0	-0.105	-0.042	16.423	0.078	0.078	0.000	0.000	0.000	0.000

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