FMO DATABASE

FMODB ID: ZV4RN

Calculation Name: 4K12-B-Xray372

Preferred Name: Complement factor H

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4K12

Chain ID: B

ChEMBL ID: CHEMBL4629

UniProt ID: P08603

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	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	82
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-553507.807097
FMO2-HF: Nuclear repulsion	519849.888935
FMO2-HF: Total energy	-33657.918163
FMO2-MP2: Total energy	-33755.386276

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(B:1:MET)

Summations of interaction energy for fragment #1(B: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.
-7.011	-1.621	10.953	-3.546	-12.797	-0.016

Interaction energy analysis for fragmet #1(B:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : 0.005

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	B	3	SER	0	0.020	0.011	3.342	-2.315	-0.439	0.000	-0.811	-1.065	0.002
4	B	4	GLU	-1	-0.808	-0.891	2.544	-1.368	0.011	0.602	-0.535	-1.446	0.001
5	B	5	ARG	1	0.924	0.965	2.472	1.235	1.549	4.294	-1.145	-3.462	-0.003
6	B	6	ASP	-1	-0.912	-0.947	5.309	0.078	0.153	-0.001	-0.006	-0.068	0.000
7	B	7	LYS	1	0.756	0.856	7.046	0.451	0.451	0.000	0.000	0.000	0.000
8	B	8	ALA	0	0.040	0.010	7.955	0.047	0.047	0.000	0.000	0.000	0.000
9	B	9	ARG	1	0.893	0.926	8.907	0.068	0.068	0.000	0.000	0.000	0.000
10	B	10	LYS	1	0.973	0.991	11.211	0.018	0.018	0.000	0.000	0.000	0.000
11	B	11	GLU	-1	-0.926	-0.955	12.681	0.058	0.058	0.000	0.000	0.000	0.000
12	B	12	VAL	0	0.012	-0.005	13.109	-0.004	-0.004	0.000	0.000	0.000	0.000
13	B	13	GLU	-1	-0.928	-0.960	15.246	-0.006	-0.006	0.000	0.000	0.000	0.000
14	B	14	GLU	-1	-0.956	-0.985	17.181	0.015	0.015	0.000	0.000	0.000	0.000
15	B	15	TYR	0	-0.087	-0.064	18.447	-0.006	-0.006	0.000	0.000	0.000	0.000
16	B	16	VAL	0	0.041	0.007	19.501	-0.005	-0.005	0.000	0.000	0.000	0.000
17	B	17	LYS	1	0.929	0.966	20.245	-0.023	-0.023	0.000	0.000	0.000	0.000
18	B	18	LYS	1	0.936	0.990	22.936	-0.034	-0.034	0.000	0.000	0.000	0.000
19	B	19	ILE	0	0.040	0.026	24.015	-0.003	-0.003	0.000	0.000	0.000	0.000
20	B	20	VAL	0	-0.003	0.003	25.211	-0.003	-0.003	0.000	0.000	0.000	0.000
21	B	21	GLY	0	0.006	0.000	27.134	-0.002	-0.002	0.000	0.000	0.000	0.000
22	B	22	GLU	-1	-0.936	-0.974	28.572	0.021	0.021	0.000	0.000	0.000	0.000
23	B	23	SER	0	-0.083	-0.055	29.533	-0.001	-0.001	0.000	0.000	0.000	0.000
24	B	24	TYR	0	-0.031	-0.028	30.526	-0.001	-0.001	0.000	0.000	0.000	0.000
25	B	25	ALA	0	-0.044	-0.004	33.150	-0.001	-0.001	0.000	0.000	0.000	0.000
26	B	26	LYS	1	0.918	0.955	33.615	-0.019	-0.019	0.000	0.000	0.000	0.000
27	B	27	SER	0	-0.011	0.018	36.109	0.000	0.000	0.000	0.000	0.000	0.000
28	B	28	THR	0	0.044	0.019	37.875	-0.001	-0.001	0.000	0.000	0.000	0.000
29	B	29	LYS	1	0.974	0.958	41.240	-0.009	-0.009	0.000	0.000	0.000	0.000
30	B	30	LYS	1	0.955	0.973	43.286	-0.009	-0.009	0.000	0.000	0.000	0.000
31	B	31	ARG	1	0.902	0.970	34.423	-0.017	-0.017	0.000	0.000	0.000	0.000
32	B	32	HIS	0	0.028	0.021	37.850	0.001	0.001	0.000	0.000	0.000	0.000
33	B	33	THR	0	0.021	-0.010	37.336	0.001	0.001	0.000	0.000	0.000	0.000
34	B	34	ILE	0	0.021	0.027	35.172	0.001	0.001	0.000	0.000	0.000	0.000
35	B	35	THR	0	-0.008	-0.018	33.316	0.002	0.002	0.000	0.000	0.000	0.000
36	B	36	VAL	0	-0.002	0.005	32.431	0.001	0.001	0.000	0.000	0.000	0.000
37	B	37	ALA	0	-0.029	-0.011	31.884	0.001	0.001	0.000	0.000	0.000	0.000
38	B	38	LEU	0	0.040	0.024	28.941	0.001	0.001	0.000	0.000	0.000	0.000
39	B	39	VAL	0	0.014	0.003	27.766	0.003	0.003	0.000	0.000	0.000	0.000
40	B	40	ASN	0	-0.033	-0.021	26.870	0.002	0.002	0.000	0.000	0.000	0.000
41	B	41	GLU	-1	-0.904	-0.950	26.217	0.035	0.035	0.000	0.000	0.000	0.000
42	B	42	LEU	0	0.014	-0.001	24.094	0.005	0.005	0.000	0.000	0.000	0.000
43	B	43	ASN	0	-0.013	-0.023	22.262	0.006	0.006	0.000	0.000	0.000	0.000
44	B	44	ASN	0	-0.026	-0.001	21.396	0.001	0.001	0.000	0.000	0.000	0.000
45	B	45	ILE	0	0.036	0.020	19.676	0.004	0.004	0.000	0.000	0.000	0.000
46	B	46	LYS	1	0.931	0.972	17.595	-0.019	-0.019	0.000	0.000	0.000	0.000
47	B	47	ASN	0	-0.015	-0.013	16.504	0.004	0.004	0.000	0.000	0.000	0.000
48	B	48	GLU	-1	-0.914	-0.947	16.193	0.084	0.084	0.000	0.000	0.000	0.000
49	B	49	TYR	0	0.003	-0.022	14.058	0.004	0.004	0.000	0.000	0.000	0.000
50	B	50	LEU	0	-0.036	-0.009	12.102	0.036	0.036	0.000	0.000	0.000	0.000
51	B	51	ASN	0	-0.003	-0.010	11.203	-0.027	-0.027	0.000	0.000	0.000	0.000
52	B	52	LYS	1	0.896	0.960	11.279	-0.150	-0.150	0.000	0.000	0.000	0.000
53	B	53	ILE	0	-0.005	-0.004	7.083	0.075	0.075	0.000	0.000	0.000	0.000
54	B	54	VAL	0	-0.071	-0.038	6.479	-0.019	-0.019	0.000	0.000	0.000	0.000
55	B	55	GLU	-1	-0.923	-0.949	6.806	-0.287	-0.287	0.000	0.000	0.000	0.000
56	B	56	SER	0	-0.094	-0.029	5.355	0.404	0.404	0.000	0.000	0.000	0.000
57	B	57	THR	0	-0.034	-0.032	3.368	-0.935	-0.329	0.027	-0.166	-0.468	0.000
58	B	58	SER	0	-0.004	-0.008	2.410	-2.261	-1.228	1.832	-1.015	-1.850	-0.006
59	B	59	GLU	-1	-0.830	-0.939	2.145	-0.981	-1.567	3.906	0.222	-3.541	-0.010
60	B	60	SER	0	-0.003	-0.005	3.715	-0.209	-0.100	0.019	0.050	-0.178	0.000
61	B	61	GLU	-1	-0.863	-0.924	6.170	0.770	0.770	0.000	0.000	0.000	0.000
62	B	62	LEU	0	0.033	0.018	3.557	-0.965	-0.381	0.274	-0.140	-0.719	0.000
63	B	63	GLN	0	-0.010	-0.017	7.138	-0.326	-0.326	0.000	0.000	0.000	0.000
64	B	64	ILE	0	0.009	-0.003	9.939	-0.114	-0.114	0.000	0.000	0.000	0.000
65	B	65	LEU	0	0.016	0.010	8.726	-0.104	-0.104	0.000	0.000	0.000	0.000
66	B	66	MET	0	-0.041	0.003	9.390	-0.117	-0.117	0.000	0.000	0.000	0.000
67	B	67	MET	0	-0.068	-0.012	13.007	-0.054	-0.054	0.000	0.000	0.000	0.000
68	B	68	GLU	-1	-0.914	-0.967	15.013	0.149	0.149	0.000	0.000	0.000	0.000
69	B	69	SER	0	0.021	0.014	15.536	-0.035	-0.035	0.000	0.000	0.000	0.000
70	B	70	ARG	1	0.949	0.977	17.281	-0.077	-0.077	0.000	0.000	0.000	0.000
71	B	71	SER	0	0.002	0.005	19.319	-0.017	-0.017	0.000	0.000	0.000	0.000
72	B	72	LYS	1	0.977	0.993	20.093	-0.081	-0.081	0.000	0.000	0.000	0.000
73	B	73	VAL	0	-0.004	0.001	20.894	-0.010	-0.010	0.000	0.000	0.000	0.000
74	B	74	ASP	-1	-0.817	-0.891	23.260	0.040	0.040	0.000	0.000	0.000	0.000
75	B	75	GLU	-1	-0.948	-0.977	24.924	0.039	0.039	0.000	0.000	0.000	0.000
76	B	76	ALA	0	0.013	0.019	26.043	-0.005	-0.005	0.000	0.000	0.000	0.000
77	B	77	VAL	0	-0.009	-0.007	27.357	-0.005	-0.005	0.000	0.000	0.000	0.000
78	B	78	SER	0	-0.174	-0.102	29.376	-0.004	-0.004	0.000	0.000	0.000	0.000
79	B	79	LYS	1	0.930	0.977	29.253	-0.034	-0.034	0.000	0.000	0.000	0.000
80	B	80	PHE	0	0.020	0.018	32.596	-0.002	-0.002	0.000	0.000	0.000	0.000
81	B	81	GLU	-1	-0.893	-0.931	35.025	0.014	0.014	0.000	0.000	0.000	0.000
82	B	82	LYS	1	0.929	0.962	33.197	-0.020	-0.020	0.000	0.000	0.000	0.000

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