FMO DATABASE

FMODB ID: R87N8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-553997.314591
FMO2-HF: Nuclear repulsion	520339.013933
FMO2-HF: Total energy	-33658.300658
FMO2-MP2: Total energy	-33755.793493

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.
-7.79	0.321	7.129	-3.403	-11.837	-0.022

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 : 0.033 / 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

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	B	3	SER	0	0.002	0.006	3.278	-2.115	-0.208	0.001	-0.826	-1.082	0.002
4	B	4	GLU	-1	-0.767	-0.870	2.580	-1.045	0.212	0.461	-0.483	-1.236	0.001
5	B	5	ARG	1	0.897	0.928	2.738	0.462	2.977	1.158	-0.918	-2.755	-0.005
6	B	6	ASP	-1	-0.913	-0.949	5.331	0.055	0.141	-0.001	-0.005	-0.079	0.000
7	B	7	LYS	1	0.732	0.838	6.987	0.283	0.283	0.000	0.000	0.000	0.000
8	B	8	ALA	0	0.044	0.013	7.997	0.040	0.040	0.000	0.000	0.000	0.000
9	B	9	ARG	1	0.916	0.936	9.182	0.088	0.088	0.000	0.000	0.000	0.000
10	B	10	LYS	1	0.946	0.979	11.241	-0.007	-0.007	0.000	0.000	0.000	0.000
11	B	11	GLU	-1	-0.915	-0.955	12.720	0.096	0.096	0.000	0.000	0.000	0.000
12	B	12	VAL	0	0.020	0.004	13.326	-0.007	-0.007	0.000	0.000	0.000	0.000
13	B	13	GLU	-1	-0.867	-0.924	15.315	-0.014	-0.014	0.000	0.000	0.000	0.000
14	B	14	GLU	-1	-0.918	-0.958	17.222	0.024	0.024	0.000	0.000	0.000	0.000
15	B	15	TYR	0	-0.061	-0.052	18.486	-0.006	-0.006	0.000	0.000	0.000	0.000
16	B	16	VAL	0	0.027	0.001	19.508	-0.007	-0.007	0.000	0.000	0.000	0.000
17	B	17	LYS	1	0.808	0.897	18.649	-0.028	-0.028	0.000	0.000	0.000	0.000
18	B	18	LYS	1	0.845	0.928	22.977	-0.046	-0.046	0.000	0.000	0.000	0.000
19	B	19	ILE	0	0.012	0.012	24.331	-0.004	-0.004	0.000	0.000	0.000	0.000
20	B	20	VAL	0	0.009	0.008	25.297	-0.004	-0.004	0.000	0.000	0.000	0.000
21	B	21	GLY	0	0.019	0.008	27.184	-0.003	-0.003	0.000	0.000	0.000	0.000
22	B	22	GLU	-1	-0.851	-0.921	28.286	0.034	0.034	0.000	0.000	0.000	0.000
23	B	23	SER	0	-0.084	-0.051	29.589	-0.002	-0.002	0.000	0.000	0.000	0.000
24	B	24	TYR	0	-0.015	-0.023	30.494	-0.002	-0.002	0.000	0.000	0.000	0.000
25	B	25	ALA	0	-0.050	-0.006	33.204	-0.001	-0.001	0.000	0.000	0.000	0.000
26	B	26	LYS	1	0.925	0.967	32.678	-0.027	-0.027	0.000	0.000	0.000	0.000
27	B	27	SER	0	-0.010	0.019	36.174	-0.001	-0.001	0.000	0.000	0.000	0.000
28	B	28	THR	0	0.042	0.011	37.933	-0.001	-0.001	0.000	0.000	0.000	0.000
29	B	29	LYS	1	0.975	0.962	41.292	-0.010	-0.010	0.000	0.000	0.000	0.000
30	B	30	LYS	1	0.956	0.974	43.336	-0.011	-0.011	0.000	0.000	0.000	0.000
31	B	31	ARG	1	0.865	0.935	34.836	-0.021	-0.021	0.000	0.000	0.000	0.000
32	B	32	HIS	0	0.036	0.026	37.377	0.001	0.001	0.000	0.000	0.000	0.000
33	B	33	THR	0	0.023	-0.005	37.382	0.001	0.001	0.000	0.000	0.000	0.000
34	B	34	ILE	0	0.022	0.022	35.279	0.000	0.000	0.000	0.000	0.000	0.000
35	B	35	THR	0	-0.008	-0.014	33.408	0.002	0.002	0.000	0.000	0.000	0.000
36	B	36	VAL	0	0.016	0.011	32.481	0.001	0.001	0.000	0.000	0.000	0.000
37	B	37	ALA	0	-0.018	0.001	31.925	0.001	0.001	0.000	0.000	0.000	0.000
38	B	38	LEU	0	0.044	0.028	29.031	0.001	0.001	0.000	0.000	0.000	0.000
39	B	39	VAL	0	0.019	0.001	27.827	0.003	0.003	0.000	0.000	0.000	0.000
40	B	40	ASN	0	-0.055	-0.033	26.912	0.001	0.001	0.000	0.000	0.000	0.000
41	B	41	GLU	-1	-0.904	-0.947	26.282	0.036	0.036	0.000	0.000	0.000	0.000
42	B	42	LEU	0	0.009	-0.004	24.156	0.005	0.005	0.000	0.000	0.000	0.000
43	B	43	ASN	0	-0.028	-0.021	22.320	0.004	0.004	0.000	0.000	0.000	0.000
44	B	44	ASN	0	-0.015	0.007	21.426	-0.003	-0.003	0.000	0.000	0.000	0.000
45	B	45	ILE	0	0.024	0.012	19.822	0.003	0.003	0.000	0.000	0.000	0.000
46	B	46	LYS	1	0.906	0.951	17.631	-0.015	-0.015	0.000	0.000	0.000	0.000
47	B	47	ASN	0	-0.009	-0.015	16.547	0.004	0.004	0.000	0.000	0.000	0.000
48	B	48	GLU	-1	-0.896	-0.925	16.217	0.085	0.085	0.000	0.000	0.000	0.000
49	B	49	TYR	0	-0.041	-0.071	13.862	-0.002	-0.002	0.000	0.000	0.000	0.000
50	B	50	LEU	0	-0.033	-0.008	12.147	0.038	0.038	0.000	0.000	0.000	0.000
51	B	51	ASN	0	-0.008	-0.014	11.216	-0.036	-0.036	0.000	0.000	0.000	0.000
52	B	52	LYS	1	0.855	0.936	11.294	-0.160	-0.160	0.000	0.000	0.000	0.000
53	B	53	ILE	0	-0.007	-0.008	7.247	0.086	0.086	0.000	0.000	0.000	0.000
54	B	54	VAL	0	-0.076	-0.038	6.518	-0.001	-0.001	0.000	0.000	0.000	0.000
55	B	55	GLU	-1	-0.924	-0.951	6.750	-0.422	-0.422	0.000	0.000	0.000	0.000
56	B	56	SER	0	-0.115	-0.059	5.543	0.380	0.499	-0.001	-0.015	-0.103	0.000
57	B	57	THR	0	-0.032	-0.033	3.476	-0.935	-0.295	0.039	-0.164	-0.515	0.000
58	B	58	SER	0	-0.002	-0.011	2.199	-2.937	-1.994	3.015	-1.659	-2.298	-0.010
59	B	59	GLU	-1	-0.852	-0.947	2.251	-0.406	-0.460	2.313	0.805	-3.065	-0.010
60	B	60	SER	0	-0.007	-0.004	3.919	-0.405	-0.258	0.009	-0.021	-0.135	0.000
61	B	61	GLU	-1	-0.830	-0.885	6.173	0.963	0.963	0.000	0.000	0.000	0.000
62	B	62	LEU	0	0.040	0.022	3.749	-0.973	-0.422	0.135	-0.117	-0.569	0.000
63	B	63	GLN	0	-0.012	-0.012	7.312	-0.340	-0.340	0.000	0.000	0.000	0.000
64	B	64	ILE	0	0.008	-0.005	10.159	-0.129	-0.129	0.000	0.000	0.000	0.000
65	B	65	LEU	0	0.017	0.011	8.767	-0.112	-0.112	0.000	0.000	0.000	0.000
66	B	66	MET	0	-0.023	0.010	9.686	-0.124	-0.124	0.000	0.000	0.000	0.000
67	B	67	MET	0	-0.064	-0.020	13.188	-0.058	-0.058	0.000	0.000	0.000	0.000
68	B	68	GLU	-1	-0.845	-0.901	15.171	0.152	0.152	0.000	0.000	0.000	0.000
69	B	69	SER	0	0.012	0.010	15.568	-0.037	-0.037	0.000	0.000	0.000	0.000
70	B	70	ARG	1	0.933	0.975	17.419	-0.103	-0.103	0.000	0.000	0.000	0.000
71	B	71	SER	0	-0.010	0.005	19.488	-0.017	-0.017	0.000	0.000	0.000	0.000
72	B	72	LYS	1	0.926	0.944	20.322	-0.082	-0.082	0.000	0.000	0.000	0.000
73	B	73	VAL	0	0.006	0.003	21.043	-0.012	-0.012	0.000	0.000	0.000	0.000
74	B	74	ASP	-1	-0.811	-0.894	23.403	0.054	0.054	0.000	0.000	0.000	0.000
75	B	75	GLU	-1	-0.823	-0.882	25.075	0.044	0.044	0.000	0.000	0.000	0.000
76	B	76	ALA	0	0.024	0.030	26.177	-0.006	-0.006	0.000	0.000	0.000	0.000
77	B	77	VAL	0	0.000	-0.003	27.507	-0.005	-0.005	0.000	0.000	0.000	0.000
78	B	78	SER	0	-0.171	-0.103	29.531	-0.004	-0.004	0.000	0.000	0.000	0.000
79	B	79	LYS	1	0.859	0.920	28.674	-0.040	-0.040	0.000	0.000	0.000	0.000
80	B	80	PHE	0	0.020	0.017	32.238	-0.003	-0.003	0.000	0.000	0.000	0.000
81	B	81	GLU	-1	-0.878	-0.912	35.180	0.019	0.019	0.000	0.000	0.000	0.000
82	B	82	LYS	1	0.918	0.956	33.324	-0.027	-0.027	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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