FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: P376L

Calculation Name: 3VSX-B-Xray39

Preferred Name: Renin

Target Type: SINGLE PROTEIN

Ligand Name: (2s,4s,5s)-5-amino-n-(3-amino-2,2-dimethyl-3-oxopropyl)-6-[4-(2-chlorophenyl)-2,2-dimethyl-5-oxopiperazin-1-yl]-4-hydroxy-2-(propan-2-yl)hexanamide

ligand 3-letter code: R32

PDB ID: 3VSX

Chain ID: B

ChEMBL ID: CHEMBL286

UniProt ID: P00797

Base Structure: X-ray

Registration Date: 2019-02-15

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Homology modeling
Water No
Procedure Auto-FMO protocol ver. 1.20171228
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 334
LigandResidueName R32
LigandFragmentNumber 334
LigandCharge R32=1
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5244355.072791
FMO2-HF: Nuclear repulsion 5113023.433846
FMO2-HF: Total energy -131331.638945
FMO2-MP2: Total energy -131711.2921


3D Structure
Snapshot
 
Ligand structure

R32

ligand structure
Ligand Interaction
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.
-404.723-374.454114.437-47.739-96.9690.310


Interactive mode: IFIE and PIEDA for fragment #334(B:402:R32)


Summations of interaction energy for fragment #334(B:402:R32)
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.
-404.723-374.454114.437-47.739-96.969-0.31
Interaction energy analysis for fragmet #334(B:402:R32)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.689 / q_NPA : 0.855
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   
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].
1B8SER10.7480.85319.20715.32315.3230.0000.0000.0000.000
2B9SER00.0480.03317.988-0.617-0.6170.0000.0000.0000.000
3B10VAL00.0190.00212.7380.7030.7030.0000.0000.0000.000
4B11ILE0-0.0010.00814.961-0.736-0.7360.0000.0000.0000.000
5B12LEU0-0.041-0.02310.163-0.803-0.8030.0000.0000.0000.000
6B13THR00.0170.01110.8691.7721.7720.0000.0000.0000.000
7B14ASN0-0.030-0.0199.515-3.677-3.6770.0000.0000.0000.000
8B15TYR00.0670.0325.3392.0982.0980.0000.0000.0000.000
9B16MET00.003-0.0116.823-2.215-2.2150.0000.0000.0000.000
10B17ASP-1-0.786-0.8928.161-21.234-21.2340.0000.0000.0000.000
11B18THR0-0.129-0.0633.479-2.650-2.3740.005-0.045-0.2360.000
12B19GLN00.0200.0252.493-10.472-8.1313.277-1.596-4.023-0.009
13B20TYR00.0610.0474.6633.4203.5510.000-0.013-0.1170.000
14B21TYR00.013-0.0067.239-2.962-2.9620.0000.0000.0000.000
15B22GLY00.0760.0568.8482.3062.3060.0000.0000.0000.000
16B23GLU-1-0.927-0.97910.754-20.933-20.9330.0000.0000.0000.000
17B24ILE0-0.066-0.02411.3260.2130.2130.0000.0000.0000.000
18B25GLY0-0.032-0.01714.1040.3860.3860.0000.0000.0000.000
19B26ILE00.0130.01213.109-0.307-0.3070.0000.0000.0000.000
20B27GLY00.0580.02217.6310.4220.4220.0000.0000.0000.000
21B28THR0-0.122-0.02721.0010.1470.1470.0000.0000.0000.000
22B29PRO00.086-0.00724.4520.3300.3300.0000.0000.0000.000
23B30PRO0-0.019-0.00620.184-0.252-0.2520.0000.0000.0000.000
24B31GLN0-0.0080.01218.006-0.180-0.1800.0000.0000.0000.000
25B32THR0-0.042-0.04216.253-0.511-0.5110.0000.0000.0000.000
26B33PHE00.0010.00311.2030.4660.4660.0000.0000.0000.000
27B34LYS10.9861.01510.00618.82418.8240.0000.0000.0000.000
28B35VAL0-0.0020.0036.795-0.897-0.8970.0000.0000.0000.000
29B36VAL00.0490.0311.9841.475-0.9755.868-0.770-2.648-0.005
30B37PHE00.003-0.0144.611-1.219-1.024-0.001-0.014-0.1800.000
31B38ASP-1-0.685-0.7921.602-148.928-154.89830.694-13.837-10.887-0.142
32B39THR0-0.032-0.0114.3801.1661.5000.000-0.042-0.2930.000
33B40GLY00.0310.0252.2896.7836.4724.552-2.113-2.1280.010
34B41SER0-0.071-0.0482.1444.0558.5627.215-3.397-8.325-0.024
35B42SER00.026-0.0122.6743.2200.8590.0803.482-1.200-0.002
36B43ASN0-0.027-0.0094.3520.4930.7480.000-0.019-0.2360.000
37B44VAL00.0460.0286.610-2.394-2.3940.0000.0000.0000.000
38B45TRP0-0.032-0.0083.6143.4534.0080.006-0.068-0.4930.000
39B46VAL00.0410.0237.946-1.799-1.7990.0000.0000.0000.000
40B47PRO00.0130.0098.5550.8470.8470.0000.0000.0000.000
41B48SER0-0.011-0.03711.1330.9870.9870.0000.0000.0000.000
42B49SER00.0150.00714.7340.1600.1600.0000.0000.0000.000
43B50LYS10.8420.92417.94212.91512.9150.0000.0000.0000.000
44B51CYS00.0110.02614.589-0.234-0.2340.0000.0000.0000.000
45B52SER0-0.0230.00916.8970.6080.6080.0000.0000.0000.000
46B53ARG10.9990.97516.68912.41312.4130.0000.0000.0000.000
47B54LEU0-0.0050.00218.1260.1990.1990.0000.0000.0000.000
48B55TYR0-0.0080.00612.723-0.106-0.1060.0000.0000.0000.000
49B56THR00.012-0.03011.685-0.079-0.0790.0000.0000.0000.000
50B57ALA00.025-0.0038.6630.1470.1470.0000.0000.0000.000
51B58CYS0-0.003-0.00310.462-0.463-0.4630.0000.0000.0000.000
52B59VAL0-0.077-0.02812.8880.4460.4460.0000.0000.0000.000
53B60TYR0-0.054-0.04810.9030.8130.8130.0000.0000.0000.000
54B61HIS00.0160.0316.594-0.131-0.1310.0000.0000.0000.000
55B62LYS10.8730.96012.10216.12316.1230.0000.0000.0000.000
56B63LEU0-0.042-0.03513.012-0.691-0.6910.0000.0000.0000.000
57B64PHE0-0.019-0.00414.5510.7080.7080.0000.0000.0000.000
58B65ASP-1-0.788-0.90816.294-12.102-12.1020.0000.0000.0000.000
59B66ALA00.007-0.00119.8140.3580.3580.0000.0000.0000.000
60B67SER0-0.125-0.06121.2890.5010.5010.0000.0000.0000.000
61B68ASP-1-0.924-0.95422.836-10.888-10.8880.0000.0000.0000.000
62B69SER0-0.143-0.07121.9210.1860.1860.0000.0000.0000.000
63B70SER0-0.031-0.03124.0370.0210.0210.0000.0000.0000.000
64B71SER0-0.057-0.04223.2700.3340.3340.0000.0000.0000.000
65B72TYR00.0250.02520.216-0.003-0.0030.0000.0000.0000.000
66B73LYS10.8770.94022.20212.00012.0000.0000.0000.0000.000
67B74HIS00.0400.02521.192-0.592-0.5920.0000.0000.0000.000
68B75ASN00.8080.91017.61614.10414.1040.0000.0000.0000.000
69B76GLY00.022-0.00618.4670.5240.5240.0000.0000.0000.000
70B77THR0-0.032-0.00913.9890.2730.2730.0000.0000.0000.000
71B78GLU-1-0.872-0.92614.016-15.579-15.5790.0000.0000.0000.000
72B79LEU0-0.053-0.0307.844-0.344-0.3440.0000.0000.0000.000
73B80THR0-0.004-0.0027.2470.5810.5810.0000.0000.0000.000
74B81LEU0-0.046-0.0204.350-1.331-1.0350.000-0.016-0.2790.000
75B82ARG10.9660.9733.54421.65522.3650.009-0.123-0.5960.000
76B83TYR00.0630.0192.022-13.021-5.69710.850-5.878-12.296-0.017
77B84SER00.003-0.0091.825-8.148-12.60011.920-1.212-6.2560.021
78B85THR0-0.018-0.0032.198-7.442-5.6622.822-1.713-2.8890.015
79B86GLY00.0520.0145.0302.2382.547-0.001-0.011-0.2970.000
80B87THR0-0.078-0.0545.890-0.922-0.9220.0000.0000.0000.000
81B88VAL00.0120.0356.1611.4321.4320.0000.0000.0000.000
82B89SER00.015-0.0058.725-1.390-1.3900.0000.0000.0000.000
83B90GLY00.0680.03311.4340.2280.2280.0000.0000.0000.000
84B91PHE00.0150.03613.3440.2570.2570.0000.0000.0000.000
85B92LEU0-0.039-0.02811.161-0.596-0.5960.0000.0000.0000.000
86B93SER0-0.009-0.01314.6761.4391.4390.0000.0000.0000.000
87B94GLN00.0210.00316.257-0.422-0.4220.0000.0000.0000.000
88B95ASP-1-0.695-0.80018.691-12.916-12.9160.0000.0000.0000.000
89B96ILE0-0.056-0.02219.265-0.635-0.6350.0000.0000.0000.000
90B97ILE00.0540.01413.520-0.199-0.1990.0000.0000.0000.000
91B98THR0-0.075-0.04317.3410.5800.5800.0000.0000.0000.000
92B99VAL00.0590.02213.813-0.672-0.6720.0000.0000.0000.000
93B100GLY00.0980.05016.1460.5410.5410.0000.0000.0000.000
94B101GLY0-0.057-0.01118.0560.5880.5880.0000.0000.0000.000
95B102ILE0-0.015-0.00719.0630.7580.7580.0000.0000.0000.000
96B103THR0-0.003-0.00119.514-0.446-0.4460.0000.0000.0000.000
97B104VAL00.0130.01017.3860.3780.3780.0000.0000.0000.000
98B105THR0-0.030-0.01019.362-0.320-0.3200.0000.0000.0000.000
99B106GLN00.004-0.01112.3590.2820.2820.0000.0000.0000.000
100B107MET0-0.044-0.00413.6770.8340.8340.0000.0000.0000.000
101B108PHE0-0.009-0.00711.902-1.435-1.4350.0000.0000.0000.000
102B109GLY00.0360.00111.3451.3431.3430.0000.0000.0000.000
103B110GLU-1-0.793-0.86511.643-16.472-16.4720.0000.0000.0000.000
104B111VAL0-0.033-0.0128.3460.6780.6780.0000.0000.0000.000
105B112THR0-0.015-0.02511.7660.4070.4070.0000.0000.0000.000
106B113GLU-1-0.914-0.96212.571-14.887-14.8870.0000.0000.0000.000
107B114MET00.0170.0077.727-1.382-1.3820.0000.0000.0000.000
108B115PRO0-0.0150.0077.4051.0991.0990.0000.0000.0000.000
109B116ALA00.0480.0027.554-0.681-0.6810.0000.0000.0000.000
110B117LEU0-0.0130.0346.703-0.693-0.6930.0000.0000.0000.000
111B118PRO00.007-0.0383.054-1.353-0.2350.983-0.386-1.7150.003
112B119PHE00.0980.0062.759-5.178-2.3651.872-1.016-3.670-0.005
113B120MET0-0.0170.0374.688-0.403-0.3130.0020.002-0.0940.000
114B121LEU0-0.087-0.0282.8650.5931.3280.073-0.124-0.6840.000
115B122ALA0-0.046-0.0122.612-5.562-3.3490.730-0.863-2.080-0.003
116B123GLU-1-0.899-0.9563.495-18.832-18.6390.0400.055-0.2870.000
117B124PHE0-0.108-0.0452.260-4.911-1.6034.194-1.522-5.979-0.005
118B125ASP-1-0.787-0.9037.272-20.386-20.3860.0000.0000.0000.000
119B126GLY0-0.003-0.0295.6240.4690.4690.0000.0000.0000.000
120B127VAL0-0.057-0.0102.340-4.457-4.2293.100-0.501-2.827-0.004
121B128VAL00.0120.0024.7264.6294.765-0.001-0.013-0.1230.000
122B129GLY0-0.031-0.0155.762-2.775-2.7750.0000.0000.0000.000
123B130MET0-0.063-0.0386.4555.8125.8120.0000.0000.0000.000
124B131GLY00.0290.0185.3332.4702.4700.0000.0000.0000.000
125B132PHE0-0.0320.0006.3852.1822.1820.0000.0000.0000.000
126B133ILE00.0600.0136.053-1.615-1.6150.0000.0000.0000.000
127B134GLU-1-0.919-0.9607.416-19.171-19.1710.0000.0000.0000.000
128B135GLN0-0.074-0.0202.555-5.339-2.4070.891-1.370-2.4540.019
129B136ALA0-0.0100.0002.969-7.485-6.3210.140-0.640-0.664-0.006
130B137ILE0-0.054-0.0202.4092.9303.2481.232-0.228-1.3220.000
131B138GLY00.0320.0056.0480.3500.3500.0000.0000.0000.000
132B139ARG10.8900.9349.01517.56817.5680.0000.0000.0000.000
133B140VAL0-0.0070.0119.4801.1151.1150.0000.0000.0000.000
134B141THR0-0.002-0.0089.201-1.323-1.3230.0000.0000.0000.000
135B142PRO00.0570.0497.655-0.025-0.0250.0000.0000.0000.000
136B143ILE00.0760.0319.9451.5001.5000.0000.0000.0000.000
137B144PHE00.0120.00012.0891.3981.3980.0000.0000.0000.000
138B145ASP-1-0.835-0.90511.349-19.069-19.0690.0000.0000.0000.000
139B146ASN00.002-0.01114.2502.0242.0240.0000.0000.0000.000
140B147ILE0-0.0070.00115.9781.0341.0340.0000.0000.0000.000
141B148ILE0-0.033-0.00516.8181.0071.0070.0000.0000.0000.000
142B149SER0-0.036-0.02718.0150.9820.9820.0000.0000.0000.000
143B150GLN0-0.085-0.04320.5000.3610.3610.0000.0000.0000.000
144B151GLY0-0.025-0.00222.6870.5310.5310.0000.0000.0000.000
145B152VAL0-0.032-0.02123.3530.3840.3840.0000.0000.0000.000
146B153LEU0-0.045-0.01619.1950.1150.1150.0000.0000.0000.000
147B154LYS10.9260.95623.45812.54912.5490.0000.0000.0000.000
148B155GLU-1-0.912-0.94922.286-13.531-13.5310.0000.0000.0000.000
149B156ASP-1-0.817-0.91217.020-17.448-17.4480.0000.0000.0000.000
150B157VAL0-0.0030.00117.468-0.590-0.5900.0000.0000.0000.000
151B158PHE0-0.007-0.01110.9460.5680.5680.0000.0000.0000.000
152B159SER00.0210.00315.027-0.864-0.8640.0000.0000.0000.000
153B160PHE0-0.043-0.0458.347-0.425-0.4250.0000.0000.0000.000
154B161TYR00.0160.02113.5200.3580.3580.0000.0000.0000.000
155B162TYR0-0.044-0.0447.1040.1960.1960.0000.0000.0000.000
156B163ASN00.0360.01313.4060.8510.8510.0000.0000.0000.000
157B164ARG10.8880.92713.17315.27415.2740.0000.0000.0000.000
158B165ASP-1-0.802-0.91313.681-15.211-15.2110.0000.0000.0000.000
159B166SER0-0.042-0.00712.134-0.645-0.6450.0000.0000.0000.000
160B167GLU-1-0.844-0.93613.339-16.588-16.5880.0000.0000.0000.000
161B168ASN0-0.066-0.03415.9781.1281.1280.0000.0000.0000.000
162B169SER0-0.131-0.04917.6760.4730.4730.0000.0000.0000.000
163B170GLN00.0040.00018.573-0.536-0.5360.0000.0000.0000.000
164B171SER0-0.087-0.03518.496-0.295-0.2950.0000.0000.0000.000
165B172LEU00.0200.02817.315-0.352-0.3520.0000.0000.0000.000
166B173GLY00.0750.03413.833-0.213-0.2130.0000.0000.0000.000
167B174GLY00.0570.00413.361-1.186-1.1860.0000.0000.0000.000
168B175GLN0-0.036-0.02314.6760.8740.8740.0000.0000.0000.000
169B176ILE00.0180.0349.982-0.504-0.5040.0000.0000.0000.000
170B177VAL0-0.030-0.01214.3541.4041.4040.0000.0000.0000.000
171B178LEU0-0.005-0.01613.808-0.287-0.2870.0000.0000.0000.000
172B179GLY00.002-0.01817.6071.0351.0350.0000.0000.0000.000
173B180GLY00.0490.02319.6650.8920.8920.0000.0000.0000.000
174B181SER00.0180.02319.335-0.891-0.8910.0000.0000.0000.000
175B182ASP-1-0.860-0.93320.515-13.439-13.4390.0000.0000.0000.000
176B183PRO0-0.041-0.03222.274-0.286-0.2860.0000.0000.0000.000
177B184GLN0-0.056-0.04924.0171.0411.0410.0000.0000.0000.000
178B185HIS00.0110.02219.8780.2050.2050.0000.0000.0000.000
179B186TYR0-0.0070.00921.018-0.578-0.5780.0000.0000.0000.000
180B187GLU-1-0.940-0.95022.866-11.824-11.8240.0000.0000.0000.000
181B188GLY0-0.051-0.02525.338-0.230-0.2300.0000.0000.0000.000
182B189ASN0-0.041-0.03726.100-0.088-0.0880.0000.0000.0000.000
183B190PHE00.0140.01219.000-0.194-0.1940.0000.0000.0000.000
184B191HIS0-0.023-0.00421.3540.7890.7890.0000.0000.0000.000
185B192TYR0-0.061-0.04918.797-0.337-0.3370.0000.0000.0000.000
186B193ILE0-0.055-0.01615.3390.8490.8490.0000.0000.0000.000
187B194ASN0-0.007-0.01216.118-1.098-1.0980.0000.0000.0000.000
188B195LEU0-0.0150.00311.564-0.329-0.3290.0000.0000.0000.000
189B196ILE0-0.055-0.01811.2271.1141.1140.0000.0000.0000.000
190B197LYS10.9360.9579.80018.58018.5800.0000.0000.0000.000
191B198THR0-0.005-0.00911.705-1.145-1.1450.0000.0000.0000.000
192B199GLY00.0360.0149.1090.5490.5490.0000.0000.0000.000
193B200VAL0-0.004-0.0165.258-1.709-1.7090.0000.0000.0000.000
194B201TRP00.0060.0027.1002.9062.9060.0000.0000.0000.000
195B202GLN0-0.054-0.0366.341-1.294-1.2940.0000.0000.0000.000
196B203ILE00.0130.0009.0261.9731.9730.0000.0000.0000.000
197B204GLN00.001-0.00911.429-0.249-0.2490.0000.0000.0000.000
198B205MET0-0.046-0.00411.745-0.036-0.0360.0000.0000.0000.000
199B206LYS10.7650.87014.63714.18414.1840.0000.0000.0000.000
200B207GLY00.0930.03017.9350.4330.4330.0000.0000.0000.000
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