FMO DATABASE

FMODB ID: 6NZVZ

Calculation Name: 1CMI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1CMI

Chain ID: A

ChEMBL ID:

UniProt ID: P63167

Base Structure: X-ray

Registration Date: 2023-06-22

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	85
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-615767.614562
FMO2-HF: Nuclear repulsion	580932.187044
FMO2-HF: Total energy	-34835.427518
FMO2-MP2: Total energy	-34936.173119

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:5:LYS)

Summations of interaction energy for fragment #1(A:5:LYS)

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.
1.027	3.274	0.019	-0.801	-1.466	0.002

Interaction energy analysis for fragmet #1(A:5:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.949 / q_NPA : 0.959

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

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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	7	VAL	0	-0.029	-0.020	3.774	-1.260	0.196	-0.011	-0.559	-0.887	0.002
4	A	8	ILE	0	0.032	0.018	6.208	1.779	1.779	0.000	0.000	0.000	0.000
5	A	9	LYS	1	0.870	0.951	8.765	32.027	32.027	0.000	0.000	0.000	0.000
6	A	10	ASN	0	-0.017	-0.018	12.274	1.782	1.782	0.000	0.000	0.000	0.000
7	A	11	ALA	0	0.026	0.019	14.120	-0.160	-0.160	0.000	0.000	0.000	0.000
8	A	12	ASP	-1	-0.829	-0.916	16.134	-12.704	-12.704	0.000	0.000	0.000	0.000
9	A	13	MET	0	-0.051	0.004	16.154	0.426	0.426	0.000	0.000	0.000	0.000
10	A	14	SER	0	-0.002	-0.026	18.103	-0.550	-0.550	0.000	0.000	0.000	0.000
11	A	15	GLU	-1	-0.901	-0.964	15.487	-15.691	-15.691	0.000	0.000	0.000	0.000
12	A	16	GLU	-1	-0.850	-0.901	14.902	-14.081	-14.081	0.000	0.000	0.000	0.000
13	A	17	MET	0	-0.011	0.005	15.700	-0.625	-0.625	0.000	0.000	0.000	0.000
14	A	18	GLN	0	-0.024	-0.031	12.012	-1.858	-1.858	0.000	0.000	0.000	0.000
15	A	19	GLN	0	0.016	0.009	11.059	-1.617	-1.617	0.000	0.000	0.000	0.000
16	A	20	ASP	-1	-0.751	-0.836	11.107	-16.301	-16.301	0.000	0.000	0.000	0.000
17	A	21	SER	0	-0.036	-0.023	12.026	0.179	0.179	0.000	0.000	0.000	0.000
18	A	22	VAL	0	-0.016	-0.011	5.795	-1.022	-1.022	0.000	0.000	0.000	0.000
19	A	23	GLU	-1	-0.903	-0.929	8.116	-19.133	-19.133	0.000	0.000	0.000	0.000
20	A	24	CYS	0	-0.007	0.011	9.499	0.146	0.146	0.000	0.000	0.000	0.000
21	A	25	ALA	0	0.017	-0.012	8.843	0.400	0.400	0.000	0.000	0.000	0.000
22	A	26	THR	0	-0.062	-0.047	5.861	-1.838	-1.838	0.000	0.000	0.000	0.000
23	A	27	GLN	0	0.015	0.019	7.961	0.841	0.841	0.000	0.000	0.000	0.000
24	A	28	ALA	0	-0.041	-0.018	11.413	0.777	0.777	0.000	0.000	0.000	0.000
25	A	29	LEU	0	-0.029	-0.023	7.436	0.435	0.435	0.000	0.000	0.000	0.000
26	A	30	GLU	-1	-0.957	-0.965	8.845	-22.940	-22.940	0.000	0.000	0.000	0.000
27	A	31	LYS	1	0.861	0.943	11.475	15.349	15.349	0.000	0.000	0.000	0.000
28	A	32	TYR	0	-0.055	-0.035	14.366	1.520	1.520	0.000	0.000	0.000	0.000
29	A	33	ASN	0	0.023	0.006	14.612	-1.626	-1.626	0.000	0.000	0.000	0.000
30	A	34	ILE	0	-0.010	0.000	16.759	-0.403	-0.403	0.000	0.000	0.000	0.000
31	A	35	GLU	-1	-0.837	-0.924	15.364	-18.051	-18.051	0.000	0.000	0.000	0.000
32	A	36	LYS	1	0.836	0.912	17.086	12.941	12.941	0.000	0.000	0.000	0.000
33	A	37	ASP	-1	-0.822	-0.915	19.142	-13.108	-13.108	0.000	0.000	0.000	0.000
34	A	38	ILE	0	0.020	0.021	12.644	0.113	0.113	0.000	0.000	0.000	0.000
35	A	39	ALA	0	-0.002	-0.011	15.725	-0.127	-0.127	0.000	0.000	0.000	0.000
36	A	40	ALA	0	-0.056	-0.031	17.347	0.459	0.459	0.000	0.000	0.000	0.000
37	A	41	HIS	0	0.025	0.016	15.099	0.779	0.779	0.000	0.000	0.000	0.000
38	A	42	ILE	0	0.075	0.022	12.395	0.330	0.330	0.000	0.000	0.000	0.000
39	A	43	LYS	1	0.773	0.870	16.272	12.325	12.325	0.000	0.000	0.000	0.000
40	A	44	LYS	1	0.955	0.959	19.676	12.420	12.420	0.000	0.000	0.000	0.000
41	A	45	GLU	-1	-0.813	-0.896	17.196	-12.631	-12.631	0.000	0.000	0.000	0.000
42	A	46	PHE	0	0.023	0.007	14.993	0.362	0.362	0.000	0.000	0.000	0.000
43	A	47	ASP	-1	-0.780	-0.882	20.022	-11.258	-11.258	0.000	0.000	0.000	0.000
44	A	48	LYS	1	0.733	0.863	21.650	12.824	12.824	0.000	0.000	0.000	0.000
45	A	49	LYS	1	0.858	0.921	17.538	14.664	14.664	0.000	0.000	0.000	0.000
46	A	50	TYR	0	-0.024	-0.045	18.285	0.318	0.318	0.000	0.000	0.000	0.000
47	A	51	ASN	0	-0.020	-0.005	23.562	0.396	0.396	0.000	0.000	0.000	0.000
48	A	52	PRO	0	0.001	0.016	25.402	-0.342	-0.342	0.000	0.000	0.000	0.000
49	A	53	THR	0	-0.044	-0.024	26.369	0.246	0.246	0.000	0.000	0.000	0.000
50	A	54	TRP	0	-0.015	-0.009	19.300	-0.392	-0.392	0.000	0.000	0.000	0.000
51	A	55	HIS	0	-0.032	0.001	21.656	0.268	0.268	0.000	0.000	0.000	0.000
52	A	56	CYS	0	-0.065	-0.030	16.277	-0.788	-0.788	0.000	0.000	0.000	0.000
53	A	57	ILE	0	0.005	0.012	17.578	0.556	0.556	0.000	0.000	0.000	0.000
54	A	58	VAL	0	0.033	0.014	13.108	-1.095	-1.095	0.000	0.000	0.000	0.000
55	A	59	GLY	0	0.047	0.022	14.204	1.123	1.123	0.000	0.000	0.000	0.000
56	A	60	ARG	1	0.899	0.925	9.116	25.365	25.365	0.000	0.000	0.000	0.000
57	A	61	ASN	0	-0.053	-0.030	13.504	0.163	0.163	0.000	0.000	0.000	0.000
58	A	62	PHE	0	0.044	0.030	15.413	0.881	0.881	0.000	0.000	0.000	0.000
59	A	63	GLY	0	0.033	0.032	18.519	-0.685	-0.685	0.000	0.000	0.000	0.000
60	A	64	SER	0	-0.056	-0.040	20.572	0.396	0.396	0.000	0.000	0.000	0.000
61	A	65	TYR	0	0.031	0.012	22.959	-0.266	-0.266	0.000	0.000	0.000	0.000
62	A	66	VAL	0	-0.010	0.005	22.928	0.321	0.321	0.000	0.000	0.000	0.000
63	A	67	THR	0	0.004	0.007	26.157	0.091	0.091	0.000	0.000	0.000	0.000
64	A	68	HIS	1	0.833	0.908	23.477	12.911	12.911	0.000	0.000	0.000	0.000
65	A	69	GLU	-1	-0.792	-0.892	25.624	-10.508	-10.508	0.000	0.000	0.000	0.000
66	A	70	THR	0	-0.022	-0.009	24.596	-0.378	-0.378	0.000	0.000	0.000	0.000
67	A	71	LYS	1	0.938	0.955	22.297	11.471	11.471	0.000	0.000	0.000	0.000
68	A	72	HIS	0	-0.024	-0.005	20.905	-0.277	-0.277	0.000	0.000	0.000	0.000
69	A	73	PHE	0	0.000	-0.019	18.402	0.187	0.187	0.000	0.000	0.000	0.000
70	A	74	ILE	0	0.026	0.010	12.019	-0.395	-0.395	0.000	0.000	0.000	0.000
71	A	75	TYR	0	0.021	0.021	13.614	-0.553	-0.553	0.000	0.000	0.000	0.000
72	A	76	PHE	0	-0.019	-0.017	7.717	-0.714	-0.714	0.000	0.000	0.000	0.000
73	A	77	TYR	0	0.002	-0.009	6.366	0.944	0.944	0.000	0.000	0.000	0.000
74	A	78	LEU	0	0.066	0.029	3.244	-4.858	-4.424	0.032	-0.171	-0.295	0.000
75	A	79	GLY	0	0.039	0.041	4.124	3.891	4.211	-0.001	-0.059	-0.260	0.000
76	A	80	GLN	0	-0.044	-0.027	4.631	-7.676	-7.639	-0.001	-0.012	-0.024	0.000
77	A	81	VAL	0	0.014	0.016	6.786	4.283	4.283	0.000	0.000	0.000	0.000
78	A	82	ALA	0	-0.017	0.000	8.809	-3.082	-3.082	0.000	0.000	0.000	0.000
79	A	83	ILE	0	0.023	-0.004	9.751	1.980	1.980	0.000	0.000	0.000	0.000
80	A	84	LEU	0	-0.007	0.005	12.931	-0.494	-0.494	0.000	0.000	0.000	0.000
81	A	85	LEU	0	-0.007	0.003	15.183	0.646	0.646	0.000	0.000	0.000	0.000
82	A	86	PHE	0	0.004	-0.013	17.142	-0.079	-0.079	0.000	0.000	0.000	0.000
83	A	87	LYS	1	0.907	0.978	20.465	11.317	11.317	0.000	0.000	0.000	0.000
84	A	88	SER	0	-0.009	-0.021	23.588	-0.013	-0.013	0.000	0.000	0.000	0.000
85	A	89	GLY	0	0.022	0.025	27.111	-0.026	-0.026	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:LYS)