Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: XVV21

Calculation Name: 3MXN-B-Xray42

Preferred Name:

Target Type:

Ligand Name: benzamidine

ligand 3-letter code: BEN

PDB ID: 3MXN

Chain ID: B

ChEMBL ID:

UniProt ID: Q9H9A7

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 Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 194
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1295250.347666
FMO2-HF: Nuclear repulsion 1238502.253807
FMO2-HF: Total energy -56748.093859
FMO2-MP2: Total energy -56907.177344


3D Structure
Snapshot
 
Ligand structure

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.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(B:16:ACE)


Summations of interaction energy for fragment #1(B:16:ACE)
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.
-0.3051.3520.221-0.816-1.061-0.002
Interaction energy analysis for fragmet #1(B:16:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / 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   
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].
3B18PRO0-0.0160.0173.227-0.0071.2600.053-0.602-0.718-0.001
4B19ARG11.0011.0045.4010.3630.3630.0000.0000.0000.000
5B20SER00.0350.0438.0480.1190.1190.0000.0000.0000.000
6B21PRO00.0590.0217.9840.0640.0640.0000.0000.0000.000
7B22PRO0-0.016-0.0107.027-0.098-0.0980.0000.0000.0000.000
8B23LEU00.0270.0289.4350.0190.0190.0000.0000.0000.000
9B24LYS10.8490.91013.231-0.284-0.2840.0000.0000.0000.000
10B25VAL00.0050.01215.291-0.036-0.0360.0000.0000.0000.000
11B26LEU00.0540.03217.5030.0180.0180.0000.0000.0000.000
12B27ALA0-0.016-0.02920.043-0.010-0.0100.0000.0000.0000.000
13B28GLU-1-0.932-0.98620.9470.0620.0620.0000.0000.0000.000
14B29GLN00.0460.02920.5130.0040.0040.0000.0000.0000.000
15B30LEU0-0.010-0.00616.078-0.012-0.0120.0000.0000.0000.000
16B31ARG10.8330.89920.550-0.067-0.0670.0000.0000.0000.000
17B32ARG10.7590.86023.701-0.061-0.0610.0000.0000.0000.000
18B33ASP-1-0.744-0.83623.5350.0450.0450.0000.0000.0000.000
19B34ALA0-0.0160.00020.487-0.003-0.0030.0000.0000.0000.000
20B35GLU-1-0.956-0.98022.101-0.006-0.0060.0000.0000.0000.000
21B36GLY0-0.040-0.02021.576-0.004-0.0040.0000.0000.0000.000
22B37GLY00.028-0.00220.8620.0060.0060.0000.0000.0000.000
23B38PRO00.004-0.00617.483-0.007-0.0070.0000.0000.0000.000
24B39GLY0-0.041-0.01115.385-0.008-0.0080.0000.0000.0000.000
25B40ALA0-0.031-0.01316.461-0.008-0.0080.0000.0000.0000.000
26B41TRP0-0.0070.01215.3810.0220.0220.0000.0000.0000.000
27B42ARG10.9520.97618.0270.0300.0300.0000.0000.0000.000
28B43LEU00.0090.01519.1890.0030.0030.0000.0000.0000.000
29B44SER00.0130.01421.2770.0010.0010.0000.0000.0000.000
30B45ARG10.8050.86022.420-0.046-0.0460.0000.0000.0000.000
31B46ALA00.0110.00526.3770.0010.0010.0000.0000.0000.000
32B47ALA0-0.002-0.00129.897-0.001-0.0010.0000.0000.0000.000
33B48ALA0-0.028-0.00827.8140.0000.0000.0000.0000.0000.000
34B49GLY00.0000.00529.9570.0020.0020.0000.0000.0000.000
35B50ARG10.8500.93725.589-0.055-0.0550.0000.0000.0000.000
36B51GLY00.0300.01426.018-0.004-0.0040.0000.0000.0000.000
37B52PRO00.0070.00222.9650.0080.0080.0000.0000.0000.000
38B53LEU00.0170.02417.824-0.003-0.0030.0000.0000.0000.000
39B54ASP-1-0.845-0.89116.765-0.029-0.0290.0000.0000.0000.000
40B55LEU0-0.016-0.01114.1130.0240.0240.0000.0000.0000.000
41B56ALA0-0.036-0.01510.714-0.045-0.0450.0000.0000.0000.000
42B57ALA0-0.031-0.0267.377-0.011-0.0110.0000.0000.0000.000
43B58VAL00.0020.0079.2670.0040.0040.0000.0000.0000.000
44B59TRP0-0.051-0.0389.8710.1550.1550.0000.0000.0000.000
45B60MET0-0.025-0.00311.808-0.067-0.0670.0000.0000.0000.000
46B61GLN00.0270.00214.3910.0870.0870.0000.0000.0000.000
47B62GLY00.0610.02617.157-0.026-0.0260.0000.0000.0000.000
48B63ARG10.7810.87819.923-0.103-0.1030.0000.0000.0000.000
49B64VAL0-0.0080.00719.399-0.007-0.0070.0000.0000.0000.000
50B65VAL0-0.029-0.01121.954-0.008-0.0080.0000.0000.0000.000
51B66MET0-0.017-0.02323.361-0.009-0.0090.0000.0000.0000.000
52B67ALA0-0.010-0.01021.1150.0090.0090.0000.0000.0000.000
53B68ASP-1-0.889-0.93121.6730.0160.0160.0000.0000.0000.000
54B69ARG10.9270.96516.3360.0130.0130.0000.0000.0000.000
55B70GLY0-0.015-0.01716.9360.0140.0140.0000.0000.0000.000
56B71GLU-1-0.972-0.98816.300-0.011-0.0110.0000.0000.0000.000
57B72ALA00.0250.00817.6760.0060.0060.0000.0000.0000.000
58B73ARG10.8770.95019.072-0.049-0.0490.0000.0000.0000.000
59B74LEU0-0.015-0.02016.5540.0070.0070.0000.0000.0000.000
60B75ARG10.8340.89320.622-0.078-0.0780.0000.0000.0000.000
61B76ASP-1-0.687-0.80020.5560.1330.1330.0000.0000.0000.000
62B77PRO0-0.012-0.02122.707-0.011-0.0110.0000.0000.0000.000
63B78SER0-0.0080.00123.264-0.010-0.0100.0000.0000.0000.000
64B79GLY00.0090.00124.746-0.011-0.0110.0000.0000.0000.000
65B80ASP-1-0.771-0.84522.9600.0780.0780.0000.0000.0000.000
66B81PHE00.0420.00815.589-0.003-0.0030.0000.0000.0000.000
67B82SER0-0.030-0.01518.7100.0020.0020.0000.0000.0000.000
68B83VAL0-0.0170.00612.9280.0050.0050.0000.0000.0000.000
69B84ARG10.9790.99214.1850.0120.0120.0000.0000.0000.000
70B85GLY00.0220.01212.5480.0070.0070.0000.0000.0000.000
71B86LEU00.0330.01312.0360.0050.0050.0000.0000.0000.000
72B87GLU-1-0.811-0.91013.616-0.022-0.0220.0000.0000.0000.000
73B88ARG10.8850.95410.1240.2110.2110.0000.0000.0000.000
74B89VAL0-0.0360.0228.651-0.005-0.0050.0000.0000.0000.000
75B90PRO00.0080.0077.799-0.063-0.0630.0000.0000.0000.000
76B91ARG10.9370.95310.668-0.062-0.0620.0000.0000.0000.000
77B92GLY00.0200.02514.236-0.007-0.0070.0000.0000.0000.000
78B93ARG10.9080.94215.572-0.240-0.2400.0000.0000.0000.000
79B94PRO00.0410.03318.0520.0190.0190.0000.0000.0000.000
80B95CYS0-0.023-0.01716.7190.0010.0010.0000.0000.0000.000
81B96LEU00.0230.02317.2530.0010.0010.0000.0000.0000.000
82B97VAL0-0.025-0.01519.897-0.015-0.0150.0000.0000.0000.000
83B98PRO00.0250.01323.3000.0100.0100.0000.0000.0000.000
84B99GLY00.0310.01825.030-0.004-0.0040.0000.0000.0000.000
85B100LYS10.9140.97521.229-0.134-0.1340.0000.0000.0000.000
86B101TYR00.0090.00220.1720.0040.0040.0000.0000.0000.000
87B102VAL00.000-0.00716.0980.0130.0130.0000.0000.0000.000
88B103MET00.0210.05410.1400.0250.0250.0000.0000.0000.000
89B104VAL0-0.002-0.02310.8450.0190.0190.0000.0000.0000.000
90B105MET00.0080.0193.6660.0440.1650.007-0.040-0.0870.000
91B106GLY00.028-0.0077.8600.0020.0020.0000.0000.0000.000
92B107VAL0-0.017-0.0036.9750.0120.0120.0000.0000.0000.000
93B108VAL00.0340.0159.554-0.006-0.0060.0000.0000.0000.000
94B109GLN0-0.022-0.01412.723-0.065-0.0650.0000.0000.0000.000
95B110ALA00.002-0.00915.562-0.012-0.0120.0000.0000.0000.000
96B111CYS00.0010.01318.2140.0200.0200.0000.0000.0000.000
97B112SER00.0530.04820.4180.0090.0090.0000.0000.0000.000
98B113PRO00.0180.00824.056-0.007-0.0070.0000.0000.0000.000
99B114GLU-1-0.832-0.91121.7820.0530.0530.0000.0000.0000.000
100B115PRO00.0380.04918.425-0.010-0.0100.0000.0000.0000.000
101B116CYS0-0.089-0.00817.2310.0070.0070.0000.0000.0000.000
102B117LEU00.0050.00211.819-0.015-0.0150.0000.0000.0000.000
103B118GLN00.0080.00310.2610.0250.0250.0000.0000.0000.000
104B119ALA00.004-0.0029.1750.0240.0240.0000.0000.0000.000
105B120VAL0-0.032-0.0052.825-0.392-0.1230.161-0.174-0.256-0.001
106B121LYS10.8920.9245.806-0.922-0.9220.0000.0000.0000.000
107B122MET00.0450.0388.133-0.088-0.0880.0000.0000.0000.000
108B123THR0-0.088-0.00811.2410.0140.0140.0000.0000.0000.000
109B124ASP-1-0.739-0.88113.9260.1730.1730.0000.0000.0000.000
110B125LEU0-0.059-0.01216.2320.0210.0210.0000.0000.0000.000
111B126SER00.024-0.02019.330-0.020-0.0200.0000.0000.0000.000
112B127ASP-1-0.900-0.91922.1630.1850.1850.0000.0000.0000.000
113B128ASN00.0390.02222.955-0.026-0.0260.0000.0000.0000.000
114B129PRO00.0520.03723.9980.0100.0100.0000.0000.0000.000
115B130ILE00.010-0.00724.705-0.002-0.0020.0000.0000.0000.000
116B131HIS00.007-0.00219.2890.0020.0020.0000.0000.0000.000
117B132GLU-1-0.745-0.84222.1470.1250.1250.0000.0000.0000.000
118B133SER0-0.038-0.01823.568-0.009-0.0090.0000.0000.0000.000
119B134MET0-0.0140.00922.191-0.012-0.0120.0000.0000.0000.000
120B135TRP0-0.0310.00415.4650.0110.0110.0000.0000.0000.000
121B136GLU-1-0.727-0.82721.5170.1030.1030.0000.0000.0000.000
122B137LEU00.0210.02023.884-0.003-0.0030.0000.0000.0000.000
123B138GLU-1-0.780-0.85518.4500.2580.2580.0000.0000.0000.000
124B139VAL0-0.0160.00818.6920.0090.0090.0000.0000.0000.000
125B140GLU-1-0.885-0.93520.6950.0850.0850.0000.0000.0000.000
126B141ASP-1-0.874-0.93822.8280.1270.1270.0000.0000.0000.000
127B142LEU0-0.002-0.00315.6600.0000.0000.0000.0000.0000.000
128B143HIS00.0020.00018.312-0.024-0.0240.0000.0000.0000.000
129B144ARG10.9360.97721.781-0.097-0.0970.0000.0000.0000.000
130B145ASN0-0.086-0.04621.741-0.019-0.0190.0000.0000.0000.000
131B146ILE0-0.0270.01017.8150.0070.0070.0000.0000.0000.000
132B147PRO-1-0.771-0.84720.6080.0410.0410.0000.0000.0000.000
133A10HOH00.0140.00311.3620.0500.0500.0000.0000.0000.000
134A12HOH00.0030.00319.5190.0130.0130.0000.0000.0000.000
135A30HOH0-0.018-0.02415.2780.0100.0100.0000.0000.0000.000
136A78HOH0-0.035-0.02519.6720.0000.0000.0000.0000.0000.000
137A163HOH00.0230.01215.879-0.002-0.0020.0000.0000.0000.000
138B148HOH0-0.038-0.03024.672-0.003-0.0030.0000.0000.0000.000
139B149HOH00.011-0.00122.838-0.004-0.0040.0000.0000.0000.000
140B150HOH0-0.040-0.03519.8130.0090.0090.0000.0000.0000.000
141B151HOH00.000-0.02910.5390.0610.0610.0000.0000.0000.000
142B155HOH0-0.009-0.01626.1100.0020.0020.0000.0000.0000.000
143B156HOH0-0.009-0.01417.9980.0090.0090.0000.0000.0000.000
144B157HOH00.0190.00513.7730.0040.0040.0000.0000.0000.000
145B158HOH0-0.041-0.03526.739-0.003-0.0030.0000.0000.0000.000
146B159HOH0-0.0070.00626.608-0.002-0.0020.0000.0000.0000.000
147B160HOH00.005-0.00610.3660.0580.0580.0000.0000.0000.000
148B162HOH0-0.019-0.02924.7410.0030.0030.0000.0000.0000.000
149B163HOH0-0.023-0.02023.5980.0000.0000.0000.0000.0000.000
150B164HOH0-0.039-0.04114.4070.0060.0060.0000.0000.0000.000
151B165HOH00.003-0.00421.265-0.004-0.0040.0000.0000.0000.000
152B166HOH0-0.0040.00622.8560.0070.0070.0000.0000.0000.000
153B167HOH0-0.047-0.0399.218-0.043-0.0430.0000.0000.0000.000
154B168HOH0-0.041-0.02212.204-0.014-0.0140.0000.0000.0000.000
155B171HOH0-0.013-0.01417.0100.0030.0030.0000.0000.0000.000
156B174HOH00.0300.02012.5610.0110.0110.0000.0000.0000.000
157B175HOH0-0.031-0.04524.108-0.002-0.0020.0000.0000.0000.000
158B176HOH00.0350.04119.040-0.004-0.0040.0000.0000.0000.000
159B177HOH0-0.010-0.01922.415-0.002-0.0020.0000.0000.0000.000
160B178HOH0-0.053-0.04217.1150.0160.0160.0000.0000.0000.000
161B179HOH0-0.030-0.02424.5360.0000.0000.0000.0000.0000.000
162B180HOH00.0250.01732.6590.0010.0010.0000.0000.0000.000
163B181HOH0-0.032-0.02526.308-0.001-0.0010.0000.0000.0000.000
164B182HOH0-0.033-0.02325.145-0.002-0.0020.0000.0000.0000.000
165B183HOH0-0.013-0.01021.957-0.003-0.0030.0000.0000.0000.000
166B185HOH0-0.034-0.02925.025-0.001-0.0010.0000.0000.0000.000
167B187HOH0-0.074-0.05418.352-0.008-0.0080.0000.0000.0000.000
168B188HOH00.0480.03022.1900.0020.0020.0000.0000.0000.000
169B189HOH0-0.035-0.05327.0770.0040.0040.0000.0000.0000.000
170B191HOH0-0.025-0.01625.996-0.003-0.0030.0000.0000.0000.000
171B193HOH0-0.030-0.02821.9420.0000.0000.0000.0000.0000.000
172B195HOH0-0.031-0.01325.069-0.004-0.0040.0000.0000.0000.000
173B196HOH0-0.021-0.02222.7280.0010.0010.0000.0000.0000.000
174B199HOH0-0.010-0.01824.7250.0040.0040.0000.0000.0000.000
175B200HOH00.009-0.00225.5000.0030.0030.0000.0000.0000.000
176B202HOH0-0.046-0.03628.779-0.002-0.0020.0000.0000.0000.000
177B204HOH0-0.018-0.02327.4600.0000.0000.0000.0000.0000.000
178B205HOH0-0.035-0.03718.6000.0060.0060.0000.0000.0000.000
179B206HOH0-0.0020.00415.5030.0040.0040.0000.0000.0000.000
180B207HOH0-0.017-0.00325.658-0.003-0.0030.0000.0000.0000.000
181B209HOH0-0.066-0.04913.108-0.010-0.0100.0000.0000.0000.000
182B210HOH0-0.025-0.0197.4530.0940.0940.0000.0000.0000.000
183B211HOH0-0.030-0.01519.770-0.004-0.0040.0000.0000.0000.000
184B212HOH0-0.019-0.00826.407-0.003-0.0030.0000.0000.0000.000
185B213HOH00.0210.01726.7620.0010.0010.0000.0000.0000.000
186B214HOH0-0.025-0.01327.358-0.003-0.0030.0000.0000.0000.000
187B215HOH0-0.022-0.02223.7690.0050.0050.0000.0000.0000.000
188B217HOH0-0.033-0.02619.991-0.006-0.0060.0000.0000.0000.000
189B233HOH0-0.023-0.01519.5180.0000.0000.0000.0000.0000.000
190B234HOH0-0.062-0.06012.016-0.015-0.0150.0000.0000.0000.000
191B235HOH00.0180.0099.443-0.053-0.0530.0000.0000.0000.000
192B238HOH00.0380.02510.513-0.019-0.0190.0000.0000.0000.000
193B241HOH0-0.031-0.02527.637-0.002-0.0020.0000.0000.0000.000
194B242HOH0-0.042-0.05320.989-0.002-0.0020.0000.0000.0000.000