FMO DATABASE

FMODB ID: 3991L

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

Total energy (hartree)

FMO2-HF: Electronic energy	-503012.208023
FMO2-HF: Nuclear repulsion	468617.000728
FMO2-HF: Total energy	-34395.207295
FMO2-MP2: Total energy	-34493.928889

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.
-7.293	-2.615	0.46	-1.949	-3.188	0.001

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 : 0.046 / q_NPA : 0.013

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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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	-0.895	-0.941	2.681	-3.171	-0.778	0.213	-1.039	-1.566	0.000
4	A	25	SER	0	-0.027	-0.019	2.398	-0.403	0.730	0.228	-0.460	-0.901	0.000
5	A	26	LEU	0	0.048	0.008	3.309	-0.457	0.568	0.020	-0.442	-0.603	0.001
6	A	27	GLN	0	0.046	0.023	4.994	-0.375	-0.248	-0.001	-0.008	-0.118	0.000
7	A	28	LYS	1	0.923	0.972	7.110	0.372	0.372	0.000	0.000	0.000	0.000
8	A	29	LEU	0	0.018	-0.009	7.476	-0.016	-0.016	0.000	0.000	0.000	0.000
9	A	30	VAL	0	0.050	0.035	9.172	-0.035	-0.035	0.000	0.000	0.000	0.000
10	A	31	ASN	0	0.029	0.033	11.283	-0.107	-0.107	0.000	0.000	0.000	0.000
11	A	32	ARG	1	0.912	0.954	12.280	-0.013	-0.013	0.000	0.000	0.000	0.000
12	A	33	LEU	0	0.038	0.019	12.356	-0.024	-0.024	0.000	0.000	0.000	0.000
13	A	34	SER	0	0.038	0.021	15.373	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	35	ARG	1	0.851	0.915	15.091	-0.127	-0.127	0.000	0.000	0.000	0.000
15	A	36	ILE	0	0.021	0.016	17.132	-0.013	-0.013	0.000	0.000	0.000	0.000
16	A	37	GLU	-1	-0.815	-0.873	19.725	0.140	0.140	0.000	0.000	0.000	0.000
17	A	38	GLY	0	-0.040	-0.036	21.516	-0.008	-0.008	0.000	0.000	0.000	0.000
18	A	39	HIS	0	-0.057	-0.037	23.047	-0.006	-0.006	0.000	0.000	0.000	0.000
19	A	40	ILE	0	0.027	0.011	22.969	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	41	ARG	1	0.830	0.893	22.433	-0.120	-0.120	0.000	0.000	0.000	0.000
21	A	42	GLY	0	0.000	0.008	27.563	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	43	VAL	0	0.032	0.005	28.731	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	44	LYS	1	0.878	0.938	30.422	-0.057	-0.057	0.000	0.000	0.000	0.000
24	A	45	THR	0	-0.037	-0.027	32.125	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	46	MET	0	-0.015	0.006	33.440	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	47	VAL	0	0.012	0.015	34.952	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	48	GLN	0	-0.009	-0.004	35.330	0.001	0.001	0.000	0.000	0.000	0.000
28	A	49	GLU	-1	-0.902	-0.939	37.476	0.037	0.037	0.000	0.000	0.000	0.000
29	A	50	ASN	0	-0.062	-0.031	40.211	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	51	ARG	1	0.840	0.923	36.010	-0.032	-0.032	0.000	0.000	0.000	0.000
31	A	52	PRO	0	0.031	0.014	40.221	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	53	CYS	0	0.017	0.007	38.764	0.000	0.000	0.000	0.000	0.000	0.000
33	A	54	PRO	0	0.058	0.008	37.552	0.000	0.000	0.000	0.000	0.000	0.000
34	A	55	GLU	-1	-0.795	-0.890	36.292	0.022	0.022	0.000	0.000	0.000	0.000
35	A	56	VAL	0	0.002	0.007	34.063	0.002	0.002	0.000	0.000	0.000	0.000
36	A	57	LEU	0	-0.007	-0.021	32.832	0.001	0.001	0.000	0.000	0.000	0.000
37	A	58	ILE	0	0.000	0.005	32.143	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	59	GLN	0	0.029	0.027	29.048	0.001	0.001	0.000	0.000	0.000	0.000
39	A	60	VAL	0	0.009	-0.003	28.112	0.001	0.001	0.000	0.000	0.000	0.000
40	A	61	ALA	0	-0.019	0.002	27.644	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	62	ALA	0	0.003	0.012	26.029	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	63	VAL	0	-0.002	0.000	23.457	0.000	0.000	0.000	0.000	0.000	0.000
43	A	64	ARG	1	0.957	0.979	22.734	0.011	0.011	0.000	0.000	0.000	0.000
44	A	65	GLY	0	0.056	0.031	22.822	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	66	ALA	0	-0.100	-0.071	19.686	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	67	LEU	0	0.025	0.006	18.278	0.000	0.000	0.000	0.000	0.000	0.000
47	A	68	ASP	-1	-0.847	-0.917	18.250	-0.048	-0.048	0.000	0.000	0.000	0.000
48	A	69	ARG	1	0.885	0.944	17.101	0.001	0.001	0.000	0.000	0.000	0.000
49	A	70	VAL	0	-0.029	-0.016	13.027	-0.022	-0.022	0.000	0.000	0.000	0.000
50	A	71	ALA	0	0.040	0.023	13.621	-0.020	-0.020	0.000	0.000	0.000	0.000
51	A	72	ARG	1	0.820	0.882	14.894	0.182	0.182	0.000	0.000	0.000	0.000
52	A	73	LEU	0	-0.040	-0.033	10.732	-0.025	-0.025	0.000	0.000	0.000	0.000
53	A	74	ILE	0	0.001	0.004	10.237	-0.065	-0.065	0.000	0.000	0.000	0.000
54	A	75	LEU	0	0.006	0.013	11.272	-0.060	-0.060	0.000	0.000	0.000	0.000
55	A	76	ASP	-1	-0.823	-0.885	12.115	-0.303	-0.303	0.000	0.000	0.000	0.000
56	A	77	ASP	-1	-0.920	-0.966	6.597	-1.027	-1.027	0.000	0.000	0.000	0.000
57	A	78	HIS	0	-0.057	-0.027	9.325	-0.109	-0.109	0.000	0.000	0.000	0.000
58	A	79	MET	0	-0.016	-0.021	11.654	-0.015	-0.015	0.000	0.000	0.000	0.000
59	A	80	ASN	0	-0.023	-0.011	7.926	0.116	0.116	0.000	0.000	0.000	0.000
60	A	81	GLU	-1	-0.909	-0.942	8.429	-1.114	-1.114	0.000	0.000	0.000	0.000
61	A	82	CYS	0	-0.013	0.011	10.926	0.043	0.043	0.000	0.000	0.000	0.000
62	A	83	ILE	0	-0.040	-0.027	14.572	0.043	0.043	0.000	0.000	0.000	0.000
63	A	84	THR	0	-0.036	-0.025	10.478	0.054	0.054	0.000	0.000	0.000	0.000
64	A	85	ARG	1	0.801	0.876	12.347	0.597	0.597	0.000	0.000	0.000	0.000
65	A	86	ALA	0	-0.010	0.007	14.697	0.052	0.052	0.000	0.000	0.000	0.000
66	A	87	ALA	0	-0.071	-0.035	16.420	0.040	0.040	0.000	0.000	0.000	0.000
67	A	88	ALA	0	-0.063	-0.025	15.276	0.033	0.033	0.000	0.000	0.000	0.000
68	A	89	GLU	-1	-0.939	-0.977	15.766	-0.424	-0.424	0.000	0.000	0.000	0.000
69	A	90	GLY	0	-0.045	-0.005	19.209	0.026	0.026	0.000	0.000	0.000	0.000
70	A	91	ASN	0	-0.037	-0.033	20.202	0.003	0.003	0.000	0.000	0.000	0.000
71	A	92	ILE	0	0.070	0.020	21.718	-0.010	-0.010	0.000	0.000	0.000	0.000
72	A	93	GLU	-1	-0.937	-0.968	22.907	-0.164	-0.164	0.000	0.000	0.000	0.000
73	A	94	GLN	0	0.035	0.002	21.746	0.000	0.000	0.000	0.000	0.000	0.000
74	A	95	GLU	-1	-0.729	-0.829	16.725	-0.412	-0.412	0.000	0.000	0.000	0.000
75	A	96	LEU	0	-0.051	-0.030	19.756	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	97	ALA	0	-0.045	-0.033	22.231	0.010	0.010	0.000	0.000	0.000	0.000
77	A	98	GLU	-1	-0.771	-0.894	15.847	-0.378	-0.378	0.000	0.000	0.000	0.000
78	A	99	LEU	0	-0.039	-0.005	16.855	0.003	0.003	0.000	0.000	0.000	0.000
79	A	100	LYS	1	0.891	0.943	19.537	0.174	0.174	0.000	0.000	0.000	0.000
80	A	101	GLU	-1	-0.787	-0.866	21.604	-0.157	-0.157	0.000	0.000	0.000	0.000
81	A	102	ALA	0	-0.042	-0.021	17.361	0.017	0.017	0.000	0.000	0.000	0.000
82	A	103	LEU	0	-0.025	-0.032	19.427	0.015	0.015	0.000	0.000	0.000	0.000
83	A	104	ASP	-1	-0.922	-0.952	21.537	-0.111	-0.111	0.000	0.000	0.000	0.000
84	A	105	ARG	1	0.736	0.852	20.513	0.169	0.169	0.000	0.000	0.000	0.000
85	A	106	PHE	0	-0.046	-0.011	17.899	0.009	0.009	0.000	0.000	0.000	0.000
86	A	107	LEU	0	-0.044	-0.004	21.162	0.016	0.016	0.000	0.000	0.000	0.000

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