FMO DATABASE

FMODB ID: JLL59

Calculation Name: 5FMN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5FMN

Chain ID: A

ChEMBL ID:

UniProt ID: Q55554

Base Structure: X-ray

Registration Date: 2023-06-21

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	86
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-502607.992592
FMO2-HF: Nuclear repulsion	468213.471272
FMO2-HF: Total energy	-34394.52132
FMO2-MP2: Total energy	-34493.254867

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:22:SER)

Summations of interaction energy for fragment #1(A:22:SER)

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.
-13.455	-8.412	0.318	-2.182	-3.178	0.011

Interaction energy analysis for fragmet #1(A:22:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.049 / 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

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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	24	GLU	-1	-0.917	-0.956	3.086	-0.706	1.840	0.114	-1.111	-1.548	0.005
4	A	25	SER	0	0.002	0.006	2.949	-3.929	-2.586	0.185	-0.579	-0.949	0.004
5	A	26	LEU	0	0.041	0.008	3.307	-2.240	-1.196	0.020	-0.485	-0.579	0.002
6	A	27	GLN	0	0.063	0.027	4.984	-0.855	-0.745	-0.001	-0.007	-0.102	0.000
7	A	28	LYS	1	0.988	0.987	7.352	-1.540	-1.540	0.000	0.000	0.000	0.000
8	A	29	LEU	0	0.014	0.001	7.227	-0.313	-0.313	0.000	0.000	0.000	0.000
9	A	30	VAL	0	0.033	0.030	9.203	-0.216	-0.216	0.000	0.000	0.000	0.000
10	A	31	ASN	0	-0.043	-0.019	11.272	-0.273	-0.273	0.000	0.000	0.000	0.000
11	A	32	ARG	1	0.871	0.940	12.498	-0.725	-0.725	0.000	0.000	0.000	0.000
12	A	33	LEU	0	0.045	0.018	12.287	-0.086	-0.086	0.000	0.000	0.000	0.000
13	A	34	SER	0	0.049	0.036	15.374	-0.065	-0.065	0.000	0.000	0.000	0.000
14	A	35	ARG	1	0.895	0.941	15.698	-0.568	-0.568	0.000	0.000	0.000	0.000
15	A	36	ILE	0	0.010	0.012	17.244	-0.040	-0.040	0.000	0.000	0.000	0.000
16	A	37	GLU	-1	-0.907	-0.945	19.603	0.267	0.267	0.000	0.000	0.000	0.000
17	A	38	GLY	0	-0.052	-0.042	21.509	-0.029	-0.029	0.000	0.000	0.000	0.000
18	A	39	HIS	0	-0.041	-0.024	23.042	-0.007	-0.007	0.000	0.000	0.000	0.000
19	A	40	ILE	0	0.030	0.014	23.183	-0.021	-0.021	0.000	0.000	0.000	0.000
20	A	41	ARG	1	0.917	0.957	22.884	-0.266	-0.266	0.000	0.000	0.000	0.000
21	A	42	GLY	0	0.017	0.018	27.559	-0.013	-0.013	0.000	0.000	0.000	0.000
22	A	43	VAL	0	0.038	0.007	28.645	-0.012	-0.012	0.000	0.000	0.000	0.000
23	A	44	LYS	1	0.921	0.969	29.945	-0.150	-0.150	0.000	0.000	0.000	0.000
24	A	45	THR	0	0.002	-0.005	32.119	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	46	MET	0	-0.045	-0.017	33.400	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	47	VAL	0	0.002	0.011	34.899	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	48	GLN	0	-0.046	-0.026	35.779	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	49	GLU	-1	-0.958	-0.970	38.033	0.106	0.106	0.000	0.000	0.000	0.000
29	A	50	ASN	0	-0.057	-0.022	40.205	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	51	ARG	1	0.861	0.917	36.100	-0.114	-0.114	0.000	0.000	0.000	0.000
31	A	52	PRO	0	0.032	0.018	40.220	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	53	CYS	0	0.021	0.002	38.984	0.006	0.006	0.000	0.000	0.000	0.000
33	A	54	PRO	0	0.051	0.005	37.553	0.005	0.005	0.000	0.000	0.000	0.000
34	A	55	GLU	-1	-0.781	-0.863	36.286	0.108	0.108	0.000	0.000	0.000	0.000
35	A	56	VAL	0	0.021	0.011	33.982	0.010	0.010	0.000	0.000	0.000	0.000
36	A	57	LEU	0	-0.013	-0.023	32.833	0.008	0.008	0.000	0.000	0.000	0.000
37	A	58	ILE	0	0.003	0.009	32.113	0.005	0.005	0.000	0.000	0.000	0.000
38	A	59	GLN	0	0.023	0.016	29.045	0.022	0.022	0.000	0.000	0.000	0.000
39	A	60	VAL	0	0.000	-0.001	28.114	0.013	0.013	0.000	0.000	0.000	0.000
40	A	61	ALA	0	-0.017	-0.002	27.645	0.005	0.005	0.000	0.000	0.000	0.000
41	A	62	ALA	0	0.009	0.014	25.991	0.008	0.008	0.000	0.000	0.000	0.000
42	A	63	VAL	0	-0.010	-0.003	23.383	0.022	0.022	0.000	0.000	0.000	0.000
43	A	64	ARG	1	0.976	0.984	22.736	-0.103	-0.103	0.000	0.000	0.000	0.000
44	A	65	GLY	0	0.052	0.030	22.826	0.004	0.004	0.000	0.000	0.000	0.000
45	A	66	ALA	0	-0.105	-0.068	19.591	0.019	0.019	0.000	0.000	0.000	0.000
46	A	67	LEU	0	0.028	0.004	18.283	0.041	0.041	0.000	0.000	0.000	0.000
47	A	68	ASP	-1	-0.850	-0.912	18.252	0.157	0.157	0.000	0.000	0.000	0.000
48	A	69	ARG	1	0.875	0.933	17.129	-0.295	-0.295	0.000	0.000	0.000	0.000
49	A	70	VAL	0	-0.033	-0.015	13.130	0.047	0.047	0.000	0.000	0.000	0.000
50	A	71	ALA	0	0.047	0.024	13.625	0.016	0.016	0.000	0.000	0.000	0.000
51	A	72	ARG	1	0.841	0.914	14.899	-0.162	-0.162	0.000	0.000	0.000	0.000
52	A	73	LEU	0	-0.030	-0.033	10.709	0.017	0.017	0.000	0.000	0.000	0.000
53	A	74	ILE	0	0.022	0.020	10.241	0.021	0.021	0.000	0.000	0.000	0.000
54	A	75	LEU	0	-0.008	0.001	11.276	-0.093	-0.093	0.000	0.000	0.000	0.000
55	A	76	ASP	-1	-0.846	-0.917	12.071	0.120	0.120	0.000	0.000	0.000	0.000
56	A	77	ASP	-1	-0.941	-0.970	7.002	0.517	0.517	0.000	0.000	0.000	0.000
57	A	78	HIS	0	0.006	0.007	9.339	-0.220	-0.220	0.000	0.000	0.000	0.000
58	A	79	MET	0	0.003	-0.018	11.659	-0.055	-0.055	0.000	0.000	0.000	0.000
59	A	80	ASN	0	-0.016	-0.003	7.751	0.013	0.013	0.000	0.000	0.000	0.000
60	A	81	GLU	-1	-0.936	-0.962	8.425	-1.413	-1.413	0.000	0.000	0.000	0.000
61	A	82	CYS	0	-0.015	0.013	10.975	0.007	0.007	0.000	0.000	0.000	0.000
62	A	83	ILE	0	-0.025	-0.020	14.527	0.020	0.020	0.000	0.000	0.000	0.000
63	A	84	THR	0	-0.044	-0.031	10.478	0.030	0.030	0.000	0.000	0.000	0.000
64	A	85	ARG	1	0.871	0.913	12.131	0.644	0.644	0.000	0.000	0.000	0.000
65	A	86	ALA	0	-0.001	0.011	14.814	0.040	0.040	0.000	0.000	0.000	0.000
66	A	87	ALA	0	-0.071	-0.034	16.460	0.033	0.033	0.000	0.000	0.000	0.000
67	A	88	ALA	0	-0.066	-0.027	15.309	0.024	0.024	0.000	0.000	0.000	0.000
68	A	89	GLU	-1	-0.954	-0.985	16.054	-0.602	-0.602	0.000	0.000	0.000	0.000
69	A	90	GLY	0	-0.051	-0.005	19.342	0.029	0.029	0.000	0.000	0.000	0.000
70	A	91	ASN	0	-0.013	-0.021	20.289	0.011	0.011	0.000	0.000	0.000	0.000
71	A	92	ILE	0	0.060	0.013	21.769	-0.006	-0.006	0.000	0.000	0.000	0.000
72	A	93	GLU	-1	-0.971	-0.980	22.956	-0.135	-0.135	0.000	0.000	0.000	0.000
73	A	94	GLN	0	0.027	-0.002	21.667	0.007	0.007	0.000	0.000	0.000	0.000
74	A	95	GLU	-1	-0.736	-0.836	16.961	-0.434	-0.434	0.000	0.000	0.000	0.000
75	A	96	LEU	0	-0.055	-0.025	19.759	0.015	0.015	0.000	0.000	0.000	0.000
76	A	97	ALA	0	-0.037	-0.032	22.249	0.021	0.021	0.000	0.000	0.000	0.000
77	A	98	GLU	-1	-0.832	-0.924	16.249	-0.381	-0.381	0.000	0.000	0.000	0.000
78	A	99	LEU	0	-0.094	-0.033	16.761	0.022	0.022	0.000	0.000	0.000	0.000
79	A	100	LYS	1	0.919	0.947	19.542	0.130	0.130	0.000	0.000	0.000	0.000
80	A	101	GLU	-1	-0.891	-0.935	21.703	-0.141	-0.141	0.000	0.000	0.000	0.000
81	A	102	ALA	0	-0.055	-0.025	17.396	0.019	0.019	0.000	0.000	0.000	0.000
82	A	103	LEU	0	-0.024	-0.031	19.427	0.031	0.031	0.000	0.000	0.000	0.000
83	A	104	ASP	-1	-0.917	-0.949	21.542	-0.047	-0.047	0.000	0.000	0.000	0.000
84	A	105	ARG	1	0.853	0.926	20.142	0.132	0.132	0.000	0.000	0.000	0.000
85	A	106	PHE	0	-0.041	-0.013	17.575	0.024	0.024	0.000	0.000	0.000	0.000
86	A	107	LEU	0	-0.058	-0.007	21.163	0.025	0.025	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:22:SER)